From 87d6bcfbd4a57b1009edcd9916e22e6ebb30e6e8 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Tue, 19 Jan 2021 12:00:11 +0100
Subject: [PATCH 001/154] scripts to build rpm packages - initial build

---
 packages/.gitignore                     |  4 ++
 packages/Makefile                       | 82 ++++++++++++++++++++++
 packages/rpm/SOURCES/inforex.httpd.conf | 46 +++++++++++++
 packages/rpm/SPECS/inforex.spec         | 91 +++++++++++++++++++++++++
 4 files changed, 223 insertions(+)
 create mode 100644 packages/.gitignore
 create mode 100644 packages/Makefile
 create mode 100644 packages/rpm/SOURCES/inforex.httpd.conf
 create mode 100644 packages/rpm/SPECS/inforex.spec

diff --git a/packages/.gitignore b/packages/.gitignore
new file mode 100644
index 00000000..8bfcebde
--- /dev/null
+++ b/packages/.gitignore
@@ -0,0 +1,4 @@
+*~
+*.swp
+*.rpm
+rpm/SOURCES/inforex.tgz
diff --git a/packages/Makefile b/packages/Makefile
new file mode 100644
index 00000000..f1f55a88
--- /dev/null
+++ b/packages/Makefile
@@ -0,0 +1,82 @@
+# local path from current dir
+RPM_SPEC_DIR = rpm/SPECS
+RPM_SOURCES_DIR = rpm/SOURCES
+
+RPMBUILD = $(shell if [ -e /usr/bin/rpmbuild ]; then echo /usr/bin/rpmbuild; else bin/rpm; fi)
+HAVE_RPMBUILD = "no"$(RPMBUILD)
+RPM = rpm
+PACKAGE = inforex
+GITHASH=`git log --oneline |head -1|cut -d" " -f 1`
+VERSION = 0.1
+RELNO = 1
+RELEASE = $(shell if [ ! -z '$(GITHASH)' ]; then echo -n "$(RELNO)v.$(GITHASH)"; else echo -n "$(RELNO)";fi)
+
+RELSPECTAG = RELEASE_TAG
+
+# glob cannot work here
+TARITIFEXISTS = tests phpunit.xml data
+FILES2TAR = composer.json apps LICENCE.md local sonar-project.properties config/README.md documentations phpunit engine gfx public_html database INSTALL.md README.md $(foreach wrd,$(TARITIFEXISTS),$(wrd))
+
+$(RPM_SOURCES_DIR)/$(PACKAGE).tgz: ../.git/index 
+	@(tar -C .. -cvzf $(RPM_SOURCES_DIR)/$(PACKAGE).tgz $(FILES2TAR) > /dev/null )
+
+.PHONY: rpm-local srpm-common rpm-common srpm rpm all clean 
+
+all: rpm
+
+# to wymaga podania w wywołaniu parametrów w zmiennych środowiska
+#  rpmbuild="katalog_do_budowania" i rpmspec="nazwa_pliku_spec"
+rpm-local: $(RPM_SOURCES_DIR)/$(PACKAGE).tgz
+	@(if test "${HAVE_RPMBUILD}" = "no"; then \
+                echo -e "\n" \
+        "*** Required util ${RPMBUILD} missing.  Please install the\n" \
+        "*** package for your distribution which provides ${RPMBUILD},\n" \
+        "*** re-run configure, and try again.\n"; \
+                exit 1; \
+        fi; \
+        mkdir -p $(rpmbuild)/TMP && \
+        mkdir -p $(rpmbuild)/BUILD && \
+        mkdir -p $(rpmbuild)/RPMS && \
+        mkdir -p $(rpmbuild)/SRPMS && \
+        mkdir -p $(rpmbuild)/SPECS && \
+        cat ${RPM_SPEC_DIR}/$(rpmspec) | sed -e 's/${RELSPECTAG}/${RELEASE}/' > $(rpmbuild)/SPECS/$(rpmspec) && \
+        mkdir -p $(rpmbuild)/SOURCES && \
+	if ls -A ${RPM_SOURCES_DIR} ; then \
+		cp ${RPM_SOURCES_DIR}/* $(rpmbuild)/SOURCES; \
+	fi)
+
+srpm-common:
+	@(rpmspec=$(PACKAGE).spec; \
+	rpmbuild=`mktemp -t -d $(PACKAGE)-build-$$USER-XXXXXXXX`; \
+	$(MAKE) $(AM_MAKEFLAGS) \
+		rpmbuild="$$rpmbuild" \
+		rpmspec="$$rpmspec" \
+		rpm-local || exit 1; \
+	LANG=C $(RPMBUILD) \
+                --define "_tmppath $$rpmbuild/TMP" \
+                --define "_topdir $$rpmbuild" \
+                $(def) -bs $$rpmbuild/SPECS/$$rpmspec || exit 1; \
+	cp $$rpmbuild/SRPMS/*.src.rpm . || exit 1; \
+        rm -R $$rpmbuild)
+
+ 
+rpm-common: 
+	@(rpmpkg=$(PACKAGE)-$(VERSION)-$(RELEASE)*src.rpm; \
+        rpmspec=$(PACKAGE).spec; \
+        rpmbuild=`mktemp -t -d $(PACKAGE)-build-$$USER-XXXXXXXX`; \
+	$(MAKE) $(AM_MAKEFLAGS) \
+                rpmbuild="$$rpmbuild" \
+                rpmspec="$$rpmspec" \
+                rpm-local || exit 1; \
+	LANG=C ${RPMBUILD} \
+                --define "_tmppath $$rpmbuild/TMP" \
+                --define "_topdir $$rpmbuild" \
+                $(def) --rebuild $$rpmpkg || exit 1; \
+	cp $$rpmbuild/RPMS/*/* . || exit 1; \
+        rm -R $$rpmbuild)
+
+rpm: srpm-common rpm-common
+srpm: srpm-common
+
+clean:
+	rm -f $(PACKAGE)*.rpm
diff --git a/packages/rpm/SOURCES/inforex.httpd.conf b/packages/rpm/SOURCES/inforex.httpd.conf
new file mode 100644
index 00000000..7961c625
--- /dev/null
+++ b/packages/rpm/SOURCES/inforex.httpd.conf
@@ -0,0 +1,46 @@
+# To offer inforex via Apache, add the following Alias
+# to your server's configuration
+# Alias /inforex "INFOREXDIR"
+
+<Directory "INFOREXDIR">
+  Options None
+  AllowOverride None
+  <IfModule mod_php5.c>
+      php_admin_flag safe_mode off
+      php_admin_value open_basedir INFOREXDIR/:INFOREXDATAROOT/:PHPLIBDIR:/tmp
+  </IfModule>
+
+  <IfVersion >= 2.4>
+    <IfModule mod_access_compat.c>
+      Order allow,deny
+      #Allow from 127.0.0.1
+      Allow from all
+    </IfModule>
+    Require all granted
+  </IfVersion>
+  <IfVersion < 2.4>
+    Order allow,deny
+    #Allow from 127.0.0.1
+    Allow from all
+  </IfVersion>
+</Directory>
+
+<Directory "INFOREXDATAROOT">
+  <IfVersion >= 2.4>
+    Require all denied
+  </IfVersion>
+  <IfVersion < 2.4>
+    Order allow,deny
+    Deny from all
+  </IfVersion>
+</Directory>
+
+<Directory "INFOREXDIR/testy">
+  <IfVersion >= 2.4>
+    Require all denied
+  </IfVersion>
+  <IfVersion < 2.4>
+    Order allow,deny
+    Deny from all
+  </IfVersion>
+</Directory>
diff --git a/packages/rpm/SPECS/inforex.spec b/packages/rpm/SPECS/inforex.spec
new file mode 100644
index 00000000..29f9ba0b
--- /dev/null
+++ b/packages/rpm/SPECS/inforex.spec
@@ -0,0 +1,91 @@
+%define _unpackaged_files_terminate_build 1
+%define __brp_mangle_shebangs  /usr/bin/true
+
+%define        httpduser         apache
+%define        httpdgroup        apache
+%define        httpconfdir       /etc/httpd
+#% define        phplibdir         %{_datadir}/php
+%define        phplibdir         /var/www/html
+%define        inforexdir        %{phplibdir}/%{name}
+
+Name:       inforex
+Version:    0.1
+Release:    RELEASE_TAG
+Summary:    dummy package to testing rpm builds
+License:    GLGPL v3
+Group:      Productivity/Networking/Web/Frontends
+URL:        https://github.com/CLARIN-PL/Inforex
+
+Source0:	%{name}.tgz
+Source1:        %{name}.httpd.conf
+
+BuildRequires:  httpd-devel
+BuildRequires:  httpd
+BuildRequires:  php-devel
+
+Requires:       httpd
+Requires:       mysql
+
+Buildarch: noarch
+
+%global debug_package %{nil}
+
+%description
+This skeleton is intentionaly developed as absolute minimal specification
+to test all phases of building rpm process
+
+%prep
+%setup -q -c
+
+# remove .htaccess files
+#find . -name \.htaccess -print | xargs rm -f
+
+# remove several scripts not used in the package
+#rm -rf  vendor/ezyang/htmlpurifier/maintenance/
+
+%build
+
+%install
+rm -rf $RPM_BUILD_ROOT
+mkdir $RPM_BUILD_ROOT
+install -m 755 -d %{buildroot}%{inforexdir}
+# data dir may not exists
+mkdir %{buildroot}%{inforexdir}/data
+# copy all files
+cp -r . %{buildroot}%{inforexdir}
+
+# move data directory to /var/lib/ and set symlink
+install -m 755 -d %{buildroot}%{_localstatedir}/lib/
+mv %{buildroot}%{inforexdir}/data %{buildroot}%{_localstatedir}/lib/%{name}
+ln -s %{_localstatedir}/lib/%{name} %{buildroot}%{inforexdir}/data
+
+# install (empty) configuration-file
+touch %{buildroot}%{_localstatedir}/lib/%{name}/config.ini.php
+
+# install apache config-file and fix paths
+install -m 755 -d %{buildroot}%{httpconfdir}/conf.d
+install -m 644 %{SOURCE1} %{buildroot}%{httpconfdir}/conf.d/%{name}.conf
+sed -i -e 's|INFOREXDIR|%{inforexdir}|g ;
+        s|INFOREXDATAROOT|%{_localstatedir}/lib/%{name}|g ;
+        s|# Alias|Alias| ;
+        s|PHPLIBDIR|%{phplibdir}|g' %{buildroot}%{httpconfdir}/conf.d/%{name}.conf
+
+%post
+if [ -x %{_sbindir}/semanage ] ; then
+        # check is SELinux is installed and update settings
+        semanage fcontext -a -t httpd_var_lib_t %{_localstatedir}/lib/%{name}
+fi
+
+%files
+%defattr(644,root,root,755)
+
+%dir %{inforexdir}
+%{inforexdir}/*
+
+%{_localstatedir}/lib/%{name}/config.ini.php
+
+%{httpconfdir}/conf.d/%{name}.conf
+
+%changelog
+* Thu Jan 14 2021 Seweryn Walentynowicz <seweryn@walor.torun.pl>
+- Initial rpm spec file

From 90d64a8f848b69d394ee1749520167341a900784 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Tue, 19 Jan 2021 21:43:11 +0100
Subject: [PATCH 002/154] set of various problems solved

---
 .gitignore                     | 3 ++-
 engine/Config/Config.php       | 2 +-
 engine/external/pear/Auth.php  | 2 +-
 engine/include/CInforexWeb.php | 9 ++++++---
 engine/include/CPage.php       | 2 +-
 engine/page/page_home.php      | 2 +-
 public_html/index.php          | 2 +-
 7 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/.gitignore b/.gitignore
index 5afeda68..fc978b20 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,4 +10,5 @@ secured_data/import
 *.aux
 *.log
 *.backup
-*.swp
\ No newline at end of file
+*.swp
+composer.lock
diff --git a/engine/Config/Config.php b/engine/Config/Config.php
index 8a793fbc..ed5f29a4 100644
--- a/engine/Config/Config.php
+++ b/engine/Config/Config.php
@@ -39,7 +39,7 @@ class Config extends Singleton\Singleton{
 
 	static private $url = 'http://localhost/inforex';
 	static private $dsn = array(
-    		'phptype'  => 'mysql',
+    		'phptype'  => 'mysqli',
     		'username' => 'inforex',
     		'password' => 'password',
     		'hostspec' => 'localhost',
diff --git a/engine/external/pear/Auth.php b/engine/external/pear/Auth.php
index 648880d1..52fe7ae3 100644
--- a/engine/external/pear/Auth.php
+++ b/engine/external/pear/Auth.php
@@ -466,7 +466,7 @@ function &_factory($driver, $options = '')
     {
         $storage_class = 'Auth_Container_' . $driver;
         include_once 'Auth/Container/' . $driver . '.php';
-        $obj =& new $storage_class($options);
+        $obj = new $storage_class($options);
         return $obj;
     }
 
diff --git a/engine/include/CInforexWeb.php b/engine/include/CInforexWeb.php
index bd07e706..5921b76b 100644
--- a/engine/include/CInforexWeb.php
+++ b/engine/include/CInforexWeb.php
@@ -184,7 +184,7 @@ function doPage($page, &$variables)
         $o->set('user', $user);
         $o->set('page', $page);
         $o->set('corpus', $corpus);
-        $o->set('release', RELEASE);
+        $o->set('release', defined("RELEASE") ? RELEASE : "RELEASE" );
         $o->set('config', Config::Config());
         $o->set('rev', $this->getRevisionKey());
 
@@ -252,7 +252,7 @@ function execute()
 
         /* Gather the data about an activity */
         $activity_page = array();
-        $activity_page['ip_id'] = $db->get_entry_key("ips", "ip_id", array("ip" => $_SERVER["REMOTE_ADDR"]));
+        $activity_page['ip_id'] = $db->get_entry_key("ips", "ip_id", array("ip" => isset($_SERVER["REMOTE_ADDR"]) ? $_SERVER["REMOTE_ADDR"] : "CLI local" ));
         $activity_page['user_id'] = isset($user) ? $user['user_id'] : null;
         $activity_page['corpus_id'] = isset($corpus) ? $corpus['id'] : null;
         $activity_page['report_id'] = RequestLoader::getDocumentId();
@@ -284,7 +284,10 @@ function execute()
 
     function getRevisionKey()
     {
-        $commitHash = exec("git rev-list -n 1 master");
+        // last tag 
+        //$commitHash = exec("git describe --tags `git rev-list --tags --max-count=1`");
+        // last revision
+        $commitHash = exec("git rev-list --tags --max-count=1");
         $revKey = substr($commitHash, 0, 8);
         return $revKey;
     }
diff --git a/engine/include/CPage.php b/engine/include/CPage.php
index 58b1626b..9afb6e72 100644
--- a/engine/include/CPage.php
+++ b/engine/include/CPage.php
@@ -78,7 +78,7 @@ function CPage($name=null,$description=null){
 		$this->description = $description;
 		$this->template = new Smarty();
 		$this->template->compile_dir = Config::Config()->get_path_engine() . "/templates_c";
-		$this->set('RELEASE', "RELEASE");
+		$this->set('RELEASE', defined('RELEASE') ? RELEASE : "RELEASE");
 
 		/**
 		 * Include default JS and CSS files for the page
diff --git a/engine/page/page_home.php b/engine/page/page_home.php
index 482c3209..fa60a5dd 100644
--- a/engine/page/page_home.php
+++ b/engine/page/page_home.php
@@ -17,7 +17,7 @@ function __construct()
     function execute(){
 		global $user;
 
-        $user_id = intval($user[user_id]);
+        $user_id = intval($user["user_id"]);
 		
 		$private_corpora = DbCorpus::getPrivateCorporaForUser($user_id, intval(hasRole(USER_ROLE_ADMIN)));
 		$public_corpora = DbCorpus::getCorpora(1);
diff --git a/public_html/index.php b/public_html/index.php
index 87c13113..51ee1987 100644
--- a/public_html/index.php
+++ b/public_html/index.php
@@ -56,7 +56,7 @@
 		}
     }
 
-	chdir("../engine");
+	chdir(__DIR__ . "/../engine/");
 
 	$p->execute();
 

From c5cc67e5632baa14810efa55e32156ff68197c15 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Mon, 25 Jan 2021 19:49:26 +0100
Subject: [PATCH 003/154] bad assign by referencje for object removed from Auth
 module

---
 engine/external/pear/Auth/Container/DBLite.php       | 4 ++--
 engine/external/pear/Auth/Container/MDB.php          | 2 +-
 engine/external/pear/Auth/Container/MDB2.php         | 2 +-
 engine/external/pear/Auth/Container/NetVPOPMaild.php | 2 +-
 engine/external/pear/Auth/Container/POP3.php         | 2 +-
 engine/external/pear/Auth/Controller.php             | 2 +-
 6 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/engine/external/pear/Auth/Container/DBLite.php b/engine/external/pear/Auth/Container/DBLite.php
index 29961089..2f0f17b2 100644
--- a/engine/external/pear/Auth/Container/DBLite.php
+++ b/engine/external/pear/Auth/Container/DBLite.php
@@ -120,9 +120,9 @@ function _connect(&$dsn)
     {
         $this->log('Auth_Container_DBLite::_connect() called.', AUTH_LOG_DEBUG);
         if (is_string($dsn) || is_array($dsn)) {
-            $this->db =& DB::connect($dsn, $this->options['db_options']);
+            $this->db = DB::connect($dsn, $this->options['db_options']);
         } elseif (is_subclass_of($dsn, "db_common")) {
-            $this->db =& $dsn;
+            $this->db = $dsn;
         } else {
             return PEAR::raiseError("Invalid dsn or db object given");
         }
diff --git a/engine/external/pear/Auth/Container/MDB.php b/engine/external/pear/Auth/Container/MDB.php
index 019a122a..a6a92d61 100644
--- a/engine/external/pear/Auth/Container/MDB.php
+++ b/engine/external/pear/Auth/Container/MDB.php
@@ -111,7 +111,7 @@ function _connect($dsn)
     {
         $this->log('Auth_Container_MDB::_connect() called.', AUTH_LOG_DEBUG);
         if (is_string($dsn) || is_array($dsn)) {
-            $this->db =& MDB::connect($dsn, $this->options['db_options']);
+            $this->db = MDB::connect($dsn, $this->options['db_options']);
         } elseif (is_subclass_of($dsn, 'mdb_common')) {
             $this->db = $dsn;
         } elseif (is_object($dsn) && MDB::isError($dsn)) {
diff --git a/engine/external/pear/Auth/Container/MDB2.php b/engine/external/pear/Auth/Container/MDB2.php
index a3c26b7d..0d8a35c7 100644
--- a/engine/external/pear/Auth/Container/MDB2.php
+++ b/engine/external/pear/Auth/Container/MDB2.php
@@ -111,7 +111,7 @@ function _connect($dsn)
     {
         $this->log('Auth_Container_MDB2::_connect() called.', AUTH_LOG_DEBUG);
         if (is_string($dsn) || is_array($dsn)) {
-            $this->db =& MDB2::connect($dsn, $this->options['db_options']);
+            $this->db = MDB2::connect($dsn, $this->options['db_options']);
         } elseif (is_subclass_of($dsn, 'MDB2_Driver_Common')) {
             $this->db = $dsn;
         } elseif (is_object($dsn) && MDB2::isError($dsn)) {
diff --git a/engine/external/pear/Auth/Container/NetVPOPMaild.php b/engine/external/pear/Auth/Container/NetVPOPMaild.php
index 634fab51..b9d78a13 100644
--- a/engine/external/pear/Auth/Container/NetVPOPMaild.php
+++ b/engine/external/pear/Auth/Container/NetVPOPMaild.php
@@ -108,7 +108,7 @@ function Auth_Container_Vpopmaild($server=null)
     function fetchData($username, $password)
     {
         $this->log('Auth_Container_Vpopmaild::fetchData() called.', AUTH_LOG_DEBUG);
-        $vpopmaild =& new Net_Vpopmaild();
+        $vpopmaild = new Net_Vpopmaild();
         // Connect
         try {
             $res = $vpopmaild->connect($this->server, $this->port, $this->method);
diff --git a/engine/external/pear/Auth/Container/POP3.php b/engine/external/pear/Auth/Container/POP3.php
index 0bfab1b5..5278092d 100644
--- a/engine/external/pear/Auth/Container/POP3.php
+++ b/engine/external/pear/Auth/Container/POP3.php
@@ -128,7 +128,7 @@ function Auth_Container_POP3($server=null)
     function fetchData($username, $password)
     {
         $this->log('Auth_Container_POP3::fetchData() called.', AUTH_LOG_DEBUG);
-        $pop3 =& new Net_POP3();
+        $pop3 = new Net_POP3();
         $res = $pop3->connect($this->server, $this->port, $this->method);
         if (!$res) {
             $this->log('Connection to POP3 server failed.', AUTH_LOG_DEBUG);
diff --git a/engine/external/pear/Auth/Controller.php b/engine/external/pear/Auth/Controller.php
index 92d9f80a..b1c707f8 100644
--- a/engine/external/pear/Auth/Controller.php
+++ b/engine/external/pear/Auth/Controller.php
@@ -106,7 +106,7 @@ class Auth_Controller
      */
     function Auth_Controller(&$auth_obj, $login='login.php', $default='index.php', $accessList=array())
     {
-        $this->auth =& $auth_obj;
+        $this->auth = $auth_obj;
         $this->_loginPage = $login;
         $this->_defaultPage = $default;
         @session_start();

From e8176530826358d4636ebcdb4e95128c328e1085 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Fri, 29 Jan 2021 22:14:31 +0100
Subject: [PATCH 004/154] ajax_test_wccl syntax error

---
 engine/ajax/ajax_test_wccl_rules.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/engine/ajax/ajax_test_wccl_rules.php b/engine/ajax/ajax_test_wccl_rules.php
index eb797899..1b65acb1 100644
--- a/engine/ajax/ajax_test_wccl_rules.php
+++ b/engine/ajax/ajax_test_wccl_rules.php
@@ -8,7 +8,7 @@ function execute(){
 		$offset = intval($_POST['offset']);
 		$rules = strval($_POST['wccl_rules']);
 		$corpus = intval($_POST['corpus']);
-		$corpus_path = {Config::Config()->get_wccl_match_tester_corpora()}[$corpus]["path"];
+		$corpus_path = Config::Config()->get_wccl_match_tester_corpora()[$corpus]["path"];
 
 		$cmd = "python ".Config::Config()->get_wccl_match_tester_script()." -s %d -o %d -r %s -c %s 2>&1";
 		$cmd = sprintf($cmd, $start, $offset, escapeshellarg($rules), $corpus_path);

From 98ae7e3caecb5d913e1f61830fb33d59c4f11766 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Mon, 1 Feb 2021 19:31:20 +0100
Subject: [PATCH 005/154] /var/lib/inforex dir added to rpm, some correct to
 error solving

---
 engine/ajax/ajax_test_wccl_rules.php | 10 ++++++----
 packages/rpm/SPECS/inforex.spec      |  2 +-
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/engine/ajax/ajax_test_wccl_rules.php b/engine/ajax/ajax_test_wccl_rules.php
index 1b65acb1..ef57413d 100644
--- a/engine/ajax/ajax_test_wccl_rules.php
+++ b/engine/ajax/ajax_test_wccl_rules.php
@@ -36,10 +36,12 @@ function execute(){
 		
 		$return = array();
 		$return["errors"] = $errors;
-		$return["finished"] = $response->processed == 0;
-		$return["total_processed"] = $start + $response->processed;  
-		$return["items"] = $response->items;
-		$return["total_documents"] = $response->total;
+		if(isset($response->processed)) {
+			$return["finished"] = $response->processed == 0;
+			$return["total_processed"] = $start + $response->processed;  
+		}
+		$return["items"] = isset($response->items) ? $response->items : 0;
+		$return["total_documents"] = isset($response->total) ? $response->total : 0;
 									
 		return $return;
 	}
diff --git a/packages/rpm/SPECS/inforex.spec b/packages/rpm/SPECS/inforex.spec
index 29f9ba0b..4ab63da2 100644
--- a/packages/rpm/SPECS/inforex.spec
+++ b/packages/rpm/SPECS/inforex.spec
@@ -4,7 +4,6 @@
 %define        httpduser         apache
 %define        httpdgroup        apache
 %define        httpconfdir       /etc/httpd
-#% define        phplibdir         %{_datadir}/php
 %define        phplibdir         /var/www/html
 %define        inforexdir        %{phplibdir}/%{name}
 
@@ -82,6 +81,7 @@ fi
 %dir %{inforexdir}
 %{inforexdir}/*
 
+%dir %{_localstatedir}/lib/%{name}
 %{_localstatedir}/lib/%{name}/config.ini.php
 
 %{httpconfdir}/conf.d/%{name}.conf

From aaadf323e7a877b3928e835a7d5562b9a891c691 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Wed, 17 Feb 2021 19:13:14 +0100
Subject: [PATCH 006/154] final rpm cut, solving selinux context problem

---
 packages/rpm/SOURCES/inforex.httpd.conf |  2 +-
 packages/rpm/SPECS/inforex.spec         | 17 ++++++++++++++++-
 2 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/packages/rpm/SOURCES/inforex.httpd.conf b/packages/rpm/SOURCES/inforex.httpd.conf
index 7961c625..2d6f730c 100644
--- a/packages/rpm/SOURCES/inforex.httpd.conf
+++ b/packages/rpm/SOURCES/inforex.httpd.conf
@@ -1,6 +1,6 @@
 # To offer inforex via Apache, add the following Alias
 # to your server's configuration
-# Alias /inforex "INFOREXDIR"
+# Alias /inforex "INFOREXDIR/public_html"
 
 <Directory "INFOREXDIR">
   Options None
diff --git a/packages/rpm/SPECS/inforex.spec b/packages/rpm/SPECS/inforex.spec
index 4ab63da2..5cf469a1 100644
--- a/packages/rpm/SPECS/inforex.spec
+++ b/packages/rpm/SPECS/inforex.spec
@@ -58,6 +58,13 @@ install -m 755 -d %{buildroot}%{_localstatedir}/lib/
 mv %{buildroot}%{inforexdir}/data %{buildroot}%{_localstatedir}/lib/%{name}
 ln -s %{_localstatedir}/lib/%{name} %{buildroot}%{inforexdir}/data
 
+# create one initial sql dump from all patches
+rm -rf %{buildroot}/%{inforexdir}/database
+mkdir -p %{buildroot}/%{inforexdir}/database/init
+SQL_DUMP_FILE=%{buildroot}%{inforexdir}/database/init/initDB.sql
+cat ./database/init/inforex-v1.0.sql |grep -v "50013 DEFINER=" > $SQL_DUMP_FILE
+cat ./database/inforex-v1.0-changelog.sql |sed -e 's/endDelimiter:#/\nDELIMITER #/' | sed -e 's/^#/#\nDELIMITER ;/' >> $SQL_DUMP_FILE
+
 # install (empty) configuration-file
 touch %{buildroot}%{_localstatedir}/lib/%{name}/config.ini.php
 
@@ -72,7 +79,11 @@ sed -i -e 's|INFOREXDIR|%{inforexdir}|g ;
 %post
 if [ -x %{_sbindir}/semanage ] ; then
         # check is SELinux is installed and update settings
-        semanage fcontext -a -t httpd_var_lib_t %{_localstatedir}/lib/%{name}
+	if ( %{_sbindir}/semanage fcontext -l |grep %{_localstatedir}/lib/%{name} > /dev/null ) ; then 
+		%{_sbindir}/semanage fcontext -d %{_localstatedir}/lib/%{name}
+	fi
+        %{_sbindir}/semanage fcontext -a -t httpd_var_lib_t %{_localstatedir}/lib/%{name}
+	%{_sbindir}/restorecon %{_localstatedir}/lib/%{name}
 fi
 
 %files
@@ -87,5 +98,9 @@ fi
 %{httpconfdir}/conf.d/%{name}.conf
 
 %changelog
+* Wed Feb 17 2021 Seweryn Walentynowicz <seweryn@walor.torun.pl>
+- solved selinux context installation problems
+* Mon Feb 15 2021 Seweryn Walentynowicz <seweryn@walor.torun.pl>
+- Initial complete sql dump added
 * Thu Jan 14 2021 Seweryn Walentynowicz <seweryn@walor.torun.pl>
 - Initial rpm spec file

From ad643c4902b5db1a45c03f7bd70a7b15fe1cfc08 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 27 Feb 2021 09:56:58 +0100
Subject: [PATCH 007/154] added composer.lock to .gitignore

---
 .gitignore | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 5afeda68..fc978b20 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,4 +10,5 @@ secured_data/import
 *.aux
 *.log
 *.backup
-*.swp
\ No newline at end of file
+*.swp
+composer.lock

From 768cdc7935d69acad0c39da4a7f0f3b8729cca3d Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 27 Feb 2021 10:04:40 +0100
Subject: [PATCH 008/154] eliminated ZERO DATE from initial db structure

---
 database/init/inforex-v1.0.sql | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/database/init/inforex-v1.0.sql b/database/init/inforex-v1.0.sql
index c45af4ec..a9a02759 100644
--- a/database/init/inforex-v1.0.sql
+++ b/database/init/inforex-v1.0.sql
@@ -1614,7 +1614,7 @@ DROP TABLE IF EXISTS `tasks`;
 CREATE TABLE `tasks` (
   `task_id` int(11) NOT NULL AUTO_INCREMENT,
   `datetime` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP COMMENT 'Data i czas utworzenia zadania.',
-  `datetime_start` timestamp NOT NULL DEFAULT '0000-00-00 00:00:00',
+  `datetime_start` timestamp NULL DEFAULT NULL,
   `type` varchar(32) COLLATE utf8mb4_unicode_ci NOT NULL COMMENT 'Identyfikator zadania.',
   `description` text COLLATE utf8mb4_unicode_ci,
   `parameters` text COLLATE utf8mb4_unicode_ci NOT NULL,

From d6c7571ad05717962753fe6f4bd588ec1523d1e6 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 27 Feb 2021 17:25:27 +0100
Subject: [PATCH 009/154] DEFINER lines for unexistent DB user removed

---
 database/init/inforex-v1.0.sql | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/database/init/inforex-v1.0.sql b/database/init/inforex-v1.0.sql
index a9a02759..20113c55 100644
--- a/database/init/inforex-v1.0.sql
+++ b/database/init/inforex-v1.0.sql
@@ -1988,7 +1988,6 @@ UNLOCK TABLES;
 /*!50001 SET character_set_results     = utf8 */;
 /*!50001 SET collation_connection      = utf8_general_ci */;
 /*!50001 CREATE ALGORITHM=UNDEFINED */
-/*!50013 DEFINER=`gpw`@`localhost` SQL SECURITY DEFINER */
 /*!50001 VIEW `activities_view_users` AS select `u`.`screename` AS `screename`,count(0) AS `COUNT(*)`,max(`a`.`datetime`) AS `last_datetime`,`a`.`activity_page_id` AS `activity_page_id`,`a`.`datetime` AS `datetime`,`a`.`ip_id` AS `ip_id`,`a`.`user_id` AS `user_id`,`a`.`corpus_id` AS `corpus_id`,`a`.`report_id` AS `report_id`,`a`.`activity_type_id` AS `activity_type_id`,`a`.`execution_time` AS `execution_time` from (`activities` `a` join `users` `u` on((`a`.`user_id` = `u`.`user_id`))) group by `a`.`user_id` */;
 /*!50001 SET character_set_client      = @saved_cs_client */;
 /*!50001 SET character_set_results     = @saved_cs_results */;
@@ -2006,7 +2005,6 @@ UNLOCK TABLES;
 /*!50001 SET character_set_results     = utf8 */;
 /*!50001 SET collation_connection      = utf8_general_ci */;
 /*!50001 CREATE ALGORITHM=UNDEFINED */
-/*!50013 DEFINER=`root`@`localhost` SQL SECURITY DEFINER */
 /*!50001 VIEW `reports_annotations` AS select `ra`.`id` AS `id`,`ra`.`report_id` AS `report_id`,`ra`.`type_id` AS `type_id`,`at`.`name` AS `type`,`ra`.`from` AS `from`,`ra`.`to` AS `to`,`ra`.`text` AS `text`,`ra`.`user_id` AS `user_id`,`ra`.`creation_time` AS `creation_time`,`ra`.`stage` AS `stage`,`ra`.`source` AS `source` from (`reports_annotations_optimized` `ra` left join `annotation_types` `at` on((`at`.`annotation_type_id` = `ra`.`type_id`))) */;
 /*!50001 SET character_set_client      = @saved_cs_client */;
 /*!50001 SET character_set_results     = @saved_cs_results */;
@@ -2024,7 +2022,6 @@ UNLOCK TABLES;
 /*!50001 SET character_set_results     = utf8 */;
 /*!50001 SET collation_connection      = utf8_general_ci */;
 /*!50001 CREATE ALGORITHM=UNDEFINED */
-/*!50013 DEFINER=`root`@`localhost` SQL SECURITY DEFINER */
 /*!50001 VIEW `tokens_tags` AS select `tt`.`token_tag_id` AS `token_tag_id`,`tt`.`token_id` AS `token_id`,`b`.`text` AS `base`,`tt`.`base_id` AS `base_id`,`tokens_tags_ctags`.`ctag` AS `ctag`,`tt`.`disamb` AS `disamb` from ((`tokens_tags_optimized` `tt` left join `bases` `b` on((`b`.`id` = `tt`.`base_id`))) left join `tokens_tags_ctags` on((`tt`.`ctag_id` = `tokens_tags_ctags`.`id`))) */;
 /*!50001 SET character_set_client      = @saved_cs_client */;
 /*!50001 SET character_set_results     = @saved_cs_results */;

From c22c2b9a0f54970678d868f5a589f714cea0b940 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 27 Feb 2021 17:28:16 +0100
Subject: [PATCH 010/154] DB initialization sql_mode hint is no longer needed

---
 engine/include/database/MDB2DatabaseEngine.php | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/engine/include/database/MDB2DatabaseEngine.php b/engine/include/database/MDB2DatabaseEngine.php
index 48bd3c56..04dcd0c4 100644
--- a/engine/include/database/MDB2DatabaseEngine.php
+++ b/engine/include/database/MDB2DatabaseEngine.php
@@ -33,13 +33,6 @@ public function __construct($dsn) {
 		}
 		$this->mdb2->loadModule('Extended');
 		$this->mdb2->query("SET SESSION query_cache_type = ON");    
-		// hint for default using '0000-00-00' datetime field in tasks table :o(
-        $this->mdb2->query("SET @old_sql_mode := @@sql_mode");
-        $this->mdb2->query("SET @new_sql_mode := @old_sql_mode");
-        $this->mdb2->query("SET @new_sql_mode := TRIM(BOTH ',' FROM REPLACE(CONCAT(',',@new_sql_mode,','),',NO_ZERO_DATE,' ,','))");
-        $this->mdb2->query("SET @new_sql_mode := TRIM(BOTH ',' FROM REPLACE(CONCAT(',',@new_sql_mode,','),',NO_ZERO_IN_DATE,',','))");
-        $this->mdb2->query("SET @@sql_mode := @new_sql_mode;");
-    
 	} // __construct()
 
     public function prepareAndExecute($sql,$args=null) {

From 636a181544f9a47a1656d01897b63184c32739fe Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Tue, 2 Mar 2021 11:05:26 +0100
Subject: [PATCH 011/154] delete database/update load files for gwp database -
 no longer needed

---
 .../update/update_001_user_activities.sql     | 10 ---
 .../update/update_002_report_perspective.sql  | 62 --------------
 database/update/update_003_images.sql         | 13 ---
 database/update/update_004_relation_types.sql | 36 --------
 database/update/update_005_events.sql         | 83 -------------------
 .../update/update_006_reports_annotations.sql | 17 ----
 .../update/update_007_annotation_types.sql    |  2 -
 database/update/update_008_tokens.sql         | 19 -----
 .../update/update_009_annotation_types.sql    |  3 -
 .../update_010_corpus_perspective_roles.sql   | 27 ------
 .../update/update_011_report_perspectives.sql |  9 --
 .../update/update_012_corpus_subcorpora.sql   | 24 ------
 database/update/update_013_flags.sql          | 69 ---------------
 database/update/update_014_flags.sql          |  1 -
 .../update/update_015_report_perspectives.sql |  8 --
 database/update/update_016_tokens_tags.sql    | 13 ---
 .../update/update_017_reports_annotations.sql |  7 --
 database/update/update_018_relations.sql      |  4 -
 .../update/update_019_relations_groups.sql    | 13 ---
 database/update/update_020_tokens.sql         |  1 -
 database/update/update_021_tokens_tags.sql    |  2 -
 database/update/update_022_reports_diffs.sql  |  1 -
 database/update/update_023_reports_groups.sql |  1 -
 database/update/update_024_flags_sort.sql     |  2 -
 database/update/update_025_statuses.sql       |  9 --
 .../update_026_reports_tokenization.sql       |  1 -
 database/update/update_027_common_types.sql   | 29 -------
 .../update/update_028_reports_ext_kpwr.sql    |  9 --
 database/update/update_029_reports_types.sql  | 32 -------
 database/update/update_030_1_bases.sql        | 56 -------------
 .../update_030_2_reports_annotations.sql      | 26 ------
 .../update_030_reports_annotation_lemma.sql   | 40 ---------
 .../update_031_tokens_tags_ctags_pos.sql      | 11 ---
 .../update/update_033_tokens_tags_reload.sql  |  5 --
 database/update/update_034_ctag_unique.sql    |  1 -
 ...update_035_no_cascade_delete_for_types.sql | 20 -----
 .../update/update_036_report_content_size.sql |  1 -
 .../update/update_037_shared_attributes.sql   | 39 ---------
 .../update_038_shared_attributes_enum.sql     | 48 -----------
 ..._reports_annotations_shared_attributes.sql | 54 ------------
 ...040_annotation_types_shared_attributes.sql | 49 -----------
 database/update/update_041_agreement.sql      |  3 -
 database/update/update_042_create_corpus.sql  |  3 -
 database/update/update_043_email.sql          |  1 -
 database/update/update_044_tasks.sql          | 46 ----------
 database/update/update_045_tasks_update.sql   |  2 -
 database/update/update_046_wccl_rules.sql     | 14 ----
 .../update/update_047_user_login_max_size.sql |  1 -
 .../update_048_tasks_datetime_start.sql       |  2 -
 .../update_048_wccl_match_annotations.sql     |  1 -
 database/update/update_050_no_cascade.sql     |  9 --
 database/update/update_051_agreement.sql      | 14 ----
 .../update/update_052_flag_description.sql    |  1 -
 .../update_053_role_delete_annotations.sql    |  1 -
 database/update/update_054_exports.sql        | 28 -------
 database/update/update_055_checkboxes.sql     | 36 --------
 database/update/update_055_missing_field.sql  |  1 -
 database/update/update_056_report_lang.sql    |  2 -
 .../update_057_report_user_selection.sql      |  1 -
 .../update/update_058_annotation_types.sql    | 12 ---
 .../update/update_059_annotation_access.sql   |  2 -
 .../update/update_059_users_acitivities.sql   | 33 --------
 .../update/update_060_annotation_sets.sql     | 11 ---
 database/update/update_061_relation_edit.sql  |  1 -
 database/update/update_062_relation_sets.sql  |  6 --
 .../update_063_shared_annotation_sets.sql     |  4 -
 .../update_064_private_relation_sets.sql      |  2 -
 .../update_065_annotation_sets_corpora.sql    |  7 --
 database/update/update_066_morpho_disamb.sql  | 53 ------------
 database/update/update_066_relations.sql      |  1 -
 .../update_067_federation_login_clarin.sql    |  3 -
 .../update_068_morphodisamb_agreement.sql     |  6 --
 ..._adding_report_prespectives_for_morpho.sql |  5 --
 .../update/update_070_relation_agreement.sql  |  2 -
 .../update_071_annotation_agreement.sql       |  1 -
 database/update/update_071_default_nulls.sql  |  1 -
 .../update/update_072_tonekization_null.sql   |  1 -
 database/update/update_073_reports_nulls.sql  |  5 --
 database/update/update_074_exports.sql        | 19 -----
 ...update_075_add_tagger_field_to_exports.sql |  1 -
 database/update/update_075_corpora_date.sql   |  1 -
 database/update/update_075_upload.sql         |  8 --
 database/update/update_076_flags.sql          | 59 -------------
 database/update/update_076_roles.sql          | 24 ------
 database/update/update_077_tagsets.sql        |  2 -
 ...update_078_annotation_types_attributes.sql | 32 -------
 database/update/update_078_message_null.sql   |  1 -
 .../update/update_079_import_annotations.sql  |  1 -
 .../update/update_080_report_translations.sql |  4 -
 .../update/update_081_import_languages.sql    | 21 -----
 .../update_082_cascade_flag_history.sql       |  4 -
 ...te_083_reports_uesrs_selection_indices.sql |  9 --
 .../update_084_report_annotation_table.sql    |  1 -
 database/update/update_085_tagsets.sql        |  2 -
 database/update/update_086_orths.sql          | 34 --------
 .../update_087_attribute_value_length.sql     |  5 --
 ..._088_perspective_annotation_attributes.sql |  1 -
 .../update/update_089_fix_perspective_id.sql  |  1 -
 database/update/update_091_corpus_css.sql     |  1 -
 database/update/update_092_report_deleted.sql |  1 -
 100 files changed, 1411 deletions(-)
 delete mode 100644 database/update/update_001_user_activities.sql
 delete mode 100644 database/update/update_002_report_perspective.sql
 delete mode 100644 database/update/update_003_images.sql
 delete mode 100644 database/update/update_004_relation_types.sql
 delete mode 100644 database/update/update_005_events.sql
 delete mode 100644 database/update/update_006_reports_annotations.sql
 delete mode 100644 database/update/update_007_annotation_types.sql
 delete mode 100644 database/update/update_008_tokens.sql
 delete mode 100644 database/update/update_009_annotation_types.sql
 delete mode 100644 database/update/update_010_corpus_perspective_roles.sql
 delete mode 100644 database/update/update_011_report_perspectives.sql
 delete mode 100644 database/update/update_012_corpus_subcorpora.sql
 delete mode 100644 database/update/update_013_flags.sql
 delete mode 100644 database/update/update_014_flags.sql
 delete mode 100644 database/update/update_015_report_perspectives.sql
 delete mode 100644 database/update/update_016_tokens_tags.sql
 delete mode 100644 database/update/update_017_reports_annotations.sql
 delete mode 100644 database/update/update_018_relations.sql
 delete mode 100644 database/update/update_019_relations_groups.sql
 delete mode 100644 database/update/update_020_tokens.sql
 delete mode 100644 database/update/update_021_tokens_tags.sql
 delete mode 100644 database/update/update_022_reports_diffs.sql
 delete mode 100644 database/update/update_023_reports_groups.sql
 delete mode 100644 database/update/update_024_flags_sort.sql
 delete mode 100644 database/update/update_025_statuses.sql
 delete mode 100644 database/update/update_026_reports_tokenization.sql
 delete mode 100644 database/update/update_027_common_types.sql
 delete mode 100644 database/update/update_028_reports_ext_kpwr.sql
 delete mode 100644 database/update/update_029_reports_types.sql
 delete mode 100644 database/update/update_030_1_bases.sql
 delete mode 100644 database/update/update_030_2_reports_annotations.sql
 delete mode 100644 database/update/update_030_reports_annotation_lemma.sql
 delete mode 100644 database/update/update_031_tokens_tags_ctags_pos.sql
 delete mode 100644 database/update/update_033_tokens_tags_reload.sql
 delete mode 100644 database/update/update_034_ctag_unique.sql
 delete mode 100644 database/update/update_035_no_cascade_delete_for_types.sql
 delete mode 100644 database/update/update_036_report_content_size.sql
 delete mode 100644 database/update/update_037_shared_attributes.sql
 delete mode 100644 database/update/update_038_shared_attributes_enum.sql
 delete mode 100644 database/update/update_039_reports_annotations_shared_attributes.sql
 delete mode 100644 database/update/update_040_annotation_types_shared_attributes.sql
 delete mode 100644 database/update/update_041_agreement.sql
 delete mode 100644 database/update/update_042_create_corpus.sql
 delete mode 100644 database/update/update_043_email.sql
 delete mode 100644 database/update/update_044_tasks.sql
 delete mode 100644 database/update/update_045_tasks_update.sql
 delete mode 100644 database/update/update_046_wccl_rules.sql
 delete mode 100644 database/update/update_047_user_login_max_size.sql
 delete mode 100644 database/update/update_048_tasks_datetime_start.sql
 delete mode 100644 database/update/update_048_wccl_match_annotations.sql
 delete mode 100644 database/update/update_050_no_cascade.sql
 delete mode 100644 database/update/update_051_agreement.sql
 delete mode 100644 database/update/update_052_flag_description.sql
 delete mode 100644 database/update/update_053_role_delete_annotations.sql
 delete mode 100644 database/update/update_054_exports.sql
 delete mode 100644 database/update/update_055_checkboxes.sql
 delete mode 100644 database/update/update_055_missing_field.sql
 delete mode 100644 database/update/update_056_report_lang.sql
 delete mode 100644 database/update/update_057_report_user_selection.sql
 delete mode 100644 database/update/update_058_annotation_types.sql
 delete mode 100644 database/update/update_059_annotation_access.sql
 delete mode 100644 database/update/update_059_users_acitivities.sql
 delete mode 100644 database/update/update_060_annotation_sets.sql
 delete mode 100644 database/update/update_061_relation_edit.sql
 delete mode 100644 database/update/update_062_relation_sets.sql
 delete mode 100644 database/update/update_063_shared_annotation_sets.sql
 delete mode 100644 database/update/update_064_private_relation_sets.sql
 delete mode 100644 database/update/update_065_annotation_sets_corpora.sql
 delete mode 100644 database/update/update_066_morpho_disamb.sql
 delete mode 100644 database/update/update_066_relations.sql
 delete mode 100644 database/update/update_067_federation_login_clarin.sql
 delete mode 100644 database/update/update_068_morphodisamb_agreement.sql
 delete mode 100644 database/update/update_069_adding_report_prespectives_for_morpho.sql
 delete mode 100644 database/update/update_070_relation_agreement.sql
 delete mode 100644 database/update/update_071_annotation_agreement.sql
 delete mode 100644 database/update/update_071_default_nulls.sql
 delete mode 100644 database/update/update_072_tonekization_null.sql
 delete mode 100644 database/update/update_073_reports_nulls.sql
 delete mode 100644 database/update/update_074_exports.sql
 delete mode 100644 database/update/update_075_add_tagger_field_to_exports.sql
 delete mode 100644 database/update/update_075_corpora_date.sql
 delete mode 100644 database/update/update_075_upload.sql
 delete mode 100644 database/update/update_076_flags.sql
 delete mode 100644 database/update/update_076_roles.sql
 delete mode 100644 database/update/update_077_tagsets.sql
 delete mode 100644 database/update/update_078_annotation_types_attributes.sql
 delete mode 100644 database/update/update_078_message_null.sql
 delete mode 100644 database/update/update_079_import_annotations.sql
 delete mode 100644 database/update/update_080_report_translations.sql
 delete mode 100644 database/update/update_081_import_languages.sql
 delete mode 100644 database/update/update_082_cascade_flag_history.sql
 delete mode 100644 database/update/update_083_reports_uesrs_selection_indices.sql
 delete mode 100644 database/update/update_084_report_annotation_table.sql
 delete mode 100644 database/update/update_085_tagsets.sql
 delete mode 100644 database/update/update_086_orths.sql
 delete mode 100644 database/update/update_087_attribute_value_length.sql
 delete mode 100644 database/update/update_088_perspective_annotation_attributes.sql
 delete mode 100644 database/update/update_089_fix_perspective_id.sql
 delete mode 100644 database/update/update_091_corpus_css.sql
 delete mode 100644 database/update/update_092_report_deleted.sql

diff --git a/database/update/update_001_user_activities.sql b/database/update/update_001_user_activities.sql
deleted file mode 100644
index 7f18eec4..00000000
--- a/database/update/update_001_user_activities.sql
+++ /dev/null
@@ -1,10 +0,0 @@
-CREATE TABLE `gpw`.`user_activities` (
-`user_id` INT NOT NULL ,
-`started` DATETIME NOT NULL ,
-`ended` DATETIME NOT NULL ,
-`counter` INT NOT NULL ,
-INDEX ( `user_id` , `ended` )
-) ENGINE = MYISAM ;
-
-ALTER TABLE `user_activities` ADD `login` BOOLEAN NOT NULL ;
-ALTER TABLE `user_activities` ADD `id` BIGINT NOT NULL AUTO_INCREMENT PRIMARY KEY FIRST ;
diff --git a/database/update/update_002_report_perspective.sql b/database/update/update_002_report_perspective.sql
deleted file mode 100644
index 0efd08b9..00000000
--- a/database/update/update_002_report_perspective.sql
+++ /dev/null
@@ -1,62 +0,0 @@
---
--- Struktura tabeli dla  `corpus_and_report_perspectives`
---
-
-CREATE TABLE IF NOT EXISTS `corpus_and_report_perspectives` (
-  `perspective_id` varchar(32) NOT NULL,
-  `corpus_id` int(11) NOT NULL,
-  `access` enum('public','loggedin','role') NOT NULL,
-  PRIMARY KEY (`perspective_id`,`corpus_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=utf8;
-
---
--- Zrzut danych tabeli `corpus_and_report_perspectives`
---
-
-INSERT INTO `corpus_and_report_perspectives` (`perspective_id`, `corpus_id`, `access`) VALUES
-('transcription', 3, 'public'),
-('preview', 1, 'public'),
-('html', 1, 'public'),
-('report', 1, 'public'),
-('takipi', 1, 'public'),
-('edit', 1, 'loggedin'),
-('edit_raw', 1, 'loggedin'),
-('annotator', 1, 'loggedin'),
-('tei', 1, 'public'),
-('preview', 5, 'public'),
-('html', 5, 'public'),
-('report', 5, 'public'),
-('takipi', 5, 'public'),
-('edit', 5, 'loggedin'),
-('edit_raw', 5, 'loggedin'),
-('annotator', 5, 'loggedin'),
-('tei', 5, 'public');
-
--- --------------------------------------------------------
-
---
--- Struktura tabeli dla  `report_perspectives`
---
-
-CREATE TABLE IF NOT EXISTS `report_perspectives` (
-  `id` varchar(32) NOT NULL,
-  `title` varchar(255) NOT NULL,
-  `order` int(11) NOT NULL,
-  PRIMARY KEY (`id`)
-) ENGINE=MyISAM DEFAULT CHARSET=utf8;
-
---
--- Zrzut danych tabeli `report_perspectives`
---
-
-INSERT INTO `report_perspectives` (`id`, `title`, `order`) VALUES
-('transcription', 'Transcription', 10),
-('preview', 'Text', 20),
-('html', 'HTML', 30),
-('raw', 'Źródłowy dokument', 40),
-('takipi', 'TaKIPI', 50),
-('edit', 'Edycja', 60),
-('edit_raw', 'Edycja / źródło', 70),
-('annotator', 'Anotacja', 80),
-('tei', 'TEI', 90);
-
diff --git a/database/update/update_003_images.sql b/database/update/update_003_images.sql
deleted file mode 100644
index c9c4ea3f..00000000
--- a/database/update/update_003_images.sql
+++ /dev/null
@@ -1,13 +0,0 @@
-CREATE TABLE `images` (
-	`id` BIGINT NOT NULL AUTO_INCREMENT PRIMARY KEY ,
-	`corpus_id` INT NOT NULL,
-	`original_name` VARCHAR(64) NOT NULL ,
-	`hash_name` VARCHAR(32) NOT NULL
-) ;
-
-CREATE TABLE `reports_and_images` (
-	`report_id` INT NOT NULL ,
-	`images_id` INT NOT NULL ,
-	`position` INT NOT NULL ,
-	PRIMARY KEY ( `report_id` , `images_id` )
-) ;
\ No newline at end of file
diff --git a/database/update/update_004_relation_types.sql b/database/update/update_004_relation_types.sql
deleted file mode 100644
index 1ab22b11..00000000
--- a/database/update/update_004_relation_types.sql
+++ /dev/null
@@ -1,36 +0,0 @@
-/*
-Tabela typów relacji powinna zawierać:
-
-    * identyfikator relacji (może być liczba, auto increment),
-    * nazwa relacji, do 64 znaków,
-    * opis relacji, text,
-    * identyfikator kategorii (z tabeli annotation_sets) --- informaja, między jakimi typami jednostek będzie można tworzyć relacje.
-*/
-CREATE TABLE `relation_types` (
-  `id` INT NOT NULL AUTO_INCREMENT,
-  `name` VARCHAR(64)  NOT NULL,
-  `description` TEXT  NOT NULL,
-  `annotation_set_id` INT  NOT NULL,
-  PRIMARY KEY (`id`)
-);
- 
-
-/*
-Tabela instancji relacji powinna zawierać:
-
-    * identyfikator instancji (liczba, auto increment),
-    * identyfikator typu relacji (z powyższej tabeli),
-    * jednostka źródłowa (identyfikator jednostki, z tabeli report_annotations),
-    * jednostka docelowa (j/w),
-    * data dodania,
-    * identyfikator użytkownika, który dodał relację.
-*/
-CREATE TABLE `relations` (
-  `id` BIGINT(20)  NOT NULL AUTO_INCREMENT,
-  `relation_type_id` INT  NOT NULL,
-  `source_id` BIGINT(20)  NOT NULL,
-  `target_id` BIGINT(20)  NOT NULL,
-  `date` DATE  NOT NULL,
-  `user_id` INT  NOT NULL,
-  PRIMARY KEY (`id`)
-);
\ No newline at end of file
diff --git a/database/update/update_005_events.sql b/database/update/update_005_events.sql
deleted file mode 100644
index 4bc9634d..00000000
--- a/database/update/update_005_events.sql
+++ /dev/null
@@ -1,83 +0,0 @@
-/*Grupy zdarzeń
-event_groups
-* event_group_id INT KEY AUTO_INREMENT
-* name VARCHAR(64)
-* description TEXT
-*/
-CREATE TABLE `event_groups` (
-	`event_group_id` INT NOT NULL AUTO_INCREMENT PRIMARY KEY ,
-	`name` VARCHAR( 64 ) NOT NULL ,
-	`description` TEXT NOT NULL
-);
-
-/*Typy zdarzeń przypisane do grup:
-event_types
-* event_type_id INT KEY AUTO_INREMENT
-* name VARCHAR(64)
-* description TEXT
-* event_group_id INT
-*/
-CREATE TABLE `event_types` (
-	`event_type_id` INT NOT NULL AUTO_INCREMENT PRIMARY KEY ,
-	`name` VARCHAR( 64 ) NOT NULL ,
-	`description` TEXT NOT NULL ,
-	`event_group_id` INT NOT NULL
-);
-
-/*Typy slotów przypisane do typów zdarzeń:
-
-event_type_slots
-* event_type_slot INT KEY AUTO_INCREMENT
-* name VARCHAR(64)
-* description TEXT
-* event_type_id INT*/
-CREATE TABLE `event_type_slots` (
-	`event_type_slot_id` INT NOT NULL AUTO_INCREMENT PRIMARY KEY ,
-	`name` VARCHAR( 64 ) NOT NULL ,
-	`description` TEXT NOT NULL ,
-	`event_type_id` INT NOT NULL
-);
-
-
-
-/*Przypisanie grup zdarzeń do korpusów:
-corpus_event_groups
-* corpus_id INT
-* event_group_id INT*/
-CREATE TABLE `corpus_event_groups` (
-	`corpus_id` INT NOT NULL,
-	`event_group_id` INT NOT NULL
-);
-
-/*Instancje zdarzeń:
-
-reports_events
-* report_event_id INT KEY AUTO_INCREMENT
-* report_id INT
-* event_type_id INT
-* user_id INT
-* creation_time DATETIME*/
-CREATE TABLE `reports_events` (
-	`report_event_id` INT NOT NULL AUTO_INCREMENT PRIMARY KEY ,
-	`report_id` INT NOT NULL ,
-	`event_type_id` INT NOT NULL ,
-	`user_id` INT NOT NULL ,
-	`creation_time` DATETIME NOT NULL
-);
-
-
-/*Sloty instancji zdarzenia:
-reports_events_slots
-* report_event_slot_id INT KEY AUTO_INCREMENT
-* report_event_id INT
-* report_annotation_id INT*/
-CREATE TABLE `reports_events_slots` (
-	`report_event_slot_id` INT NOT NULL AUTO_INCREMENT PRIMARY KEY ,
-	`report_event_id` INT NOT NULL ,
-	`report_annotation_id` INT NULL,
-	`event_type_slot_id` INT NOT NULL,
-	`user_id` INT NOT NULL,
-	`creation_time` DATETIME NOT NULL,
- 	`user_update_id` INT NOT NULL,
- 	`update_time` DATETIME NOT NULL	
-);
diff --git a/database/update/update_006_reports_annotations.sql b/database/update/update_006_reports_annotations.sql
deleted file mode 100644
index e3da3045..00000000
--- a/database/update/update_006_reports_annotations.sql
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
-Dodanie pola `user_id` dla `report_annotation_attribute`
-Należy dodać pole `user_id` do tabeli `report_annotation_attribute` jako klucz obcy do tabeli `users`. Pole ustawiane jest TYLKO przy utworzeniu atrybutu i wartość pola równa jest identyfikatorowi użytkownika, który dodał pole. Edycja nie zmienia wartości tego pola.
-
-Klucz dla tej tabeli powinien być zmieniony z (annotation_id, annotation_attribute_id) na (annotation_id, annotation_attribute_id, user_id)
-*/
-ALTER TABLE `reports_annotations_attributes` ADD `user_id` INT(11) NOT NULL ;
-ALTER TABLE `reports_annotations_attributes` ADD CONSTRAINT `user_id` FOREIGN KEY ( `user_id` ) REFERENCES `users` ( `user_id` ) ;
-ALTER TABLE `reports_annotations_attributes` DROP PRIMARY KEY;
-ALTER TABLE `reports_annotations_attributes` ADD PRIMARY KEY ( `annotation_id` , `annotation_attribute_id` , `user_id` );
-
-/*
-Pole `stage` w tabeli `report_annotations` będzie polem wyliczeniowym przyjmującym jedną z wartości: candidate, user, final.
-Domyślną wartością jest `user`.
-*/
-ALTER TABLE `reports_annotations` ADD `stage` ENUM( 'candidate', 'user', 'final' ) NOT NULL DEFAULT 'user';
-
diff --git a/database/update/update_007_annotation_types.sql b/database/update/update_007_annotation_types.sql
deleted file mode 100644
index c0e61bbe..00000000
--- a/database/update/update_007_annotation_types.sql
+++ /dev/null
@@ -1,2 +0,0 @@
-/*Kolumna `short_description` typu VARCHAR będzie zawierała skrócony opis typu anotacji.*/
-ALTER TABLE `annotation_types` ADD `short_description` VARCHAR( 64 ) NULL DEFAULT NULL ;
\ No newline at end of file
diff --git a/database/update/update_008_tokens.sql b/database/update/update_008_tokens.sql
deleted file mode 100644
index ff7fa1b9..00000000
--- a/database/update/update_008_tokens.sql
+++ /dev/null
@@ -1,19 +0,0 @@
-/*Tabela `tokens` definiuje segmentację tekstu na tokeny. Jeżeli dla danego dokumentu została zdefiniowana segmentacja, to anotacje muszą być spójne z określoną segmentacją.
-
-tokens
-* token_id BIGINT
-* report_id INT FOREIGN KEY na reports.id
-* from INT
-* to INT
-*/
-CREATE TABLE `tokens` (
-  `token_id` BIGINT (20) NOT NULL AUTO_INCREMENT,
-  `report_id` BIGINT(20)  NOT NULL,
-  `from` INT  NOT NULL,
-  `to` INT  NOT NULL,
-  PRIMARY KEY (`token_id`),
-  CONSTRAINT `fk_report_id` FOREIGN KEY  (`report_id`)
-    REFERENCES `reports` (`id`)
-    ON UPDATE CASCADE
-)
-ENGINE = InnoDB;
diff --git a/database/update/update_009_annotation_types.sql b/database/update/update_009_annotation_types.sql
deleted file mode 100644
index 0477675b..00000000
--- a/database/update/update_009_annotation_types.sql
+++ /dev/null
@@ -1,3 +0,0 @@
-/*Do tabeli anotacji należy dodać pole `css`, w którym będą przechowywany styl anotacji (tło, czcionka, ramka, etc.). 
-Może to być pole typu VARCHAR, w którym będzie przchowywany opis css.*/
-ALTER TABLE `annotation_types` ADD `css` VARCHAR( 255 ) NULL;
\ No newline at end of file
diff --git a/database/update/update_010_corpus_perspective_roles.sql b/database/update/update_010_corpus_perspective_roles.sql
deleted file mode 100644
index 2c6bddff..00000000
--- a/database/update/update_010_corpus_perspective_roles.sql
+++ /dev/null
@@ -1,27 +0,0 @@
-/*
-Jako trzeci typ dostępu do perspektywy będzie `role`. Oznacza to, że perspektywa będzie dostępna wybranym użytkownikom. Do przechowania informacji o dostępie do perspektywy w trybie `role` będzie trzeba utworzyć tablicę:
-corpus_perspective_roles
-
-    * user_id
-    * corpus_id
-    * report_perspective_id
-
-Wpis w tej tablicy będzie oznaczał, że użytkownik user_id ma dostęp do perspektywy report_perspective_id w korpusie corpus_id.
-
-Jeżeli użytkownik nie będzie miał dostępu do perspektywy, to nie powinna być ona widoczna w menu perspektyw.
-*/
-CREATE TABLE `corpus_perspective_roles` (
-  `user_id` INT NOT NULL,
-  `corpus_id` INT NOT NULL,
-  `report_perspective_id` VARCHAR(32) NOT NULL,
-  CONSTRAINT `fk_user_id` FOREIGN KEY  (`user_id`)
-    REFERENCES `users` (`user_id`)
-    ON UPDATE CASCADE,
-  CONSTRAINT `fk_corpus_id` FOREIGN KEY  (`corpus_id`)
-    REFERENCES `corpora` (`id`)
-    ON UPDATE CASCADE,
-  CONSTRAINT `fk_report_perspective_id` FOREIGN KEY  (`report_perspective_id`)
-    REFERENCES `report_perspectives` (`id`)
-    ON UPDATE CASCADE
-)
-ENGINE = InnoDB;
\ No newline at end of file
diff --git a/database/update/update_011_report_perspectives.sql b/database/update/update_011_report_perspectives.sql
deleted file mode 100644
index e75fd9ad..00000000
--- a/database/update/update_011_report_perspectives.sql
+++ /dev/null
@@ -1,9 +0,0 @@
-/*Dodać perspektywę dokumentu o nazwie Tokenization.*/
-INSERT INTO `report_perspectives` (
-`id` ,
-`title` ,
-`order`
-)
-VALUES (
-'tokenization', 'Tokenization', '100'
-);
\ No newline at end of file
diff --git a/database/update/update_012_corpus_subcorpora.sql b/database/update/update_012_corpus_subcorpora.sql
deleted file mode 100644
index fa4e54a7..00000000
--- a/database/update/update_012_corpus_subcorpora.sql
+++ /dev/null
@@ -1,24 +0,0 @@
-/*Dodać tabelę*/
-
-CREATE TABLE `corpus_subcorpora` (
-	`subcorpus_id` INT NULL AUTO_INCREMENT,
-	`corpus_id` INT NOT NULL,
-	`name` VARCHAR( 256 ) NOT NULL ,
-	`description` TEXT NOT NULL ,
-	PRIMARY KEY ( `subcorpus_id` )
-) ENGINE = InnoDB;
-
-
-/*Rozszerzyć schemat tabeli `reports` o kolumnę `subcorpus_id`.*/
-ALTER TABLE `reports` ADD `subcorpus_id` INT NULL;
-
-/*tymczasowo nie ustawialem kluczy obcych!*/
-
-ALTER TABLE `reports` ADD CONSTRAINT `fk_subcorpus_id` FOREIGN KEY (`subcorpus_id`) REFERENCES `corpus_subcorpora` (`subcorpus_id`) ON UPDATE CASCADE;
-
-ALTER TABLE `corpus_subcorpora` ADD INDEX ( `corpus_id` ) ;
-
-ALTER TABLE `corpus_subcorpora` ADD FOREIGN KEY ( `corpus_id` ) REFERENCES `gpw`.`corpora` (
-`id`
-) ON DELETE CASCADE ON UPDATE CASCADE ;
-
diff --git a/database/update/update_013_flags.sql b/database/update/update_013_flags.sql
deleted file mode 100644
index 6613af13..00000000
--- a/database/update/update_013_flags.sql
+++ /dev/null
@@ -1,69 +0,0 @@
-/*W bazie należy dodać tabelę, która będzie definicją możliwych statusów postępu prac.
-
-flags
-  flag_id INT AUTO_INCREMENT
-  name VARCHAR(64)
-  description TEXT
-  
-  CREATE TABLE `corpus_perspective_roles` (
-  `user_id` INT NOT NULL,
-  `corpus_id` INT NOT NULL,
-  `report_perspective_id` VARCHAR(32) NOT NULL,
-  CONSTRAINT `fk_user_id` FOREIGN KEY  (`user_id`)
-    REFERENCES `users` (`user_id`)
-    ON UPDATE CASCADE,
-  CONSTRAINT `fk_corpus_id` FOREIGN KEY  (`corpus_id`)
-    REFERENCES `corpora` (`id`)
-    ON UPDATE CASCADE,
-  CONSTRAINT `fk_report_perspective_id` FOREIGN KEY  (`report_perspective_id`)
-    REFERENCES `report_perspectives` (`id`)
-    ON UPDATE CASCADE
-)
-  
-  
-  */
-
-CREATE TABLE `flags` (
-	`flag_id` INT NOT NULL AUTO_INCREMENT ,
-	`name` VARCHAR( 64 ) NOT NULL ,
-	`description` TEXT NOT NULL ,
-	PRIMARY KEY ( `flag_id` )
-) ENGINE = InnoDB;
-
-CREATE TABLE `corpora_flags` (
-	`corpora_flag_id` INT NOT NULL AUTO_INCREMENT ,
-	`corpora_id` INT NOT NULL ,
-	`name` VARCHAR( 128 ) NOT NULL ,
-	PRIMARY KEY (`corpora_flag_id`) ,
-	CONSTRAINT `fk_corpora_id` FOREIGN KEY (`corpora_id`)
-	  REFERENCES `corpora` (`id`) 
-) ENGINE = InnoDB;
-
-CREATE TABLE `reports_flags` (
-	`corpora_flag_id` INT NOT NULL,
-	`report_id` BIGINT(20) NOT NULL, 
-	`flag_id` INT NOT NULL,
-	CONSTRAINT `fk_corpora_flag_id` FOREIGN KEY (`corpora_flag_id`)
-	  REFERENCES `corpora_flags` (`corpora_flag_id`),
-	CONSTRAINT `fk1_report_id` FOREIGN KEY (`report_id`)
-	  REFERENCES `reports` (`id`),
-	CONSTRAINT `fk_flag_id` FOREIGN KEY (`flag_id`)
-	  REFERENCES `flags` (`flag_id`) 
-) ENGINE = InnoDB;
-
-INSERT INTO `gpw`.`flags` (
-`flag_id` ,
-`name` ,
-`description`
-)
-VALUES (
-1 , 'nowy', 'dokument nie został jeszcze sprawdzony'
-), (
-2 , 'w opracowaniu', 'dokument jest w trakcie opracowania'
-), (
-3 , 'gotowy', 'praca nad dokumentem została zakończone i wymaga sprawdzenia'
-), (
-4 , 'sprawdzony', 'dokument został pomyślnie sprawdzony'
-), (
-5 , 'do poprawy', 'dokument wymaga poprawy'
-);
diff --git a/database/update/update_014_flags.sql b/database/update/update_014_flags.sql
deleted file mode 100644
index a8b4f2e6..00000000
--- a/database/update/update_014_flags.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE `reports_flags` ADD UNIQUE `corpora_flag_id_unique` ( `corpora_flag_id` , `report_id` )
\ No newline at end of file
diff --git a/database/update/update_015_report_perspectives.sql b/database/update/update_015_report_perspectives.sql
deleted file mode 100644
index 41eb45e8..00000000
--- a/database/update/update_015_report_perspectives.sql
+++ /dev/null
@@ -1,8 +0,0 @@
-INSERT INTO `report_perspectives` (
-`id` ,
-`title` ,
-`order`
-)
-VALUES (
-'autoextension', 'Automatic Extension', '110'
-);
\ No newline at end of file
diff --git a/database/update/update_016_tokens_tags.sql b/database/update/update_016_tokens_tags.sql
deleted file mode 100644
index 1d28e9a6..00000000
--- a/database/update/update_016_tokens_tags.sql
+++ /dev/null
@@ -1,13 +0,0 @@
-CREATE TABLE `tokens_tags` (
-	`token_tag_id` BIGINT( 20 ) NOT NULL AUTO_INCREMENT ,
-	`token_id` BIGINT( 20 ) NOT NULL ,
-	`base` VARCHAR( 32 ) NOT NULL ,
-	`ctag` VARCHAR( 32 ) NOT NULL ,
-	`disamb` BOOLEAN NOT NULL ,
-	PRIMARY KEY ( `token_tag_id` ) ,
-	CONSTRAINT `fk_token_id` FOREIGN KEY  (`token_id`)
-    	REFERENCES `tokens` (`token_id`)
-    	ON UPDATE CASCADE
-    	ON DELETE CASCADE
-) ENGINE = InnoDB;
-
diff --git a/database/update/update_017_reports_annotations.sql b/database/update/update_017_reports_annotations.sql
deleted file mode 100644
index 22fe9747..00000000
--- a/database/update/update_017_reports_annotations.sql
+++ /dev/null
@@ -1,7 +0,0 @@
-ALTER TABLE `reports_annotations` ADD `source` ENUM( 'user', 'bootstrapping' ) NOT NULL DEFAULT 'user';
-UPDATE `reports_annotations` SET `source` = "user" WHERE `stage` = "user";
-UPDATE `reports_annotations` SET `source` = "bootstrapping" WHERE `stage` = "candidate";
-ALTER TABLE `reports_annotations` CHANGE `stage` `stage` ENUM( 'new', 'final', 'discarded' ) NOT NULL DEFAULT 'final';
-UPDATE `reports_annotations` SET `stage` = "final" WHERE `source` = "user";
-UPDATE `reports_annotations` SET `stage` = "new" WHERE `source` = "bootstrapping";
-UPDATE `report_perspectives` SET `title` = 'Annotation Bootstrapping' WHERE `report_perspectives`.`id` = 'autoextension';
\ No newline at end of file
diff --git a/database/update/update_018_relations.sql b/database/update/update_018_relations.sql
deleted file mode 100644
index 1fb52994..00000000
--- a/database/update/update_018_relations.sql
+++ /dev/null
@@ -1,4 +0,0 @@
-ALTER TABLE `relations` DROP FOREIGN KEY `relations_ibfk_2`;
-ALTER TABLE `relations` ADD CONSTRAINT `relations_ibfk_2` FOREIGN KEY (`source_id`) REFERENCES `reports_annotations` (`id`) ON DELETE CASCADE;
-ALTER TABLE `relations` DROP FOREIGN KEY `relations_ibfk_3`;
-ALTER TABLE `relations` ADD CONSTRAINT `relations_ibfk_3` FOREIGN KEY (`target_id`) REFERENCES `reports_annotations` (`id`) ON DELETE CASCADE;
\ No newline at end of file
diff --git a/database/update/update_019_relations_groups.sql b/database/update/update_019_relations_groups.sql
deleted file mode 100644
index f1cdbcf4..00000000
--- a/database/update/update_019_relations_groups.sql
+++ /dev/null
@@ -1,13 +0,0 @@
-CREATE TABLE `relations_groups` (
-  `relation_type_id` int(11) NOT NULL,
-  `part` enum('source','target') NOT NULL,
-  `annotation_set_id` int(11) DEFAULT NULL,
-  `annotation_subset_id` int(11) DEFAULT NULL,
-  KEY `relation_type_id` (`relation_type_id`),
-  KEY `annotation_set_id` (`annotation_set_id`),
-  KEY `annotation_subset_id` (`annotation_subset_id`)  
-) ENGINE=InnoDB;
-
-ALTER TABLE `relations_groups` ADD FOREIGN KEY ( `relation_type_id` ) REFERENCES `relation_types` (`id`) ON DELETE CASCADE ON UPDATE CASCADE ;
-ALTER TABLE `relations_groups` ADD FOREIGN KEY ( `annotation_set_id` ) REFERENCES `annotation_sets` (`annotation_set_id`) ON DELETE CASCADE ON UPDATE CASCADE ;
-ALTER TABLE `relations_groups` ADD FOREIGN KEY ( `annotation_subset_id` ) REFERENCES `annotation_subsets` (`annotation_subset_id`) ON DELETE CASCADE ON UPDATE CASCADE ;
\ No newline at end of file
diff --git a/database/update/update_020_tokens.sql b/database/update/update_020_tokens.sql
deleted file mode 100644
index 2a7cdbc5..00000000
--- a/database/update/update_020_tokens.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE `tokens` ADD `eos` BOOLEAN NOT NULL;
\ No newline at end of file
diff --git a/database/update/update_021_tokens_tags.sql b/database/update/update_021_tokens_tags.sql
deleted file mode 100644
index 256cb443..00000000
--- a/database/update/update_021_tokens_tags.sql
+++ /dev/null
@@ -1,2 +0,0 @@
-ALTER TABLE `tokens_tags` CHANGE `base` `base` TEXT CHARACTER SET utf8 COLLATE utf8_general_ci NOT NULL;
-ALTER TABLE `tokens_tags` CHANGE `ctag` `ctag` VARCHAR( 100 ) CHARACTER SET utf8 COLLATE utf8_general_ci NOT NULL;
diff --git a/database/update/update_022_reports_diffs.sql b/database/update/update_022_reports_diffs.sql
deleted file mode 100644
index 5ac3e10e..00000000
--- a/database/update/update_022_reports_diffs.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE `reports_diffs` ADD `comment` TEXT NULL ;
diff --git a/database/update/update_023_reports_groups.sql b/database/update/update_023_reports_groups.sql
deleted file mode 100644
index bc9ee4e8..00000000
--- a/database/update/update_023_reports_groups.sql
+++ /dev/null
@@ -1 +0,0 @@
-INSERT INTO relations_groups (relation_type_id, part, annotation_set_id) SELECT "1" AS relation_type_id, "source" AS part,  annotation_set_id FROM annotation_sets UNION SELECT "1" AS relation_type_id, "target" AS part,  annotation_set_id FROM annotation_sets;
diff --git a/database/update/update_024_flags_sort.sql b/database/update/update_024_flags_sort.sql
deleted file mode 100644
index 3040d27c..00000000
--- a/database/update/update_024_flags_sort.sql
+++ /dev/null
@@ -1,2 +0,0 @@
-ALTER TABLE `corpora_flags` ADD `short` VARCHAR( 16 ) NOT NULL ,
-ADD `sort` INT NOT NULL 
diff --git a/database/update/update_025_statuses.sql b/database/update/update_025_statuses.sql
deleted file mode 100644
index 11d862e5..00000000
--- a/database/update/update_025_statuses.sql
+++ /dev/null
@@ -1,9 +0,0 @@
-INSERT INTO `gpw`.`reports_statuses` (
-`id` ,
-`status` ,
-`description` ,
-`order`
-)
-VALUES (
-NULL , 'Do usunięcia', 'Dokument powinien zostać usunięty', '8'
-);
diff --git a/database/update/update_026_reports_tokenization.sql b/database/update/update_026_reports_tokenization.sql
deleted file mode 100644
index 874faf0c..00000000
--- a/database/update/update_026_reports_tokenization.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE `reports` ADD `tokenization` VARCHAR( 32 ) NOT NULL ;
diff --git a/database/update/update_027_common_types.sql b/database/update/update_027_common_types.sql
deleted file mode 100644
index 4cc71c0c..00000000
--- a/database/update/update_027_common_types.sql
+++ /dev/null
@@ -1,29 +0,0 @@
-CREATE TABLE IF NOT EXISTS `annotation_types_common` (
-  `annotation_name` varchar(32) NOT NULL,
-  KEY `annotation_name` (`annotation_name`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8;
-
---
--- Dumping data for table `annotation_types_common`
---
-
-INSERT INTO `annotation_types_common` (`annotation_name`) VALUES
-('admin1_nam'),
-('admin2_nam'),
-('admin3_nam'),
-('award_nam'),
-('brand_nam'),
-('city_nam'),
-('country_nam'),
-('event_nam'),
-('facility_nam'),
-('historical_region_nam'),
-('institution_nam'),
-('nation_nam'),
-('organization_nam'),
-('person_add_nam'),
-('person_first_nam'),
-('person_last_nam'),
-('person_nam'),
-('road_nam'),
-('title_nam');
diff --git a/database/update/update_028_reports_ext_kpwr.sql b/database/update/update_028_reports_ext_kpwr.sql
deleted file mode 100644
index 4fd7f21b..00000000
--- a/database/update/update_028_reports_ext_kpwr.sql
+++ /dev/null
@@ -1,9 +0,0 @@
-CREATE TABLE `gpw`.`reports_ext_kpwr` (
-`id` BIGINT NOT NULL ,
-`keywords` TEXT NOT NULL ,
-PRIMARY KEY ( `report_id` )
-) ENGINE = InnoDB;
-
-ALTER TABLE `reports_ext_kpwr` ADD FOREIGN KEY ( `id` ) REFERENCES `gpw`.`reports` (
-`id`
-) ON DELETE CASCADE ON UPDATE CASCADE ;
diff --git a/database/update/update_029_reports_types.sql b/database/update/update_029_reports_types.sql
deleted file mode 100644
index 8b2e0c8a..00000000
--- a/database/update/update_029_reports_types.sql
+++ /dev/null
@@ -1,32 +0,0 @@
-SET SQL_MODE = "NO_AUTO_VALUE_ON_ZERO";
-SET time_zone = "+00:00";
-
-
-/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
-/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
-/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
-/*!40101 SET NAMES utf8 */;
-
-CREATE TABLE IF NOT EXISTS `reports_formats` (
-  `id` int(11) NOT NULL AUTO_INCREMENT,
-  `format` varchar(32) NOT NULL,
-  PRIMARY KEY (`id`)
-) ENGINE=InnoDB  DEFAULT CHARSET=latin1 AUTO_INCREMENT=5 ;
-
-
-INSERT INTO `reports_formats` (`id`, `format`) VALUES
-(1, 'xml'),
-(2, 'plain'),
-(3, 'premorph');
-
-
-ALTER TABLE  `reports` ADD  `format_id` INT NOT NULL DEFAULT  '1';
-ALTER TABLE  `reports` ADD INDEX (  `format_id` ) ;
-
-ALTER TABLE  `reports` ADD FOREIGN KEY (  `format_id` ) REFERENCES  `inforex`.`reports_formats` (`id`) ON DELETE RESTRICT ON UPDATE RESTRICT ;
-
-/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
-/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
-/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
-
-
diff --git a/database/update/update_030_1_bases.sql b/database/update/update_030_1_bases.sql
deleted file mode 100644
index 507172ed..00000000
--- a/database/update/update_030_1_bases.sql
+++ /dev/null
@@ -1,56 +0,0 @@
-CREATE TABLE `bases` (
-	`id` BIGINT(20) NOT NULL AUTO_INCREMENT,
-	`text` VARCHAR(255) NOT NULL COLLATE 'utf8_bin',
-	PRIMARY KEY (`id`),
-	UNIQUE INDEX `text` (`text`)
-)
-COLLATE='utf8_bin'
-ENGINE=InnoDB;
-
-INSERT IGNORE INTO bases (text) 
-SELECT base FROM tokens_tags GROUP BY HEX(base);
-
-ALTER TABLE `tokens_tags`
-	ADD COLUMN `base_id` BIGINT(20) NOT NULL AFTER `token_id`;
-
-SET @count = 0;
-UPDATE `bases` SET `bases`.`id` = @count:= @count + 1;
-ALTER TABLE bases AUTO_INCREMENT = 1;
-UPDATE tokens_tags SET base_id = (SELECT id FROM bases WHERE text=tokens_tags.base COLLATE utf8_bin) WHERE base_id = 0;
-
-RENAME TABLE `tokens_tags` TO `tokens_tags_optimized`;
-ALTER TABLE `tokens_tags_optimized`
-	ADD CONSTRAINT `FK_tokens_tags_optimized_bases` FOREIGN KEY (`base_id`) REFERENCES `bases` (`id`) ON UPDATE RESTRICT ON DELETE RESTRICT;
-	
-ALTER TABLE `tokens_tags_optimized`
-	DROP COLUMN `base`;	
-	
-CREATE ALGORITHM = UNDEFINED VIEW `tokens_tags` AS 
-    SELECT token_tag_id,token_id,b.text as base,base_id,ctag,disamb
-    FROM tokens_tags_optimized AS tt
-    LEFT JOIN bases AS b ON b.id=tt.base_id;
-    
-DELIMITER $$
-CREATE PROCEDURE `bases_delete_unused_bases`()
-	LANGUAGE SQL
-	NOT DETERMINISTIC
-	MODIFIES SQL DATA
-	SQL SECURITY INVOKER
-	COMMENT ''
-BEGIN
-	DROP TABLE IF EXISTS bases_temp;
-	
-	CREATE TEMPORARY TABLE bases_temp (	`base_id` BIGINT NOT NULL,
-		PRIMARY KEY (`base_id`)) ENGINE=MEMORY;
-	
-	INSERT INTO bases_temp (base_id)
-		SELECT base_id
-		FROM tokens_tags_optimized
-		GROUP BY base_id;
-		
-	DELETE
-	FROM bases
-	WHERE id NOT IN (SELECT * FROM bases_temp);
-	DROP TABLE bases_temp;
-END$$
-DELIMITER $$
diff --git a/database/update/update_030_2_reports_annotations.sql b/database/update/update_030_2_reports_annotations.sql
deleted file mode 100644
index 0d65f561..00000000
--- a/database/update/update_030_2_reports_annotations.sql
+++ /dev/null
@@ -1,26 +0,0 @@
-ALTER TABLE `annotation_types`
-	ADD COLUMN `annotation_type_id` INT NOT NULL AUTO_INCREMENT FIRST,
-	ADD PRIMARY KEY (`annotation_type_id`);
-	
-ALTER TABLE `reports_annotations`
-	ADD COLUMN `type_id` INT(11) NULL DEFAULT NULL AFTER `type`;
-	
-ALTER TABLE `reports_annotations`
-	DROP FOREIGN KEY `reports_annotations_ibfk_1`;
-	
-UPDATE reports_annotations 
-SET type_id = (SELECT annotation_type_id FROM annotation_types WHERE annotation_types.name=reports_annotations.type COLLATE utf8_bin);
-
-ALTER TABLE `reports_annotations`
-	DROP COLUMN `type`;
-
-ALTER TABLE `reports_annotations`
-	ADD CONSTRAINT `FK_annotations_types` FOREIGN KEY (`type_id`) REFERENCES `annotation_types` (`annotation_type_id`) ON UPDATE CASCADE ON DELETE CASCADE;
-
-RENAME TABLE `reports_annotations` TO `reports_annotations_optimized`;
-
-CREATE ALGORITHM = UNDEFINED VIEW `reports_annotations` AS 
-	SELECT ra.id, report_id, type_id, at.name AS type, `from`, `to`, text, user_id, creation_time, stage, source
-	FROM reports_annotations_optimized AS ra
-	LEFT JOIN annotation_types AS at ON at.annotation_type_id=ra.type_id 
-    
\ No newline at end of file
diff --git a/database/update/update_030_reports_annotation_lemma.sql b/database/update/update_030_reports_annotation_lemma.sql
deleted file mode 100644
index 33fb52a6..00000000
--- a/database/update/update_030_reports_annotation_lemma.sql
+++ /dev/null
@@ -1,40 +0,0 @@
-INSERT INTO `report_perspectives` (`id`, `title`, `description`, `order`) VALUES ('annotation_lemma', 'Annotation Lemmas', '', '15');
-
--- phpMyAdmin SQL Dump
--- version 4.0.5deb1
--- http://www.phpmyadmin.net
---
--- Host: localhost
--- Generation Time: Sep 06, 2013 at 02:36 PM
--- Server version: 5.5.32-0ubuntu3
--- PHP Version: 5.5.3-1ubuntu1
-
-SET SQL_MODE = "NO_AUTO_VALUE_ON_ZERO";
-SET time_zone = "+00:00";
-
---
--- Database: `inforex`
---
-
--- --------------------------------------------------------
-
---
--- Table structure for table `reports_annotations_lemma`
---
-
-CREATE TABLE IF NOT EXISTS `reports_annotations_lemma` (
-  `report_annotation_id` bigint(20) NOT NULL,
-  `lemma` mediumtext COLLATE utf8_polish_ci NOT NULL,
-  UNIQUE KEY `report_annotation_id` (`report_annotation_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_polish_ci;
-
---
--- Constraints for dumped tables
---
-
---
--- Constraints for table `reports_annotations_lemma`
---
-ALTER TABLE `reports_annotations_lemma`
-  ADD CONSTRAINT `reports_annotations_lemma_ibfk_1` FOREIGN KEY (`report_annotation_id`) REFERENCES `reports_annotations_optimized` (`id`) ON DELETE CASCADE ON UPDATE NO ACTION;
-
diff --git a/database/update/update_031_tokens_tags_ctags_pos.sql b/database/update/update_031_tokens_tags_ctags_pos.sql
deleted file mode 100644
index ed9b66ae..00000000
--- a/database/update/update_031_tokens_tags_ctags_pos.sql
+++ /dev/null
@@ -1,11 +0,0 @@
-ALTER TABLE  `tokens_tags_optimized` ADD FOREIGN KEY (  `ctag_id` ) REFERENCES  `tokens_tags_ctags` (`id`) ON DELETE RESTRICT ON UPDATE RESTRICT;
-
-INSERT INTO `tokens_tags_ctags`(`ctag`) SELECT DISTINCT ctag FROM `tokens_tags_optimized`;
-UPDATE `tokens_tags_optimized` tto JOIN `tokens_tags_ctags` ttc USING(ctag) SET tto.ctag_id = ttc.id;
-
-ALTER TABLE  `tokens_tags_optimized` ADD  `pos` VARCHAR( 20 ) NOT NULL ;
-
-UPDATE `tokens_tags_optimized` SET pos = SUBSTRING_INDEX( SUBSTRING_INDEX(ctag,  ':', 1 ) ,  ':', -1 );
-
-ALTER TABLE `tokens_tags_optimized`  DROP `ctag`;
-ALTER TABLE `tokens_tags_optimized` CHANGE `ctag_id` `ctag_id` INT( 11 ) NOT NULL ;
diff --git a/database/update/update_033_tokens_tags_reload.sql b/database/update/update_033_tokens_tags_reload.sql
deleted file mode 100644
index 58fa55e0..00000000
--- a/database/update/update_033_tokens_tags_reload.sql
+++ /dev/null
@@ -1,5 +0,0 @@
-CREATE ALGORITHM = UNDEFINED VIEW `tokens_tags` AS 
-SELECT token_tag_id,token_id,b.text as base,base_id,ctag,disamb
-FROM tokens_tags_optimized AS tt
-LEFT JOIN bases AS b ON b.id=tt.base_id
-LEFT JOIN tokens_tags_ctags ON(tt.ctag_id = tokens_tags_ctags.id);
\ No newline at end of file
diff --git a/database/update/update_034_ctag_unique.sql b/database/update/update_034_ctag_unique.sql
deleted file mode 100644
index 9e65aa10..00000000
--- a/database/update/update_034_ctag_unique.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE `tokens_tags_ctags` ADD UNIQUE INDEX `ctag_UNIQUE` (`ctag` ASC) ;
\ No newline at end of file
diff --git a/database/update/update_035_no_cascade_delete_for_types.sql b/database/update/update_035_no_cascade_delete_for_types.sql
deleted file mode 100644
index 38f81d80..00000000
--- a/database/update/update_035_no_cascade_delete_for_types.sql
+++ /dev/null
@@ -1,20 +0,0 @@
-ALTER TABLE `reports_annotations_optimized` DROP FOREIGN KEY `FK_reports_annotations_annotation_types` ,
-ADD FOREIGN KEY ( `type_id` ) REFERENCES `gpw`.`annotation_types` (
-`annotation_type_id`
-) ON DELETE RESTRICT ON UPDATE CASCADE ;
-
-ALTER TABLE `relations` DROP FOREIGN KEY `relations_ibfk_5` ,
-ADD FOREIGN KEY ( `relation_type_id` ) REFERENCES `gpw`.`relation_types` (
-`id`
-) ON DELETE RESTRICT ON UPDATE CASCADE ;
-
-ALTER TABLE `relations` DROP FOREIGN KEY `relations_ibfk_7` ,
-ADD FOREIGN KEY ( `source_id` ) REFERENCES `gpw`.`reports_annotations_optimized` (
-`id`
-) ON DELETE RESTRICT ON UPDATE CASCADE ;
-
-ALTER TABLE `relations` DROP FOREIGN KEY `relations_ibfk_8` ,
-ADD FOREIGN KEY ( `target_id` ) REFERENCES `gpw`.`reports_annotations_optimized` (
-`id`
-) ON DELETE RESTRICT ON UPDATE CASCADE ;
-
diff --git a/database/update/update_036_report_content_size.sql b/database/update/update_036_report_content_size.sql
deleted file mode 100644
index 462f2098..00000000
--- a/database/update/update_036_report_content_size.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE `reports` CHANGE `content` `content` MEDIUMTEXT CHARACTER SET utf8 COLLATE utf8_general_ci NOT NULL;
diff --git a/database/update/update_037_shared_attributes.sql b/database/update/update_037_shared_attributes.sql
deleted file mode 100644
index e9090960..00000000
--- a/database/update/update_037_shared_attributes.sql
+++ /dev/null
@@ -1,39 +0,0 @@
--- phpMyAdmin SQL Dump
--- version 4.0.10deb1
--- http://www.phpmyadmin.net
---
--- Host: localhost
--- Generation Time: Feb 05, 2015 at 01:55 PM
--- Server version: 5.5.41-0ubuntu0.14.04.1
--- PHP Version: 5.5.9-1ubuntu4.5
-
-SET SQL_MODE = "NO_AUTO_VALUE_ON_ZERO";
-SET time_zone = "+00:00";
-
-
-/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
-/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
-/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
-/*!40101 SET NAMES utf8 */;
-
---
--- Database: `inforex`
---
-
--- --------------------------------------------------------
-
---
--- Table structure for table `shared_attributes`
---
-
-CREATE TABLE IF NOT EXISTS `shared_attributes` (
-  `id` int(11) NOT NULL AUTO_INCREMENT,
-  `name` varchar(45) CHARACTER SET utf8 DEFAULT NULL,
-  `type` enum('enum','string') CHARACTER SET utf8 DEFAULT NULL,
-  `description` varchar(45) CHARACTER SET utf8 DEFAULT NULL,
-  PRIMARY KEY (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1 AUTO_INCREMENT=1 ;
-
-/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
-/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
-/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
diff --git a/database/update/update_038_shared_attributes_enum.sql b/database/update/update_038_shared_attributes_enum.sql
deleted file mode 100644
index 0d8f5ac7..00000000
--- a/database/update/update_038_shared_attributes_enum.sql
+++ /dev/null
@@ -1,48 +0,0 @@
--- phpMyAdmin SQL Dump
--- version 4.0.10deb1
--- http://www.phpmyadmin.net
---
--- Host: localhost
--- Generation Time: Feb 05, 2015 at 01:55 PM
--- Server version: 5.5.41-0ubuntu0.14.04.1
--- PHP Version: 5.5.9-1ubuntu4.5
-
-SET SQL_MODE = "NO_AUTO_VALUE_ON_ZERO";
-SET time_zone = "+00:00";
-
-
-/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
-/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
-/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
-/*!40101 SET NAMES utf8 */;
-
---
--- Database: `inforex`
---
-
--- --------------------------------------------------------
-
---
--- Table structure for table `shared_attributes_enum`
---
-
-CREATE TABLE IF NOT EXISTS `shared_attributes_enum` (
-  `shared_attribute_id` int(11) NOT NULL AUTO_INCREMENT,
-  `value` varchar(45) CHARACTER SET utf8 NOT NULL,
-  `description` varchar(45) CHARACTER SET utf8 NOT NULL,
-  KEY `shared_attribute_id` (`shared_attribute_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1 AUTO_INCREMENT=1 ;
-
---
--- Constraints for dumped tables
---
-
---
--- Constraints for table `shared_attributes_enum`
---
-ALTER TABLE `shared_attributes_enum`
-  ADD CONSTRAINT `shared_attributes_enum_ibfk_1` FOREIGN KEY (`shared_attribute_id`) REFERENCES `shared_attributes` (`id`) ON DELETE CASCADE ON UPDATE NO ACTION;
-
-/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
-/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
-/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
diff --git a/database/update/update_039_reports_annotations_shared_attributes.sql b/database/update/update_039_reports_annotations_shared_attributes.sql
deleted file mode 100644
index 335f765a..00000000
--- a/database/update/update_039_reports_annotations_shared_attributes.sql
+++ /dev/null
@@ -1,54 +0,0 @@
--- phpMyAdmin SQL Dump
--- version 4.0.10deb1
--- http://www.phpmyadmin.net
---
--- Host: localhost
--- Generation Time: Feb 05, 2015 at 12:56 PM
--- Server version: 5.5.41-0ubuntu0.14.04.1
--- PHP Version: 5.5.9-1ubuntu4.5
-
-SET SQL_MODE = "NO_AUTO_VALUE_ON_ZERO";
-SET time_zone = "+00:00";
-
-
-/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
-/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
-/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
-/*!40101 SET NAMES utf8 */;
-
---
--- Database: `inforex`
---
-
--- --------------------------------------------------------
-
---
--- Table structure for table `reports_annotations_shared_attributes`
---
-
-CREATE TABLE IF NOT EXISTS `reports_annotations_shared_attributes` (
-  `annotation_id` bigint(20) NOT NULL,
-  `shared_attribute_id` int(11) NOT NULL,
-  `value` varchar(45) CHARACTER SET utf8 NOT NULL,
-  `user_id` int(11) NOT NULL,
-  UNIQUE KEY `unique_annotations_shared_attributes_values` (`annotation_id`,`shared_attribute_id`),
-  KEY `annotation_id` (`annotation_id`),
-  KEY `shared_attribute_id` (`shared_attribute_id`),
-  KEY `user_id` (`user_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-
---
--- Constraints for dumped tables
---
-
---
--- Constraints for table `reports_annotations_shared_attributes`
---
-ALTER TABLE `reports_annotations_shared_attributes`
-  ADD CONSTRAINT `reports_annotations_shared_attributes_ibfk_1` FOREIGN KEY (`annotation_id`) REFERENCES `reports_annotations_optimized` (`id`) ON DELETE CASCADE ON UPDATE NO ACTION,
-  ADD CONSTRAINT `reports_annotations_shared_attributes_ibfk_2` FOREIGN KEY (`shared_attribute_id`) REFERENCES `shared_attributes` (`id`) ON DELETE CASCADE ON UPDATE NO ACTION,
-  ADD CONSTRAINT `reports_annotations_shared_attributes_ibfk_3` FOREIGN KEY (`user_id`) REFERENCES `users` (`user_id`) ON DELETE CASCADE ON UPDATE NO ACTION;
-
-/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
-/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
-/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
diff --git a/database/update/update_040_annotation_types_shared_attributes.sql b/database/update/update_040_annotation_types_shared_attributes.sql
deleted file mode 100644
index a6dbbdaa..00000000
--- a/database/update/update_040_annotation_types_shared_attributes.sql
+++ /dev/null
@@ -1,49 +0,0 @@
--- phpMyAdmin SQL Dump
--- version 4.0.10deb1
--- http://www.phpmyadmin.net
---
--- Host: localhost
--- Generation Time: Feb 03, 2015 at 06:22 PM
--- Server version: 5.5.41-0ubuntu0.14.04.1
--- PHP Version: 5.5.9-1ubuntu4.5
-
-SET SQL_MODE = "NO_AUTO_VALUE_ON_ZERO";
-SET time_zone = "+00:00";
-
-
-/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
-/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
-/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
-/*!40101 SET NAMES utf8 */;
-
---
--- Database: `inforex`
---
-
--- --------------------------------------------------------
-
---
--- Table structure for table `annotation_types_shared_attributes`
---
-
-CREATE TABLE IF NOT EXISTS `annotation_types_shared_attributes` (
-  `annotation_type_id` int(11) NOT NULL,
-  `shared_attribute_id` int(11) NOT NULL,
-  KEY `annotation_type_id` (`annotation_type_id`),
-  KEY `shared_attribute_id` (`shared_attribute_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-
---
--- Constraints for dumped tables
---
-
---
--- Constraints for table `annotation_types_shared_attributes`
---
-ALTER TABLE `annotation_types_shared_attributes`
-  ADD CONSTRAINT `annotation_types_shared_attributes_ibfk_2` FOREIGN KEY (`annotation_type_id`) REFERENCES `annotation_types` (`annotation_type_id`) ON DELETE CASCADE ON UPDATE NO ACTION,
-  ADD CONSTRAINT `annotation_types_shared_attributes_ibfk_1` FOREIGN KEY (`shared_attribute_id`) REFERENCES `shared_attributes` (`id`) ON DELETE CASCADE ON UPDATE NO ACTION;
-
-/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
-/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
-/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
diff --git a/database/update/update_041_agreement.sql b/database/update/update_041_agreement.sql
deleted file mode 100644
index 354fe5e5..00000000
--- a/database/update/update_041_agreement.sql
+++ /dev/null
@@ -1,3 +0,0 @@
-UPDATE `corpus_roles` SET `description` = 'Edycja anotacji publicznych' WHERE `corpus_roles`.`role` = 'annotate';
-
-INSERT INTO `corpus_roles` (`role`, `description`) VALUES ('', ''), ('annotate_agreement', 'Edycja anotacji prywatnych na potrzeby badania zgodności.');
diff --git a/database/update/update_042_create_corpus.sql b/database/update/update_042_create_corpus.sql
deleted file mode 100644
index 3a01f034..00000000
--- a/database/update/update_042_create_corpus.sql
+++ /dev/null
@@ -1,3 +0,0 @@
-INSERT INTO `roles` (`role`, `description`) VALUES ('create_corpus', 'Prawo do tworzenia nowych korpusów.');
-
-ALTER TABLE `corpora` CHANGE `ext` `ext` VARCHAR(32) CHARACTER SET utf8 COLLATE utf8_polish_ci NULL;
diff --git a/database/update/update_043_email.sql b/database/update/update_043_email.sql
deleted file mode 100644
index 7f44d9fd..00000000
--- a/database/update/update_043_email.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE `users` CHANGE `email` `email` VARCHAR(256) CHARACTER SET utf8 COLLATE utf8_polish_ci NOT NULL DEFAULT 'unknown';
diff --git a/database/update/update_044_tasks.sql b/database/update/update_044_tasks.sql
deleted file mode 100644
index eb3ebfc8..00000000
--- a/database/update/update_044_tasks.sql
+++ /dev/null
@@ -1,46 +0,0 @@
---
--- Struktura tabeli dla tabeli `tasks`
---
-
-CREATE TABLE IF NOT EXISTS `tasks` (
-  `task_id` int(11) NOT NULL AUTO_INCREMENT,
-  `datetime` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP COMMENT 'Data i czas utworzenia zadania.',
-  `type` varchar(32) COLLATE utf8_polish_ci NOT NULL COMMENT 'Identyfikator zadania.',
-  `parameters` text COLLATE utf8_polish_ci NOT NULL,
-  `corpus_id` int(11) NOT NULL,
-  `user_id` int(11) DEFAULT NULL,
-  `max_steps` int(11) NOT NULL,
-  `current_step` int(11) NOT NULL,
-  `status` enum('new','process','done','error') COLLATE utf8_polish_ci NOT NULL DEFAULT 'new',
-  PRIMARY KEY (`task_id`),
-  KEY `corpus_id` (`corpus_id`),
-  KEY `user_id` (`user_id`)
-) ENGINE=InnoDB  DEFAULT CHARSET=utf8 COLLATE=utf8_polish_ci AUTO_INCREMENT=44 ;
-
---
--- Ograniczenia dla zrzutów tabel
---
-
---
--- Ograniczenia dla tabeli `tasks`
---
-ALTER TABLE `tasks`
-  ADD CONSTRAINT `tasks_ibfk_2` FOREIGN KEY (`user_id`) REFERENCES `users` (`user_id`) ON DELETE SET NULL ON UPDATE CASCADE,
-  ADD CONSTRAINT `tasks_ibfk_1` FOREIGN KEY (`corpus_id`) REFERENCES `corpora` (`id`) ON DELETE CASCADE ON UPDATE CASCADE;
-
-CREATE TABLE IF NOT EXISTS `tasks_reports` (
-  `task_id` int(11) NOT NULL,
-  `report_id` bigint(11) NOT NULL,
-  `status` enum('new','process','done','error') COLLATE utf8_polish_ci NOT NULL,
-  `message` TEXT,
-  KEY `document_id` (`report_id`),
-  KEY `task_id` (`task_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_polish_ci;
-
-
-ALTER TABLE `tasks_reports`
-  ADD CONSTRAINT `tasks_reports_ibfk_2` FOREIGN KEY (`report_id`) REFERENCES `reports` (`id`) ON DELETE CASCADE ON UPDATE CASCADE,
-  ADD CONSTRAINT `tasks_reports_ibfk_1` FOREIGN KEY (`task_id`) REFERENCES `tasks` (`task_id`) ON DELETE CASCADE ON UPDATE CASCADE;
-
-
-INSERT INTO `corpus_roles` (`role`, `description`) VALUES ('tasks', 'Wykonywanie masowych zadań na dokumentach');
diff --git a/database/update/update_045_tasks_update.sql b/database/update/update_045_tasks_update.sql
deleted file mode 100644
index 383fa6a9..00000000
--- a/database/update/update_045_tasks_update.sql
+++ /dev/null
@@ -1,2 +0,0 @@
-ALTER TABLE `tasks` ADD `description` TEXT NULL AFTER `type`;
-ALTER TABLE `tasks` ADD `message` TEXT NULL ;
diff --git a/database/update/update_046_wccl_rules.sql b/database/update/update_046_wccl_rules.sql
deleted file mode 100644
index 1d6dd216..00000000
--- a/database/update/update_046_wccl_rules.sql
+++ /dev/null
@@ -1,14 +0,0 @@
-CREATE TABLE IF NOT EXISTS `wccl_rules` (
-  `wccl_rule_id` int(11) NOT NULL AUTO_INCREMENT,
-  `user_id` int(11) NOT NULL,
-  `corpus_id` int(11) NOT NULL,
-  `rules` text COLLATE utf8_polish_ci,
-  PRIMARY KEY (`wccl_rule_id`),
-  UNIQUE KEY `user_id` (`user_id`,`corpus_id`),
-  KEY `user_id_2` (`user_id`),
-  KEY `corpus_id` (`corpus_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_polish_ci AUTO_INCREMENT=1 ;
-
-ALTER TABLE `wccl_rules`
-  ADD CONSTRAINT `wccl_rules_ibfk_2` FOREIGN KEY (`corpus_id`) REFERENCES `corpora` (`id`) ON DELETE CASCADE ON UPDATE CASCADE,
-  ADD CONSTRAINT `wccl_rules_ibfk_1` FOREIGN KEY (`user_id`) REFERENCES `users` (`user_id`) ON DELETE CASCADE ON UPDATE CASCADE;
diff --git a/database/update/update_047_user_login_max_size.sql b/database/update/update_047_user_login_max_size.sql
deleted file mode 100644
index 00706c2d..00000000
--- a/database/update/update_047_user_login_max_size.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE `users` CHANGE `login` `login` VARCHAR( 64 ) CHARACTER SET utf8 COLLATE utf8_general_ci NOT NULL;
\ No newline at end of file
diff --git a/database/update/update_048_tasks_datetime_start.sql b/database/update/update_048_tasks_datetime_start.sql
deleted file mode 100644
index 77a29972..00000000
--- a/database/update/update_048_tasks_datetime_start.sql
+++ /dev/null
@@ -1,2 +0,0 @@
-ALTER TABLE `tasks` 
-ADD COLUMN `datetime_start` TIMESTAMP NULL DEFAULT NULL AFTER `datetime`;
diff --git a/database/update/update_048_wccl_match_annotations.sql b/database/update/update_048_wccl_match_annotations.sql
deleted file mode 100644
index ec726933..00000000
--- a/database/update/update_048_wccl_match_annotations.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE `wccl_rules` ADD `annotations` TEXT NULL ;
\ No newline at end of file
diff --git a/database/update/update_050_no_cascade.sql b/database/update/update_050_no_cascade.sql
deleted file mode 100644
index 80c928eb..00000000
--- a/database/update/update_050_no_cascade.sql
+++ /dev/null
@@ -1,9 +0,0 @@
-ALTER TABLE `reports` DROP FOREIGN KEY `reports_ibfk_7` ,
-ADD FOREIGN KEY ( `subcorpus_id` ) REFERENCES `inforex`.`corpus_subcorpora` (
-`subcorpus_id`
-) ON DELETE SET NULL ON UPDATE CASCADE ;
-
-ALTER TABLE `reports` DROP FOREIGN KEY `reports_ibfk_8` ,
-ADD FOREIGN KEY ( `type` ) REFERENCES `inforex`.`reports_types` (
-`id`
-) ON DELETE SET NULL ON UPDATE CASCADE ;
diff --git a/database/update/update_051_agreement.sql b/database/update/update_051_agreement.sql
deleted file mode 100644
index cb3c0b14..00000000
--- a/database/update/update_051_agreement.sql
+++ /dev/null
@@ -1,14 +0,0 @@
-UPDATE `corpus_roles` SET description='Edycja anotacji prywatnych' WHERE role='annotate_agreement';
-
-ALTER TABLE  `reports_annotations_optimized` CHANGE  `stage`  `stage` ENUM(  'new',  'final',  'discarded',  'agreement' ) CHARACTER SET utf8 COLLATE utf8_polish_ci NOT NULL DEFAULT  'final';
-
-ALTER TABLE `corpus_roles` ADD `description_long` TEXT NOT NULL ;
-
-INSERT INTO `corpus_roles` (
-`role` ,
-`description` ,
-`description_long`
-)
-VALUES (
-'agreement_check', 'Sprawdzanie zgodności anotatorów', 'Dostęp do strony z wynikami zgodności anotatorów. '
-);
diff --git a/database/update/update_052_flag_description.sql b/database/update/update_052_flag_description.sql
deleted file mode 100644
index 70b3bb26..00000000
--- a/database/update/update_052_flag_description.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE `corpora_flags` ADD `description` TEXT NOT NULL ;
\ No newline at end of file
diff --git a/database/update/update_053_role_delete_annotations.sql b/database/update/update_053_role_delete_annotations.sql
deleted file mode 100644
index 6ecb3d9a..00000000
--- a/database/update/update_053_role_delete_annotations.sql
+++ /dev/null
@@ -1 +0,0 @@
-INSERT INTO `corpus_roles` (`role`, `description`, `description_long`) VALUES ('delete_annotations', 'Prawo do usuwania anotacji', 'Użytkownik może usuwać anotacje (dotyczy anotacji publicznych i prywatnych)');
\ No newline at end of file
diff --git a/database/update/update_054_exports.sql b/database/update/update_054_exports.sql
deleted file mode 100644
index 085563b8..00000000
--- a/database/update/update_054_exports.sql
+++ /dev/null
@@ -1,28 +0,0 @@
-CREATE TABLE IF NOT EXISTS `exports` (
-  `export_id` bigint(20) NOT NULL AUTO_INCREMENT,
-  `corpus_id` int(20) NOT NULL,
-  `datetime_submit` datetime NOT NULL,
-  `datetime_start` datetime DEFAULT NULL,
-  `datetime_finish` datetime DEFAULT NULL,
-  `status` enum('new','process','done','error') COLLATE utf8_polish_ci NOT NULL DEFAULT 'new',
-  `description` text COLLATE utf8_polish_ci NOT NULL,
-  `selectors` text COLLATE utf8_polish_ci NOT NULL,
-  `extractors` text COLLATE utf8_polish_ci NOT NULL,
-  `indices` text COLLATE utf8_polish_ci NOT NULL,
-  `message` text COLLATE utf8_polish_ci NOT NULL,
-  PRIMARY KEY (`export_id`),
-  KEY `corpus_id` (`corpus_id`),
-  KEY `status` (`status`)
-) ENGINE=InnoDB  DEFAULT CHARSET=utf8 COLLATE=utf8_polish_ci COMMENT='Tabela z historią zadań eksportu korpusów' AUTO_INCREMENT=1 ;
-
-ALTER TABLE `exports`
-  ADD CONSTRAINT `exports_ibfk_1` FOREIGN KEY (`corpus_id`) REFERENCES `corpora` (`id`) ON DELETE CASCADE ON UPDATE CASCADE;
-
-INSERT INTO  `corpus_roles` (
-`role` ,
-`description` ,
-`description_long`
-)
-VALUES (
-'export',  'Eksport korpusu',  'Umożliwia wyeksportowanie określonych dokumentów i danych do postaci plików.'
-);
\ No newline at end of file
diff --git a/database/update/update_055_checkboxes.sql b/database/update/update_055_checkboxes.sql
deleted file mode 100644
index fd5b22f1..00000000
--- a/database/update/update_055_checkboxes.sql
+++ /dev/null
@@ -1,36 +0,0 @@
--- phpMyAdmin SQL Dump
--- version 4.0.10deb1
--- http://www.phpmyadmin.net
---
--- Host: localhost
--- Generation Time: Feb 28, 2017 at 10:15 AM
--- Server version: 5.5.54-0ubuntu0.14.04.1
--- PHP Version: 5.5.9-1ubuntu4.21
-
-SET SQL_MODE = "NO_AUTO_VALUE_ON_ZERO";
-SET time_zone = "+00:00";
-
-
-/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
-/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
-/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
-/*!40101 SET NAMES utf8 */;
-
---
--- Database: `inforex`
---
-
--- --------------------------------------------------------
-
---
--- Table structure for table `users_checkboxes`
---
-
-CREATE TABLE IF NOT EXISTS `users_checkboxes` (
-  `user_id` int(11) NOT NULL,
-  `report_id` bigint(20) NOT NULL
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-
-/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
-/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
-/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
\ No newline at end of file
diff --git a/database/update/update_055_missing_field.sql b/database/update/update_055_missing_field.sql
deleted file mode 100644
index 18438967..00000000
--- a/database/update/update_055_missing_field.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE  `tasks` ADD  `datetime_start` TIMESTAMP NOT NULL AFTER  `datetime`;
\ No newline at end of file
diff --git a/database/update/update_056_report_lang.sql b/database/update/update_056_report_lang.sql
deleted file mode 100644
index abf6971a..00000000
--- a/database/update/update_056_report_lang.sql
+++ /dev/null
@@ -1,2 +0,0 @@
-ALTER TABLE  `reports` ADD  `lang` VARCHAR( 3 ) NULL ,
-ADD INDEX (  `lang` );
\ No newline at end of file
diff --git a/database/update/update_057_report_user_selection.sql b/database/update/update_057_report_user_selection.sql
deleted file mode 100644
index 439288ef..00000000
--- a/database/update/update_057_report_user_selection.sql
+++ /dev/null
@@ -1 +0,0 @@
-RENAME TABLE `users_checkboxes` TO `reports_users_selection`;
\ No newline at end of file
diff --git a/database/update/update_058_annotation_types.sql b/database/update/update_058_annotation_types.sql
deleted file mode 100644
index f06d2720..00000000
--- a/database/update/update_058_annotation_types.sql
+++ /dev/null
@@ -1,12 +0,0 @@
-CREATE TABLE IF NOT EXISTS `annotation_types_shortlist` (
-  `annotation_type_id` int(11) NOT NULL,
-  `user_id` int(11) NOT NULL,
-  `shortlist` int(11) NOT NULL
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-
-ALTER TABLE `annotation_types`
-ADD `shortlist` int(11) DEFAULT 0;
-
-UPDATE `annotation_types` SET `shortlist`= 0 WHERE 1;
-
-DROP TABLE `annotation_types_common`;
diff --git a/database/update/update_059_annotation_access.sql b/database/update/update_059_annotation_access.sql
deleted file mode 100644
index 36ac316b..00000000
--- a/database/update/update_059_annotation_access.sql
+++ /dev/null
@@ -1,2 +0,0 @@
-ALTER TABLE  `annotation_sets` ADD  `public` INT NOT NULL DEFAULT  '1';
-ALTER TABLE  `annotation_sets` ADD  `user_id` INT( 11 ) NOT NULL DEFAULT  '1';
\ No newline at end of file
diff --git a/database/update/update_059_users_acitivities.sql b/database/update/update_059_users_acitivities.sql
deleted file mode 100644
index 1c81c062..00000000
--- a/database/update/update_059_users_acitivities.sql
+++ /dev/null
@@ -1,33 +0,0 @@
-CREATE TABLE IF NOT EXISTS `ips` (
-  `ip_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `ip` char(39) COLLATE utf8_bin NOT NULL,
-  PRIMARY KEY (`ip_id`),
-  UNIQUE KEY `ip` (`ip`)
-) ENGINE=InnoDB  DEFAULT CHARSET=utf8 COLLATE=utf8_bin ;
-
-CREATE TABLE IF NOT EXISTS `activity_types` (
-  `activity_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `category` varchar(16) COLLATE utf8_bin NOT NULL,
-  `name` varchar(32) COLLATE utf8_bin DEFAULT NULL,
-  KEY `activity_type_id` (`activity_type_id`)
-) ENGINE=InnoDB  DEFAULT CHARSET=utf8 COLLATE=utf8_bin;
-
-CREATE TABLE IF NOT EXISTS `activities` (
-  `activity_page_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
-  `datetime` datetime NOT NULL,
-  `ip_id` int(10) unsigned NOT NULL,
-  `user_id` int(11) DEFAULT NULL,
-  `corpus_id` int(11) DEFAULT NULL,
-  `report_id` int(11) DEFAULT NULL,
-  `activity_type_id` int(11) NOT NULL,
-  `execution_time` smallint(5) unsigned DEFAULT NULL,
-  PRIMARY KEY (`activity_page_id`),
-  KEY `ip_id` (`ip_id`),
-  KEY `user_id` (`user_id`),
-  KEY `corpus_id` (`corpus_id`),
-  KEY `report_id` (`report_id`),
-  KEY `activity_type_id` (`activity_type_id`),
-  KEY `datetime` (`datetime`)
-) ENGINE=InnoDB  DEFAULT CHARSET=utf8 COLLATE=utf8_bin;
-
-CREATE  VIEW `activities_view_users` AS select `u`.`screename` AS `screename`,count(0) AS `COUNT(*)`,max(`a`.`datetime`) AS `last_datetime`,`a`.`activity_page_id` AS `activity_page_id`,`a`.`datetime` AS `datetime`,`a`.`ip_id` AS `ip_id`,`a`.`user_id` AS `user_id`,`a`.`corpus_id` AS `corpus_id`,`a`.`report_id` AS `report_id`,`a`.`activity_type_id` AS `activity_type_id`,`a`.`execution_time` AS `execution_time` from (`activities` `a` join `users` `u` on((`a`.`user_id` = `u`.`user_id`))) group by `a`.`user_id`;
diff --git a/database/update/update_060_annotation_sets.sql b/database/update/update_060_annotation_sets.sql
deleted file mode 100644
index 2ee62cb4..00000000
--- a/database/update/update_060_annotation_sets.sql
+++ /dev/null
@@ -1,11 +0,0 @@
-ALTER TABLE `annotation_sets` CHANGE `nested` `nested` TINYINT(1) NOT NULL DEFAULT '0';
-ALTER TABLE `annotation_types` CHANGE `cross_sentence` `cross_sentence` TINYINT(1) NOT NULL DEFAULT '0';
-
-ALTER TABLE `annotation_sets` CHANGE `description` `name` VARCHAR(255) CHARACTER SET utf8 COLLATE utf8_general_ci NOT NULL;
-ALTER TABLE `annotation_sets` ADD `description` TEXT NOT NULL AFTER `name`;
-
-ALTER TABLE `annotation_subsets` CHANGE `description` `name` VARCHAR(64) CHARACTER SET utf8 COLLATE utf8_general_ci NOT NULL;
-ALTER TABLE `annotation_subsets` ADD `description` TEXT CHARACTER SET utf8 COLLATE utf8_general_ci NOT NULL AFTER `name`;
-
-ALTER TABLE `activity_types` CHANGE `name` `name` VARCHAR(128) CHARACTER SET utf8 COLLATE utf8_bin NULL DEFAULT NULL;
-ALTER TABLE `annotation_types` CHANGE `level` `level` INT(11) NOT NULL DEFAULT '0';
\ No newline at end of file
diff --git a/database/update/update_061_relation_edit.sql b/database/update/update_061_relation_edit.sql
deleted file mode 100644
index 9b90c0bb..00000000
--- a/database/update/update_061_relation_edit.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE  `relations_groups` ADD  `annotation_type_id` INT( 11 ) NULL DEFAULT NULL AFTER  `annotation_subset_id` ;
diff --git a/database/update/update_062_relation_sets.sql b/database/update/update_062_relation_sets.sql
deleted file mode 100644
index daac1fc1..00000000
--- a/database/update/update_062_relation_sets.sql
+++ /dev/null
@@ -1,6 +0,0 @@
-ALTER TABLE  `relation_sets` ADD  `description` TEXT NOT NULL ;
-
-CREATE TABLE IF NOT EXISTS `corpora_relations` (
-  `corpus_id` int(11) NOT NULL,
-  `relation_set_id` int(11) NOT NULL
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
\ No newline at end of file
diff --git a/database/update/update_063_shared_annotation_sets.sql b/database/update/update_063_shared_annotation_sets.sql
deleted file mode 100644
index cbddccad..00000000
--- a/database/update/update_063_shared_annotation_sets.sql
+++ /dev/null
@@ -1,4 +0,0 @@
-CREATE TABLE IF NOT EXISTS `users_annotation_sets` (
-  `user_id` int(11) NOT NULL,
-  `annotation_set_id` int(11) NOT NULL
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
\ No newline at end of file
diff --git a/database/update/update_064_private_relation_sets.sql b/database/update/update_064_private_relation_sets.sql
deleted file mode 100644
index 14bd4b05..00000000
--- a/database/update/update_064_private_relation_sets.sql
+++ /dev/null
@@ -1,2 +0,0 @@
-ALTER TABLE  `relation_sets` ADD  `public` INT( 1 ) NOT NULL DEFAULT  '0',
-  ADD  `user_id` INT( 11 ) NOT NULL DEFAULT  '1';
\ No newline at end of file
diff --git a/database/update/update_065_annotation_sets_corpora.sql b/database/update/update_065_annotation_sets_corpora.sql
deleted file mode 100644
index b5115318..00000000
--- a/database/update/update_065_annotation_sets_corpora.sql
+++ /dev/null
@@ -1,7 +0,0 @@
-CREATE TABLE IF NOT EXISTS `annotation_sets_corpora` (
-  `annotation_set_id` int(11) NOT NULL,
-  `corpus_id` int(11) NOT NULL,
-  PRIMARY KEY (`annotation_set_id`,`corpus_id`),
-  KEY `annotation_set_id` (`annotation_set_id`),
-  KEY `corpus_id` (`corpus_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_polish_ci;
\ No newline at end of file
diff --git a/database/update/update_066_morpho_disamb.sql b/database/update/update_066_morpho_disamb.sql
deleted file mode 100644
index aceee914..00000000
--- a/database/update/update_066_morpho_disamb.sql
+++ /dev/null
@@ -1,53 +0,0 @@
--- create table tagsets
-
-CREATE TABLE IF NOT EXISTS `tagsets` (
-  `tagset_id` int(11) NOT NULL AUTO_INCREMENT,
-  `name` varchar(30) NOT NULL,
-  PRIMARY KEY (`tagset_id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_polish_ci;
-
-
--- add fields to tokens_tags_optimized
---  user default NULL
-
-ALTER TABLE  `tokens_tags_optimized` ADD  `user_id` INT NULL DEFAULT NULL;
-
--- adding foreign key constraints
-ALTER TABLE `tokens_tags_optimized`
-ADD FOREIGN KEY (`user_id`) REFERENCES `users`(`user_id`);
-
--- adding tagset_id to tags
-ALTER TABLE  `tokens_tags_ctags`
-ADD COLUMN tagset_id INT DEFAULT NULL ,
-ADD FOREIGN KEY  `fk_tagset` ( tagset_id ) REFERENCES tagsets( tagset_id ) ;
-
--- delete unique on ctag
-ALTER TABLE  `tokens_tags_ctags` DROP INDEX  `ctag_UNIQUE` ;
-
--- add uniqe on ctag and tagset
-ALTER TABLE  `tokens_tags_ctags` ADD CONSTRAINT  `ctag_tagset_UNIQUE` UNIQUE (
-`ctag` ,
-`tagset_id`
-);
-
--- adding new role into corpus_roles
-INSERT INTO  `corpus_roles` (
-`role` ,
-`description` ,
-`description_long`
-)
-VALUES (
-'agreement_morpho',  'Sprawdzanie zgodności dezambiguacji morfologicznych i wybór ostatecznej wersji.',  'Użytkownik widzi decyzje anotatorów i wybiera ostateczną wersję.'
-);
-
--- inserting NKJP tagset into `tagsets`
-INSERT INTO `tagsets` (`name`) VALUES ("nkjp");
-
--- setting tagset_id of all tokens_tags_ctags to that of "nkjp"
-UPDATE  `tokens_tags_ctags` dest,
-(
-SELECT *
-FROM  `tagsets`
-WHERE  `name` LIKE  "nkjp"
-)src
-SET dest.`tagset_id` = src.`tagset_id`;
\ No newline at end of file
diff --git a/database/update/update_066_relations.sql b/database/update/update_066_relations.sql
deleted file mode 100644
index 611b41b3..00000000
--- a/database/update/update_066_relations.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE `relations` ADD `stage` ENUM( 'final', 'discarded', 'agreement' ) NOT NULL DEFAULT 'final';
\ No newline at end of file
diff --git a/database/update/update_067_federation_login_clarin.sql b/database/update/update_067_federation_login_clarin.sql
deleted file mode 100644
index 3616fd50..00000000
--- a/database/update/update_067_federation_login_clarin.sql
+++ /dev/null
@@ -1,3 +0,0 @@
--- alter table
-
-ALTER TABLE  `users` ADD  `clarin_login` VARCHAR( 256 ) CHARACTER SET utf8 COLLATE utf8_general_ci NULL ;
diff --git a/database/update/update_068_morphodisamb_agreement.sql b/database/update/update_068_morphodisamb_agreement.sql
deleted file mode 100644
index 2d3500c8..00000000
--- a/database/update/update_068_morphodisamb_agreement.sql
+++ /dev/null
@@ -1,6 +0,0 @@
--- add stage field to tokens_tags_optimized
-
-ALTER TABLE  `tokens_tags_optimized`
-ADD  `stage` ENUM(  'tagger',  'agreement',  'final' )
-CHARACTER SET utf8 COLLATE utf8_general_ci NOT NULL DEFAULT  'tagger'
-COMMENT  'Describes stage of chosen tag, tagger- generated by tagger, agreement- set by user, final- set by final user with agreement check';
\ No newline at end of file
diff --git a/database/update/update_069_adding_report_prespectives_for_morpho.sql b/database/update/update_069_adding_report_prespectives_for_morpho.sql
deleted file mode 100644
index d431a3a3..00000000
--- a/database/update/update_069_adding_report_prespectives_for_morpho.sql
+++ /dev/null
@@ -1,5 +0,0 @@
--- inserting pages morphodisamb and morphodisambagreement
-
-INSERT INTO `report_perspectives` (`id`, `title`, `description`, `order`) VALUES
-("morphodisamb","Morphological Disambiguation","Show and edit user morphological disamgibuations",300),
-("morphodisambagreement","Morphological Disambiguation Agreement","Show and edit final morphological disambiguations",310);
\ No newline at end of file
diff --git a/database/update/update_070_relation_agreement.sql b/database/update/update_070_relation_agreement.sql
deleted file mode 100644
index e36ed911..00000000
--- a/database/update/update_070_relation_agreement.sql
+++ /dev/null
@@ -1,2 +0,0 @@
-ALTER TABLE  `relations` ADD INDEX (  `stage` ) ;
-INSERT INTO `report_perspectives` (`id`, `title`, `description`, `order`) VALUES ('relation_agreement', 'Relation agreement', '', '11');
\ No newline at end of file
diff --git a/database/update/update_071_annotation_agreement.sql b/database/update/update_071_annotation_agreement.sql
deleted file mode 100644
index 3985adb6..00000000
--- a/database/update/update_071_annotation_agreement.sql
+++ /dev/null
@@ -1 +0,0 @@
-UPDATE `report_perspectives` SET  `title` =  'Annotation agreement' WHERE  `report_perspectives`.`id` =  'agreement';
\ No newline at end of file
diff --git a/database/update/update_071_default_nulls.sql b/database/update/update_071_default_nulls.sql
deleted file mode 100644
index 436ab4c5..00000000
--- a/database/update/update_071_default_nulls.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE `exports` CHANGE `description` `description` TEXT CHARACTER SET utf8 COLLATE utf8_polish_ci NULL, CHANGE `selectors` `selectors` TEXT CHARACTER SET utf8 COLLATE utf8_polish_ci NULL, CHANGE `extractors` `extractors` TEXT CHARACTER SET utf8 COLLATE utf8_polish_ci NULL, CHANGE `indices` `indices` TEXT CHARACTER SET utf8 COLLATE utf8_polish_ci NULL, CHANGE `message` `message` TEXT CHARACTER SET utf8 COLLATE utf8_polish_ci NULL;
\ No newline at end of file
diff --git a/database/update/update_072_tonekization_null.sql b/database/update/update_072_tonekization_null.sql
deleted file mode 100644
index ca687160..00000000
--- a/database/update/update_072_tonekization_null.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE `reports` CHANGE `tokenization` `tokenization` VARCHAR(32) CHARACTER SET utf8 COLLATE utf8_polish_ci NULL DEFAULT NULL;
\ No newline at end of file
diff --git a/database/update/update_073_reports_nulls.sql b/database/update/update_073_reports_nulls.sql
deleted file mode 100644
index 67cfb663..00000000
--- a/database/update/update_073_reports_nulls.sql
+++ /dev/null
@@ -1,5 +0,0 @@
-ALTER TABLE  `reports` CHANGE  `date`  `date` DATE NULL DEFAULT NULL ,
-CHANGE  `title`  `title` TEXT CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL ,
-CHANGE  `source`  `source` TEXT CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL ,
-CHANGE  `author`  `author` VARCHAR( 128 ) CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL ,
-CHANGE  `content`  `content` MEDIUMTEXT CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL
\ No newline at end of file
diff --git a/database/update/update_074_exports.sql b/database/update/update_074_exports.sql
deleted file mode 100644
index d30cf5b0..00000000
--- a/database/update/update_074_exports.sql
+++ /dev/null
@@ -1,19 +0,0 @@
-ALTER TABLE  `exports` ADD  `progress` INT NOT NULL DEFAULT  '0';
-ALTER TABLE `exports` ADD `statistics` TEXT NULL DEFAULT NULL AFTER `progress`;
-
-CREATE TABLE `export_errors` (
-  `id` int(11) NOT NULL,
-  `export_id` int(11) NOT NULL,
-  `message` text NOT NULL
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-
-ALTER TABLE `export_errors`
-  ADD PRIMARY KEY (`id`);
-
-ALTER TABLE `export_errors`
-  MODIFY `id` int(11) NOT NULL AUTO_INCREMENT;
-
-ALTER TABLE `export_errors` ADD `error_details` TEXT NOT NULL AFTER `message`;
-ALTER TABLE `export_errors` ADD `count` INT NOT NULL AFTER `error_details`;
-ALTER TABLE `export_errors` CHANGE `message` `message` TEXT CHARACTER SET utf8 COLLATE utf8_general_ci NOT NULL;
-ALTER TABLE `export_errors` CHANGE `error_details` `error_details` TEXT CHARACTER SET utf8 COLLATE utf8_general_ci NOT NULL;
\ No newline at end of file
diff --git a/database/update/update_075_add_tagger_field_to_exports.sql b/database/update/update_075_add_tagger_field_to_exports.sql
deleted file mode 100644
index 9671a0ed..00000000
--- a/database/update/update_075_add_tagger_field_to_exports.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE  `exports` ADD  `tagging` VARCHAR( 16 ) DEFAULT "tagger" NOT NULL AFTER  `indices`;
\ No newline at end of file
diff --git a/database/update/update_075_corpora_date.sql b/database/update/update_075_corpora_date.sql
deleted file mode 100644
index 2cc4305b..00000000
--- a/database/update/update_075_corpora_date.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE `corpora` ADD `date_created` DATETIME NULL DEFAULT NULL AFTER `ext`;
\ No newline at end of file
diff --git a/database/update/update_075_upload.sql b/database/update/update_075_upload.sql
deleted file mode 100644
index a03ecd8e..00000000
--- a/database/update/update_075_upload.sql
+++ /dev/null
@@ -1,8 +0,0 @@
-ALTER TABLE `reports` ADD `filename` TEXT NULL AFTER `lang`;
-ALTER TABLE `reports` CHANGE `tokenization` `tokenization` VARCHAR(32) CHARACTER SET utf8 COLLATE utf8_polish_ci NULL;
-
-ALTER TABLE `reports` CHANGE `date` `date` DATE NULL,
-CHANGE `title` `title` TEXT CHARACTER SET utf8 COLLATE utf8_general_ci NULL,
-CHANGE `source` `source` TEXT CHARACTER SET utf8 COLLATE utf8_general_ci NULL,
-CHANGE `author` `author` VARCHAR(128) CHARACTER SET utf8 COLLATE utf8_general_ci NULL,
-CHANGE `content` `content` MEDIUMTEXT CHARACTER SET utf8 COLLATE utf8_general_ci NULL;
\ No newline at end of file
diff --git a/database/update/update_076_flags.sql b/database/update/update_076_flags.sql
deleted file mode 100644
index 99617908..00000000
--- a/database/update/update_076_flags.sql
+++ /dev/null
@@ -1,59 +0,0 @@
--- Flag status history table.
-CREATE TABLE `flag_status_history` (
-  `report_id` bigint(20) NOT NULL,
-  `flag_id` int(11) NOT NULL,
-  `user_id` int(11) NOT NULL,
-  `new_status` int(11) NOT NULL,
-  `old_status` int(11) NOT NULL,
-  `date` DATETIME NOT NULL
-) ENGINE=InnoDB;
-
-ALTER TABLE `flag_status_history`
-  ADD KEY `report_id` (`report_id`),
-  ADD KEY `flag_id` (`flag_id`),
-  ADD KEY `user_id` (`user_id`),
-  ADD KEY `new_status` (`new_status`),
-  ADD KEY `old_status` (`old_status`);
-
-ALTER TABLE `flag_status_history`
-  ADD CONSTRAINT `flag_status_history_ibfk_1` FOREIGN KEY (`report_id`) REFERENCES `reports` (`id`),
-  ADD CONSTRAINT `flag_status_history_ibfk_2` FOREIGN KEY (`flag_id`) REFERENCES `corpora_flags` (`corpora_flag_id`),
-  ADD CONSTRAINT `flag_status_history_ibfk_3` FOREIGN KEY (`user_id`) REFERENCES `users` (`user_id`),
-  ADD CONSTRAINT `flag_status_history_ibfk_4` FOREIGN KEY (`new_status`) REFERENCES `flags` (`flag_id`),
-  ADD CONSTRAINT `flag_status_history_ibfk_5` FOREIGN KEY (`old_status`) REFERENCES `flags` (`flag_id`);
-
-ALTER TABLE `flag_status_history` ADD `id` BIGINT(22) NOT NULL AUTO_INCREMENT FIRST, ADD PRIMARY KEY (`id`);
-
--- Stored procedure
-DROP procedure IF EXISTS `changeFlagStatus`;
-
-DELIMITER $$
-CREATE PROCEDURE `changeFlagStatus`(
-  IN flag_id INT(11),
-  IN flag_status INT(11),
-  IN report_id INT(11),
-  IN user_id INT(11))
-  BEGIN
-    -- Previous flag status.
-    DECLARE old_status INT(11);
-
-    -- Store the previous flag status into old_status variable.
-    SELECT rf.flag_id INTO old_status FROM reports_flags rf
-    WHERE (rf.report_id = report_id AND rf.corpora_flag_id = flag_id);
-
-    -- Update the document's flag status.
-    REPLACE INTO reports_flags(corpora_flag_id, report_id, flag_id)
-    VALUES(flag_id, report_id, flag_status);
-
-    -- Store the change in the flag status history table.
-    INSERT INTO flag_status_history (date, report_id, flag_id, user_id, new_status, old_status)
-    VALUES (CURRENT_TIMESTAMP, report_id, flag_id, user_id, flag_status, IFNULL(old_status,-1));
-  END$$
-
-DELIMITER ;
-
--- Adding perspective
-INSERT INTO `report_perspectives` (`id`, `title`, `description`, `order`) VALUES ('flag_history', 'Flag history', 'Show the history of flag changes.', '320');
-
--- Adding corpus role
-INSERT INTO `corpus_roles` (`role`, `description`, `description_long`) VALUES ('flag_history', 'Sprawdzanie historii flag', '');
diff --git a/database/update/update_076_roles.sql b/database/update/update_076_roles.sql
deleted file mode 100644
index 5178f202..00000000
--- a/database/update/update_076_roles.sql
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
-Changing the length of the role column in roles and users_roles tables.
- */
-LOCK TABLES
-roles WRITE,
-users_roles WRITE;
-
-ALTER TABLE users_roles
-DROP FOREIGN KEY users_roles_ibfk_2;
-
-ALTER TABLE users_roles MODIFY role varchar(32);
-
-ALTER TABLE roles MODIFY role varchar(32);
-ALTER TABLE users_roles
-ADD CONSTRAINT users_roles_ibfk_2 FOREIGN KEY (role)
-REFERENCES roles (role);
-
-UNLOCK TABLES;
-
-/*
-Adding new roles
- */
-INSERT INTO `roles` (`role`, `description`) VALUES ('editor_schema_events', 'Edit schema events.');
-INSERT INTO `roles` (`role`, `description`) VALUES ('editor_schema_relations', 'Edit schema relations.');
\ No newline at end of file
diff --git a/database/update/update_077_tagsets.sql b/database/update/update_077_tagsets.sql
deleted file mode 100644
index 3696b7b1..00000000
--- a/database/update/update_077_tagsets.sql
+++ /dev/null
@@ -1,2 +0,0 @@
-INSERT INTO `tagsets` (`tagset_id`, `name`) VALUES ('2', 'English'), ('3', 'German');
-ALTER TABLE `reports` CHANGE `tokenization` `tokenization` VARCHAR(255) CHARACTER SET utf8 COLLATE utf8_polish_ci NULL DEFAULT NULL;
\ No newline at end of file
diff --git a/database/update/update_078_annotation_types_attributes.sql b/database/update/update_078_annotation_types_attributes.sql
deleted file mode 100644
index e4c747c8..00000000
--- a/database/update/update_078_annotation_types_attributes.sql
+++ /dev/null
@@ -1,32 +0,0 @@
-START TRANSACTION;
-
-DROP TABLE IF EXISTS `annotation_types_attributes_temp`;
-
-CREATE TABLE `annotation_types_attributes_temp` ( `id` INT(11) NOT NULL , `annotation_type_id` INT(11) NOT NULL , `name` VARCHAR(32) NOT NULL , `type` ENUM('radio', 'string') NOT NULL ) ENGINE = InnoDB;
-
-INSERT INTO annotation_types_attributes_temp (id, annotation_type_id, name, type)
-  SELECT ata.id, at.annotation_type_id, ata.name, ata.type FROM `annotation_types_attributes` ata
-    JOIN annotation_types at ON at.name = ata.annotation_type;
-
-SET FOREIGN_KEY_CHECKS = 0;
-
-DROP TABLE IF EXISTS `annotation_types_attributes`;
-
-SET FOREIGN_KEY_CHECKS = 1;
-
-CREATE TABLE `annotation_types_attributes` (
-  `id` int(11) NOT NULL AUTO_INCREMENT,
-  `annotation_type_id` INT(11) NOT NULL,
-  `name` varchar(32) CHARACTER SET utf8 NOT NULL,
-  `type` enum('radio','string') CHARACTER SET utf8 NOT NULL,
-  PRIMARY KEY (`id`),
-  KEY `annotation_type_id` (`annotation_type_id`),
-  CONSTRAINT `annotation_types_attributes_ibfk_1` FOREIGN KEY (`annotation_type_id`) REFERENCES `annotation_types` (`annotation_type_id`) ON DELETE CASCADE ON UPDATE CASCADE
-) ENGINE=InnoDB AUTO_INCREMENT=147 DEFAULT CHARSET=utf8 COLLATE=utf8_polish_ci;
-
-INSERT INTO annotation_types_attributes (id, annotation_type_id, name, type)
-  SELECT * FROM `annotation_types_attributes_temp`;
-
-DROP TABLE `annotation_types_attributes_temp`;
-
-COMMIT;
\ No newline at end of file
diff --git a/database/update/update_078_message_null.sql b/database/update/update_078_message_null.sql
deleted file mode 100644
index 2632d78d..00000000
--- a/database/update/update_078_message_null.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE `tasks_reports` CHANGE `message` `message` TEXT CHARACTER SET utf8 COLLATE utf8_polish_ci NULL;
\ No newline at end of file
diff --git a/database/update/update_079_import_annotations.sql b/database/update/update_079_import_annotations.sql
deleted file mode 100644
index d1c67818..00000000
--- a/database/update/update_079_import_annotations.sql
+++ /dev/null
@@ -1 +0,0 @@
-INSERT INTO `report_perspectives` (`id`, `title`, `description`, `order`) VALUES ('importannotations', 'Import annotations', 'Import annotations from a .CCL file.', '150');
diff --git a/database/update/update_080_report_translations.sql b/database/update/update_080_report_translations.sql
deleted file mode 100644
index 818ba2f9..00000000
--- a/database/update/update_080_report_translations.sql
+++ /dev/null
@@ -1,4 +0,0 @@
-ALTER TABLE `reports` ADD `parent_report_id` BIGINT(20) NULL DEFAULT NULL AFTER `filename`;
-ALTER TABLE reports ADD CONSTRAINT fk_parent_report_id FOREIGN KEY (parent_report_id) REFERENCES reports(id);
-INSERT INTO `report_perspectives` (`id`, `title`, `description`, `order`) VALUES ('edittranslation', 'Edit translation', 'Edit document translation', '320');
-INSERT INTO `report_perspectives` (`id`, `title`, `description`, `order`) VALUES ('extendedmetadata', 'Extended metadata', 'Metadata including translations, images and document content.', '325');
\ No newline at end of file
diff --git a/database/update/update_081_import_languages.sql b/database/update/update_081_import_languages.sql
deleted file mode 100644
index f9727b96..00000000
--- a/database/update/update_081_import_languages.sql
+++ /dev/null
@@ -1,21 +0,0 @@
-CREATE TABLE `lang` (
-  `code` varchar(3),
-  `language` varchar(255) NOT NULL
-) ENGINE=InnoDB DEFAULT CHARSET=latin1;
-
-ALTER TABLE `lang` ADD PRIMARY KEY(`code`);
-
-INSERT INTO lang (code, language) VALUES ("aar", "Afar"),("abk", "Abkhazian"),("ace", "Achinese"),("ach", "Acoli"),("ada", "Adangme"),("ady", "Adyghe; Adygei"),("afa", "Afro-Asiatic languages"),("afh", "Afrihili"),("afr", "Afrikaans"),("ain", "Ainu"),("aka", "Akan"),("akk", "Akkadian"),("alb", "Albanian"),("ale", "Aleut"),("alg", "Algonquian languages"),("alt", "Southern Altai"),("amh", "Amharic"),("ang", "English, Old (ca.450-1100)"),("anp", "Angika"),("apa", "Apache languages"),("ara", "Arabic"),("arc", "Official Aramaic (700-300 BCE); Imperial Aramaic (700-300 BCE)"),("arg", "Aragonese"),("arm", "Armenian"),("arn", "Mapudungun; Mapuche"),("arp", "Arapaho"),("art", "Artificial languages"),("arw", "Arawak"),("asm", "Assamese"),("ast", "Asturian; Bable; Leonese; Asturleonese"),("ath", "Athapascan languages"),("aus", "Australian languages"),("ava", "Avaric"),("ave", "Avestan"),("awa", "Awadhi"),("aym", "Aymara"),("aze", "Azerbaijani"),("bad", "Banda languages"),("bai", "Bamileke languages"),("bak", "Bashkir"),("bal", "Baluchi"),("bam", "Bambara"),("ban", "Balinese"),("baq", "Basque"),("bas", "Basa"),("bat", "Baltic languages"),("bej", "Beja; Bedawiyet"),("bel", "Belarusian"),("bem", "Bemba"),("ben", "Bengali"),("ber", "Berber languages"),("bho", "Bhojpuri"),("bih", "Bihari languages"),("bik", "Bikol"),("bin", "Bini; Edo"),("bis", "Bislama"),("bla", "Siksika"),("bnt", "Bantu (Other)"),("bos", "Bosnian"),("bra", "Braj"),("bre", "Breton"),("btk", "Batak languages"),("bua", "Buriat"),("bug", "Buginese"),("bul", "Bulgarian"),("bur", "Burmese"),("byn", "Blin; Bilin"),("cad", "Caddo"),("cai", "Central American Indian languages"),("car", "Galibi Carib"),("cat", "Catalan; Valencian"),("cau", "Caucasian languages"),("ceb", "Cebuano"),("cel", "Celtic languages"),("cha", "Chamorro"),("chb", "Chibcha"),("che", "Chechen"),("chg", "Chagatai"),("chi", "Chinese"),("chk", "Chuukese"),("chm", "Mari"),("chn", "Chinook jargon"),("cho", "Choctaw"),("chp", "Chipewyan; Dene Suline"),("chr", "Cherokee"),("chu", "Church Slavic; Old Slavonic; Church Slavonic; Old Bulgarian; Old Church Slavonic"),("chv", "Chuvash"),("chy", "Cheyenne"),("cmc", "Chamic languages"),("cop", "Coptic"),("cor", "Cornish"),("cos", "Corsican"),("cpe", "Creoles and pidgins, English based"),("cpf", "Creoles and pidgins, French-based "),("cpp", "Creoles and pidgins, Portuguese-based "),("cre", "Cree"),("crh", "Crimean Tatar; Crimean Turkish"),("crp", "Creoles and pidgins "),("csb", "Kashubian"),("cus", "Cushitic languages"),("cze", "Czech"),("dak", "Dakota"),("dan", "Danish"),("dar", "Dargwa"),("day", "Land Dayak languages"),("del", "Delaware"),("den", "Slave (Athapascan)"),("dgr", "Dogrib"),("din", "Dinka"),("div", "Divehi; Dhivehi; Maldivian"),("doi", "Dogri"),("dra", "Dravidian languages"),("dsb", "Lower Sorbian"),("dua", "Duala"),("dum", "Dutch, Middle (ca.1050-1350)"),("dut", "Dutch; Flemish"),("dyu", "Dyula"),("dzo", "Dzongkha"),("efi", "Efik"),("egy", "Egyptian (Ancient)"),("eka", "Ekajuk"),("elx", "Elamite"),("eng", "English"),("enm", "English, Middle (1100-1500)"),("epo", "Esperanto"),("est", "Estonian"),("ewe", "Ewe"),("ewo", "Ewondo"),("fan", "Fang"),("fao", "Faroese"),("fat", "Fanti"),("fij", "Fijian"),("fil", "Filipino; Pilipino"),("fin", "Finnish"),("fiu", "Finno-Ugrian languages"),("fon", "Fon"),("fre", "French"),("frm", "French, Middle (ca.1400-1600)"),("fro", "French, Old (842-ca.1400)"),("frr", "Northern Frisian"),("frs", "Eastern Frisian"),("fry", "Western Frisian"),("ful", "Fulah"),("fur", "Friulian"),("gaa", "Ga"),("gay", "Gayo"),("gba", "Gbaya"),("gem", "Germanic languages"),("geo", "Georgian"),("ger", "German"),("gez", "Geez"),("gil", "Gilbertese"),("gla", "Gaelic; Scottish Gaelic"),("gle", "Irish"),("glg", "Galician"),("glv", "Manx"),("gmh", "German, Middle High (ca.1050-1500)"),("goh", "German, Old High (ca.750-1050)"),("gon", "Gondi"),("gor", "Gorontalo"),("got", "Gothic"),("grb", "Grebo"),("grc", "Greek, Ancient (to 1453)"),("gre", "Greek, Modern (1453-)"),("grn", "Guarani"),("gsw", "Swiss German; Alemannic; Alsatian"),("guj", "Gujarati"),("gwi", "Gwich'in"),("hai", "Haida"),("hat", "Haitian; Haitian Creole"),("hau", "Hausa"),("haw", "Hawaiian"),("heb", "Hebrew"),("her", "Herero"),("hil", "Hiligaynon"),("him", "Himachali languages; Western Pahari languages"),("hin", "Hindi"),("hit", "Hittite"),("hmn", "Hmong; Mong"),("hmo", "Hiri Motu"),("hrv", "Croatian"),("hsb", "Upper Sorbian"),("hun", "Hungarian"),("hup", "Hupa"),("iba", "Iban"),("ibo", "Igbo"),("ice", "Icelandic"),("ido", "Ido"),("iii", "Sichuan Yi; Nuosu"),("ijo", "Ijo languages"),("iku", "Inuktitut"),("ile", "Interlingue; Occidental"),("ilo", "Iloko"),("ina", "Interlingua (International Auxiliary Language Association)"),("inc", "Indic languages"),("ind", "Indonesian"),("ine", "Indo-European languages"),("inh", "Ingush"),("ipk", "Inupiaq"),("ira", "Iranian languages"),("iro", "Iroquoian languages"),("ita", "Italian"),("jav", "Javanese"),("jbo", "Lojban"),("jpn", "Japanese"),("jpr", "Judeo-Persian"),("jrb", "Judeo-Arabic"),("kaa", "Kara-Kalpak"),("kab", "Kabyle"),("kac", "Kachin; Jingpho"),("kal", "Kalaallisut; Greenlandic"),("kam", "Kamba"),("kan", "Kannada"),("kar", "Karen languages"),("kas", "Kashmiri"),("kau", "Kanuri"),("kaw", "Kawi"),("kaz", "Kazakh"),("kbd", "Kabardian"),("kha", "Khasi"),("khi", "Khoisan languages"),("khm", "Central Khmer"),("kho", "Khotanese; Sakan"),("kik", "Kikuyu; Gikuyu"),("kin", "Kinyarwanda"),("kir", "Kirghiz; Kyrgyz"),("kmb", "Kimbundu"),("kok", "Konkani"),("kom", "Komi"),("kon", "Kongo"),("kor", "Korean"),("kos", "Kosraean"),("kpe", "Kpelle"),("krc", "Karachay-Balkar"),("krl", "Karelian"),("kro", "Kru languages"),("kru", "Kurukh"),("kua", "Kuanyama; Kwanyama"),("kum", "Kumyk"),("kur", "Kurdish"),("kut", "Kutenai"),("lad", "Ladino"),("lah", "Lahnda"),("lam", "Lamba"),("lao", "Lao"),("lat", "Latin"),("lav", "Latvian"),("lez", "Lezghian"),("lim", "Limburgan; Limburger; Limburgish"),("lin", "Lingala"),("lit", "Lithuanian"),("lol", "Mongo"),("loz", "Lozi"),("ltz", "Luxembourgish; Letzeburgesch"),("lua", "Luba-Lulua"),("lub", "Luba-Katanga"),("lug", "Ganda"),("lui", "Luiseno"),("lun", "Lunda"),("luo", "Luo (Kenya and Tanzania)"),("lus", "Lushai"),("mac", "Macedonian"),("mad", "Madurese"),("mag", "Magahi"),("mah", "Marshallese"),("mai", "Maithili"),("mak", "Makasar"),("mal", "Malayalam"),("man", "Mandingo"),("mao", "Maori"),("map", "Austronesian languages"),("mar", "Marathi"),("mas", "Masai"),("may", "Malay"),("mdf", "Moksha"),("mdr", "Mandar"),("men", "Mende"),("mga", "Irish, Middle (900-1200)"),("mic", "Mi'kmaq; Micmac"),("min", "Minangkabau"),("mis", "Uncoded languages"),("mkh", "Mon-Khmer languages"),("mlg", "Malagasy"),("mlt", "Maltese"),("mnc", "Manchu"),("mni", "Manipuri"),("mno", "Manobo languages"),("moh", "Mohawk"),("mon", "Mongolian"),("mos", "Mossi"),("mul", "Multiple languages"),("mun", "Munda languages"),("mus", "Creek"),("mwl", "Mirandese"),("mwr", "Marwari"),("myn", "Mayan languages"),("myv", "Erzya"),("nah", "Nahuatl languages"),("nai", "North American Indian languages"),("nap", "Neapolitan"),("nau", "Nauru"),("nav", "Navajo; Navaho"),("nbl", "Ndebele, South; South Ndebele"),("nde", "Ndebele, North; North Ndebele"),("ndo", "Ndonga"),("nds", "Low German; Low Saxon; German, Low; Saxon, Low"),("nep", "Nepali"),("new", "Nepal Bhasa; Newari"),("nia", "Nias"),("nic", "Niger-Kordofanian languages"),("niu", "Niuean"),("nno", "Norwegian Nynorsk; Nynorsk, Norwegian"),("nob", "Bokmål, Norwegian; Norwegian Bokmål"),("nog", "Nogai"),("non", "Norse, Old"),("nor", "Norwegian"),("nqo", "N'Ko"),("nso", "Pedi; Sepedi; Northern Sotho"),("nub", "Nubian languages"),("nwc", "Classical Newari; Old Newari; Classical Nepal Bhasa"),("nya", "Chichewa; Chewa; Nyanja"),("nym", "Nyamwezi"),("nyn", "Nyankole"),("nyo", "Nyoro"),("nzi", "Nzima"),("oci", "Occitan (post 1500); Provençal"),("oji", "Ojibwa"),("ori", "Oriya"),("orm", "Oromo"),("osa", "Osage"),("oss", "Ossetian; Ossetic"),("ota", "Turkish, Ottoman (1500-1928)"),("oto", "Otomian languages"),("paa", "Papuan languages"),("pag", "Pangasinan"),("pal", "Pahlavi"),("pam", "Pampanga; Kapampangan"),("pan", "Panjabi; Punjabi"),("pap", "Papiamento"),("pau", "Palauan"),("peo", "Persian, Old (ca.600-400 B.C.)"),("per", "Persian"),("phi", "Philippine languages"),("phn", "Phoenician"),("pli", "Pali"),("pol", "Polish"),("pon", "Pohnpeian"),("por", "Portuguese"),("pra", "Prakrit languages"),("pro", "Provençal, Old (to 1500)"),("pus", "Pushto; Pashto"),("que", "Quechua"),("raj", "Rajasthani"),("rap", "Rapanui"),("rar", "Rarotongan; Cook Islands Maori"),("roa", "Romance languages"),("roh", "Romansh"),("rom", "Romany"),("rum", "Romanian; Moldavian; Moldovan"),("run", "Rundi"),("rup", "Aromanian; Arumanian; Macedo-Romanian"),("rus", "Russian"),("sad", "Sandawe"),("sag", "Sango"),("sah", "Yakut"),("sai", "South American Indian (Other)"),("sal", "Salishan languages"),("sam", "Samaritan Aramaic"),("san", "Sanskrit"),("sas", "Sasak"),("sat", "Santali"),("scn", "Sicilian"),("sco", "Scots"),("sel", "Selkup"),("sem", "Semitic languages"),("sga", "Irish, Old (to 900)"),("sgn", "Sign Languages"),("shn", "Shan"),("sid", "Sidamo"),("sin", "Sinhala; Sinhalese"),("sio", "Siouan languages"),("sit", "Sino-Tibetan languages"),("sla", "Slavic languages"),("slo", "Slovak"),("slv", "Slovenian"),("sma", "Southern Sami"),("sme", "Northern Sami"),("smi", "Sami languages"),("smj", "Lule Sami"),("smn", "Inari Sami"),("smo", "Samoan"),("sms", "Skolt Sami"),("sna", "Shona"),("snd", "Sindhi"),("snk", "Soninke"),("sog", "Sogdian"),("som", "Somali"),("son", "Songhai languages"),("sot", "Sotho, Southern"),("spa", "Spanish; Castilian"),("srd", "Sardinian"),("srn", "Sranan Tongo"),("srp", "Serbian"),("srr", "Serer"),("ssa", "Nilo-Saharan languages"),("ssw", "Swati"),("suk", "Sukuma"),("sun", "Sundanese"),("sus", "Susu"),("sux", "Sumerian"),("swa", "Swahili"),("swe", "Swedish"),("syc", "Classical Syriac"),("syr", "Syriac"),("tah", "Tahitian"),("tai", "Tai languages"),("tam", "Tamil"),("tat", "Tatar"),("tel", "Telugu"),("tem", "Timne"),("ter", "Tereno"),("tet", "Tetum"),("tgk", "Tajik"),("tgl", "Tagalog"),("tha", "Thai"),("tib", "Tibetan"),("tig", "Tigre"),("tir", "Tigrinya"),("tiv", "Tiv"),("tkl", "Tokelau"),("tlh", "Klingon; tlhIngan-Hol"),("tli", "Tlingit"),("tmh", "Tamashek"),("tog", "Tonga (Nyasa)"),("ton", "Tonga (Tonga Islands)"),("tpi", "Tok Pisin"),("tsi", "Tsimshian"),("tsn", "Tswana"),("tso", "Tsonga"),("tuk", "Turkmen"),("tum", "Tumbuka"),("tup", "Tupi languages"),("tur", "Turkish"),("tut", "Altaic languages"),("tvl", "Tuvalu"),("twi", "Twi"),("tyv", "Tuvinian"),("udm", "Udmurt"),("uga", "Ugaritic"),("uig", "Uighur; Uyghur"),("ukr", "Ukrainian"),("umb", "Umbundu"),("und", "Undetermined"),("urd", "Urdu"),("uzb", "Uzbek"),("vai", "Vai"),("ven", "Venda"),("vie", "Vietnamese"),("vol", "Volapük"),("vot", "Votic"),("wak", "Wakashan languages"),("wal", "Walamo"),("war", "Waray"),("was", "Washo"),("wel", "Welsh"),("wen", "Sorbian languages"),("wln", "Walloon"),("wol", "Wolof"),("xal", "Kalmyk; Oirat"),("xho", "Xhosa"),("yao", "Yao"),("yap", "Yapese"),("yid", "Yiddish"),("yor", "Yoruba"),("ypk", "Yupik languages"),("zap", "Zapotec"),("zbl", "Blissymbols; Blissymbolics; Bliss"),("zen", "Zenaga"),("zha", "Zhuang; Chuang"),("znd", "Zande languages"),("zul", "Zulu"),("zun", "Zuni"),("zxx", "No linguistic content; Not applicable"),("zza", "Zaza; Dimili; Dimli; Kirdki; Kirmanjki; Zazaki");
-
-ALTER TABLE reports MODIFY lang VARCHAR(3);
-
-CREATE INDEX reports_lang_index ON reports (lang);
-
-UPDATE reports SET lang = CASE WHEN lang = 'cz' THEN 'cze' WHEN lang = 'hr' THEN 'hun' WHEN lang = 'pl' THEN 'pol' WHEN lang = 'ru' THEN 'rus' WHEN lang = 'sk' THEN 'slo' WHEN lang = 'sl' THEN 'slv' WHEN lang = 'uk' THEN 'ukr' ELSE NULL END;
-
-ALTER TABLE reports MODIFY lang CHAR(3);
-ALTER TABLE `reports` CHANGE `lang` `lang` CHAR(3) CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL;
-
-ALTER TABLE `lang` CHANGE `code` `code` CHAR(3) CHARACTER SET utf8 COLLATE utf8_general_ci NOT NULL;
-
-ALTER TABLE reports ADD FOREIGN KEY (lang) REFERENCES lang(code);
diff --git a/database/update/update_082_cascade_flag_history.sql b/database/update/update_082_cascade_flag_history.sql
deleted file mode 100644
index 1989ad89..00000000
--- a/database/update/update_082_cascade_flag_history.sql
+++ /dev/null
@@ -1,4 +0,0 @@
-ALTER TABLE  `flag_status_history` DROP FOREIGN KEY  `flag_status_history_ibfk_1` ,
-ADD FOREIGN KEY (  `report_id` ) REFERENCES  `reports` (
-`id`
-) ON DELETE CASCADE ON UPDATE RESTRICT ;
\ No newline at end of file
diff --git a/database/update/update_083_reports_uesrs_selection_indices.sql b/database/update/update_083_reports_uesrs_selection_indices.sql
deleted file mode 100644
index 6005de4b..00000000
--- a/database/update/update_083_reports_uesrs_selection_indices.sql
+++ /dev/null
@@ -1,9 +0,0 @@
-ALTER TABLE `reports_users_selection` ADD INDEX(`user_id`);
-
-ALTER TABLE `reports_users_selection` ADD FOREIGN KEY (`user_id`) REFERENCES `users`(`user_id`) ON DELETE CASCADE ON UPDATE CASCADE;
-
-ALTER TABLE `reports_users_selection` ADD INDEX(`report_id`);
-
-ALTER TABLE `reports_users_selection` ADD  FOREIGN KEY (`report_id`) REFERENCES `reports`(`id`) ON DELETE CASCADE ON UPDATE CASCADE;
-
-ALTER TABLE `reports_users_selection` ADD UNIQUE( `user_id`, `report_id`);
\ No newline at end of file
diff --git a/database/update/update_084_report_annotation_table.sql b/database/update/update_084_report_annotation_table.sql
deleted file mode 100644
index 2f5ba03d..00000000
--- a/database/update/update_084_report_annotation_table.sql
+++ /dev/null
@@ -1 +0,0 @@
-INSERT INTO `report_perspectives` (`id`, `title`, `description`, `order`) VALUES ('annotation_table', 'Annotation table', 'Display a summary of annotations', '100');
\ No newline at end of file
diff --git a/database/update/update_085_tagsets.sql b/database/update/update_085_tagsets.sql
deleted file mode 100644
index c5864c80..00000000
--- a/database/update/update_085_tagsets.sql
+++ /dev/null
@@ -1,2 +0,0 @@
-INSERT INTO `tagsets` (`tagset_id`, `name`) VALUES ('4', 'Hebrew UDPipe'), ('5', 'Russian UDPipe');
-INSERT INTO `tagsets` (`tagset_id`, `name`) VALUES ('6', 'Czech UDPipe'), ('7', 'Bulgarian UDPipe');
\ No newline at end of file
diff --git a/database/update/update_086_orths.sql b/database/update/update_086_orths.sql
deleted file mode 100644
index e102e8cc..00000000
--- a/database/update/update_086_orths.sql
+++ /dev/null
@@ -1,34 +0,0 @@
---
--- Struktura tabeli dla tabeli `orths`
---
-
-CREATE TABLE `orths` (
-  `orth_id` bigint(20) NOT NULL,
-  `orth` varchar(190) NOT NULL
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4_bin;
-
---
--- Indeksy dla zrzutów tabel
---
-
---
--- Indexes for table `orths`
---
-ALTER TABLE `orths`
-  ADD PRIMARY KEY (`orth_id`),
-  ADD KEY `orth` (`orth`);
-
---
--- AUTO_INCREMENT for dumped tables
---
-
---
--- AUTO_INCREMENT dla tabeli `orths`
---
-ALTER TABLE `orths`
-  MODIFY `orth_id` bigint(20) NOT NULL AUTO_INCREMENT;
-
-ALTER TABLE `orths` ADD UNIQUE(`orth`);
-
-ALTER TABLE `tokens` ADD `orth_id` BIGINT NULL AFTER `eos`;
-
diff --git a/database/update/update_087_attribute_value_length.sql b/database/update/update_087_attribute_value_length.sql
deleted file mode 100644
index 50a4c880..00000000
--- a/database/update/update_087_attribute_value_length.sql
+++ /dev/null
@@ -1,5 +0,0 @@
-ALTER TABLE `reports_annotations_shared_attributes` CHANGE `value` `value` VARCHAR(128) CHARACTER SET utf8 COLLATE utf8_general_ci NOT NULL;
-
-ALTER TABLE `shared_attributes_enum` CHANGE `value` `value` VARCHAR(128) CHARACTER SET utf8 COLLATE utf8_general_ci NOT NULL;
-
-ALTER TABLE `shared_attributes_enum` CHANGE `description` `description` VARCHAR(255) CHARACTER SET utf8 COLLATE utf8_general_ci NOT NULL;
\ No newline at end of file
diff --git a/database/update/update_088_perspective_annotation_attributes.sql b/database/update/update_088_perspective_annotation_attributes.sql
deleted file mode 100644
index 0e639a26..00000000
--- a/database/update/update_088_perspective_annotation_attributes.sql
+++ /dev/null
@@ -1 +0,0 @@
-INSERT INTO `report_perspectives` (`id`, `title`, `description`, `order`) VALUES ('annotation_attributes', 'Annotation attributes', 'Batch editor of annotation attributes', '110');
\ No newline at end of file
diff --git a/database/update/update_089_fix_perspective_id.sql b/database/update/update_089_fix_perspective_id.sql
deleted file mode 100644
index 3212fe70..00000000
--- a/database/update/update_089_fix_perspective_id.sql
+++ /dev/null
@@ -1 +0,0 @@
-UPDATE `report_perspectives` SET `id` = 'importAnnotations' WHERE `report_perspectives`.`id` = 'importannotations';
\ No newline at end of file
diff --git a/database/update/update_091_corpus_css.sql b/database/update/update_091_corpus_css.sql
deleted file mode 100644
index 0583aecd..00000000
--- a/database/update/update_091_corpus_css.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE `corpora` ADD `css` TEXT NULL AFTER `date_created`;
\ No newline at end of file
diff --git a/database/update/update_092_report_deleted.sql b/database/update/update_092_report_deleted.sql
deleted file mode 100644
index e07ef980..00000000
--- a/database/update/update_092_report_deleted.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE `reports` ADD `deleted` BOOLEAN NOT NULL DEFAULT FALSE AFTER `parent_report_id`, ADD INDEX `reports_deleted_idx` (`deleted`);
\ No newline at end of file

From e4f459eacdf4648abed9b6e544212bd5726f373d Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Tue, 2 Mar 2021 11:08:31 +0100
Subject: [PATCH 012/154] another unused query files removed and moved to
 documentations

---
 database/queries/annotations_delete_by_corpus_id_and_stage.sql | 3 ---
 .../direct.query.examples}/statistics_activity.sql             | 0
 2 files changed, 3 deletions(-)
 delete mode 100644 database/queries/annotations_delete_by_corpus_id_and_stage.sql
 rename {database/queries => documentations/direct.query.examples}/statistics_activity.sql (100%)

diff --git a/database/queries/annotations_delete_by_corpus_id_and_stage.sql b/database/queries/annotations_delete_by_corpus_id_and_stage.sql
deleted file mode 100644
index a005f269..00000000
--- a/database/queries/annotations_delete_by_corpus_id_and_stage.sql
+++ /dev/null
@@ -1,3 +0,0 @@
-SET @corpus_id=51;
-SET @stage='new';
-DELETE an FROM `reports_annotations_optimized` an JOIN reports r ON (an.report_id=r.id) WHERE r.corpora=@corpus_id AND an.stage=@stage;
\ No newline at end of file
diff --git a/database/queries/statistics_activity.sql b/documentations/direct.query.examples/statistics_activity.sql
similarity index 100%
rename from database/queries/statistics_activity.sql
rename to documentations/direct.query.examples/statistics_activity.sql

From 7ce8c850abd2a18fce92b990482db42ff53dac09 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 6 Mar 2021 14:11:46 +0100
Subject: [PATCH 013/154] actualize files in TARITIFEXISTS

---
 packages/Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/packages/Makefile b/packages/Makefile
index f1f55a88..5de35af8 100644
--- a/packages/Makefile
+++ b/packages/Makefile
@@ -14,7 +14,7 @@ RELEASE = $(shell if [ ! -z '$(GITHASH)' ]; then echo -n "$(RELNO)v.$(GITHASH)";
 RELSPECTAG = RELEASE_TAG
 
 # glob cannot work here
-TARITIFEXISTS = tests phpunit.xml data
+TARITIFEXISTS = 
 FILES2TAR = composer.json apps LICENCE.md local sonar-project.properties config/README.md documentations phpunit engine gfx public_html database INSTALL.md README.md $(foreach wrd,$(TARITIFEXISTS),$(wrd))
 
 $(RPM_SOURCES_DIR)/$(PACKAGE).tgz: ../.git/index 

From 48b19763532c2fece23d6cae0eb22a994291ae44 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 6 Mar 2021 19:46:56 +0100
Subject: [PATCH 014/154] rw rights to templetes_c dir in rpm package

---
 packages/rpm/SPECS/inforex.spec | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/packages/rpm/SPECS/inforex.spec b/packages/rpm/SPECS/inforex.spec
index 5cf469a1..ded62c7a 100644
--- a/packages/rpm/SPECS/inforex.spec
+++ b/packages/rpm/SPECS/inforex.spec
@@ -42,6 +42,9 @@ to test all phases of building rpm process
 # remove several scripts not used in the package
 #rm -rf  vendor/ezyang/htmlpurifier/maintenance/
 
+# remove precompiled templtates from devel dir
+rm -rf engine/templates_c/*
+
 %build
 
 %install
@@ -84,6 +87,8 @@ if [ -x %{_sbindir}/semanage ] ; then
 	fi
         %{_sbindir}/semanage fcontext -a -t httpd_var_lib_t %{_localstatedir}/lib/%{name}
 	%{_sbindir}/restorecon %{_localstatedir}/lib/%{name}
+	%{_sbindir}/semanage fcontext -a -t httpd_sys_rw_content_t %{inforexdir}/engine/templates_c
+	%{_sbindir}/restorecon %{inforexdir}/engine/templates_c
 fi
 
 %files
@@ -92,6 +97,8 @@ fi
 %dir %{inforexdir}
 %{inforexdir}/*
 
+%attr(775,-,%{httpdgroup}) %{inforexdir}/engine/templates_c
+
 %dir %{_localstatedir}/lib/%{name}
 %{_localstatedir}/lib/%{name}/config.ini.php
 

From 075a43e556a0653f5559dceee43d1f12b62ac2c8 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 6 Mar 2021 20:56:24 +0100
Subject: [PATCH 015/154] deprecated preg_replace in Smarty class

---
 .../Smarty-2.6.22/libs/Smarty_Compiler.class.php    | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/engine/external/Smarty-2.6.22/libs/Smarty_Compiler.class.php b/engine/external/Smarty-2.6.22/libs/Smarty_Compiler.class.php
index 374ba3d0..c4ac6cbe 100644
--- a/engine/external/Smarty-2.6.22/libs/Smarty_Compiler.class.php
+++ b/engine/external/Smarty-2.6.22/libs/Smarty_Compiler.class.php
@@ -271,13 +271,12 @@ function _compile_file($resource_name, $source_content, &$compiled_content)
         reset($this->_folded_blocks);
 
         /* replace special blocks by "{php}" */
-        $source_content = preg_replace($search.'e', "'"
-                                       . $this->_quote_replace($this->left_delimiter) . 'php'
-                                       . "' . str_repeat(\"\n\", substr_count('\\0', \"\n\")) .'"
-                                       . $this->_quote_replace($this->right_delimiter)
-                                       . "'"
-                                       , $source_content);
-
+        $source_content = preg_replace_callback($search,
+            function($matches) {
+                return $this->_quote_replace($this->left_delimiter) . 'php' . str_repeat($this->_quote_replace("\n"),substr_count($matches[0], $this->_quote_replace("\n"))).$this->_quote_replace($this->right_delimiter);
+            },
+            $source_content
+        );
         /* Gather all template tags. */
         preg_match_all("~{$ldq}\s*(.*?)\s*{$rdq}~s", $source_content, $_match);
         $template_tags = $_match[1];

From c4b5765bfeefc6eaead84a650cb97ff695acb5b0 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 6 Mar 2021 21:06:16 +0100
Subject: [PATCH 016/154] quota missing in string constant

---
 engine/templates/inc_header2.tpl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/engine/templates/inc_header2.tpl b/engine/templates/inc_header2.tpl
index 40a360fa..db18073a 100644
--- a/engine/templates/inc_header2.tpl
+++ b/engine/templates/inc_header2.tpl
@@ -66,7 +66,7 @@
 		<script type="text/javascript" src="js/c_autoresize.js?{$rev}"></script>
 
 
-	{if $page==wccl_match_tester || $page==corpus_wccl_match}
+	{if $page=="wccl_match_tester" || $page=="corpus_wccl_match"}
 		<script type="text/javascript" src="js/codemirror/codemirror.js"></script>
 		<link rel="StyleSheet" href="js/codemirror/codemirror.css" TYPE="text/css"/>
 		<script type="text/javascript" src="js/codemirror/mode/wccl.js?{$rev}"></script>

From 5f34e95d03e88db97625a21a95bae03d316b4cd1 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Mon, 8 Mar 2021 11:19:20 +0100
Subject: [PATCH 017/154] nonexistent index in templates generate warnings

---
 engine/settings.php              | 10 +++++++++-
 engine/templates/inc_header2.tpl |  6 +++---
 engine/templates/inc_menu2.tpl   |  4 ++--
 3 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/engine/settings.php b/engine/settings.php
index b4e8608c..d4cfc4ca 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -16,5 +16,13 @@
 ini_set("short_open_tag",1);
 setlocale(LC_CTYPE, "en_US.UTF-8");		
 
- 
+error_reporting(E_ALL);
+
+function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0) {
+	print("[".$level."] ".$message." in ".$file.":".$line."<br/>\n");
+	//throw new ErrorException($message, 0, $level, $file, $line);
+}
+
+set_error_handler(inforexCentralErrorHandler);
+
 ?>
diff --git a/engine/templates/inc_header2.tpl b/engine/templates/inc_header2.tpl
index db18073a..65b0c1b5 100644
--- a/engine/templates/inc_header2.tpl
+++ b/engine/templates/inc_header2.tpl
@@ -105,7 +105,7 @@
 		<b>Status:</b> <span id="status_icon"></span> <span id="status_text">Tutaj będzie wyświetlany status.</span>	
 	</div>
 
-	{if $exception}
+	{if isset($exception)}
 		<div id="fatal_error" style="text-align: left"><h2>Exception:</h2><pre>{$exception}</pre></div>
 	{/if}
 
@@ -114,14 +114,14 @@
 	
     <div id="page_content">
 		
-	{if $error}
+	{if isset($error)}
 		<div style="padding: 0pt 0.7em; margin: 10px;" class="ui-state-highlight ui-corner-all"> 
 			<p style="padding: 10px"><span style="float: left; margin-right: 0.3em;" class="ui-icon ui-icon-info"></span>
 			<strong>Error</strong> {$error}</p>
 		</div>
 	{/if}
 	
-	{if $info}
+	{if isset($info)}
 		<div style="padding: 0pt 0.7em; margin: 10px;" class="ui-state-highlight ui-corner-all"> 
 			<p style="padding: 10px"><span style="float: left; margin-right: 0.3em;" class="ui-icon ui-icon-info"></span>
 			<strong>Info</strong> {$info}</p>
diff --git a/engine/templates/inc_menu2.tpl b/engine/templates/inc_menu2.tpl
index 89eb9e6e..88b9395a 100644
--- a/engine/templates/inc_menu2.tpl
+++ b/engine/templates/inc_menu2.tpl
@@ -15,7 +15,7 @@
 				<li class="{if $page=="home"} active{/if}">
 					<a href="index.php?page=home">Corpora</a>
 				</li>
-                {if $corpus.id}
+                {if isset($corpus.id)}
 					<li class="active dropdown navbar-sub corpus_select_nav">
 						<a class="dropdown-toggle" data-toggle="dropdown" href="index.php?page=start&amp;corpus={$corpus.id}">
 							<span class="glyphicon glyphicon-menu-hamburger" aria-hidden="true" title="Show a list of corpora"></span> <b>{$corpus.name}</b>
@@ -68,7 +68,7 @@
 						</ul>
 					</li>
                 {/if}
-                {if $corpus.id && ( "read"|has_corpus_role_or_owner || "admin"|has_role || $corpus.public ) }
+                {if isset($corpus.id) && ( "read"|has_corpus_role_or_owner || "admin"|has_role || $corpus.public ) }
 
                     <li class="navbar-sub dropdown nav_corpus_pages" style="background: #eee">
 						<a class="dropdown-toggle" data-toggle="dropdown" href="#">

From 61f603435ed10524474965346fccc0d888c3d194 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Mon, 8 Mar 2021 12:19:16 +0100
Subject: [PATCH 018/154] missing static properties in Config added

---
 engine/Config/Config.php | 25 ++++++++++++++-----------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/engine/Config/Config.php b/engine/Config/Config.php
index ed5f29a4..2a94f690 100644
--- a/engine/Config/Config.php
+++ b/engine/Config/Config.php
@@ -32,6 +32,7 @@ class Config extends Singleton\Singleton{
 	static private $path_engine       = 'ABSOLUTE_PATH_TO:inforex/engine';
 	static private $path_www          = 'ABSOLUTE_PATH_TO:inforex/public_html';	
 	static private $path_secured_data = 'ABSOLUTE_PATH_TO:inforex/data';
+	static private $path_exports 	  = 'ABSOLUTE_PATH_TO:inforex/data/exports';
 
 	/* set $federationLoginUrl to null if regular login is to be used */
     static private $federationLoginUrl = null;
@@ -47,6 +48,8 @@ class Config extends Singleton\Singleton{
 	);
 
 	static private $wccl_match_enable = false;
+	static private $wccl_match_tester_script = "ABSOLUTE_PATH_TO:inforex/apps/wccl/wccl-gateway.py";
+	static private $wccl_match_script = "ABSOLUTE_PATH_TO:inforex/apps/wccl/wccl-gateway-run.py";
 	
 	static private $wccl_match_tester_corpora = array(
 			array("name"=>"KPWr 1.2.2 TimeML train &ndash; all (1&ndash;551)", 
@@ -94,20 +97,20 @@ final protected function __construct(){
 
         parent::__construct();
 
-		$this->session_time = 60 * 60 * 24 * 356 * 2;
+		self::put_session_time(60 * 60 * 24 * 356 * 2);
 
 		// Setup default paths
 		$path_engine = realpath(__DIR__ . DIRECTORY_SEPARATOR . "..");
 		$path_inforex = realpath($path_engine . DIRECTORY_SEPARATOR . '..');
 
-		$this->path_engine       = $path_engine;
-		$this->path_www          = $path_inforex . DIRECTORY_SEPARATOR . 'public_html';	
-		$this->path_secured_data = $path_inforex . DIRECTORY_SEPARATOR . 'secured_data';
+		self::put_path_engine($path_engine);
+		self::put_path_www($path_inforex . DIRECTORY_SEPARATOR . 'public_html');	
+		self::put_path_secured_data($path_inforex . DIRECTORY_SEPARATOR . 'secured_data');
 		
-		$this->path_exports      = $this->path_secured_data . DIRECTORY_SEPARATOR . 'exports';
+		self::put_path_exports(self::get_path_secured_data() . DIRECTORY_SEPARATOR . 'exports');
 		
-		$this->wccl_match_tester_script = $path_engine . "/../apps/wccl/wccl-gateway.py";
-		$this->wccl_match_script = $path_engine . "/../apps/wccl/wccl-gateway-run.py";		
+		self::put_wccl_match_tester_script($path_engine . "/../apps/wccl/wccl-gateway.py");
+		self::put_wccl_match_script($path_engine . "/../apps/wccl/wccl-gateway-run.py");		
 
 	}
 
@@ -120,8 +123,8 @@ function __call($method,$arguments){
 		if ( substr($method, 0, 4) == "get_" ){
 			$parameter_name = substr($method, 4);
 			if (  property_exists($this,$parameter_name) ) {
-				if ( isset($this->$parameter_name ) ) {
-					return $this->$parameter_name;
+				if ( isset(self::$parameter_name ) ) {
+					return self::$parameter_name;
 				} elseif ( isset(self::${$parameter_name})) { 
 					return self::${$parameter_name};
 				} else
@@ -134,9 +137,9 @@ function __call($method,$arguments){
             // implementation of put_<sth>($value) method
             $parameter_name = substr($method, 4);
             $value = $arguments[0];
-            $this->{$parameter_name}=$value;
+            self::$$parameter_name=$value;
             if($parameter_name=="localConfigFilename"){
-                $this->loadConfigFromFile($this->localConfigFilename);
+                $this->loadConfigFromFile(self::get_localConfigFilename());
             }
         } 
 		else

From 5df1ee33e45ffd6348144793663acf67175c188a Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Mon, 8 Mar 2021 12:30:40 +0100
Subject: [PATCH 019/154] unexistent variables in CInforexWeb generate warnings

---
 engine/include/CInforexWeb.php | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/engine/include/CInforexWeb.php b/engine/include/CInforexWeb.php
index 5921b76b..b3bf7bfd 100644
--- a/engine/include/CInforexWeb.php
+++ b/engine/include/CInforexWeb.php
@@ -245,16 +245,16 @@ function execute()
 
         $variables = array();
         $variables['exceptions'] = array();
-        $action = $_POST['action'];
-        $ajax = $_POST['ajax'];
-        $page = $_GET['page'];
+        $action = isset($_POST['action']) ? $_POST['action'] : null;
+        $ajax = isset($_POST['ajax']) ? $_POST['ajax'] : null;
+        $page = isset($_GET['page']) ? $_GET['page'] : null;
         $stamp_start = time();
 
         /* Gather the data about an activity */
         $activity_page = array();
         $activity_page['ip_id'] = $db->get_entry_key("ips", "ip_id", array("ip" => isset($_SERVER["REMOTE_ADDR"]) ? $_SERVER["REMOTE_ADDR"] : "CLI local" ));
         $activity_page['user_id'] = isset($user) ? $user['user_id'] : null;
-        $activity_page['corpus_id'] = isset($corpus) ? $corpus['id'] : null;
+        $activity_page['corpus_id'] = isset($corpus['id']) ? $corpus['id'] : null;
         $activity_page['report_id'] = RequestLoader::getDocumentId();
         $activity_page['datetime'] = date("Y-m-d H:i:s");
 

From 92447dffbd15d4a6d82f7884f652b698732c489f Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Mon, 8 Mar 2021 12:37:42 +0100
Subject: [PATCH 020/154] unexistent index tested

---
 public_html/index.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public_html/index.php b/public_html/index.php
index 51ee1987..fbf70336 100644
--- a/public_html/index.php
+++ b/public_html/index.php
@@ -33,7 +33,7 @@
 	$db = new Database(Config::Config()->get_dsn(), Config::Config()->get_log_sql(), Config::Config()->get_log_output(), Config::Config()->get_db_charset());
 	
 	$auth = new UserAuthorize(Config::Config()->get_dsn());
-	$auth->authorize($_POST['logout']=="1");
+	$auth->authorize(isset($_POST['logout']) && ($_POST['logout']=="1"));
 	$user = $auth->getUserData();
 	$corpus = RequestLoader::loadCorpus();
 

From e2dc1141d99064c2f55c195936557d3792625464 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Mon, 8 Mar 2021 13:22:32 +0100
Subject: [PATCH 021/154] missing login data displayed in template

---
 engine/include/CUserAuthorize.php | 1 +
 1 file changed, 1 insertion(+)

diff --git a/engine/include/CUserAuthorize.php b/engine/include/CUserAuthorize.php
index f4f7bedc..d982d156 100644
--- a/engine/include/CUserAuthorize.php
+++ b/engine/include/CUserAuthorize.php
@@ -36,6 +36,7 @@ function getUserData(){
 		if ($user){
 			$roles = $db->fetch_rows("SELECT * FROM users_roles us JOIN roles USING (role) WHERE user_id=?", array($user['user_id']));
 			$login = $db->fetch_one("SELECT login FROM users WHERE user_id=?", array($user['user_id']));
+			$user['login'] = $login;
             $user['role'][ROLE_SYSTEM_USER_PUBLIC] = "Has access to public pages";
 			$user['role'][ROLE_SYSTEM_USER_LOGGEDIN] = "User is loggedin to the system";
 			foreach ($roles as $role){

From 242cda133e3036c21c684dec79a2e756c678c67e Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Mon, 8 Mar 2021 13:30:10 +0100
Subject: [PATCH 022/154] unset indexes tested in templates

---
 engine/templates/inc_system_messages.tpl | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/engine/templates/inc_system_messages.tpl b/engine/templates/inc_system_messages.tpl
index 20ed8204..e011d995 100644
--- a/engine/templates/inc_system_messages.tpl
+++ b/engine/templates/inc_system_messages.tpl
@@ -6,28 +6,28 @@
  *}
  
 {* Komunikaty systemowe *}
-{if $action_permission_denied}
+{if isset($action_permission_denied)}
 <div style="background: #A6001C; padding: 2px; margin: 2px; ">
 	<div style="float: left; color: white; padding: 5px; font-weight: bold;">Access denied:</div>
 	<div style="background: #FFF194; margin-left: 150px; padding: 5px; color: #A6001C">{$action_permission_denied}</div>
 </div>
 {/if}
 
-{if $action_error}
+{if isset($action_error)}
 <div style="background: #E03D19; padding: 2px; margin: 2px; ">
 	<div style="float: left; color: white; padding: 5px; font-weight: bold;">Error:</div>
 	<div style="background: #FFF194; margin-left: 150px; padding: 5px; color: #733B0E">{$action_error}</div>
 </div>
 {/if}
 
-{if $action_performed}
+{if isset($action_performed)}
 <div style="background: #6B9100; padding: 2px; margin: 2px; ">
 	<div style="float: left; color: white; padding: 5px; font-weight: bold;">Success:</div>
 	<div style="background: #FFF194; margin-left: 150px; padding: 5px; color: #3E5400">{$action_performed}</div>
 </div>
 {/if}
 
-{if $page_permission_denied}
+{if isset($page_permission_denied)}
 <div style="background: #A6001C; padding: 2px; margin: 2px; ">
 	<div style="float: left; color: white; padding: 5px; font-weight: bold;">Access denied:</div>
 	<div style="background: #FFF194; margin-left: 150px; padding: 5px; color: #A6001C">&raquo;{$page_permission_denied}</div>

From 19284c05ccbefa1466cf508da99abe5bb2481b22 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Mon, 8 Mar 2021 15:31:42 +0100
Subject: [PATCH 023/154] Config reingeenering allowed set non existens
 parameters

---
 engine/Config/Config.php | 98 +++++++++++++++++++++-------------------
 engine/settings.php      |  2 +-
 2 files changed, 52 insertions(+), 48 deletions(-)

diff --git a/engine/Config/Config.php b/engine/Config/Config.php
index 2a94f690..902f1f04 100644
--- a/engine/Config/Config.php
+++ b/engine/Config/Config.php
@@ -22,36 +22,36 @@ public function __call($name, $arguments)
  */
 class Config extends Singleton\Singleton{
 
-    static private $sid = "gpw";
-	//var $sid = "gpw";
-	static private $session_time = 0;
-	static private $offline = false;
-    static private $db_charset = "utf8mb4";
+	static private $confVariables = array (
+    	"sid" => "gpw",
+	    "session_time" => 0,
+		"offline" => false,
+    	"db_charset" => "utf8mb4",
 	
 	/* Inforex basic configuration */
-	static private $path_engine       = 'ABSOLUTE_PATH_TO:inforex/engine';
-	static private $path_www          = 'ABSOLUTE_PATH_TO:inforex/public_html';	
-	static private $path_secured_data = 'ABSOLUTE_PATH_TO:inforex/data';
-	static private $path_exports 	  = 'ABSOLUTE_PATH_TO:inforex/data/exports';
+		"path_engine" => 'ABSOLUTE_PATH_TO:inforex/engine',
+		"path_www"    => 'ABSOLUTE_PATH_TO:inforex/public_html',	
+		"path_secured_data" => 'ABSOLUTE_PATH_TO:inforex/data',
+	//static private $path_exports 	  = 'ABSOLUTE_PATH_TO:inforex/data/exports';
 
 	/* set $federationLoginUrl to null if regular login is to be used */
-    static private $federationLoginUrl = null;
-    static private $federationValidateTokenUrl = null;
+        "federationLoginUrl" => null,
+    	"federationValidateTokenUrl" => null,
 
-	static private $url = 'http://localhost/inforex';
-	static private $dsn = array(
+		"url" => 'http://localhost/inforex',
+		"dsn" => array(
     		'phptype'  => 'mysqli',
     		'username' => 'inforex',
     		'password' => 'password',
     		'hostspec' => 'localhost',
     		'database' => 'inforex',
-	);
+		),
 
-	static private $wccl_match_enable = false;
-	static private $wccl_match_tester_script = "ABSOLUTE_PATH_TO:inforex/apps/wccl/wccl-gateway.py";
-	static private $wccl_match_script = "ABSOLUTE_PATH_TO:inforex/apps/wccl/wccl-gateway-run.py";
+		"wccl_match_enable" => false,
+		//"wccl_match_tester_script" => "ABSOLUTE_PATH_TO:inforex/apps/wccl/wccl-gateway.py";
+		//static private $wccl_match_script = "ABSOLUTE_PATH_TO:inforex/apps/wccl/wccl-gateway-run.py";
 	
-	static private $wccl_match_tester_corpora = array(
+		"wccl_match_tester_corpora" => array(
 			array("name"=>"KPWr 1.2.2 TimeML train &ndash; all (1&ndash;551)", 
 					"path"=>"/nlp/corpora/pwr/kpwr-release/kpwr-1.2.2-time-disamb/index_time_train.txt"),
 			array("name"=>"KPWr 1.2.2 TimeML train &ndash; A (1&ndash;100)", "path"=>"/index_time_a.txt"),
@@ -60,30 +60,31 @@ class Config extends Singleton\Singleton{
 			array("name"=>"KPWr 1.2.2 TimeML train &ndash; D (301&ndash;551)", "path"=>"/index_time_d.txt"),
 			array("name"=>"KPWr 1.2.2 TimeML tune","path"=>"/index_time_tune.txt"),
 			array("name"=>"KPWr 1.2.7 TimeML train&ndash; all",	"path"=>"/index_time_train.txt")
-		); 	
+		), 	
 		
-	static private $wccl_match_daemon = null;
+		"wccl_match_daemon" => null,
 
 	/* Advanced parameters */
-	static private $path_python       = 'python';
-	static private $path_liner        = null;
-	static private $path_liner2       = null;
-	static private $path_nerd         = null;
-	static private $path_wcrft        = null;
-	static private $path_semql        = null;
-	static private $file_with_rules   = null; 
-	static private $takipi_wsdl       = null;
-	static private $liner_wsdl        = null;
-	static private $serel_liner_wsdl  = null;
-	static private $path_wcrft_model  = "";
-	static private $wcrft_config	   = "nkjp_s2.ini";
-	static private $wcrft2_config	   = "nkjp_e2";
-	static private $log_sql           = false;
-	static private $log_output		   = "fb";
-	static private $path_grabber	   = null;
+		"path_python"       => 'python',
+		"path_liner"        => null,
+		"path_liner2"       => null,
+		"path_nerd"         => null,
+		"path_wcrft"        => null,
+		"path_semql"        => null,
+		"file_with_rules"   => null, 
+		"takipi_wsdl"       => null,
+		"liner_wsdl"        => null,
+		"serel_liner_wsdl"  => null,
+		"path_wcrft_model"  => "",
+		"wcrft_config"	   => "nkjp_s2.ini",
+		"wcrft2_config"	   => "nkjp_e2",
+		"log_sql"           => false,
+		"log_output"		=> "fb",
+		"path_grabber"	   => null,
 	
     // path for local config file - if exists
-    static private $localConfigFilename  = "";
+    	"localConfigFilename"  => ""
+	);
 		
 	// for more friendly call only...
     final public static function Config(){
@@ -97,20 +98,20 @@ final protected function __construct(){
 
         parent::__construct();
 
-		self::put_session_time(60 * 60 * 24 * 356 * 2);
+		$this->put_session_time(60 * 60 * 24 * 356 * 2);
 
 		// Setup default paths
 		$path_engine = realpath(__DIR__ . DIRECTORY_SEPARATOR . "..");
 		$path_inforex = realpath($path_engine . DIRECTORY_SEPARATOR . '..');
 
-		self::put_path_engine($path_engine);
-		self::put_path_www($path_inforex . DIRECTORY_SEPARATOR . 'public_html');	
-		self::put_path_secured_data($path_inforex . DIRECTORY_SEPARATOR . 'secured_data');
+		$this->put_path_engine($path_engine);
+		$this->put_path_www($path_inforex . DIRECTORY_SEPARATOR . 'public_html');	
+		$this->put_path_secured_data($path_inforex . DIRECTORY_SEPARATOR . 'secured_data');
 		
-		self::put_path_exports(self::get_path_secured_data() . DIRECTORY_SEPARATOR . 'exports');
+		$this->put_path_exports($this->get_path_secured_data() . DIRECTORY_SEPARATOR . 'exports');
 		
-		self::put_wccl_match_tester_script($path_engine . "/../apps/wccl/wccl-gateway.py");
-		self::put_wccl_match_script($path_engine . "/../apps/wccl/wccl-gateway-run.py");		
+		$this->put_wccl_match_tester_script($path_engine . "/../apps/wccl/wccl-gateway.py");
+		$this->put_wccl_match_script($path_engine . "/../apps/wccl/wccl-gateway-run.py");		
 
 	}
 
@@ -122,9 +123,12 @@ function __call($method,$arguments){
         }
 		if ( substr($method, 0, 4) == "get_" ){
 			$parameter_name = substr($method, 4);
+			if ( array_key_exists($parameter_name,self::$confVariables) ) {
+				return self::$confVariables[$parameter_name];
+			} 
 			if (  property_exists($this,$parameter_name) ) {
-				if ( isset(self::$parameter_name ) ) {
-					return self::$parameter_name;
+				if ( isset($this->$parameter_name ) ) {
+					return $this->$parameter_name;
 				} elseif ( isset(self::${$parameter_name})) { 
 					return self::${$parameter_name};
 				} else
@@ -137,7 +141,7 @@ function __call($method,$arguments){
             // implementation of put_<sth>($value) method
             $parameter_name = substr($method, 4);
             $value = $arguments[0];
-            self::$$parameter_name=$value;
+            self::$confVariables[$parameter_name]=$value;
             if($parameter_name=="localConfigFilename"){
                 $this->loadConfigFromFile(self::get_localConfigFilename());
             }
diff --git a/engine/settings.php b/engine/settings.php
index d4cfc4ca..842f863f 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -23,6 +23,6 @@ function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0)
 	//throw new ErrorException($message, 0, $level, $file, $line);
 }
 
-set_error_handler(inforexCentralErrorHandler);
+set_error_handler("inforexCentralErrorHandler");
 
 ?>

From 2b61f7ec4c22d971c1195a6131a10bb4cbe467db Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Tue, 9 Mar 2021 18:13:04 +0100
Subject: [PATCH 024/154] test environment to two constructors problem

---
 .gitignore                  | 2 ++
 engine/Config/Singleton.php | 2 +-
 engine/settings.php         | 6 ++++++
 3 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index fc978b20..af94741c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,3 +12,5 @@ secured_data/import
 *.backup
 *.swp
 composer.lock
+config.local.php.*
+tests/
diff --git a/engine/Config/Singleton.php b/engine/Config/Singleton.php
index 562fca0e..4e14ad8f 100644
--- a/engine/Config/Singleton.php
+++ b/engine/Config/Singleton.php
@@ -13,7 +13,7 @@
 
 abstract class Singleton {
 
-    protected static $_instance = NULL;
+    protected static $_instance = null;
 
     /**
      * Prevent direct object creation
diff --git a/engine/settings.php b/engine/settings.php
index 842f863f..c3d468a1 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -16,7 +16,13 @@
 ini_set("short_open_tag",1);
 setlocale(LC_CTYPE, "en_US.UTF-8");		
 
+// to psuje podwójne konstruktory
 error_reporting(E_ALL);
+// a dowolny z poniższych blokuje te komunikaty
+//error_reporting(E_ALL ^ E_STRICT);
+ini_set("error_reporting", E_ALL & ~E_STRICT );
+// mój handler poniżej nie jest wrażliwy na ustawienia error_reporting
+// i wywala wszystko zawsze:
 
 function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0) {
 	print("[".$level."] ".$message." in ".$file.":".$line."<br/>\n");

From 23a191fbd213bdca982ffc30e282accb41ec9525 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Tue, 9 Mar 2021 19:08:14 +0100
Subject: [PATCH 025/154] bypass double constructor problem in PHP 5.x

---
 engine/settings.php | 25 ++++++++++++++++---------
 local/agreement.php |  2 +-
 2 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/engine/settings.php b/engine/settings.php
index c3d468a1..5ebf61f2 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -16,18 +16,25 @@
 ini_set("short_open_tag",1);
 setlocale(LC_CTYPE, "en_US.UTF-8");		
 
-// to psuje podwójne konstruktory
+// We need all messages for developer usage
 error_reporting(E_ALL);
-// a dowolny z poniższych blokuje te komunikaty
-//error_reporting(E_ALL ^ E_STRICT);
-ini_set("error_reporting", E_ALL & ~E_STRICT );
-// mój handler poniżej nie jest wrażliwy na ustawienia error_reporting
-// i wywala wszystko zawsze:
+// our handler isn't depends from above setting
 
 function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0) {
-	print("[".$level."] ".$message." in ".$file.":".$line."<br/>\n");
-	//throw new ErrorException($message, 0, $level, $file, $line);
-}
+
+	//print("[".$level."] ".$message." in ".$file.":".$line."<br/>\n");
+	
+	// silently drop ugly strict double constructor report in PHP < 7
+	if(version_compare(phpversion(),'7.0.0','<')) {
+		if(preg_match("/^Redefining already defined constructor for class Config/",$message)) {
+			return;
+		}
+	} // ver < 7.0
+
+	// converts all errors to exceptions
+	throw new ErrorException($message, 0, $level, $file, $line);
+
+}  // inforexCentralErrorHandler()
 
 set_error_handler("inforexCentralErrorHandler");
 
diff --git a/local/agreement.php b/local/agreement.php
index 21a18bac..071639f4 100644
--- a/local/agreement.php
+++ b/local/agreement.php
@@ -22,7 +22,7 @@
 $config = null;
 
 try {
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null );
 
 	$config->dsn1 = parse_database_uri($opt->getRequired("db-uri1"));
 	$config->dsn2 = parse_database_uri($opt->getRequired("db-uri2"));

From f0165b73bdbd88e8d6600f3a9fc6feab5ad1ed9b Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Tue, 9 Mar 2021 21:10:15 +0100
Subject: [PATCH 026/154] some potentially nonexistent variables

---
 engine/clioptcommon.php       | 12 +++++++-----
 engine/settings.php           |  2 +-
 local/ccl2iob.php             |  2 +-
 local/cli-liner2-nlprest2.php |  2 +-
 local/cli-restore-corpus.php  |  2 +-
 local/cli-upload-txt.php      |  2 +-
 local/daemon-cleanup.php      |  2 +-
 7 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/engine/clioptcommon.php b/engine/clioptcommon.php
index 882deeca..3c6ab37b 100644
--- a/engine/clioptcommon.php
+++ b/engine/clioptcommon.php
@@ -9,10 +9,12 @@
 class CliOptCommon {
 
     static function parseDbParameters($opt, $defaultDsn=array()){
-        $dbUser = $defaultDsn['username'];
-        $dbPass = $defaultDsn['password'];
-        $dbName = $defaultDsn['database'];
-        list($dbHost, $dbPort) = explode(":", $defaultDsn['hostspec']);
+        $dbUser = array_key_exists('username',$defaultDsn) ? $defaultDsn['username'] : "";
+        $dbPass = array_key_exists('password',$defaultDsn) ? $defaultDsn['password'] : "";
+        $dbName = array_key_exists('database',$defaultDsn) ? $defaultDsn['database'] : "";
+	$hostspecArray = array_key_exists('hostspec',$defaultDsn) ? explode(":", $defaultDsn['hostspec']) : array() ;
+	$dbHost = isset($hostspecArray[0]) ? $hostspecArray[0] : "";
+	$dbPort = isset($hostspecArray[1]) ? $hostspecArray[1] : "";
 
         if ( $opt->exists("db-uri")){
             $uri = $opt->getRequired("db-uri");
@@ -140,4 +142,4 @@ static function validateFlags($flags, $corpusId){
         }
     }
 
-}
\ No newline at end of file
+}
diff --git a/engine/settings.php b/engine/settings.php
index 5ebf61f2..8eae876f 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -22,7 +22,7 @@
 
 function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0) {
 
-	//print("[".$level."] ".$message." in ".$file.":".$line."<br/>\n");
+	print("[".$level."] ".$message." in ".$file.":".$line."<br/>\n");
 	
 	// silently drop ugly strict double constructor report in PHP < 7
 	if(version_compare(phpversion(),'7.0.0','<')) {
diff --git a/local/ccl2iob.php b/local/ccl2iob.php
index 9fb6c2cb..4de40b12 100644
--- a/local/ccl2iob.php
+++ b/local/ccl2iob.php
@@ -29,7 +29,7 @@
 //get parameters
 $config = null;
 try {
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	$input = $opt->getRequired("input");
 } 
 catch(Exception $ex){
diff --git a/local/cli-liner2-nlprest2.php b/local/cli-liner2-nlprest2.php
index a3fb7273..00f097b0 100644
--- a/local/cli-liner2-nlprest2.php
+++ b/local/cli-liner2-nlprest2.php
@@ -35,7 +35,7 @@
 /******************** parse cli *********************************************/
 try{
     /** Parse cli parameters */
-    $opt->parseCli($argv);
+    $opt->parseCli(isset($argv) ? $argv : null);
 
     $modelsAnnotationSets = array("n82"=>1, "timex4"=>15);
 
diff --git a/local/cli-restore-corpus.php b/local/cli-restore-corpus.php
index e0cd5132..72a645f5 100644
--- a/local/cli-restore-corpus.php
+++ b/local/cli-restore-corpus.php
@@ -27,7 +27,7 @@
 /******************** parse cli *********************************************/
 try{
     /** Parse cli parameters */
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
     $dsn = CliOptCommon::parseDbParameters($opt, Config::Config()->get_dsn());
 	$corpusId = $opt->getRequired("corpus");
 	$output = $opt->getOptional("output", null);
diff --git a/local/cli-upload-txt.php b/local/cli-upload-txt.php
index ea24f222..8bee3821 100644
--- a/local/cli-upload-txt.php
+++ b/local/cli-upload-txt.php
@@ -28,7 +28,7 @@
 /******************** parse cli *********************************************/
 try{
     /** Parse cli parameters */
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
     $dsn = CliOptCommon::parseDbParameters($opt, array("localhost", "root", null, "gpw", "3306"));
 	$sourceFolder = $opt->getRequired("folder");
 	$targetSubcorpusId = $opt->getRequired("subcorpus");
diff --git a/local/daemon-cleanup.php b/local/daemon-cleanup.php
index 9ec89bce..3a4fe5c2 100644
--- a/local/daemon-cleanup.php
+++ b/local/daemon-cleanup.php
@@ -25,7 +25,7 @@
 /******************** parse cli *********************************************/
 
 try{
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	Config::Config()->put_dsn(CliOptCommon::parseDbParameters($opt, Config::Config()->get_dsn()));
 }catch(Exception $ex){
 	print "!! ". $ex->getMessage() . " !!\n\n";

From 5b483dac97a40d2b27550ea7fe1cc0f0a4256c7f Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Wed, 10 Mar 2021 21:27:35 +0100
Subject: [PATCH 027/154] all local db calls realize via mysqli

---
 engine/clioptcommon.php                    | 7 +++++--
 engine/external/pear/MDB2/Driver/mysql.php | 2 +-
 engine/settings.php                        | 2 +-
 local/agreement.php                        | 4 ++--
 local/daemon-cleanup.php                   | 3 ++-
 local/daemon-export.php                    | 2 +-
 local/daemon-grab.php                      | 2 +-
 local/daemon-upload.php                    | 2 +-
 local/export-corpus.php                    | 2 +-
 local/flags.php                            | 2 +-
 local/import-ccl.php                       | 4 ++--
 local/import-tei.php                       | 2 +-
 local/liner2.php                           | 2 +-
 local/tokenize.php                         | 2 +-
 local/wsd-annotate.php                     | 2 +-
 15 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/engine/clioptcommon.php b/engine/clioptcommon.php
index 3c6ab37b..4065a791 100644
--- a/engine/clioptcommon.php
+++ b/engine/clioptcommon.php
@@ -29,10 +29,13 @@ static function parseDbParameters($opt, $defaultDsn=array()){
             }
         }
         $dsn = array();
-        $dsn['phptype'] = 'mysql';
+        $dsn['phptype'] = 'mysqli';
         $dsn['username'] = $dbUser;
         $dsn['password'] = $dbPass;
-        $dsn['hostspec'] = $dbHost . ":" . $dbPort;
+        $dsn['hostspec'] = $dbHost;
+	if($dbPort!="") { 
+		$dsn['hostspec'] .= ":" . $dbPort;
+	}
         $dsn['database'] = $dbName;
         return $dsn;
     }
diff --git a/engine/external/pear/MDB2/Driver/mysql.php b/engine/external/pear/MDB2/Driver/mysql.php
index 0bf0ab71..b9fd4e8c 100644
--- a/engine/external/pear/MDB2/Driver/mysql.php
+++ b/engine/external/pear/MDB2/Driver/mysql.php
@@ -921,7 +921,7 @@ function &prepare($query, $types = null, $result_types = null, $lobs = array())
         }
 
         $class_name = 'MDB2_Statement_'.$this->phptype;
-        $obj =& new $class_name($this, $statement_name, $positions, $query, $types, $result_types, $is_manip, $limit, $offset);
+        $obj = new $class_name($this, $statement_name, $positions, $query, $types, $result_types, $is_manip, $limit, $offset);
         $this->debug($query, __FUNCTION__, array('is_manip' => $is_manip, 'when' => 'post', 'result' => $obj));
         return $obj;
     }
diff --git a/engine/settings.php b/engine/settings.php
index 8eae876f..5ebf61f2 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -22,7 +22,7 @@
 
 function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0) {
 
-	print("[".$level."] ".$message." in ".$file.":".$line."<br/>\n");
+	//print("[".$level."] ".$message." in ".$file.":".$line."<br/>\n");
 	
 	// silently drop ugly strict double constructor report in PHP < 7
 	if(version_compare(phpversion(),'7.0.0','<')) {
diff --git a/local/agreement.php b/local/agreement.php
index 071639f4..c334fd24 100644
--- a/local/agreement.php
+++ b/local/agreement.php
@@ -26,8 +26,8 @@
 
 	$config->dsn1 = parse_database_uri($opt->getRequired("db-uri1"));
 	$config->dsn2 = parse_database_uri($opt->getRequired("db-uri2"));
-	$config->dns1['phptype'] = 'mysql';
-	$config->dns2['phptype'] = 'mysql';
+	$config->dns1['phptype'] = 'mysqli';
+	$config->dns2['phptype'] = 'mysqli';
 	
 	$config->sql = "SELECT r.id, a.from, a.to, a.type_id, a.text
  FROM `reports_annotations_optimized` a
diff --git a/local/daemon-cleanup.php b/local/daemon-cleanup.php
index 3a4fe5c2..98525d9f 100644
--- a/local/daemon-cleanup.php
+++ b/local/daemon-cleanup.php
@@ -30,7 +30,8 @@
 }catch(Exception $ex){
 	print "!! ". $ex->getMessage() . " !!\n\n";
 	$opt->printHelp();
-	die("\n");
+	print("\n");
+	return;
 }
 
 try{
diff --git a/local/daemon-export.php b/local/daemon-export.php
index 62dfc7c0..eff59576 100644
--- a/local/daemon-export.php
+++ b/local/daemon-export.php
@@ -51,7 +51,7 @@
 					"DB URI is incorrect. Given '$uri', but expected" .
 					" 'user:pass@host:port/name'");
 		$dsn = array();
-		$dsn['phptype'] = 'mysql';
+		$dsn['phptype'] = 'mysqli';
 		$dsn['username'] = $dbUser;
 		$dsn['password'] = $dbPass;
 		$dsn['hostspec'] = $dbHost . ":" . $dbPort;
diff --git a/local/daemon-grab.php b/local/daemon-grab.php
index d2d35944..8a030205 100644
--- a/local/daemon-grab.php
+++ b/local/daemon-grab.php
@@ -50,7 +50,7 @@
 					"DB URI is incorrect. Given '$uri', but exptected" .
 					" 'user:pass@host:port/name'");	
 		$dsn = array();	
-		$dsn['phptype'] = 'mysql';
+		$dsn['phptype'] = 'mysqli';
 		$dsn['username'] = $dbUser;
 		$dsn['password'] = $dbPass;
 		$dsn['hostspec'] = $dbHost . ":" . $dbPort;
diff --git a/local/daemon-upload.php b/local/daemon-upload.php
index 037b1213..546a9eac 100644
--- a/local/daemon-upload.php
+++ b/local/daemon-upload.php
@@ -50,7 +50,7 @@
 					"DB URI is incorrect. Given '$uri', but exptected" .
 					" 'user:pass@host:port/name'");	
 		$dsn = array();	
-		$dsn['phptype'] = 'mysql';
+		$dsn['phptype'] = 'mysqli';
 		$dsn['username'] = $dbUser;
 		$dsn['password'] = $dbPass;
 		$dsn['hostspec'] = $dbHost . ":" . $dbPort;
diff --git a/local/export-corpus.php b/local/export-corpus.php
index 30dd7e47..7cd9455c 100644
--- a/local/export-corpus.php
+++ b/local/export-corpus.php
@@ -67,7 +67,7 @@
 		$dbPass = $m[2];
 		$dbHost = $m[3];
 		$dbName = $m[4];
-		$config->dsn = array('phptype'  => 'mysql', 'username' => $dbUser, 'password' => $dbPass,
+		$config->dsn = array('phptype'  => 'mysqli', 'username' => $dbUser, 'password' => $dbPass,
     							'hostspec' => $dbHost, 'database' => $dbName);		    			
 		
 	}else{
diff --git a/local/flags.php b/local/flags.php
index c756b3af..8389d36d 100644
--- a/local/flags.php
+++ b/local/flags.php
@@ -42,7 +42,7 @@
 	}
 	
 	$config->dsn = array(
-	    			'phptype'  => 'mysql',
+	    			'phptype'  => 'mysqli',
 	    			'username' => $dbUser,
 	    			'password' => $dbPass,
 	    			'hostspec' => $dbHost,
diff --git a/local/import-ccl.php b/local/import-ccl.php
index ed5a59a8..fa304f88 100644
--- a/local/import-ccl.php
+++ b/local/import-ccl.php
@@ -638,7 +638,7 @@ function parseArgs($argv){
 			}
 				
 			$this->config->dsn = array(
-			    			'phptype'  => 'mysql',
+			    			'phptype'  => 'mysqli',
 			    			'username' => $this->dbUser,
 			    			'password' => $this->dbPass,
 			    			'hostspec' => $this->dbHost,
@@ -673,4 +673,4 @@ function import($db){
 $db = new Database($ccl_importer->getDbConfig());
 $ccl_importer->import($db);
 
-?>
\ No newline at end of file
+?>
diff --git a/local/import-tei.php b/local/import-tei.php
index 3f1d1ec0..00f04f40 100755
--- a/local/import-tei.php
+++ b/local/import-tei.php
@@ -551,7 +551,7 @@ function parseArgs($argv){
 			}
 				
 			$this->config = array(
-			    			'phptype'  => 'mysql',
+			    			'phptype'  => 'mysqli',
 			    			'username' => $this->dbUser,
 			    			'password' => $this->dbPass,
 			    			'hostspec' => $this->dbHost,
diff --git a/local/liner2.php b/local/liner2.php
index 8d64874d..ad73ed8f 100644
--- a/local/liner2.php
+++ b/local/liner2.php
@@ -43,7 +43,7 @@
 	}
 	
 	Config::Config()->put_dsn(array(
-	    			'phptype'  => 'mysql',
+	    			'phptype'  => 'mysqli',
 	    			'username' => $dbUser,
 	    			'password' => $dbPass,
 	    			'hostspec' => $dbHost,
diff --git a/local/tokenize.php b/local/tokenize.php
index 508b9b4d..e4da129a 100644
--- a/local/tokenize.php
+++ b/local/tokenize.php
@@ -58,7 +58,7 @@
     Config::Config()->put_tagsetName('nkjp');
 
 	$dsn = array();
-	$dsn['phptype'] = 'mysql';
+	$dsn['phptype'] = 'mysqli';
 	$dsn['username'] = $dbUser;
 	$dsn['password'] = $dbPass;
 	$dsn['hostspec'] = $dbHost . ":" . $dbPort;
diff --git a/local/wsd-annotate.php b/local/wsd-annotate.php
index 835b085f..a665363d 100644
--- a/local/wsd-annotate.php
+++ b/local/wsd-annotate.php
@@ -52,7 +52,7 @@
 		}
 	}
 	
-	$config->dsn['phptype'] = 'mysql';
+	$config->dsn['phptype'] = 'mysqli';
 	$config->dsn['username'] = $dbUser;
 	$config->dsn['password'] = $dbPass;
 	$config->dsn['hostspec'] = $dbHost . ":" . $dbPort;

From 2ff58227d5d1e4a9550d2057fedb4c73251554c8 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Wed, 10 Mar 2021 22:21:17 +0100
Subject: [PATCH 028/154] empty argument parseCli

---
 engine/settings.php              | 2 +-
 local/agreement.php              | 2 +-
 local/ccl2iob.php                | 2 +-
 local/cli-liner2-nlprest2.php    | 2 +-
 local/cli-restore-corpus.php     | 2 +-
 local/cli-upload-txt.php         | 2 +-
 local/daemon-cleanup.php         | 2 +-
 local/daemon-export.php          | 4 ++--
 local/daemon-grab.php            | 4 ++--
 local/daemon-tasks.php           | 4 ++--
 local/daemon-upload.php          | 4 ++--
 local/export-corpus.php          | 4 ++--
 local/flags.php                  | 4 ++--
 local/import-ccl.php             | 4 ++--
 local/import-corpus-cli.php      | 4 ++--
 local/import-sherlock.php        | 4 ++--
 local/import-tei.php             | 2 +-
 local/import-wsd-annotations.php | 4 ++--
 local/liner2.php                 | 4 ++--
 local/slavicner2019-annotate.php | 4 ++--
 local/slavicner2019.php          | 4 ++--
 local/tokenize-update.php        | 4 ++--
 local/tokenize.php               | 4 ++--
 local/upload.php                 | 4 ++--
 local/wsd-annotate.php           | 4 ++--
 25 files changed, 42 insertions(+), 42 deletions(-)

diff --git a/engine/settings.php b/engine/settings.php
index 5ebf61f2..8eae876f 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -22,7 +22,7 @@
 
 function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0) {
 
-	//print("[".$level."] ".$message." in ".$file.":".$line."<br/>\n");
+	print("[".$level."] ".$message." in ".$file.":".$line."<br/>\n");
 	
 	// silently drop ugly strict double constructor report in PHP < 7
 	if(version_compare(phpversion(),'7.0.0','<')) {
diff --git a/local/agreement.php b/local/agreement.php
index c334fd24..eccc0944 100644
--- a/local/agreement.php
+++ b/local/agreement.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("UTF-8");
diff --git a/local/ccl2iob.php b/local/ccl2iob.php
index 4de40b12..9a11e8a2 100644
--- a/local/ccl2iob.php
+++ b/local/ccl2iob.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("UTF-8");
diff --git a/local/cli-liner2-nlprest2.php b/local/cli-liner2-nlprest2.php
index 00f097b0..1271c6c5 100644
--- a/local/cli-liner2-nlprest2.php
+++ b/local/cli-liner2-nlprest2.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
diff --git a/local/cli-restore-corpus.php b/local/cli-restore-corpus.php
index 72a645f5..4d323ef7 100644
--- a/local/cli-restore-corpus.php
+++ b/local/cli-restore-corpus.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
diff --git a/local/cli-upload-txt.php b/local/cli-upload-txt.php
index 8bee3821..ad2a79e9 100644
--- a/local/cli-upload-txt.php
+++ b/local/cli-upload-txt.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
diff --git a/local/daemon-cleanup.php b/local/daemon-cleanup.php
index 98525d9f..4e2f670c 100644
--- a/local/daemon-cleanup.php
+++ b/local/daemon-cleanup.php
@@ -10,7 +10,7 @@
 require_once($enginePath."/settings.php");
 require_once($enginePath.'/include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath."/../config/")."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath.DIRECTORY_SEPARATOR."..".DIRECTORY_SEPARATOR."config"). DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
diff --git a/local/daemon-export.php b/local/daemon-export.php
index eff59576..6f82c8bd 100644
--- a/local/daemon-export.php
+++ b/local/daemon-export.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
@@ -32,7 +32,7 @@
 $formats['premorph'] = 3;
 
 try{
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	if ( $opt->exists("db-uri")){
 		$dbHost = "localhost";
 		$dbUser = "root";
diff --git a/local/daemon-grab.php b/local/daemon-grab.php
index 8a030205..39c60b25 100644
--- a/local/daemon-grab.php
+++ b/local/daemon-grab.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("utf-8");
@@ -31,7 +31,7 @@
 $formats['premorph'] = 3;
 
 try{
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	if ( $opt->exists("db-uri")){
 		$dbHost = "localhost";
 		$dbUser = "root";
diff --git a/local/daemon-tasks.php b/local/daemon-tasks.php
index fc7f6789..dce68361 100644
--- a/local/daemon-tasks.php
+++ b/local/daemon-tasks.php
@@ -10,7 +10,7 @@
 require_once($enginePath."/settings.php");
 require_once($enginePath.'/include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath."/../config/")."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath."/../config").DIRECTORY_SEPARATOR."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
@@ -31,7 +31,7 @@
 $formats['premorph'] = 3;
 
 try{
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	
 	$dbHost = "localhost";
 	$dbUser = "root";
diff --git a/local/daemon-upload.php b/local/daemon-upload.php
index 546a9eac..efb1b34f 100644
--- a/local/daemon-upload.php
+++ b/local/daemon-upload.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("utf-8");
@@ -31,7 +31,7 @@
 $formats['premorph'] = 3;
 
 try{
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	if ( $opt->exists("db-uri")){
 		$dbHost = "localhost";
 		$dbUser = "root";
diff --git a/local/export-corpus.php b/local/export-corpus.php
index 7cd9455c..10016ac0 100644
--- a/local/export-corpus.php
+++ b/local/export-corpus.php
@@ -35,7 +35,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("utf-8");
@@ -58,7 +58,7 @@
 $dns = null;
 $config->selectors = array();
 try {
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 
 	// Parsowanie db-uri 
 	$uri = $opt->getRequired("db-uri");
diff --git a/local/flags.php b/local/flags.php
index 8389d36d..1805afdd 100644
--- a/local/flags.php
+++ b/local/flags.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("UTF-8");
@@ -27,7 +27,7 @@
 $opt->addParameter(new ClioptParameter("init", null, null, "init only not set flags"));
 $config = null;
 try {
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	
 	if ( $opt->exists("db-uri")){
 		$uri = $opt->getRequired("db-uri");
diff --git a/local/import-ccl.php b/local/import-ccl.php
index fa304f88..69bc0dc9 100644
--- a/local/import-ccl.php
+++ b/local/import-ccl.php
@@ -616,9 +616,9 @@ function __construct(){
 		$this->opt->addParameter(new ClioptParameter("db-name", null, "name", "database name"));
 	}
 
-	function parseArgs($argv){
+	function parseArgs(isset($argv) ? $argv : null){
 		try {
-			$this->opt->parseCli($argv);
+			$this->opt->parseCli(isset($argv) ? $argv : null);
 			
 			$this->dbUser = $this->opt->getOptional("db-user", "root");
 			$this->dbPass = $this->opt->getOptional("db-pass", "sql");
diff --git a/local/import-corpus-cli.php b/local/import-corpus-cli.php
index e9c209f1..af9b8a18 100644
--- a/local/import-corpus-cli.php
+++ b/local/import-corpus-cli.php
@@ -4,7 +4,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
@@ -28,7 +28,7 @@
 ini_set('memory_limit', '1024M');
 
 try {
-    $opt->parseCli($argv);
+    $opt->parseCli(isset($argv) ? $argv : null);
     $dsn = CliOptCommon::parseDbParameters($opt, Config::Config()->get_dsn());
     $verbose = $opt->exists("verbose");
     $corpusDir = $opt->getRequired("corpus-directory");
diff --git a/local/import-sherlock.php b/local/import-sherlock.php
index b652f0a1..ccaacb76 100644
--- a/local/import-sherlock.php
+++ b/local/import-sherlock.php
@@ -4,7 +4,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
@@ -22,7 +22,7 @@
 /******************** parse cli *********************************************/
 
 try{
-    $opt->parseCli($argv);
+    $opt->parseCli(isset($argv) ? $argv : null);
     $dsn = CliOptCommon::parseDbParameters($opt, Config::Config()->get_dsn());
     $verbose = $opt->exists("verbose");
     $jsonPath = $opt->getRequired("json");
diff --git a/local/import-tei.php b/local/import-tei.php
index 00f04f40..b9dda496 100755
--- a/local/import-tei.php
+++ b/local/import-tei.php
@@ -531,7 +531,7 @@ function __construct(){
 
 	function parseArgs($argv){
 		try {
-			$this->opt->parseCli($argv);
+			$this->opt->parseCli(isset($argv) ? $argv : null);
 			
 			$this->dbUser = $this->opt->getOptional("db-user", "root");
 			$this->dbPass = $this->opt->getOptional("db-pass", "sql");
diff --git a/local/import-wsd-annotations.php b/local/import-wsd-annotations.php
index 8eb7bc14..c578c32d 100644
--- a/local/import-wsd-annotations.php
+++ b/local/import-wsd-annotations.php
@@ -4,7 +4,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
@@ -23,7 +23,7 @@
 
 try {
     ini_set('memory_limit', '1024M');
-    $opt->parseCli($argv);
+    $opt->parseCli(isset($argv) ? $argv : null);
     $dsn = CliOptCommon::parseDbParameters($opt, Config::Config()->get_dsn());
     $verbose = $opt->exists("verbose");
     $jsonPath = $opt->getRequired("json");
diff --git a/local/liner2.php b/local/liner2.php
index ad73ed8f..384e12fd 100644
--- a/local/liner2.php
+++ b/local/liner2.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("utf-8");
@@ -28,7 +28,7 @@
 /******************** parse cli *********************************************/
 
 try{
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	
 	if ( $opt->exists("db-uri")){
 		$uri = $opt->getRequired("db-uri");
diff --git a/local/slavicner2019-annotate.php b/local/slavicner2019-annotate.php
index ebb7dcac..bc6a79c1 100644
--- a/local/slavicner2019-annotate.php
+++ b/local/slavicner2019-annotate.php
@@ -4,7 +4,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
@@ -57,7 +57,7 @@ function printHelp(){
     }
 
     function parseArgv($argv){
-        $this->opt->parseCli($argv);
+        $this->opt->parseCli(isset($argv) ? $argv : null);
         $this->dsn = CliOptCommon::parseDbParameters($this->opt, array("localhost", "root", null, "gpw", "3306"));
         $this->folder = $this->opt->getRequired("folder");
         $this->corpusId = $this->opt->getRequired("corpus");
diff --git a/local/slavicner2019.php b/local/slavicner2019.php
index e7077f20..c7e5d232 100644
--- a/local/slavicner2019.php
+++ b/local/slavicner2019.php
@@ -3,7 +3,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
@@ -20,7 +20,7 @@
 
 /******************** scripts entry point   *********************************************/
 function process($opt, $argv){
-    $opt->parseCli($argv);
+    $opt->parseCli(isset($argv) ? $argv : null);
     $dsn = CliOptCommon::parseDbParameters($opt, array("localhost", "root", null, "gpw", "3306"));
     $flags = CliOptCommon::parseFlag($opt->getParameters("flag"));
     $folder = $opt->getRequired("folder");
diff --git a/local/tokenize-update.php b/local/tokenize-update.php
index f1c03063..c4974700 100644
--- a/local/tokenize-update.php
+++ b/local/tokenize-update.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("utf-8");
@@ -35,7 +35,7 @@
 /******************** parse cli *********************************************/
 //$config = null;
 try{
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	
 	$dbHost = "localhost";
 	$dbUser = "root";
diff --git a/local/tokenize.php b/local/tokenize.php
index e4da129a..32e86558 100644
--- a/local/tokenize.php
+++ b/local/tokenize.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("utf-8");
@@ -33,7 +33,7 @@
 /******************** parse cli *********************************************/
 //$config = null;
 try{
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	
 	$dbHost = "localhost";
 	$dbUser = "root";
diff --git a/local/upload.php b/local/upload.php
index 8a6d3008..19553e9c 100644
--- a/local/upload.php
+++ b/local/upload.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("utf-32");
@@ -38,7 +38,7 @@
 $formats['premorph'] = 3;
 
 try{
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	
 	$dbHost = "localhost";
 	$dbUser = "root";
diff --git a/local/wsd-annotate.php b/local/wsd-annotate.php
index a665363d..10f2e119 100644
--- a/local/wsd-annotate.php
+++ b/local/wsd-annotate.php
@@ -8,7 +8,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("UTF-8");
@@ -31,7 +31,7 @@
 
 $config = null;
 try {
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	
 	$dbHost = "localhost";
 	$dbUser = "root";

From ecced915642298430c63d8cbf9465d1393de38aa Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Wed, 10 Mar 2021 22:21:17 +0100
Subject: [PATCH 029/154] empty argument parseCli

---
 engine/settings.php              | 2 +-
 local/agreement.php              | 2 +-
 local/ccl2iob.php                | 2 +-
 local/cli-liner2-nlprest2.php    | 2 +-
 local/cli-restore-corpus.php     | 2 +-
 local/cli-upload-txt.php         | 2 +-
 local/daemon-cleanup.php         | 2 +-
 local/daemon-export.php          | 4 ++--
 local/daemon-grab.php            | 4 ++--
 local/daemon-tasks.php           | 4 ++--
 local/daemon-upload.php          | 4 ++--
 local/export-corpus.php          | 4 ++--
 local/flags.php                  | 4 ++--
 local/import-ccl.php             | 4 ++--
 local/import-corpus-cli.php      | 4 ++--
 local/import-sherlock.php        | 4 ++--
 local/import-tei.php             | 2 +-
 local/import-wsd-annotations.php | 4 ++--
 local/liner2.php                 | 4 ++--
 local/slavicner2019-annotate.php | 8 ++++----
 local/slavicner2019.php          | 6 +++---
 local/tokenize-update.php        | 4 ++--
 local/tokenize.php               | 4 ++--
 local/upload.php                 | 6 +++---
 local/wsd-annotate.php           | 4 ++--
 25 files changed, 46 insertions(+), 46 deletions(-)

diff --git a/engine/settings.php b/engine/settings.php
index 5ebf61f2..8eae876f 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -22,7 +22,7 @@
 
 function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0) {
 
-	//print("[".$level."] ".$message." in ".$file.":".$line."<br/>\n");
+	print("[".$level."] ".$message." in ".$file.":".$line."<br/>\n");
 	
 	// silently drop ugly strict double constructor report in PHP < 7
 	if(version_compare(phpversion(),'7.0.0','<')) {
diff --git a/local/agreement.php b/local/agreement.php
index c334fd24..eccc0944 100644
--- a/local/agreement.php
+++ b/local/agreement.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("UTF-8");
diff --git a/local/ccl2iob.php b/local/ccl2iob.php
index 4de40b12..9a11e8a2 100644
--- a/local/ccl2iob.php
+++ b/local/ccl2iob.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("UTF-8");
diff --git a/local/cli-liner2-nlprest2.php b/local/cli-liner2-nlprest2.php
index 00f097b0..1271c6c5 100644
--- a/local/cli-liner2-nlprest2.php
+++ b/local/cli-liner2-nlprest2.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
diff --git a/local/cli-restore-corpus.php b/local/cli-restore-corpus.php
index 72a645f5..4d323ef7 100644
--- a/local/cli-restore-corpus.php
+++ b/local/cli-restore-corpus.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
diff --git a/local/cli-upload-txt.php b/local/cli-upload-txt.php
index 8bee3821..ad2a79e9 100644
--- a/local/cli-upload-txt.php
+++ b/local/cli-upload-txt.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
diff --git a/local/daemon-cleanup.php b/local/daemon-cleanup.php
index 98525d9f..4e2f670c 100644
--- a/local/daemon-cleanup.php
+++ b/local/daemon-cleanup.php
@@ -10,7 +10,7 @@
 require_once($enginePath."/settings.php");
 require_once($enginePath.'/include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath."/../config/")."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath.DIRECTORY_SEPARATOR."..".DIRECTORY_SEPARATOR."config"). DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
diff --git a/local/daemon-export.php b/local/daemon-export.php
index eff59576..6f82c8bd 100644
--- a/local/daemon-export.php
+++ b/local/daemon-export.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
@@ -32,7 +32,7 @@
 $formats['premorph'] = 3;
 
 try{
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	if ( $opt->exists("db-uri")){
 		$dbHost = "localhost";
 		$dbUser = "root";
diff --git a/local/daemon-grab.php b/local/daemon-grab.php
index 8a030205..39c60b25 100644
--- a/local/daemon-grab.php
+++ b/local/daemon-grab.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("utf-8");
@@ -31,7 +31,7 @@
 $formats['premorph'] = 3;
 
 try{
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	if ( $opt->exists("db-uri")){
 		$dbHost = "localhost";
 		$dbUser = "root";
diff --git a/local/daemon-tasks.php b/local/daemon-tasks.php
index fc7f6789..dce68361 100644
--- a/local/daemon-tasks.php
+++ b/local/daemon-tasks.php
@@ -10,7 +10,7 @@
 require_once($enginePath."/settings.php");
 require_once($enginePath.'/include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath."/../config/")."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath."/../config").DIRECTORY_SEPARATOR."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
@@ -31,7 +31,7 @@
 $formats['premorph'] = 3;
 
 try{
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	
 	$dbHost = "localhost";
 	$dbUser = "root";
diff --git a/local/daemon-upload.php b/local/daemon-upload.php
index 546a9eac..efb1b34f 100644
--- a/local/daemon-upload.php
+++ b/local/daemon-upload.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("utf-8");
@@ -31,7 +31,7 @@
 $formats['premorph'] = 3;
 
 try{
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	if ( $opt->exists("db-uri")){
 		$dbHost = "localhost";
 		$dbUser = "root";
diff --git a/local/export-corpus.php b/local/export-corpus.php
index 7cd9455c..10016ac0 100644
--- a/local/export-corpus.php
+++ b/local/export-corpus.php
@@ -35,7 +35,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("utf-8");
@@ -58,7 +58,7 @@
 $dns = null;
 $config->selectors = array();
 try {
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 
 	// Parsowanie db-uri 
 	$uri = $opt->getRequired("db-uri");
diff --git a/local/flags.php b/local/flags.php
index 8389d36d..1805afdd 100644
--- a/local/flags.php
+++ b/local/flags.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("UTF-8");
@@ -27,7 +27,7 @@
 $opt->addParameter(new ClioptParameter("init", null, null, "init only not set flags"));
 $config = null;
 try {
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	
 	if ( $opt->exists("db-uri")){
 		$uri = $opt->getRequired("db-uri");
diff --git a/local/import-ccl.php b/local/import-ccl.php
index fa304f88..69bc0dc9 100644
--- a/local/import-ccl.php
+++ b/local/import-ccl.php
@@ -616,9 +616,9 @@ function __construct(){
 		$this->opt->addParameter(new ClioptParameter("db-name", null, "name", "database name"));
 	}
 
-	function parseArgs($argv){
+	function parseArgs(isset($argv) ? $argv : null){
 		try {
-			$this->opt->parseCli($argv);
+			$this->opt->parseCli(isset($argv) ? $argv : null);
 			
 			$this->dbUser = $this->opt->getOptional("db-user", "root");
 			$this->dbPass = $this->opt->getOptional("db-pass", "sql");
diff --git a/local/import-corpus-cli.php b/local/import-corpus-cli.php
index e9c209f1..af9b8a18 100644
--- a/local/import-corpus-cli.php
+++ b/local/import-corpus-cli.php
@@ -4,7 +4,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
@@ -28,7 +28,7 @@
 ini_set('memory_limit', '1024M');
 
 try {
-    $opt->parseCli($argv);
+    $opt->parseCli(isset($argv) ? $argv : null);
     $dsn = CliOptCommon::parseDbParameters($opt, Config::Config()->get_dsn());
     $verbose = $opt->exists("verbose");
     $corpusDir = $opt->getRequired("corpus-directory");
diff --git a/local/import-sherlock.php b/local/import-sherlock.php
index b652f0a1..ccaacb76 100644
--- a/local/import-sherlock.php
+++ b/local/import-sherlock.php
@@ -4,7 +4,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
@@ -22,7 +22,7 @@
 /******************** parse cli *********************************************/
 
 try{
-    $opt->parseCli($argv);
+    $opt->parseCli(isset($argv) ? $argv : null);
     $dsn = CliOptCommon::parseDbParameters($opt, Config::Config()->get_dsn());
     $verbose = $opt->exists("verbose");
     $jsonPath = $opt->getRequired("json");
diff --git a/local/import-tei.php b/local/import-tei.php
index 00f04f40..b9dda496 100755
--- a/local/import-tei.php
+++ b/local/import-tei.php
@@ -531,7 +531,7 @@ function __construct(){
 
 	function parseArgs($argv){
 		try {
-			$this->opt->parseCli($argv);
+			$this->opt->parseCli(isset($argv) ? $argv : null);
 			
 			$this->dbUser = $this->opt->getOptional("db-user", "root");
 			$this->dbPass = $this->opt->getOptional("db-pass", "sql");
diff --git a/local/import-wsd-annotations.php b/local/import-wsd-annotations.php
index 8eb7bc14..c578c32d 100644
--- a/local/import-wsd-annotations.php
+++ b/local/import-wsd-annotations.php
@@ -4,7 +4,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
@@ -23,7 +23,7 @@
 
 try {
     ini_set('memory_limit', '1024M');
-    $opt->parseCli($argv);
+    $opt->parseCli(isset($argv) ? $argv : null);
     $dsn = CliOptCommon::parseDbParameters($opt, Config::Config()->get_dsn());
     $verbose = $opt->exists("verbose");
     $jsonPath = $opt->getRequired("json");
diff --git a/local/liner2.php b/local/liner2.php
index ad73ed8f..384e12fd 100644
--- a/local/liner2.php
+++ b/local/liner2.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("utf-8");
@@ -28,7 +28,7 @@
 /******************** parse cli *********************************************/
 
 try{
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	
 	if ( $opt->exists("db-uri")){
 		$uri = $opt->getRequired("db-uri");
diff --git a/local/slavicner2019-annotate.php b/local/slavicner2019-annotate.php
index ebb7dcac..9706d5e5 100644
--- a/local/slavicner2019-annotate.php
+++ b/local/slavicner2019-annotate.php
@@ -4,7 +4,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
@@ -57,7 +57,7 @@ function printHelp(){
     }
 
     function parseArgv($argv){
-        $this->opt->parseCli($argv);
+        $this->opt->parseCli(isset($argv) ? $argv : null);
         $this->dsn = CliOptCommon::parseDbParameters($this->opt, array("localhost", "root", null, "gpw", "3306"));
         $this->folder = $this->opt->getRequired("folder");
         $this->corpusId = $this->opt->getRequired("corpus");
@@ -328,8 +328,8 @@ function logWarning($warning){
 /******************** scripts entry point   *********************************************/
 try{
     $action = new ActionAnnotateTsv();
-    $action->parseArgv($argv);
-    $action->process($argv);
+    $action->parseArgv(isset($argv) ? $argv : null);
+    $action->process(isset($argv) ? $argv : null);
 }catch(Exception $ex){
     print "!! ". $ex->getMessage() . " !!\n\n";
     $action->printHelp();
diff --git a/local/slavicner2019.php b/local/slavicner2019.php
index e7077f20..3f10f245 100644
--- a/local/slavicner2019.php
+++ b/local/slavicner2019.php
@@ -3,7 +3,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
@@ -20,7 +20,7 @@
 
 /******************** scripts entry point   *********************************************/
 function process($opt, $argv){
-    $opt->parseCli($argv);
+    $opt->parseCli(isset($argv) ? $argv : null);
     $dsn = CliOptCommon::parseDbParameters($opt, array("localhost", "root", null, "gpw", "3306"));
     $flags = CliOptCommon::parseFlag($opt->getParameters("flag"));
     $folder = $opt->getRequired("folder");
@@ -134,7 +134,7 @@ function createFolderIfNotExists($folder){
 
 /******************** scripts entry point   *********************************************/
 try{
-    process($opt, $argv);
+    process($opt, isset($argv) ? $argv : null);
 }catch(Exception $ex){
     print "!! ". $ex->getMessage() . " !!\n\n";
     $opt->printHelp();
diff --git a/local/tokenize-update.php b/local/tokenize-update.php
index f1c03063..c4974700 100644
--- a/local/tokenize-update.php
+++ b/local/tokenize-update.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("utf-8");
@@ -35,7 +35,7 @@
 /******************** parse cli *********************************************/
 //$config = null;
 try{
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	
 	$dbHost = "localhost";
 	$dbUser = "root";
diff --git a/local/tokenize.php b/local/tokenize.php
index e4da129a..32e86558 100644
--- a/local/tokenize.php
+++ b/local/tokenize.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("utf-8");
@@ -33,7 +33,7 @@
 /******************** parse cli *********************************************/
 //$config = null;
 try{
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	
 	$dbHost = "localhost";
 	$dbUser = "root";
diff --git a/local/upload.php b/local/upload.php
index 8a6d3008..b4264fc8 100644
--- a/local/upload.php
+++ b/local/upload.php
@@ -10,7 +10,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("utf-32");
@@ -38,7 +38,7 @@
 $formats['premorph'] = 3;
 
 try{
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	
 	$dbHost = "localhost";
 	$dbUser = "root";
@@ -126,7 +126,7 @@ function main ($config){
 	
 	$sql = sprintf("SELECT * FROM corpus_subcorpora WHERE subcorpus_id = %d", $config->subcorpus);
 	$corpus = $db->fetch($sql);
-	$corpus_id = intval($corpus[corpus_id]);
+	$corpus_id = intval($corpus['corpus_id']);
 			
 	if ( $corpus_id == 0 )
 		die("Unrecognized subcorpus id {$config->cobcorpus}\n\n");
diff --git a/local/wsd-annotate.php b/local/wsd-annotate.php
index a665363d..10f2e119 100644
--- a/local/wsd-annotate.php
+++ b/local/wsd-annotate.php
@@ -8,7 +8,7 @@
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" . DIRECTORY_SEPARATOR )."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 
 mb_internal_encoding("UTF-8");
@@ -31,7 +31,7 @@
 
 $config = null;
 try {
-	$opt->parseCli($argv);
+	$opt->parseCli(isset($argv) ? $argv : null);
 	
 	$dbHost = "localhost";
 	$dbUser = "root";

From 6208e7d4b1c57156e583c71225759dce539b6bd0 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Thu, 11 Mar 2021 21:51:19 +0100
Subject: [PATCH 030/154] null object as local config

---
 engine/settings.php |  2 +-
 local/flags.php     | 12 +++++++-----
 local/liner2.php    |  8 ++++----
 3 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/engine/settings.php b/engine/settings.php
index 8eae876f..5ebf61f2 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -22,7 +22,7 @@
 
 function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0) {
 
-	print("[".$level."] ".$message." in ".$file.":".$line."<br/>\n");
+	//print("[".$level."] ".$message." in ".$file.":".$line."<br/>\n");
 	
 	// silently drop ugly strict double constructor report in PHP < 7
 	if(version_compare(phpversion(),'7.0.0','<')) {
diff --git a/local/flags.php b/local/flags.php
index 1805afdd..2886d4dc 100644
--- a/local/flags.php
+++ b/local/flags.php
@@ -25,7 +25,8 @@
 $opt->addParameter(new ClioptParameter("flag-to-set", null, "flag name", "name of flag to set"));
 $opt->addParameter(new ClioptParameter("status", "v", "id", "flag status id"));
 $opt->addParameter(new ClioptParameter("init", null, null, "init only not set flags"));
-$config = null;
+class LocalConfigArrayClass { };
+$config = new LocalConfigArrayClass;
 try {
 	$opt->parseCli(isset($argv) ? $argv : null);
 	
@@ -43,10 +44,11 @@
 	
 	$config->dsn = array(
 	    			'phptype'  => 'mysqli',
-	    			'username' => $dbUser,
-	    			'password' => $dbPass,
-	    			'hostspec' => $dbHost,
-	    			'database' => $dbName);	$config->corpus = $opt->getParameters("corpus");
+	    			'username' => isset($dbUser) ? $dbUser : "",
+	    			'password' => isset($dbPass) ? $dbPass : "",
+	    			'hostspec' => isset($dbHost) ? $dbHost : "localhost",
+	    			'database' => isset($dbName) ? $dbName : "");	
+	$config->corpus = $opt->getParameters("corpus");
 	$config->subcorpus = $opt->getParameters("subcorpus");
 	$config->documents = $opt->getParameters("document");
 	$config->flag = $opt->getOptional("flag", null);
diff --git a/local/liner2.php b/local/liner2.php
index 384e12fd..3ecf8347 100644
--- a/local/liner2.php
+++ b/local/liner2.php
@@ -44,10 +44,10 @@
 	
 	Config::Config()->put_dsn(array(
 	    			'phptype'  => 'mysqli',
-	    			'username' => $dbUser,
-	    			'password' => $dbPass,
-	    			'hostspec' => $dbHost,
-	    			'database' => $dbName));	
+	    			'username' => isset($dbUser) ? $dbUser : "",
+	    			'password' => isset($dbPass) ? $dbPass : "",
+	    			'hostspec' => isset($dbHost) ? $dbHost : "localhost",
+	    			'database' => isset($dbName) ? $dbName : ""));	
 	$db = new Database(Config::Config()->get_dsn());
 	$db->set_encoding('utf8'); 	
 	// SET CHARACTER SET sets only subset of SET NAMES params

From 9ba26d9d779aa3b36e7a38e58c6437f92c9bf83c Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Fri, 12 Mar 2021 19:53:52 +0100
Subject: [PATCH 031/154] selinux removes former settings in rpm build

---
 packages/rpm/SPECS/inforex.spec | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/packages/rpm/SPECS/inforex.spec b/packages/rpm/SPECS/inforex.spec
index ded62c7a..a7a1608e 100644
--- a/packages/rpm/SPECS/inforex.spec
+++ b/packages/rpm/SPECS/inforex.spec
@@ -87,6 +87,10 @@ if [ -x %{_sbindir}/semanage ] ; then
 	fi
         %{_sbindir}/semanage fcontext -a -t httpd_var_lib_t %{_localstatedir}/lib/%{name}
 	%{_sbindir}/restorecon %{_localstatedir}/lib/%{name}
+	# %{inforexdir}/engine/templates_c for rw
+	if ( %{_sbindir}/semanage fcontext -l |grep %{inforexdir}/engine/templates_c  > /dev/null ) ; then
+		%{_sbindir}/semanage fcontext -d %{inforexdir}/engine/templates_c 
+	fi
 	%{_sbindir}/semanage fcontext -a -t httpd_sys_rw_content_t %{inforexdir}/engine/templates_c
 	%{_sbindir}/restorecon %{inforexdir}/engine/templates_c
 fi

From 33cdd85bc70689c09cacb9065cfe3c79b889ba89 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 13 Mar 2021 10:10:08 +0100
Subject: [PATCH 032/154] dockerfile configured to php7.3

---
 docker/www/Dockerfile | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/docker/www/Dockerfile b/docker/www/Dockerfile
index e802fd80..90ebdcd3 100644
--- a/docker/www/Dockerfile
+++ b/docker/www/Dockerfile
@@ -1,4 +1,4 @@
-FROM php:5.6-apache as php-base
+FROM php:7.3-apache as php-base
 
 RUN apt-get update -y && apt-get upgrade -y
 RUN apt-get install software-properties-common wget -y
@@ -18,12 +18,13 @@ RUN a2enmod headers
 RUN a2enmod expires
 
 #Installing some PHP libraries
-RUN apt-get install libmcrypt-dev zlib1g zlib1g-dev -y \
-	&& docker-php-ext-install mcrypt \
-	&& docker-php-ext-install mysql \
+RUN apt-get install libmcrypt-dev zlib1g zlib1g-dev -y libzip-dev \
+	&& docker-php-ext-install mysqli \
 	&& docker-php-ext-install zip \
 	&& docker-php-ext-install gd \
-	&& apt-get install re2c -y
+	&& apt-get install re2c -y \
+    	&& pecl install mcrypt-1.0.3 \
+    	&& docker-php-ext-enable mcrypt
 
 # Xdiff install
 RUN curl -L -o /tmp/xdiff.tar.gz "http://www.xmailserver.org/libxdiff-0.23.tar.gz" \
@@ -32,7 +33,7 @@ RUN curl -L -o /tmp/xdiff.tar.gz "http://www.xmailserver.org/libxdiff-0.23.tar.g
     && rm /tmp/xdiff.tar.gz \
     && cd /usr/src/xdiff \
     && ./configure  && make && make install \
-    &&  pecl install xdiff-1.5.2 && docker-php-ext-enable xdiff
+    &&  pecl install xdiff-2.0.1 && docker-php-ext-enable xdiff
 
 # Supervisor
 RUN apt-get update -y && apt-get install supervisor -y

From 2343b3994ed86d4c25f24a71343a227de0978d0a Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 13 Mar 2021 11:23:48 +0100
Subject: [PATCH 033/154] check using mysql driver on PHP7 -> exception

---
 engine/external/pear/MDB2/Driver/mysql.php | 2 +-
 engine/include/database/Database.php       | 7 +++++++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/engine/external/pear/MDB2/Driver/mysql.php b/engine/external/pear/MDB2/Driver/mysql.php
index b9fd4e8c..10d307de 100644
--- a/engine/external/pear/MDB2/Driver/mysql.php
+++ b/engine/external/pear/MDB2/Driver/mysql.php
@@ -1187,7 +1187,7 @@ function &fetchRow($fetchmode = MDB2_FETCHMODE_DEFAULT, $rownum = null)
             if ($object_class == 'stdClass') {
                 $row = (object) $row;
             } else {
-                $row = &new $object_class($row);
+                $row = new $object_class($row);
             }
         }
         ++$this->rownum;
diff --git a/engine/include/database/Database.php b/engine/include/database/Database.php
index a6b154ce..768f6092 100644
--- a/engine/include/database/Database.php
+++ b/engine/include/database/Database.php
@@ -25,6 +25,13 @@ class Database{
 	 * @param log_output {String} -- where to print logs: fb (use fb function), print (use print),
 	 */
 	public function __construct($dsn, $log=false, $log_output="chrome_php", $encoding="utf8mb4"){
+        // mysql library driver is not supported in PHP 7.x at all
+        if(array_key_exists('phptype',$dsn) 
+           && ($dsn['phptype']=='mysql')
+           && version_compare(phpversion(),'7.0.0','>=')
+          ) {
+            throw new DatabaseException("Driver 'mysql' is not supported in PHP7, check your configuration 'phptype' setting, try using 'mysqli'."); 
+        }
 		$this->mdb2 = new MDB2DatabaseEngine($dsn);
 		$this->set_encoding($encoding);
 		$this->log = $log;

From 25c04428fca7f222c9f8352ea5783141ff5c3f0e Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 13 Mar 2021 11:29:17 +0100
Subject: [PATCH 034/154] docker local config file upgraded

---
 docker/www/sample.config.local.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/www/sample.config.local.php b/docker/www/sample.config.local.php
index 91d09df6..6c72156a 100644
--- a/docker/www/sample.config.local.php
+++ b/docker/www/sample.config.local.php
@@ -3,7 +3,7 @@
 Config::Config()->put_path_www('/home/inforex/public_html');
 Config::Config()->put_path_secured_data('/home/inforex/secured_data');
 Config::Config()->put_dsn(array(
-    'phptype'  => 'mysql',
+    'phptype'  => 'mysqli',
     'username' => 'inforex', 'port' => '3306', 'password' => 'password',
     'hostspec' => 'db',
     'database' => 'inforex',

From 5e87c47782b695aabe5dc4424ce13e577ee167f5 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 13 Mar 2021 12:44:10 +0100
Subject: [PATCH 035/154] strict errors in PHP7 environment

---
 engine/external/Smarty-2.6.22/libs/Smarty.class.php | 2 +-
 engine/external/pear/Auth.php                       | 2 +-
 engine/external/pear/Auth/Container.php             | 2 +-
 engine/external/pear/Auth/Container/MDB2.php        | 2 +-
 engine/external/pear/MDB2/Driver/mysqli.php         | 2 +-
 engine/include/CInforexWeb.php                      | 2 +-
 engine/include/CPage.php                            | 2 +-
 engine/settings.php                                 | 3 ++-
 8 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/engine/external/Smarty-2.6.22/libs/Smarty.class.php b/engine/external/Smarty-2.6.22/libs/Smarty.class.php
index 95ec67ba..9074a8d6 100644
--- a/engine/external/Smarty-2.6.22/libs/Smarty.class.php
+++ b/engine/external/Smarty-2.6.22/libs/Smarty.class.php
@@ -565,7 +565,7 @@ class Smarty
     /**
      * The class constructor.
      */
-    function Smarty()
+    function __construct()
     {
       $this->assign('SCRIPT_NAME', isset($_SERVER['SCRIPT_NAME']) ? $_SERVER['SCRIPT_NAME']
                     : @$GLOBALS['HTTP_SERVER_VARS']['SCRIPT_NAME']);
diff --git a/engine/external/pear/Auth.php b/engine/external/pear/Auth.php
index 52fe7ae3..4f2dd55c 100644
--- a/engine/external/pear/Auth.php
+++ b/engine/external/pear/Auth.php
@@ -330,7 +330,7 @@ class Auth {
      * @param boolean   Should the login form be displayed if necessary?
      * @return void
      */
-    function Auth($storageDriver, $options = '', $loginFunction = '', $showLogin = true)
+    function __construct($storageDriver, $options = '', $loginFunction = '', $showLogin = true)
     {
         $this->applyAuthOptions($options);
 
diff --git a/engine/external/pear/Auth/Container.php b/engine/external/pear/Auth/Container.php
index 5724d7d6..0024099f 100644
--- a/engine/external/pear/Auth/Container.php
+++ b/engine/external/pear/Auth/Container.php
@@ -63,7 +63,7 @@ class Auth_Container
      *
      * @access public
      */
-    function Auth_Container()
+    function __construct()
     {
     }
 
diff --git a/engine/external/pear/Auth/Container/MDB2.php b/engine/external/pear/Auth/Container/MDB2.php
index 0d8a35c7..97b320da 100644
--- a/engine/external/pear/Auth/Container/MDB2.php
+++ b/engine/external/pear/Auth/Container/MDB2.php
@@ -83,7 +83,7 @@ class Auth_Container_MDB2 extends Auth_Container
      * @param  string Connection data or MDB2 object
      * @return object Returns an error object if something went wrong
      */
-    function Auth_Container_MDB2($dsn)
+    function __construct($dsn)
     {
         $this->_setDefaults();
 
diff --git a/engine/external/pear/MDB2/Driver/mysqli.php b/engine/external/pear/MDB2/Driver/mysqli.php
index f49e8eb8..4e18f9c3 100644
--- a/engine/external/pear/MDB2/Driver/mysqli.php
+++ b/engine/external/pear/MDB2/Driver/mysqli.php
@@ -1151,7 +1151,7 @@ function prepare($query, $types = null, $result_types = null, $lobs = array())
 
         if (!$is_manip) {
             static $prep_statement_counter = 1;
-            $statement_name = sprintf($this->options['statement_format'], $this->phptype, $prep_statement_counter++ . sha1(microtime() + mt_rand()));
+            $statement_name = sprintf($this->options['statement_format'], $this->phptype, $prep_statement_counter++ . sha1(microtime() . strval(mt_rand())));
             $statement_name = substr(strtolower($statement_name), 0, $this->options['max_identifiers_length']);
             $query = "PREPARE $statement_name FROM ".$this->quote($query, 'text');
 
diff --git a/engine/include/CInforexWeb.php b/engine/include/CInforexWeb.php
index b3bf7bfd..f0e78aae 100644
--- a/engine/include/CInforexWeb.php
+++ b/engine/include/CInforexWeb.php
@@ -196,7 +196,7 @@ function doPage($page, &$variables)
                 $variables['exceptions'][] = $ex;
             }
             $o->set('page_generation_time', (time() - $stamp_start));
-            $o->set('compact_mode', $_COOKIE['compact_mode']);
+            $o->set('compact_mode', isset($_COOKIE['compact_mode']) ? $_COOKIE['compact_mode'] : "");
             $o->set('warnings', $o->getWarnings());
             $o->set('exceptions', $variables['exceptions']);
 			$o->set('Config',array(
diff --git a/engine/include/CPage.php b/engine/include/CPage.php
index 9afb6e72..7fa227af 100644
--- a/engine/include/CPage.php
+++ b/engine/include/CPage.php
@@ -73,7 +73,7 @@ class CPage extends CRequest{
 	 */
 	var $include_files = array();
 	
-	function CPage($name=null,$description=null){
+	function __construct($name=null,$description=null){
 		$this->name = $name;
 		$this->description = $description;
 		$this->template = new Smarty();
diff --git a/engine/settings.php b/engine/settings.php
index 5ebf61f2..3e317e31 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -32,7 +32,8 @@ function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0)
 	} // ver < 7.0
 
 	// converts all errors to exceptions
-	throw new ErrorException($message, 0, $level, $file, $line);
+    $extended_message = "[".$level."] ".$message." in ".$file.":".$line;
+	throw new ErrorException($extended_message, 0, $level, $file, $line);
 
 }  // inforexCentralErrorHandler()
 

From 915e03f7d1e3a60052ae2ca565a6cfc42541ac9f Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 13 Mar 2021 13:31:17 +0100
Subject: [PATCH 036/154] reference of new operator is now disabled

---
 engine/include/utils/CDocumentConverter.php | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/engine/include/utils/CDocumentConverter.php b/engine/include/utils/CDocumentConverter.php
index 5c6608aa..74246f65 100644
--- a/engine/include/utils/CDocumentConverter.php
+++ b/engine/include/utils/CDocumentConverter.php
@@ -13,7 +13,7 @@ class DocumentConverter{
 	 */
 	static function wcclDocument2AnnotatedDocument($wccl){
 
-		$doc = &new AnnotatedDocument($wccl->name);
+		$doc = new AnnotatedDocument($wccl->name);
 		
 		$sentence_id = 1;
 		$sentencecs = array();
@@ -22,19 +22,19 @@ static function wcclDocument2AnnotatedDocument($wccl){
 		
 		foreach($wccl->chunks as $c){
 			
-			$chunk = &new AnnotatedDocumentChunk($c->id);
+			$chunk = new AnnotatedDocumentChunk($c->id);
 			$doc->addChunk($chunk);
 						
 			foreach($c->sentences as $s){
 
-				$sentene = &new AnnotatedDocumentSentence($s->id);
+				$sentene = new AnnotatedDocumentSentence($s->id);
 				$chunk->addSentence($sentene);	
 				
 				$token_id = 1;
 				$annotation_id = 1;
 								
 				foreach($s->tokens as &$t){
-					$token = &new AnnotatedDocumentToken($token_id++, $t->orth, $t->ns);
+					$token = new AnnotatedDocumentToken($token_id++, $t->orth, $t->ns);
 					$sentene->addToken($token);
 									
 					if (!is_array($t->lexemes) ){
@@ -44,7 +44,7 @@ static function wcclDocument2AnnotatedDocument($wccl){
 						
 					
 					foreach ($t->lexemes as $l){
-						$lexem = &new AnnotatedDocumentLexem($l->base, $l->ctag, $l->disamb); 
+						$lexem = new AnnotatedDocumentLexem($l->base, $l->ctag, $l->disamb); 
 						$token->addLexem($lexem);
 					}
 				}
@@ -58,7 +58,7 @@ static function wcclDocument2AnnotatedDocument($wccl){
 							$t = $s->tokens[$i];
 							if ($t->channels[$name] != $last_num && $first_index !== null){
 								// dodaj anotacje
-								$ad = &new AnnotatedDocumentAnnotation($annotation_id++, $sentene, $first_index, $i-1, $name, trim($text));
+								$ad = new AnnotatedDocumentAnnotation($annotation_id++, $sentene, $first_index, $i-1, $name, trim($text));
 								$sentene->addAnnotation($ad);
 								
 								$hash = sprintf("%s_%s_%s", $s->id, $name, $last_num);
@@ -80,7 +80,7 @@ static function wcclDocument2AnnotatedDocument($wccl){
 							}
 						}
 						if ($last_num != 0){
-							$ad = &new AnnotatedDocumentAnnotation($annotation_id++, $sentene, $first_index, $i-1, $name, trim($text));
+							$ad = new AnnotatedDocumentAnnotation($annotation_id++, $sentene, $first_index, $i-1, $name, trim($text));
 							$sentene->addAnnotation($ad);
 
 							$hash = sprintf("%s_%s_%s", $s->id, $name, $last_num);
@@ -116,4 +116,4 @@ static function wcclDocument2AnnotatedDocument($wccl){
 	
 }
 
-?>
\ No newline at end of file
+?>

From b96df7ef4963d5ec80e4c275b210fa036ff05567 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Tue, 16 Mar 2021 21:39:08 +0100
Subject: [PATCH 037/154] next corrections for work in php7 environment

---
 .../libs/Smarty_Compiler.class.php            |  4 +--
 .../database/CDbAnnotationSharedAttribute.php | 26 +++++++++----------
 ...istration_annotation_shared_attributes.php |  2 +-
 engine/page/page_ccl_viewer.php               |  4 +--
 ...istration_annotation_shared_attributes.tpl |  4 ++-
 engine/templates/page_ccl_viewer.tpl          |  4 +--
 6 files changed, 23 insertions(+), 21 deletions(-)

diff --git a/engine/external/Smarty-2.6.22/libs/Smarty_Compiler.class.php b/engine/external/Smarty-2.6.22/libs/Smarty_Compiler.class.php
index c4ac6cbe..e20ef9ef 100644
--- a/engine/external/Smarty-2.6.22/libs/Smarty_Compiler.class.php
+++ b/engine/external/Smarty-2.6.22/libs/Smarty_Compiler.class.php
@@ -81,7 +81,7 @@ class Smarty_Compiler extends Smarty {
     /**
      * The class constructor.
      */
-    function Smarty_Compiler()
+    function __construct()
     {
         $this->_phpversion = substr(phpversion(),0,1);
 
@@ -564,7 +564,7 @@ function _compile_tag($template_tag)
 
             case 'php':
                 /* handle folded tags replaced by {php} */
-                list(, $block) = each($this->_folded_blocks);
+                $block = current($this->_folded_blocks);
                 $this->_current_line_no += substr_count($block[0], "\n");
                 /* the number of matched elements in the regexp in _compile_file()
                    determins the type of folded tag that was found */
diff --git a/engine/include/database/CDbAnnotationSharedAttribute.php b/engine/include/database/CDbAnnotationSharedAttribute.php
index f317d6e2..c2a9d597 100644
--- a/engine/include/database/CDbAnnotationSharedAttribute.php
+++ b/engine/include/database/CDbAnnotationSharedAttribute.php
@@ -8,43 +8,43 @@
 
 class CDbAnnotationSharedAttribute{
 
-    function getAll(){
+    static function getAll(){
         global $db;
         $sql = "SELECT * FROM shared_attributes ORDER BY description";
         return $db->fetch_rows($sql);
     }
 
-    function get($sharedAttributeId){
+    static function get($sharedAttributeId){
         global $db;
         $sql = "SELECT * FROM shared_attributes WHERE id = ?";
         return $db->fetch($sql, array($sharedAttributeId));
     }
 
-    function existsAttributeEnumValue($sharedAttributeId, $value){
+    static function existsAttributeEnumValue($sharedAttributeId, $value){
         global $db;
         $sql = "SELECT * FROM shared_attributes_enum WHERE shared_attribute_id = ? AND `value` = ?";
         return count($db->fetch_rows($sql, array($sharedAttributeId, $value)))>0;
     }
 
-    function addAttributeEnumValue($sharedAttributeId, $value){
+    static function addAttributeEnumValue($sharedAttributeId, $value){
         global $db;
         $sql = "INSERT IGNORE INTO shared_attributes_enum (shared_attribute_id, `value`) VALUES(?, ?)";
         $db->execute($sql, array($sharedAttributeId, $value));
     }
 
-    function addAttributeEnumValueWithDescription($sharedAttributeId, $value, $description){
+    static function addAttributeEnumValueWithDescription($sharedAttributeId, $value, $description){
         global $db;
         $sql = "INSERT INTO shared_attributes_enum (shared_attribute_id, `value`, description) VALUES(?, ?, ?)";
         $db->execute($sql, array($sharedAttributeId, $value, $description));
     }
 
-    function deleteAttributeValue($attributeId, $value){
+    static function deleteAttributeValue($attributeId, $value){
         global $db;
         $sql = "DELETE FROM shared_attributes_enum WHERE shared_attribute_id=? AND value=?";
         $db->execute($sql, array($attributeId, $value));
     }
 
-    function getAnnotationSharedAttributes($annotationId){
+    static function getAnnotationSharedAttributes($annotationId){
         global $db;
         $sql = "SELECT atsa.*, sa.*, rasa.value
             FROM reports_annotations_optimized an
@@ -55,7 +55,7 @@ function getAnnotationSharedAttributes($annotationId){
         return $db->fetch_rows($sql, array($annotationId));
     }
 
-    function getAttributeAnnotationValues($corpusId, $attributeId=null, $lang=null, $subcorpusId=null){
+    static function getAttributeAnnotationValues($corpusId, $attributeId=null, $lang=null, $subcorpusId=null){
         global $db;
         $builder = new SqlBuilder("reports_annotations_shared_attributes", "rasa");
         $builder->addSelectColumn(new SqlBuilderSelect("rasa.value", "value"));
@@ -82,7 +82,7 @@ function getAttributeAnnotationValues($corpusId, $attributeId=null, $lang=null,
         return $db->fetch_rows($sql, $params);
     }
 
-    function getAnnotationsWithAttributeValue(
+    static function getAnnotationsWithAttributeValue(
             $corpusId, $attributeId=null, $attributeValue=null, $lang=null, $subcorpusId=null){
         global $db;
         $builder = new SqlBuilder("reports_annotations_shared_attributes", "rasa");
@@ -119,21 +119,21 @@ function getAnnotationsWithAttributeValue(
         return $db->fetch_rows($sql, $params);
     }
 
-    function updateAttributeDescription($attributeId, $value, $description){
+    static function updateAttributeDescription($attributeId, $value, $description){
         global $db;
         $sql = "UPDATE shared_attributes_enum SET description = ? WHERE shared_attribute_id = ? AND value = ?";
         $db->execute($sql, array($description, $attributeId, $value));
     }
 
-    function updateAttributeValue($attributeId, $valueOld, $valueNew){
+    static function updateAttributeValue($attributeId, $valueOld, $valueNew){
         global $db;
         $sql = "UPDATE shared_attributes_enum SET value = ? WHERE shared_attribute_id = ? AND value = ?";
         $db->execute($sql, array($valueNew, $attributeId, $valueOld));
     }
 
-    function updateAnnotationAttributeValues($attributeId, $valueOld, $valueNew){
+    static function updateAnnotationAttributeValues($attributeId, $valueOld, $valueNew){
         global $db;
         $sql = "UPDATE reports_annotations_shared_attributes SET value = ? WHERE shared_attribute_id = ? AND value = ?";
         $db->execute($sql, array($valueNew, $attributeId, $valueOld));
     }
-}
\ No newline at end of file
+}
diff --git a/engine/page/page_administration_annotation_shared_attributes.php b/engine/page/page_administration_annotation_shared_attributes.php
index f4411788..8422a1dc 100644
--- a/engine/page/page_administration_annotation_shared_attributes.php
+++ b/engine/page/page_administration_annotation_shared_attributes.php
@@ -11,4 +11,4 @@ class Page_administration_annotation_shared_attributes extends CPageAdministrati
 	function execute(){
 		$this->set("sharedAttributes", CDbAnnotationSharedAttribute::getAll());
 	}
-}
\ No newline at end of file
+}
diff --git a/engine/page/page_ccl_viewer.php b/engine/page/page_ccl_viewer.php
index 66bb2b04..b42abdb2 100644
--- a/engine/page/page_ccl_viewer.php
+++ b/engine/page/page_ccl_viewer.php
@@ -253,14 +253,14 @@ function set_navigation_elements($elements, $htmlStr, &$chunksToInset, &$show_re
 	
 
 	function set_panels(){
-		$this->set('showRight', $_COOKIE['showRight']=="true"?true:false);
+		$this->set('showRight', array_key_exists('showRight',$_COOKIE) and ($_COOKIE['showRight']=="true")?true:false);
 	}
 	
 	
 	function set_relation_sets(){
 		$sql = 	"SELECT * FROM relation_sets ";
 		$relation_sets = $this->getDb()->fetch_rows($sql);
-		$types = explode(",",preg_replace("/\:1|id|\{|\}|\"|\\\/","",$_COOKIE['active_annotation_types']));
+		$types = explode(",",preg_replace("/\:1|id|\{|\}|\"|\\\/","",array_key_exists('active_annotation_types',$_COOKIE)?$_COOKIE['active_annotation_types']:""));
 		foreach($relation_sets as $key => $rel_set)
 			$relation_sets[$key]['active'] = ($_COOKIE['active_annotation_types'] ? (in_array($rel_set['relation_set_id'],$types) ? 1 : 0) : 1 );
 		$this->set('relation_sets', $relation_sets);
diff --git a/engine/templates/page_administration_annotation_shared_attributes.tpl b/engine/templates/page_administration_annotation_shared_attributes.tpl
index ade7b528..e520ea94 100644
--- a/engine/templates/page_administration_annotation_shared_attributes.tpl
+++ b/engine/templates/page_administration_annotation_shared_attributes.tpl
@@ -25,6 +25,7 @@
                         </tr>
                         </thead>
                         <tbody>
+			{if isset($sharedAttributes)}
                         {foreach from=$sharedAttributes item=shared_attribute}
                             <tr>
                                 <td class="num">{$shared_attribute.id}</td>
@@ -33,6 +34,7 @@
                                 <td>{$shared_attribute.description}</td>
                             </tr>
                         {/foreach}
+			{/if}
                         </tbody>
                     </table>
                 </div>
@@ -209,4 +211,4 @@
     </div>
 </div>
 
-{include file="inc_footer.tpl"}
\ No newline at end of file
+{include file="inc_footer.tpl"}
diff --git a/engine/templates/page_ccl_viewer.tpl b/engine/templates/page_ccl_viewer.tpl
index 6150a543..ffca0bad 100644
--- a/engine/templates/page_ccl_viewer.tpl
+++ b/engine/templates/page_ccl_viewer.tpl
@@ -15,7 +15,7 @@
 			<div class="panel-body">
 				<div class="column" id="widget_text">
 					<div id="leftContent" style="float:left; width: {if $showRight}50%; border-right: 1px solid #E0CFC2;{else}100%;{/if}" class="annotations scrolling content">
-						  <div style="margin: 5px" class="contentBox">{$content_inline|format_annotations}</div>
+						  <div style="margin: 5px" class="contentBox">{if isset($content_inline)}{$content_inline|format_annotations}{/if}</div>
 					</div>
 					<div id="rightContent" style="{if !$showRight}display: none{/if};" class="annotations scrolling content rightPanel">
 						  <div style="margin: 5px" class="contentBox">{$content_inline2|format_annotations}</div>
@@ -37,4 +37,4 @@
 
 </div>
 
-{include file="inc_footer.tpl"}
\ No newline at end of file
+{include file="inc_footer.tpl"}

From 48ed9db4f051ae072e7a971cddd48adc8654bd15 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Sat, 20 Mar 2021 10:25:59 +0100
Subject: [PATCH 038/154] all errors are catchable by handlers

---
 engine/settings.php | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/engine/settings.php b/engine/settings.php
index 3e317e31..16db97ac 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -39,4 +39,40 @@ function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0)
 
 set_error_handler("inforexCentralErrorHandler");
 
+function inforexInitialExceptionHandler ($e) {
+
+    // common handler for all exceptiom before CInforexWebPage was 
+    // constructed.
+
+    // reports to http server logs anyway
+    error_log($e);
+    http_response_code(500);
+    // if set display_errors write information on screen
+    if (ini_get(’display_errors’)) {
+        echo $e;
+    } else {
+        // dummy message for user
+        echo "<h1>500 Internal Server Error</h1>
+        An internal server error has been occurred.<br>
+        Please try again later.";
+    }
+
+} // inforexInitialExceptionHandler()
+
+set_exception_handler("inforexInitialExceptionHandler");
+
+function inforexShutdownFunction() {
+
+    $error = error_get_last();
+    if ($error !== null) {
+        $e = new ErrorException(
+            $error[’message’], 0, $error[’type’], $error[’file’], $error[’line’]
+        );
+        nforexInitialExceptionHandler($e);
+    }
+
+} // inforexShutdownFunction()  
+
+register_shutdown_function("inforexShutdownFunction");
+
 ?>

From 410a27d9d9f8fe9ad67a6de00989dc03afab73c4 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Sat, 20 Mar 2021 13:42:07 +0100
Subject: [PATCH 039/154] tunning of redirection in error handlers

---
 engine/settings.php | 57 ++++++++++++++++++++++++++++++---------------
 1 file changed, 38 insertions(+), 19 deletions(-)

diff --git a/engine/settings.php b/engine/settings.php
index 16db97ac..0ab75220 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -16,22 +16,28 @@
 ini_set("short_open_tag",1);
 setlocale(LC_CTYPE, "en_US.UTF-8");		
 
-// We need all messages for developer usage
-error_reporting(E_ALL);
-// our handler isn't depends from above setting
-
 function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0) {
 
-	//print("[".$level."] ".$message." in ".$file.":".$line."<br/>\n");
-	
+    //print("inforexCentralErrorHandler \n");
+    // mask errors on error_reporting() settings
+    // here we have them all
+    $systemErrorReporting = error_reporting();
+    if( ($systemErrorReporting & $level) == 0 ) {
+        // this error level is masked by system settings
+        error_clear_last();
+        return;
+    }   
+
 	// silently drop ugly strict double constructor report in PHP < 7
 	if(version_compare(phpversion(),'7.0.0','<')) {
 		if(preg_match("/^Redefining already defined constructor for class Config/",$message)) {
+            error_clear_last();
 			return;
 		}
 	} // ver < 7.0
 
-	// converts all errors to exceptions
+	// converts all not masked errors to exceptions
+    //  there are no return from exception to code continue...
     $extended_message = "[".$level."] ".$message." in ".$file.":".$line;
 	throw new ErrorException($extended_message, 0, $level, $file, $line);
 
@@ -43,19 +49,28 @@ function inforexInitialExceptionHandler ($e) {
 
     // common handler for all exceptiom before CInforexWebPage was 
     // constructed.
+    //print("inforexInitialExceptionHandler \n");
 
+    // Uncaught exception reporting main code
     // reports to http server logs anyway
     error_log($e);
-    http_response_code(500);
-    // if set display_errors write information on screen
-    if (ini_get(’display_errors’)) {
-        echo $e;
-    } else {
-        // dummy message for user
-        echo "<h1>500 Internal Server Error</h1>
-        An internal server error has been occurred.<br>
-        Please try again later.";
-    }
+    // on CLI console all was done, do nothing more
+    if (php_sapi_name() !== "cli") {
+        // there actions for browser environment
+        http_response_code(500);
+        // if set display_errors write information on screen
+        if (ini_get("display_errors")) {
+            echo $e;
+        } else {
+            // dummy message for user
+            echo "<h1>500 Internal Server Error</h1>
+            An internal server error has been occurred.<br>
+            Please try again later.";
+        } // display_errors
+    } // ! CLI
+
+    // serviced errors shouldn't be processed again
+    error_clear_last();
 
 } // inforexInitialExceptionHandler()
 
@@ -63,12 +78,16 @@ function inforexInitialExceptionHandler ($e) {
 
 function inforexShutdownFunction() {
 
+    //print("inforexShutdownFunction \n");
+    // returns null or array( "type"=>, "message"=>, "file"=>, "line"=> )
+    // if earlier inforexInitialExceptionHandler was called, there not
+    // will be reported twice 
     $error = error_get_last();
     if ($error !== null) {
         $e = new ErrorException(
-            $error[’message’], 0, $error[’type’], $error[’file’], $error[’line’]
+            $error["message"], 0, $error["type"], $error["file"], $error["line"]
         );
-        nforexInitialExceptionHandler($e);
+        inforexInitialExceptionHandler($e);
     }
 
 } // inforexShutdownFunction()  

From 9dea7c536a235a04fddd48555eb27de096bf7614 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Sat, 20 Mar 2021 19:51:56 +0100
Subject: [PATCH 040/154] all w/o last_errors() on PHP5

---
 engine/include/CPage.php                | 12 ++++++++++--
 engine/include/functions/func_roles.php | 12 +++++++++++-
 engine/templates/inc_menu2.tpl          | 10 +++++-----
 3 files changed, 26 insertions(+), 8 deletions(-)

diff --git a/engine/include/CPage.php b/engine/include/CPage.php
index 7fa227af..646ed01d 100644
--- a/engine/include/CPage.php
+++ b/engine/include/CPage.php
@@ -149,7 +149,11 @@ function hasAccess($user=null, $corpus=null){
                 if (hasUserCorpusRole($user, $corpus, $this->anyCorpusRole)) {
                     return true;
                 } else {
-                    $userCorpusRoles = is_array($corpus['role'][$user['user_id']]) ? array_keys($corpus['role'][$user['user_id']]) : array(ROLE_SYSTEM_USER_PUBLIC);
+			if(isset($corpus['role'][$user['user_id']])) {
+                    		$userCorpusRoles = is_array($corpus['role'][$user['user_id']]) ? array_keys($corpus['role'][$user['user_id']]) : array(ROLE_SYSTEM_USER_PUBLIC);
+			} else {
+				$userCorpusRoles = array(ROLE_SYSTEM_USER_PUBLIC);
+			}
                     $rolesRequired = array_merge($rolesRequired, $this->anyCorpusRole);
                     $rolesUser = array_merge($rolesUser, $userCorpusRoles);
                 }
@@ -158,7 +162,11 @@ function hasAccess($user=null, $corpus=null){
                 if ( hasUserSystemRole($user, $this->anySystemRole) ){
                     return true;
                 } else {
-                    $userSystemRoles = is_array($user['role']) ? array_keys($user['role']) : array(ROLE_SYSTEM_USER_PUBLIC=>"");
+			if(isset($user['role'])) {
+                    		$userSystemRoles = is_array($user['role']) ? array_keys($user['role']) : array(ROLE_SYSTEM_USER_PUBLIC=>"");
+			} else {
+				$userSystemRoles = array(ROLE_SYSTEM_USER_PUBLIC=>"");
+			}
                     $rolesRequired = array_merge($rolesRequired, $this->anySystemRole);
                     $rolesUser = array_merge($rolesUser, $userSystemRoles);
 				}
diff --git a/engine/include/functions/func_roles.php b/engine/include/functions/func_roles.php
index e30369ba..9a4adee6 100644
--- a/engine/include/functions/func_roles.php
+++ b/engine/include/functions/func_roles.php
@@ -11,7 +11,11 @@ function hasUserSystemRole($user, $anyRole){
     if (in_array(ROLE_SYSTEM_USER_PUBLIC, $anyRole)){
         return true;
     } else {
-        $userRoles = array_keys(is_array($user['role']) ? $user['role'] : array(ROLE_SYSTEM_USER_PUBLIC=>""));
+	if(isset($user['role'])) {
+        	$userRoles = array_keys(is_array($user['role']) ? $user['role'] : array(ROLE_SYSTEM_USER_PUBLIC=>""));
+	} else {
+		$userRoles = array(ROLE_SYSTEM_USER_PUBLIC=>"");
+	}
         return count(array_intersect($userRoles, $anyRole)) > 0;
     }
 }
@@ -56,6 +60,12 @@ function hasCorpusRole($role){
  */
 function isCorpusOwner(){
 	global $corpus, $user;
+	if( !isset($user['user_id']) ) {
+		return False;
+	}
+        if( !isset($corpus['user_id']) ) {
+                return False;  // maybe True ?
+        }
 	return $user['user_id'] == $corpus['user_id'];
 }
 
diff --git a/engine/templates/inc_menu2.tpl b/engine/templates/inc_menu2.tpl
index 88b9395a..36c02c58 100644
--- a/engine/templates/inc_menu2.tpl
+++ b/engine/templates/inc_menu2.tpl
@@ -18,7 +18,7 @@
                 {if isset($corpus.id)}
 					<li class="active dropdown navbar-sub corpus_select_nav">
 						<a class="dropdown-toggle" data-toggle="dropdown" href="index.php?page=start&amp;corpus={$corpus.id}">
-							<span class="glyphicon glyphicon-menu-hamburger" aria-hidden="true" title="Show a list of corpora"></span> <b>{$corpus.name}</b>
+							<span class="glyphicon glyphicon-menu-hamburger" aria-hidden="true" title="Show a list of corpora"></span> <b>{if isset($corpus.name)}{$corpus.name}{/if}</b>
 							<!--<span class="caret"></span>--></a>
 						<ul class="dropdown-menu">
 
@@ -40,7 +40,7 @@
                                     <a tabindex="-1" href="#"><span class="glyphicon glyphicon-globe" aria-hidden="true"></span> Public corpora</a>
                                     <ul class="dropdown-menu corpus_dropdown_menu">
                                         {foreach from=$corpus.public_corpora item=element}
-                                            <li><a href="index.php?page={if $row.title}browse{else}{$page}{/if}&amp;corpus={$element.corpus_id}">{$element.name} <strong>({$element.screename})</strong></a></li>
+                                            <li><a href="index.php?page={if $row.title}browse{else}{$page}{/if}&amp;corpus={$element.corpus_id}">{$element.name} <strong>({if isset($element.screename)}{$element.screename}{/if})</strong></a></li>
                                         {/foreach}
                                     </ul>
                                 </li>
@@ -51,7 +51,7 @@
                                     <a tabindex="-1" href="#"><span class="glyphicon glyphicon-lock" aria-hidden="true"></span> Private corpora</a>
                                     <ul class="dropdown-menu corpus_dropdown_menu">
                                         {foreach from=$corpus.private_corpora item=element}
-                                            <li><a href="index.php?page={if $row.title}browse{else}{$page}{/if}&amp;corpus={$element.corpus_id}">{$element.name} <strong>({$element.screename})</strong></a></li>
+                                            <li><a href="index.php?page={if $row.title}browse{else}{$page}{/if}&amp;corpus={$element.corpus_id}">{$element.name} <strong>({if isset($element.screename)}{$element.screename}{/if})</strong></a></li>
                                         {/foreach}
                                     </ul>
                                 </li>
@@ -68,7 +68,7 @@
 						</ul>
 					</li>
                 {/if}
-                {if isset($corpus.id) && ( "read"|has_corpus_role_or_owner || "admin"|has_role || $corpus.public ) }
+                {if isset($corpus.id) && ( "read"|has_corpus_role_or_owner || "admin"|has_role || !empty($corpus.public) ) }
 
                     <li class="navbar-sub dropdown nav_corpus_pages" style="background: #eee">
 						<a class="dropdown-toggle" data-toggle="dropdown" href="#">
@@ -185,7 +185,7 @@
 			</ul>
 			<ul class="nav navbar-nav navbar-right" style="margin-right:50px;">
 				{if $user}
-				<li><a href="index.php?page=user_roles"><b>{$user.login} {if $user.screename}[{$user.screename}]{/if}</b></a></li>
+				<li><a href="index.php?page=user_roles"><b>{if isset($user.login)}{$user.login}{/if} {if isset($element.screename)}{$element.screename}{/if}</b></a></li>
 				{/if}
 				<li>
 					{*if not using federation login show usual login buttons*}

From d641ac75837656d22a469eead7b2b48fe00eecab Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Mon, 22 Mar 2021 06:21:29 +0100
Subject: [PATCH 041/154] advanced to PHP 7.4 docker image

---
 docker/www/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/www/Dockerfile b/docker/www/Dockerfile
index 90ebdcd3..cb11d041 100644
--- a/docker/www/Dockerfile
+++ b/docker/www/Dockerfile
@@ -1,4 +1,4 @@
-FROM php:7.3-apache as php-base
+FROM php:7.4-apache as php-base
 
 RUN apt-get update -y && apt-get upgrade -y
 RUN apt-get install software-properties-common wget -y

From 9e4250cd3e77e2befaa7a234b162c9783dc8133f Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Tue, 30 Mar 2021 20:15:54 +0200
Subject: [PATCH 042/154] specialized exceptions

---
 engine/Config/Config.php                                   | 6 +++---
 .../ajax_report_delete_annotation_relation_anaphora.php    | 2 +-
 engine/ajax/ajax_report_update_annotation.php              | 6 +++---
 engine/include/CRequest.php                                | 2 +-
 engine/include/exceptions/ajax/GeneralAjaxException.php    | 7 +++++++
 engine/include/exceptions/config/ConfigException.php       | 7 +++++++
 engine/include/exceptions/include/CRequestException.php    | 7 +++++++
 7 files changed, 29 insertions(+), 8 deletions(-)
 create mode 100644 engine/include/exceptions/ajax/GeneralAjaxException.php
 create mode 100644 engine/include/exceptions/config/ConfigException.php
 create mode 100644 engine/include/exceptions/include/CRequestException.php

diff --git a/engine/Config/Config.php b/engine/Config/Config.php
index 902f1f04..1970a3d9 100644
--- a/engine/Config/Config.php
+++ b/engine/Config/Config.php
@@ -10,7 +10,7 @@ class Phantom {
 
     public function __call($name, $arguments)
     {
-        throw new Exception("Method {$name} is not supported.");
+        throw new ConfigException("Method {$name} is not supported.");
     }
 
 } // Phamtom class
@@ -135,7 +135,7 @@ function __call($method,$arguments){
 					// last case - null is not catch by isset()
 					return null;
 			} else {
-				throw new Exception("Parameter '$parameter_name' not defined in the configuration file.");
+				throw new ConfigException("Parameter '$parameter_name' not defined in the configuration file.");
 			}
 		} else if ( substr($method, 0, 4) == "put_" ){
             // implementation of put_<sth>($value) method
@@ -175,7 +175,7 @@ public function loadConfigFromFile($pathname) {
                 try {
                     include($pathname);
                 } catch( Exception $e ) {
-                    throw new Exception("Error loading configuration file '$pathname'.");
+                    throw new ConfigException("Error loading configuration file '$pathname'.");
                 } // try..catch() new syntax
             }  // try...catch() old syntax
         } // if file_exists()
diff --git a/engine/ajax/ajax_report_delete_annotation_relation_anaphora.php b/engine/ajax/ajax_report_delete_annotation_relation_anaphora.php
index 554e0e0d..fdd57a65 100644
--- a/engine/ajax/ajax_report_delete_annotation_relation_anaphora.php
+++ b/engine/ajax/ajax_report_delete_annotation_relation_anaphora.php
@@ -17,7 +17,7 @@ function execute(){
 		global $user;
 
 		if (!intval($user['user_id'])){
-			throw new Exception("Brak identyfikatora użytkownika");
+			throw new GeneralAjaxException("Brak identyfikatora użytkownika");
 		}
 
 		$relation_id = intval($_POST['relation_id']);
diff --git a/engine/ajax/ajax_report_update_annotation.php b/engine/ajax/ajax_report_update_annotation.php
index 9c9fa113..65cb15a4 100644
--- a/engine/ajax/ajax_report_update_annotation.php
+++ b/engine/ajax/ajax_report_update_annotation.php
@@ -44,7 +44,7 @@ function execute(){
 			    DbAnnotation::removeUnusedAnnotationSharedAttributes($annotation_id);
             }
 		} else {
-			throw new Exception("An error occurred while saving the annotation");
+			throw new GeneralAjaxException("An error occurred while saving the annotation");
 			return;			
 		}
 
@@ -62,7 +62,7 @@ function execute(){
      * @param $from
      * @param $to
      * @param $type_id
-     * @throws Exception
+     * @throws GeneralAjaxException
      */
 	function validateText($row, $text, $from, $to, $type_id){
         $content = $row['content'];
@@ -81,7 +81,7 @@ function validateText($row, $text, $from, $to, $type_id){
                 "Position: [<b>$from,$to</b>]<br/>" .
                 "Sent phrase: <b>'$text'</b><br/>" .
                 "Database phrase: <b>'$html_revalidate'</b>";
-            throw new Exception($error);
+            throw new GeneralAjaxException($error);
         }
     }
 
diff --git a/engine/include/CRequest.php b/engine/include/CRequest.php
index de92d645..c16b145e 100644
--- a/engine/include/CRequest.php
+++ b/engine/include/CRequest.php
@@ -22,7 +22,7 @@ function getRequestParameterRequired($name){
         if ( isset($_REQUEST[$name]) ) {
             return  $_REQUEST[$name];
         } else {
-            throw new Exception("Missing parameter in the request: $name");
+            throw new CRequestException("Missing parameter in the request: $name");
         }
     }
 
diff --git a/engine/include/exceptions/ajax/GeneralAjaxException.php b/engine/include/exceptions/ajax/GeneralAjaxException.php
new file mode 100644
index 00000000..19b9bd1d
--- /dev/null
+++ b/engine/include/exceptions/ajax/GeneralAjaxException.php
@@ -0,0 +1,7 @@
+<?php
+
+class GeneralAjaxException extends Exception {
+
+}
+
+?>
diff --git a/engine/include/exceptions/config/ConfigException.php b/engine/include/exceptions/config/ConfigException.php
new file mode 100644
index 00000000..16ea0614
--- /dev/null
+++ b/engine/include/exceptions/config/ConfigException.php
@@ -0,0 +1,7 @@
+<?php
+
+class ConfigException extends Exception {
+
+}
+
+?>
diff --git a/engine/include/exceptions/include/CRequestException.php b/engine/include/exceptions/include/CRequestException.php
new file mode 100644
index 00000000..970cc38d
--- /dev/null
+++ b/engine/include/exceptions/include/CRequestException.php
@@ -0,0 +1,7 @@
+<?php
+
+class CRequestException extends Exception {
+
+}
+
+?>

From cc637b3d9d82b94d9adce105cee68dd5b9e25d6e Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Tue, 30 Mar 2021 22:49:44 +0200
Subject: [PATCH 043/154] excluding from test suite

---
 engine/external/pear/HTML/Select.php |  2 +-
 engine/settings.php                  | 42 +++++++++++++++++++++++++---
 2 files changed, 39 insertions(+), 5 deletions(-)

diff --git a/engine/external/pear/HTML/Select.php b/engine/external/pear/HTML/Select.php
index 47f4bd88..7cfde676 100644
--- a/engine/external/pear/HTML/Select.php
+++ b/engine/external/pear/HTML/Select.php
@@ -103,7 +103,7 @@ function apiVersion()
     function setSelectedValues($values)
     {
         if (is_string($values)) {
-            $values = split("[ ]?,[ ]?", $values);
+            $values = explode("[ ]?,[ ]?", $values);
         }
         if (!is_array($values)) {
             $values = array($values);
diff --git a/engine/settings.php b/engine/settings.php
index 0ab75220..294ea986 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -16,6 +16,24 @@
 ini_set("short_open_tag",1);
 setlocale(LC_CTYPE, "en_US.UTF-8");		
 
+function errorClearLast() {
+
+       if(version_compare(phpversion(),'7.0.0','<')) {
+               // for PHP5 there is no error_clear_last()
+               // hint: dummy handler ignore all errors from level 0
+               set_error_handler('var_dump', 0);
+               // call dummy handler for error undef var
+               // resets internal register
+               // @ for not console reporting
+               @$undef_var;
+               // restore previous handler
+               restore_error_handler();
+       } else {
+               error_clear_last();
+       }
+
+} // errorClearLast()
+
 function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0) {
 
     //print("inforexCentralErrorHandler \n");
@@ -24,14 +42,14 @@ function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0)
     $systemErrorReporting = error_reporting();
     if( ($systemErrorReporting & $level) == 0 ) {
         // this error level is masked by system settings
-        error_clear_last();
+	errorClearLast();
         return;
     }   
 
 	// silently drop ugly strict double constructor report in PHP < 7
 	if(version_compare(phpversion(),'7.0.0','<')) {
 		if(preg_match("/^Redefining already defined constructor for class Config/",$message)) {
-            error_clear_last();
+			errorClearLast();
 			return;
 		}
 	} // ver < 7.0
@@ -70,7 +88,7 @@ function inforexInitialExceptionHandler ($e) {
     } // ! CLI
 
     // serviced errors shouldn't be processed again
-    error_clear_last();
+    errorClearLast();
 
 } // inforexInitialExceptionHandler()
 
@@ -92,6 +110,22 @@ function inforexShutdownFunction() {
 
 } // inforexShutdownFunction()  
 
-register_shutdown_function("inforexShutdownFunction");
+function isPHPUnitRunning() {
+
+	// detect if code running under PHPUnit control
+	//  two constatnts are defined by this system
+	if (! defined('PHPUNIT_COMPOSER_INSTALL') && ! defined('__PHPUNIT_PHAR__')) {
+    		// is not PHPUnit run
+    		return False;
+	} else {
+		return True;
+	}
+
+} // isPHPUnitRunning()
+
+if(! isPHPUnitRunning()) {
+	// under PHPUnit this one not works
+	register_shutdown_function("inforexShutdownFunction");
+}
 
 ?>

From bcc9ff2641553b3d4f50200a9f69df3e00341e26 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <seweryn@walor.torun.pl>
Date: Wed, 31 Mar 2021 18:36:47 +0200
Subject: [PATCH 044/154] handler backported to PHP5

---
 engine/settings.php | 33 ++++++++++++++++++++++++++++-----
 1 file changed, 28 insertions(+), 5 deletions(-)

diff --git a/engine/settings.php b/engine/settings.php
index 294ea986..e6bb8cd8 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -20,13 +20,15 @@ function errorClearLast() {
 
        if(version_compare(phpversion(),'7.0.0','<')) {
                // for PHP5 there is no error_clear_last()
-               // hint: dummy handler ignore all errors from level 0
+               // hint: dummy handler convert all errors from level 0
+               //  to well recognizable specific error
+               //  below former handler is pushed to internal stack
                set_error_handler('var_dump', 0);
                // call dummy handler for error undef var
-               // resets internal register
+               // sets internal register to specific error
                // @ for not console reporting
-               @$undef_var;
-               // restore previous handler
+               @$undef_var_with_ambigous_characteristic_name;
+               // restore ( pop ) previous handler from internal stack
                restore_error_handler();
        } else {
                error_clear_last();
@@ -34,6 +36,27 @@ function errorClearLast() {
 
 } // errorClearLast()
 
+function errorGetLast() {
+
+        $result = error_get_last();
+        if(version_compare(phpversion(),'7.0.0','<')) {
+                // detect:
+                // ["message"]=="Undefined variable: undef_var_with_ambigous_characteristic_name"
+		if(is_array($result)
+                   && ( isset($result["message"])
+                        && preg_match('/undef_var_with_ambigous_characteristic_name/',$result["message"])                                                                             )
+                  ) {
+                        // error was reseted by errorClearLast()
+                        return null;
+                } else {
+                        return $result;
+                }
+        } else {
+                return $result;
+        }
+
+}  // errorGetLast()
+ 
 function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0) {
 
     //print("inforexCentralErrorHandler \n");
@@ -100,7 +123,7 @@ function inforexShutdownFunction() {
     // returns null or array( "type"=>, "message"=>, "file"=>, "line"=> )
     // if earlier inforexInitialExceptionHandler was called, there not
     // will be reported twice 
-    $error = error_get_last();
+    $error = errorGetLast();
     if ($error !== null) {
         $e = new ErrorException(
             $error["message"], 0, $error["type"], $error["file"], $error["line"]

From 85197a86736cb76dece690e5ce0c64f7924df588 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 12 Jun 2021 08:22:56 +0200
Subject: [PATCH 045/154] operator [] on empty string is an error now

---
 engine/include/database/Database.php | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/engine/include/database/Database.php b/engine/include/database/Database.php
index 768f6092..6879091b 100644
--- a/engine/include/database/Database.php
+++ b/engine/include/database/Database.php
@@ -224,7 +224,7 @@ function last_id(){
          *         DatabaseException thrown on error
 	 */
 	function update($table, $values, $keys){
-		$value = "";
+		$value = array();
 		if(is_array($values)){
 			foreach ($values as $k=>$v)
 				$value[] = "`$k`=?";
@@ -235,7 +235,7 @@ function update($table, $values, $keys){
 			// followed implode() fails....
 			throw new DatabaseException("2-nd argument of Database->update() must be non empty array.",$values);
 		}
-		$key = "";
+		$key = array();
 		if(is_array($keys)){
 			foreach ($keys as $k=>$v)
 				$key[] = "`$k`=?";

From 3897bdd514562a8a4a6d55d823c43cbb458379fc Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 12 Jun 2021 12:29:34 +0200
Subject: [PATCH 046/154] Unproper static call to unstatic method
 set_users_roles - ugly solution but works

---
 engine/page/corpus_perspectives/PerspectivePerspectives.php | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/engine/page/corpus_perspectives/PerspectivePerspectives.php b/engine/page/corpus_perspectives/PerspectivePerspectives.php
index bb52b812..484cafb3 100644
--- a/engine/page/corpus_perspectives/PerspectivePerspectives.php
+++ b/engine/page/corpus_perspectives/PerspectivePerspectives.php
@@ -12,7 +12,11 @@ function execute()
 	{
 		$this->set_corpus_perspectives();
 		$this->set_users_perspectives();
-		PerspectiveUsers_roles::set_users_roles();
+        // [SW] metoda set_users_roles() nie jest statyczna, używa własności 
+        // page konstrukcja poniżej kieruje ją do instancji strony istniejącej
+		// PerspectiveUsers_roles::set_users_roles();
+        $PerspectiveUsers_rolesInstanceForPage = new PerspectiveUsers_roles($this->page);
+        $PerspectiveUsers_rolesInstanceForPage->set_users_roles();
 	}
 	
 	function set_corpus_perspectives(){

From ecae8d87daa847730a0799166ba264baa68931de Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 12 Jun 2021 12:41:03 +0200
Subject: [PATCH 047/154] Unproper static call to unstatic method
 set_users_roles - more clearly solution

---
 engine/include/CCorpusPerspective.php         | 22 +++++++++++++++++++
 .../PerspectivePerspectives.php               |  6 +----
 .../PerspectiveUsers_roles.php                | 21 ------------------
 3 files changed, 23 insertions(+), 26 deletions(-)

diff --git a/engine/include/CCorpusPerspective.php b/engine/include/CCorpusPerspective.php
index 0d3a84e2..4ae2f399 100644
--- a/engine/include/CCorpusPerspective.php
+++ b/engine/include/CCorpusPerspective.php
@@ -22,6 +22,28 @@ function __construct(CPage &$page)
     }
 	
 	abstract function execute();
+
+    // this method is used also by PerspectivePerspectives
+    function set_users_roles(){
+        global $corpus;
+        $roles = ($this->page->getDb())->fetch_rows("SELECT *" .
+                " FROM users_corpus_roles us " .
+                " RIGHT JOIN users u ON (us.user_id=u.user_id AND us.corpus_id={$corpus['id']})" .
+                " WHERE u.user_id != {$corpus['user_id']}" .
+                " ORDER BY u.screename");
+
+        $users_roles = array();
+        foreach ($roles as $role){
+            $users_roles[$role['user_id']]['role'][] = $role['role'];
+            $users_roles[$role['user_id']]['screename'] = $role['screename'];
+            $users_roles[$role['user_id']]['user_id'] = $role['user_id'];
+        }
+        foreach($users_roles as $key => $u_roles){
+            if(!in_array(CORPUS_ROLE_READ,$u_roles['role']))
+                unset($users_roles[$key]);
+        }
+        $this->page->set('users_roles', $users_roles);
+    } // set_users_roles()
 	
 }
 ?>
diff --git a/engine/page/corpus_perspectives/PerspectivePerspectives.php b/engine/page/corpus_perspectives/PerspectivePerspectives.php
index 484cafb3..6b159e99 100644
--- a/engine/page/corpus_perspectives/PerspectivePerspectives.php
+++ b/engine/page/corpus_perspectives/PerspectivePerspectives.php
@@ -12,11 +12,7 @@ function execute()
 	{
 		$this->set_corpus_perspectives();
 		$this->set_users_perspectives();
-        // [SW] metoda set_users_roles() nie jest statyczna, używa własności 
-        // page konstrukcja poniżej kieruje ją do instancji strony istniejącej
-		// PerspectiveUsers_roles::set_users_roles();
-        $PerspectiveUsers_rolesInstanceForPage = new PerspectiveUsers_roles($this->page);
-        $PerspectiveUsers_rolesInstanceForPage->set_users_roles();
+		$this->set_users_roles();
 	}
 	
 	function set_corpus_perspectives(){
diff --git a/engine/page/corpus_perspectives/PerspectiveUsers_roles.php b/engine/page/corpus_perspectives/PerspectiveUsers_roles.php
index 48a6c694..4c9353db 100644
--- a/engine/page/corpus_perspectives/PerspectiveUsers_roles.php
+++ b/engine/page/corpus_perspectives/PerspectiveUsers_roles.php
@@ -14,27 +14,6 @@ function execute()
 		$this->set_corpus_roles();
 	}
 	
-	function set_users_roles(){
-		global $corpus, $db;
-		$roles = $db->fetch_rows("SELECT *" .
-				" FROM users_corpus_roles us " .
-				" RIGHT JOIN users u ON (us.user_id=u.user_id AND us.corpus_id={$corpus['id']})" .
-				" WHERE u.user_id != {$corpus['user_id']}" .
-				" ORDER BY u.screename");
-
-		$users_roles = array();
-		foreach ($roles as $role){
-			$users_roles[$role['user_id']]['role'][] = $role['role'];
-			$users_roles[$role['user_id']]['screename'] = $role['screename']; 
-			$users_roles[$role['user_id']]['user_id'] = $role['user_id']; 
-		}
-		foreach($users_roles as $key => $u_roles){
-			if(!in_array(CORPUS_ROLE_READ,$u_roles['role']))
-				unset($users_roles[$key]);
-		}
-		$this->page->set('users_roles', $users_roles);
-	}
-	
 	function set_corpus_roles(){
 		global $db;
 		$corpus_roles = $db->fetch_rows("SELECT * FROM corpus_roles WHERE role != 'read'");

From 75fd25460750f2164dba4ba9f2baa1e6931b962b Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Wed, 16 Jun 2021 21:51:18 +0200
Subject: [PATCH 048/154] literal smarty tags removed from document browser

---
 engine/templates/page_corpus_documents.tpl    | 16 ++++----
 .../templates/page_corpus_documents_old.tpl   | 37 +++++++++++--------
 2 files changed, 30 insertions(+), 23 deletions(-)

diff --git a/engine/templates/page_corpus_documents.tpl b/engine/templates/page_corpus_documents.tpl
index c8036d41..1dc160ad 100644
--- a/engine/templates/page_corpus_documents.tpl
+++ b/engine/templates/page_corpus_documents.tpl
@@ -22,19 +22,21 @@
                 <script type="text/javascript">
                     var init_from = {$from};
                     var colModel = [
-                            {literal}{
-                            {/literal}display: "<input class='select_all' type='checkbox' name='select_action'>",
+                        {ldelim}
+                            display: "<input class='select_all' type='checkbox' name='select_action'>",
                             name: "checkbox_action",
                             width: 30,
-                            align: 'center'{literal}}{/literal},
+                            align: 'center'
+			{rdelim},
                         {foreach from=$columns item=c}
                             {if $c->isVisible() || $c->isPinned()}
-                                {literal}{
-                                {/literal}display: "{$c->getHeader()}",
+                                {ldelim}
+                                display: "{$c->getHeader()}",
                                 name: "{$c->getKey()}",
                                 width: {$c->getWidth()},
                                 sortable: false,
-                                align: '{$c->getAlign()}'{literal}}{/literal},
+                                align: '{$c->getAlign()}'
+				{rdelim},
                             {/if}
                         {/foreach}
                     ];
@@ -241,4 +243,4 @@
 {else}
     {include file="inc_no_access.tpl"}
 {/if}
-{include file="inc_footer.tpl"}
\ No newline at end of file
+{include file="inc_footer.tpl"}
diff --git a/engine/templates/page_corpus_documents_old.tpl b/engine/templates/page_corpus_documents_old.tpl
index f061e689..6accaa4f 100644
--- a/engine/templates/page_corpus_documents_old.tpl
+++ b/engine/templates/page_corpus_documents_old.tpl
@@ -26,37 +26,41 @@
                     var colModel = [
                         {foreach from=$columns item=c key=k}
                         {if preg_match("/^flag/",$k)}
-                            {literal}{
-                            {/literal}display: "{$c.short}",
+                            {ldelim}
+                            display: "{$c.short}",
                             name: "{$k|lower}",
                             width: 40,
                             sortable: true,
-                            align: 'center'{literal}}{/literal},
+                            align: 'center'
+			    {rdelim},
                         {elseif preg_match("/found_base_form/", $k)}
-                            {literal}{
-                            {/literal}display: "{$c}",
+                            {ldelim}
+                            display: "{$c}",
                             name: "{$k|lower}",
                             width: 200,
                             sortable: true,
-                            align: 'center'{literal}}{/literal},
+                            align: 'center'
+			    {rdelim},
                         {elseif $c=="Subcorpus"}
-                            {literal}{
-                            {/literal}display: "{$c}",
+                            {ldelim}
+                            display: "{$c}",
                             name: "{$k|lower}",
                             width: 100,
                             sortable: true,
-                            align: 'left'{literal}}{/literal},
+                            align: 'left'
+		            {rdelim},
                         {elseif $c=="checkbox"}
-                            {literal}{
-                            {/literal}display: "<input class = 'select_all' type='checkbox' name='select_action'>",
+                            {ldelim}
+                            display: "<input class = 'select_all' type='checkbox' name='select_action'>",
                             name: "{$k|lower}",
                             width: 50,
-                            align: 'center'{literal}}{/literal},
+                            align: 'center'
+			    {rdelim},
 
                         {else}
                         {if !preg_match("/lp/", $k)}
-                            {literal}{
-                            {/literal}display: "{$c}", name: "{$k|lower}",
+                            {ldelim}
+                            display: "{$c}", name: "{$k|lower}",
 
                             {if preg_match("/title/", $k)}
                             width: 50, align: 'left',
@@ -70,7 +74,8 @@
                             width: 50, align: 'center',
                             {/if}
 
-                            sortable: true{literal}}{/literal},
+                            sortable: true
+			    {rdelim},
                         {/if}
 
                         {/if}
@@ -221,4 +226,4 @@
 {else}
     {include file="inc_no_access.tpl"}
 {/if}
-{include file="inc_footer.tpl"}
\ No newline at end of file
+{include file="inc_footer.tpl"}

From 4f15a26b0a42f2d19b6d049c791a1f919426bcc2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tomasz=20Naskr=C4=99t?= <tomasz.naskret@pwr.edu.pl>
Date: Thu, 17 Jun 2021 14:47:26 +0200
Subject: [PATCH 049/154] fixed small errors to get access to perspectives

---
 engine/ajax/ajax_annotation_edit_delete.php   |  2 +-
 engine/ajax/ajax_annotation_edit_update.php   |  2 +-
 engine/include/database/CDbAnnotation.php     |  2 +-
 engine/include/database/CDbCorpus.php         |  5 +++--
 .../filters/ReportFilterEnumFlag.php          |  2 +-
 .../PerspectiveAnaphora.php                   | 21 ++++++++++---------
 .../PerspectiveAnnotator.php                  |  2 +-
 .../PerspectiveAnnotator_anaphora.php         |  6 +++---
 .../report_perspectives/PerspectiveEdit.php   |  2 +-
 9 files changed, 23 insertions(+), 21 deletions(-)

diff --git a/engine/ajax/ajax_annotation_edit_delete.php b/engine/ajax/ajax_annotation_edit_delete.php
index a795c5e7..ca7f1309 100644
--- a/engine/ajax/ajax_annotation_edit_delete.php
+++ b/engine/ajax/ajax_annotation_edit_delete.php
@@ -16,7 +16,7 @@ function __construct(){
     /**
      * ToDo: implement custom permissions to this action
      */
-    function customPermissionRule($user, $corpus){
+    function customPermissionRule($user=null, $corpus=null){
         return true;
     }
 
diff --git a/engine/ajax/ajax_annotation_edit_update.php b/engine/ajax/ajax_annotation_edit_update.php
index 99180534..32e9b408 100644
--- a/engine/ajax/ajax_annotation_edit_update.php
+++ b/engine/ajax/ajax_annotation_edit_update.php
@@ -11,7 +11,7 @@ class Ajax_annotation_edit_update extends CPageCorpus {
     /**
      * ToDo: implement custom permissions to this action
      */
-    function customPermissionRule($user, $corpus){
+    function customPermissionRule($user=null, $corpus=null){
         return true;
     }
 
diff --git a/engine/include/database/CDbAnnotation.php b/engine/include/database/CDbAnnotation.php
index e3647c0f..4716b3d1 100755
--- a/engine/include/database/CDbAnnotation.php
+++ b/engine/include/database/CDbAnnotation.php
@@ -850,7 +850,7 @@ static function getUserAnnotationCount($corpus_id=null, $subcorpus_ids=null, $re
 		}
 
 		if ( $annotation_type_ids !== null ){
-			$annotation_type_ids = array_map(intval, $annotation_type_ids);
+			$annotation_type_ids = array_map('intval', $annotation_type_ids);
 			if ( count($annotation_type_ids) > 0 ){
 				$params_where = array_merge($params_where, $annotation_type_ids);
 				$sql_where[] = "a.type_id IN (" . implode(",", array_fill(0, count($annotation_type_ids), "?")) .")";
diff --git a/engine/include/database/CDbCorpus.php b/engine/include/database/CDbCorpus.php
index 4b4131e7..c87926c9 100644
--- a/engine/include/database/CDbCorpus.php
+++ b/engine/include/database/CDbCorpus.php
@@ -333,8 +333,9 @@ static function getCorpusExtColumns($table_name){
 				if (preg_match('/^enum\((.*)\)$/', $row['Type'], $match)){
 					$field['type'] = 'enum';
 					$values = array();
-					foreach ( split(",", $match[1]) as $v )
-						$values[] = trim($v, "'");
+					foreach ( preg_split("~,~", $match[1]) as $v ) {
+                        $values[] = trim($v, "'");
+                    }
 					$field['field_values'] = $values;
 				}
 				else
diff --git a/engine/include/utils/reportlist/filters/ReportFilterEnumFlag.php b/engine/include/utils/reportlist/filters/ReportFilterEnumFlag.php
index eae2f035..c0670d04 100644
--- a/engine/include/utils/reportlist/filters/ReportFilterEnumFlag.php
+++ b/engine/include/utils/reportlist/filters/ReportFilterEnumFlag.php
@@ -22,7 +22,7 @@ function __construct($flagId, $flagName){
         $this->template = "report_filters/inc_filter_flag.tpl";
     }
 
-    function applyTo(&$sqlBuilder){
+    function applyTo($sqlBuilder){
         $flagKey = "fl_" . $this->flagId;
         $sqlBuilder->addJoinTable(new SqlBuilderJoin("reports_flags", $flagKey, "r.id = $flagKey.report_id AND $flagKey.corpora_flag_id = ?", array($this->flagId)));
 
diff --git a/engine/page/report_perspectives/PerspectiveAnaphora.php b/engine/page/report_perspectives/PerspectiveAnaphora.php
index cde27ef9..06b0dd36 100644
--- a/engine/page/report_perspectives/PerspectiveAnaphora.php
+++ b/engine/page/report_perspectives/PerspectiveAnaphora.php
@@ -10,7 +10,7 @@ class PerspectiveAnaphora extends CPerspective {
 	
 	function execute()
 	{
-		$document_id = $this->document[id];
+		$document_id = $this->document['id'];
 		
 		$rows = $this->page->getDb()->fetch_rows("SELECT ans.from AS ans_from, ans.to AS ans_to, ans.type AS ans_type, ans.text AS ans_text," .
 									" ant.from AS ant_from, ant.to AS ant_to, ant.type AS ant_type, ant.text AS ant_text," .
@@ -45,43 +45,44 @@ function load_document_content($relations){
 			$htmlStr = new HtmlStr($this->document['content']);
 			
 			foreach ($relations as $ann){			
-				if ( !isset($elements[$ann[target_id]]) ){
+				if ( !isset($elements[$ann['target_id']]) ){
 					$annotation = sprintf("<an#%d:%s>", $ann['target_id'], $ann['ant_type']);
-					$elements[$ann[target_id]] = array("annotation"=>$annotation,
+					$elements[$ann['target_id']] = array("annotation"=>$annotation,
 														"from"=>$ann['ant_from'],
 														"to"=>$ann['ant_to'],
 														"before"=>"", 
 														"after"=>array());
 
 					$element_id = $next_id++;
-					$index[$ann[target_id]]	= $element_id;
+					$index[$ann['target_id']]	= $element_id;
 					$sup = "<#$element_id>";
 					
-					$elements[$ann[target_id]][before] = $sup;
+					$elements[$ann['target_id']]['before'] = $sup;
 				}				
 			}
 					
 			foreach ($relations as $ann){
-				$element_id = $index[$ann[target_id]];
+				$element_id = $index[$ann['target_id']];
 				$sup = "<#↦$element_id>";
 				
-				if ( !isset($elements[$ann[source_id]]) ){
+				if ( !isset($elements[$ann['source_id']]) ){
 					$annotation = sprintf("<an#%d:%s>", $ann['source_id'], $ann['ans_type']);
-					$elements[$ann[source_id]] = array("annotation"=>$annotation, 
+					$elements[$ann['source_id']] = array("annotation"=>$annotation,
 														"from"=>$ann['ans_from'],
 														"to"=>$ann['ans_to'],
 														"before"=>"", 
 														"after"=>array());					
 				}
 				
-				$elements[$ann[source_id]][after][] = $sup;
+				$elements[$ann['source_id']]['after'][] = $sup;
 				
 			}
 			
 			foreach ($elements as $id=>$e){
-				$htmlStr->insertTag($e['from'], $e[before].$e[annotation], $e['to']+1, "</an>" . implode($e[after]));				
+				$htmlStr->insertTag($e['from'], $e['before'].$e['annotation'], $e['to']+1, "</an>" . implode($e['after']));
 			}
 		}catch (Exception $ex){
+			//TODO Check what is this handler
 			custom_exception_handler($ex);
 		}
 		
diff --git a/engine/page/report_perspectives/PerspectiveAnnotator.php b/engine/page/report_perspectives/PerspectiveAnnotator.php
index abce254c..b3e9f14c 100644
--- a/engine/page/report_perspectives/PerspectiveAnnotator.php
+++ b/engine/page/report_perspectives/PerspectiveAnnotator.php
@@ -206,7 +206,7 @@ function set_annotation_menu(){
 				$annotation_grouped[$set][$set_name][$subset]['notcommon'] = !$an['common'];
 				$annotationsSubsets[] = $an['subsetid'];
 			}
-			$annotation_grouped[$set][$set_name][$subset][$an[name]] = $an;
+			$annotation_grouped[$set][$set_name][$subset][$an['name']] = $an;
 			$annotation_grouped[$set][$set_name][$subset]['notcommon'] |= !$an['common'];
 		}
 		if (!$_COOKIE['clearedLayer']){
diff --git a/engine/page/report_perspectives/PerspectiveAnnotator_anaphora.php b/engine/page/report_perspectives/PerspectiveAnnotator_anaphora.php
index bee08f1b..1787c9af 100644
--- a/engine/page/report_perspectives/PerspectiveAnnotator_anaphora.php
+++ b/engine/page/report_perspectives/PerspectiveAnnotator_anaphora.php
@@ -180,10 +180,10 @@ function set_annotations(){
 		$relations = $this->page->getDb()->fetch_rows($sql_relations, array($id));
 		
 		foreach ($relations as $r){
-			if ($r[group_id] == 1)
-				$htmlStr2->insert($r[to]+1, "<sup class='rel' target='".$r['target_id']."'></sup>", false, true, false);
+			if ($r['group_id'] == 1)
+				$htmlStr2->insert($r['to']+1, "<sup class='rel' target='".$r['target_id']."'></sup>", false, true, false);
 			else
-				$htmlStr->insert($r[to]+1, "<sup class='rel' target='".$r['target_id']."'/></sup>", false, true, false);
+				$htmlStr->insert($r['to']+1, "<sup class='rel' target='".$r['target_id']."'/></sup>", false, true, false);
 		}
 		
 		$this->page->set('content_inline', Reformat::xmlToHtml($htmlStr->getContent()));
diff --git a/engine/page/report_perspectives/PerspectiveEdit.php b/engine/page/report_perspectives/PerspectiveEdit.php
index 2102419c..7c3155b4 100644
--- a/engine/page/report_perspectives/PerspectiveEdit.php
+++ b/engine/page/report_perspectives/PerspectiveEdit.php
@@ -23,7 +23,7 @@ function set_dropdown_lists()
 		$select_format = DbReport::getAllFormatsByName();
 		
 		$sql = "SELECT COUNT(*) FROM reports_annotations WHERE report_id = ?";
-		$annotations_count = $this->page->getDb()->fetch_one($sql, $this->document[id]);
+		$annotations_count = $this->page->getDb()->fetch_one($sql, $this->document['id']);
 
 		try{
 			$content = $this->document['content'];

From b1a490be28994ac2c990b678aec8cdf3bd8dc3a8 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 19 Jun 2021 18:19:27 +0200
Subject: [PATCH 050/154] correct some potential errors about mixing smarty
 comments with literal

---
 engine/templates/inc_footer.tpl               | 18 +++++------
 engine/templates/inc_report_annotator_wsd.tpl |  2 --
 engine/templates/inc_report_morphodisamb.tpl  |  8 ++---
 .../inc_report_morphodisambagreement.tpl      | 15 ++++-----
 .../page_corpus_agreement_morphology.tpl      | 32 +++++++++----------
 5 files changed, 32 insertions(+), 43 deletions(-)

diff --git a/engine/templates/inc_footer.tpl b/engine/templates/inc_footer.tpl
index 09869b3d..ee4f5273 100644
--- a/engine/templates/inc_footer.tpl
+++ b/engine/templates/inc_footer.tpl
@@ -10,27 +10,25 @@
 		</div>
 		{if $Config.federationLoginUrl}
 		{*inclusion of clarin bar*}
-			{literal}
 				<script src="https://ctj.clarin-pl.eu/clarin_bar/script.js"></script>
 				<script>
-					$(document).ready(function() {
-                        new ClarinModule({
-                            offset: {
+					$(document).ready(function() {ldelim}
+                        new ClarinModule({ldelim}
+                            offset: {ldelim}
                                 'top': 0,
                                 'right': 0,
                                 'bottom': null,
                                 'left': null
-                            },
-                            arrow: {
+                            {rdelim},
+                            arrow: {ldelim}
                                 'initial-orientation': "left",// up || down || right || left
                                 'rotation-hover': 180
-                            },
+                            {rdelim},
                             themeColor: '#337ab7',
                             compactMode: true
-                        });
-                    });
+                        {rdelim});
+                    {rdelim});
 				</script>
-			{/literal}
         {/if}
 		<div id="footer">
 			<span style="float: left">
diff --git a/engine/templates/inc_report_annotator_wsd.tpl b/engine/templates/inc_report_annotator_wsd.tpl
index 1571cc68..c3e7180b 100644
--- a/engine/templates/inc_report_annotator_wsd.tpl
+++ b/engine/templates/inc_report_annotator_wsd.tpl
@@ -128,9 +128,7 @@
 	</div>
 </div>
 
-{literal}
 	<script>
         // global variable used in different places
 		var annotationModeFieldName = 'annotation_mode_wsd';
 	</script>
-{/literal}
\ No newline at end of file
diff --git a/engine/templates/inc_report_morphodisamb.tpl b/engine/templates/inc_report_morphodisamb.tpl
index cd2e3ffd..871b0981 100644
--- a/engine/templates/inc_report_morphodisamb.tpl
+++ b/engine/templates/inc_report_morphodisamb.tpl
@@ -149,11 +149,9 @@
 
 </div>
 
-{literal}
 <script>
-    $(function () {
-        var morphoTokenTags = {/literal}{$tokensTags|@json_encode};{literal}
+    $(function () {ldelim}
+        var morphoTokenTags = {$tokensTags|@json_encode};
         var morphoModule = new MorphoTagger($('#morpho-tagger'), $('span.token'), morphoTokenTags, $('#editable-select'));
-    });
+    {rdelim});
 </script>
-{/literal}
diff --git a/engine/templates/inc_report_morphodisambagreement.tpl b/engine/templates/inc_report_morphodisambagreement.tpl
index 66639777..b266a46d 100644
--- a/engine/templates/inc_report_morphodisambagreement.tpl
+++ b/engine/templates/inc_report_morphodisambagreement.tpl
@@ -136,21 +136,18 @@
 
 
 <script>
-    {literal}
 
     setupUserSelectionAB("morpho");
 
-    $(function () {
-        var morphoTokenTags = {/literal}{$tokensTags|@json_encode};{literal}
-		var finalDecision = {/literal}{$finalTagsDecision|@json_encode};{literal}
-        var annotatorADecisions = {/literal}{$tokensTagsAnnotatorA|@json_encode};{literal}
-        var annotatorBDecisions = {/literal}{$tokensTagsAnnotatorB|@json_encode};{literal}
+    $(function () {ldelim}
+        var morphoTokenTags = {$tokensTags|@json_encode};
+	var finalDecision = {$finalTagsDecision|@json_encode};
+        var annotatorADecisions = {$tokensTagsAnnotatorA|@json_encode};
+        var annotatorBDecisions = {$tokensTagsAnnotatorB|@json_encode};
 
 
         var morphoModuleAgree = new MorphoTaggerAgree($('#morpho-tagger'), $('span.token'), morphoTokenTags, $('#editable-select'), finalDecision, annotatorADecisions, annotatorBDecisions);
-    });
+    {rdelim});
 
-
-	{/literal}
 </script>
 
diff --git a/engine/templates/page_corpus_agreement_morphology.tpl b/engine/templates/page_corpus_agreement_morphology.tpl
index cb3674ed..6ae171fa 100644
--- a/engine/templates/page_corpus_agreement_morphology.tpl
+++ b/engine/templates/page_corpus_agreement_morphology.tpl
@@ -149,37 +149,36 @@
     </div>
 </div>
 
-{literal}
 <script>
-	var reports = {/literal}{$reports|@json_encode};{literal}
-	var subcorp = {/literal}{$selectedSubcorp|@json_encode};{literal}
-	var usersMorphoDisamb = []; //{/literal}{$usersMorphoDisambSet|@json_encode}; {literal}
-	var annotator_a_id = {/literal}{$annotator_a_id|@json_encode}; {literal}
-	var annotator_b_id = {/literal}{$annotator_b_id|@json_encode}; {literal}
-	var annotators = {/literal}{$annotators|@json_encode}; {literal}
+	var reports = {$reports|@json_encode};
+	var subcorp = {$selectedSubcorp|@json_encode};
+	var usersMorphoDisamb = []; //{$usersMorphoDisambSet|@json_encode};
+	var annotator_a_id = {$annotator_a_id|@json_encode}; 
+	var annotator_b_id = {$annotator_b_id|@json_encode}; 
+	var annotators = {$annotators|@json_encode}; 
 
 	var selectedAnnotators = [];
 	selectedAnnotators.push(annotators.find(
-	    function(it){
+	    function(it){ldelim}
 	        return it.user_id === annotator_a_id;
-        }));
+        {rdelim}));
 
     selectedAnnotators.push(annotators.find(
-	    function(it){
+	    function(it){ldelim}
 	        return it.user_id === annotator_b_id;
-        }));
+        {rdelim}));
 
-    var reportsTable = $('#reports_table').DataTable( {
+    var reportsTable = $('#reports_table').DataTable( {ldelim}
         scrollY:        "65vh",
         scrollX:        true,
         scrollCollapse: true,
         paging:         false,
-        fixedColumns:   {
+        fixedColumns:   {ldelim}
             leftColumns: 2
-        },
+        {rdelim},
         fixedColumns:   true,
         bInfo:			false,
-    } );
+    {rdelim} );
 
     var diffTable = $('#difference_table');
 
@@ -192,5 +191,4 @@
 		usersMorphoDisamb
 	);
 </script>
-{/literal}
-{include file="inc_footer.tpl"}
\ No newline at end of file
+{include file="inc_footer.tpl"}

From d3bbaac9113a0416c3aae07212f523bbb3d7f5d3 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Sat, 19 Jun 2021 19:20:52 +0200
Subject: [PATCH 051/154] unquoting literal in template of corpus settings

---
 engine/templates/page_corpus_settings.tpl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/engine/templates/page_corpus_settings.tpl b/engine/templates/page_corpus_settings.tpl
index 39870501..e67ac34c 100644
--- a/engine/templates/page_corpus_settings.tpl
+++ b/engine/templates/page_corpus_settings.tpl
@@ -19,7 +19,7 @@
                     </li>
                 {/foreach}
                 {if isCorpusOwner() || "admin"|has_role}
-                    <li class="{if $subpage==corpus_delete}active{/if}">
+                    <li class="{if $subpage=="corpus_delete"}active{/if}">
                         <a href="index.php?page=corpus_settings&amp;corpus={$corpus.id}&amp;subpage=corpus_delete">Delete corpus</a>
                     </li>
                 {/if}
@@ -54,4 +54,4 @@
 </div>
 
 
-{include file="inc_footer.tpl"}
\ No newline at end of file
+{include file="inc_footer.tpl"}

From dcceafc24db072b6d3e323ce45e5e5f7f90a2ed2 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Tue, 22 Jun 2021 18:00:36 +0200
Subject: [PATCH 052/154] bad screename error in page header solved

---
 engine/templates/inc_menu2.tpl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/engine/templates/inc_menu2.tpl b/engine/templates/inc_menu2.tpl
index 36c02c58..33f04593 100644
--- a/engine/templates/inc_menu2.tpl
+++ b/engine/templates/inc_menu2.tpl
@@ -185,7 +185,7 @@
 			</ul>
 			<ul class="nav navbar-nav navbar-right" style="margin-right:50px;">
 				{if $user}
-				<li><a href="index.php?page=user_roles"><b>{if isset($user.login)}{$user.login}{/if} {if isset($element.screename)}{$element.screename}{/if}</b></a></li>
+				<li><a href="index.php?page=user_roles"><b>{if isset($user.login)}{$user.login}{/if} {if isset($user.screename)}{$user.screename}{/if}</b></a></li>
 				{/if}
 				<li>
 					{*if not using federation login show usual login buttons*}

From 0caed9ec756e8fbd8b7740c4b5c139da00c439f1 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Thu, 24 Jun 2021 14:39:21 +0200
Subject: [PATCH 053/154] improving rpm package building - version management

---
 packages/Makefile               | 10 +++++-----
 packages/rpm/SPECS/inforex.spec | 15 +++++++--------
 2 files changed, 12 insertions(+), 13 deletions(-)

diff --git a/packages/Makefile b/packages/Makefile
index 5de35af8..f5eb870d 100644
--- a/packages/Makefile
+++ b/packages/Makefile
@@ -7,10 +7,11 @@ HAVE_RPMBUILD = "no"$(RPMBUILD)
 RPM = rpm
 PACKAGE = inforex
 GITHASH=`git log --oneline |head -1|cut -d" " -f 1`
-VERSION = 0.1
+VERSION = 0.2
 RELNO = 1
 RELEASE = $(shell if [ ! -z '$(GITHASH)' ]; then echo -n "$(RELNO)v.$(GITHASH)"; else echo -n "$(RELNO)";fi)
 
+VERSPECTAG = VERSION_TAG
 RELSPECTAG = RELEASE_TAG
 
 # glob cannot work here
@@ -39,7 +40,7 @@ rpm-local: $(RPM_SOURCES_DIR)/$(PACKAGE).tgz
         mkdir -p $(rpmbuild)/RPMS && \
         mkdir -p $(rpmbuild)/SRPMS && \
         mkdir -p $(rpmbuild)/SPECS && \
-        cat ${RPM_SPEC_DIR}/$(rpmspec) | sed -e 's/${RELSPECTAG}/${RELEASE}/' > $(rpmbuild)/SPECS/$(rpmspec) && \
+        cat ${RPM_SPEC_DIR}/$(rpmspec) | sed -e 's/${RELSPECTAG}/${RELEASE}/' | sed -e 's/${VERSPECTAG}/${VERSION}/' > $(rpmbuild)/SPECS/$(rpmspec) && \
         mkdir -p $(rpmbuild)/SOURCES && \
 	if ls -A ${RPM_SOURCES_DIR} ; then \
 		cp ${RPM_SOURCES_DIR}/* $(rpmbuild)/SOURCES; \
@@ -61,8 +62,7 @@ srpm-common:
 
  
 rpm-common: 
-	@(rpmpkg=$(PACKAGE)-$(VERSION)-$(RELEASE)*src.rpm; \
-        rpmspec=$(PACKAGE).spec; \
+	@(rpmspec=$(PACKAGE).spec; \
         rpmbuild=`mktemp -t -d $(PACKAGE)-build-$$USER-XXXXXXXX`; \
 	$(MAKE) $(AM_MAKEFLAGS) \
                 rpmbuild="$$rpmbuild" \
@@ -71,7 +71,7 @@ rpm-common:
 	LANG=C ${RPMBUILD} \
                 --define "_tmppath $$rpmbuild/TMP" \
                 --define "_topdir $$rpmbuild" \
-                $(def) --rebuild $$rpmpkg || exit 1; \
+                $(def) -bb $$rpmbuild/SPECS/$$rpmspec || exit 1; \
 	cp $$rpmbuild/RPMS/*/* . || exit 1; \
         rm -R $$rpmbuild)
 
diff --git a/packages/rpm/SPECS/inforex.spec b/packages/rpm/SPECS/inforex.spec
index a7a1608e..f7237a9a 100644
--- a/packages/rpm/SPECS/inforex.spec
+++ b/packages/rpm/SPECS/inforex.spec
@@ -8,7 +8,7 @@
 %define        inforexdir        %{phplibdir}/%{name}
 
 Name:       inforex
-Version:    0.1
+Version:    VERSION_TAG
 Release:    RELEASE_TAG
 Summary:    dummy package to testing rpm builds
 License:    GLGPL v3
@@ -36,12 +36,6 @@ to test all phases of building rpm process
 %prep
 %setup -q -c
 
-# remove .htaccess files
-#find . -name \.htaccess -print | xargs rm -f
-
-# remove several scripts not used in the package
-#rm -rf  vendor/ezyang/htmlpurifier/maintenance/
-
 # remove precompiled templtates from devel dir
 rm -rf engine/templates_c/*
 
@@ -61,6 +55,9 @@ install -m 755 -d %{buildroot}%{_localstatedir}/lib/
 mv %{buildroot}%{inforexdir}/data %{buildroot}%{_localstatedir}/lib/%{name}
 ln -s %{_localstatedir}/lib/%{name} %{buildroot}%{inforexdir}/data
 
+# install templates_c empty workdir for Smarty cache
+install -m 775 -d %{buildroot}%{inforexdir}/engine/templates_c
+
 # create one initial sql dump from all patches
 rm -rf %{buildroot}/%{inforexdir}/database
 mkdir -p %{buildroot}/%{inforexdir}/database/init
@@ -100,7 +97,7 @@ fi
 
 %dir %{inforexdir}
 %{inforexdir}/*
-
+%exclude %{inforexdir}/engine/templates_c
 %attr(775,-,%{httpdgroup}) %{inforexdir}/engine/templates_c
 
 %dir %{_localstatedir}/lib/%{name}
@@ -109,6 +106,8 @@ fi
 %{httpconfdir}/conf.d/%{name}.conf
 
 %changelog
+* Thu Jun 24 2021 Seweryn Walentynowicz <seweryn@walor.torun.pl>
+- templates_c directory must exists before packaging rpm
 * Wed Feb 17 2021 Seweryn Walentynowicz <seweryn@walor.torun.pl>
 - solved selinux context installation problems
 * Mon Feb 15 2021 Seweryn Walentynowicz <seweryn@walor.torun.pl>

From 3787e16ca668298d6e831935f3334bb5b6fa8e44 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Tue, 27 Jul 2021 18:55:47 +0200
Subject: [PATCH 054/154] solve Auth library error

---
 engine/external/pear/Auth/Container/Array.php | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/engine/external/pear/Auth/Container/Array.php b/engine/external/pear/Auth/Container/Array.php
index 334080cb..d0e63f38 100644
--- a/engine/external/pear/Auth/Container/Array.php
+++ b/engine/external/pear/Auth/Container/Array.php
@@ -124,9 +124,10 @@ function Auth_Container_Array($data)
      *
      * @param  string Username
      * @param  string Password
+     * @param   boolean not used, for compatibility with ancestor interface
      * @return boolean|PEAR_Error Error object or boolean
      */
-    function fetchData($user, $pass)
+    function fetchData($user, $pass, $isChallengeResponse = false)
     {
         $this->log('Auth_Container_Array::fetchData() called.', AUTH_LOG_DEBUG);
         if (   isset($this->users[$user])

From 51a52cb4d48d2fae3cb4af94914c9fe467933d49 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Tue, 27 Jul 2021 19:08:02 +0200
Subject: [PATCH 055/154] move corpus loading after set clarin user procedure

---
 public_html/index.php | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/public_html/index.php b/public_html/index.php
index fbf70336..bcd42d8c 100644
--- a/public_html/index.php
+++ b/public_html/index.php
@@ -35,7 +35,6 @@
 	$auth = new UserAuthorize(Config::Config()->get_dsn());
 	$auth->authorize(isset($_POST['logout']) && ($_POST['logout']=="1"));
 	$user = $auth->getUserData();
-	$corpus = RequestLoader::loadCorpus();
 
 	// federation login is enabled
 	if(Config::Config()->get_federationLoginUrl()){
@@ -56,6 +55,9 @@
 		}
     }
 
+    // load corpus after finally set $user data
+    $corpus = RequestLoader::loadCorpus();
+
 	chdir(__DIR__ . "/../engine/");
 
 	$p->execute();

From a206fd3c2c9f06b000378e87aeee9e4c207e7e79 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <S.Walentynowicz@walor.torun.pl>
Date: Thu, 12 Aug 2021 18:02:31 +0200
Subject: [PATCH 056/154] external curl request separation

---
 engine/include/CUserAuthorize.php | 41 +++++++++++++++++++------------
 1 file changed, 25 insertions(+), 16 deletions(-)

diff --git a/engine/include/CUserAuthorize.php b/engine/include/CUserAuthorize.php
index d982d156..3e394cf8 100644
--- a/engine/include/CUserAuthorize.php
+++ b/engine/include/CUserAuthorize.php
@@ -73,26 +73,35 @@ function getClarinUser(){
 
         // sudo apt-get install php5-curl
         if(isset($_COOKIE['clarin-pl-token'])) {
-            $token = $_COOKIE['clarin-pl-token'];
-            $curl = curl_init(Config::Config()->get_federationValidateTokenUrl() . $token);
+            return $this->getClarinUserByToken($_COOKIE['clarin-pl-token']);
+        } else {
+            return null;
+        }
 
-            curl_setopt($curl, CURLOPT_POST, true);
-            curl_setopt($curl, CURLOPT_POSTFIELDS, '');
-            curl_setopt($curl, CURLOPT_HTTPHEADER, array('Content-Type:application/json'));
-            curl_setopt($curl, CURLOPT_RETURNTRANSFER, true);
+    } // getClarinUser()
 
-            $response = curl_exec($curl);
-            $httpcode = curl_getinfo($curl, CURLINFO_HTTP_CODE);
-            curl_close($curl);
+    private function getClarinUserByToken($token){
 
-            // invalid token
-            if ($httpcode !== 200) {
-                return null;
-            }
-            return json_decode($response, true);
+        // using system curl command
+        // sudo apt-get install php5-curl
+        $curl = curl_init(Config::Config()->get_federationValidateTokenUrl() . $token);
+
+        curl_setopt($curl, CURLOPT_POST, true);
+        curl_setopt($curl, CURLOPT_POSTFIELDS, '');
+        curl_setopt($curl, CURLOPT_HTTPHEADER, array('Content-Type:application/json'));
+        curl_setopt($curl, CURLOPT_RETURNTRANSFER, true);
+
+        $response = curl_exec($curl);
+        $httpcode = curl_getinfo($curl, CURLINFO_HTTP_CODE);
+        curl_close($curl);
+
+        // invalid token
+        if ($httpcode !== 200) {
+            return null;
         }
-        return null;
-    }
+        return json_decode($response, true);
+
+    } // getClarinUserByToken()
 
 	function getClarinLogin()
     {

From 539c35a8ee224f510a63d413403c514c1e0a5ddf Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Thu, 14 Oct 2021 12:03:14 +0200
Subject: [PATCH 057/154] revKey when no git

---
 engine/include/CInforexWeb.php | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/engine/include/CInforexWeb.php b/engine/include/CInforexWeb.php
index f0e78aae..ac3b55e8 100644
--- a/engine/include/CInforexWeb.php
+++ b/engine/include/CInforexWeb.php
@@ -287,8 +287,15 @@ function getRevisionKey()
         // last tag 
         //$commitHash = exec("git describe --tags `git rev-list --tags --max-count=1`");
         // last revision
-        $commitHash = exec("git rev-list --tags --max-count=1");
-        $revKey = substr($commitHash, 0, 8);
+        $output = array();
+        $result_code = null; // integer
+        $commitHash = exec("git rev-list --tags --max-count=1 2>/dev/null",$output,$result_code);
+        if(($result_code==0) and (count($output)>0)) {
+            $commitHash = $output[0];
+            $revKey = substr($commitHash, 0, 8);
+        } else {
+            $revKey = "no git revision available";
+        }
         return $revKey;
     }
 

From 4f3322b76c31ae6084086e55e3a82835345aa9b3 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Thu, 14 Oct 2021 18:24:42 +0200
Subject: [PATCH 058/154] missing slash added in local config name

---
 docker/www/sample.config.local.php | 4 +++-
 public_html/css.php                | 2 +-
 public_html/image.php              | 2 +-
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/docker/www/sample.config.local.php b/docker/www/sample.config.local.php
index 6c72156a..8a06e3fd 100644
--- a/docker/www/sample.config.local.php
+++ b/docker/www/sample.config.local.php
@@ -4,7 +4,9 @@
 Config::Config()->put_path_secured_data('/home/inforex/secured_data');
 Config::Config()->put_dsn(array(
     'phptype'  => 'mysqli',
-    'username' => 'inforex', 'port' => '3306', 'password' => 'password',
+    'username' => 'inforex', 
+    'port' => '3306', 
+    'password' => 'password',
     'hostspec' => 'db',
     'database' => 'inforex',
 ));
diff --git a/public_html/css.php b/public_html/css.php
index 28b05e76..9ce6135b 100644
--- a/public_html/css.php
+++ b/public_html/css.php
@@ -10,7 +10,7 @@
 require_once($enginePath."/settings.php");
 require_once($enginePath.'/include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath."/../config/")."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath."/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 /********************************************************************8
  * Połączenie z bazą danych (nowy sposób)
diff --git a/public_html/image.php b/public_html/image.php
index 7b2850f8..7be2fe79 100644
--- a/public_html/image.php
+++ b/public_html/image.php
@@ -10,7 +10,7 @@
 require_once($enginePath."/settings.php");
 require_once($enginePath.'/include.php');
 Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath."/../config/")."config.local.php");
+Config::Config()->put_localConfigFilename(realpath($enginePath."/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 /********************************************************************8
  * Połączenie z bazą danych (nowy sposób)

From 51a39b825d20749972db3a8483425d3a736ce348 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Wed, 1 Dec 2021 13:48:38 +0100
Subject: [PATCH 059/154] reduce html code sending size for page_report_preview

---
 engine/ajax/ajax_annotation_type_tree.php     |  18 +++
 engine/include/CPage.php                      |   4 +-
 engine/templates/inc_header2.tpl              |   9 +-
 .../inc_widget_annotation_type_tree.tpl       |  52 +------
 ...dget_annotation_type_tree_set_template.tpl |  25 ++++
 ...t_annotation_type_tree_subset_template.tpl |  26 ++++
 ...et_annotation_type_tree_types_template.tpl |  25 ++++
 public_html/js/page_report_preview.js         | 131 +++++++++++++++++-
 8 files changed, 238 insertions(+), 52 deletions(-)
 create mode 100644 engine/ajax/ajax_annotation_type_tree.php
 create mode 100644 engine/templates/inc_widget_annotation_type_tree_set_template.tpl
 create mode 100644 engine/templates/inc_widget_annotation_type_tree_subset_template.tpl
 create mode 100644 engine/templates/inc_widget_annotation_type_tree_types_template.tpl

diff --git a/engine/ajax/ajax_annotation_type_tree.php b/engine/ajax/ajax_annotation_type_tree.php
new file mode 100644
index 00000000..b2836b9b
--- /dev/null
+++ b/engine/ajax/ajax_annotation_type_tree.php
@@ -0,0 +1,18 @@
+<?php
+/**
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ * See LICENCE
+ */
+
+
+class Ajax_annotation_type_tree extends CPagePublic {
+
+	function execute(){
+		$cid = strval($_POST['corpusId']);
+        $annotation_sets =  DbAnnotation::getAnnotationStructureByCorpora($cid);
+		return $annotation_sets;
+	}
+
+} // Ajax_annotation_type_tree
diff --git a/engine/include/CPage.php b/engine/include/CPage.php
index 2d8c4a52..e2d07645 100644
--- a/engine/include/CPage.php
+++ b/engine/include/CPage.php
@@ -218,8 +218,8 @@ function set_by_ref($name, &$object){
      * @return variable value or null if the variable is undefined
 	 */
 	function get($name){
-		if (isset($this->template->_tpl_vars[$name])) {
-            return $this->template->_tpl_vars[$name];
+		if (isset($this->template->tpl_vars[$name])) {
+            return $this->template->tpl_vars[$name];
         } else {
             return null;
         }
diff --git a/engine/templates/inc_header2.tpl b/engine/templates/inc_header2.tpl
index 40a360fa..c8835d17 100644
--- a/engine/templates/inc_header2.tpl
+++ b/engine/templates/inc_header2.tpl
@@ -93,10 +93,13 @@
 
 		<script type="text/javascript" src="libs/sprintf.min.js?{$rev}"></script>
 	{foreach from=$include_files item=f}
-		{if $f.type == "js"}<script type="text/javascript" src="{$f.file}?{$rev}"></script>{*
-		*}{elseif $f.type == "css"}<link rel="stylesheet" type="text/css" href="{$f.file}?{$rev}" />{/if}
+{if $f.type == "js"}
+	<script type="text/javascript" src="{$f.file}?{$rev}"></script>
+{elseif $f.type == "css"}
+	<link rel="stylesheet" type="text/css" href="{$f.file}?{$rev}" />
+{/if}
 	{/foreach}
-	</head>
+</head>
 <body>
 <div id="page" class="{$page}{if $compact_mode} compact{/if}">
 
diff --git a/engine/templates/inc_widget_annotation_type_tree.tpl b/engine/templates/inc_widget_annotation_type_tree.tpl
index 04aceb14..65d1f068 100644
--- a/engine/templates/inc_widget_annotation_type_tree.tpl
+++ b/engine/templates/inc_widget_annotation_type_tree.tpl
@@ -14,54 +14,14 @@
                     <th style="text-align:center; width: 100px" title="Dynamically show/hide layer">Display</th>
                 </tr>
 			</thead>
-			<tbody>
-		    {foreach from=$annotation_types item=set key=k name=groups}
-			    <tr class="layerRow hiddenRow" setid="{$set.groupid}">
-			    	<td style="vertical-align: middle;" class="layersList">
-			    		<span class="count" title="Number of selected annotation types from this layer" style="float: right; font-size: 10px; color: #445967; font-weight: normal;"></span>
-			    		<span class="toggleLayer ui-icon ui-icon-circlesmall-plus" style="float:left"></span>
-			    		<span class="layerName" style="clear:both">{$set.name}</span>
-			    	</td>
-			    	<td style="vertical-align: middle;text-align:center">
-			    		<input name="layerId-{$k}" type="checkbox" class="group_cb" /> 
-			    	</td>
-			    </tr>
-		    	{foreach from=$set item=subset key=sk name=subsets}
-					{if $sk != "name"}
-					<tr class="sublayerRow" subsetid="{$sk}" style="display:none">
-						<td style="vertical-align: middle;" class="layersList">
-							<span class="count" title="Number of selected annotation types from this subset" style="float: right; font-size: 10px; color: #445967; font-weight: normal;"></span>
-							<span class="ui-icon ui-icon-carat-1-sw" style="float:left"></span>
-							<span class="toggleSubLayer ui-icon ui-icon-circlesmall-plus" style="float:left"></span>
-							<span class="layerName" style="margin-left:10px;clear:both">{$subset.name}</span>
-						</td>
-			    		<td style="vertical-align: middle;text-align:center">
-			    			<input name="subsetId-{$sk}" type="checkbox" class="subset_cb" /> 
-			    		</td>
-					</tr>
-					{foreach from=$subset item=type key=tk name=types}
-						{if $tk != "name"}
-					<tr class="typelayerRow" typeid="{$tk}" style="display:none">
-						<td style="vertical-align: middle;" class="layersList">
-							<span class="ui-icon ui-icon-carat-1-sw" style="float:left"></span>
-							<span class="ui-icon ui-icon-carat-1-sw" style="float:left"></span>
-							<span class="layerName" style="margin-left:20px;clear:both;font-weight:normal;">{$type}</span>
-						</td>
-				    	<td style="vertical-align: middle;text-align:center">
-				    		<input name="typeId-{$tk}" type="checkbox" class="leftLayer type_cb" /> 
-				    	</td>
-					</tr>
-						{/if}
-					{/foreach}					
-					{/if}		    	
-		    	{/foreach}	
-		    {/foreach}
-			{if $annotation_types|@count==0}
+			<tbody class="annotationTypesTree" >
 				<tr>
 					<td colspan="2"><i>No layers, subsets nor types to display</i></td>
 				</tr>
-			{/if}		    
-		    </tbody>		
+			</tbody>    <!-- class=annotationTypesTree -->
     	</table>	
     	</div>    
-	</div>	
\ No newline at end of file
+	</div>	
+{include file="inc_widget_annotation_type_tree_set_template.tpl"}
+{include file="inc_widget_annotation_type_tree_subset_template.tpl"}
+{include file="inc_widget_annotation_type_tree_types_template.tpl"}
diff --git a/engine/templates/inc_widget_annotation_type_tree_set_template.tpl b/engine/templates/inc_widget_annotation_type_tree_set_template.tpl
new file mode 100644
index 00000000..6e908f3e
--- /dev/null
+++ b/engine/templates/inc_widget_annotation_type_tree_set_template.tpl
@@ -0,0 +1,25 @@
+{*
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ * See LICENCE
+ *}
+{* HTML template to generate dynamically row for annotation types set row
+    setRowTpl
+   Parameters to set in each row by JS code:
+	setRowId - set in checkbox.name as "layerId-".setRowId
+	         - not originally set in place of group.id  ?!?
+	setRowName - set as content in .layerName element
+*}
+<template id="setRowTpl">
+                            <tr class="layerRow hiddenRow" setid="">
+                                <td style="vertical-align: middle;" class="layersList">
+                                        <span class="count" title="Number of selected annotation types from this layer" style="float: right; font-size: 10px; color: #445967; font-weight: normal;"></span>
+                                        <span class="toggleLayer ui-icon ui-icon-circlesmall-plus" style="float:left"></span>
+                                        <span class="layerName" style="clear:both">setRowName</span>
+                                </td>
+                                <td style="vertical-align: middle;text-align:center">
+                                        <input name="layerId-setRowId" type="checkbox" class="group_cb" />
+                                </td>
+                            </tr>
+</template> 
diff --git a/engine/templates/inc_widget_annotation_type_tree_subset_template.tpl b/engine/templates/inc_widget_annotation_type_tree_subset_template.tpl
new file mode 100644
index 00000000..23fc6da2
--- /dev/null
+++ b/engine/templates/inc_widget_annotation_type_tree_subset_template.tpl
@@ -0,0 +1,26 @@
+{*
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ * See LICENCE
+ *}
+{* HTML template to generate dynamically row for annotation types subset row
+    subsetRowTpl
+   Parameters to set in each row by JS code:
+	subsetRowId - set checkboxa.name as "subsetId-".subsetRowId
+	            - set subsetid attr in tr tag .sublayerRow 
+	setRowName - set as content in .layerName element
+*}
+<template id="subsetRowTpl">
+                                        <tr class="sublayerRow" subsetid="subsetRowId" style="display:none">
+                                                <td style="vertical-align: middle;" class="layersList">
+                                                        <span class="count" title="Number of selected annotation types from this subset" style="float: right; font-size: 10px; color: #445967; font-weight: normal;"></span>
+                                                        <span class="ui-icon ui-icon-carat-1-sw" style="float:left"></span>
+                                                        <span class="toggleSubLayer ui-icon ui-icon-circlesmall-plus" style="float:left"></span>
+                                                        <span class="layerName" style="margin-left:10px;clear:both">subsetRowName</span>
+                                                </td>
+                                        <td style="vertical-align: middle;text-align:center">
+                                                <input name="subsetId-subsetRowId" type="checkbox" class="subset_cb" />
+                                        </td>
+                                        </tr>
+</template> 
diff --git a/engine/templates/inc_widget_annotation_type_tree_types_template.tpl b/engine/templates/inc_widget_annotation_type_tree_types_template.tpl
new file mode 100644
index 00000000..a0a0f7bd
--- /dev/null
+++ b/engine/templates/inc_widget_annotation_type_tree_types_template.tpl
@@ -0,0 +1,25 @@
+{*
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ * See LICENCE
+ *}
+{* HTML template to generate dynamically row for annotation type row
+    typeRowTpl
+   Parameters to set in each row by JS code:
+	typeRowId - set checkboxa.name as "typeId-".typeRowId
+	            - set typeid attr in tr tag .typelayerRow 
+	typeRowName - set as content in .layerName element
+*}
+<template id="typeRowTpl">
+                                        <tr class="typelayerRow" typeid="typeRowId" style="display:none">
+                                                <td style="vertical-align: middle;" class="layersList">
+                                                        <span class="ui-icon ui-icon-carat-1-sw" style="float:left"></span>
+                                                        <span class="ui-icon ui-icon-carat-1-sw" style="float:left"></span>
+                                                        <span class="layerName" style="margin-left:20px;clear:both;font-weight:normal;">typeRowName</span>
+                                                </td>
+                                        <td style="vertical-align: middle;text-align:center">
+                                                <input name="typeId-typeRowId" type="checkbox" class="leftLayer type_cb" />
+                                        </td>
+                                        </tr>
+</template> 
diff --git a/public_html/js/page_report_preview.js b/public_html/js/page_report_preview.js
index ae9920d9..0fd22190 100644
--- a/public_html/js/page_report_preview.js
+++ b/public_html/js/page_report_preview.js
@@ -9,10 +9,139 @@ var wRelationSets = null;
 var url = $.url(window.location.href);
 var corpus_id = url.param("corpus");
 var report_id = url.param("id");
+
+function createSetRowFromTemplate(container,setId,setName) {
+
+	/* from HTML template in DOM named id='setRowTpl'
+	 * creates code of set row for parametres setId,setName
+	 * and place it on the end of container element
+      	*/
+        const setRowTemplateId = "setRowTpl";
+        let setRow = null;
+        const template = document.querySelector("#"+setRowTemplateId);
+        if(template) {
+                setRow = template.content.cloneNode(true);
+                if(setRow){
+                        setRow.querySelector("input").setAttribute("name","layerId-"+setId);
+                        setRow.querySelector(".layerName").innerText = setName;
+                        if(container) {
+                                container.append(setRow);
+                        }
+                } else {
+                        console.log("Cannot clone DOM element for template with id="+setRowTemplateId);
+                }
+        } else {
+                console.log("Cannot create DOM element from template with id="+setRowTemplateId);
+        }
+
+} // createSetRowfromTemplate()
+
+function createSubsetRowFromTemplate(container,subsetId,subsetName) {
+
+        /* from HTML template in DOM named id='subsetRowTpl'
+         * creates code of subset row for parametres subsetId, subsetName
+ 	 * and place it on the end of container element                       
+	 */
+        const subsetRowTemplateId = "subsetRowTpl";
+        let subsetRow = null;
+        const template = document.querySelector("#"+subsetRowTemplateId);
+        if(template) {
+                subsetRow = template.content.cloneNode(true);
+                if(subsetRow){
+			subsetRow.querySelector("input").setAttribute("name","subsetId-"+subsetId);
+                        subsetRow.querySelector("tr").setAttribute("subsetid",subsetId);
+                        subsetRow.querySelector(".layerName").innerText = subsetName;
+                        if(container) {
+                                container.append(subsetRow);
+                        }
+                } else {
+                        console.log("Cannot clone DOM element for template with id="+subsetRowTemplateId);
+                }
+        } else {
+                console.log("Cannot create DOM element from template with id="+subsetRowTemplateId);
+        }
+
+} // createSubsetRowfromTemplate()
+ 
+function createTypeRowFromTemplate(container,typeId,typeName) {
+
+        /* from HTML template in DOM named id='typeRowTpl'
+         * creates code of type row for parametres typeId, typeName
+         * and place it on the end of container element                      
+         */
+        const typeRowTemplateId = "typeRowTpl";
+        let typeRow = null;
+        const template = document.querySelector("#"+typeRowTemplateId);
+        if(template) {
+                typeRow = template.content.cloneNode(true);
+                if(typeRow){
+			typeRow.querySelector("input").setAttribute("name","typeId-"+typeId);
+                        typeRow.querySelector("tr").setAttribute("typeid",typeId);
+                        typeRow.querySelector(".layerName").innerText = typeName;
+                        if(container) {
+                                container.append(typeRow);
+                        }
+                } else {
+                        console.log("Cannot clone DOM element for template with id="+typeRowTemplateId);
+                }
+        } else {
+                console.log("Cannot create DOM element from template with id="+typeRowTemplateId);
+        }
+
+} // createTypeRowFromTemplate()
+ 
+/**
+ *  loads rows with sets, subsets & types of annotations from templates
+ *  and pure JSON data from ajax request
+ */
+function loadAnnotationTypesFromTemplates() {
+
+	// loading all data from ajax service
+	const serviceName = "annotation_type_tree";
+	const getTypesSuccess = function(data) {
+
+		// create rows for sets, subsets and types
+		if(!data){ return; }
+		if(data.length==0){ return; }
+		// element, which holds all rows
+		const container = $(".annotationTypesTree");
+		// remove default content for empty set
+		$(container).find("tr").remove();
+		// array of setId => set_array, 
+		$.each(data,function(setId,setArray){
+			const setName = setArray.name;
+			createSetRowFromTemplate(container,setId,setName); 
+			$.each(setArray,function(subsetId,subsetArray){
+				if(subsetId!='name'){
+					const subsetName = subsetArray.name;
+					createSubsetRowFromTemplate(container,subsetId,subsetName);
+					$.each(subsetArray,function(typeId,typeName){
+						if(typeId!='name'){
+							createTypeRowFromTemplate(container,typeId,typeName);
+						}; // typeId<>'name'	
+					}); // each subsetArray
+				}; // subsetId <> 'name'
+			}); // each setArray
+		}); // each data
+
+	};
+        const getTypesError = function() {
+                console.log("Error on ajax request for "+serviceName);
+        };
+        doAjaxSync( serviceName ,
+		{ 'corpusId' : corpus_id },
+                getTypesSuccess,
+                getTypesError,
+                null  // getTypesComplete
+        );
+ 	
+} // loadAnnotationTypesFromTemplates()
+
 /**
  * Przypisanie akcji po wczytaniu się strony.
  */
 $(document).ready(function(){
+    loadAnnotationTypesFromTemplates();
     wRelationSets = new WidgetRelationSetSelector("#relation-sets", corpus_id);
     wRelationSets.load();
 
@@ -228,4 +357,4 @@ function saveViewConfiguration(){
     } else{
         $.cookie(report_id + '_preview_user', null);
     }
-}
\ No newline at end of file
+}

From 4da86e70b86d830d64d7ccedc10489017694874f Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Tue, 7 Dec 2021 14:30:52 +0100
Subject: [PATCH 060/154] limit count of types displayed in preview tree of
 types

---
 engine/config/Config.php                      |  2 +
 engine/include/database/CDbAnnotation.php     | 62 ++++++++++++++-----
 .../PerspectivePreview.php                    |  3 +-
 engine/settings.php                           |  7 ++-
 .../inc_widget_annotation_type_tree.tpl       |  4 +-
 5 files changed, 60 insertions(+), 18 deletions(-)

diff --git a/engine/config/Config.php b/engine/config/Config.php
index 8d4cfeeb..60c44312 100644
--- a/engine/config/Config.php
+++ b/engine/config/Config.php
@@ -81,6 +81,8 @@ class Config extends Singleton\Singleton
     static private $log_output = "fb";
     static private $path_grabber = null;
 
+    static private $max_types_limit_threshold = MAX_TYPES_LIMIT_THRESHOLD;
+
     // path for local config file - if exists
     static private $localConfigFilename = "";
 
diff --git a/engine/include/database/CDbAnnotation.php b/engine/include/database/CDbAnnotation.php
index 2789ed2f..28fd23b1 100755
--- a/engine/include/database/CDbAnnotation.php
+++ b/engine/include/database/CDbAnnotation.php
@@ -711,7 +711,51 @@ static function getAnnotationTags($corpus_id, $annotation_type, $session){
 		return  $db->fetch_rows($sql, $params);
 	}
 
-	static function getAnnotationStructureByCorpora($corpus_id){
+    static private function annotationStructureFromDBToArrayTree($dbResult,$limited = false) {
+
+        if($limited){
+            // key for this array is [set_id,subset_id]
+            $typesCountForSetSubset = array();
+            $maxTypesLimitThreshold = Config::Config()->get_max_types_limit_threshold();
+        }
+
+        $annotation_sets = array();
+        foreach($dbResult as $at){
+            $set_id = $at['set_id'];
+            $subset_id = $at['subset_id'];
+            if (!isset($annotation_sets[$set_id])){
+                $annotation_sets[$set_id] = array('name' => $at['set_name']);
+            }
+            if (!isset($annotation_sets[$set_id][$subset_id])){
+                $annotation_sets[$set_id][$subset_id] = array('name' => $at['subset_name']);
+            }
+
+            if($limited){
+                // counts types for set,subset
+                $typesCountForSetSubset[$set_id][$subset_id] = 1 +
+                    ( isset($typesCountForSetSubset[$set_id][$subset_id])
+                        ? $typesCountForSetSubset[$set_id][$subset_id] : 0 );
+                // test threshold
+                if($typesCountForSetSubset[$set_id][$subset_id]
+                    == $maxTypesLimitThreshold ) {
+                    $annotation_sets[$set_id][$subset_id][MAX_TYPES_LABEL_INDEX] = MAX_TYPES_NAME_LABEL;
+                }
+                if($typesCountForSetSubset[$set_id][$subset_id]
+                    < $maxTypesLimitThreshold ) {
+                    $annotation_sets[$set_id][$subset_id][$at['type_id']] = $at['type_name'];
+                }
+            } else {
+                // old method generating very big html structure
+                $annotation_sets[$set_id][$subset_id][$at['type_id']] = $at['type_name'];
+            } // if !limited
+
+        } // foreach()
+
+        return $annotation_sets;
+
+    } // annotationStructureFromDBToArrayTree
+
+	static function getAnnotationStructureByCorpora($corpus_id,$limited = false){
 		global $db;
 
 		$sql = "SELECT ans.annotation_set_id AS set_id, ans.name AS set_name, ansub.annotation_subset_id AS subset_id, ".
@@ -723,21 +767,9 @@ static function getAnnotationStructureByCorpora($corpus_id){
 
 		$annotation_types = $db->fetch_rows($sql,array($corpus_id));
 
-		$annotation_sets = array();
-		foreach($annotation_types as $at){
-			$set_id = $at['set_id'];
-			$subset_id = $at['subset_id'];
-			if (!isset($annotation_sets[$set_id])){
-				$annotation_sets[$set_id] = array('name' => $at['set_name']);
-			}
-			if (!isset($annotation_sets[$set_id][$subset_id])){
-				$annotation_sets[$set_id][$subset_id] = array('name' => $at['subset_name']);
-			}
+		return self::annotationStructureFromDBToArrayTree($annotation_types,$limited);
 
-			$annotation_sets[$set_id][$subset_id][$at['type_id']] = $at['type_name'];
-		}
-		return $annotation_sets;
-	}
+	} // getAnnotationStructureByCorpora()
 
     /*
      *  for one integer $corpus_id returns list of all annotation sets
diff --git a/engine/page/report_perspectives/PerspectivePreview.php b/engine/page/report_perspectives/PerspectivePreview.php
index 02027b94..7b599d1e 100644
--- a/engine/page/report_perspectives/PerspectivePreview.php
+++ b/engine/page/report_perspectives/PerspectivePreview.php
@@ -71,7 +71,8 @@ function execute()
         $this->page->set("stage_relations", $stage_relations);
         $this->page->set("stages_annotations", $stages_annotations);
         $this->page->set("stages_relations", $stages_relations);
-        $this->page->set('annotation_types', DbAnnotation::getAnnotationStructureByCorpora($corpusId));
+        $this->page->set('annotation_types', DbAnnotation::getAnnotationStructureByCorpora($corpusId,True));
+        $this->page->set('annotation_types_threshold_name',MAX_TYPES_NAME_LABEL); 
         $this->page->set('relation_sets', DbRelationSet::getRelationSetsAssignedToCorpus($corpusId));
         $this->page->set("annotations", $annotations);
         $this->page->set("relations", $relations);
diff --git a/engine/settings.php b/engine/settings.php
index b4e8608c..0c846316 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -16,5 +16,10 @@
 ini_set("short_open_tag",1);
 setlocale(LC_CTYPE, "en_US.UTF-8");		
 
- 
+// threshold of count types for one set/subset combination
+define('MAX_TYPES_LIMIT_THRESHOLD',300);
+define('MAX_TYPES_LABEL_INDEX',999999999999); // over autoincrement id
+define('MAX_TYPES_NAME_LABEL','...');
+  
+
 ?>
diff --git a/engine/templates/inc_widget_annotation_type_tree.tpl b/engine/templates/inc_widget_annotation_type_tree.tpl
index 04aceb14..cd38a4a9 100644
--- a/engine/templates/inc_widget_annotation_type_tree.tpl
+++ b/engine/templates/inc_widget_annotation_type_tree.tpl
@@ -48,7 +48,9 @@
 							<span class="layerName" style="margin-left:20px;clear:both;font-weight:normal;">{$type}</span>
 						</td>
 				    	<td style="vertical-align: middle;text-align:center">
+						{if $type != $annotation_types_threshold_name}
 				    		<input name="typeId-{$tk}" type="checkbox" class="leftLayer type_cb" /> 
+						{/if}
 				    	</td>
 					</tr>
 						{/if}
@@ -64,4 +66,4 @@
 		    </tbody>		
     	</table>	
     	</div>    
-	</div>	
\ No newline at end of file
+	</div>	

From 6bdbfb0b9d6e0b00c59989a6676f4fb2cee0e7fb Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Sat, 11 Dec 2021 19:00:21 +0100
Subject: [PATCH 061/154] too many </div> in footer of page

---
 engine/include/CInforexWeb.php  | 3 ++-
 engine/templates/inc_footer.tpl | 5 ++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/engine/include/CInforexWeb.php b/engine/include/CInforexWeb.php
index ac3b55e8..77797e16 100644
--- a/engine/include/CInforexWeb.php
+++ b/engine/include/CInforexWeb.php
@@ -294,7 +294,8 @@ function getRevisionKey()
             $commitHash = $output[0];
             $revKey = substr($commitHash, 0, 8);
         } else {
-            $revKey = "no git revision available";
+            // no git revision available
+            $revKey = "no_git_rev";
         }
         return $revKey;
     }
diff --git a/engine/templates/inc_footer.tpl b/engine/templates/inc_footer.tpl
index ee4f5273..b63ea83c 100644
--- a/engine/templates/inc_footer.tpl
+++ b/engine/templates/inc_footer.tpl
@@ -7,7 +7,7 @@
  
 {* Zamknięcie szablonu strony. Szablon rozpoczynający: inc_header *}
 
-		</div>
+		</div> <!-- id="page_content" -->
 		{if $Config.federationLoginUrl}
 		{*inclusion of clarin bar*}
 				<script src="https://ctj.clarin-pl.eu/clarin_bar/script.js"></script>
@@ -46,8 +46,7 @@
 				<div style="text-align: left; background: red; color: white; padding: 3px;"><b>Warning:</b> SQL logging is ON. To disable it set <em style="color: yellow">Config::Config()->put_log_sql(false);</em> in <em style="color: yellow">config.local.php</em>.</div>
 			{/if}
 			</span>
-		</div>
-	</div>
+	</div> <!-- id="page" -->
 	
    </body>
 </html>

From aa005990e111703b6948cb80a5cd59cfe57c7244 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Fri, 17 Dec 2021 19:52:58 +0100
Subject: [PATCH 062/154] docker configuration tuning

---
 docker/www/Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/docker/www/Dockerfile b/docker/www/Dockerfile
index cb11d041..3a852d88 100644
--- a/docker/www/Dockerfile
+++ b/docker/www/Dockerfile
@@ -1,7 +1,8 @@
 FROM php:7.4-apache as php-base
 
 RUN apt-get update -y && apt-get upgrade -y
-RUN apt-get install software-properties-common wget -y
+RUN apt-get install apt-utils -y
+RUN apt-get install software-properties-common wget less -y
 RUN apt-get install vim p7zip-full libpng-dev -y
 
 # Workaround for write permission on write to MacOS X volumes

From 9f03b3da5e5a4605c131adebe72f06d8069d4090 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Sat, 18 Dec 2021 11:51:06 +0100
Subject: [PATCH 063/154] remove not opened /optgroup tags

---
 engine/templates/page_corpus_documents.tpl | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/engine/templates/page_corpus_documents.tpl b/engine/templates/page_corpus_documents.tpl
index 1dc160ad..4673994a 100644
--- a/engine/templates/page_corpus_documents.tpl
+++ b/engine/templates/page_corpus_documents.tpl
@@ -177,7 +177,6 @@
                                                         <option value="" selected="selected">-Flag-</option>
                                                         {foreach from=$corpus_flag_ids  item="set"}
                                                             <option value="{$set.corpora_flag_id}">{$set.name}</option>
-                                                            </optgroup>
                                                         {/foreach}
                                                     </select>
                                                 </div>
@@ -190,7 +189,6 @@
                                                         <option value="" selected="selected">-Status-</option>
                                                         {foreach from=$available_flags  item="set"}
                                                             <option value="{$set.flag_id}">{$set.name}</option>
-                                                            </optgroup>
                                                         {/foreach}
                                                     </select>
                                                 </div>
@@ -208,7 +206,6 @@
                                                         <option value="-1" selected="selected">-Subcorpus-</option>
                                                         {foreach from=$subcorpora  item="set"}
                                                             <option value="{$set.subcorpus_id}">{$set.name}</option>
-                                                            </optgroup>
                                                         {/foreach}
                                                     </select>
                                                 </div>

From 777026136829004b3ba101d57484204e4f7783c0 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Mon, 20 Dec 2021 19:59:54 +0100
Subject: [PATCH 064/154] throwing out internal Smarty variables, not supported
 in 3+ versions

---
 engine/include/CPage.php | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/engine/include/CPage.php b/engine/include/CPage.php
index 646ed01d..3f5c9148 100644
--- a/engine/include/CPage.php
+++ b/engine/include/CPage.php
@@ -219,12 +219,13 @@ function set_by_ref($name, &$object){
 	 * Get an variable value assign to the page.
 	 * @param $name -- a variable name
      * @return variable value or null if the variable is undefined
+     *          or array of all template variables if $name=null
 	 */
 	function get($name){
-		if (isset($this->template->_tpl_vars[$name])) {
-            return $this->template->_tpl_vars[$name];
-        } else {
-            return null;
+        if(method_exists($this->template,"getTemplateVars" )) { // Smarty version 3+
+            return $this->template->getTemplateVars($name);
+        } else { // Smarty version below 3
+            return $this->template->get_template_vars($name);
         }
 	}
 		

From 3b2cae649a6f8690ce5c64f571254757b928fca1 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Fri, 31 Dec 2021 19:19:48 +0100
Subject: [PATCH 065/154] fatal errors should be logged as default

---
 docker/www/php.ini | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/docker/www/php.ini b/docker/www/php.ini
index 2a89579a..d1987673 100644
--- a/docker/www/php.ini
+++ b/docker/www/php.ini
@@ -1,4 +1,5 @@
 [PHP]
+log_errors = 1
 upload_max_filesize = 30M
 post_max_size = 30M
-memory_limit = 256M
+memory_limit = 2048M

From 13e81cc27ac005b8d06353d5f5798a6715bfa8a4 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Sat, 15 Jan 2022 11:46:48 +0100
Subject: [PATCH 066/154] raise http request header limit as in docker branch

---
 docker/www/Dockerfile | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/docker/www/Dockerfile b/docker/www/Dockerfile
index 3a852d88..83e74415 100644
--- a/docker/www/Dockerfile
+++ b/docker/www/Dockerfile
@@ -48,6 +48,9 @@ WORKDIR /var/www
 #Setting up virtual host
 RUN echo "  Alias /inforex $inforex_location/public_html\n  <Directory $inforex_location/public_html>\n    Require all granted\n  </Directory>\n" | tee /etc/apache2/sites-available/inforex.conf
 
+# Raise RequestFieldLimit for many annotation selected cookies
+RUN echo "\nLimitRequestFieldSize 16384" >> /etc/apache2/ports.conf
+
 #Set up symbolinc link
 WORKDIR /etc/apache2/sites-enabled/
 RUN ln -s ../sites-available/inforex.conf inforex.conf

From afaedfa1d92814f3abe544df635d5125cb70074f Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Wed, 9 Mar 2022 19:38:53 +0100
Subject: [PATCH 067/154] extract function dummyMessage4User

---
 engine/settings.php | 25 ++++++++++++++++++++++---
 1 file changed, 22 insertions(+), 3 deletions(-)

diff --git a/engine/settings.php b/engine/settings.php
index e6bb8cd8..5a5f945d 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -104,9 +104,7 @@ function inforexInitialExceptionHandler ($e) {
             echo $e;
         } else {
             // dummy message for user
-            echo "<h1>500 Internal Server Error</h1>
-            An internal server error has been occurred.<br>
-            Please try again later.";
+            dummyMessage4User();
         } // display_errors
     } // ! CLI
 
@@ -115,6 +113,21 @@ function inforexInitialExceptionHandler ($e) {
 
 } // inforexInitialExceptionHandler()
 
+function dummyMessage4User() {
+
+    // dummy message masks error details for user
+    // and writes general error information
+    $NL='';
+    if (php_sapi_name() !== "cli") {
+        $NL = '<br/>';
+    } 
+    $NL .= "\n";
+    print("<h1>500 Internal Server Error</h1>".$NL);
+    print("An internal server error has been occurred.".$NL);
+    print("Please try again later.".$NL);
+
+} // dummyMessage4User
+
 set_exception_handler("inforexInitialExceptionHandler");
 
 function inforexShutdownFunction() {
@@ -125,10 +138,16 @@ function inforexShutdownFunction() {
     // will be reported twice 
     $error = errorGetLast();
     if ($error !== null) {
+        /*
         $e = new ErrorException(
             $error["message"], 0, $error["type"], $error["file"], $error["line"]
         );
         inforexInitialExceptionHandler($e);
+        */
+        // dummy message if not errors displayed by system
+        if (!ini_get("display_errors")) {
+            dummyMessage4User();
+        }
     }
 
 } // inforexShutdownFunction()  

From 94c36b806906bd2cec09bb429ccfd987a6189300 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Thu, 10 Mar 2022 19:36:33 +0100
Subject: [PATCH 068/154] remove html tags from fatal error message on console

---
 engine/settings.php | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/engine/settings.php b/engine/settings.php
index 5a5f945d..f79572fd 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -118,11 +118,13 @@ function dummyMessage4User() {
     // dummy message masks error details for user
     // and writes general error information
     $NL='';
+    $H1Open=''; $H1Close='';
     if (php_sapi_name() !== "cli") {
         $NL = '<br/>';
-    } 
+        $H1Open='<h1>'; $H1Close='</h1>';
+    }
     $NL .= "\n";
-    print("<h1>500 Internal Server Error</h1>".$NL);
+    print($H1Open."500 Internal Server Error".$H1Close.$NL);
     print("An internal server error has been occurred.".$NL);
     print("Please try again later.".$NL);
 

From 424098da4f0623eb7853c7003e59ba9f84d2e15a Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Sat, 12 Mar 2022 12:57:05 +0100
Subject: [PATCH 069/154] remove apt-utils from docker config, cause
 interactive problems

---
 docker/www/Dockerfile | 1 -
 1 file changed, 1 deletion(-)

diff --git a/docker/www/Dockerfile b/docker/www/Dockerfile
index 83e74415..84842ec7 100644
--- a/docker/www/Dockerfile
+++ b/docker/www/Dockerfile
@@ -1,7 +1,6 @@
 FROM php:7.4-apache as php-base
 
 RUN apt-get update -y && apt-get upgrade -y
-RUN apt-get install apt-utils -y
 RUN apt-get install software-properties-common wget less -y
 RUN apt-get install vim p7zip-full libpng-dev -y
 

From d7332475884edfac5d10c43d8aae9624ad01ab57 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Wed, 16 Mar 2022 21:18:37 +0100
Subject: [PATCH 070/154] implementing changes from docker branch -
 docker_config_fix

---
 docker-compose.yml          |  2 +-
 docker/liquibase/Dockerfile |  4 ++--
 docker/liquibase/run.sh     | 15 ++++++++-------
 3 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/docker-compose.yml b/docker-compose.yml
index 5a4dfe45..08e711be 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -21,7 +21,7 @@ services:
        - "7080:80"
       depends_on:
        - db
-    liuqibase:
+    liquibase:
       build: ./docker/liquibase
       links:
       - db
diff --git a/docker/liquibase/Dockerfile b/docker/liquibase/Dockerfile
index d498566d..b72a2cca 100644
--- a/docker/liquibase/Dockerfile
+++ b/docker/liquibase/Dockerfile
@@ -3,7 +3,7 @@ FROM openjdk:8
 WORKDIR /workdir
 
 RUN apt-get install unzip -y
-RUN apt-get update && apt-get install -y netcat
+RUN apt-get update && apt-get install -y 
 
 RUN wget https://github.com/liquibase/liquibase/releases/download/liquibase-parent-3.5.5/liquibase-3.5.5-bin.tar.gz
 RUN tar -xvf liquibase-3.5.5-bin.tar.gz
@@ -13,4 +13,4 @@ RUN wget http://www.java2s.com/Code/JarDownload/mysql/mysql-connector-java-5.1.2
 RUN unzip mysql-connector-java-5.1.21.jar.zip
 
 COPY liquibase.properties /workdir
-COPY run.sh /workdir
\ No newline at end of file
+COPY run.sh /workdir
diff --git a/docker/liquibase/run.sh b/docker/liquibase/run.sh
index 25c859c5..54bb2cbb 100644
--- a/docker/liquibase/run.sh
+++ b/docker/liquibase/run.sh
@@ -1,10 +1,11 @@
 #!/bin/bash
 
-while [ "`nc -vz db 3306 2>&1 | grep open -o`" != "open" ]
-do
-    nc -vz db 3306 2>&1
-    echo "waiting for db .."
-    sleep 1
-done
+# Wait or database server is up
+# exit after one hour anyway
+export TIMEOUT=3600
+# DB server name and port
+export HOST="db"
+export PORT=3306
+timeout $TIMEOUT bash -c 'until printf "" 2>>/dev/null >>/dev/tcp/$0/$1; do echo "waiting for db .."; sleep 1; done' $HOST $PORT
 
-java -jar liquibase.jar --changeLogFile database/inforex-v1.0-changelog.sql update
\ No newline at end of file
+java -jar liquibase.jar --changeLogFile database/inforex-v1.0-changelog.sql update

From 3b1a37f4004d362a9a5ee68bc907a2121424f1f8 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Thu, 17 Mar 2022 19:04:33 +0100
Subject: [PATCH 071/154] FirePHP update to version supported by php7

---
 composer.json                                 |    1 +
 .../pear/FirePHPCore/FirePHP.class.php        | 1784 -----------------
 .../pear/FirePHPCore/FirePHP.class.php4       | 1332 ------------
 engine/external/pear/FirePHPCore/LICENSE      |   29 -
 engine/external/pear/FirePHPCore/fb.php       |  276 ---
 engine/external/pear/FirePHPCore/fb.php4      |  251 ---
 6 files changed, 1 insertion(+), 3672 deletions(-)
 delete mode 100644 engine/external/pear/FirePHPCore/FirePHP.class.php
 delete mode 100644 engine/external/pear/FirePHPCore/FirePHP.class.php4
 delete mode 100644 engine/external/pear/FirePHPCore/LICENSE
 delete mode 100644 engine/external/pear/FirePHPCore/fb.php
 delete mode 100644 engine/external/pear/FirePHPCore/fb.php4

diff --git a/composer.json b/composer.json
index fd3d722d..8e0de6fa 100644
--- a/composer.json
+++ b/composer.json
@@ -43,6 +43,7 @@
     "ext-json": "*"
   },
     "require-dev": {
+	"firephp/firephp-core": "^0.5.3",
         "phpunit/phpunit": "4.8.",
         "phpunit/dbunit": "1.4.*"
     }
diff --git a/engine/external/pear/FirePHPCore/FirePHP.class.php b/engine/external/pear/FirePHPCore/FirePHP.class.php
deleted file mode 100644
index 67ef84f4..00000000
--- a/engine/external/pear/FirePHPCore/FirePHP.class.php
+++ /dev/null
@@ -1,1784 +0,0 @@
-<?php
-/**
- * *** BEGIN LICENSE BLOCK *****
- *  
- * This file is part of FirePHP (http://www.firephp.org/).
- * 
- * Software License Agreement (New BSD License)
- * 
- * Copyright (c) 2006-2010, Christoph Dorn
- * All rights reserved.
- * 
- * Redistribution and use in source and binary forms, with or without modification,
- * are permitted provided that the following conditions are met:
- * 
- *     * Redistributions of source code must retain the above copyright notice,
- *       this list of conditions and the following disclaimer.
- * 
- *     * Redistributions in binary form must reproduce the above copyright notice,
- *       this list of conditions and the following disclaimer in the documentation
- *       and/or other materials provided with the distribution.
- * 
- *     * Neither the name of Christoph Dorn nor the names of its
- *       contributors may be used to endorse or promote products derived from this
- *       software without specific prior written permission.
- * 
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
- * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
- * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- * 
- * ***** END LICENSE BLOCK *****
- * 
- * @copyright       Copyright (C) 2007-2009 Christoph Dorn
- * @author          Christoph Dorn <christoph@christophdorn.com>
- * @license         http://www.opensource.org/licenses/bsd-license.php
- * @package         FirePHPCore
- */
-
-/**
- * @see http://code.google.com/p/firephp/issues/detail?id=112
- */
-if (!defined('E_STRICT')) {
-    define('E_STRICT', 2048);
-}
-if (!defined('E_RECOVERABLE_ERROR')) {
-    define('E_RECOVERABLE_ERROR', 4096);
-}
-if (!defined('E_DEPRECATED')) {
-    define('E_DEPRECATED', 8192);
-}
-if (!defined('E_USER_DEPRECATED')) {
-    define('E_USER_DEPRECATED', 16384);
-} 
- 
-/**
- * Sends the given data to the FirePHP Firefox Extension.
- * The data can be displayed in the Firebug Console or in the
- * "Server" request tab.
- * 
- * For more information see: http://www.firephp.org/
- * 
- * @copyright       Copyright (C) 2007-2009 Christoph Dorn
- * @author          Christoph Dorn <christoph@christophdorn.com>
- * @license         http://www.opensource.org/licenses/bsd-license.php
- * @package         FirePHPCore
- */
-class FirePHP {
-
-    /**
-     * FirePHP version
-     *
-     * @var string
-     */
-    const VERSION = '0.3';    // @pinf replace '0.3' with '%%package.version%%'
-
-    /**
-     * Firebug LOG level
-     *
-     * Logs a message to firebug console.
-     * 
-     * @var string
-     */
-    const LOG = 'LOG';
-  
-    /**
-     * Firebug INFO level
-     *
-     * Logs a message to firebug console and displays an info icon before the message.
-     * 
-     * @var string
-     */
-    const INFO = 'INFO';
-    
-    /**
-     * Firebug WARN level
-     *
-     * Logs a message to firebug console, displays an warning icon before the message and colors the line turquoise.
-     * 
-     * @var string
-     */
-    const WARN = 'WARN';
-    
-    /**
-     * Firebug ERROR level
-     *
-     * Logs a message to firebug console, displays an error icon before the message and colors the line yellow. Also increments the firebug error count.
-     * 
-     * @var string
-     */
-    const ERROR = 'ERROR';
-    
-    /**
-     * Dumps a variable to firebug's server panel
-     *
-     * @var string
-     */
-    const DUMP = 'DUMP';
-    
-    /**
-     * Displays a stack trace in firebug console
-     *
-     * @var string
-     */
-    const TRACE = 'TRACE';
-    
-    /**
-     * Displays an exception in firebug console
-     * 
-     * Increments the firebug error count.
-     *
-     * @var string
-     */
-    const EXCEPTION = 'EXCEPTION';
-    
-    /**
-     * Displays an table in firebug console
-     *
-     * @var string
-     */
-    const TABLE = 'TABLE';
-    
-    /**
-     * Starts a group in firebug console
-     * 
-     * @var string
-     */
-    const GROUP_START = 'GROUP_START';
-    
-    /**
-     * Ends a group in firebug console
-     * 
-     * @var string
-     */
-    const GROUP_END = 'GROUP_END';
-    
-    /**
-     * Singleton instance of FirePHP
-     *
-     * @var FirePHP
-     */
-    protected static $instance = null;
-    
-    /**
-     * Flag whether we are logging from within the exception handler
-     * 
-     * @var boolean
-     */
-    protected $inExceptionHandler = false;
-    
-    /**
-     * Flag whether to throw PHP errors that have been converted to ErrorExceptions
-     * 
-     * @var boolean
-     */
-    protected $throwErrorExceptions = true;
-    
-    /**
-     * Flag whether to convert PHP assertion errors to Exceptions
-     * 
-     * @var boolean
-     */
-    protected $convertAssertionErrorsToExceptions = true;
-    
-    /**
-     * Flag whether to throw PHP assertion errors that have been converted to Exceptions
-     * 
-     * @var boolean
-     */
-    protected $throwAssertionExceptions = false;
-
-    /**
-     * Wildfire protocol message index
-     *
-     * @var int
-     */
-    protected $messageIndex = 1;
-    
-    /**
-     * Options for the library
-     * 
-     * @var array
-     */
-    protected $options = array('maxDepth' => 10,
-                               'maxObjectDepth' => 5,
-                               'maxArrayDepth' => 5,
-                               'useNativeJsonEncode' => true,
-                               'includeLineNumbers' => true);
-
-    /**
-     * Filters used to exclude object members when encoding
-     * 
-     * @var array
-     */
-    protected $objectFilters = array(
-        'firephp' => array('objectStack', 'instance', 'json_objectStack'),
-        'firephp_test_class' => array('objectStack', 'instance', 'json_objectStack')
-    );
-
-    /**
-     * A stack of objects used to detect recursion during object encoding
-     * 
-     * @var object
-     */
-    protected $objectStack = array();
-
-    /**
-     * Flag to enable/disable logging
-     * 
-     * @var boolean
-     */
-    protected $enabled = true;
-
-    /**
-     * The insight console to log to if applicable
-     * 
-     * @var object
-     */
-    protected $logToInsightConsole = null;
-
-    /**
-     * When the object gets serialized only include specific object members.
-     * 
-     * @return array
-     */  
-    public function __sleep()
-    {
-        return array('options','objectFilters','enabled');
-    }
-    
-    /**
-     * Gets singleton instance of FirePHP
-     *
-     * @param boolean $AutoCreate
-     * @return FirePHP
-     */
-    public static function getInstance($AutoCreate = false)
-    {
-        if ($AutoCreate===true && !self::$instance) {
-            self::init();
-        }
-        return self::$instance;
-    }
-    
-    /**
-     * Creates FirePHP object and stores it for singleton access
-     *
-     * @return FirePHP
-     */
-    public static function init()
-    {
-        return self::setInstance(new self());
-    }
-
-    /**
-     * Set the instance of the FirePHP singleton
-     * 
-     * @param FirePHP $instance The FirePHP object instance
-     * @return FirePHP
-     */
-    public static function setInstance($instance)
-    {
-        return self::$instance = $instance;
-    }
-
-    /**
-     * Set an Insight console to direct all logging calls to
-     * 
-     * @param object $console The console object to log to
-     * @return void
-     */
-    public function setLogToInsightConsole($console)
-    {
-        if(is_string($console)) {
-            if(get_class($this)!='FirePHP_Insight' && !is_subclass_of($this, 'FirePHP_Insight')) {
-                throw new Exception('FirePHP instance not an instance or subclass of FirePHP_Insight!');
-            }
-            $this->logToInsightConsole = $this->to('request')->console($console);
-        } else {
-            $this->logToInsightConsole = $console;
-        }
-    }
-
-    /**
-     * Enable and disable logging to Firebug
-     * 
-     * @param boolean $Enabled TRUE to enable, FALSE to disable
-     * @return void
-     */
-    public function setEnabled($Enabled)
-    {
-       $this->enabled = $Enabled;
-    }
-    
-    /**
-     * Check if logging is enabled
-     * 
-     * @return boolean TRUE if enabled
-     */
-    public function getEnabled()
-    {
-        return $this->enabled;
-    }
-    
-    /**
-     * Specify a filter to be used when encoding an object
-     * 
-     * Filters are used to exclude object members.
-     * 
-     * @param string $Class The class name of the object
-     * @param array $Filter An array of members to exclude
-     * @return void
-     */
-    public function setObjectFilter($Class, $Filter)
-    {
-        $this->objectFilters[strtolower($Class)] = $Filter;
-    }
-  
-    /**
-     * Set some options for the library
-     * 
-     * Options:
-     *  - maxDepth: The maximum depth to traverse (default: 10)
-     *  - maxObjectDepth: The maximum depth to traverse objects (default: 5)
-     *  - maxArrayDepth: The maximum depth to traverse arrays (default: 5)
-     *  - useNativeJsonEncode: If true will use json_encode() (default: true)
-     *  - includeLineNumbers: If true will include line numbers and filenames (default: true)
-     * 
-     * @param array $Options The options to be set
-     * @return void
-     */
-    public function setOptions($Options)
-    {
-        $this->options = array_merge($this->options,$Options);
-    }
-
-    /**
-     * Get options from the library
-     *
-     * @return array The currently set options
-     */
-    public function getOptions()
-    {
-        return $this->options;
-    }
-
-    /**
-     * Set an option for the library
-     * 
-     * @param string $Name
-     * @param mixed $Value
-     * @throws Exception
-     * @return void
-     */  
-    public function setOption($Name, $Value)
-    {
-        if (!isset($this->options[$Name])) {
-            throw $this->newException('Unknown option: ' . $Name);
-        }
-        $this->options[$Name] = $Value;
-    }
-
-    /**
-     * Get an option from the library
-     *
-     * @param string $Name
-     * @throws Exception
-     * @return mixed
-     */
-    public function getOption($Name)
-    {
-        if (!isset($this->options[$Name])) {
-            throw $this->newException('Unknown option: ' . $Name);
-        }
-        return $this->options[$Name];
-    }
-
-    /**
-     * Register FirePHP as your error handler
-     * 
-     * Will throw exceptions for each php error.
-     * 
-     * @return mixed Returns a string containing the previously defined error handler (if any)
-     */
-    public function registerErrorHandler($throwErrorExceptions = false)
-    {
-        //NOTE: The following errors will not be caught by this error handler:
-        //      E_ERROR, E_PARSE, E_CORE_ERROR,
-        //      E_CORE_WARNING, E_COMPILE_ERROR,
-        //      E_COMPILE_WARNING, E_STRICT
-    
-        $this->throwErrorExceptions = $throwErrorExceptions;
-    
-        return set_error_handler(array($this,'errorHandler'));     
-    }
-
-    /**
-     * FirePHP's error handler
-     * 
-     * Throws exception for each php error that will occur.
-     *
-     * @param int $errno
-     * @param string $errstr
-     * @param string $errfile
-     * @param int $errline
-     * @param array $errcontext
-     */
-    public function errorHandler($errno, $errstr, $errfile, $errline, $errcontext)
-    {
-        // Don't throw exception if error reporting is switched off
-        if (error_reporting() == 0) {
-            return;
-        }
-        // Only throw exceptions for errors we are asking for
-        if (error_reporting() & $errno) {
-
-            $exception = new ErrorException($errstr, 0, $errno, $errfile, $errline);
-            if ($this->throwErrorExceptions) {
-                throw $exception;
-            } else {
-                $this->fb($exception);
-            }
-        }
-    }
-  
-    /**
-     * Register FirePHP as your exception handler
-     * 
-     * @return mixed Returns the name of the previously defined exception handler,
-     *               or NULL on error.
-     *               If no previous handler was defined, NULL is also returned.
-     */
-    public function registerExceptionHandler()
-    {
-        return set_exception_handler(array($this,'exceptionHandler'));     
-    }
-  
-    /**
-     * FirePHP's exception handler
-     * 
-     * Logs all exceptions to your firebug console and then stops the script.
-     *
-     * @param Exception $Exception
-     * @throws Exception
-     */
-    function exceptionHandler($Exception)
-    {
-    
-        $this->inExceptionHandler = true;
-    
-        header('HTTP/1.1 500 Internal Server Error');
-    
-        try {
-            $this->fb($Exception);
-        } catch (Exception $e) {
-            echo 'We had an exception: ' . $e;
-        }
-        $this->inExceptionHandler = false;
-    }
-  
-    /**
-     * Register FirePHP driver as your assert callback
-     * 
-     * @param boolean $convertAssertionErrorsToExceptions
-     * @param boolean $throwAssertionExceptions
-     * @return mixed Returns the original setting or FALSE on errors
-     */
-    public function registerAssertionHandler($convertAssertionErrorsToExceptions = true, $throwAssertionExceptions = false)
-    {
-        $this->convertAssertionErrorsToExceptions = $convertAssertionErrorsToExceptions;
-        $this->throwAssertionExceptions = $throwAssertionExceptions;
-        
-        if ($throwAssertionExceptions && !$convertAssertionErrorsToExceptions) {
-            throw $this->newException('Cannot throw assertion exceptions as assertion errors are not being converted to exceptions!');
-        }
-        
-        return assert_options(ASSERT_CALLBACK, array($this, 'assertionHandler'));
-    }
-  
-    /**
-     * FirePHP's assertion handler
-     *
-     * Logs all assertions to your firebug console and then stops the script.
-     *
-     * @param string $file File source of assertion
-     * @param int    $line Line source of assertion
-     * @param mixed  $code Assertion code
-     */
-    public function assertionHandler($file, $line, $code)
-    {
-        if ($this->convertAssertionErrorsToExceptions) {
-          
-          $exception = new ErrorException('Assertion Failed - Code[ '.$code.' ]', 0, null, $file, $line);
-    
-          if ($this->throwAssertionExceptions) {
-              throw $exception;
-          } else {
-              $this->fb($exception);
-          }
-        
-        } else {
-            $this->fb($code, 'Assertion Failed', FirePHP::ERROR, array('File'=>$file,'Line'=>$line));
-        }
-    }
-  
-    /**
-     * Start a group for following messages.
-     * 
-     * Options:
-     *   Collapsed: [true|false]
-     *   Color:     [#RRGGBB|ColorName]
-     *
-     * @param string $Name
-     * @param array $Options OPTIONAL Instructions on how to log the group
-     * @return true
-     * @throws Exception
-     */
-    public function group($Name, $Options = null)
-    {
-    
-        if (!$Name) {
-            throw $this->newException('You must specify a label for the group!');
-        }
-        
-        if ($Options) {
-            if (!is_array($Options)) {
-                throw $this->newException('Options must be defined as an array!');
-            }
-            if (array_key_exists('Collapsed', $Options)) {
-                $Options['Collapsed'] = ($Options['Collapsed'])?'true':'false';
-            }
-        }
-        
-        return $this->fb(null, $Name, FirePHP::GROUP_START, $Options);
-    }
-  
-    /**
-     * Ends a group you have started before
-     *
-     * @return true
-     * @throws Exception
-     */
-    public function groupEnd()
-    {
-        return $this->fb(null, null, FirePHP::GROUP_END);
-    }
-
-    /**
-     * Log object with label to firebug console
-     *
-     * @see FirePHP::LOG
-     * @param mixes $Object
-     * @param string $Label
-     * @return true
-     * @throws Exception
-     */
-    public function log($Object, $Label = null, $Options = array())
-    {
-        return $this->fb($Object, $Label, FirePHP::LOG, $Options);
-    } 
-
-    /**
-     * Log object with label to firebug console
-     *
-     * @see FirePHP::INFO
-     * @param mixes $Object
-     * @param string $Label
-     * @return true
-     * @throws Exception
-     */
-    public function info($Object, $Label = null, $Options = array())
-    {
-        return $this->fb($Object, $Label, FirePHP::INFO, $Options);
-    } 
-
-    /**
-     * Log object with label to firebug console
-     *
-     * @see FirePHP::WARN
-     * @param mixes $Object
-     * @param string $Label
-     * @return true
-     * @throws Exception
-     */
-    public function warn($Object, $Label = null, $Options = array())
-    {
-        return $this->fb($Object, $Label, FirePHP::WARN, $Options);
-    } 
-
-    /**
-     * Log object with label to firebug console
-     *
-     * @see FirePHP::ERROR
-     * @param mixes $Object
-     * @param string $Label
-     * @return true
-     * @throws Exception
-     */
-    public function error($Object, $Label = null, $Options = array())
-    {
-        return $this->fb($Object, $Label, FirePHP::ERROR, $Options);
-    } 
-
-    /**
-     * Dumps key and variable to firebug server panel
-     *
-     * @see FirePHP::DUMP
-     * @param string $Key
-     * @param mixed $Variable
-     * @return true
-     * @throws Exception
-     */
-    public function dump($Key, $Variable, $Options = array())
-    {
-        if (!is_string($Key)) {
-            throw $this->newException('Key passed to dump() is not a string');
-        }
-        if (strlen($Key)>100) {
-            throw $this->newException('Key passed to dump() is longer than 100 characters');
-        }
-        if (!preg_match_all('/^[a-zA-Z0-9-_\.:]*$/', $Key, $m)) {
-            throw $this->newException('Key passed to dump() contains invalid characters [a-zA-Z0-9-_\.:]');
-        }
-        return $this->fb($Variable, $Key, FirePHP::DUMP, $Options);
-    }
-  
-    /**
-     * Log a trace in the firebug console
-     *
-     * @see FirePHP::TRACE
-     * @param string $Label
-     * @return true
-     * @throws Exception
-     */
-    public function trace($Label)
-    {
-        return $this->fb($Label, FirePHP::TRACE);
-    } 
-
-    /**
-     * Log a table in the firebug console
-     *
-     * @see FirePHP::TABLE
-     * @param string $Label
-     * @param string $Table
-     * @return true
-     * @throws Exception
-     */
-    public function table($Label, $Table, $Options = array())
-    {
-        return $this->fb($Table, $Label, FirePHP::TABLE, $Options);
-    }
-
-    /**
-     * Insight API wrapper
-     * 
-     * @see Insight_Helper::to()
-     */
-    public static function to()
-    {
-        $instance = self::getInstance();
-        if (!method_exists($instance, "_to")) {
-            throw new Exception("FirePHP::to() implementation not loaded");
-        }
-        $args = func_get_args();
-        return call_user_func_array(array($instance, '_to'), $args);
-    }
-
-    /**
-     * Insight API wrapper
-     * 
-     * @see Insight_Helper::plugin()
-     */
-    public static function plugin()
-    {
-        $instance = self::getInstance();
-        if (!method_exists($instance, "_plugin")) {
-            throw new Exception("FirePHP::plugin() implementation not loaded");
-        }
-        $args = func_get_args();
-        return call_user_func_array(array($instance, '_plugin'), $args);
-    }
-
-    /**
-     * Check if FirePHP is installed on client
-     *
-     * @return boolean
-     */
-    public function detectClientExtension()
-    {
-        // Check if FirePHP is installed on client via User-Agent header
-        if (@preg_match_all('/\sFirePHP\/([\.\d]*)\s?/si',$this->getUserAgent(),$m) &&
-           version_compare($m[1][0],'0.0.6','>=')) {
-            return true;
-        } else
-        // Check if FirePHP is installed on client via X-FirePHP-Version header
-        if (@preg_match_all('/^([\.\d]*)$/si',$this->getRequestHeader("X-FirePHP-Version"),$m) &&
-           version_compare($m[1][0],'0.0.6','>=')) {
-            return true;
-        }
-        return false;
-    }
- 
-    /**
-     * Log varible to Firebug
-     * 
-     * @see http://www.firephp.org/Wiki/Reference/Fb
-     * @param mixed $Object The variable to be logged
-     * @return true Return TRUE if message was added to headers, FALSE otherwise
-     * @throws Exception
-     */
-    public function fb($Object)
-    {
-        if($this instanceof FirePHP_Insight && method_exists($this, '_logUpgradeClientMessage')) {
-            if(!FirePHP_Insight::$upgradeClientMessageLogged) {    // avoid infinite recursion as _logUpgradeClientMessage() logs a message
-                $this->_logUpgradeClientMessage();
-            }
-        }
-
-        static $insightGroupStack = array();
-
-        if (!$this->getEnabled()) {
-            return false;
-        }
-
-        if ($this->headersSent($filename, $linenum)) {
-            // If we are logging from within the exception handler we cannot throw another exception
-            if ($this->inExceptionHandler) {
-                // Simply echo the error out to the page
-                echo '<div style="border: 2px solid red; font-family: Arial; font-size: 12px; background-color: lightgray; padding: 5px;"><span style="color: red; font-weight: bold;">FirePHP ERROR:</span> Headers already sent in <b>'.$filename.'</b> on line <b>'.$linenum.'</b>. Cannot send log data to FirePHP. You must have Output Buffering enabled via ob_start() or output_buffering ini directive.</div>';
-            } else {
-                throw $this->newException('Headers already sent in '.$filename.' on line '.$linenum.'. Cannot send log data to FirePHP. You must have Output Buffering enabled via ob_start() or output_buffering ini directive.');
-            }
-        }
-      
-        $Type = null;
-        $Label = null;
-        $Options = array();
-      
-        if (func_num_args()==1) {
-        } else
-        if (func_num_args()==2) {
-            switch(func_get_arg(1)) {
-                case self::LOG:
-                case self::INFO:
-                case self::WARN:
-                case self::ERROR:
-                case self::DUMP:
-                case self::TRACE:
-                case self::EXCEPTION:
-                case self::TABLE:
-                case self::GROUP_START:
-                case self::GROUP_END:
-                    $Type = func_get_arg(1);
-                    break;
-                default:
-                    $Label = func_get_arg(1);
-                    break;
-            }
-        } else
-        if (func_num_args()==3) {
-            $Type = func_get_arg(2);
-            $Label = func_get_arg(1);
-        } else
-        if (func_num_args()==4) {
-            $Type = func_get_arg(2);
-            $Label = func_get_arg(1);
-            $Options = func_get_arg(3);
-        } else {
-            throw $this->newException('Wrong number of arguments to fb() function!');
-        }
-
-        if($this->logToInsightConsole!==null && (get_class($this)=='FirePHP_Insight' || is_subclass_of($this, 'FirePHP_Insight'))) {
-            $msg = $this->logToInsightConsole;
-            if ($Object instanceof Exception) {
-                $Type = self::EXCEPTION;
-            }
-            if($Label && $Type!=self::TABLE && $Type!=self::GROUP_START) {
-                $msg = $msg->label($Label);
-            }
-            switch($Type) {
-                case self::DUMP:
-                case self::LOG:
-                    return $msg->log($Object);
-                case self::INFO:
-                    return $msg->info($Object);
-                case self::WARN:
-                    return $msg->warn($Object);
-                case self::ERROR:
-                    return $msg->error($Object);
-                case self::TRACE:
-                    return $msg->trace($Object);
-                case self::EXCEPTION:
-                	return $this->plugin('engine')->handleException($Object, $msg);
-                case self::TABLE:
-                    if (isset($Object[0]) && !is_string($Object[0]) && $Label) {
-                        $Object = array($Label, $Object);
-                    }
-                    return $msg->table($Object[0], array_slice($Object[1],1), $Object[1][0]);
-                case self::GROUP_START:
-                	$insightGroupStack[] = $msg->group(md5($Label))->open();
-                    return $msg->log($Label);
-                case self::GROUP_END:
-                	if(count($insightGroupStack)==0) {
-                	    throw new Error('Too many groupEnd() as opposed to group() calls!');
-                	}
-                	$group = array_pop($insightGroupStack);
-                    return $group->close();
-	            default:
-                    return $msg->log($Object);
-            }
-        }
-
-        if (!$this->detectClientExtension()) {
-            return false;
-        }
-      
-        $meta = array();
-        $skipFinalObjectEncode = false;
-      
-        if ($Object instanceof Exception) {
-    
-            $meta['file'] = $this->_escapeTraceFile($Object->getFile());
-            $meta['line'] = $Object->getLine();
-          
-            $trace = $Object->getTrace();
-            if ($Object instanceof ErrorException
-               && isset($trace[0]['function'])
-               && $trace[0]['function']=='errorHandler'
-               && isset($trace[0]['class'])
-               && $trace[0]['class']=='FirePHP') {
-               
-                $severity = false;
-                switch($Object->getSeverity()) {
-                    case E_WARNING: $severity = 'E_WARNING'; break;
-                    case E_NOTICE: $severity = 'E_NOTICE'; break;
-                    case E_USER_ERROR: $severity = 'E_USER_ERROR'; break;
-                    case E_USER_WARNING: $severity = 'E_USER_WARNING'; break;
-                    case E_USER_NOTICE: $severity = 'E_USER_NOTICE'; break;
-                    case E_STRICT: $severity = 'E_STRICT'; break;
-                    case E_RECOVERABLE_ERROR: $severity = 'E_RECOVERABLE_ERROR'; break;
-                    case E_DEPRECATED: $severity = 'E_DEPRECATED'; break;
-                    case E_USER_DEPRECATED: $severity = 'E_USER_DEPRECATED'; break;
-                }
-                   
-                $Object = array('Class'=>get_class($Object),
-                                'Message'=>$severity.': '.$Object->getMessage(),
-                                'File'=>$this->_escapeTraceFile($Object->getFile()),
-                                'Line'=>$Object->getLine(),
-                                'Type'=>'trigger',
-                                'Trace'=>$this->_escapeTrace(array_splice($trace,2)));
-                $skipFinalObjectEncode = true;
-            } else {
-                $Object = array('Class'=>get_class($Object),
-                                'Message'=>$Object->getMessage(),
-                                'File'=>$this->_escapeTraceFile($Object->getFile()),
-                                'Line'=>$Object->getLine(),
-                                'Type'=>'throw',
-                                'Trace'=>$this->_escapeTrace($trace));
-                $skipFinalObjectEncode = true;
-            }
-            $Type = self::EXCEPTION;
-          
-        } else
-        if ($Type==self::TRACE) {
-          
-            $trace = debug_backtrace();
-            if (!$trace) return false;
-            for( $i=0 ; $i<sizeof($trace) ; $i++ ) {
-    
-                if (isset($trace[$i]['class'])
-                   && isset($trace[$i]['file'])
-                   && ($trace[$i]['class']=='FirePHP'
-                       || $trace[$i]['class']=='FB')
-                   && (substr($this->_standardizePath($trace[$i]['file']),-18,18)=='FirePHPCore/fb.php'
-                       || substr($this->_standardizePath($trace[$i]['file']),-29,29)=='FirePHPCore/FirePHP.class.php')) {
-                    /* Skip - FB::trace(), FB::send(), $firephp->trace(), $firephp->fb() */
-                } else
-                if (isset($trace[$i]['class'])
-                   && isset($trace[$i+1]['file'])
-                   && $trace[$i]['class']=='FirePHP'
-                   && substr($this->_standardizePath($trace[$i+1]['file']),-18,18)=='FirePHPCore/fb.php') {
-                    /* Skip fb() */
-                } else
-                if ($trace[$i]['function']=='fb'
-                   || $trace[$i]['function']=='trace'
-                   || $trace[$i]['function']=='send') {
-
-                    $Object = array('Class'=>isset($trace[$i]['class'])?$trace[$i]['class']:'',
-                                    'Type'=>isset($trace[$i]['type'])?$trace[$i]['type']:'',
-                                    'Function'=>isset($trace[$i]['function'])?$trace[$i]['function']:'',
-                                    'Message'=>$trace[$i]['args'][0],
-                                    'File'=>isset($trace[$i]['file'])?$this->_escapeTraceFile($trace[$i]['file']):'',
-                                    'Line'=>isset($trace[$i]['line'])?$trace[$i]['line']:'',
-                                    'Args'=>isset($trace[$i]['args'])?$this->encodeObject($trace[$i]['args']):'',
-                                    'Trace'=>$this->_escapeTrace(array_splice($trace,$i+1)));
-        
-                    $skipFinalObjectEncode = true;
-                    $meta['file'] = isset($trace[$i]['file'])?$this->_escapeTraceFile($trace[$i]['file']):'';
-                    $meta['line'] = isset($trace[$i]['line'])?$trace[$i]['line']:'';
-                    break;
-                }
-            }
-    
-        } else
-        if ($Type==self::TABLE) {
-          
-            if (isset($Object[0]) && is_string($Object[0])) {
-                $Object[1] = $this->encodeTable($Object[1]);
-            } else {
-                $Object = $this->encodeTable($Object);
-            }
-    
-            $skipFinalObjectEncode = true;
-          
-        } else
-        if ($Type==self::GROUP_START) {
-          
-            if (!$Label) {
-                throw $this->newException('You must specify a label for the group!');
-            }
-          
-        } else {
-            if ($Type===null) {
-                $Type = self::LOG;
-            }
-        }
-        
-        if ($this->options['includeLineNumbers']) {
-            if (!isset($meta['file']) || !isset($meta['line'])) {
-    
-                $trace = debug_backtrace();
-                for( $i=0 ; $trace && $i<sizeof($trace) ; $i++ ) {
-          
-                    if (isset($trace[$i]['class'])
-                       && isset($trace[$i]['file'])
-                       && ($trace[$i]['class']=='FirePHP'
-                           || $trace[$i]['class']=='FB')
-                       && (substr($this->_standardizePath($trace[$i]['file']),-18,18)=='FirePHPCore/fb.php'
-                           || substr($this->_standardizePath($trace[$i]['file']),-29,29)=='FirePHPCore/FirePHP.class.php')) {
-                        /* Skip - FB::trace(), FB::send(), $firephp->trace(), $firephp->fb() */
-                    } else
-                    if (isset($trace[$i]['class'])
-                       && isset($trace[$i+1]['file'])
-                       && $trace[$i]['class']=='FirePHP'
-                       && substr($this->_standardizePath($trace[$i+1]['file']),-18,18)=='FirePHPCore/fb.php') {
-                        /* Skip fb() */
-                    } else
-                    if (isset($trace[$i]['file'])
-                       && substr($this->_standardizePath($trace[$i]['file']),-18,18)=='FirePHPCore/fb.php') {
-                        /* Skip FB::fb() */
-                    } else {
-                        $meta['file'] = isset($trace[$i]['file'])?$this->_escapeTraceFile($trace[$i]['file']):'';
-                        $meta['line'] = isset($trace[$i]['line'])?$trace[$i]['line']:'';
-                        break;
-                    }
-                }      
-            }
-        } else {
-            unset($meta['file']);
-            unset($meta['line']);
-        }
-
-        $this->setHeader('X-Wf-Protocol-1','http://meta.wildfirehq.org/Protocol/JsonStream/0.2');
-        $this->setHeader('X-Wf-1-Plugin-1','http://meta.firephp.org/Wildfire/Plugin/FirePHP/Library-FirePHPCore/'.self::VERSION);
-     
-        $structure_index = 1;
-        if ($Type==self::DUMP) {
-            $structure_index = 2;
-            $this->setHeader('X-Wf-1-Structure-2','http://meta.firephp.org/Wildfire/Structure/FirePHP/Dump/0.1');
-        } else {
-            $this->setHeader('X-Wf-1-Structure-1','http://meta.firephp.org/Wildfire/Structure/FirePHP/FirebugConsole/0.1');
-        }
-      
-        if ($Type==self::DUMP) {
-            $msg = '{"'.$Label.'":'.$this->jsonEncode($Object, $skipFinalObjectEncode).'}';
-        } else {
-            $msg_meta = $Options;
-            $msg_meta['Type'] = $Type;
-            if ($Label!==null) {
-                $msg_meta['Label'] = $Label;
-            }
-            if (isset($meta['file']) && !isset($msg_meta['File'])) {
-                $msg_meta['File'] = $meta['file'];
-            }
-            if (isset($meta['line']) && !isset($msg_meta['Line'])) {
-                $msg_meta['Line'] = $meta['line'];
-            }
-            $msg = '['.$this->jsonEncode($msg_meta).','.$this->jsonEncode($Object, $skipFinalObjectEncode).']';
-        }
-        
-        $parts = explode("\n",chunk_split($msg, 5000, "\n"));
-    
-        for( $i=0 ; $i<count($parts) ; $i++) {
-            
-            $part = $parts[$i];
-            if ($part) {
-                
-                if (count($parts)>2) {
-                    // Message needs to be split into multiple parts
-                    $this->setHeader('X-Wf-1-'.$structure_index.'-'.'1-'.$this->messageIndex,
-                                     (($i==0)?strlen($msg):'')
-                                     . '|' . $part . '|'
-                                     . (($i<count($parts)-2)?'\\':''));
-                } else {
-                    $this->setHeader('X-Wf-1-'.$structure_index.'-'.'1-'.$this->messageIndex,
-                                     strlen($part) . '|' . $part . '|');
-                }
-                
-                $this->messageIndex++;
-                
-                if ($this->messageIndex > 99999) {
-                    throw $this->newException('Maximum number (99,999) of messages reached!');             
-                }
-            }
-        }
-    
-        $this->setHeader('X-Wf-1-Index',$this->messageIndex-1);
-    
-        return true;
-    }
-  
-    /**
-     * Standardizes path for windows systems.
-     *
-     * @param string $Path
-     * @return string
-     */
-    protected function _standardizePath($Path)
-    {
-        return preg_replace('/\\\\+/','/',$Path);    
-    }
-  
-    /**
-     * Escape trace path for windows systems
-     *
-     * @param array $Trace
-     * @return array
-     */
-    protected function _escapeTrace($Trace)
-    {
-        if (!$Trace) return $Trace;
-        for( $i=0 ; $i<sizeof($Trace) ; $i++ ) {
-            if (isset($Trace[$i]['file'])) {
-                $Trace[$i]['file'] = $this->_escapeTraceFile($Trace[$i]['file']);
-            }
-            if (isset($Trace[$i]['args'])) {
-                $Trace[$i]['args'] = $this->encodeObject($Trace[$i]['args']);
-            }
-        }
-        return $Trace;    
-    }
-  
-    /**
-     * Escape file information of trace for windows systems
-     *
-     * @param string $File
-     * @return string
-     */
-    protected function _escapeTraceFile($File)
-    {
-        /* Check if we have a windows filepath */
-        if (strpos($File,'\\')) {
-            /* First strip down to single \ */
-          
-            $file = preg_replace('/\\\\+/','\\',$File);
-          
-            return $file;
-        }
-        return $File;
-    }
-
-    /**
-     * Check if headers have already been sent
-     *
-     * @param string $Filename
-     * @param integer $Linenum
-     */
-    protected function headersSent(&$Filename, &$Linenum)
-    {
-        return headers_sent($Filename, $Linenum);
-    }
-
-    /**
-     * Send header
-     *
-     * @param string $Name
-     * @param string $Value
-     */
-    protected function setHeader($Name, $Value)
-    {
-        return header($Name.': '.$Value);
-    }
-
-    /**
-     * Get user agent
-     *
-     * @return string|false
-     */
-    protected function getUserAgent()
-    {
-        if (!isset($_SERVER['HTTP_USER_AGENT'])) return false;
-        return $_SERVER['HTTP_USER_AGENT'];
-    }
-
-    /**
-     * Get all request headers
-     * 
-     * @return array
-     */
-    public static function getAllRequestHeaders() {
-        static $_cached_headers = false;
-        if($_cached_headers!==false) {
-            return $_cached_headers;
-        }
-        $headers = array();
-        if(function_exists('getallheaders')) {
-            foreach( getallheaders() as $name => $value ) {
-                $headers[strtolower($name)] = $value;
-            }
-        } else {
-            foreach($_SERVER as $name => $value) {
-                if(substr($name, 0, 5) == 'HTTP_') {
-                    $headers[strtolower(str_replace(' ', '-', str_replace('_', ' ', substr($name, 5))))] = $value;
-                }
-            }
-        }
-        return $_cached_headers = $headers;
-    }
-
-    /**
-     * Get a request header
-     *
-     * @return string|false
-     */
-    protected function getRequestHeader($Name)
-    {
-        $headers = self::getAllRequestHeaders();
-        if (isset($headers[strtolower($Name)])) {
-            return $headers[strtolower($Name)];
-        }
-        return false;
-    }
-
-    /**
-     * Returns a new exception
-     *
-     * @param string $Message
-     * @return Exception
-     */
-    protected function newException($Message)
-    {
-        return new Exception($Message);
-    }
-  
-    /**
-     * Encode an object into a JSON string
-     * 
-     * Uses PHP's jeson_encode() if available
-     * 
-     * @param object $Object The object to be encoded
-     * @return string The JSON string
-     */
-    public function jsonEncode($Object, $skipObjectEncode = false)
-    {
-        if (!$skipObjectEncode) {
-            $Object = $this->encodeObject($Object);
-        }
-        
-        if (function_exists('json_encode')
-           && $this->options['useNativeJsonEncode']!=false) {
-    
-            return json_encode($Object);
-        } else {
-            return $this->json_encode($Object);
-        }
-    }
-
-    /**
-     * Encodes a table by encoding each row and column with encodeObject()
-     * 
-     * @param array $Table The table to be encoded
-     * @return array
-     */  
-    protected function encodeTable($Table)
-    {
-    
-        if (!$Table) return $Table;
-        
-        $new_table = array();
-        foreach($Table as $row) {
-      
-            if (is_array($row)) {
-                $new_row = array();
-            
-                foreach($row as $item) {
-                    $new_row[] = $this->encodeObject($item);
-                }
-            
-                $new_table[] = $new_row;
-            }
-        }
-        
-        return $new_table;
-    }
-
-    /**
-     * Encodes an object including members with
-     * protected and private visibility
-     * 
-     * @param Object $Object The object to be encoded
-     * @param int $Depth The current traversal depth
-     * @return array All members of the object
-     */
-    protected function encodeObject($Object, $ObjectDepth = 1, $ArrayDepth = 1, $MaxDepth = 1)
-    {
-        if ($MaxDepth > $this->options['maxDepth']) {
-            return '** Max Depth ('.$this->options['maxDepth'].') **';
-        }
-
-        $return = array();
-    
-        if (is_resource($Object)) {
-    
-            return '** '.(string)$Object.' **';
-    
-        } else    
-        if (is_object($Object)) {
-    
-            if ($ObjectDepth > $this->options['maxObjectDepth']) {
-                return '** Max Object Depth ('.$this->options['maxObjectDepth'].') **';
-            }
-            
-            foreach ($this->objectStack as $refVal) {
-                if ($refVal === $Object) {
-                    return '** Recursion ('.get_class($Object).') **';
-                }
-            }
-            array_push($this->objectStack, $Object);
-                    
-            $return['__className'] = $class = get_class($Object);
-            $class_lower = strtolower($class);
-    
-            $reflectionClass = new ReflectionClass($class);  
-            $properties = array();
-            foreach( $reflectionClass->getProperties() as $property) {
-                $properties[$property->getName()] = $property;
-            }
-                
-            $members = (array)$Object;
-    
-            foreach( $properties as $plain_name => $property ) {
-    
-                $name = $raw_name = $plain_name;
-                if ($property->isStatic()) {
-                    $name = 'static:'.$name;
-                }
-                if ($property->isPublic()) {
-                    $name = 'public:'.$name;
-                } else
-                if ($property->isPrivate()) {
-                    $name = 'private:'.$name;
-                    $raw_name = "\0".$class."\0".$raw_name;
-                } else
-                if ($property->isProtected()) {
-                    $name = 'protected:'.$name;
-                    $raw_name = "\0".'*'."\0".$raw_name;
-                }
-    
-                if (!(isset($this->objectFilters[$class_lower])
-                     && is_array($this->objectFilters[$class_lower])
-                     && in_array($plain_name,$this->objectFilters[$class_lower]))) {
-    
-                    if (array_key_exists($raw_name,$members)
-                       && !$property->isStatic()) {
-                  
-                        $return[$name] = $this->encodeObject($members[$raw_name], $ObjectDepth + 1, 1, $MaxDepth + 1);      
-                
-                    } else {
-                        if (method_exists($property,'setAccessible')) {
-                            $property->setAccessible(true);
-                            $return[$name] = $this->encodeObject($property->getValue($Object), $ObjectDepth + 1, 1, $MaxDepth + 1);
-                        } else
-                        if ($property->isPublic()) {
-                            $return[$name] = $this->encodeObject($property->getValue($Object), $ObjectDepth + 1, 1, $MaxDepth + 1);
-                        } else {
-                            $return[$name] = '** Need PHP 5.3 to get value **';
-                        }
-                    }
-                } else {
-                    $return[$name] = '** Excluded by Filter **';
-                }
-            }
-            
-            // Include all members that are not defined in the class
-            // but exist in the object
-            foreach( $members as $raw_name => $value ) {
-    
-                $name = $raw_name;
-              
-                if ($name{0} == "\0") {
-                    $parts = explode("\0", $name);
-                    $name = $parts[2];
-                }
-              
-                $plain_name = $name;
-    
-                if (!isset($properties[$name])) {
-                    $name = 'undeclared:'.$name;
-    
-                    if (!(isset($this->objectFilters[$class_lower])
-                         && is_array($this->objectFilters[$class_lower])
-                         && in_array($plain_name,$this->objectFilters[$class_lower]))) {
-    
-                        $return[$name] = $this->encodeObject($value, $ObjectDepth + 1, 1, $MaxDepth + 1);
-                    } else {
-                        $return[$name] = '** Excluded by Filter **';
-                    }
-                }
-            }
-            
-            array_pop($this->objectStack);
-            
-        } elseif (is_array($Object)) {
-    
-            if ($ArrayDepth > $this->options['maxArrayDepth']) {
-                return '** Max Array Depth ('.$this->options['maxArrayDepth'].') **';
-            }
-          
-            foreach ($Object as $key => $val) {
-              
-                // Encoding the $GLOBALS PHP array causes an infinite loop
-                // if the recursion is not reset here as it contains
-                // a reference to itself. This is the only way I have come up
-                // with to stop infinite recursion in this case.
-                if ($key=='GLOBALS'
-                   && is_array($val)
-                   && array_key_exists('GLOBALS',$val)) {
-                    $val['GLOBALS'] = '** Recursion (GLOBALS) **';
-                }
-              
-                $return[$key] = $this->encodeObject($val, 1, $ArrayDepth + 1, $MaxDepth + 1);
-            }
-        } else {
-            if (self::is_utf8($Object)) {
-                return $Object;
-            } else {
-                return utf8_encode($Object);
-            }
-        }
-        return $return;
-    }
-
-    /**
-     * Returns true if $string is valid UTF-8 and false otherwise.
-     *
-     * @param mixed $str String to be tested
-     * @return boolean
-     */
-    protected static function is_utf8($str)
-    {
-        if(function_exists('mb_detect_encoding')) {
-            return (mb_detect_encoding($str) == 'UTF-8');
-        }
-        $c=0; $b=0;
-        $bits=0;
-        $len=strlen($str);
-        for($i=0; $i<$len; $i++){
-            $c=ord($str[$i]);
-            if ($c > 128){
-                if (($c >= 254)) return false;
-                elseif ($c >= 252) $bits=6;
-                elseif ($c >= 248) $bits=5;
-                elseif ($c >= 240) $bits=4;
-                elseif ($c >= 224) $bits=3;
-                elseif ($c >= 192) $bits=2;
-                else return false;
-                if (($i+$bits) > $len) return false;
-                while($bits > 1){
-                    $i++;
-                    $b=ord($str[$i]);
-                    if ($b < 128 || $b > 191) return false;
-                    $bits--;
-                }
-            }
-        }
-        return true;
-    } 
-
-    /**
-     * Converts to and from JSON format.
-     *
-     * JSON (JavaScript Object Notation) is a lightweight data-interchange
-     * format. It is easy for humans to read and write. It is easy for machines
-     * to parse and generate. It is based on a subset of the JavaScript
-     * Programming Language, Standard ECMA-262 3rd Edition - December 1999.
-     * This feature can also be found in  Python. JSON is a text format that is
-     * completely language independent but uses conventions that are familiar
-     * to programmers of the C-family of languages, including C, C++, C#, Java,
-     * JavaScript, Perl, TCL, and many others. These properties make JSON an
-     * ideal data-interchange language.
-     *
-     * This package provides a simple encoder and decoder for JSON notation. It
-     * is intended for use with client-side Javascript applications that make
-     * use of HTTPRequest to perform server communication functions - data can
-     * be encoded into JSON notation for use in a client-side javascript, or
-     * decoded from incoming Javascript requests. JSON format is native to
-     * Javascript, and can be directly eval()'ed with no further parsing
-     * overhead
-     *
-     * All strings should be in ASCII or UTF-8 format!
-     *
-     * LICENSE: Redistribution and use in source and binary forms, with or
-     * without modification, are permitted provided that the following
-     * conditions are met: Redistributions of source code must retain the
-     * above copyright notice, this list of conditions and the following
-     * disclaimer. Redistributions in binary form must reproduce the above
-     * copyright notice, this list of conditions and the following disclaimer
-     * in the documentation and/or other materials provided with the
-     * distribution.
-     *
-     * THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESS OR IMPLIED
-     * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-     * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN
-     * NO EVENT SHALL CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
-     * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
-     * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
-     * OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-     * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
-     * TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
-     * USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-     * DAMAGE.
-     *
-     * @category
-     * @package     Services_JSON
-     * @author      Michal Migurski <mike-json@teczno.com>
-     * @author      Matt Knapp <mdknapp[at]gmail[dot]com>
-     * @author      Brett Stimmerman <brettstimmerman[at]gmail[dot]com>
-     * @author      Christoph Dorn <christoph@christophdorn.com>
-     * @copyright   2005 Michal Migurski
-     * @version     CVS: $Id: JSON.php,v 1.31 2006/06/28 05:54:17 migurski Exp $
-     * @license     http://www.opensource.org/licenses/bsd-license.php
-     * @link        http://pear.php.net/pepr/pepr-proposal-show.php?id=198
-     */
-   
-     
-    /**
-     * Keep a list of objects as we descend into the array so we can detect recursion.
-     */
-    private $json_objectStack = array();
-
-
-   /**
-    * convert a string from one UTF-8 char to one UTF-16 char
-    *
-    * Normally should be handled by mb_convert_encoding, but
-    * provides a slower PHP-only method for installations
-    * that lack the multibye string extension.
-    *
-    * @param    string  $utf8   UTF-8 character
-    * @return   string  UTF-16 character
-    * @access   private
-    */
-    private function json_utf82utf16($utf8)
-    {
-        // oh please oh please oh please oh please oh please
-        if (function_exists('mb_convert_encoding')) {
-            return mb_convert_encoding($utf8, 'UTF-16', 'UTF-8');
-        }
-
-        switch(strlen($utf8)) {
-            case 1:
-                // this case should never be reached, because we are in ASCII range
-                // see: http://www.cl.cam.ac.uk/~mgk25/unicode.html#utf-8
-                return $utf8;
-
-            case 2:
-                // return a UTF-16 character from a 2-byte UTF-8 char
-                // see: http://www.cl.cam.ac.uk/~mgk25/unicode.html#utf-8
-                return chr(0x07 & (ord($utf8{0}) >> 2))
-                       . chr((0xC0 & (ord($utf8{0}) << 6))
-                       | (0x3F & ord($utf8{1})));
-
-            case 3:
-                // return a UTF-16 character from a 3-byte UTF-8 char
-                // see: http://www.cl.cam.ac.uk/~mgk25/unicode.html#utf-8
-                return chr((0xF0 & (ord($utf8{0}) << 4))
-                       | (0x0F & (ord($utf8{1}) >> 2)))
-                       . chr((0xC0 & (ord($utf8{1}) << 6))
-                       | (0x7F & ord($utf8{2})));
-        }
-
-        // ignoring UTF-32 for now, sorry
-        return '';
-    }
-
-   /**
-    * encodes an arbitrary variable into JSON format
-    *
-    * @param    mixed   $var    any number, boolean, string, array, or object to be encoded.
-    *                           see argument 1 to Services_JSON() above for array-parsing behavior.
-    *                           if var is a strng, note that encode() always expects it
-    *                           to be in ASCII or UTF-8 format!
-    *
-    * @return   mixed   JSON string representation of input var or an error if a problem occurs
-    * @access   public
-    */
-    private function json_encode($var)
-    {
-    
-        if (is_object($var)) {
-            if (in_array($var,$this->json_objectStack)) {
-                return '"** Recursion **"';
-            }
-        }
-          
-        switch (gettype($var)) {
-            case 'boolean':
-                return $var ? 'true' : 'false';
-
-            case 'NULL':
-                return 'null';
-
-            case 'integer':
-                return (int) $var;
-
-            case 'double':
-            case 'float':
-                return (float) $var;
-
-            case 'string':
-                // STRINGS ARE EXPECTED TO BE IN ASCII OR UTF-8 FORMAT
-                $ascii = '';
-                $strlen_var = strlen($var);
-
-               /*
-                * Iterate over every character in the string,
-                * escaping with a slash or encoding to UTF-8 where necessary
-                */
-                for ($c = 0; $c < $strlen_var; ++$c) {
-
-                    $ord_var_c = ord($var{$c});
-
-                    switch (true) {
-                        case $ord_var_c == 0x08:
-                            $ascii .= '\b';
-                            break;
-                        case $ord_var_c == 0x09:
-                            $ascii .= '\t';
-                            break;
-                        case $ord_var_c == 0x0A:
-                            $ascii .= '\n';
-                            break;
-                        case $ord_var_c == 0x0C:
-                            $ascii .= '\f';
-                            break;
-                        case $ord_var_c == 0x0D:
-                            $ascii .= '\r';
-                            break;
-
-                        case $ord_var_c == 0x22:
-                        case $ord_var_c == 0x2F:
-                        case $ord_var_c == 0x5C:
-                            // double quote, slash, slosh
-                            $ascii .= '\\'.$var{$c};
-                            break;
-
-                        case (($ord_var_c >= 0x20) && ($ord_var_c <= 0x7F)):
-                            // characters U-00000000 - U-0000007F (same as ASCII)
-                            $ascii .= $var{$c};
-                            break;
-
-                        case (($ord_var_c & 0xE0) == 0xC0):
-                            // characters U-00000080 - U-000007FF, mask 110XXXXX
-                            // see http://www.cl.cam.ac.uk/~mgk25/unicode.html#utf-8
-                            $char = pack('C*', $ord_var_c, ord($var{$c + 1}));
-                            $c += 1;
-                            $utf16 = $this->json_utf82utf16($char);
-                            $ascii .= sprintf('\u%04s', bin2hex($utf16));
-                            break;
-
-                        case (($ord_var_c & 0xF0) == 0xE0):
-                            // characters U-00000800 - U-0000FFFF, mask 1110XXXX
-                            // see http://www.cl.cam.ac.uk/~mgk25/unicode.html#utf-8
-                            $char = pack('C*', $ord_var_c,
-                                         ord($var{$c + 1}),
-                                         ord($var{$c + 2}));
-                            $c += 2;
-                            $utf16 = $this->json_utf82utf16($char);
-                            $ascii .= sprintf('\u%04s', bin2hex($utf16));
-                            break;
-
-                        case (($ord_var_c & 0xF8) == 0xF0):
-                            // characters U-00010000 - U-001FFFFF, mask 11110XXX
-                            // see http://www.cl.cam.ac.uk/~mgk25/unicode.html#utf-8
-                            $char = pack('C*', $ord_var_c,
-                                         ord($var{$c + 1}),
-                                         ord($var{$c + 2}),
-                                         ord($var{$c + 3}));
-                            $c += 3;
-                            $utf16 = $this->json_utf82utf16($char);
-                            $ascii .= sprintf('\u%04s', bin2hex($utf16));
-                            break;
-
-                        case (($ord_var_c & 0xFC) == 0xF8):
-                            // characters U-00200000 - U-03FFFFFF, mask 111110XX
-                            // see http://www.cl.cam.ac.uk/~mgk25/unicode.html#utf-8
-                            $char = pack('C*', $ord_var_c,
-                                         ord($var{$c + 1}),
-                                         ord($var{$c + 2}),
-                                         ord($var{$c + 3}),
-                                         ord($var{$c + 4}));
-                            $c += 4;
-                            $utf16 = $this->json_utf82utf16($char);
-                            $ascii .= sprintf('\u%04s', bin2hex($utf16));
-                            break;
-
-                        case (($ord_var_c & 0xFE) == 0xFC):
-                            // characters U-04000000 - U-7FFFFFFF, mask 1111110X
-                            // see http://www.cl.cam.ac.uk/~mgk25/unicode.html#utf-8
-                            $char = pack('C*', $ord_var_c,
-                                         ord($var{$c + 1}),
-                                         ord($var{$c + 2}),
-                                         ord($var{$c + 3}),
-                                         ord($var{$c + 4}),
-                                         ord($var{$c + 5}));
-                            $c += 5;
-                            $utf16 = $this->json_utf82utf16($char);
-                            $ascii .= sprintf('\u%04s', bin2hex($utf16));
-                            break;
-                    }
-                }
-
-                return '"'.$ascii.'"';
-
-            case 'array':
-                /*
-                 * As per JSON spec if any array key is not an integer
-                 * we must treat the the whole array as an object. We
-                 * also try to catch a sparsely populated associative
-                 * array with numeric keys here because some JS engines
-                 * will create an array with empty indexes up to
-                 * max_index which can cause memory issues and because
-                 * the keys, which may be relevant, will be remapped
-                 * otherwise.
-                 *
-                 * As per the ECMA and JSON specification an object may
-                 * have any string as a property. Unfortunately due to
-                 * a hole in the ECMA specification if the key is a
-                 * ECMA reserved word or starts with a digit the
-                 * parameter is only accessible using ECMAScript's
-                 * bracket notation.
-                 */
-
-                // treat as a JSON object
-                if (is_array($var) && count($var) && (array_keys($var) !== range(0, sizeof($var) - 1))) {
-                  
-                    $this->json_objectStack[] = $var;
-
-                    $properties = array_map(array($this, 'json_name_value'),
-                                            array_keys($var),
-                                            array_values($var));
-
-                    array_pop($this->json_objectStack);
-
-                    foreach($properties as $property) {
-                        if ($property instanceof Exception) {
-                            return $property;
-                        }
-                    }
-
-                    return '{' . join(',', $properties) . '}';
-                }
-
-                $this->json_objectStack[] = $var;
-
-                // treat it like a regular array
-                $elements = array_map(array($this, 'json_encode'), $var);
-
-                array_pop($this->json_objectStack);
-
-                foreach($elements as $element) {
-                    if ($element instanceof Exception) {
-                        return $element;
-                    }
-                }
-
-                return '[' . join(',', $elements) . ']';
-
-            case 'object':
-                $vars = self::encodeObject($var);
-
-                $this->json_objectStack[] = $var;
-
-                $properties = array_map(array($this, 'json_name_value'),
-                                        array_keys($vars),
-                                        array_values($vars));
-
-                array_pop($this->json_objectStack);
-              
-                foreach($properties as $property) {
-                    if ($property instanceof Exception) {
-                        return $property;
-                    }
-                }
-                     
-                return '{' . join(',', $properties) . '}';
-
-            default:
-                return null;
-        }
-    }
-
-   /**
-    * array-walking function for use in generating JSON-formatted name-value pairs
-    *
-    * @param    string  $name   name of key to use
-    * @param    mixed   $value  reference to an array element to be encoded
-    *
-    * @return   string  JSON-formatted name-value pair, like '"name":value'
-    * @access   private
-    */
-    private function json_name_value($name, $value)
-    {
-        // Encoding the $GLOBALS PHP array causes an infinite loop
-        // if the recursion is not reset here as it contains
-        // a reference to itself. This is the only way I have come up
-        // with to stop infinite recursion in this case.
-        if ($name=='GLOBALS'
-           && is_array($value)
-           && array_key_exists('GLOBALS',$value)) {
-            $value['GLOBALS'] = '** Recursion **';
-        }
-    
-        $encoded_value = $this->json_encode($value);
-
-        if ($encoded_value instanceof Exception) {
-            return $encoded_value;
-        }
-
-        return $this->json_encode(strval($name)) . ':' . $encoded_value;
-    }
-
-    /**
-     * @deprecated
-     */    
-    public function setProcessorUrl($URL)
-    {
-        trigger_error("The FirePHP::setProcessorUrl() method is no longer supported", E_USER_DEPRECATED);
-    }
-
-    /**
-     * @deprecated
-     */
-    public function setRendererUrl($URL)
-    {
-        trigger_error("The FirePHP::setRendererUrl() method is no longer supported", E_USER_DEPRECATED);
-    }  
-}
diff --git a/engine/external/pear/FirePHPCore/FirePHP.class.php4 b/engine/external/pear/FirePHPCore/FirePHP.class.php4
deleted file mode 100644
index 407a6596..00000000
--- a/engine/external/pear/FirePHPCore/FirePHP.class.php4
+++ /dev/null
@@ -1,1332 +0,0 @@
-<?php
-/**
- * *** BEGIN LICENSE BLOCK *****
- *  
- * This file is part of FirePHP (http://www.firephp.org/).
- * 
- * Software License Agreement (New BSD License)
- * 
- * Copyright (c) 2006-2010, Christoph Dorn
- * All rights reserved.
- * 
- * Redistribution and use in source and binary forms, with or without modification,
- * are permitted provided that the following conditions are met:
- * 
- *     * Redistributions of source code must retain the above copyright notice,
- *       this list of conditions and the following disclaimer.
- * 
- *     * Redistributions in binary form must reproduce the above copyright notice,
- *       this list of conditions and the following disclaimer in the documentation
- *       and/or other materials provided with the distribution.
- * 
- *     * Neither the name of Christoph Dorn nor the names of its
- *       contributors may be used to endorse or promote products derived from this
- *       software without specific prior written permission.
- * 
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
- * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
- * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- * 
- * ***** END LICENSE BLOCK *****
- * 
- * This verion of FirePHPCore is for use with PHP4. If you do not require PHP4 
- * compatibility, it is suggested you use FirePHPCore.class.php instead.
- * 
- * @copyright   Copyright (C) 2007-2009 Christoph Dorn
- * @author      Christoph Dorn <christoph@christophdorn.com>
- * @author      Michael Day <manveru.alma@gmail.com>
- * @license     http://www.opensource.org/licenses/bsd-license.php
- * @package     FirePHPCore
- */
- 
-/**
- * FirePHP version
- * 
- * @var string
- */
-define('FirePHP_VERSION', '0.3');   // @pinf replace '0.3' with '%%package.version%%'
-
-/**
- * Firebug LOG level
- * 
- * Logs a message to firebug console
- * 
- * @var string
- */
-define('FirePHP_LOG', 'LOG');
-
-/**
- * Firebug INFO level
- * 
- * Logs a message to firebug console and displays an info icon before the message
- *
- * @var string
- */
-define('FirePHP_INFO', 'INFO');
-
-/**
- * Firebug WARN level
- * 
- * Logs a message to firebug console, displays a warning icon before the message and colors the line turquoise
- *
- * @var string
- */
-define('FirePHP_WARN', 'WARN');
-
-/**
- * Firebug ERROR level
- * 
- * Logs a message to firebug console, displays an error icon before the message and colors the line yellow. Also increments the firebug error count.
- *
- * @var string
- */
-define('FirePHP_ERROR', 'ERROR');
-
-/**
- * Dumps a variable to firebug's server panel
- *
- * @var string
- */
-define('FirePHP_DUMP', 'DUMP');
-
-/**
- * Displays a stack trace in firebug console
- * 
- * @var string
- */
-define('FirePHP_TRACE', 'TRACE');
-
-/**
- * Displays a table in firebug console
- *
- * @var string
- */
-define('FirePHP_TABLE', 'TABLE');
- 
-/**
- * Starts a group in firebug console
- *
- * @var string
- */
-define('FirePHP_GROUP_START', 'GROUP_START');
-
-/**
- * Ends a group in firebug console
- * 
- * @var string
- */
-define('FirePHP_GROUP_END', 'GROUP_END');
-
-/**
- * Sends the given data to the FirePHP Firefox Extension.
- * The data can be displayed in the Firebug Console or in the
- * "Server" request tab.
- * 
- * For more information see: http://www.firephp.org/
- * 
- * @copyright   Copyright (C) 2007-2009 Christoph Dorn
- * @author      Christoph Dorn <christoph@christophdorn.com>
- * @author      Michael Day <manveru.alma@gmail.com>
- * @license     http://www.opensource.org/licenses/bsd-license.php
- * @package     FirePHPCore
- */
-class FirePHP {
-  /**
-   * Wildfire protocol message index
-   *
-   * @var int
-   */
-  var $messageIndex = 1;
-    
-  /**
-   * Options for the library
-   * 
-   * @var array
-   */
-  var $options = array('maxObjectDepth' => 5,
-                       'maxArrayDepth' => 5,
-                       'useNativeJsonEncode' => true,
-                       'includeLineNumbers' => true);
-
-  /**
-   * Filters used to exclude object members when encoding
-   * 
-   * @var array
-   */
-  var $objectFilters = array();
-  
-  /**
-   * A stack of objects used to detect recursion during object encoding
-   * 
-   * @var object
-   */
-  var $objectStack = array();
-  
-  /**
-   * Flag to enable/disable logging
-   * 
-   * @var boolean
-   */
-  var $enabled = true;
-
-  /**
-   * The object constructor
-   */
-  function FirePHP() {
-  }
-
-    
-  /**
-   * When the object gets serialized only include specific object members.
-   * 
-   * @return array
-   */  
-  function __sleep() {
-    return array('options','objectFilters','enabled');
-  }
-
-  /**
-   * Gets singleton instance of FirePHP
-   *
-   * @param boolean $AutoCreate
-   * @return FirePHP
-   */
-  function &getInstance($AutoCreate=false) {
-  	global $FirePHP_Instance;
-  	
-  	if($AutoCreate===true && !$FirePHP_Instance) {
-  		$FirePHP_Instance = new FirePHP();
-  	}
-  	
-  	return $FirePHP_Instance;
-  }
-    
-  /**
-   * Enable and disable logging to Firebug
-   * 
-   * @param boolean $Enabled TRUE to enable, FALSE to disable
-   * @return void
-   */
-  function setEnabled($Enabled) {
-    $this->enabled = $Enabled;
-  }
-  
-  /**
-   * Check if logging is enabled
-   * 
-   * @return boolean TRUE if enabled
-   */
-  function getEnabled() {
-    return $this->enabled;
-  }
-  
-  /**
-   * Specify a filter to be used when encoding an object
-   * 
-   * Filters are used to exclude object members.
-   * 
-   * @param string $Class The class name of the object
-   * @param array $Filter An array of members to exclude
-   * @return void
-   */
-  function setObjectFilter($Class, $Filter) {
-    $this->objectFilters[strtolower($Class)] = $Filter;
-  }
-  
-  /**
-   * Set some options for the library
-   * 
-   * Options:
-   *  - maxObjectDepth: The maximum depth to traverse objects (default: 5)
-   *  - maxArrayDepth: The maximum depth to traverse arrays (default: 5)
-   *  - useNativeJsonEncode: If true will use json_encode() (default: true)
-   *  - includeLineNumbers: If true will include line numbers and filenames (default: true)
-   * 
-   * @param array $Options The options to be set
-   * @return void
-   */
-  function setOptions($Options) {
-    $this->options = array_merge($this->options,$Options);
-  }
-  
-  /**
-   * Get options from the library
-   *
-   * @return array The currently set options
-   */
-  function getOptions() {
-    return $this->options;
-  }
-  
-  /**
-   * Register FirePHP as your error handler
-   * 
-   * Will use FirePHP to log each php error.
-   *
-   * @return mixed Returns a string containing the previously defined error handler (if any)
-   */
-  function registerErrorHandler()
-  {
-    //NOTE: The following errors will not be caught by this error handler:
-    //      E_ERROR, E_PARSE, E_CORE_ERROR,
-    //      E_CORE_WARNING, E_COMPILE_ERROR,
-    //      E_COMPILE_WARNING, E_STRICT
-    
-    return set_error_handler(array($this,'errorHandler'));     
-  }
-
-  /**
-   * FirePHP's error handler
-   * 
-   * Logs each php error that will occur.
-   *
-   * @param int $errno
-   * @param string $errstr
-   * @param string $errfile
-   * @param int $errline
-   * @param array $errcontext
-   */
-  function errorHandler($errno, $errstr, $errfile, $errline, $errcontext)
-  {
-  	global $FirePHP_Instance;
-    // Don't log error if error reporting is switched off
-    if (error_reporting() == 0) {
-      return;
-    }
-    // Only log error for errors we are asking for
-    if (error_reporting() & $errno) {
-      $FirePHP_Instance->group($errstr);
-      $FirePHP_Instance->error("{$errfile}, line $errline");
-      $FirePHP_Instance->groupEnd();
-    }
-  }
-  
-  /**
-   * Register FirePHP driver as your assert callback
-   * 
-   * @return mixed Returns the original setting
-   */
-  function registerAssertionHandler()
-  {
-    return assert_options(ASSERT_CALLBACK, array($this, 'assertionHandler'));
-  }
-  
-  /**
-   * FirePHP's assertion handler
-   *
-   * Logs all assertions to your firebug console and then stops the script.
-   *
-   * @param string $file File source of assertion
-   * @param int    $line Line source of assertion
-   * @param mixed  $code Assertion code
-   */
-  function assertionHandler($file, $line, $code)
-  {
-    $this->fb($code, 'Assertion Failed', FirePHP_ERROR, array('File'=>$file,'Line'=>$line));
-  }  
-  
-  /**
-   * Set custom processor url for FirePHP
-   *
-   * @param string $URL
-   */    
-  function setProcessorUrl($URL)
-  {
-    $this->setHeader('X-FirePHP-ProcessorURL', $URL);
-  }
-
-  /**
-   * Set custom renderer url for FirePHP
-   *
-   * @param string $URL
-   */
-  function setRendererUrl($URL)
-  {
-    $this->setHeader('X-FirePHP-RendererURL', $URL);
-  }
-  
-  /**
-   * Start a group for following messages.
-   * 
-   * Options:
-   *   Collapsed: [true|false]
-   *   Color:     [#RRGGBB|ColorName]
-   *
-   * @param string $Name
-   * @param array $Options OPTIONAL Instructions on how to log the group
-   * @return true
-   * @throws Exception
-   */
-  function group($Name, $Options=null) {
-    
-    if(!$Name) {
-      trigger_error('You must specify a label for the group!');
-    }
-    
-    if($Options) {
-      if(!is_array($Options)) {
-        trigger_error('Options must be defined as an array!');
-      }
-      if(array_key_exists('Collapsed', $Options)) {
-        $Options['Collapsed'] = ($Options['Collapsed'])?'true':'false';
-      }
-    }
-    
-    return $this->fb(null, $Name, FirePHP_GROUP_START, $Options);
-  }
-  
-  /**
-   * Ends a group you have started before
-   *
-   * @return true
-   * @throws Exception
-   */
-  function groupEnd() {
-    return $this->fb(null, null, FirePHP_GROUP_END);
-  }
-
-  /**
-   * Log object with label to firebug console
-   *
-   * @see FirePHP::LOG
-   * @param mixes $Object
-   * @param string $Label
-   * @return true
-   * @throws Exception
-   */
-  function log($Object, $Label=null) {
-    return $this->fb($Object, $Label, FirePHP_LOG);
-  } 
-
-  /**
-   * Log object with label to firebug console
-   *
-   * @see FirePHP::INFO
-   * @param mixes $Object
-   * @param string $Label
-   * @return true
-   * @throws Exception
-   */
-  function info($Object, $Label=null) {
-    return $this->fb($Object, $Label, FirePHP_INFO);
-  } 
-
-  /**
-   * Log object with label to firebug console
-   *
-   * @see FirePHP::WARN
-   * @param mixes $Object
-   * @param string $Label
-   * @return true
-   * @throws Exception
-   */
-  function warn($Object, $Label=null) {
-    return $this->fb($Object, $Label, FirePHP_WARN);
-  } 
-
-  /**
-   * Log object with label to firebug console
-   *
-   * @see FirePHP::ERROR
-   * @param mixes $Object
-   * @param string $Label
-   * @return true
-   * @throws Exception
-   */
-  function error($Object, $Label=null) {
-    return $this->fb($Object, $Label, FirePHP_ERROR);
-  } 
-
-  /**
-   * Dumps key and variable to firebug server panel
-   *
-   * @see FirePHP::DUMP
-   * @param string $Key
-   * @param mixed $Variable
-   * @return true
-   * @throws Exception
-   */
-  function dump($Key, $Variable) {
-    return $this->fb($Variable, $Key, FirePHP_DUMP);
-  }
-  
-  /**
-   * Log a trace in the firebug console
-   *
-   * @see FirePHP::TRACE
-   * @param string $Label
-   * @return true
-   * @throws Exception
-   */
-  function trace($Label) {
-    return $this->fb($Label, FirePHP_TRACE);
-  } 
-
-  /**
-   * Log a table in the firebug console
-   *
-   * @see FirePHP::TABLE
-   * @param string $Label
-   * @param string $Table
-   * @return true
-   * @throws Exception
-   */
-  function table($Label, $Table) {
-    return $this->fb($Table, $Label, FirePHP_TABLE);
-  }
-  
-  /**
-   * Check if FirePHP is installed on client
-   *
-   * @return boolean
-   */
-  function detectClientExtension() {
-    // Check if FirePHP is installed on client via User-Agent header
-    if(@preg_match_all('/\sFirePHP\/([\.\d]*)\s?/si',$this->getUserAgent(),$m) &&
-       version_compare($m[1][0],'0.0.6','>=')) {
-      return true;
-    } else
-    // Check if FirePHP is installed on client via X-FirePHP-Version header
-    if(@preg_match_all('/^([\.\d]*)$/si',$this->getRequestHeader("X-FirePHP-Version"),$m) &&
-       version_compare($m[1][0],'0.0.6','>=')) {
-      return true;
-    }
-    return false;
-  }
- 
-  /**
-   * Log varible to Firebug
-   * 
-   * @see http://www.firephp.org/Wiki/Reference/Fb
-   * @param mixed $Object The variable to be logged
-   * @return true Return TRUE if message was added to headers, FALSE otherwise
-   * @throws Exception
-   */
-  function fb($Object) {
-  
-    if(!$this->enabled) {
-      return false;
-    }
-  
-    if (headers_sent($filename, $linenum)) {
-        trigger_error('Headers already sent in '.$filename.' on line '.$linenum.'. Cannot send log data to FirePHP. You must have Output Buffering enabled via ob_start() or output_buffering ini directive.');
-    }
-  
-    $Type = null;
-    $Label = null;
-    $Options = array();
-  
-    if(func_num_args()==1) {
-    } else
-    if(func_num_args()==2) {
-      switch(func_get_arg(1)) {
-        case FirePHP_LOG:
-        case FirePHP_INFO:
-        case FirePHP_WARN:
-        case FirePHP_ERROR:
-        case FirePHP_DUMP:
-        case FirePHP_TRACE:
-        case FirePHP_TABLE:
-        case FirePHP_GROUP_START:
-        case FirePHP_GROUP_END:
-          $Type = func_get_arg(1);
-          break;
-        default:
-          $Label = func_get_arg(1);
-          break;
-      }
-    } else
-    if(func_num_args()==3) {
-      $Type = func_get_arg(2);
-      $Label = func_get_arg(1);
-    } else
-    if(func_num_args()==4) {
-      $Type = func_get_arg(2);
-      $Label = func_get_arg(1);
-      $Options = func_get_arg(3);
-    } else {
-      trigger_error('Wrong number of arguments to fb() function!');
-    }
-  
-  
-    if(!$this->detectClientExtension()) {
-      return false;
-    }
-  
-    $meta = array();
-    $skipFinalObjectEncode = false;
-  
-    if($Type==FirePHP_TRACE) {
-      
-      $trace = debug_backtrace();
-      if(!$trace) return false;
-      for( $i=0 ; $i<sizeof($trace) ; $i++ ) {
-
-        if(isset($trace[$i]['class'])
-           && isset($trace[$i]['file'])
-           && ($trace[$i]['class']=='FirePHP'
-               || $trace[$i]['class']=='FB')
-           && (substr($this->_standardizePath($trace[$i]['file']),-18,18)=='FirePHPCore/fb.php'
-               || substr($this->_standardizePath($trace[$i]['file']),-29,29)=='FirePHPCore/FirePHP.class.php')) {
-          /* Skip - FB::trace(), FB::send(), $firephp->trace(), $firephp->fb() */
-        } else
-        if(isset($trace[$i]['class'])
-           && isset($trace[$i+1]['file'])
-           && $trace[$i]['class']=='FirePHP'
-           && substr($this->_standardizePath($trace[$i+1]['file']),-18,18)=='FirePHPCore/fb.php') {
-          /* Skip fb() */
-        } else
-        if($trace[$i]['function']=='fb'
-           || $trace[$i]['function']=='trace'
-           || $trace[$i]['function']=='send') {
-          $Object = array('Class'=>isset($trace[$i]['class'])?$trace[$i]['class']:'',
-                          'Type'=>isset($trace[$i]['type'])?$trace[$i]['type']:'',
-                          'Function'=>isset($trace[$i]['function'])?$trace[$i]['function']:'',
-                          'Message'=>$trace[$i]['args'][0],
-                          'File'=>isset($trace[$i]['file'])?$this->_escapeTraceFile($trace[$i]['file']):'',
-                          'Line'=>isset($trace[$i]['line'])?$trace[$i]['line']:'',
-                          'Args'=>isset($trace[$i]['args'])?$this->encodeObject($trace[$i]['args']):'',
-                          'Trace'=>$this->_escapeTrace(array_splice($trace,$i+1)));
-
-          $skipFinalObjectEncode = true;
-          $meta['file'] = isset($trace[$i]['file'])?$this->_escapeTraceFile($trace[$i]['file']):'';
-          $meta['line'] = isset($trace[$i]['line'])?$trace[$i]['line']:'';
-          break;
-        }
-      }
-
-    } else
-    if($Type==FirePHP_TABLE) {
-      
-      if(isset($Object[0]) && is_string($Object[0])) {
-        $Object[1] = $this->encodeTable($Object[1]);
-      } else {
-        $Object = $this->encodeTable($Object);
-      }
-
-      $skipFinalObjectEncode = true;
-      
-    } else
-    if($Type==FirePHP_GROUP_START) {
-      
-      if(!$Label) {
-        trigger_error('You must specify a label for the group!');
-      }
-    } else {
-      if($Type===null) {
-        $Type = FirePHP_LOG;
-      }
-    }
-    
-    if($this->options['includeLineNumbers']) {
-      if(!isset($meta['file']) || !isset($meta['line'])) {
-
-        $trace = debug_backtrace();
-        for( $i=0 ; $trace && $i<sizeof($trace) ; $i++ ) {
-  
-          if(isset($trace[$i]['class'])
-             && isset($trace[$i]['file'])
-             && ($trace[$i]['class']=='FirePHP'
-                 || $trace[$i]['class']=='FB')
-             && (substr($this->_standardizePath($trace[$i]['file']),-18,18)=='FirePHPCore/fb.php'
-                 || substr($this->_standardizePath($trace[$i]['file']),-29,29)=='FirePHPCore/FirePHP.class.php')) {
-            /* Skip - FB::trace(), FB::send(), $firephp->trace(), $firephp->fb() */
-          } else
-          if(isset($trace[$i]['class'])
-             && isset($trace[$i+1]['file'])
-             && $trace[$i]['class']=='FirePHP'
-             && substr($this->_standardizePath($trace[$i+1]['file']),-18,18)=='FirePHPCore/fb.php') {
-            /* Skip fb() */
-          } else
-          if(isset($trace[$i]['file'])
-             && substr($this->_standardizePath($trace[$i]['file']),-18,18)=='FirePHPCore/fb.php') {
-            /* Skip FB::fb() */
-          } else {
-            $meta['file'] = isset($trace[$i]['file'])?$this->_escapeTraceFile($trace[$i]['file']):'';
-            $meta['line'] = isset($trace[$i]['line'])?$trace[$i]['line']:'';
-            break;
-          }
-        }      
-      
-      }
-    } else {
-      unset($meta['file']);
-      unset($meta['line']);
-    }
-
-  	$this->setHeader('X-Wf-Protocol-1','http://meta.wildfirehq.org/Protocol/JsonStream/0.2');
-  	$this->setHeader('X-Wf-1-Plugin-1','http://meta.firephp.org/Wildfire/Plugin/FirePHP/Library-FirePHPCore/'.FirePHP_VERSION);
- 
-    $structure_index = 1;
-    if($Type==FirePHP_DUMP) {
-      $structure_index = 2;
-    	$this->setHeader('X-Wf-1-Structure-2','http://meta.firephp.org/Wildfire/Structure/FirePHP/Dump/0.1');
-    } else {
-    	$this->setHeader('X-Wf-1-Structure-1','http://meta.firephp.org/Wildfire/Structure/FirePHP/FirebugConsole/0.1');
-    }
-  
-    if($Type==FirePHP_DUMP) {
-    	$msg = '{"'.$Label.'":'.$this->jsonEncode($Object, $skipFinalObjectEncode).'}';
-    } else {
-      $msg_meta = $Options;
-      $msg_meta['Type'] = $Type;
-      if($Label!==null) {
-        $msg_meta['Label'] = $Label;
-      }
-      if(isset($meta['file']) && !isset($msg_meta['File'])) {
-        $msg_meta['File'] = $meta['file'];
-      }
-      if(isset($meta['line']) && !isset($msg_meta['Line'])) {
-        $msg_meta['Line'] = $meta['line'];
-      }
-    	$msg = '['.$this->jsonEncode($msg_meta).','.$this->jsonEncode($Object, $skipFinalObjectEncode).']';
-    }
-    
-    $parts = explode("\n",chunk_split($msg, 5000, "\n"));
-
-    for( $i=0 ; $i<count($parts) ; $i++) {
-        
-        $part = $parts[$i];
-        if ($part) {
-            
-            if(count($parts)>2) {
-              // Message needs to be split into multiple parts
-              $this->setHeader('X-Wf-1-'.$structure_index.'-'.'1-'.$this->messageIndex,
-                               (($i==0)?strlen($msg):'')
-                               . '|' . $part . '|'
-                               . (($i<count($parts)-2)?'\\':''));
-            } else {
-              $this->setHeader('X-Wf-1-'.$structure_index.'-'.'1-'.$this->messageIndex,
-                               strlen($part) . '|' . $part . '|');
-            }
-            
-            $this->messageIndex++;
-            
-            if ($this->messageIndex > 99999) {
-                trigger_error('Maximum number (99,999) of messages reached!');             
-            }
-        }
-    }
-
-  	$this->setHeader('X-Wf-1-Index',$this->messageIndex-1);
-
-    return true;
-  }
-  
-  
-  /**
-   * Standardizes path for windows systems.
-   *
-   * @param string $Path
-   * @return string
-   */
-   function _standardizePath($Path) {
-    return preg_replace('/\\\\+/','/',$Path);    
-  }
-  
-  /**
-   * Escape trace path for windows systems
-   *
-   * @param array $Trace
-   * @return array
-   */
-   function _escapeTrace($Trace) {
-    if(!$Trace) return $Trace;
-    for( $i=0 ; $i<sizeof($Trace) ; $i++ ) {
-      if(isset($Trace[$i]['file'])) {
-        $Trace[$i]['file'] = $this->_escapeTraceFile($Trace[$i]['file']);
-      }
-      if(isset($Trace[$i]['args'])) {
-        $Trace[$i]['args'] = $this->encodeObject($Trace[$i]['args']);
-      }
-    }
-    return $Trace;    
-  }
-  
-  /**
-   * Escape file information of trace for windows systems
-   *
-   * @param string $File
-   * @return string
-   */
-   function _escapeTraceFile($File) {
-    /* Check if we have a windows filepath */
-    if(strpos($File,'\\')) {
-      /* First strip down to single \ */
-      
-      $file = preg_replace('/\\\\+/','\\',$File);
-      
-      return $file;
-    }
-    return $File;
-  }
-
-  /**
-   * Send header
-   *
-   * @param string $Name
-   * @param string_type $Value
-   */
-   function setHeader($Name, $Value) {
-    return header($Name.': '.$Value);
-  }
-
-  /**
-   * Get user agent
-   *
-   * @return string|false
-   */
-   function getUserAgent() {
-    if(!isset($_SERVER['HTTP_USER_AGENT'])) return false;
-    return $_SERVER['HTTP_USER_AGENT'];
-  }
-
-    /**
-     * Get all request headers
-     * 
-     * @return array
-     */
-    function getAllRequestHeaders() {
-        $headers = array();
-        if(function_exists('getallheaders')) {
-            foreach( getallheaders() as $name => $value ) {
-                $headers[strtolower($name)] = $value;
-            }
-        } else {
-            foreach($_SERVER as $name => $value) {
-                if(substr($name, 0, 5) == 'HTTP_') {
-                    $headers[strtolower(str_replace(' ', '-', str_replace('_', ' ', substr($name, 5))))] = $value;
-                }
-            }
-        }
-        return $headers;
-    }
-
-    /**
-     * Get a request header
-     *
-     * @return string|false
-     */
-    function getRequestHeader($Name)
-    {
-        $headers = $this->getAllRequestHeaders();
-        if (isset($headers[strtolower($Name)])) {
-            return $headers[strtolower($Name)];
-        }
-        return false;
-    }
-  
-  /**
-   * Encode an object into a JSON string
-   * 
-   * Uses PHP's jeson_encode() if available
-   * 
-   * @param object $Object The object to be encoded
-   * @return string The JSON string
-   */
-   function jsonEncode($Object, $skipObjectEncode=false)
-  {
-    if(!$skipObjectEncode) {
-      $Object = $this->encodeObject($Object);
-    }
-    
-    if(function_exists('json_encode')
-       && $this->options['useNativeJsonEncode']!=false) {
-
-      return json_encode($Object);
-    } else {
-      return $this->json_encode($Object);
-    }
-  }
-  
-  /**
-   * Encodes a table by encoding each row and column with encodeObject()
-   * 
-   * @param array $Table The table to be encoded
-   * @return array
-   */  
-   function encodeTable($Table) {
-    
-    if(!$Table) return $Table;
-    
-    $new_table = array();
-    foreach($Table as $row) {
-  
-      if(is_array($row)) {
-        $new_row = array();
-        
-        foreach($row as $item) {
-          $new_row[] = $this->encodeObject($item);
-        }
-        
-        $new_table[] = $new_row;
-      }
-    }
-    
-    return $new_table;
-  }
-  
-  /**
-   * Encodes an object
-   * 
-   * @param Object $Object The object to be encoded
-   * @param int $Depth The current traversal depth
-   * @return array All members of the object
-   */
-   function encodeObject($Object, $ObjectDepth = 1, $ArrayDepth = 1)
-  {
-    $return = array();
-
-    if (is_resource($Object)) {
-
-      return '** '.(string)$Object.' **';
-
-    } else    
-    if (is_object($Object)) {
-
-        if ($ObjectDepth > $this->options['maxObjectDepth']) {
-          return '** Max Object Depth ('.$this->options['maxObjectDepth'].') **';
-        }
-        
-        foreach ($this->objectStack as $refVal) {
-            if ($refVal === $Object) {
-                return '** Recursion ('.get_class($Object).') **';
-            }
-        }
-        array_push($this->objectStack, $Object);
-                
-        $return['__className'] = $class = get_class($Object);
-        $class_lower = strtolower($class);
-
-        $members = (array)$Object;
-            
-        // Include all members that are not defined in the class
-        // but exist in the object
-        foreach( $members as $raw_name => $value ) {
-          
-          $name = $raw_name;
-          
-          if ($name{0} == "\0") {
-            $parts = explode("\0", $name);
-            $name = $parts[2];
-          }
-          
-          if(!isset($properties[$name])) {
-            $name = 'undeclared:'.$name;
-              
-            if(!(isset($this->objectFilters[$class_lower])
-                 && is_array($this->objectFilters[$class_lower])
-                 && in_array($raw_name,$this->objectFilters[$class_lower]))) {
-              
-              $return[$name] = $this->encodeObject($value, $ObjectDepth + 1, 1);
-            } else {
-              $return[$name] = '** Excluded by Filter **';
-            }
-          }
-        }
-        
-        array_pop($this->objectStack);
-        
-    } elseif (is_array($Object)) {
-
-        if ($ArrayDepth > $this->options['maxArrayDepth']) {
-          return '** Max Array Depth ('.$this->options['maxArrayDepth'].') **';
-        }
-      
-        foreach ($Object as $key => $val) {
-          
-          // Encoding the $GLOBALS PHP array causes an infinite loop
-          // if the recursion is not reset here as it contains
-          // a reference to itself. This is the only way I have come up
-          // with to stop infinite recursion in this case.
-          if($key=='GLOBALS'
-             && is_array($val)
-             && array_key_exists('GLOBALS',$val)) {
-            $val['GLOBALS'] = '** Recursion (GLOBALS) **';
-          }
-          
-          $return[$key] = $this->encodeObject($val, 1, $ArrayDepth + 1);
-        }
-    } else {
-      if($this->is_utf8($Object)) {
-        return $Object;
-      } else {
-        return utf8_encode($Object);
-      }
-    }
-    return $return;
-  	
-  }
-
-  /**
-   * Returns true if $string is valid UTF-8 and false otherwise.
-   *
-   * @param mixed $str String to be tested
-   * @return boolean
-   */
-   function is_utf8($str) {
-    $c=0; $b=0;
-    $bits=0;
-    $len=strlen($str);
-    for($i=0; $i<$len; $i++){
-        $c=ord($str[$i]);
-        if($c > 128){
-            if(($c >= 254)) return false;
-            elseif($c >= 252) $bits=6;
-            elseif($c >= 248) $bits=5;
-            elseif($c >= 240) $bits=4;
-            elseif($c >= 224) $bits=3;
-            elseif($c >= 192) $bits=2;
-            else return false;
-            if(($i+$bits) > $len) return false;
-            while($bits > 1){
-                $i++;
-                $b=ord($str[$i]);
-                if($b < 128 || $b > 191) return false;
-                $bits--;
-            }
-        }
-    }
-    return true;
-  } 
-
-  /**
-   * Converts to and from JSON format.
-   *
-   * JSON (JavaScript Object Notation) is a lightweight data-interchange
-   * format. It is easy for humans to read and write. It is easy for machines
-   * to parse and generate. It is based on a subset of the JavaScript
-   * Programming Language, Standard ECMA-262 3rd Edition - December 1999.
-   * This feature can also be found in  Python. JSON is a text format that is
-   * completely language independent but uses conventions that are familiar
-   * to programmers of the C-family of languages, including C, C++, C#, Java,
-   * JavaScript, Perl, TCL, and many others. These properties make JSON an
-   * ideal data-interchange language.
-   *
-   * This package provides a simple encoder and decoder for JSON notation. It
-   * is intended for use with client-side Javascript applications that make
-   * use of HTTPRequest to perform server communication functions - data can
-   * be encoded into JSON notation for use in a client-side javascript, or
-   * decoded from incoming Javascript requests. JSON format is native to
-   * Javascript, and can be directly eval()'ed with no further parsing
-   * overhead
-   *
-   * All strings should be in ASCII or UTF-8 format!
-   *
-   * LICENSE: Redistribution and use in source and binary forms, with or
-   * without modification, are permitted provided that the following
-   * conditions are met: Redistributions of source code must retain the
-   * above copyright notice, this list of conditions and the following
-   * disclaimer. Redistributions in binary form must reproduce the above
-   * copyright notice, this list of conditions and the following disclaimer
-   * in the documentation and/or other materials provided with the
-   * distribution.
-   *
-   * THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESS OR IMPLIED
-   * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-   * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN
-   * NO EVENT SHALL CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
-   * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
-   * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
-   * OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-   * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
-   * TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
-   * USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-   * DAMAGE.
-   *
-   * @category
-   * @package     Services_JSON
-   * @author      Michal Migurski <mike-json@teczno.com>
-   * @author      Matt Knapp <mdknapp[at]gmail[dot]com>
-   * @author      Brett Stimmerman <brettstimmerman[at]gmail[dot]com>
-   * @author      Christoph Dorn <christoph@christophdorn.com>
-   * @copyright   2005 Michal Migurski
-   * @version     CVS: $Id: JSON.php,v 1.31 2006/06/28 05:54:17 migurski Exp $
-   * @license     http://www.opensource.org/licenses/bsd-license.php
-   * @link        http://pear.php.net/pepr/pepr-proposal-show.php?id=198
-   */
-   
-     
-  /**
-   * Keep a list of objects as we descend into the array so we can detect recursion.
-   */
-  var $json_objectStack = array();
-
-
- /**
-  * convert a string from one UTF-8 char to one UTF-16 char
-  *
-  * Normally should be handled by mb_convert_encoding, but
-  * provides a slower PHP-only method for installations
-  * that lack the multibye string extension.
-  *
-  * @param    string  $utf8   UTF-8 character
-  * @return   string  UTF-16 character
-  * @access   private
-  */
-  function json_utf82utf16($utf8)
-  {
-      // oh please oh please oh please oh please oh please
-      if(function_exists('mb_convert_encoding')) {
-          return mb_convert_encoding($utf8, 'UTF-16', 'UTF-8');
-      }
-
-      switch(strlen($utf8)) {
-          case 1:
-              // this case should never be reached, because we are in ASCII range
-              // see: http://www.cl.cam.ac.uk/~mgk25/unicode.html#utf-8
-              return $utf8;
-
-          case 2:
-              // return a UTF-16 character from a 2-byte UTF-8 char
-              // see: http://www.cl.cam.ac.uk/~mgk25/unicode.html#utf-8
-              return chr(0x07 & (ord($utf8{0}) >> 2))
-                   . chr((0xC0 & (ord($utf8{0}) << 6))
-                       | (0x3F & ord($utf8{1})));
-
-          case 3:
-              // return a UTF-16 character from a 3-byte UTF-8 char
-              // see: http://www.cl.cam.ac.uk/~mgk25/unicode.html#utf-8
-              return chr((0xF0 & (ord($utf8{0}) << 4))
-                       | (0x0F & (ord($utf8{1}) >> 2)))
-                   . chr((0xC0 & (ord($utf8{1}) << 6))
-                       | (0x7F & ord($utf8{2})));
-      }
-
-      // ignoring UTF-32 for now, sorry
-      return '';
-  }
-
- /**
-  * encodes an arbitrary variable into JSON format
-  *
-  * @param    mixed   $var    any number, boolean, string, array, or object to be encoded.
-  *                           see argument 1 to Services_JSON() above for array-parsing behavior.
-  *                           if var is a strng, note that encode() always expects it
-  *                           to be in ASCII or UTF-8 format!
-  *
-  * @return   mixed   JSON string representation of input var or an error if a problem occurs
-  * @access   public
-  */
-  function json_encode($var)
-  {
-    
-    if(is_object($var)) {
-      if(in_array($var,$this->json_objectStack)) {
-        return '"** Recursion **"';
-      }
-    }
-          
-      switch (gettype($var)) {
-          case 'boolean':
-              return $var ? 'true' : 'false';
-
-          case 'NULL':
-              return 'null';
-
-          case 'integer':
-              return (int) $var;
-
-          case 'double':
-          case 'float':
-              return (float) $var;
-
-          case 'string':
-              // STRINGS ARE EXPECTED TO BE IN ASCII OR UTF-8 FORMAT
-              $ascii = '';
-              $strlen_var = strlen($var);
-
-             /*
-              * Iterate over every character in the string,
-              * escaping with a slash or encoding to UTF-8 where necessary
-              */
-              for ($c = 0; $c < $strlen_var; ++$c) {
-
-                  $ord_var_c = ord($var{$c});
-
-                  switch (true) {
-                      case $ord_var_c == 0x08:
-                          $ascii .= '\b';
-                          break;
-                      case $ord_var_c == 0x09:
-                          $ascii .= '\t';
-                          break;
-                      case $ord_var_c == 0x0A:
-                          $ascii .= '\n';
-                          break;
-                      case $ord_var_c == 0x0C:
-                          $ascii .= '\f';
-                          break;
-                      case $ord_var_c == 0x0D:
-                          $ascii .= '\r';
-                          break;
-
-                      case $ord_var_c == 0x22:
-                      case $ord_var_c == 0x2F:
-                      case $ord_var_c == 0x5C:
-                          // double quote, slash, slosh
-                          $ascii .= '\\'.$var{$c};
-                          break;
-
-                      case (($ord_var_c >= 0x20) && ($ord_var_c <= 0x7F)):
-                          // characters U-00000000 - U-0000007F (same as ASCII)
-                          $ascii .= $var{$c};
-                          break;
-
-                      case (($ord_var_c & 0xE0) == 0xC0):
-                          // characters U-00000080 - U-000007FF, mask 110XXXXX
-                          // see http://www.cl.cam.ac.uk/~mgk25/unicode.html#utf-8
-                          $char = pack('C*', $ord_var_c, ord($var{$c + 1}));
-                          $c += 1;
-                          $utf16 = $this->json_utf82utf16($char);
-                          $ascii .= sprintf('\u%04s', bin2hex($utf16));
-                          break;
-
-                      case (($ord_var_c & 0xF0) == 0xE0):
-                          // characters U-00000800 - U-0000FFFF, mask 1110XXXX
-                          // see http://www.cl.cam.ac.uk/~mgk25/unicode.html#utf-8
-                          $char = pack('C*', $ord_var_c,
-                                       ord($var{$c + 1}),
-                                       ord($var{$c + 2}));
-                          $c += 2;
-                          $utf16 = $this->json_utf82utf16($char);
-                          $ascii .= sprintf('\u%04s', bin2hex($utf16));
-                          break;
-
-                      case (($ord_var_c & 0xF8) == 0xF0):
-                          // characters U-00010000 - U-001FFFFF, mask 11110XXX
-                          // see http://www.cl.cam.ac.uk/~mgk25/unicode.html#utf-8
-                          $char = pack('C*', $ord_var_c,
-                                       ord($var{$c + 1}),
-                                       ord($var{$c + 2}),
-                                       ord($var{$c + 3}));
-                          $c += 3;
-                          $utf16 = $this->json_utf82utf16($char);
-                          $ascii .= sprintf('\u%04s', bin2hex($utf16));
-                          break;
-
-                      case (($ord_var_c & 0xFC) == 0xF8):
-                          // characters U-00200000 - U-03FFFFFF, mask 111110XX
-                          // see http://www.cl.cam.ac.uk/~mgk25/unicode.html#utf-8
-                          $char = pack('C*', $ord_var_c,
-                                       ord($var{$c + 1}),
-                                       ord($var{$c + 2}),
-                                       ord($var{$c + 3}),
-                                       ord($var{$c + 4}));
-                          $c += 4;
-                          $utf16 = $this->json_utf82utf16($char);
-                          $ascii .= sprintf('\u%04s', bin2hex($utf16));
-                          break;
-
-                      case (($ord_var_c & 0xFE) == 0xFC):
-                          // characters U-04000000 - U-7FFFFFFF, mask 1111110X
-                          // see http://www.cl.cam.ac.uk/~mgk25/unicode.html#utf-8
-                          $char = pack('C*', $ord_var_c,
-                                       ord($var{$c + 1}),
-                                       ord($var{$c + 2}),
-                                       ord($var{$c + 3}),
-                                       ord($var{$c + 4}),
-                                       ord($var{$c + 5}));
-                          $c += 5;
-                          $utf16 = $this->json_utf82utf16($char);
-                          $ascii .= sprintf('\u%04s', bin2hex($utf16));
-                          break;
-                  }
-              }
-
-              return '"'.$ascii.'"';
-
-          case 'array':
-             /*
-              * As per JSON spec if any array key is not an integer
-              * we must treat the the whole array as an object. We
-              * also try to catch a sparsely populated associative
-              * array with numeric keys here because some JS engines
-              * will create an array with empty indexes up to
-              * max_index which can cause memory issues and because
-              * the keys, which may be relevant, will be remapped
-              * otherwise.
-              *
-              * As per the ECMA and JSON specification an object may
-              * have any string as a property. Unfortunately due to
-              * a hole in the ECMA specification if the key is a
-              * ECMA reserved word or starts with a digit the
-              * parameter is only accessible using ECMAScript's
-              * bracket notation.
-              */
-
-              // treat as a JSON object
-              if (is_array($var) && count($var) && (array_keys($var) !== range(0, sizeof($var) - 1))) {
-                  
-                  $this->json_objectStack[] = $var;
-
-                  $properties = array_map(array($this, 'json_name_value'),
-                                          array_keys($var),
-                                          array_values($var));
-
-                  array_pop($this->json_objectStack);
-
-                  return '{' . join(',', $properties) . '}';
-              }
-
-              $this->json_objectStack[] = $var;
-
-              // treat it like a regular array
-              $elements = array_map(array($this, 'json_encode'), $var);
-
-              array_pop($this->json_objectStack);
-
-              return '[' . join(',', $elements) . ']';
-
-          case 'object':
-              $vars = FirePHP::encodeObject($var);
-
-              $this->json_objectStack[] = $var;
-
-              $properties = array_map(array($this, 'json_name_value'),
-                                      array_keys($vars),
-                                      array_values($vars));
-
-              array_pop($this->json_objectStack);
-              
-              return '{' . join(',', $properties) . '}';
-
-          default:
-              return null;
-      }
-  }
-
- /**
-  * array-walking function for use in generating JSON-formatted name-value pairs
-  *
-  * @param    string  $name   name of key to use
-  * @param    mixed   $value  reference to an array element to be encoded
-  *
-  * @return   string  JSON-formatted name-value pair, like '"name":value'
-  * @access   private
-  */
-  function json_name_value($name, $value)
-  {
-      // Encoding the $GLOBALS PHP array causes an infinite loop
-      // if the recursion is not reset here as it contains
-      // a reference to itself. This is the only way I have come up
-      // with to stop infinite recursion in this case.
-      if($name=='GLOBALS'
-         && is_array($value)
-         && array_key_exists('GLOBALS',$value)) {
-        $value['GLOBALS'] = '** Recursion **';
-      }
-    
-      $encoded_value = $this->json_encode($value);
-
-      return $this->json_encode(strval($name)) . ':' . $encoded_value;
-  }
-}
-
diff --git a/engine/external/pear/FirePHPCore/LICENSE b/engine/external/pear/FirePHPCore/LICENSE
deleted file mode 100644
index 3e390f9d..00000000
--- a/engine/external/pear/FirePHPCore/LICENSE
+++ /dev/null
@@ -1,29 +0,0 @@
-Software License Agreement (New BSD License)
-
-Copyright (c) 2006-2009, Christoph Dorn
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without modification,
-are permitted provided that the following conditions are met:
-
-    * Redistributions of source code must retain the above copyright notice,
-      this list of conditions and the following disclaimer.
-
-    * Redistributions in binary form must reproduce the above copyright notice,
-      this list of conditions and the following disclaimer in the documentation
-      and/or other materials provided with the distribution.
-
-    * Neither the name of Christoph Dorn nor the names of its
-      contributors may be used to endorse or promote products derived from this
-      software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
-ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/engine/external/pear/FirePHPCore/fb.php b/engine/external/pear/FirePHPCore/fb.php
deleted file mode 100644
index 9ed9c423..00000000
--- a/engine/external/pear/FirePHPCore/fb.php
+++ /dev/null
@@ -1,276 +0,0 @@
-<?php
-
-/* ***** BEGIN LICENSE BLOCK *****
- *  
- * This file is part of FirePHP (http://www.firephp.org/).
- * 
- * Software License Agreement (New BSD License)
- * 
- * Copyright (c) 2006-2010, Christoph Dorn
- * All rights reserved.
- * 
- * Redistribution and use in source and binary forms, with or without modification,
- * are permitted provided that the following conditions are met:
- * 
- *     * Redistributions of source code must retain the above copyright notice,
- *       this list of conditions and the following disclaimer.
- * 
- *     * Redistributions in binary form must reproduce the above copyright notice,
- *       this list of conditions and the following disclaimer in the documentation
- *       and/or other materials provided with the distribution.
- * 
- *     * Neither the name of Christoph Dorn nor the names of its
- *       contributors may be used to endorse or promote products derived from this
- *       software without specific prior written permission.
- * 
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
- * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
- * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- * 
- * ***** END LICENSE BLOCK *****
- * 
- * @copyright   Copyright (C) 2007-2009 Christoph Dorn
- * @author      Christoph Dorn <christoph@christophdorn.com>
- * @license     http://www.opensource.org/licenses/bsd-license.php
- * @package     FirePHPCore
- */
-
-if(!class_exists('FirePHP')) {
-    require_once dirname(__FILE__) . DIRECTORY_SEPARATOR . 'FirePHP.class.php';
-}
-
-/**
- * Sends the given data to the FirePHP Firefox Extension.
- * The data can be displayed in the Firebug Console or in the
- * "Server" request tab.
- * 
- * @see http://www.firephp.org/Wiki/Reference/Fb
- * @param mixed $Object
- * @return true
- * @throws Exception
- */
-function fb()
-{
-    $instance = FirePHP::getInstance(true);
-  
-    $args = func_get_args();
-    return call_user_func_array(array($instance,'fb'),$args);
-}
-
-
-class FB
-{
-    /**
-     * Enable and disable logging to Firebug
-     * 
-     * @see FirePHP->setEnabled()
-     * @param boolean $Enabled TRUE to enable, FALSE to disable
-     * @return void
-     */
-    public static function setEnabled($Enabled)
-    {
-        $instance = FirePHP::getInstance(true);
-        $instance->setEnabled($Enabled);
-    }
-  
-    /**
-     * Check if logging is enabled
-     * 
-     * @see FirePHP->getEnabled()
-     * @return boolean TRUE if enabled
-     */
-    public static function getEnabled()
-    {
-        $instance = FirePHP::getInstance(true);
-        return $instance->getEnabled();
-    }  
-  
-    /**
-     * Specify a filter to be used when encoding an object
-     * 
-     * Filters are used to exclude object members.
-     * 
-     * @see FirePHP->setObjectFilter()
-     * @param string $Class The class name of the object
-     * @param array $Filter An array or members to exclude
-     * @return void
-     */
-    public static function setObjectFilter($Class, $Filter)
-    {
-      $instance = FirePHP::getInstance(true);
-      $instance->setObjectFilter($Class, $Filter);
-    }
-  
-    /**
-     * Set some options for the library
-     * 
-     * @see FirePHP->setOptions()
-     * @param array $Options The options to be set
-     * @return void
-     */
-    public static function setOptions($Options)
-    {
-        $instance = FirePHP::getInstance(true);
-        $instance->setOptions($Options);
-    }
-
-    /**
-     * Get options for the library
-     * 
-     * @see FirePHP->getOptions()
-     * @return array The options
-     */
-    public static function getOptions()
-    {
-        $instance = FirePHP::getInstance(true);
-        return $instance->getOptions();
-    }
-
-    /**
-     * Log object to firebug
-     * 
-     * @see http://www.firephp.org/Wiki/Reference/Fb
-     * @param mixed $Object
-     * @return true
-     * @throws Exception
-     */
-    public static function send()
-    {
-        $instance = FirePHP::getInstance(true);
-        $args = func_get_args();
-        return call_user_func_array(array($instance,'fb'),$args);
-    }
-
-    /**
-     * Start a group for following messages
-     * 
-     * Options:
-     *   Collapsed: [true|false]
-     *   Color:     [#RRGGBB|ColorName]
-     *
-     * @param string $Name
-     * @param array $Options OPTIONAL Instructions on how to log the group
-     * @return true
-     */
-    public static function group($Name, $Options=null)
-    {
-        $instance = FirePHP::getInstance(true);
-        return $instance->group($Name, $Options);
-    }
-
-    /**
-     * Ends a group you have started before
-     *
-     * @return true
-     * @throws Exception
-     */
-    public static function groupEnd()
-    {
-        return self::send(null, null, FirePHP::GROUP_END);
-    }
-
-    /**
-     * Log object with label to firebug console
-     *
-     * @see FirePHP::LOG
-     * @param mixes $Object
-     * @param string $Label
-     * @return true
-     * @throws Exception
-     */
-    public static function log($Object, $Label=null)
-    {
-        return self::send($Object, $Label, FirePHP::LOG);
-    } 
-
-    /**
-     * Log object with label to firebug console
-     *
-     * @see FirePHP::INFO
-     * @param mixes $Object
-     * @param string $Label
-     * @return true
-     * @throws Exception
-     */
-    public static function info($Object, $Label=null)
-    {
-        return self::send($Object, $Label, FirePHP::INFO);
-    } 
-
-    /**
-     * Log object with label to firebug console
-     *
-     * @see FirePHP::WARN
-     * @param mixes $Object
-     * @param string $Label
-     * @return true
-     * @throws Exception
-     */
-    public static function warn($Object, $Label=null)
-    {
-        return self::send($Object, $Label, FirePHP::WARN);
-    } 
-
-    /**
-     * Log object with label to firebug console
-     *
-     * @see FirePHP::ERROR
-     * @param mixes $Object
-     * @param string $Label
-     * @return true
-     * @throws Exception
-     */
-    public static function error($Object, $Label=null)
-    {
-        return self::send($Object, $Label, FirePHP::ERROR);
-    } 
-
-    /**
-     * Dumps key and variable to firebug server panel
-     *
-     * @see FirePHP::DUMP
-     * @param string $Key
-     * @param mixed $Variable
-     * @return true
-     * @throws Exception
-     */
-    public static function dump($Key, $Variable)
-    {
-        return self::send($Variable, $Key, FirePHP::DUMP);
-    } 
-
-    /**
-     * Log a trace in the firebug console
-     *
-     * @see FirePHP::TRACE
-     * @param string $Label
-     * @return true
-     * @throws Exception
-     */
-    public static function trace($Label)
-    {
-        return self::send($Label, FirePHP::TRACE);
-    } 
-
-    /**
-     * Log a table in the firebug console
-     *
-     * @see FirePHP::TABLE
-     * @param string $Label
-     * @param string $Table
-     * @return true
-     * @throws Exception
-     */
-    public static function table($Label, $Table)
-    {
-        return self::send($Table, $Label, FirePHP::TABLE);
-    } 
-
-}
diff --git a/engine/external/pear/FirePHPCore/fb.php4 b/engine/external/pear/FirePHPCore/fb.php4
deleted file mode 100644
index b0688cfe..00000000
--- a/engine/external/pear/FirePHPCore/fb.php4
+++ /dev/null
@@ -1,251 +0,0 @@
-<?php
-
-/* ***** BEGIN LICENSE BLOCK *****
- *  
- * This file is part of FirePHP (http://www.firephp.org/).
- * 
- * Software License Agreement (New BSD License)
- * 
- * Copyright (c) 2006-2010, Christoph Dorn
- * All rights reserved.
- * 
- * Redistribution and use in source and binary forms, with or without modification,
- * are permitted provided that the following conditions are met:
- * 
- *     * Redistributions of source code must retain the above copyright notice,
- *       this list of conditions and the following disclaimer.
- * 
- *     * Redistributions in binary form must reproduce the above copyright notice,
- *       this list of conditions and the following disclaimer in the documentation
- *       and/or other materials provided with the distribution.
- * 
- *     * Neither the name of Christoph Dorn nor the names of its
- *       contributors may be used to endorse or promote products derived from this
- *       software without specific prior written permission.
- * 
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
- * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
- * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- * 
- * ***** END LICENSE BLOCK *****
- * 
- * @copyright   Copyright (C) 2007-2009 Christoph Dorn
- * @author      Christoph Dorn <christoph@christophdorn.com>
- * @author      Michael Day <manveru.alma@gmail.com>
- * @license     http://www.opensource.org/licenses/bsd-license.php
- * @package     FirePHPCore
- */
-
-require_once dirname(__FILE__).'/FirePHP.class.php4';
-
-/**
- * Sends the given data to the FirePHP Firefox Extension.
- * The data can be displayed in the Firebug Console or in the
- * "Server" request tab.
- * 
- * @see http://www.firephp.org/Wiki/Reference/Fb
- * @param mixed $Object
- * @return true
- * @throws Exception
- */
-function fb()
-{
-  $instance =& FirePHP::getInstance(true);
-
-  $args = func_get_args();
-  return call_user_func_array(array(&$instance,'fb'),$args);
-}
-
-
-class FB
-{
-  /**
-   * Enable and disable logging to Firebug
-   * 
-   * @see FirePHP->setEnabled()
-   * @param boolean $Enabled TRUE to enable, FALSE to disable
-   * @return void
-   */
-  function setEnabled($Enabled) {
-    $instance =& FirePHP::getInstance(true);
-    $instance->setEnabled($Enabled);
-  }
-  
-  /**
-   * Check if logging is enabled
-   * 
-   * @see FirePHP->getEnabled()
-   * @return boolean TRUE if enabled
-   */
-  function getEnabled() {
-    $instance =& FirePHP::getInstance(true);
-    return $instance->getEnabled();
-  }  
-  
-  /**
-   * Specify a filter to be used when encoding an object
-   * 
-   * Filters are used to exclude object members.
-   * 
-   * @see FirePHP->setObjectFilter()
-   * @param string $Class The class name of the object
-   * @param array $Filter An array or members to exclude
-   * @return void
-   */
-  function setObjectFilter($Class, $Filter) {
-    $instance =& FirePHP::getInstance(true);
-    $instance->setObjectFilter($Class, $Filter);
-  }
-  
-  /**
-   * Set some options for the library
-   * 
-   * @see FirePHP->setOptions()
-   * @param array $Options The options to be set
-   * @return void
-   */
-  function setOptions($Options) {
-    $instance =& FirePHP::getInstance(true);
-    $instance->setOptions($Options);
-  }
-
-  /**
-   * Get options for the library
-   * 
-   * @see FirePHP->getOptions()
-   * @return array The options
-   */
-  function getOptions() {
-    $instance =& FirePHP::getInstance(true);
-    return $instance->getOptions();
-  }
-
-  /**
-   * Log object to firebug
-   * 
-   * @see http://www.firephp.org/Wiki/Reference/Fb
-   * @param mixed $Object
-   * @return true
-   */
-  function send()
-  {
-    $instance =& FirePHP::getInstance(true);
-    $args = func_get_args();
-    return call_user_func_array(array(&$instance,'fb'),$args);
-  }
-
-  /**
-   * Start a group for following messages
-   * 
-   * Options:
-   *   Collapsed: [true|false]
-   *   Color:     [#RRGGBB|ColorName]
-   *
-   * @param string $Name
-   * @param array $Options OPTIONAL Instructions on how to log the group
-   * @return true
-   */
-  function group($Name, $Options=null) {
-    $instance =& FirePHP::getInstance(true);
-    return $instance->group($Name, $Options);
-  }
-
-  /**
-   * Ends a group you have started before
-   *
-   * @return true
-   */
-  function groupEnd() {
-    return FB::send(null, null, FirePHP_GROUP_END);
-  }
-
-  /**
-   * Log object with label to firebug console
-   *
-   * @see FirePHP::LOG
-   * @param mixes $Object
-   * @param string $Label
-   * @return true
-   */
-  function log($Object, $Label=null) {
-    return FB::send($Object, $Label, FirePHP_LOG);
-  } 
-
-  /**
-   * Log object with label to firebug console
-   *
-   * @see FirePHP::INFO
-   * @param mixes $Object
-   * @param string $Label
-   * @return true
-   */
-  function info($Object, $Label=null) {
-    return FB::send($Object, $Label, FirePHP_INFO);
-  } 
-
-  /**
-   * Log object with label to firebug console
-   *
-   * @see FirePHP::WARN
-   * @param mixes $Object
-   * @param string $Label
-   * @return true
-   */
-  function warn($Object, $Label=null) {
-    return FB::send($Object, $Label, FirePHP_WARN);
-  } 
-
-  /**
-   * Log object with label to firebug console
-   *
-   * @see FirePHP::ERROR
-   * @param mixes $Object
-   * @param string $Label
-   * @return true
-   */
-  function error($Object, $Label=null) {
-    return FB::send($Object, $Label, FirePHP_ERROR);
-  } 
-
-  /**
-   * Dumps key and variable to firebug server panel
-   *
-   * @see FirePHP::DUMP
-   * @param string $Key
-   * @param mixed $Variable
-   * @return true
-   */
-  function dump($Key, $Variable) {
-    return FB::send($Variable, $Key, FirePHP_DUMP);
-  } 
-
-  /**
-   * Log a trace in the firebug console
-   *
-   * @see FirePHP::TRACE
-   * @param string $Label
-   * @return true
-   */
-  function trace($Label) {
-    return FB::send($Label, FirePHP_TRACE);
-  } 
-
-  /**
-   * Log a table in the firebug console
-   *
-   * @see FirePHP::TABLE
-   * @param string $Label
-   * @param string $Table
-   * @return true
-   */
-  function table($Label, $Table) {
-    return FB::send($Table, $Label, FirePHP_TABLE);
-  } 
-}

From 8dfe64e685ab6cb7fd2e673ee634b9e933149963 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Thu, 17 Mar 2022 19:23:41 +0100
Subject: [PATCH 072/154] test if logged before get user_id

---
 engine/page/page_home.php | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/engine/page/page_home.php b/engine/page/page_home.php
index fa60a5dd..e721ab1a 100644
--- a/engine/page/page_home.php
+++ b/engine/page/page_home.php
@@ -17,7 +17,9 @@ function __construct()
     function execute(){
 		global $user;
 
-        $user_id = intval($user["user_id"]);
+        $user_id = isset($user["user_id"]) 
+                    ? intval($user["user_id"])
+                    : null ;
 		
 		$private_corpora = DbCorpus::getPrivateCorporaForUser($user_id, intval(hasRole(USER_ROLE_ADMIN)));
 		$public_corpora = DbCorpus::getCorpora(1);

From 1c7f6f7de0d2425a412f18a87065858f0d6fe333 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Fri, 18 Mar 2022 09:14:31 +0100
Subject: [PATCH 073/154] FirePHP module included only in developement
 environment

---
 engine/include/CInforexWeb.php       | 7 ++++---
 engine/include/database/Database.php | 5 ++++-
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/engine/include/CInforexWeb.php b/engine/include/CInforexWeb.php
index 77797e16..6bfcd9d7 100644
--- a/engine/include/CInforexWeb.php
+++ b/engine/include/CInforexWeb.php
@@ -24,10 +24,11 @@ function __construct()
         set_exception_handler('InforexWeb::custom_exception_handler');
 
         /********************************************************************8
-         * Aktywuj FireBug-a
+         * Aktywuj FireBug-a - only in developement environment
          */
-        FB::setEnabled(true);
-
+        if (class_exists('FB')) {
+            FB::setEnabled(true);
+        }
         /********************************************************************8
          * Rozpocznij sesję
          */
diff --git a/engine/include/database/Database.php b/engine/include/database/Database.php
index 6879091b..ef7da250 100644
--- a/engine/include/database/Database.php
+++ b/engine/include/database/Database.php
@@ -93,7 +93,10 @@ private function log_sql($sql, $args){
 				ChromePhp::log($args);
 				ChromePhp::log($backtrace);
 			}
-			elseif ($this->log_output == "fb"){
+            // FB class included only in dev environment
+			elseif (    ($this->log_output == "fb")
+                        && (class_exists('FB'))
+                   ) {
 				FB::info($sql, "SQL LOG");
 				fb($args, "Args");
 				fb($backtrace, "Backtrace");

From b367d37ec22ce8675fa3d2337011cce512d7a17d Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Sat, 26 Mar 2022 09:34:01 +0100
Subject: [PATCH 074/154] missing default config state insertSentenceTags

---
 engine/Config/Config.php | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/engine/Config/Config.php b/engine/Config/Config.php
index 1970a3d9..8670a654 100644
--- a/engine/Config/Config.php
+++ b/engine/Config/Config.php
@@ -13,7 +13,7 @@ public function __call($name, $arguments)
         throw new ConfigException("Method {$name} is not supported.");
     }
 
-} // Phamtom class
+} // Phantom class
 
 use engine\Config\Singleton as Singleton;
 
@@ -63,6 +63,8 @@ class Config extends Singleton\Singleton{
 		), 	
 		
 		"wccl_match_daemon" => null,
+        // default settings for wccl import
+        "insertSentenceTags" => true,
 
 	/* Advanced parameters */
 		"path_python"       => 'python',

From bd540671bd795f318af7365365a88b2f4faf5c06 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Sat, 26 Mar 2022 13:14:53 +0100
Subject: [PATCH 075/154] main catch service should be smarter

---
 public_html/index.php | 27 ++++++++++++++++++++++++---
 1 file changed, 24 insertions(+), 3 deletions(-)

diff --git a/public_html/index.php b/public_html/index.php
index bcd42d8c..2820b461 100644
--- a/public_html/index.php
+++ b/public_html/index.php
@@ -12,6 +12,7 @@
 	$enginePath = realpath(__DIR__ . "/../engine/");
 	require_once($enginePath."/settings.php");
 	require_once($enginePath.'/include.php');
+    
 	Config::Config()->put_path_engine($enginePath);
 	Config::Config()->put_localConfigFilename(realpath($enginePath."/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
@@ -65,7 +66,27 @@
 	print trim(ob_get_clean());
 }
 catch(Exception $e){
-	print "Unexpected exception: <b>" . $e->getMessage() . "</b>";
-	print "<pre>".$e->getTraceAsString()."</pre>";
-    print trim(ob_get_clean());
+	//print "Unexpected exception: <b>" . $e->getMessage() . "</b>";
+	//print "<pre>".$e->getTraceAsString()."</pre>";
+    //print trim(ob_get_clean());
+
+    $NL=''; $BOpen=''; $BClose=''; $PreOpen=''; $PreClose='';
+    if (php_sapi_name() !== "cli") {
+        $NL = '<br/>'; $BOpen='<b>'; $BClose='</b>'; $PreOpen='<pre>'; $PreClose='<pre/>';
+    }
+    $NL .= "\n";
+    if(ini_get('display_errors')){
+        print("Uncaught exception: ".$BOpen. $e->getMessage().$BClose.$NL);
+        print($PreOpen." in file ".$e->getFile()." on line ".$e->getLine().$PreClose.$NL);
+        print($PreOpen.$e->getTraceAsString().$PreClose.$NL);
+    } else {
+        print($BOpen."Uncaught exception has been occurred.".$BClose.$NL);
+        print("Please try again later.".$NL);
+    }
+    // komunikat o błędzie do logu - zawsze, chyba że zablokujemy w ogóle
+    if(ini_get('log_errors')){
+        //error_log("Uncaught exception: ".print_r($e,true));
+        error_log("Uncaught exception: ".$e->getMessage()." in file ".$e->getFile()." on line ".$e->getLine()." Trace:".$e->getTraceAsString());
+    }
+
 }

From dbb17623d2974895f2093821f47d0aa41debfe6e Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Mon, 28 Mar 2022 21:41:14 +0200
Subject: [PATCH 076/154] move exception service to static class

---
 .../exceptions/UncaughtExceptionService.php   | 104 +++++++++++++++++
 engine/include/utils/PHPUnitTools.php         |  27 +++++
 engine/settings.php                           | 110 +-----------------
 public_html/index.php                         |  32 +----
 4 files changed, 141 insertions(+), 132 deletions(-)
 create mode 100644 engine/include/exceptions/UncaughtExceptionService.php
 create mode 100644 engine/include/utils/PHPUnitTools.php

diff --git a/engine/include/exceptions/UncaughtExceptionService.php b/engine/include/exceptions/UncaughtExceptionService.php
new file mode 100644
index 00000000..c030fe8d
--- /dev/null
+++ b/engine/include/exceptions/UncaughtExceptionService.php
@@ -0,0 +1,104 @@
+<?php
+/**
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ * See LICENCE
+ */
+
+class UncaughtExceptionService {
+
+    static public function errorClearLast() {
+
+        if(version_compare(phpversion(),'7.0.0','<')) {
+            // for PHP5 there is no error_clear_last()
+            // hint: dummy handler convert all errors from level 0
+            //  to well recognizable specific error
+            //  below former handler is pushed to internal stack
+            set_error_handler('var_dump', 0);
+            // call dummy handler for error undef var
+            // sets internal register to specific error
+            // @ for not console reporting
+            @$undef_var_with_ambigous_characteristic_name;
+            // restore ( pop ) previous handler from internal stack
+            restore_error_handler();
+        } else {
+            error_clear_last();
+        }
+
+    } // errorClearLast()
+
+    static public function errorGetLast() {
+
+        $result = error_get_last();
+        if(version_compare(phpversion(),'7.0.0','<')) {
+            // detect:
+            // ["message"]=="Undefined variable: undef_var_with_ambigous_characteristic_name"
+            if(is_array($result)
+                && ( isset($result["message"])
+                    && preg_match('/undef_var_with_ambigous_characteristic_name/',$result["message"])
+                )
+            ) {
+                // error was reseted by errorClearLast()
+                return null;
+            } else {
+                return $result;
+            }
+        } else {
+            return $result;
+        }
+
+    }  // errorGetLast()
+ 
+
+    static public function dummyMessage4User() {
+
+        // dummy message masks error details for user
+        // and writes general error information
+        $NL='';
+        $H1Open=''; $H1Close='';
+        if (php_sapi_name() !== "cli") {
+            $NL = '<br/>';
+            $H1Open='<h1>'; $H1Close='</h1>';
+        }
+        $NL .= "\n";
+
+        print($H1Open."500 Internal Server Error".$H1Close.$NL);
+        print("An internal server error has been occurred.".$NL);
+        print("Please try again later.".$NL);
+
+    } // dummyMessage4User
+
+    static public function UncaughtException(Exception $e) {
+
+        $NL=''; $BOpen=''; $BClose=''; $PreOpen=''; $PreClose='';
+        if (php_sapi_name() !== "cli") {
+            $NL = '<br/>'; $BOpen='<b>'; $BClose='</b>'; $PreOpen='<pre>'; $PreClose='<pre/>';
+            // there actions for browser environment
+            http_response_code(500);
+        }
+        $NL .= "\n";
+
+        if(ini_get('display_errors')){
+            print("Uncaught exception: ".$BOpen. $e->getMessage().$BClose.$NL);
+            print($PreOpen." in file ".$e->getFile()." on line ".$e->getLine().$PreClose.$NL);
+            print($PreOpen.$e->getTraceAsString().$PreClose.$NL);
+        } else {
+            print($BOpen."Uncaught exception has been occurred.".$BClose.$NL);
+            print("Please try again later.".$NL);
+        }
+        // komunikat o błędzie do logu - zawsze, chyba że zablokujemy w ogóle
+        if(ini_get('log_errors')){
+            //error_log("Uncaught exception: ".print_r($e,true));
+            error_log("Uncaught exception: ".$e->getMessage()." in file ".$e->getFile()." on line ".$e->getLine()." Trace:".$e->getTraceAsString());
+        }
+   
+        // serviced errors shouldn't be processed again
+        self::errorClearLast();
+
+    } // UncaughtException()
+
+
+} // UncaughtExceptionService class
+
+?>
diff --git a/engine/include/utils/PHPUnitTools.php b/engine/include/utils/PHPUnitTools.php
new file mode 100644
index 00000000..2ba5583c
--- /dev/null
+++ b/engine/include/utils/PHPUnitTools.php
@@ -0,0 +1,27 @@
+<?php
+/**
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ * See LICENCE
+ */
+
+class PHPUnitTools {
+
+    static public function isPHPUnitRunning() {
+
+        // detect if code running under PHPUnit control
+        //  two constatnts are defined by this system
+        if (! defined('PHPUNIT_COMPOSER_INSTALL') 
+            && ! defined('__PHPUNIT_PHAR__')) {
+            // is not PHPUnit run
+            return False;
+        } else {
+            return True;
+        } 
+
+    } // isPHPUnitRunning()
+
+} // PHPUnitTools class
+
+?>
diff --git a/engine/settings.php b/engine/settings.php
index f79572fd..b6bb3a3e 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -16,47 +16,6 @@
 ini_set("short_open_tag",1);
 setlocale(LC_CTYPE, "en_US.UTF-8");		
 
-function errorClearLast() {
-
-       if(version_compare(phpversion(),'7.0.0','<')) {
-               // for PHP5 there is no error_clear_last()
-               // hint: dummy handler convert all errors from level 0
-               //  to well recognizable specific error
-               //  below former handler is pushed to internal stack
-               set_error_handler('var_dump', 0);
-               // call dummy handler for error undef var
-               // sets internal register to specific error
-               // @ for not console reporting
-               @$undef_var_with_ambigous_characteristic_name;
-               // restore ( pop ) previous handler from internal stack
-               restore_error_handler();
-       } else {
-               error_clear_last();
-       }
-
-} // errorClearLast()
-
-function errorGetLast() {
-
-        $result = error_get_last();
-        if(version_compare(phpversion(),'7.0.0','<')) {
-                // detect:
-                // ["message"]=="Undefined variable: undef_var_with_ambigous_characteristic_name"
-		if(is_array($result)
-                   && ( isset($result["message"])
-                        && preg_match('/undef_var_with_ambigous_characteristic_name/',$result["message"])                                                                             )
-                  ) {
-                        // error was reseted by errorClearLast()
-                        return null;
-                } else {
-                        return $result;
-                }
-        } else {
-                return $result;
-        }
-
-}  // errorGetLast()
- 
 function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0) {
 
     //print("inforexCentralErrorHandler \n");
@@ -65,14 +24,14 @@ function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0)
     $systemErrorReporting = error_reporting();
     if( ($systemErrorReporting & $level) == 0 ) {
         // this error level is masked by system settings
-	errorClearLast();
+	    UncaughtExceptionService::errorClearLast();
         return;
     }   
 
 	// silently drop ugly strict double constructor report in PHP < 7
 	if(version_compare(phpversion(),'7.0.0','<')) {
 		if(preg_match("/^Redefining already defined constructor for class Config/",$message)) {
-			errorClearLast();
+			UncaughtExceptionService::errorClearLast();
 			return;
 		}
 	} // ver < 7.0
@@ -86,59 +45,13 @@ function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0)
 
 set_error_handler("inforexCentralErrorHandler");
 
-function inforexInitialExceptionHandler ($e) {
-
-    // common handler for all exceptiom before CInforexWebPage was 
-    // constructed.
-    //print("inforexInitialExceptionHandler \n");
-
-    // Uncaught exception reporting main code
-    // reports to http server logs anyway
-    error_log($e);
-    // on CLI console all was done, do nothing more
-    if (php_sapi_name() !== "cli") {
-        // there actions for browser environment
-        http_response_code(500);
-        // if set display_errors write information on screen
-        if (ini_get("display_errors")) {
-            echo $e;
-        } else {
-            // dummy message for user
-            dummyMessage4User();
-        } // display_errors
-    } // ! CLI
-
-    // serviced errors shouldn't be processed again
-    errorClearLast();
-
-} // inforexInitialExceptionHandler()
-
-function dummyMessage4User() {
-
-    // dummy message masks error details for user
-    // and writes general error information
-    $NL='';
-    $H1Open=''; $H1Close='';
-    if (php_sapi_name() !== "cli") {
-        $NL = '<br/>';
-        $H1Open='<h1>'; $H1Close='</h1>';
-    }
-    $NL .= "\n";
-    print($H1Open."500 Internal Server Error".$H1Close.$NL);
-    print("An internal server error has been occurred.".$NL);
-    print("Please try again later.".$NL);
-
-} // dummyMessage4User
-
-set_exception_handler("inforexInitialExceptionHandler");
-
 function inforexShutdownFunction() {
 
     //print("inforexShutdownFunction \n");
     // returns null or array( "type"=>, "message"=>, "file"=>, "line"=> )
     // if earlier inforexInitialExceptionHandler was called, there not
     // will be reported twice 
-    $error = errorGetLast();
+    $error = UncaughtExceptionService::errorGetLast();
     if ($error !== null) {
         /*
         $e = new ErrorException(
@@ -148,26 +61,13 @@ function inforexShutdownFunction() {
         */
         // dummy message if not errors displayed by system
         if (!ini_get("display_errors")) {
-            dummyMessage4User();
+            UncaughtExceptionService::dummyMessage4User();
         }
     }
 
 } // inforexShutdownFunction()  
 
-function isPHPUnitRunning() {
-
-	// detect if code running under PHPUnit control
-	//  two constatnts are defined by this system
-	if (! defined('PHPUNIT_COMPOSER_INSTALL') && ! defined('__PHPUNIT_PHAR__')) {
-    		// is not PHPUnit run
-    		return False;
-	} else {
-		return True;
-	}
-
-} // isPHPUnitRunning()
-
-if(! isPHPUnitRunning()) {
+if(! PHPUnitTools::isPHPUnitRunning()) {
 	// under PHPUnit this one not works
 	register_shutdown_function("inforexShutdownFunction");
 }
diff --git a/public_html/index.php b/public_html/index.php
index 2820b461..0d120c72 100644
--- a/public_html/index.php
+++ b/public_html/index.php
@@ -7,12 +7,12 @@
  */
 
 ob_start();
+$enginePath = realpath(__DIR__ . "/../engine/");
+require_once($enginePath.'/include.php');
+require_once($enginePath."/settings.php");
+//require_once($enginePath.'/include.php');
 try{
 	/********************************************************************/
-	$enginePath = realpath(__DIR__ . "/../engine/");
-	require_once($enginePath."/settings.php");
-	require_once($enginePath.'/include.php');
-    
 	Config::Config()->put_path_engine($enginePath);
 	Config::Config()->put_localConfigFilename(realpath($enginePath."/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
@@ -66,27 +66,5 @@
 	print trim(ob_get_clean());
 }
 catch(Exception $e){
-	//print "Unexpected exception: <b>" . $e->getMessage() . "</b>";
-	//print "<pre>".$e->getTraceAsString()."</pre>";
-    //print trim(ob_get_clean());
-
-    $NL=''; $BOpen=''; $BClose=''; $PreOpen=''; $PreClose='';
-    if (php_sapi_name() !== "cli") {
-        $NL = '<br/>'; $BOpen='<b>'; $BClose='</b>'; $PreOpen='<pre>'; $PreClose='<pre/>';
-    }
-    $NL .= "\n";
-    if(ini_get('display_errors')){
-        print("Uncaught exception: ".$BOpen. $e->getMessage().$BClose.$NL);
-        print($PreOpen." in file ".$e->getFile()." on line ".$e->getLine().$PreClose.$NL);
-        print($PreOpen.$e->getTraceAsString().$PreClose.$NL);
-    } else {
-        print($BOpen."Uncaught exception has been occurred.".$BClose.$NL);
-        print("Please try again later.".$NL);
-    }
-    // komunikat o błędzie do logu - zawsze, chyba że zablokujemy w ogóle
-    if(ini_get('log_errors')){
-        //error_log("Uncaught exception: ".print_r($e,true));
-        error_log("Uncaught exception: ".$e->getMessage()." in file ".$e->getFile()." on line ".$e->getLine()." Trace:".$e->getTraceAsString());
-    }
-
+    UncaughtExceptionService::UncaughtException($e);
 }

From 96069e67f7e95ce7392cff072f5e97c7c967a643 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Fri, 1 Apr 2022 09:27:27 +0200
Subject: [PATCH 077/154] error to exception smart conversion

---
 engine/settings.php | 172 +++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 171 insertions(+), 1 deletion(-)

diff --git a/engine/settings.php b/engine/settings.php
index b6bb3a3e..30e4603c 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -38,12 +38,182 @@ function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0)
 
 	// converts all not masked errors to exceptions
     //  there are no return from exception to code continue...
+    $severities = [
+        E_ERROR => 'ERROR',
+        E_WARNING => 'WARNING',
+        E_PARSE => 'PARSE',
+        E_NOTICE => 'NOTICE',
+        E_CORE_ERROR => 'CORE_ERROR',
+        E_CORE_WARNING => 'CORE_WARNING',
+        E_COMPILE_ERROR => 'COMPILE_ERROR',
+        E_COMPILE_WARNING => 'COMPILE_WARNING',
+        E_USER_ERROR => 'USER_ERROR',
+        E_USER_WARNING => 'USER_WARNING',
+        E_USER_NOTICE => 'USER_NOTICE',
+        E_STRICT => 'STRICT',
+        E_RECOVERABLE_ERROR => 'RECOVERABLE_ERROR',
+        E_DEPRECATED => 'DEPRECATED',
+        E_USER_DEPRECATED => 'USER_DEPRECATED',
+    ];
     $extended_message = "[".$level."] ".$message." in ".$file.":".$line;
-	throw new ErrorException($extended_message, 0, $level, $file, $line);
+    $e = new Exception($extended_message, 0);
+    // Just remove the current point from the trace
+    $reflection = new ReflectionProperty(get_class($e), 'trace');
+    $reflection->setAccessible(true);
+    $trace = $reflection->getValue($e);
+    array_shift($trace);
+    $reflection->setValue($e, $trace);
+
+    $text = '';
+    $text .= ($severities[$level] ?? $level) . ': ';
+    $text .= "$message in $file($line)\n";
+    $text .= "Stack trace:\n";
+    $text .= $e->getTraceAsString();
+
+    throw($e);
+
+    //throw new ErrorException($text, 0, $level, $file, $line);
+
+    //$extended_message = "[".$level."] ".$message." in ".$file.":".$line;
+	//throw new ErrorException($extended_message, 0, $level, $file, $line);
 
 }  // inforexCentralErrorHandler()
 
+function process_error_backtrace($errno, $errstr, $errfile, $errline, $errcontext) {
+    if(!(error_reporting() & $errno))
+        return;
+    switch($errno) {
+    case E_WARNING      :
+    case E_USER_WARNING :
+    case E_STRICT       :
+    case E_NOTICE       :
+    case E_USER_NOTICE  :
+        $type = 'warning';
+        $fatal = false;
+        break;
+    default             :
+        $type = 'fatal error';
+        $fatal = true;
+        break;
+    }
+    $trace = array_reverse(debug_backtrace());
+    array_pop($trace);
+    if(php_sapi_name() == 'cli') {
+        echo 'Backtrace from ' . $type . ' \'' . $errstr . '\' at ' . $errfile . ' ' . $errline . ':' . "\n";
+        foreach($trace as $item)
+            echo '  ' . (isset($item['file']) ? $item['file'] : '<unknown file>') . ' ' . (isset($item['line']) ? $item['line'] : '<unknown line>') . ' calling ' . $item['function'] . '()' . "\n";
+    } else {
+        echo '<p class="error_backtrace">' . "\n";
+        echo '  Backtrace from ' . $type . ' \'' . $errstr . '\' at ' . $errfile . ' ' . $errline . ':' . "\n";
+        echo '  <ol>' . "\n";
+        foreach($trace as $item)
+            echo '    <li>' . (isset($item['file']) ? $item['file'] : '<unknown file>') . ' ' . (isset($item['line']) ? $item['line'] : '<unknown line>') . ' calling ' . $item['function'] . '()</li>' . "\n";
+        echo '  </ol>' . "\n";
+        echo '</p>' . "\n";
+    }
+    if(ini_get('log_errors')) {
+        $items = array();
+        foreach($trace as $item)
+            $items[] = (isset($item['file']) ? $item['file'] : '<unknown file>') . ' ' . (isset($item['line']) ? $item['line'] : '<unknown line>') . ' calling ' . $item['function'] . '()';
+        $message = 'Backtrace from ' . $type . ' \'' . $errstr . '\' at ' . $errfile . ' ' . $errline . ': ' . join(' | ', $items);
+        error_log($message);
+    }
+    if($fatal)
+        exit(1);
+}
+
 set_error_handler("inforexCentralErrorHandler");
+//set_error_handler("process_error_backtrace");
+/*
+set_error_handler(function(int $severity, string $message, string $file, int $line) {
+    if (!(error_reporting() & $severity)) {
+        return false;
+    }
+
+    $severities = [
+        E_ERROR => 'ERROR',
+        E_WARNING => 'WARNING',
+        E_PARSE => 'PARSE',
+        E_NOTICE => 'NOTICE',
+        E_CORE_ERROR => 'CORE_ERROR',
+        E_CORE_WARNING => 'CORE_WARNING',
+        E_COMPILE_ERROR => 'COMPILE_ERROR',
+        E_COMPILE_WARNING => 'COMPILE_WARNING',
+        E_USER_ERROR => 'USER_ERROR',
+        E_USER_WARNING => 'USER_WARNING',
+        E_USER_NOTICE => 'USER_NOTICE',
+        E_STRICT => 'STRICT',
+        E_RECOVERABLE_ERROR => 'RECOVERABLE_ERROR',
+        E_DEPRECATED => 'DEPRECATED',
+        E_USER_DEPRECATED => 'USER_DEPRECATED',
+    ];
+
+    $e = new \Exception;
+
+    // Just remove the current point from the trace
+    $reflection = new \ReflectionProperty(get_class($e), 'trace');
+    $reflection->setAccessible(true);
+    $trace = $reflection->getValue($e);
+    array_shift($trace);
+    $reflection->setValue($e, $trace);
+
+    $text = '';
+    $text .= ($severities[$severity] ?? $severity) . ': ';
+    $text .= "$message in $file($line)\n";
+    $text .= "Stack trace:\n";
+    $text .= $e->getTraceAsString();
+
+    error_log($text);
+
+    if (in_array($severity, [
+        E_CORE_ERROR,
+        E_ERROR,
+        E_RECOVERABLE_ERROR,
+        E_PARSE,
+        E_COMPILE_ERROR,
+        E_USER_ERROR,
+    ], true)) {
+        http_response_code(500);
+        exit(255);
+    }
+
+    return true;
+});
+*/
+// Give an extra parameter to the filename
+// to save multiple log files
+function _fatalog_($extra = false)
+{
+    static $last_extra;
+
+    // CHANGE THIS TO: A writeable filepath in your system...
+    $filepath = '/var/www/html/sites/default/files/fatal-'.($extra === false ? $last_extra : $extra).'.log';
+
+    if ($extra===false) {
+        unlink($filepath);
+    } else {
+        // we write a log file with the debug info
+        file_put_contents($filepath, json_encode(debug_backtrace()));
+        // saving last extra parameter for future unlink... if possible...
+        $last_extra = $extra;
+    }
+}
+/*
+Here's an example of how to use it:
+
+// A function which will produce a fatal error
+function fatal_example()
+{
+    _fatalog_(time()); // writing the log
+    $some_fatal_code = array()/3; // fatality!
+    _fatalog_(); // if we get here then delete last file log
+}
+
+Finally to read the contents of the log...
+
+var_dump(json_decode(file_get_contents('/path/to-the-fatal.log')));
+
+*/
 
 function inforexShutdownFunction() {
 

From 3d14ce149a8d28e74493296e8be7fee613630a4d Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Fri, 1 Apr 2022 09:27:27 +0200
Subject: [PATCH 078/154] error to exception smart conversion

---
 engine/settings.php | 180 +++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 179 insertions(+), 1 deletion(-)

diff --git a/engine/settings.php b/engine/settings.php
index b6bb3a3e..7a28080a 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -38,12 +38,190 @@ function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0)
 
 	// converts all not masked errors to exceptions
     //  there are no return from exception to code continue...
+    $severities = [
+        E_ERROR => 'ERROR',
+        E_WARNING => 'WARNING',
+        E_PARSE => 'PARSE',
+        E_NOTICE => 'NOTICE',
+        E_CORE_ERROR => 'CORE_ERROR',
+        E_CORE_WARNING => 'CORE_WARNING',
+        E_COMPILE_ERROR => 'COMPILE_ERROR',
+        E_COMPILE_WARNING => 'COMPILE_WARNING',
+        E_USER_ERROR => 'USER_ERROR',
+        E_USER_WARNING => 'USER_WARNING',
+        E_USER_NOTICE => 'USER_NOTICE',
+        E_STRICT => 'STRICT',
+        E_RECOVERABLE_ERROR => 'RECOVERABLE_ERROR',
+        E_DEPRECATED => 'DEPRECATED',
+        E_USER_DEPRECATED => 'USER_DEPRECATED',
+    ];
     $extended_message = "[".$level."] ".$message." in ".$file.":".$line;
-	throw new ErrorException($extended_message, 0, $level, $file, $line);
+    $e = new Exception($extended_message, 0);
+    // Just remove the current point from the trace
+    $reflection = new ReflectionProperty(get_class($e), 'trace');
+    $reflection->setAccessible(true);
+    $trace = $reflection->getValue($e);
+    array_shift($trace);
+    $reflection->setValue($e, $trace);
+
+    $reflection = new ReflectionProperty(get_class($e), 'file');
+    $reflection->setAccessible(true);
+    $reflection->setValue($e, $file);
+    $reflection = new ReflectionProperty(get_class($e), 'line');
+    $reflection->setAccessible(true);
+    $reflection->setValue($e, $line);
+
+    $text = '';
+    $text .= ($severities[$level] ?? $level) . ': ';
+    $text .= "$message in $file($line)\n";
+    $text .= "Stack trace:\n";
+    $text .= $e->getTraceAsString();
+
+    throw($e);
+
+    //throw new ErrorException($text, 0, $level, $file, $line);
+
+    //$extended_message = "[".$level."] ".$message." in ".$file.":".$line;
+	//throw new ErrorException($extended_message, 0, $level, $file, $line);
 
 }  // inforexCentralErrorHandler()
 
+function process_error_backtrace($errno, $errstr, $errfile, $errline, $errcontext) {
+    if(!(error_reporting() & $errno))
+        return;
+    switch($errno) {
+    case E_WARNING      :
+    case E_USER_WARNING :
+    case E_STRICT       :
+    case E_NOTICE       :
+    case E_USER_NOTICE  :
+        $type = 'warning';
+        $fatal = false;
+        break;
+    default             :
+        $type = 'fatal error';
+        $fatal = true;
+        break;
+    }
+    $trace = array_reverse(debug_backtrace());
+    array_pop($trace);
+    if(php_sapi_name() == 'cli') {
+        echo 'Backtrace from ' . $type . ' \'' . $errstr . '\' at ' . $errfile . ' ' . $errline . ':' . "\n";
+        foreach($trace as $item)
+            echo '  ' . (isset($item['file']) ? $item['file'] : '<unknown file>') . ' ' . (isset($item['line']) ? $item['line'] : '<unknown line>') . ' calling ' . $item['function'] . '()' . "\n";
+    } else {
+        echo '<p class="error_backtrace">' . "\n";
+        echo '  Backtrace from ' . $type . ' \'' . $errstr . '\' at ' . $errfile . ' ' . $errline . ':' . "\n";
+        echo '  <ol>' . "\n";
+        foreach($trace as $item)
+            echo '    <li>' . (isset($item['file']) ? $item['file'] : '<unknown file>') . ' ' . (isset($item['line']) ? $item['line'] : '<unknown line>') . ' calling ' . $item['function'] . '()</li>' . "\n";
+        echo '  </ol>' . "\n";
+        echo '</p>' . "\n";
+    }
+    if(ini_get('log_errors')) {
+        $items = array();
+        foreach($trace as $item)
+            $items[] = (isset($item['file']) ? $item['file'] : '<unknown file>') . ' ' . (isset($item['line']) ? $item['line'] : '<unknown line>') . ' calling ' . $item['function'] . '()';
+        $message = 'Backtrace from ' . $type . ' \'' . $errstr . '\' at ' . $errfile . ' ' . $errline . ': ' . join(' | ', $items);
+        error_log($message);
+    }
+    if($fatal)
+        exit(1);
+}
+
 set_error_handler("inforexCentralErrorHandler");
+//set_error_handler("process_error_backtrace");
+/*
+set_error_handler(function(int $severity, string $message, string $file, int $line) {
+    if (!(error_reporting() & $severity)) {
+        return false;
+    }
+
+    $severities = [
+        E_ERROR => 'ERROR',
+        E_WARNING => 'WARNING',
+        E_PARSE => 'PARSE',
+        E_NOTICE => 'NOTICE',
+        E_CORE_ERROR => 'CORE_ERROR',
+        E_CORE_WARNING => 'CORE_WARNING',
+        E_COMPILE_ERROR => 'COMPILE_ERROR',
+        E_COMPILE_WARNING => 'COMPILE_WARNING',
+        E_USER_ERROR => 'USER_ERROR',
+        E_USER_WARNING => 'USER_WARNING',
+        E_USER_NOTICE => 'USER_NOTICE',
+        E_STRICT => 'STRICT',
+        E_RECOVERABLE_ERROR => 'RECOVERABLE_ERROR',
+        E_DEPRECATED => 'DEPRECATED',
+        E_USER_DEPRECATED => 'USER_DEPRECATED',
+    ];
+
+    $e = new \Exception;
+
+    // Just remove the current point from the trace
+    $reflection = new \ReflectionProperty(get_class($e), 'trace');
+    $reflection->setAccessible(true);
+    $trace = $reflection->getValue($e);
+    array_shift($trace);
+    $reflection->setValue($e, $trace);
+
+    $text = '';
+    $text .= ($severities[$severity] ?? $severity) . ': ';
+    $text .= "$message in $file($line)\n";
+    $text .= "Stack trace:\n";
+    $text .= $e->getTraceAsString();
+
+    error_log($text);
+
+    if (in_array($severity, [
+        E_CORE_ERROR,
+        E_ERROR,
+        E_RECOVERABLE_ERROR,
+        E_PARSE,
+        E_COMPILE_ERROR,
+        E_USER_ERROR,
+    ], true)) {
+        http_response_code(500);
+        exit(255);
+    }
+
+    return true;
+});
+*/
+// Give an extra parameter to the filename
+// to save multiple log files
+function _fatalog_($extra = false)
+{
+    static $last_extra;
+
+    // CHANGE THIS TO: A writeable filepath in your system...
+    //$filepath = '/var/www/html/sites/default/files/fatal-'.($extra === false ? $last_extra : $extra).'.log';
+    $filepath = '../engine/templates_c/fatal-'.($extra === false ? $last_extra : $extra).'.log';
+
+    if ($extra===false) {
+        unlink($filepath);
+    } else {
+        // we write a log file with the debug info
+        file_put_contents($filepath, json_encode(debug_backtrace()));
+        // saving last extra parameter for future unlink... if possible...
+        $last_extra = $extra;
+    }
+}
+/*
+Here's an example of how to use it:
+
+// A function which will produce a fatal error
+function fatal_example()
+{
+    _fatalog_(time()); // writing the log
+    $some_fatal_code = array()/3; // fatality!
+    _fatalog_(); // if we get here then delete last file log
+}
+
+Finally to read the contents of the log...
+
+var_dump(json_decode(file_get_contents('/path/to-the-fatal.log')));
+
+*/
 
 function inforexShutdownFunction() {
 

From c0ce5b266cdf3ce20a668c2261d3db3a9467f1df Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Fri, 1 Apr 2022 21:49:04 +0200
Subject: [PATCH 079/154] test uninitiated variables

---
 engine/include/database/CDbRelationSet.php           | 1 +
 engine/templates/inc_widget_annotation_type_tree.tpl | 4 ++--
 engine/templates/inc_widget_relation_type_tree.tpl   | 4 ++--
 engine/templates/page_corpus_agreement_relations.tpl | 4 ++--
 4 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/engine/include/database/CDbRelationSet.php b/engine/include/database/CDbRelationSet.php
index b97932e5..e172be9c 100644
--- a/engine/include/database/CDbRelationSet.php
+++ b/engine/include/database/CDbRelationSet.php
@@ -34,6 +34,7 @@ static function getRelationTypesOfSet($relation_set_id, $report_id = null){
         $params = array($relation_set_id);
 
         $relation_types = $db->fetch_rows($sql, $params);
+        $report_sql = "";
         if($report_id != null){
             $report_sql = "AND rao.report_id = ?";
         }
diff --git a/engine/templates/inc_widget_annotation_type_tree.tpl b/engine/templates/inc_widget_annotation_type_tree.tpl
index 04aceb14..f424c6c9 100644
--- a/engine/templates/inc_widget_annotation_type_tree.tpl
+++ b/engine/templates/inc_widget_annotation_type_tree.tpl
@@ -56,7 +56,7 @@
 					{/if}		    	
 		    	{/foreach}	
 		    {/foreach}
-			{if $annotation_types|@count==0}
+			{if (!is_array($annotation_types)) || $annotation_types|@count==0}
 				<tr>
 					<td colspan="2"><i>No layers, subsets nor types to display</i></td>
 				</tr>
@@ -64,4 +64,4 @@
 		    </tbody>		
     	</table>	
     	</div>    
-	</div>	
\ No newline at end of file
+	</div>	
diff --git a/engine/templates/inc_widget_relation_type_tree.tpl b/engine/templates/inc_widget_relation_type_tree.tpl
index 4e371191..d11e472b 100644
--- a/engine/templates/inc_widget_relation_type_tree.tpl
+++ b/engine/templates/inc_widget_relation_type_tree.tpl
@@ -45,7 +45,7 @@
                     {/if}
                 {/foreach}
             {/foreach}
-			{if $relation_types|@count==0}
+			{if (!is_array($relation_types)) || $relation_types|@count==0}
 				<tr>
 					<td colspan="2"><i>No layers or types to display</i></td>
 				</tr>
@@ -53,4 +53,4 @@
 		    </tbody>		
     	</table>	
     	</div>    
-	</div>	
\ No newline at end of file
+	</div>	
diff --git a/engine/templates/page_corpus_agreement_relations.tpl b/engine/templates/page_corpus_agreement_relations.tpl
index 7e4767b9..a9154fa5 100644
--- a/engine/templates/page_corpus_agreement_relations.tpl
+++ b/engine/templates/page_corpus_agreement_relations.tpl
@@ -120,7 +120,7 @@
 								<div class="panel-heading">Users</div>
 								<div class="panel-body" style="">
 
-									{if $annotators|@count == 0}
+									{if (!is_array($annotators)) || $annotators|@count == 0}
 										{capture assign=message}
 										<em>There are no users with agreement annotations for the selected criteria.</em>
 										{/capture}
@@ -185,4 +185,4 @@
 			</div>
 		</div>
 
-{include file="inc_footer.tpl"}
\ No newline at end of file
+{include file="inc_footer.tpl"}

From 25d7ee09c995f66a58547a58e5a1e827559f9953 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Fri, 1 Apr 2022 21:50:01 +0200
Subject: [PATCH 080/154] improve _fatalog_ for nested call

---
 engine/settings.php | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/engine/settings.php b/engine/settings.php
index 7a28080a..8dbaac2d 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -191,11 +191,11 @@ function process_error_backtrace($errno, $errstr, $errfile, $errline, $errcontex
 // to save multiple log files
 function _fatalog_($extra = false)
 {
-    static $last_extra;
+    static $last_extra = array();
 
     // CHANGE THIS TO: A writeable filepath in your system...
     //$filepath = '/var/www/html/sites/default/files/fatal-'.($extra === false ? $last_extra : $extra).'.log';
-    $filepath = '../engine/templates_c/fatal-'.($extra === false ? $last_extra : $extra).'.log';
+    $filepath = '../engine/templates_c/fatal-'.($extra === false ? array_pop($last_extra) : $extra).'.log';
 
     if ($extra===false) {
         unlink($filepath);
@@ -203,7 +203,7 @@ function _fatalog_($extra = false)
         // we write a log file with the debug info
         file_put_contents($filepath, json_encode(debug_backtrace()));
         // saving last extra parameter for future unlink... if possible...
-        $last_extra = $extra;
+        array_push($last_extra,$extra);
     }
 }
 /*

From 70886091a12294fffe12600422baf6837ab92151 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Fri, 1 Apr 2022 21:51:44 +0200
Subject: [PATCH 081/154] full debugging getRelationTypesOfSet

---
 engine/include/database/CDbRelationSet.php | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/engine/include/database/CDbRelationSet.php b/engine/include/database/CDbRelationSet.php
index e172be9c..bd13c889 100644
--- a/engine/include/database/CDbRelationSet.php
+++ b/engine/include/database/CDbRelationSet.php
@@ -29,11 +29,15 @@ static function getRelationSetsAssignedToCorpus($corpusId){
      */
 	static function getRelationTypesOfSet($relation_set_id, $report_id = null){
         global $db;
+        _fatalog_(strval(time()).'_start_getRelationTypesOfSet');
         $sql = "SELECT rt.* FROM relation_types rt
                 WHERE rt.relation_set_id = ?";
         $params = array($relation_set_id);
 
         $relation_types = $db->fetch_rows($sql, $params);
+        //error_log("relation_types [".$sql."] = ".var_export($relation_types,true));
+
+        _fatalog_(strval(time()).'_getRelationTypesOfSet_rtCounted');
         $report_sql = "";
         if($report_id != null){
             $report_sql = "AND rao.report_id = ?";
@@ -48,7 +52,10 @@ static function getRelationTypesOfSet($relation_set_id, $report_id = null){
         if($report_id != null){
             $params[] = $report_id;
         }
+        error_log("relation_types_counted SQL = ".$sql." params = ".var_export($params,true));
         $relation_types_counted = $db->fetch_rows($sql, $params);
+        error_log("relation_types_counted = ".var_export($relation_types_counted,true));
+        _fatalog_();
 
         $relation_types_used = 0;
         foreach($relation_types_counted as $relation_type){
@@ -56,6 +63,7 @@ static function getRelationTypesOfSet($relation_set_id, $report_id = null){
         }
 
         $relation_types['number_of_uses'] = $relation_types_used/2;
+        _fatalog_();
         return $relation_types;
     }
 
@@ -64,18 +72,26 @@ static function getRelationTypesOfSet($relation_set_id, $report_id = null){
      * @param $corpus_id
      */
 	static function getRelationTree($corpus_id, $report_id = null){
+        _fatalog_(strval(time()).'_start_getRelationTree');
         $annotation_tree = array();
         $relation_sets = self::getRelationSetsAssignedToCorpus($corpus_id);
-
+        
+        _fatalog_(strval(time()).'_beforeForeach');
+        //error_log("relation_sets=".print_r($relation_sets,true));
         foreach($relation_sets as $relation_set){
             $relation_set_id = $relation_set['relation_set_id'];
             $relation_set_name = $relation_set['name'];
 
-
+            _fatalog_(strval(time()).'_loop'.strval($relation_set_id));
+            //error_log("relation_set_id=".print_r($relation_set_id,true));
+            //error_log("report_id=".print_r($report_id,true));
             $annotation_tree[$relation_set_id] = self::getRelationTypesOfSet($relation_set_id, $report_id);
+            _fatalog_();
             $annotation_tree[$relation_set_id]['relation_set_name'] = $relation_set_name;
             $annotation_tree[$relation_set_id]['relation_set_id'] = $relation_set_id;
         }
+        _fatalog_();
+        _fatalog_();
         return $annotation_tree;
     }
 

From 431d43e3fc021327ea67a4552ed90dc11a224982 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Sat, 2 Apr 2022 11:12:32 +0200
Subject: [PATCH 082/154] sql query fix based on docker branch

---
 engine/include/database/CDbRelationSet.php | 31 +++++++---------------
 1 file changed, 9 insertions(+), 22 deletions(-)

diff --git a/engine/include/database/CDbRelationSet.php b/engine/include/database/CDbRelationSet.php
index bd13c889..75faceb8 100644
--- a/engine/include/database/CDbRelationSet.php
+++ b/engine/include/database/CDbRelationSet.php
@@ -29,33 +29,29 @@ static function getRelationSetsAssignedToCorpus($corpusId){
      */
 	static function getRelationTypesOfSet($relation_set_id, $report_id = null){
         global $db;
-        _fatalog_(strval(time()).'_start_getRelationTypesOfSet');
         $sql = "SELECT rt.* FROM relation_types rt
                 WHERE rt.relation_set_id = ?";
         $params = array($relation_set_id);
 
         $relation_types = $db->fetch_rows($sql, $params);
-        //error_log("relation_types [".$sql."] = ".var_export($relation_types,true));
-
-        _fatalog_(strval(time()).'_getRelationTypesOfSet_rtCounted');
         $report_sql = "";
         if($report_id != null){
-            $report_sql = "AND rao.report_id = ?";
+            $report_sql = "AND rao_src.report_id = ? AND rao_trg.report_id = ?";
         }
 
-        $sql = "SELECT r.*, COUNT(r.id) AS 'number_of_types' FROM relation_types rt
+        $sql = "SELECT COUNT(r.id) AS 'number_of_types' FROM relation_types rt
                 LEFT JOIN relations r ON r.relation_type_id = rt.id 
-                LEFT JOIN reports_annotations_optimized rao ON (rao.id = r.source_id OR rao.id = r.target_id)
-                WHERE (rt.relation_set_id = ? ".$report_sql." AND r.stage = 'agreement' AND rao.stage = 'final')
+                LEFT JOIN reports_annotations_optimized rao_src ON rao_src.id = r.source_id 
+                LEFT JOIN reports_annotations_optimized rao_trg ON rao_trg.id = r.target_id
+                WHERE rt.relation_set_id = ? ".$report_sql." AND r.stage = 'agreement' AND (rao_src.stage = 'final' OR rao_trg.stage = 'final')
                 GROUP BY r.id";
+
         $params = array($relation_set_id);
         if($report_id != null){
             $params[] = $report_id;
+            $params[] = $report_id;
         }
-        error_log("relation_types_counted SQL = ".$sql." params = ".var_export($params,true));
         $relation_types_counted = $db->fetch_rows($sql, $params);
-        error_log("relation_types_counted = ".var_export($relation_types_counted,true));
-        _fatalog_();
 
         $relation_types_used = 0;
         foreach($relation_types_counted as $relation_type){
@@ -63,7 +59,6 @@ static function getRelationTypesOfSet($relation_set_id, $report_id = null){
         }
 
         $relation_types['number_of_uses'] = $relation_types_used/2;
-        _fatalog_();
         return $relation_types;
     }
 
@@ -72,26 +67,18 @@ static function getRelationTypesOfSet($relation_set_id, $report_id = null){
      * @param $corpus_id
      */
 	static function getRelationTree($corpus_id, $report_id = null){
-        _fatalog_(strval(time()).'_start_getRelationTree');
         $annotation_tree = array();
         $relation_sets = self::getRelationSetsAssignedToCorpus($corpus_id);
-        
-        _fatalog_(strval(time()).'_beforeForeach');
-        //error_log("relation_sets=".print_r($relation_sets,true));
+
         foreach($relation_sets as $relation_set){
             $relation_set_id = $relation_set['relation_set_id'];
             $relation_set_name = $relation_set['name'];
 
-            _fatalog_(strval(time()).'_loop'.strval($relation_set_id));
-            //error_log("relation_set_id=".print_r($relation_set_id,true));
-            //error_log("report_id=".print_r($report_id,true));
+
             $annotation_tree[$relation_set_id] = self::getRelationTypesOfSet($relation_set_id, $report_id);
-            _fatalog_();
             $annotation_tree[$relation_set_id]['relation_set_name'] = $relation_set_name;
             $annotation_tree[$relation_set_id]['relation_set_id'] = $relation_set_id;
         }
-        _fatalog_();
-        _fatalog_();
         return $annotation_tree;
     }
 

From 855358e4bf7041e7517693957aa856f6725259b8 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Sat, 2 Apr 2022 15:05:50 +0200
Subject: [PATCH 083/154] ErrorService new implementation

---
 .../include/exceptions/BacktraceService.php   |  90 +++++++
 engine/include/exceptions/ErrorService.php    | 157 ++++++++++++
 engine/settings.php                           | 232 +-----------------
 public_html/index.php                         |   1 -
 4 files changed, 249 insertions(+), 231 deletions(-)
 create mode 100644 engine/include/exceptions/BacktraceService.php
 create mode 100644 engine/include/exceptions/ErrorService.php

diff --git a/engine/include/exceptions/BacktraceService.php b/engine/include/exceptions/BacktraceService.php
new file mode 100644
index 00000000..366c5475
--- /dev/null
+++ b/engine/include/exceptions/BacktraceService.php
@@ -0,0 +1,90 @@
+<?php
+/**
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ * See LICENCE
+ */
+
+class BacktraceService {
+
+    static public function getBacktrace($removeLevels=1) {
+        // return backtrace as array of calls
+        // remove $removeLevels calls from top of stack
+
+        $trace = array_reverse(debug_backtrace());
+        while($removeLevels && count($trace)>0) {
+            array_pop($trace);
+            $removeLevels--;
+        }
+        return $trace;        
+
+    } // getBacktrace
+
+    static private function formatCLITraceStr($traceArray) {
+
+        $result = "";
+        $index = count($traceArray)-1;
+        while($index>=0) {
+        //foreach($traceArray as $item) {
+            $item = $traceArray[$index--];
+            $result .= '  ' 
+                       .(isset($item['file']) ? $item['file'] : '<unknown file>')
+                       .' ' 
+                       .(isset($item['line']) ? $item['line'] : '<unknown line>')
+                       .' calling ' . $item['function'] . '()' 
+                       . "\n";
+        }
+        return $result; 
+
+    } // formatCLITraceStr
+
+    static private function formatHTMLTraceStr($traceArray) {
+
+        $result =    '  <ol>' . "\n";
+        $index = count($traceArray)-1;
+        while($index>=0) {
+        //foreach($traceArray as $item) {
+            $item = $traceArray[$index--];
+            $result .= '    <li>' 
+                        . (isset($item['file']) ? $item['file'] : '<unknown file>') 
+                        . ' ' 
+                        . (isset($item['line']) ? $item['line'] : '<unknown line>') 
+                        . ' calling ' . $item['function'] . '()' 
+                        . "</li>\n";
+        }
+        $result .=   '  </ol>' . "\n";
+ 
+        return $result;
+
+    } // formatHTMLTraceStr
+
+    static public function formatTraceStr($traceArray) {
+
+        if(php_sapi_name() == 'cli') {
+            return self::formatCLITraceStr($traceArray);
+        } else {
+            return self::formatHTMLTraceStr($traceArray);
+        }
+
+    } // formatTraceStr()
+
+    static public function formatTraceLogStr($traceArray) {
+
+        $items = array();
+        $index = count($traceArray)-1;
+        while($index>=0) {
+        //foreach($traceArray as $item) {
+            $item = $traceArray[$index--];
+            $items[] = (isset($item['file']) ? $item['file'] : '<unknown file>')                       . ' ' 
+                       . (isset($item['line']) ? $item['line'] : '<unknown line>') 
+                       . ' calling ' . $item['function'] . '()';
+        }
+        return join(' | ', $items);
+
+    } // formatTraceLogStr()
+
+} // BacktraceService class
+
+?>
+
diff --git a/engine/include/exceptions/ErrorService.php b/engine/include/exceptions/ErrorService.php
new file mode 100644
index 00000000..0d0a2dd7
--- /dev/null
+++ b/engine/include/exceptions/ErrorService.php
@@ -0,0 +1,157 @@
+<?php
+/**
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ * See LICENCE
+ */
+
+class ErrorService {
+
+    const severities = [
+        E_ERROR => 'ERROR',
+        E_WARNING => 'WARNING',
+        E_PARSE => 'PARSE',
+        E_NOTICE => 'NOTICE',
+        E_CORE_ERROR => 'CORE_ERROR',
+        E_CORE_WARNING => 'CORE_WARNING',
+        E_COMPILE_ERROR => 'COMPILE_ERROR',
+        E_COMPILE_WARNING => 'COMPILE_WARNING',
+        E_USER_ERROR => 'USER_ERROR',
+        E_USER_WARNING => 'USER_WARNING',
+        E_USER_NOTICE => 'USER_NOTICE',
+        E_STRICT => 'STRICT',
+        E_RECOVERABLE_ERROR => 'RECOVERABLE_ERROR',
+        E_DEPRECATED => 'DEPRECATED',
+        E_USER_DEPRECATED => 'USER_DEPRECATED',
+    ];
+
+    static private function getLevelStr($level) {
+
+        $result = "UNKNOWN ERROR";
+        if(array_key_exists($level,self::severities)) {
+            $result = self::severities[$level];
+        }
+        return $result;
+
+    } // getLevelStr()
+
+    static private function errorMsgCLIStr($level,$message,$file,$line) {
+
+        $msg = self::getLevelStr($level)
+                    . ' \'' . $message . '\' at '
+                    . $file
+                    . ' ' . $line . ' Trace: '."\n"
+                    . BacktraceService::formatTraceStr(BacktraceService::getBacktrace(4));
+        return $msg;
+
+    } // errorMsgCLIStr()
+
+    static private function errorMsgHTMLStr($level,$message,$file,$line) {
+
+        $msg = '<p class="error_backtrace">' . "\n"
+               . self::getLevelStr($level) . ' \'' . $message . '\' at ' . $file . ' ' . $line . ' Trace :<br/>'. "\n";
+        $msg .= BacktraceService::formatTraceStr(BacktraceService::getBacktrace(4));
+        $msg .= '</p>'."\n";
+        return $msg;
+
+    } // errorMsgHTMLStr()
+
+    static private function errorMsgStr($level,$message,$file,$line) {
+
+        if(php_sapi_name() == 'cli') {
+            return self::errorMsgCLIStr($level,$message,$file,$line);
+        } else {
+            return self::errorMsgHTMLStr($level,$message,$file,$line);
+        }
+
+    } // errorMsgStr()
+
+    static private function throwErrorException($level,$message,$file,$line) {
+
+        //$text = "[".$level."] ".$message." in ".$file.":".$line;
+        //throw new ErrorException($text, 0, $level, $file, $line);
+ 
+        $e = new Exception($message, 0);
+        // Just remove the current 2 points from the trace
+        $reflection = new ReflectionProperty(get_class($e), 'trace');
+        $reflection->setAccessible(true);
+        $trace = $reflection->getValue($e);
+        array_shift($trace);
+        array_shift($trace);
+        $reflection->setValue($e, $trace);
+
+        $reflection = new ReflectionProperty(get_class($e), 'file');
+        $reflection->setAccessible(true);
+        $reflection->setValue($e, $file);
+        $reflection = new ReflectionProperty(get_class($e), 'line');
+        $reflection->setAccessible(true);
+        $reflection->setValue($e, $line);
+
+        throw($e);
+        
+    } // throwErrorException
+
+    static public function errorHandler($level, $message, $file = ’’, $line = 0) {
+        // log all to logfile
+        if(ini_get('log_errors')){
+            $msg = self::getLevelStr($level) 
+                    . ' \'' . $message . '\' at ' 
+                    . $file 
+                    . ' ' . $line . ' Trace: ' 
+                    . BacktraceService::formatTraceLogStr(BacktraceService::getBacktrace(2));
+            error_log($msg);
+        }
+
+        // mask errors on error_reporting() settings
+        // here we have them all
+        $systemErrorReporting = error_reporting();
+        if( ($systemErrorReporting & $level) == 0 ) {
+            // this error level is masked by system settings
+            UncaughtExceptionService::errorClearLast();
+            return;
+        }
+
+        // notice, warnings, strict print only if display_errors = 1
+        // and continue running program
+        switch($level) {
+            case E_WARNING      :
+            case E_USER_WARNING :
+            case E_STRICT       :
+            case E_NOTICE       :
+            case E_USER_NOTICE  :
+            case E_CORE_WARNING :
+            case E_COMPILE_WARNING  :
+                if(ini_get('display_errors')){
+                    print(self::errorMsgStr($level,$message,$file,$line)); 
+                } else {
+                    // none information in this case
+                }
+                return;
+            break;
+            default             :  // fatal errors 
+                // call exception - no return
+                self::throwErrorException($level,$message,$file,$line);
+            break;
+        }
+         
+    } // errorHandler()
+
+    static public function shutdownFunction() {
+
+        // returns null or array( "type"=>, "message"=>, "file"=>, "line"=> )
+        // if earlier inforexInitialExceptionHandler was called, there not
+        // will be reported twice
+        $error = UncaughtExceptionService::errorGetLast();
+        if ($error !== null) {
+            // dummy message if not errors displayed by system
+            if (!ini_get("display_errors")) {
+                UncaughtExceptionService::dummyMessage4User();
+            } else {
+                // no action - system default
+            }
+        }
+
+    } // shutdownFunction()
+ 
+} // class ErrorService
diff --git a/engine/settings.php b/engine/settings.php
index 8dbaac2d..225efce2 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -16,238 +16,10 @@
 ini_set("short_open_tag",1);
 setlocale(LC_CTYPE, "en_US.UTF-8");		
 
-function inforexCentralErrorHandler($level, $message, $file = ’’, $line = 0) {
-
-    //print("inforexCentralErrorHandler \n");
-    // mask errors on error_reporting() settings
-    // here we have them all
-    $systemErrorReporting = error_reporting();
-    if( ($systemErrorReporting & $level) == 0 ) {
-        // this error level is masked by system settings
-	    UncaughtExceptionService::errorClearLast();
-        return;
-    }   
-
-	// silently drop ugly strict double constructor report in PHP < 7
-	if(version_compare(phpversion(),'7.0.0','<')) {
-		if(preg_match("/^Redefining already defined constructor for class Config/",$message)) {
-			UncaughtExceptionService::errorClearLast();
-			return;
-		}
-	} // ver < 7.0
-
-	// converts all not masked errors to exceptions
-    //  there are no return from exception to code continue...
-    $severities = [
-        E_ERROR => 'ERROR',
-        E_WARNING => 'WARNING',
-        E_PARSE => 'PARSE',
-        E_NOTICE => 'NOTICE',
-        E_CORE_ERROR => 'CORE_ERROR',
-        E_CORE_WARNING => 'CORE_WARNING',
-        E_COMPILE_ERROR => 'COMPILE_ERROR',
-        E_COMPILE_WARNING => 'COMPILE_WARNING',
-        E_USER_ERROR => 'USER_ERROR',
-        E_USER_WARNING => 'USER_WARNING',
-        E_USER_NOTICE => 'USER_NOTICE',
-        E_STRICT => 'STRICT',
-        E_RECOVERABLE_ERROR => 'RECOVERABLE_ERROR',
-        E_DEPRECATED => 'DEPRECATED',
-        E_USER_DEPRECATED => 'USER_DEPRECATED',
-    ];
-    $extended_message = "[".$level."] ".$message." in ".$file.":".$line;
-    $e = new Exception($extended_message, 0);
-    // Just remove the current point from the trace
-    $reflection = new ReflectionProperty(get_class($e), 'trace');
-    $reflection->setAccessible(true);
-    $trace = $reflection->getValue($e);
-    array_shift($trace);
-    $reflection->setValue($e, $trace);
-
-    $reflection = new ReflectionProperty(get_class($e), 'file');
-    $reflection->setAccessible(true);
-    $reflection->setValue($e, $file);
-    $reflection = new ReflectionProperty(get_class($e), 'line');
-    $reflection->setAccessible(true);
-    $reflection->setValue($e, $line);
-
-    $text = '';
-    $text .= ($severities[$level] ?? $level) . ': ';
-    $text .= "$message in $file($line)\n";
-    $text .= "Stack trace:\n";
-    $text .= $e->getTraceAsString();
-
-    throw($e);
-
-    //throw new ErrorException($text, 0, $level, $file, $line);
-
-    //$extended_message = "[".$level."] ".$message." in ".$file.":".$line;
-	//throw new ErrorException($extended_message, 0, $level, $file, $line);
-
-}  // inforexCentralErrorHandler()
-
-function process_error_backtrace($errno, $errstr, $errfile, $errline, $errcontext) {
-    if(!(error_reporting() & $errno))
-        return;
-    switch($errno) {
-    case E_WARNING      :
-    case E_USER_WARNING :
-    case E_STRICT       :
-    case E_NOTICE       :
-    case E_USER_NOTICE  :
-        $type = 'warning';
-        $fatal = false;
-        break;
-    default             :
-        $type = 'fatal error';
-        $fatal = true;
-        break;
-    }
-    $trace = array_reverse(debug_backtrace());
-    array_pop($trace);
-    if(php_sapi_name() == 'cli') {
-        echo 'Backtrace from ' . $type . ' \'' . $errstr . '\' at ' . $errfile . ' ' . $errline . ':' . "\n";
-        foreach($trace as $item)
-            echo '  ' . (isset($item['file']) ? $item['file'] : '<unknown file>') . ' ' . (isset($item['line']) ? $item['line'] : '<unknown line>') . ' calling ' . $item['function'] . '()' . "\n";
-    } else {
-        echo '<p class="error_backtrace">' . "\n";
-        echo '  Backtrace from ' . $type . ' \'' . $errstr . '\' at ' . $errfile . ' ' . $errline . ':' . "\n";
-        echo '  <ol>' . "\n";
-        foreach($trace as $item)
-            echo '    <li>' . (isset($item['file']) ? $item['file'] : '<unknown file>') . ' ' . (isset($item['line']) ? $item['line'] : '<unknown line>') . ' calling ' . $item['function'] . '()</li>' . "\n";
-        echo '  </ol>' . "\n";
-        echo '</p>' . "\n";
-    }
-    if(ini_get('log_errors')) {
-        $items = array();
-        foreach($trace as $item)
-            $items[] = (isset($item['file']) ? $item['file'] : '<unknown file>') . ' ' . (isset($item['line']) ? $item['line'] : '<unknown line>') . ' calling ' . $item['function'] . '()';
-        $message = 'Backtrace from ' . $type . ' \'' . $errstr . '\' at ' . $errfile . ' ' . $errline . ': ' . join(' | ', $items);
-        error_log($message);
-    }
-    if($fatal)
-        exit(1);
-}
-
-set_error_handler("inforexCentralErrorHandler");
-//set_error_handler("process_error_backtrace");
-/*
-set_error_handler(function(int $severity, string $message, string $file, int $line) {
-    if (!(error_reporting() & $severity)) {
-        return false;
-    }
-
-    $severities = [
-        E_ERROR => 'ERROR',
-        E_WARNING => 'WARNING',
-        E_PARSE => 'PARSE',
-        E_NOTICE => 'NOTICE',
-        E_CORE_ERROR => 'CORE_ERROR',
-        E_CORE_WARNING => 'CORE_WARNING',
-        E_COMPILE_ERROR => 'COMPILE_ERROR',
-        E_COMPILE_WARNING => 'COMPILE_WARNING',
-        E_USER_ERROR => 'USER_ERROR',
-        E_USER_WARNING => 'USER_WARNING',
-        E_USER_NOTICE => 'USER_NOTICE',
-        E_STRICT => 'STRICT',
-        E_RECOVERABLE_ERROR => 'RECOVERABLE_ERROR',
-        E_DEPRECATED => 'DEPRECATED',
-        E_USER_DEPRECATED => 'USER_DEPRECATED',
-    ];
-
-    $e = new \Exception;
-
-    // Just remove the current point from the trace
-    $reflection = new \ReflectionProperty(get_class($e), 'trace');
-    $reflection->setAccessible(true);
-    $trace = $reflection->getValue($e);
-    array_shift($trace);
-    $reflection->setValue($e, $trace);
-
-    $text = '';
-    $text .= ($severities[$severity] ?? $severity) . ': ';
-    $text .= "$message in $file($line)\n";
-    $text .= "Stack trace:\n";
-    $text .= $e->getTraceAsString();
-
-    error_log($text);
-
-    if (in_array($severity, [
-        E_CORE_ERROR,
-        E_ERROR,
-        E_RECOVERABLE_ERROR,
-        E_PARSE,
-        E_COMPILE_ERROR,
-        E_USER_ERROR,
-    ], true)) {
-        http_response_code(500);
-        exit(255);
-    }
-
-    return true;
-});
-*/
-// Give an extra parameter to the filename
-// to save multiple log files
-function _fatalog_($extra = false)
-{
-    static $last_extra = array();
-
-    // CHANGE THIS TO: A writeable filepath in your system...
-    //$filepath = '/var/www/html/sites/default/files/fatal-'.($extra === false ? $last_extra : $extra).'.log';
-    $filepath = '../engine/templates_c/fatal-'.($extra === false ? array_pop($last_extra) : $extra).'.log';
-
-    if ($extra===false) {
-        unlink($filepath);
-    } else {
-        // we write a log file with the debug info
-        file_put_contents($filepath, json_encode(debug_backtrace()));
-        // saving last extra parameter for future unlink... if possible...
-        array_push($last_extra,$extra);
-    }
-}
-/*
-Here's an example of how to use it:
-
-// A function which will produce a fatal error
-function fatal_example()
-{
-    _fatalog_(time()); // writing the log
-    $some_fatal_code = array()/3; // fatality!
-    _fatalog_(); // if we get here then delete last file log
-}
-
-Finally to read the contents of the log...
-
-var_dump(json_decode(file_get_contents('/path/to-the-fatal.log')));
-
-*/
-
-function inforexShutdownFunction() {
-
-    //print("inforexShutdownFunction \n");
-    // returns null or array( "type"=>, "message"=>, "file"=>, "line"=> )
-    // if earlier inforexInitialExceptionHandler was called, there not
-    // will be reported twice 
-    $error = UncaughtExceptionService::errorGetLast();
-    if ($error !== null) {
-        /*
-        $e = new ErrorException(
-            $error["message"], 0, $error["type"], $error["file"], $error["line"]
-        );
-        inforexInitialExceptionHandler($e);
-        */
-        // dummy message if not errors displayed by system
-        if (!ini_get("display_errors")) {
-            UncaughtExceptionService::dummyMessage4User();
-        }
-    }
-
-} // inforexShutdownFunction()  
-
+set_error_handler("ErrorService::errorHandler");
 if(! PHPUnitTools::isPHPUnitRunning()) {
 	// under PHPUnit this one not works
-	register_shutdown_function("inforexShutdownFunction");
+	register_shutdown_function("ErrorService::shutdownFunction");
 }
 
 ?>
diff --git a/public_html/index.php b/public_html/index.php
index 0d120c72..1778e60c 100644
--- a/public_html/index.php
+++ b/public_html/index.php
@@ -10,7 +10,6 @@
 $enginePath = realpath(__DIR__ . "/../engine/");
 require_once($enginePath.'/include.php');
 require_once($enginePath."/settings.php");
-//require_once($enginePath.'/include.php');
 try{
 	/********************************************************************/
 	Config::Config()->put_path_engine($enginePath);

From 5e33d37441ccf382a3b682dfffba67ec8281d2af Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Wed, 6 Apr 2022 18:29:12 +0200
Subject: [PATCH 084/154] throwFatalError method for testing error service

---
 engine/include/exceptions/ErrorService.php | 43 ++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/engine/include/exceptions/ErrorService.php b/engine/include/exceptions/ErrorService.php
index 0d0a2dd7..7bbf49a1 100644
--- a/engine/include/exceptions/ErrorService.php
+++ b/engine/include/exceptions/ErrorService.php
@@ -154,4 +154,47 @@ static public function shutdownFunction() {
 
     } // shutdownFunction()
  
+    // fatal error generator for testing purposes
+    // to generate fatal error - memory exhausted write
+    //      self::throwFatalError();
+    public static function throwFatalError() {
+
+        // This method generate limit exhausted memory consumption
+        // PHP Fatal error:  Allowed memory size of ... bytes exhausted
+        //
+        $bigCount = self::memoryLimitAsBytes() / 8;
+        $bigStr = str_repeat( "Hello|", $bigCount );
+        $bigArray = explode( '|', $bigStr );
+        $deadBuffer = array();
+        foreach( $bigArray as $key => $item ){
+            $deadBuffer[] = $item;
+        }
+        return $deadBuffer;
+
+    } // throwFatalError
+
+    private static function limitStrToBytes($limitStr) {
+
+        switch(strtolower(substr($limitStr,-1))) {
+            case 'g':   
+                return (int)$limitStr*1073741824;
+            case 'm':
+                return (int)$limitStr*1048576;
+            case 'k':
+                return (int)$limitStr*1024;
+            default:    
+                return (int)$limitStr;
+        }
+
+    } // limitStrToBytes()
+
+    private static function memoryLimitAsBytes() {
+
+        $limit = ini_get("memory_limit");
+        return self::limitStrToBytes($limit);
+
+    } // memoryLimitAsBytes
+
 } // class ErrorService
+
+?>

From a65b0d6369efd8e4b9b168c513ec564b0e22421e Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Thu, 7 Apr 2022 21:36:37 +0200
Subject: [PATCH 085/154] test and final error handlers tunning

---
 engine/include/exceptions/ErrorService.php    | 29 +++++++----
 .../exceptions/UncaughtExceptionService.php   | 50 +++++++++++++------
 2 files changed, 52 insertions(+), 27 deletions(-)

diff --git a/engine/include/exceptions/ErrorService.php b/engine/include/exceptions/ErrorService.php
index 7bbf49a1..0d40dc76 100644
--- a/engine/include/exceptions/ErrorService.php
+++ b/engine/include/exceptions/ErrorService.php
@@ -50,13 +50,24 @@ static private function errorMsgCLIStr($level,$message,$file,$line) {
     static private function errorMsgHTMLStr($level,$message,$file,$line) {
 
         $msg = '<p class="error_backtrace">' . "\n"
-               . self::getLevelStr($level) . ' \'' . $message . '\' at ' . $file . ' ' . $line . ' Trace :<br/>'. "\n";
+               . self::getLevelStr($level) . ' \'' . $message . '\' at ' . $file . ' ' . $line . '<br/> Trace :'. "\n";
         $msg .= BacktraceService::formatTraceStr(BacktraceService::getBacktrace(4));
         $msg .= '</p>'."\n";
         return $msg;
 
     } // errorMsgHTMLStr()
 
+    static private function errorMsgLogStr($level,$message,$file,$line) {
+
+        $msg = self::getLevelStr($level)
+                . ' \'' . $message . '\' at '
+                . $file
+                . ' ' . $line . ' Trace: '
+                . BacktraceService::formatTraceLogStr(BacktraceService::getBacktrace(3));
+        return $msg;
+
+    } // errorMsgLogStr()
+
     static private function errorMsgStr($level,$message,$file,$line) {
 
         if(php_sapi_name() == 'cli') {
@@ -72,6 +83,7 @@ static private function throwErrorException($level,$message,$file,$line) {
         //$text = "[".$level."] ".$message." in ".$file.":".$line;
         //throw new ErrorException($text, 0, $level, $file, $line);
  
+        $message = self::getLevelStr($level)." : ".$message;
         $e = new Exception($message, 0);
         // Just remove the current 2 points from the trace
         $reflection = new ReflectionProperty(get_class($e), 'trace');
@@ -93,16 +105,6 @@ static private function throwErrorException($level,$message,$file,$line) {
     } // throwErrorException
 
     static public function errorHandler($level, $message, $file = ’’, $line = 0) {
-        // log all to logfile
-        if(ini_get('log_errors')){
-            $msg = self::getLevelStr($level) 
-                    . ' \'' . $message . '\' at ' 
-                    . $file 
-                    . ' ' . $line . ' Trace: ' 
-                    . BacktraceService::formatTraceLogStr(BacktraceService::getBacktrace(2));
-            error_log($msg);
-        }
-
         // mask errors on error_reporting() settings
         // here we have them all
         $systemErrorReporting = error_reporting();
@@ -122,6 +124,10 @@ static public function errorHandler($level, $message, $file = ’’, $line = 0)
             case E_USER_NOTICE  :
             case E_CORE_WARNING :
             case E_COMPILE_WARNING  :
+                // log all to logfile
+                if(ini_get('log_errors')){
+                    error_log(self::errorMsgLogStr($level,$message,$file,$line));
+                }
                 if(ini_get('display_errors')){
                     print(self::errorMsgStr($level,$message,$file,$line)); 
                 } else {
@@ -130,6 +136,7 @@ static public function errorHandler($level, $message, $file = ’’, $line = 0)
                 return;
             break;
             default             :  // fatal errors 
+                // exception should do logfile logging
                 // call exception - no return
                 self::throwErrorException($level,$message,$file,$line);
             break;
diff --git a/engine/include/exceptions/UncaughtExceptionService.php b/engine/include/exceptions/UncaughtExceptionService.php
index c030fe8d..ffe00bdb 100644
--- a/engine/include/exceptions/UncaughtExceptionService.php
+++ b/engine/include/exceptions/UncaughtExceptionService.php
@@ -50,7 +50,6 @@ static public function errorGetLast() {
 
     }  // errorGetLast()
  
-
     static public function dummyMessage4User() {
 
         // dummy message masks error details for user
@@ -60,37 +59,56 @@ static public function dummyMessage4User() {
         if (php_sapi_name() !== "cli") {
             $NL = '<br/>';
             $H1Open='<h1>'; $H1Close='</h1>';
+            print("<h1>500 Internal Server Error</h1><br/>\n");
         }
         $NL .= "\n";
 
-        print($H1Open."500 Internal Server Error".$H1Close.$NL);
         print("An internal server error has been occurred.".$NL);
         print("Please try again later.".$NL);
 
     } // dummyMessage4User
 
-    static public function UncaughtException(Exception $e) {
+    static private function exceptionMsgCLIStr(Exception $e) {
 
-        $NL=''; $BOpen=''; $BClose=''; $PreOpen=''; $PreClose='';
-        if (php_sapi_name() !== "cli") {
-            $NL = '<br/>'; $BOpen='<b>'; $BClose='</b>'; $PreOpen='<pre>'; $PreClose='<pre/>';
-            // there actions for browser environment
+        $msg = "Uncaught exception: ".$e->getMessage()."\n"
+               ." in file ".$e->getFile()." on line ".$e->getLine()."\n"
+               .$e->getTraceAsString()."\n";
+        return $msg;
+
+    } // exceptionMsgCLIStr()
+
+    static private function exceptionMsgHTMLStr(Exception $e) {
+
+        $msg = "Uncaught exception: <b>".$e->getMessage()."</b>\n"
+            ."<pre> in file ".$e->getFile()." on line ".$e->getLine()."</pre>\n"
+            ."<pre>".$e->getTraceAsString()."</pre>\n";
+        return $msg;
+
+    } // exceptionMsgHTMLStr()
+
+    static private function exceptionMessage(Exception $e) {
+
+        if(php_sapi_name() == 'cli') {
+            print(self::exceptionMsgCLIStr($e));
+        } else {
+            // there actions for browser environment only
             http_response_code(500);
+            print(self::exceptionMsgHTMLStr($e));
         }
-        $NL .= "\n";
+
+    } // exceptionMessage()
+
+    static public function UncaughtException(Exception $e) {
 
         if(ini_get('display_errors')){
-            print("Uncaught exception: ".$BOpen. $e->getMessage().$BClose.$NL);
-            print($PreOpen." in file ".$e->getFile()." on line ".$e->getLine().$PreClose.$NL);
-            print($PreOpen.$e->getTraceAsString().$PreClose.$NL);
+            self::exceptionMessage($e);
         } else {
-            print($BOpen."Uncaught exception has been occurred.".$BClose.$NL);
-            print("Please try again later.".$NL);
+            self::dummyMessage4User(); 
         }
-        // komunikat o błędzie do logu - zawsze, chyba że zablokujemy w ogóle
+
+        // logging information to logfile always, if not disallow
         if(ini_get('log_errors')){
-            //error_log("Uncaught exception: ".print_r($e,true));
-            error_log("Uncaught exception: ".$e->getMessage()." in file ".$e->getFile()." on line ".$e->getLine()." Trace:".$e->getTraceAsString());
+            error_log("Uncaught exception: ".$e->getMessage()." in file ".$e->getFile()." on line ".$e->getLine()." Trace:".$e->getTraceAsString(),0);
         }
    
         // serviced errors shouldn't be processed again

From 3623243111e537084cb889c8ceee9bf8219858f0 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Thu, 14 Apr 2022 22:08:45 +0200
Subject: [PATCH 086/154] initial DB content for db docker container should be
 in init subdirectory

---
 database/{ => init}/inforex-v1.0.sql | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename database/{ => init}/inforex-v1.0.sql (100%)

diff --git a/database/inforex-v1.0.sql b/database/init/inforex-v1.0.sql
similarity index 100%
rename from database/inforex-v1.0.sql
rename to database/init/inforex-v1.0.sql

From 7c9ec22365be38b9716604e8bb6fff35f2e698ce Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Thu, 14 Apr 2022 22:11:42 +0200
Subject: [PATCH 087/154] unproper user gpw in db system

---
 database/init/inforex-v1.0.sql | 1 -
 1 file changed, 1 deletion(-)

diff --git a/database/init/inforex-v1.0.sql b/database/init/inforex-v1.0.sql
index c45af4ec..6b9121c3 100644
--- a/database/init/inforex-v1.0.sql
+++ b/database/init/inforex-v1.0.sql
@@ -1988,7 +1988,6 @@ UNLOCK TABLES;
 /*!50001 SET character_set_results     = utf8 */;
 /*!50001 SET collation_connection      = utf8_general_ci */;
 /*!50001 CREATE ALGORITHM=UNDEFINED */
-/*!50013 DEFINER=`gpw`@`localhost` SQL SECURITY DEFINER */
 /*!50001 VIEW `activities_view_users` AS select `u`.`screename` AS `screename`,count(0) AS `COUNT(*)`,max(`a`.`datetime`) AS `last_datetime`,`a`.`activity_page_id` AS `activity_page_id`,`a`.`datetime` AS `datetime`,`a`.`ip_id` AS `ip_id`,`a`.`user_id` AS `user_id`,`a`.`corpus_id` AS `corpus_id`,`a`.`report_id` AS `report_id`,`a`.`activity_type_id` AS `activity_type_id`,`a`.`execution_time` AS `execution_time` from (`activities` `a` join `users` `u` on((`a`.`user_id` = `u`.`user_id`))) group by `a`.`user_id` */;
 /*!50001 SET character_set_client      = @saved_cs_client */;
 /*!50001 SET character_set_results     = @saved_cs_results */;

From 0a69efff2ab5e92ff411331268e15f16541b7b78 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Thu, 14 Apr 2022 22:13:45 +0200
Subject: [PATCH 088/154] remove SQL SECURITY DEFINER forced root only to load
 dump to DB

---
 database/init/inforex-v1.0.sql | 2 --
 1 file changed, 2 deletions(-)

diff --git a/database/init/inforex-v1.0.sql b/database/init/inforex-v1.0.sql
index 6b9121c3..36dc2f6a 100644
--- a/database/init/inforex-v1.0.sql
+++ b/database/init/inforex-v1.0.sql
@@ -2005,7 +2005,6 @@ UNLOCK TABLES;
 /*!50001 SET character_set_results     = utf8 */;
 /*!50001 SET collation_connection      = utf8_general_ci */;
 /*!50001 CREATE ALGORITHM=UNDEFINED */
-/*!50013 DEFINER=`root`@`localhost` SQL SECURITY DEFINER */
 /*!50001 VIEW `reports_annotations` AS select `ra`.`id` AS `id`,`ra`.`report_id` AS `report_id`,`ra`.`type_id` AS `type_id`,`at`.`name` AS `type`,`ra`.`from` AS `from`,`ra`.`to` AS `to`,`ra`.`text` AS `text`,`ra`.`user_id` AS `user_id`,`ra`.`creation_time` AS `creation_time`,`ra`.`stage` AS `stage`,`ra`.`source` AS `source` from (`reports_annotations_optimized` `ra` left join `annotation_types` `at` on((`at`.`annotation_type_id` = `ra`.`type_id`))) */;
 /*!50001 SET character_set_client      = @saved_cs_client */;
 /*!50001 SET character_set_results     = @saved_cs_results */;
@@ -2023,7 +2022,6 @@ UNLOCK TABLES;
 /*!50001 SET character_set_results     = utf8 */;
 /*!50001 SET collation_connection      = utf8_general_ci */;
 /*!50001 CREATE ALGORITHM=UNDEFINED */
-/*!50013 DEFINER=`root`@`localhost` SQL SECURITY DEFINER */
 /*!50001 VIEW `tokens_tags` AS select `tt`.`token_tag_id` AS `token_tag_id`,`tt`.`token_id` AS `token_id`,`b`.`text` AS `base`,`tt`.`base_id` AS `base_id`,`tokens_tags_ctags`.`ctag` AS `ctag`,`tt`.`disamb` AS `disamb` from ((`tokens_tags_optimized` `tt` left join `bases` `b` on((`b`.`id` = `tt`.`base_id`))) left join `tokens_tags_ctags` on((`tt`.`ctag_id` = `tokens_tags_ctags`.`id`))) */;
 /*!50001 SET character_set_client      = @saved_cs_client */;
 /*!50001 SET character_set_results     = @saved_cs_results */;

From 3ba87f55eba7915263f738ddab0bbad7de114909 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Thu, 14 Apr 2022 22:29:49 +0200
Subject: [PATCH 089/154] string 0000-00-00 00:00:00 is not valid for timestamp
 field initialization in newer DB version

---
 database/init/inforex-v1.0.sql | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/database/init/inforex-v1.0.sql b/database/init/inforex-v1.0.sql
index 36dc2f6a..20113c55 100644
--- a/database/init/inforex-v1.0.sql
+++ b/database/init/inforex-v1.0.sql
@@ -1614,7 +1614,7 @@ DROP TABLE IF EXISTS `tasks`;
 CREATE TABLE `tasks` (
   `task_id` int(11) NOT NULL AUTO_INCREMENT,
   `datetime` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP COMMENT 'Data i czas utworzenia zadania.',
-  `datetime_start` timestamp NOT NULL DEFAULT '0000-00-00 00:00:00',
+  `datetime_start` timestamp NULL DEFAULT NULL,
   `type` varchar(32) COLLATE utf8mb4_unicode_ci NOT NULL COMMENT 'Identyfikator zadania.',
   `description` text COLLATE utf8mb4_unicode_ci,
   `parameters` text COLLATE utf8mb4_unicode_ci NOT NULL,

From c25abc3ba27165e2af667bc5f217c27539b178ac Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Fri, 15 Apr 2022 12:09:10 +0200
Subject: [PATCH 090/154] mysqli driver should be used as default now

---
 engine/config/Config.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/engine/config/Config.php b/engine/config/Config.php
index 60c44312..f852f110 100644
--- a/engine/config/Config.php
+++ b/engine/config/Config.php
@@ -41,7 +41,7 @@ class Config extends Singleton\Singleton
 
     static private $url = 'http://localhost/inforex';
     static private $dsn = array(
-        'phptype' => 'mysql',
+        'phptype' => 'mysqli',
         'username' => 'inforex',
         'password' => 'password',
         'hostspec' => 'localhost',

From 5b3a8d33df61af2e9f7de89d0ba0073dbfe51811 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Fri, 15 Apr 2022 12:49:20 +0200
Subject: [PATCH 091/154] const for threshold of count types restored

---
 engine/settings.php | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/engine/settings.php b/engine/settings.php
index 5aed2ff0..c0d70137 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -15,6 +15,12 @@
 ini_set("output_buffering", 0);
 ini_set("short_open_tag",1);
 setlocale(LC_CTYPE, "en_US.UTF-8");
+
+// threshold of count types for one set/subset combination
+define('MAX_TYPES_LIMIT_THRESHOLD',300);
+define('MAX_TYPES_LABEL_INDEX',999999999999); // over autoincrement id
+define('MAX_TYPES_NAME_LABEL','...');
+
 set_error_handler("ErrorService::errorHandler");
 if(! PHPUnitTools::isPHPUnitRunning()) {
 	// under PHPUnit this one not works

From 18e158e33fc5ab214b46c9895f424be265df3857 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tomasz=20Naskr=C4=99t?= <tomasz.naskret@pwr.edu.pl>
Date: Thu, 21 Apr 2022 10:17:24 +0200
Subject: [PATCH 092/154] fix: after merge

- https://redmine.e-science.pl/clarin/issues/1491
---
 engine/templates/inc_widget_annotation_type_tree.tpl | 1 +
 1 file changed, 1 insertion(+)

diff --git a/engine/templates/inc_widget_annotation_type_tree.tpl b/engine/templates/inc_widget_annotation_type_tree.tpl
index 693d34a5..2c942341 100644
--- a/engine/templates/inc_widget_annotation_type_tree.tpl
+++ b/engine/templates/inc_widget_annotation_type_tree.tpl
@@ -61,6 +61,7 @@
 				<tr>
 					<td colspan="2"><i>No layers, subsets nor types to display</i></td>
 				</tr>
+			{/if}
 			</tbody>    <!-- class=annotationTypesTree -->
     	</table>	
     	</div>

From 8e5db18e7d49de70d5aacc44531f94c75607b915 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tomasz=20Naskr=C4=99t?= <tomasz.naskret@pwr.edu.pl>
Date: Thu, 21 Apr 2022 10:34:56 +0200
Subject: [PATCH 093/154] doc: moving file out from init

---
 database/README.md                   | 4 ++++
 database/{init => }/inforex-v1.0.sql | 0
 2 files changed, 4 insertions(+)
 create mode 100644 database/README.md
 rename database/{init => }/inforex-v1.0.sql (100%)

diff --git a/database/README.md b/database/README.md
new file mode 100644
index 00000000..ab2b35d8
--- /dev/null
+++ b/database/README.md
@@ -0,0 +1,4 @@
+### Database Initialization
+Before you start first time database docker move inforex-v1.0.sql to init/ folder
+
+File removed form init/ folder to prevent accidental initialization.
diff --git a/database/init/inforex-v1.0.sql b/database/inforex-v1.0.sql
similarity index 100%
rename from database/init/inforex-v1.0.sql
rename to database/inforex-v1.0.sql

From 1f22feaa68addd968697aefa752a800f653c96b5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tomasz=20Naskr=C4=99t?= <tomasz.naskret@pwr.edu.pl>
Date: Fri, 22 Apr 2022 15:28:37 +0200
Subject: [PATCH 094/154] fix: loading2

https://redmine.e-science.pl/clarin/issues/1492?issue_count=3&issue_position=1&next_issue_id=1383
---
 docker/www/Dockerfile                   | 2 ++
 engine/include/utils/CReportContent.php | 4 ++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/docker/www/Dockerfile b/docker/www/Dockerfile
index 84842ec7..07e911be 100644
--- a/docker/www/Dockerfile
+++ b/docker/www/Dockerfile
@@ -38,6 +38,8 @@ RUN curl -L -o /tmp/xdiff.tar.gz "http://www.xmailserver.org/libxdiff-0.23.tar.g
 # Supervisor
 RUN apt-get update -y && apt-get install supervisor -y
 
+# Git
+RUN apt-get install git -y
 
 FROM php-base
 
diff --git a/engine/include/utils/CReportContent.php b/engine/include/utils/CReportContent.php
index 88f19223..1e0321cb 100644
--- a/engine/include/utils/CReportContent.php
+++ b/engine/include/utils/CReportContent.php
@@ -114,8 +114,8 @@ static function insertAnnotationsWithRelations(HtmlStr2 $htmlStr, $annotations,
         foreach ($annotations as $an) {
             try {
                 $after = "";
-                if ( isset($annotationRelations[$an[id]]) ){
-                    $after = implode("", $annotationRelations[$an[id]]);
+                if ( isset($annotationRelations[$an['id']]) ){
+                    $after = implode("", $annotationRelations[$an['id']]);
                 }
                 $htmlStr->insertTag($an['from'],
                     sprintf("<an#%d:annotation %s:%d:%d:'%s'>", $an['id'], $an['type'], $an['group_id'], $an['annotation_subset_id'], $an['lemma']), $an['to'] + 1, "</an>$after");

From 9b3e3e7e87f3215422ac3bc211b36652eac3543d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tomasz=20Naskr=C4=99t?= <tomasz.naskret@pwr.edu.pl>
Date: Fri, 22 Apr 2022 15:56:10 +0200
Subject: [PATCH 095/154] fix: mix content over http

---
 engine/templates/inc_footer.tpl  | 6 +++---
 engine/templates/inc_header.tpl  | 7 +++----
 engine/templates/inc_header2.tpl | 6 ++----
 3 files changed, 8 insertions(+), 11 deletions(-)

diff --git a/engine/templates/inc_footer.tpl b/engine/templates/inc_footer.tpl
index 23a593ca..7b6c84e6 100644
--- a/engine/templates/inc_footer.tpl
+++ b/engine/templates/inc_footer.tpl
@@ -33,11 +33,11 @@
 		<div id="footer">
 			<span style="float: left">
 				Praca finansowana w ramach wkładu krajowego na rzecz udziału we wspólnym międzynarodowym przedsięwzięciu
-				<a target="_blank" href="http://clarin-pl.eu">"CLARIN ERIC: Wspólne zasoby językowe i infrastruktura technologiczna"</a>
+				<a target="_blank" href="https://clarin-pl.eu">"CLARIN ERIC: Wspólne zasoby językowe i infrastruktura technologiczna"</a>
 			</span>
 			<span>
-				Copyright © <a target="_blank" href="http://pwr.wroc.pl">Politechnika Wrocławska</a>,
-				<a target="_blank" href="http://nlp.pwr.wroc.pl">Grupa Technologii Językowych G4.19</a>, 2009&ndash;2020
+				Copyright © <a target="_blank" href="https://pwr.wroc.pl">Politechnika Wrocławska</a>,
+				<a target="_blank" href="https://nlp.pwr.wroc.pl">Grupa Technologii Językowych G4.19</a>, 2009&ndash;2022
 			</span>
 		</div> <!-- id="footer" -->
 
diff --git a/engine/templates/inc_header.tpl b/engine/templates/inc_header.tpl
index af31efb1..e6d2936b 100644
--- a/engine/templates/inc_header.tpl
+++ b/engine/templates/inc_header.tpl
@@ -29,7 +29,7 @@
 	<link rel="StyleSheet" href="libs/jquery-ui-1.12.1.custom/jquery-ui.min.css" TYPE="text/css"/>
 	<script src="libs/jquery-ui-1.12.1.custom/jquery-ui.min.js" type="text/javascript"></script>
 {elseif $page == "about"}
-	<script type="text/javascript" src="http://code.jquery.com/jquery-latest.min.js"></script>
+	<script type="text/javascript" src="https://code.jquery.com/jquery-latest.min.js"></script>
 {else}
 	<script src="js/jquery/jquery-1.4.4.min.js" type="text/javascript"></script>
 	<link rel="StyleSheet" href="css/custom-theme/jquery-ui-1.7.2.custom.css?20130903" TYPE="text/css"/>
@@ -62,8 +62,8 @@
 	<link rel="stylesheet" type="text/css" href="js/jquery/markitup/skins/markitup/style.css?20130903" />
 	<link rel="stylesheet" type="text/css" href="js/jquery/markitup/sets/default/style.css?20130903" />
 
-    <link href='http://fonts.googleapis.com/css?family=Chango' rel='stylesheet' type='text/css'>
-    <link href='http://fonts.googleapis.com/css?family=Shanti' rel='stylesheet' type='text/css'>
+    <link href='https://fonts.googleapis.com/css?family=Chango' rel='stylesheet' type='text/css'>
+    <link href='https://fonts.googleapis.com/css?family=Shanti' rel='stylesheet' type='text/css'>
     <link href="https://fonts.googleapis.com/css?family=Slabo+27px" rel="stylesheet" type='text/css'>
     <!--<link rel="stylesheet" href="http://yui.yahooapis.com/pure/0.6.0/pure-min.css">-->
 
@@ -202,4 +202,3 @@
 			</p>
 		</div>
 	{/if}
-				
diff --git a/engine/templates/inc_header2.tpl b/engine/templates/inc_header2.tpl
index 52d05386..d7daaf52 100644
--- a/engine/templates/inc_header2.tpl
+++ b/engine/templates/inc_header2.tpl
@@ -53,8 +53,8 @@
 		<link rel="stylesheet" type="text/css" href="js/jquery/markitup/skins/markitup/style.css" />
 		<link rel="stylesheet" type="text/css" href="js/jquery/markitup/sets/default/style.css" />
 
-		<link href='http://fonts.googleapis.com/css?family=Chango' rel='stylesheet' type='text/css'>
-		<link href='http://fonts.googleapis.com/css?family=Shanti' rel='stylesheet' type='text/css'>
+		<link href='https://fonts.googleapis.com/css?family=Chango' rel='stylesheet' type='text/css'>
+		<link href='https://fonts.googleapis.com/css?family=Shanti' rel='stylesheet' type='text/css'>
 		<link href="https://fonts.googleapis.com/css?family=Slabo+27px" rel="stylesheet" type='text/css'>
 
 		<script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
@@ -145,5 +145,3 @@
 			</p>
 		</div>
 	{/if}
-
-

From 8dbfb07df232b2c30cc6ef2da8a52603fecf3d9c Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Sat, 23 Apr 2022 13:01:33 +0200
Subject: [PATCH 096/154] manually implementing fixes from docker branch

---
 docker/www/php.ini                            |   1 +
 .../include/diagnostics/CReportResources.php  | 117 ++++++++++++++++++
 engine/templates/page_about.tpl               |   4 +-
 3 files changed, 120 insertions(+), 2 deletions(-)
 create mode 100644 engine/include/diagnostics/CReportResources.php

diff --git a/docker/www/php.ini b/docker/www/php.ini
index d1987673..7edb71db 100644
--- a/docker/www/php.ini
+++ b/docker/www/php.ini
@@ -3,3 +3,4 @@ log_errors = 1
 upload_max_filesize = 30M
 post_max_size = 30M
 memory_limit = 2048M
+max_input_vars = 5000
diff --git a/engine/include/diagnostics/CReportResources.php b/engine/include/diagnostics/CReportResources.php
new file mode 100644
index 00000000..53dcc534
--- /dev/null
+++ b/engine/include/diagnostics/CReportResources.php
@@ -0,0 +1,117 @@
+<?php
+/**
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ * See LICENCE
+ */
+
+class ReportResources {
+
+    /* class for developers only to diagnostic memory usage and time
+       consuming needed for some code execution 
+    */
+
+    private $id = "";
+    private $time = null;
+    private $memory = null;
+
+    public function __construct($uniqueID = null) {
+
+        if($uniqueID === null) {
+            // generate unique ID for identify process in concurent
+            // logging environment
+            $uniqueID = "";
+            for($i=0;$i<4;$i++) {
+                $uniqueID .= strval($this->randomDigit());
+            }
+        } 
+        $this->id = $uniqueID;
+
+        $this->startReportResourcesCounting();
+
+    } // __constructor()
+
+    public function startReportResourcesCounting() {
+
+        // initial values. From this values diff will be counted
+        // for first step. 
+        $this->time = $this->readTime();
+        $this->memory = $this->readMemory();
+
+    } // startReportResourceCounting
+
+    public function sendReportResourceDiffToLog($msg, $timeConsumingInSeconds=null, $memoryUsageInBytes=null) {
+
+        // send to system log line with $msg string and actual
+        // measurement diff from last send... function call. If extended 
+        // parameter exists, they overwrite selfmeasuring 
+
+        if($memoryUsageInBytes==null) {
+            $memoryUsageInBytes = $this->readMemory();
+        }
+        $memoryDiff = $memoryUsageInBytes - $this->memory;
+        $this->memory = $memoryUsageInBytes;
+ 
+
+        if($timeConsumingInSeconds==null) {
+            $timeConsumingInSeconds = $this->readTime();
+        }
+        $timeDiff = $timeConsumingInSeconds - $this->time;
+        $this->time = $timeConsumingInSeconds;
+
+        $line = $this->id.": "
+                .strval($memoryDiff)." bytes "
+                .strval($timeDiff)." secs "
+                ."for ".$msg;
+        error_log($line); 
+        
+    } // sendReportResourceDiffToLog()
+
+    public function sendReportResourceToLog($msg, $timeFromMidnightInSeconds=null, $memoryUsageInBytes=null) {
+
+        // send to system log line with $msg string and actual
+        // measurement absolute values. If extended parameter
+        // exists, they overwrite selfmeasuring
+
+        if($memoryUsageInBytes==null) {
+            $memoryUsageInBytes = $this->readMemory();
+        }
+        $this->memory = $memoryUsageInBytes;
+
+        if($timeFromMidnightInSeconds==null) {
+            $timeFromMidnightInSeconds = $this->readTime();
+        }
+        $this->time = $timeFromMIdnightInSeconds;
+ 
+        $line = $this->id.": "
+                .strval($memoryUsageInBytes)." bytes "
+                .strval($timeFromMidnightInSeconds)." secs "
+                ."at ".$msg;
+        error_log($line);
+
+    } // sendReportResourceToLog()
+
+    private function randomDigit() {
+
+        return rand(0,9);    
+
+    } // randomDigit()
+
+    private function readMemory() {
+
+        // Returns the memory amount in bytes. 
+        return memory_get_usage();
+
+    } // readMemory()
+
+    private function readTime() {
+
+        // with get_as_float = true returns in seconds
+        return microtime(True);
+
+    } // readTime()
+
+} // ReportResources class
+
+?>
diff --git a/engine/templates/page_about.tpl b/engine/templates/page_about.tpl
index dbf0083b..550fc145 100644
--- a/engine/templates/page_about.tpl
+++ b/engine/templates/page_about.tpl
@@ -40,7 +40,7 @@
 							<li>export documents to a ccl format,</li>
 						</ul>
 						<br/>
-
+						{if $rev!="no_git_rev"}Code revision : {$rev}<br/>{/if}
 						Suggested browser: <a href="http://www.mozilla.com/pl/firefox/">Chrome</a> <img src="gfx/Google-Chrome-icon.png" title="Chrome" style="vertical-align: middle"/>
 					</div>
 					<div class="col-md-6">
@@ -211,4 +211,4 @@
 </div>
 -->
 
-{include file="inc_footer.tpl"}
\ No newline at end of file
+{include file="inc_footer.tpl"}

From 8b8cb5c06a20dd69c5e71825a01b960b90a63c42 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Sat, 7 May 2022 13:50:58 +0200
Subject: [PATCH 097/154] agreement changes from template_types and type_limit
 branches

---
 .../inc_widget_annotation_type_tree.tpl       | 52 +++----------------
 public_html/js/page_report_preview.js         | 11 +++-
 2 files changed, 16 insertions(+), 47 deletions(-)

diff --git a/engine/templates/inc_widget_annotation_type_tree.tpl b/engine/templates/inc_widget_annotation_type_tree.tpl
index 693d34a5..65d1f068 100644
--- a/engine/templates/inc_widget_annotation_type_tree.tpl
+++ b/engine/templates/inc_widget_annotation_type_tree.tpl
@@ -4,6 +4,7 @@
  * Wrocław University of Technology
  * See LICENCE 
  *}
+ 
 	<div id="annotation_layers">
 		<div style="overflow-y:auto" class="">
 		<table class="table table-striped" cellspacing="1" style="width: 100%">
@@ -13,55 +14,14 @@
                     <th style="text-align:center; width: 100px" title="Dynamically show/hide layer">Display</th>
                 </tr>
 			</thead>
-			<tbody>
-		    {foreach from=$annotation_types item=set key=k name=groups}
-			    <tr class="layerRow hiddenRow" setid="{$set.groupid}">
-			    	<td style="vertical-align: middle;" class="layersList">
-			    		<span class="count" title="Number of selected annotation types from this layer" style="float: right; font-size: 10px; color: #445967; font-weight: normal;"></span>
-			    		<span class="toggleLayer ui-icon ui-icon-circlesmall-plus" style="float:left"></span>
-			    		<span class="layerName" style="clear:both">{$set.name}</span>
-			    	</td>
-			    	<td style="vertical-align: middle;text-align:center">
-			    		<input name="layerId-{$k}" type="checkbox" class="group_cb" /> 
-			    	</td>
-			    </tr>
-		    	{foreach from=$set item=subset key=sk name=subsets}
-					{if $sk != "name"}
-					<tr class="sublayerRow" subsetid="{$sk}" style="display:none">
-						<td style="vertical-align: middle;" class="layersList">
-							<span class="count" title="Number of selected annotation types from this subset" style="float: right; font-size: 10px; color: #445967; font-weight: normal;"></span>
-							<span class="ui-icon ui-icon-carat-1-sw" style="float:left"></span>
-							<span class="toggleSubLayer ui-icon ui-icon-circlesmall-plus" style="float:left"></span>
-							<span class="layerName" style="margin-left:10px;clear:both">{$subset.name}</span>
-						</td>
-			    		<td style="vertical-align: middle;text-align:center">
-			    			<input name="subsetId-{$sk}" type="checkbox" class="subset_cb" /> 
-			    		</td>
-					</tr>
-					{foreach from=$subset item=type key=tk name=types}
-						{if $tk != "name"}
-					<tr class="typelayerRow" typeid="{$tk}" style="display:none">
-						<td style="vertical-align: middle;" class="layersList">
-							<span class="ui-icon ui-icon-carat-1-sw" style="float:left"></span>
-							<span class="ui-icon ui-icon-carat-1-sw" style="float:left"></span>
-							<span class="layerName" style="margin-left:20px;clear:both;font-weight:normal;">{$type}</span>
-						</td>
-				    	<td style="vertical-align: middle;text-align:center">
-						{if $type != $annotation_types_threshold_name}
-				    		<input name="typeId-{$tk}" type="checkbox" class="leftLayer type_cb" /> 
-						{/if}
-				    	</td>
-					</tr>
-						{/if}
-					{/foreach}					
-					{/if}		    	
-		    	{/foreach}	
-		    {/foreach}
-			{if (!is_array($annotation_types)) || $annotation_types|@count==0}
+			<tbody class="annotationTypesTree" >
 				<tr>
 					<td colspan="2"><i>No layers, subsets nor types to display</i></td>
 				</tr>
 			</tbody>    <!-- class=annotationTypesTree -->
     	</table>	
-    	</div>
+    	</div>    
 	</div>	
+{include file="inc_widget_annotation_type_tree_set_template.tpl"}
+{include file="inc_widget_annotation_type_tree_subset_template.tpl"}
+{include file="inc_widget_annotation_type_tree_types_template.tpl"}
diff --git a/public_html/js/page_report_preview.js b/public_html/js/page_report_preview.js
index 0fd22190..6fd32fe0 100644
--- a/public_html/js/page_report_preview.js
+++ b/public_html/js/page_report_preview.js
@@ -70,12 +70,21 @@ function createTypeRowFromTemplate(container,typeId,typeName) {
          * and place it on the end of container element                      
          */
         const typeRowTemplateId = "typeRowTpl";
+	const MAX_TYPES_NAME_LABEL = "...";
         let typeRow = null;
         const template = document.querySelector("#"+typeRowTemplateId);
         if(template) {
                 typeRow = template.content.cloneNode(true);
                 if(typeRow){
-			typeRow.querySelector("input").setAttribute("name","typeId-"+typeId);
+			if(typeName==MAX_TYPES_NAME_LABEL) {
+                		/* remove checkbox for limit threshold */
+                		elem = typeRow.querySelector("input");
+                		if(elem) {
+                        		elem.parentElement.removeChild(elem);
+                		}
+        		} else { /* type under limit */
+				typeRow.querySelector("input").setAttribute("name","typeId-"+typeId);
+			}
                         typeRow.querySelector("tr").setAttribute("typeid",typeId);
                         typeRow.querySelector(".layerName").innerText = typeName;
                         if(container) {

From 69d7607de2de2b016153f03346cc2ce08ab8f822 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Mon, 9 May 2022 19:38:03 +0200
Subject: [PATCH 098/154] bad namespaces in Config class and proper changes
 agreed

---
 composer.json                           |   2 +-
 engine/Config/Config.php                | 199 ++++++++++++++++++++++++
 engine/{config => Config}/Singleton.php |   0
 engine/config/Config.php                | 192 -----------------------
 4 files changed, 200 insertions(+), 193 deletions(-)
 create mode 100644 engine/Config/Config.php
 rename engine/{config => Config}/Singleton.php (100%)
 delete mode 100644 engine/config/Config.php

diff --git a/composer.json b/composer.json
index 7d68e006..b4466c8d 100644
--- a/composer.json
+++ b/composer.json
@@ -16,7 +16,7 @@
 		"classmap": [
             "engine/external/pear/",
 			"engine/include/",
-			"engine/config/",
+			"engine/Config/",
 			"engine/page/",
 			"engine/external/ChromePhp.php"
 		],
diff --git a/engine/Config/Config.php b/engine/Config/Config.php
new file mode 100644
index 00000000..2a5c7c7d
--- /dev/null
+++ b/engine/Config/Config.php
@@ -0,0 +1,199 @@
+<?php
+/**
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ * See LICENCE 
+ */
+
+class Phantom {
+
+    public function __call($name, $arguments)
+    {
+        throw new ConfigException("Method {$name} is not supported.");
+    }
+
+} // Phantom class
+
+use engine\Config\Singleton as Singleton;
+
+/**
+ * Inforex configuration
+ */
+class Config extends Singleton\Singleton{
+
+	static private $confVariables = array (
+    	"sid" => "gpw",
+	    "session_time" => 0,
+		"offline" => false,
+    	"db_charset" => "utf8mb4",
+	
+	/* Inforex basic configuration */
+		"path_engine" => 'ABSOLUTE_PATH_TO:inforex/engine',
+		"path_www"    => 'ABSOLUTE_PATH_TO:inforex/public_html',	
+		"path_secured_data" => 'ABSOLUTE_PATH_TO:inforex/data',
+	//static private $path_exports 	  = 'ABSOLUTE_PATH_TO:inforex/data/exports';
+
+	/* set $federationLoginUrl to null if regular login is to be used */
+        "federationLoginUrl" => null,
+    	"federationValidateTokenUrl" => null,
+
+		"url" => 'http://localhost/inforex',
+		"dsn" => array(
+    		'phptype'  => 'mysqli',
+    		'username' => 'inforex',
+    		'password' => 'password',
+    		'hostspec' => 'localhost',
+    		'database' => 'inforex',
+		),
+
+		"wccl_match_enable" => false,
+		//"wccl_match_tester_script" => "ABSOLUTE_PATH_TO:inforex/apps/wccl/wccl-gateway.py";
+		//static private $wccl_match_script = "ABSOLUTE_PATH_TO:inforex/apps/wccl/wccl-gateway-run.py";
+	
+		"wccl_match_tester_corpora" => array(
+			array("name"=>"KPWr 1.2.2 TimeML train &ndash; all (1&ndash;551)", 
+					"path"=>"/nlp/corpora/pwr/kpwr-release/kpwr-1.2.2-time-disamb/index_time_train.txt"),
+			array("name"=>"KPWr 1.2.2 TimeML train &ndash; A (1&ndash;100)", "path"=>"/index_time_a.txt"),
+			array("name"=>"KPWr 1.2.2 TimeML train &ndash; B (101&ndash;200)", "path"=>"/index_time_b.txt"),
+			array("name"=>"KPWr 1.2.2 TimeML train &ndash; C (201&ndash;300)", "path"=>"/index_time_c.txt"),
+			array("name"=>"KPWr 1.2.2 TimeML train &ndash; D (301&ndash;551)", "path"=>"/index_time_d.txt"),
+			array("name"=>"KPWr 1.2.2 TimeML tune","path"=>"/index_time_tune.txt"),
+			array("name"=>"KPWr 1.2.7 TimeML train&ndash; all",	"path"=>"/index_time_train.txt")
+		), 	
+		
+		"wccl_match_daemon" => null,
+        // default settings for wccl import
+        "insertSentenceTags" => true,
+
+	/* Advanced parameters */
+		"path_python"       => 'python',
+		"path_liner"        => null,
+		"path_liner2"       => null,
+		"path_nerd"         => null,
+		"path_wcrft"        => null,
+		"path_semql"        => null,
+		"file_with_rules"   => null, 
+		"takipi_wsdl"       => null,
+		"liner_wsdl"        => null,
+		"serel_liner_wsdl"  => null,
+		"path_wcrft_model"  => "",
+		"wcrft_config"	   => "nkjp_s2.ini",
+		"wcrft2_config"	   => "nkjp_e2",
+		"log_sql"           => false,
+		"log_output"		=> "fb",
+		"path_grabber"	   => null,
+	
+        "max_types_limit_threshold" => MAX_TYPES_LIMIT_THRESHOLD,
+
+    // path for local config file - if exists
+    	"localConfigFilename"  => ""
+	);
+		
+	// for more friendly call only...
+    final public static function Config(){
+
+        return self::getInstance();
+
+    } // Config()
+		
+	// constructor - default values of some parameters 	
+	final protected function __construct(){
+
+        parent::__construct();
+
+		$this->put_session_time(60 * 60 * 24 * 356 * 2);
+
+		// Setup default paths
+		$path_engine = realpath(__DIR__ . DIRECTORY_SEPARATOR . "..");
+		$path_inforex = realpath($path_engine . DIRECTORY_SEPARATOR . '..');
+
+		$this->put_path_engine($path_engine);
+		$this->put_path_www($path_inforex . DIRECTORY_SEPARATOR . 'public_html');	
+		$this->put_path_secured_data($path_inforex . DIRECTORY_SEPARATOR . 'secured_data');
+		
+		$this->put_path_exports($this->get_path_secured_data() . DIRECTORY_SEPARATOR . 'exports');
+		
+		$this->put_wccl_match_tester_script($path_engine . "/../apps/wccl/wccl-gateway.py");
+		$this->put_wccl_match_script($path_engine . "/../apps/wccl/wccl-gateway-run.py");		
+
+	}
+
+	function __call($method,$arguments){
+        // for crazy or lazy developers may be set_<sth> too
+        if ( substr($method, 0, 4) == "set_" ){
+            // change set_<sth> to put_<sth>
+            $method=preg_replace("/^se/","pu",$method);
+        }
+		if ( substr($method, 0, 4) == "get_" ){
+			$parameter_name = substr($method, 4);
+			if ( array_key_exists($parameter_name,self::$confVariables) ) {
+				return self::$confVariables[$parameter_name];
+			} 
+			if (  property_exists($this,$parameter_name) ) {
+				if ( isset($this->$parameter_name ) ) {
+					return $this->$parameter_name;
+				} elseif ( isset(self::${$parameter_name})) { 
+					return self::${$parameter_name};
+				} else
+					// last case - null is not catch by isset()
+					return null;
+			} else {
+				throw new ConfigException("Parameter '$parameter_name' not defined in the configuration file.");
+			}
+		} else if ( substr($method, 0, 4) == "put_" ){
+            // implementation of put_<sth>($value) method
+            $parameter_name = substr($method, 4);
+            $value = $arguments[0];
+            self::$confVariables[$parameter_name]=$value;
+            if($parameter_name=="localConfigFilename"){
+                $this->loadConfigFromFile(self::get_localConfigFilename());
+            }
+        } 
+		else
+			call_user_func_array(array($this,"_".$method),$arguments);		
+	}
+	
+    private function loadOldLocalConfig($pathname) {
+
+        $config = new Phantom();   
+        include($pathname);
+        $classVars=get_object_vars($config);
+        foreach($classVars as $name => $value) {
+                $this->{"put_".$name}($config->{$name});
+        }
+
+    } // loadOldLocalConfig()
+
+    public function loadConfigFromFile($pathname) {
+
+        if ( file_exists($pathname) ) {
+            try {
+
+                $this->loadOldLocalConfig($pathname);
+
+            } catch(Exception $e) {
+
+                // Ładowanie wg. nowego configa
+                $config = $this;
+                try {
+                    include($pathname);
+                } catch( Exception $e ) {
+                    throw new ConfigException("Error loading configuration file '$pathname'.");
+                } // try..catch() new syntax
+            }  // try...catch() old syntax
+        } // if file_exists()
+
+    } // loadConfigFromFile()
+
+	public function dumpConfigSets() {
+
+        return get_class_vars(get_class($this));
+
+	} // dumpConfigSets()
+
+
+} // Config class
+
+ 
+?>
diff --git a/engine/config/Singleton.php b/engine/Config/Singleton.php
similarity index 100%
rename from engine/config/Singleton.php
rename to engine/Config/Singleton.php
diff --git a/engine/config/Config.php b/engine/config/Config.php
deleted file mode 100644
index f852f110..00000000
--- a/engine/config/Config.php
+++ /dev/null
@@ -1,192 +0,0 @@
-<?php
-/**
- * Part of the Inforex project
- * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
- * Wrocław University of Technology
- * See LICENCE
- */
-
-class Phantom
-{
-
-    public function __call($name, $arguments)
-    {
-        throw new Exception("Method {$name} is not supported.");
-    }
-
-}
-
-use engine\Config\Singleton as Singleton;
-
-/**
- * Inforex configuration
- */
-class Config extends Singleton\Singleton
-{
-
-    static private $sid = "gpw";
-    //var $sid = "gpw";
-    static private $session_time = 0;
-    static private $offline = false;
-    static private $db_charset = "utf8mb4";
-
-    /* Inforex basic configuration */
-    static private $path_engine = 'ABSOLUTE_PATH_TO:inforex/engine';
-    static private $path_www = 'ABSOLUTE_PATH_TO:inforex/public_html';
-    static private $path_secured_data = 'ABSOLUTE_PATH_TO:inforex/data';
-
-    /* set $federationLoginUrl to null if regular login is to be used */
-    static private $federationLoginUrl = null;
-    static private $federationValidateTokenUrl = null;
-
-    static private $url = 'http://localhost/inforex';
-    static private $dsn = array(
-        'phptype' => 'mysqli',
-        'username' => 'inforex',
-        'password' => 'password',
-        'hostspec' => 'localhost',
-        'database' => 'inforex',
-    );
-
-    static private $wccl_match_enable = false;
-
-    static private $wccl_match_tester_corpora = array(
-        array("name" => "KPWr 1.2.2 TimeML train &ndash; all (1&ndash;551)",
-            "path" => "/nlp/corpora/pwr/kpwr-release/kpwr-1.2.2-time-disamb/index_time_train.txt"),
-        array("name" => "KPWr 1.2.2 TimeML train &ndash; A (1&ndash;100)", "path" => "/index_time_a.txt"),
-        array("name" => "KPWr 1.2.2 TimeML train &ndash; B (101&ndash;200)", "path" => "/index_time_b.txt"),
-        array("name" => "KPWr 1.2.2 TimeML train &ndash; C (201&ndash;300)", "path" => "/index_time_c.txt"),
-        array("name" => "KPWr 1.2.2 TimeML train &ndash; D (301&ndash;551)", "path" => "/index_time_d.txt"),
-        array("name" => "KPWr 1.2.2 TimeML tune", "path" => "/index_time_tune.txt"),
-        array("name" => "KPWr 1.2.7 TimeML train&ndash; all", "path" => "/index_time_train.txt")
-    );
-
-    static private $wccl_match_daemon = null;
-
-    /* Advanced parameters */
-    static private $path_python = 'python';
-    static private $path_liner = null;
-    static private $path_liner2 = null;
-    static private $path_nerd = null;
-    static private $path_wcrft = null;
-    static private $path_semql = null;
-    static private $file_with_rules = null;
-    static private $takipi_wsdl = null;
-    static private $liner_wsdl = null;
-    static private $serel_liner_wsdl = null;
-    static private $path_wcrft_model = "";
-    static private $wcrft_config = "nkjp_s2.ini";
-    static private $wcrft2_config = "nkjp_e2";
-    static private $log_sql = false;
-    static private $log_output = "fb";
-    static private $path_grabber = null;
-
-    static private $max_types_limit_threshold = MAX_TYPES_LIMIT_THRESHOLD;
-
-    // path for local config file - if exists
-    static private $localConfigFilename = "";
-
-    // for more friendly call only...
-    final public static function Config()
-    {
-
-        return self::getInstance();
-
-    }
-
-    // constructor - default values of some parameters
-    final protected function __construct()
-    {
-
-        parent::__construct();
-
-        $this->session_time = 60 * 60 * 24 * 356 * 2;
-
-        // Setup default paths
-        $path_engine = realpath(__DIR__ . DIRECTORY_SEPARATOR . "..");
-        $path_inforex = realpath($path_engine . DIRECTORY_SEPARATOR . '..');
-
-        $this->path_engine = $path_engine;
-        $this->path_www = $path_inforex . DIRECTORY_SEPARATOR . 'public_html';
-        $this->path_secured_data = $path_inforex . DIRECTORY_SEPARATOR . 'secured_data';
-
-        $this->path_exports = $this->path_secured_data.DIRECTORY_SEPARATOR.'exports';
-
-        $this->wccl_match_tester_script = $path_engine . "/../apps/wccl/wccl-gateway.py";
-        $this->wccl_match_script = $path_engine . "/../apps/wccl/wccl-gateway-run.py";
-
-    }
-
-    function __call($method, $arguments)
-    {
-        // for crazy or lazy developers may be set_<sth> too
-        if (substr($method, 0, 4) == "set_") {
-            // change set_<sth> to put_<sth>
-            $method = preg_replace("/^se/", "pu", $method);
-        }
-        if (substr($method, 0, 4) == "get_") {
-            $parameter_name = substr($method, 4);
-            if (property_exists($this, $parameter_name)) {
-                if (isset($this->$parameter_name)) {
-                    return $this->$parameter_name;
-                } elseif (isset(self::${$parameter_name})) {
-                    return self::${$parameter_name};
-                } else
-                    // last case - null is not catch by isset()
-                    return null;
-            } else {
-                throw new Exception("Parameter '$parameter_name' not defined in the configuration file.");
-            }
-        } else if (substr($method, 0, 4) == "put_") {
-            // implementation of put_<sth>($value) method
-            $parameter_name = substr($method, 4);
-            $value = $arguments[0];
-            $this->{$parameter_name} = $value;
-            if ($parameter_name == "localConfigFilename") {
-                $this->loadConfigFromFile($this->localConfigFilename);
-            }
-        } else
-            call_user_func_array(array($this, "_" . $method), $arguments);
-    }
-
-    private function loadOldLocalConfig($pathname)
-    {
-
-        $config = new Phantom();
-        include($pathname);
-        $classVars = get_object_vars($config);
-        foreach ($classVars as $name => $value) {
-            $this->{"put_" . $name}($config->{$name});
-        }
-
-    }
-
-    public function loadConfigFromFile($pathname)
-    {
-
-        if (file_exists($pathname)) {
-            try {
-
-                $this->loadOldLocalConfig($pathname);
-
-            } catch (Exception $e) {
-
-                // loading new config
-                $config = $this;
-                try {
-                    include($pathname);
-                } catch (Exception $e) {
-                    throw new Exception("Error loading configuration file '$pathname'.");
-                }
-            }
-        }
-
-    }
-
-    public function dumpConfigSets()
-    {
-        return get_class_vars(get_class($this));
-    }
-}
-
-?>

From 2023938e37f9e6d3178527f98a2f3b2213b90988 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Wed, 11 May 2022 19:29:40 +0200
Subject: [PATCH 099/154] some database interface improvements

---
 engine/include/database/Database.php | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/engine/include/database/Database.php b/engine/include/database/Database.php
index 20e37f89..35890d1f 100644
--- a/engine/include/database/Database.php
+++ b/engine/include/database/Database.php
@@ -6,9 +6,6 @@
  * See LICENCE
  */
 
-// dla dostępności MDB2::MDB2_PORTABILITY_NONE przy inicjowaniu $db tylko
-require_once(__DIR__."/../../../engine/external/pear/MDB2.php");
-
 /**
  * Database gateway.
  */
@@ -118,7 +115,6 @@ private function log_sql($sql, $args){
      */
     function execute($sql, $args=null){
         $time_start = microtime(TRUE);
-        //$sth = null;
         $result = null;
         try{
             $this->log_sql($sql, $args);
@@ -154,7 +150,7 @@ function fetch_rows($sql, $args = null){
     }
 
     /**
-     * Return one-dimensional array of values for given column for each row
+     * Return one-dimensional array of values from given column for each row
      * returned by the query.
      * @param $sql {String} SQL query.
      * @param $column {String} Column name.
@@ -501,7 +497,11 @@ function fetch_assoc_array($sql, $key_column_name, $value_column_name, $args = n
         $rows = $this->fetch_rows($sql, $args);
         $result = array();
         foreach ($rows as $row){
-            $result[$row[$key_column_name]] = $row[$value_column_name];
+            if( array_key_exists($key_column_name,$row) && array_key_exists($value_column_name,$row) ) {
+                $result[$row[$key_column_name]] = $row[$value_column_name];
+            } else {
+                throw new DatabaseException("Columns $key_column_name or $value_column_name doesn't exists in result of query: $sql in fetch_assoc_array() database method.");
+            }
         }
         return $result;
     } // fetch_assoc_array()
@@ -520,4 +520,4 @@ public function get_collate() {
 
 } // of Database class
 
-?>
\ No newline at end of file
+?>

From 81cf35c8be44543378a19b3cee42890167b11c8d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tomasz=20Naskr=C4=99t?= <tomasz.naskret@pwr.edu.pl>
Date: Fri, 13 May 2022 08:12:31 +0200
Subject: [PATCH 100/154] fix: remove PHPUnit from settings

---
 engine/settings.php | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/engine/settings.php b/engine/settings.php
index c0d70137..f7d0c38e 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -22,8 +22,8 @@
 define('MAX_TYPES_NAME_LABEL','...');
 
 set_error_handler("ErrorService::errorHandler");
-if(! PHPUnitTools::isPHPUnitRunning()) {
+/*if(! PHPUnitTools::isPHPUnitRunning()) {
 	// under PHPUnit this one not works
 	register_shutdown_function("ErrorService::shutdownFunction");
-}
+}*/
 ?>

From 0d6aa8cd303fab7f6b87dfd8a0ca7e75201407d8 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Tue, 17 May 2022 18:39:55 +0200
Subject: [PATCH 101/154] missing opt parse added

---
 local/daemon-tasks.php | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/local/daemon-tasks.php b/local/daemon-tasks.php
index 3021f83f..650a4a79 100644
--- a/local/daemon-tasks.php
+++ b/local/daemon-tasks.php
@@ -34,6 +34,7 @@
 try{
 
 	ini_set('memory_limit', '1024M');
+    $opt->parseCli(isset($argv) ? $argv : null);
 
 	$dbHost = "localhost";
 	$dbUser = "root";
@@ -289,7 +290,7 @@ function processNlprest2Tagger($report_id, $params){
                         $orth_sql = $index_orths[$orth];
                     } else {
                         $new_orths[$orth] = 1;
-                        $orth_sql = "(SELECT orth_id FROM orths WHERE orth='" . $orth . "')";
+                        $orth_sql = "(SELECT orth_id FROM orths WHERE orth='" . $this->db->escape($orth) . "')";
                     }
 
                     $args = array($report_id, $from, $to, $lastToken, $orth_sql);
@@ -357,7 +358,7 @@ function processNlprest2Tagger($report_id, $params){
         if ( count ($new_orths) > 0 ){
             $new_orths = array_keys($new_orths);
 			for($i=0;$i<count($new_orths);$i++) {
-				$new_orths[$i] = $new_orths[$i];
+                $new_orths[$i] = $this->db->escape($new_orths[$i]);
 			}
             $sql_new_orths = 'INSERT IGNORE INTO `orths` (`orth`) VALUES ("' . implode('"),("', $new_orths) . '");';
             $this->db->execute($sql_new_orths);

From bef82d5d631f7077806d34ea15d8abda5dea6098 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Tue, 17 May 2022 19:24:00 +0200
Subject: [PATCH 102/154] change order of include and settings

---
 engine/settings.php    | 2 ++
 local/daemon-tasks.php | 1 -
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/engine/settings.php b/engine/settings.php
index c0d70137..e0163ca0 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -21,6 +21,8 @@
 define('MAX_TYPES_LABEL_INDEX',999999999999); // over autoincrement id
 define('MAX_TYPES_NAME_LABEL','...');
 
+require_once(__DIR__ . DIRECTORY_SEPARATOR . 'include.php');
+
 set_error_handler("ErrorService::errorHandler");
 if(! PHPUnitTools::isPHPUnitRunning()) {
 	// under PHPUnit this one not works
diff --git a/local/daemon-tasks.php b/local/daemon-tasks.php
index 650a4a79..c38870d0 100644
--- a/local/daemon-tasks.php
+++ b/local/daemon-tasks.php
@@ -8,7 +8,6 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 

From d37d9b73f5028adf99346f4fafca3f42d514e8b4 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Tue, 17 May 2022 21:07:56 +0200
Subject: [PATCH 103/154] local scripts corrections

---
 engine/cliopt.php                | 2 +-
 local/agreement.php              | 1 -
 local/ccl2iob.php                | 1 -
 local/cli-liner2-nlprest2.php    | 1 -
 local/cli-restore-corpus.php     | 1 -
 local/cli-upload-txt.php         | 1 -
 local/daemon-cleanup.php         | 1 -
 local/daemon-export.php          | 3 +--
 local/daemon-grab.php            | 1 -
 local/daemon-upload.php          | 1 -
 local/export-corpus.php          | 1 -
 local/flags.php                  | 1 -
 local/import-corpus-cli.php      | 1 -
 local/import-sherlock.php        | 1 -
 local/import-wsd-annotations.php | 1 -
 local/liner2.php                 | 1 -
 local/slavicner2019-annotate.php | 1 -
 local/slavicner2019.php          | 1 -
 local/tokenize-update.php        | 1 -
 local/tokenize.php               | 1 -
 local/upload.php                 | 1 -
 local/wsd-annotate.php           | 1 -
 22 files changed, 2 insertions(+), 23 deletions(-)

diff --git a/engine/cliopt.php b/engine/cliopt.php
index 1663d3e2..7c4d0366 100644
--- a/engine/cliopt.php
+++ b/engine/cliopt.php
@@ -230,7 +230,7 @@ function printHelp(){
 		}
 		print " [parameters]\n\n";
 		
-		if (count($this->executes)){
+		if (is_array($this->executes) && count($this->executes)){
 			print " Sample execute:\n";
 			foreach ($this->executes as $e){
 				echo " ".sprintf(" # %s\n", $e[1]);
diff --git a/local/agreement.php b/local/agreement.php
index 2e576962..655a6087 100644
--- a/local/agreement.php
+++ b/local/agreement.php
@@ -8,7 +8,6 @@
  
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/local/ccl2iob.php b/local/ccl2iob.php
index f2b608ba..40573c66 100644
--- a/local/ccl2iob.php
+++ b/local/ccl2iob.php
@@ -8,7 +8,6 @@
  
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/local/cli-liner2-nlprest2.php b/local/cli-liner2-nlprest2.php
index 4d910ace..1343d77f 100644
--- a/local/cli-liner2-nlprest2.php
+++ b/local/cli-liner2-nlprest2.php
@@ -8,7 +8,6 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/local/cli-restore-corpus.php b/local/cli-restore-corpus.php
index a9e6f80c..65788193 100644
--- a/local/cli-restore-corpus.php
+++ b/local/cli-restore-corpus.php
@@ -8,7 +8,6 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/local/cli-upload-txt.php b/local/cli-upload-txt.php
index e8b61aa0..bd879f2e 100644
--- a/local/cli-upload-txt.php
+++ b/local/cli-upload-txt.php
@@ -8,7 +8,6 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/local/daemon-cleanup.php b/local/daemon-cleanup.php
index 762f68d5..874a3f27 100644
--- a/local/daemon-cleanup.php
+++ b/local/daemon-cleanup.php
@@ -8,7 +8,6 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/local/daemon-export.php b/local/daemon-export.php
index 07b7d2df..29e6f09d 100644
--- a/local/daemon-export.php
+++ b/local/daemon-export.php
@@ -8,7 +8,6 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
@@ -35,7 +34,7 @@
 try{
 
 	ini_set('memory_limit', '1024M');
-	$opt->parseCli($argv);
+    $opt->parseCli(isset($argv) ? $argv : null);
 	if ( $opt->exists("db-uri")){
 		$dbHost = "localhost";
 		$dbUser = "root";
diff --git a/local/daemon-grab.php b/local/daemon-grab.php
index dffcde4f..ed17eb6b 100644
--- a/local/daemon-grab.php
+++ b/local/daemon-grab.php
@@ -8,7 +8,6 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/local/daemon-upload.php b/local/daemon-upload.php
index 34b2cc81..2b91b2ad 100644
--- a/local/daemon-upload.php
+++ b/local/daemon-upload.php
@@ -8,7 +8,6 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/local/export-corpus.php b/local/export-corpus.php
index 6dfd066e..e64e84fb 100644
--- a/local/export-corpus.php
+++ b/local/export-corpus.php
@@ -33,7 +33,6 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/local/flags.php b/local/flags.php
index 754f6030..18cec00a 100644
--- a/local/flags.php
+++ b/local/flags.php
@@ -8,7 +8,6 @@
  
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" ). DIRECTORY_SEPARATOR ."config.local.php");
 
diff --git a/local/import-corpus-cli.php b/local/import-corpus-cli.php
index 64979aea..d37faf1d 100644
--- a/local/import-corpus-cli.php
+++ b/local/import-corpus-cli.php
@@ -2,7 +2,6 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/local/import-sherlock.php b/local/import-sherlock.php
index 2d9a8566..d0e335c3 100644
--- a/local/import-sherlock.php
+++ b/local/import-sherlock.php
@@ -2,7 +2,6 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/local/import-wsd-annotations.php b/local/import-wsd-annotations.php
index 1c111242..9e50e004 100644
--- a/local/import-wsd-annotations.php
+++ b/local/import-wsd-annotations.php
@@ -2,7 +2,6 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/local/liner2.php b/local/liner2.php
index 961439ac..c0d3a25e 100644
--- a/local/liner2.php
+++ b/local/liner2.php
@@ -8,7 +8,6 @@
  
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 
diff --git a/local/slavicner2019-annotate.php b/local/slavicner2019-annotate.php
index ff6e4c78..2081ec00 100644
--- a/local/slavicner2019-annotate.php
+++ b/local/slavicner2019-annotate.php
@@ -2,7 +2,6 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/local/slavicner2019.php b/local/slavicner2019.php
index 2e3f4145..468c3503 100644
--- a/local/slavicner2019.php
+++ b/local/slavicner2019.php
@@ -1,7 +1,6 @@
 <?php
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/local/tokenize-update.php b/local/tokenize-update.php
index 7234a619..02a4b36c 100644
--- a/local/tokenize-update.php
+++ b/local/tokenize-update.php
@@ -8,7 +8,6 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/local/tokenize.php b/local/tokenize.php
index 7d390fef..fdb2b16d 100644
--- a/local/tokenize.php
+++ b/local/tokenize.php
@@ -8,7 +8,6 @@
  
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/local/upload.php b/local/upload.php
index d5597097..03e2e21f 100644
--- a/local/upload.php
+++ b/local/upload.php
@@ -8,7 +8,6 @@
  
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/local/wsd-annotate.php b/local/wsd-annotate.php
index 7221536d..3dd3cd1a 100644
--- a/local/wsd-annotate.php
+++ b/local/wsd-annotate.php
@@ -6,7 +6,6 @@
  
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-require_once($enginePath. DIRECTORY_SEPARATOR . 'include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 

From 5a3f7a1421759e90df70a0637ef3bf767bc10c4f Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Tue, 17 May 2022 21:19:32 +0200
Subject: [PATCH 104/154] double LoadRequest loader removed

---
 public_html/css.php   | 1 -
 public_html/image.php | 1 -
 public_html/index.php | 2 --
 3 files changed, 4 deletions(-)

diff --git a/public_html/css.php b/public_html/css.php
index 6686445f..bf5626c0 100644
--- a/public_html/css.php
+++ b/public_html/css.php
@@ -8,7 +8,6 @@
 
 $enginePath = realpath(__DIR__ . "/../engine/");
 require_once($enginePath . "/settings.php");
-require_once($enginePath . '/include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/public_html/image.php b/public_html/image.php
index fdf19d4c..e6b83a13 100644
--- a/public_html/image.php
+++ b/public_html/image.php
@@ -8,7 +8,6 @@
 
 $enginePath = realpath(__DIR__ . "/../engine/");
 require_once($enginePath."/settings.php");
-require_once($enginePath.'/include.php');
 Config::Config()->put_path_engine($enginePath);
 Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
diff --git a/public_html/index.php b/public_html/index.php
index e618f043..8821173b 100644
--- a/public_html/index.php
+++ b/public_html/index.php
@@ -8,7 +8,6 @@
 
 ob_start();
 $enginePath = realpath(__DIR__ . "/../engine/");
-require_once($enginePath.'/include.php');
 require_once($enginePath."/settings.php");
 try{
 
@@ -37,7 +36,6 @@
 	$auth = new UserAuthorize(Config::Config()->get_dsn());
 	$auth->authorize(isset($_POST['logout']) && ($_POST['logout']=="1"));
 	$user = $auth->getUserData();
-	$corpus = RequestLoader::loadCorpus();
 
 	// federation login is enabled
 	if(Config::Config()->get_federationLoginUrl()){

From fbc4c499bbd4862a363a75f4bd5e57dddb82d19a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tomasz=20Naskr=C4=99t?= <tomasz.naskret@pwr.edu.pl>
Date: Thu, 19 May 2022 07:22:49 +0200
Subject: [PATCH 105/154] fix: removed left closing tag

---
 engine/templates/inc_widget_annotation_type_tree.tpl | 1 -
 1 file changed, 1 deletion(-)

diff --git a/engine/templates/inc_widget_annotation_type_tree.tpl b/engine/templates/inc_widget_annotation_type_tree.tpl
index 697069a8..65d1f068 100644
--- a/engine/templates/inc_widget_annotation_type_tree.tpl
+++ b/engine/templates/inc_widget_annotation_type_tree.tpl
@@ -18,7 +18,6 @@
 				<tr>
 					<td colspan="2"><i>No layers, subsets nor types to display</i></td>
 				</tr>
-			{/if}
 			</tbody>    <!-- class=annotationTypesTree -->
     	</table>	
     	</div>    

From 10fd22442a54310dfe4915f7f6b609cfe094f5c2 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Mon, 27 Jun 2022 14:27:03 +0200
Subject: [PATCH 106/154] missing quotas in callback function name intval

---
 engine/include/database/CDbAnnotation.php | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/engine/include/database/CDbAnnotation.php b/engine/include/database/CDbAnnotation.php
index 67260933..70a58563 100755
--- a/engine/include/database/CDbAnnotation.php
+++ b/engine/include/database/CDbAnnotation.php
@@ -1022,7 +1022,7 @@ static function getUserAnnotations($user_id=null, $corpus_id=null, $subcorpus_id
 		}
 
 		if ( $annotation_type_ids !== null ){
-			$annotation_type_ids = array_map(intval, $annotation_type_ids);
+			$annotation_type_ids = array_map('intval', $annotation_type_ids);
 			if ( count($annotation_type_ids) > 0 ){
 				$params_where = array_merge($params_where, $annotation_type_ids);
 				$sql_where[] = "a.type_id IN (" . implode(",", array_fill(0, count($annotation_type_ids), "?")) .")";
@@ -1099,7 +1099,7 @@ static function getAnnotationCount($user_id=null, $corpus_id=null, $subcorpus_id
 		}
 
 		if ( $annotation_type_ids !== null ){
-			$annotation_type_ids = array_map(intval, $annotation_type_ids);
+			$annotation_type_ids = array_map('intval', $annotation_type_ids);
 			if ( count($annotation_type_ids) > 0 ){
 				$params_where = array_merge($params_where, $annotation_type_ids);
 				$sql_where[] = "a.type_id IN (" . implode(",", array_fill(0, count($annotation_type_ids), "?")) .")";
@@ -1232,7 +1232,7 @@ static function getAnnotationDocCount($user_id=null, $corpus_id=null, $subcorpus
 		}
 
 		if ( $annotation_type_ids !== null ){
-			$annotation_type_ids = array_map(intval, $annotation_type_ids);
+			$annotation_type_ids = array_map('intval', $annotation_type_ids);
 			if ( count($annotation_type_ids) > 0 ){
 				$params_where = array_merge($params_where, $annotation_type_ids);
 				$sql_where[] = "a.type_id IN (" . implode(",", array_fill(0, count($annotation_type_ids), "?")) .")";

From 96f56d98ebff2e19e507542b13c5be0654cd6cb0 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Tue, 28 Jun 2022 10:52:10 +0200
Subject: [PATCH 107/154] extracting annotation loader to external multiusing
 script

---
 .../PerspectiveAgreement.php                  |   1 +
 .../PerspectiveAnnotation_attributes.php      |   3 +-
 .../PerspectiveAnnotation_lemma.php           |   3 +-
 .../PerspectiveAnnotator.php                  |   1 +
 .../PerspectivePreview.php                    |   1 +
 .../PerspectiveRelation_agreement.php         |   1 +
 public_html/js/page_report_agreement.js       |   3 +
 .../js/page_report_annotation_attributes.js   |   5 +-
 .../js/page_report_annotation_lemma.js        |   5 +-
 .../js/page_report_annotation_tree_loader.js  | 145 ++++++++++++++++++
 public_html/js/page_report_annotator.js       |   3 +
 public_html/js/page_report_preview.js         | 138 +----------------
 .../js/page_report_relation_agreement.js      |   1 +
 13 files changed, 169 insertions(+), 141 deletions(-)
 create mode 100644 public_html/js/page_report_annotation_tree_loader.js

diff --git a/engine/page/report_perspectives/PerspectiveAgreement.php b/engine/page/report_perspectives/PerspectiveAgreement.php
index c526dc66..fa0bc601 100644
--- a/engine/page/report_perspectives/PerspectiveAgreement.php
+++ b/engine/page/report_perspectives/PerspectiveAgreement.php
@@ -13,6 +13,7 @@ function __construct(CPage $page, $document)
         parent::__construct($page, $document);
         $this->page->includeJs("js/c_widget_annotation_type_tree.js");
         $this->page->includeJs("js/c_widget_user_selection_a_b.js");
+        $this->page->includeJs("js/page_report_annotation_tree_loader.js");
     }
 	
 	function execute(){
diff --git a/engine/page/report_perspectives/PerspectiveAnnotation_attributes.php b/engine/page/report_perspectives/PerspectiveAnnotation_attributes.php
index b8e4dd0b..0444b2f7 100644
--- a/engine/page/report_perspectives/PerspectiveAnnotation_attributes.php
+++ b/engine/page/report_perspectives/PerspectiveAnnotation_attributes.php
@@ -18,6 +18,7 @@ function __construct(CPage $page, $document){
         $this->page->includeJs("js/c_widget_annotation_type_tree.js");
 
         $this->page->includeJs("js/c_widget_annotation_details.js");
+        $this->page->includeJs("js/page_report_annotation_tree_loader.js");
     }
 
 	function execute(){
@@ -89,4 +90,4 @@ function getAnnotationMode(){
         }
         return $annotation_mode;
     }
-}
\ No newline at end of file
+}
diff --git a/engine/page/report_perspectives/PerspectiveAnnotation_lemma.php b/engine/page/report_perspectives/PerspectiveAnnotation_lemma.php
index 2c7be84f..1fb10b79 100644
--- a/engine/page/report_perspectives/PerspectiveAnnotation_lemma.php
+++ b/engine/page/report_perspectives/PerspectiveAnnotation_lemma.php
@@ -13,6 +13,7 @@ function __construct(CPage $page, $document){
         parent::__construct($page, $document);
         $this->page->includeJs("js/c_annotation_mode.js");
         $this->page->includeJs("js/c_widget_annotation_type_tree.js");
+        $this->page->includeJs("js/page_report_annotation_tree_loader.js");
     }
 
 	function execute(){
@@ -75,4 +76,4 @@ function getAnnotationMode(){
         }
         return $annotation_mode;
     }
-}
\ No newline at end of file
+}
diff --git a/engine/page/report_perspectives/PerspectiveAnnotator.php b/engine/page/report_perspectives/PerspectiveAnnotator.php
index b3e9f14c..0fa248e5 100644
--- a/engine/page/report_perspectives/PerspectiveAnnotator.php
+++ b/engine/page/report_perspectives/PerspectiveAnnotator.php
@@ -25,6 +25,7 @@ function __construct(CPage $page, $document){
         $this->page->includeJs("js/c_autoaccordionview.js");
         $this->page->includeJs("js/page_report_preview.js");
         $this->page->includeJs("libs/bootstrap-confirmation.min.js");
+        $this->page->includeJs("js/page_report_annotation_tree_loader.js");
     }
 
     function execute(){
diff --git a/engine/page/report_perspectives/PerspectivePreview.php b/engine/page/report_perspectives/PerspectivePreview.php
index 7b599d1e..6aa7291f 100644
--- a/engine/page/report_perspectives/PerspectivePreview.php
+++ b/engine/page/report_perspectives/PerspectivePreview.php
@@ -14,6 +14,7 @@ function __construct(CPage $page, $document)
         $this->page->includeJs("js/c_widget_annotation_type_tree.js");
         $this->page->includeJs("js/c_widget_relation_sets.js");
         $this->page->includeJs("js/c_autoaccordionview.js");
+        $this->page->includeJs("js/page_report_annotation_tree_loader.js");
     }
 
 	function execute()
diff --git a/engine/page/report_perspectives/PerspectiveRelation_agreement.php b/engine/page/report_perspectives/PerspectiveRelation_agreement.php
index a469668b..c885fffe 100644
--- a/engine/page/report_perspectives/PerspectiveRelation_agreement.php
+++ b/engine/page/report_perspectives/PerspectiveRelation_agreement.php
@@ -13,6 +13,7 @@ function __construct(CPage $page, $document){
         $this->page->includeJs("js/c_widget_relation_type_tree.js");
         $this->page->includeJs("js/c_widget_annotation_type_tree.js");
         $this->page->includeJs("js/c_widget_user_selection_a_b.js");
+        $this->page->includeJs("js/page_report_annotation_tree_loader.js");
     }
 	
 	function execute(){
diff --git a/public_html/js/page_report_agreement.js b/public_html/js/page_report_agreement.js
index bde1a63c..d7018391 100644
--- a/public_html/js/page_report_agreement.js
+++ b/public_html/js/page_report_agreement.js
@@ -8,6 +8,9 @@
  * Przypisanie akcji po wczytaniu się strony.
  */
 $(document).ready(function(){
+    var url = $.url(window.location.href);
+    var corpus_id = url.param('corpus');
+    loadAnnotationTypesFromTemplates(corpus_id);
     assign_click_legend();
 	assign_annotation_triggers();
 	assign_more_less();
diff --git a/public_html/js/page_report_annotation_attributes.js b/public_html/js/page_report_annotation_attributes.js
index 8b8e9e37..bfb1e35a 100644
--- a/public_html/js/page_report_annotation_attributes.js
+++ b/public_html/js/page_report_annotation_attributes.js
@@ -6,6 +6,9 @@
 
 $(document).ready(function(){
 
+    var url = $.url(window.location.href);
+    var corpus_id = url.param('corpus');
+    loadAnnotationTypesFromTemplates(corpus_id);
 	setupAnnotationTypeTree();
 	setupAnnotationMode();
 
@@ -229,4 +232,4 @@ function updateSaveButtonStatus(){
         button.addClass("btn-default");
         button.removeClass("btn-danger");
     }
-}
\ No newline at end of file
+}
diff --git a/public_html/js/page_report_annotation_lemma.js b/public_html/js/page_report_annotation_lemma.js
index 54706485..784d7033 100644
--- a/public_html/js/page_report_annotation_lemma.js
+++ b/public_html/js/page_report_annotation_lemma.js
@@ -5,6 +5,9 @@
  */
 $(document).ready(function(){
 
+    var url = $.url(window.location.href);
+    var corpus_id = url.param('corpus');
+    loadAnnotationTypesFromTemplates(corpus_id);
     assignButtonAutofillClick();
     assignButtonSaveAllClick();
 
@@ -246,4 +249,4 @@ function updateSaveButtonStatus(){
         button.addClass("btn-default");
         button.removeClass("btn-danger");
     }
-}
\ No newline at end of file
+}
diff --git a/public_html/js/page_report_annotation_tree_loader.js b/public_html/js/page_report_annotation_tree_loader.js
new file mode 100644
index 00000000..1b749a31
--- /dev/null
+++ b/public_html/js/page_report_annotation_tree_loader.js
@@ -0,0 +1,145 @@
+/**
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ */
+
+var url = $.url(window.location.href);
+var corpus_id = url.param("corpus");
+
+function createSetRowFromTemplate(container,setId,setName) {
+
+	/* from HTML template in DOM named id='setRowTpl'
+	 * creates code of set row for parametres setId,setName
+	 * and place it on the end of container element
+      	*/
+        const setRowTemplateId = "setRowTpl";
+        let setRow = null;
+        const template = document.querySelector("#"+setRowTemplateId);
+        if(template) {
+                setRow = template.content.cloneNode(true);
+                if(setRow){
+                        setRow.querySelector("input").setAttribute("name","layerId-"+setId);
+                        setRow.querySelector(".layerName").innerText = setName;
+                        if(container) {
+                                container.append(setRow);
+                        }
+                } else {
+                        console.log("Cannot clone DOM element for template with id="+setRowTemplateId);
+                }
+        } else {
+                console.log("Cannot create DOM element from template with id="+setRowTemplateId);
+        }
+
+} // createSetRowfromTemplate()
+
+function createSubsetRowFromTemplate(container,subsetId,subsetName) {
+
+        /* from HTML template in DOM named id='subsetRowTpl'
+         * creates code of subset row for parametres subsetId, subsetName
+ 	 * and place it on the end of container element                       
+	 */
+        const subsetRowTemplateId = "subsetRowTpl";
+        let subsetRow = null;
+        const template = document.querySelector("#"+subsetRowTemplateId);
+        if(template) {
+                subsetRow = template.content.cloneNode(true);
+                if(subsetRow){
+			subsetRow.querySelector("input").setAttribute("name","subsetId-"+subsetId);
+                        subsetRow.querySelector("tr").setAttribute("subsetid",subsetId);
+                        subsetRow.querySelector(".layerName").innerText = subsetName;
+                        if(container) {
+                                container.append(subsetRow);
+                        }
+                } else {
+                        console.log("Cannot clone DOM element for template with id="+subsetRowTemplateId);
+                }
+        } else {
+                console.log("Cannot create DOM element from template with id="+subsetRowTemplateId);
+        }
+
+} // createSubsetRowfromTemplate()
+ 
+function createTypeRowFromTemplate(container,typeId,typeName) {
+
+        /* from HTML template in DOM named id='typeRowTpl'
+         * creates code of type row for parametres typeId, typeName
+         * and place it on the end of container element                      
+         */
+        const typeRowTemplateId = "typeRowTpl";
+	const MAX_TYPES_NAME_LABEL = "...";
+        let typeRow = null;
+        const template = document.querySelector("#"+typeRowTemplateId);
+        if(template) {
+                typeRow = template.content.cloneNode(true);
+                if(typeRow){
+			if(typeName==MAX_TYPES_NAME_LABEL) {
+                		/* remove checkbox for limit threshold */
+                		elem = typeRow.querySelector("input");
+                		if(elem) {
+                        		elem.parentElement.removeChild(elem);
+                		}
+        		} else { /* type under limit */
+				typeRow.querySelector("input").setAttribute("name","typeId-"+typeId);
+			}
+                        typeRow.querySelector("tr").setAttribute("typeid",typeId);
+                        typeRow.querySelector(".layerName").innerText = typeName;
+                        if(container) {
+                                container.append(typeRow);
+                        }
+                } else {
+                        console.log("Cannot clone DOM element for template with id="+typeRowTemplateId);
+                }
+        } else {
+                console.log("Cannot create DOM element from template with id="+typeRowTemplateId);
+        }
+
+} // createTypeRowFromTemplate()
+ 
+/**
+ *  loads rows with sets, subsets & types of annotations from templates
+ *  and pure JSON data from ajax request
+ */
+function loadAnnotationTypesFromTemplates(corpus_id) {
+
+	// loading all data from ajax service
+	const serviceName = "annotation_type_tree";
+	const getTypesSuccess = function(data) {
+
+		// create rows for sets, subsets and types
+		if(!data){ return; }
+		if(data.length==0){ return; }
+		// element, which holds all rows
+		const container = $(".annotationTypesTree");
+		// remove default content for empty set
+		$(container).find("tr").remove();
+		// array of setId => set_array, 
+		$.each(data,function(setId,setArray){
+			const setName = setArray.name;
+			createSetRowFromTemplate(container,setId,setName); 
+			$.each(setArray,function(subsetId,subsetArray){
+				if(subsetId!='name'){
+					const subsetName = subsetArray.name;
+					createSubsetRowFromTemplate(container,subsetId,subsetName);
+					$.each(subsetArray,function(typeId,typeName){
+						if(typeId!='name'){
+							createTypeRowFromTemplate(container,typeId,typeName);
+						}; // typeId<>'name'	
+					}); // each subsetArray
+				}; // subsetId <> 'name'
+			}); // each setArray
+		}); // each data
+
+	};
+        const getTypesError = function() {
+                console.log("Error on ajax request for "+serviceName);
+        };
+        doAjaxSync( serviceName ,
+		{ 'corpusId' : corpus_id },
+                getTypesSuccess,
+                getTypesError,
+                null  // getTypesComplete
+        );
+ 	
+} // loadAnnotationTypesFromTemplates()
+
diff --git a/public_html/js/page_report_annotator.js b/public_html/js/page_report_annotator.js
index 8125a4af..f890ff53 100644
--- a/public_html/js/page_report_annotator.js
+++ b/public_html/js/page_report_annotator.js
@@ -12,6 +12,9 @@ var globalSelection = null;
 
 $(function(){
 
+	var url = $.url(window.location.href);
+	var corpus_id = url.param('corpus');
+    loadAnnotationTypesFromTemplates(corpus_id);
     setupAnnotationMode();
 
     wAnnotationDetails = new WidgetAnnotation("#annotation-details", function(){
diff --git a/public_html/js/page_report_preview.js b/public_html/js/page_report_preview.js
index 6fd32fe0..69f8f2fa 100644
--- a/public_html/js/page_report_preview.js
+++ b/public_html/js/page_report_preview.js
@@ -10,147 +10,11 @@ var url = $.url(window.location.href);
 var corpus_id = url.param("corpus");
 var report_id = url.param("id");
 
-function createSetRowFromTemplate(container,setId,setName) {
-
-	/* from HTML template in DOM named id='setRowTpl'
-	 * creates code of set row for parametres setId,setName
-	 * and place it on the end of container element
-      	*/
-        const setRowTemplateId = "setRowTpl";
-        let setRow = null;
-        const template = document.querySelector("#"+setRowTemplateId);
-        if(template) {
-                setRow = template.content.cloneNode(true);
-                if(setRow){
-                        setRow.querySelector("input").setAttribute("name","layerId-"+setId);
-                        setRow.querySelector(".layerName").innerText = setName;
-                        if(container) {
-                                container.append(setRow);
-                        }
-                } else {
-                        console.log("Cannot clone DOM element for template with id="+setRowTemplateId);
-                }
-        } else {
-                console.log("Cannot create DOM element from template with id="+setRowTemplateId);
-        }
-
-} // createSetRowfromTemplate()
-
-function createSubsetRowFromTemplate(container,subsetId,subsetName) {
-
-        /* from HTML template in DOM named id='subsetRowTpl'
-         * creates code of subset row for parametres subsetId, subsetName
- 	 * and place it on the end of container element                       
-	 */
-        const subsetRowTemplateId = "subsetRowTpl";
-        let subsetRow = null;
-        const template = document.querySelector("#"+subsetRowTemplateId);
-        if(template) {
-                subsetRow = template.content.cloneNode(true);
-                if(subsetRow){
-			subsetRow.querySelector("input").setAttribute("name","subsetId-"+subsetId);
-                        subsetRow.querySelector("tr").setAttribute("subsetid",subsetId);
-                        subsetRow.querySelector(".layerName").innerText = subsetName;
-                        if(container) {
-                                container.append(subsetRow);
-                        }
-                } else {
-                        console.log("Cannot clone DOM element for template with id="+subsetRowTemplateId);
-                }
-        } else {
-                console.log("Cannot create DOM element from template with id="+subsetRowTemplateId);
-        }
-
-} // createSubsetRowfromTemplate()
- 
-function createTypeRowFromTemplate(container,typeId,typeName) {
-
-        /* from HTML template in DOM named id='typeRowTpl'
-         * creates code of type row for parametres typeId, typeName
-         * and place it on the end of container element                      
-         */
-        const typeRowTemplateId = "typeRowTpl";
-	const MAX_TYPES_NAME_LABEL = "...";
-        let typeRow = null;
-        const template = document.querySelector("#"+typeRowTemplateId);
-        if(template) {
-                typeRow = template.content.cloneNode(true);
-                if(typeRow){
-			if(typeName==MAX_TYPES_NAME_LABEL) {
-                		/* remove checkbox for limit threshold */
-                		elem = typeRow.querySelector("input");
-                		if(elem) {
-                        		elem.parentElement.removeChild(elem);
-                		}
-        		} else { /* type under limit */
-				typeRow.querySelector("input").setAttribute("name","typeId-"+typeId);
-			}
-                        typeRow.querySelector("tr").setAttribute("typeid",typeId);
-                        typeRow.querySelector(".layerName").innerText = typeName;
-                        if(container) {
-                                container.append(typeRow);
-                        }
-                } else {
-                        console.log("Cannot clone DOM element for template with id="+typeRowTemplateId);
-                }
-        } else {
-                console.log("Cannot create DOM element from template with id="+typeRowTemplateId);
-        }
-
-} // createTypeRowFromTemplate()
- 
-/**
- *  loads rows with sets, subsets & types of annotations from templates
- *  and pure JSON data from ajax request
- */
-function loadAnnotationTypesFromTemplates() {
-
-	// loading all data from ajax service
-	const serviceName = "annotation_type_tree";
-	const getTypesSuccess = function(data) {
-
-		// create rows for sets, subsets and types
-		if(!data){ return; }
-		if(data.length==0){ return; }
-		// element, which holds all rows
-		const container = $(".annotationTypesTree");
-		// remove default content for empty set
-		$(container).find("tr").remove();
-		// array of setId => set_array, 
-		$.each(data,function(setId,setArray){
-			const setName = setArray.name;
-			createSetRowFromTemplate(container,setId,setName); 
-			$.each(setArray,function(subsetId,subsetArray){
-				if(subsetId!='name'){
-					const subsetName = subsetArray.name;
-					createSubsetRowFromTemplate(container,subsetId,subsetName);
-					$.each(subsetArray,function(typeId,typeName){
-						if(typeId!='name'){
-							createTypeRowFromTemplate(container,typeId,typeName);
-						}; // typeId<>'name'	
-					}); // each subsetArray
-				}; // subsetId <> 'name'
-			}); // each setArray
-		}); // each data
-
-	};
-        const getTypesError = function() {
-                console.log("Error on ajax request for "+serviceName);
-        };
-        doAjaxSync( serviceName ,
-		{ 'corpusId' : corpus_id },
-                getTypesSuccess,
-                getTypesError,
-                null  // getTypesComplete
-        );
- 	
-} // loadAnnotationTypesFromTemplates()
-
 /**
  * Przypisanie akcji po wczytaniu się strony.
  */
 $(document).ready(function(){
-    loadAnnotationTypesFromTemplates();
+    loadAnnotationTypesFromTemplates(corpus_id);
     wRelationSets = new WidgetRelationSetSelector("#relation-sets", corpus_id);
     wRelationSets.load();
 
diff --git a/public_html/js/page_report_relation_agreement.js b/public_html/js/page_report_relation_agreement.js
index 8bddba10..1796db88 100644
--- a/public_html/js/page_report_relation_agreement.js
+++ b/public_html/js/page_report_relation_agreement.js
@@ -9,6 +9,7 @@ var corpus_id = url.param('corpus');
  * Przypisanie akcji po wczytaniu się strony.
  */
 $(function(){
+	loadAnnotationTypesFromTemplates(corpus_id);
 	assign_click_legend();
 	assign_annotation_triggers();
 	assign_more_less();

From c6711df9432275d9464dad5cfb70d55be28e5ab0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tomasz=20Naskr=C4=99t?= <tomasz.naskret@pwr.edu.pl>
Date: Wed, 13 Jul 2022 13:34:46 +0200
Subject: [PATCH 108/154] fix: service adress http->https

---
 engine/include/utils/CNlpRest2.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/engine/include/utils/CNlpRest2.php b/engine/include/utils/CNlpRest2.php
index 9914dcd0..15d785d7 100644
--- a/engine/include/utils/CNlpRest2.php
+++ b/engine/include/utils/CNlpRest2.php
@@ -6,7 +6,7 @@ class NlpRest2{
     var $user;
     var $verbose=true;
 
-        function __construct($task, $url="http://ws.clarin-pl.eu/nlprest2/base", $user="Inforex"){
+        function __construct($task, $url="https://ws.clarin-pl.eu/nlprest2/base", $user="Inforex"){
         $this->url = $url;
         $this->task = $task;
         $this->user = $user;

From 2602007dd5393839dee5b466444099400644e0a9 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Tue, 19 Sep 2023 19:36:09 +0200
Subject: [PATCH 109/154] move vendor dir outside classmap dirs

---
 .gitignore                           | 2 +-
 composer.json                        | 3 +--
 docker-compose.yml                   | 1 +
 docker-dev-up.sh                     | 4 ++--
 engine/external/pear/HTML/Select.php | 2 +-
 engine/include.php                   | 2 +-
 6 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/.gitignore b/.gitignore
index d9734d08..108b66b9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,5 @@
 engine/templates_c/*
-engine/include/vendor
+vendor
 config/config.local.php
 docker/www/config/config.local.php
 secured_data/ccls
diff --git a/composer.json b/composer.json
index c3f6e3c9..500edcf7 100644
--- a/composer.json
+++ b/composer.json
@@ -1,7 +1,6 @@
 {
     "config": {
-	"platform": {"php":"5.6"},
-        "vendor-dir": "engine/include/vendor"
+	"platform": {"php":"5.6"}
     },
 
     "autoload": {
diff --git a/docker-compose.yml b/docker-compose.yml
index bdcc6585..de4fb4eb 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -13,6 +13,7 @@ services:
         - ./docker/www/config:/home/inforex/config
         - ./secured_data:/home/inforex/secured_data
         - ./phpunit:/home/inforex/phpunit
+        - ./vendor:/home/inforex/vendor
       depends_on:
       - db
       restart: always     
diff --git a/docker-dev-up.sh b/docker-dev-up.sh
index 7ce37345..9f940b24 100755
--- a/docker-dev-up.sh
+++ b/docker-dev-up.sh
@@ -2,7 +2,7 @@
 
 composer update
 
-AUTOLOAD=engine/include/vendor/autoload.php
+AUTOLOAD=vendor/autoload.php
 
 if [ -f $AUTOLOAD ]; then
     docker-compose build
@@ -10,4 +10,4 @@ if [ -f $AUTOLOAD ]; then
 else
     echo -e "[\e[31mERROR\e[0m] $AUTOLOAD not found"
     echo -e "Make sure that '\e[32mcomposer\e[0m' is installed in order to run '\e[32mcomposer update\e[0m' and generate $AUTOLOAD"
-fi
\ No newline at end of file
+fi
diff --git a/engine/external/pear/HTML/Select.php b/engine/external/pear/HTML/Select.php
index 47f4bd88..54dce9f1 100644
--- a/engine/external/pear/HTML/Select.php
+++ b/engine/external/pear/HTML/Select.php
@@ -13,7 +13,7 @@
  * @link     http://pear.php.net/package/HTML_Select
  */
 
-require_once __DIR__ . '/../../../include/vendor/autoload.php';
+require_once __DIR__ . '/../../../../vendor/autoload.php';
 
 /**
  * Class to dynamically create an HTML SELECT
diff --git a/engine/include.php b/engine/include.php
index 2c43a4fa..189eba19 100644
--- a/engine/include.php
+++ b/engine/include.php
@@ -5,4 +5,4 @@
 $include_paths[] = get_include_path();
 set_include_path( implode(PATH_SEPARATOR, $include_paths) );
 
-require_once __DIR__ . '/include/vendor/autoload.php';
\ No newline at end of file
+require_once __DIR__ . '/../vendor/autoload.php';

From f28b62646952847407111731e8a57d92e286c34d Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Thu, 21 Sep 2023 20:16:12 +0200
Subject: [PATCH 110/154] extract FileWriter class for export

---
 engine/include/export/ConllAndJsonFactory.php | 26 ++++++-----
 engine/include/export/FileWriter.php          | 27 ++++++++++++
 .../engine/include/export/FileWriterTest.php  | 44 +++++++++++++++++++
 3 files changed, 86 insertions(+), 11 deletions(-)
 create mode 100644 engine/include/export/FileWriter.php
 create mode 100644 phpunit/tests/engine/include/export/FileWriterTest.php

diff --git a/engine/include/export/ConllAndJsonFactory.php b/engine/include/export/ConllAndJsonFactory.php
index 68c9a4cf..fbd0778d 100644
--- a/engine/include/export/ConllAndJsonFactory.php
+++ b/engine/include/export/ConllAndJsonFactory.php
@@ -1,10 +1,9 @@
 <?php
 
-
 class ConllAndJsonFactory {
 
-    function exportToConllAndJson($file_path_without_ext, $ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id)
-    {
+    private function makeConllAndJsonExportData($ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id) {
+
         /**
          * Create a cache for 'token from' to boost processing
          */
@@ -149,13 +148,18 @@ function exportToConllAndJson($file_path_without_ext, $ccl, $tokens, $relations,
             $json_builder["chunks"][] = $json_sentences;
         }
 
-        $handle = fopen($file_path_without_ext . ".conll", "w");
-        fwrite($handle, $conll);
-        fclose($handle);
+        return array($conll,$json_builder);
+
+    } // makeConllAndJsonExportData()
+
+    public function exportToConllAndJson($file_path_without_ext, $ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id)
+    {
+ 
+        list($conll,$json_builder) = $this->makeConllAndJsonExportData($ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id);
+        $fw = new FileWriter();
+        $fw->writeTextToFile($file_path_without_ext . ".conll",$conll);
+        $fw->writeJSONToFile($file_path_without_ext . ".json",$json_builder);
 
-        $handle = fopen($file_path_without_ext . ".json", "w");
-        fwrite($handle, json_encode($json_builder, JSON_PRETTY_PRINT + JSON_UNESCAPED_UNICODE));
-        fclose($handle);
-    }
+    } // exportToConllAndJson()
 
-}
\ No newline at end of file
+} // ConllAndJsonFactory class
diff --git a/engine/include/export/FileWriter.php b/engine/include/export/FileWriter.php
new file mode 100644
index 00000000..44c6cda0
--- /dev/null
+++ b/engine/include/export/FileWriter.php
@@ -0,0 +1,27 @@
+<?php
+/**
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ * See LICENCE 
+ */
+
+class FileWriter {
+	
+    public function writeTextToFile($fileName,$text) {
+
+        $handle = fopen($fileName, "w");
+        fwrite($handle, $text);
+        fclose($handle);
+
+    } // writeTextToFile()
+
+    public function writeJSONToFile($fileName,array $jsonArray) {
+
+        $textContent = json_encode($jsonArray,
+                                    JSON_PRETTY_PRINT + JSON_UNESCAPED_UNICODE);
+        $this->writeTextToFile($fileName,$textContent);
+
+    } // writeJSONToFile()
+
+}  // FileWriter class
diff --git a/phpunit/tests/engine/include/export/FileWriterTest.php b/phpunit/tests/engine/include/export/FileWriterTest.php
new file mode 100644
index 00000000..30a4748b
--- /dev/null
+++ b/phpunit/tests/engine/include/export/FileWriterTest.php
@@ -0,0 +1,44 @@
+<?php
+
+mb_internal_encoding("UTF-8");
+//use org\bovigo\vfs\vfsStream; // for vfsStream
+
+class FileWriterTest extends PHPUnit_Framework_TestCase {
+
+    private $virtualDir = null;
+
+    protected function setUp() {
+
+        $this->virtualDir = org\bovigo\vfs\vfsStream::setup('root',null,[]);
+
+    } // setUp()
+
+    public function test_writeTextToFile() {
+
+		$fileName = $this->virtualDir->url()."/test.txt";
+		$text = "jnduie773nd n";
+		$fw = new FileWriter();
+		$fw->writeTextToFile($fileName,$text);
+		$result = file_get_contents($fileName);
+        $this->assertEquals($text,$result);
+
+    } // test_writeTextToFile()
+
+    public function test_writeJSONToFile() {
+
+		$fileName = $this->virtualDir->url()."/test.txt";
+        $jsonArray = array('a' => 1);
+        $fw = new FileWriter();
+        $fw->writeJSONToFile($fileName,$jsonArray);
+        $result = file_get_contents($fileName);
+        $expected =
+'{
+    "a": 1
+}';
+        $this->assertEquals($expected,$result);
+
+    } // test_writeJSONToFile
+
+} // FileWriterTest class
+
+?>

From 0ad37de351c6ad31fb36ac0e190e5ed04372b323 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Sat, 23 Sep 2023 15:14:47 +0200
Subject: [PATCH 111/154] fix static call of nonstatic method - trouble in
 testing

---
 engine/include/export/CorpusExporter.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index 4bcd64a4..d465e18e 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -568,7 +568,7 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
         $file_path_without_ext = $output_folder . "/" . $ccl->getFileName();
 
         /* Wygeneruj CONLL i JSON */
-		ConllAndJsonFactory::exportToConllAndJson($file_path_without_ext, $ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id);
+		(new ConllAndJsonFactory())->exportToConllAndJson($file_path_without_ext, $ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id);
 
         /* Wygeneruj xml i rel.xml */
         CclFactory::setAnnotationsAndRelations($ccl, $annotations, $relations);

From 439281b1894a9a2f5f227ede29e195fb1ee5872d Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Tue, 26 Sep 2023 17:53:04 +0200
Subject: [PATCH 112/154] unit tests for conll i json export

---
 engine/include/export/ConllAndJsonFactory.php |   3 +-
 .../export/ConllAndJsonFactoryTest.php        | 227 ++++++++++++++++++
 2 files changed, 228 insertions(+), 2 deletions(-)
 create mode 100644 phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php

diff --git a/engine/include/export/ConllAndJsonFactory.php b/engine/include/export/ConllAndJsonFactory.php
index fbd0778d..dd516bec 100644
--- a/engine/include/export/ConllAndJsonFactory.php
+++ b/engine/include/export/ConllAndJsonFactory.php
@@ -2,7 +2,7 @@
 
 class ConllAndJsonFactory {
 
-    private function makeConllAndJsonExportData($ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id) {
+    protected function makeConllAndJsonExportData($ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id) {
 
         /**
          * Create a cache for 'token from' to boost processing
@@ -154,7 +154,6 @@ private function makeConllAndJsonExportData($ccl, $tokens, $relations, $annotati
 
     public function exportToConllAndJson($file_path_without_ext, $ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id)
     {
- 
         list($conll,$json_builder) = $this->makeConllAndJsonExportData($ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id);
         $fw = new FileWriter();
         $fw->writeTextToFile($file_path_without_ext . ".conll",$conll);
diff --git a/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php b/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
new file mode 100644
index 00000000..3e333577
--- /dev/null
+++ b/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
@@ -0,0 +1,227 @@
+<?php
+
+mb_internal_encoding("UTF-8");
+//use org\bovigo\vfs\vfsStream; // for vfsStream
+
+class ConllAndJsonFactoryTest extends PHPUnit_Framework_TestCase {
+
+    private $virtualDir = null;
+    // data for test
+    private $report_id = null;
+    // data for class method
+    private $file_path_without_ext = null;
+
+    protected function setUp() {
+
+        $this->virtualDir = org\bovigo\vfs\vfsStream::setup('root',null,[]);
+        $this->generateFullTestData();
+
+    } // setUp()
+
+    private function generateReportTestData() {
+
+		// $report = DbReport::getReportById($report_id);
+		//          "SELECT * FROM reports WHERE id = $report_id"
+		//          id,corpora,date,title,source,author,content,type,
+		//          status,user_id,subcorpus_id,tokenization,format_id,
+		//          lang,filename,parent_report_id,deleted
+		$report = array( "id"=>$this->report_id, "corpora"=>12,
+                "date"=>'1970-01-01', "title"=>'tytuł', "source"=>'źródło',
+                "author"=>'Autor',
+                "content"=>'To jest duże okno. Bardzo duże.', "type"=>1,
+                "status"=>2, "user_id"=>1, "subcorpus_id"=>null,
+                "tokenization"=>null, "format_id"=>2, "lang"=>'pol',
+                "filename"=>'plik.txt', "parent_report_id"=>null,
+                "deleted"=>0
+            );
+ 		return $report;
+
+    } // generateReportTestData()
+
+	private function generateTokensTestData() {
+
+		$report_id = $this->report_id;
+		// $tokens = DbToken::getTokenByReportId($report_id, null, true);
+		//          "SELECT * FROM tokens LEFT JOIN orths USING (orth_id) WHERE report_id = ? ORDER BY `from`"
+		//          token_id, report_id, from, to, eos, orth_id, orth
+		$tokens = array(
+                ["token_id"=>1, "report_id"=>$report_id, "from"=>0, "to"=>1, "eos"=>0, "orth_id"=>1, "orth"=>'To'],
+                ["token_id"=>2, "report_id"=>$report_id, "from"=>2, "to"=>5, "eos"=>0, "orth_id"=>2, "orth"=>'jest'],
+                ["token_id"=>3, "report_id"=>$report_id, "from"=>6, "to"=>9, "eos"=>0, "orth_id"=>3, "orth"=>'duże'],
+                ["token_id"=>4, "report_id"=>$report_id, "from"=>10, "to"=>13, "eos"=>0, "orth_id"=>4, "orth"=>'okno'],
+                ["token_id"=>5, "report_id"=>$report_id, "from"=>14, "to"=>14, "eos"=>1, "orth_id"=>5, "orth"=>'.'],
+                ["token_id"=>6, "report_id"=>$report_id, "from"=>15, "to"=>20, "eos"=>0, "orth_id"=>6, "orth"=>'Bardzo'],
+                ["token_id"=>7, "report_id"=>$report_id, "from"=>21, "to"=>24, "eos"=>0, "orth_id"=>3, "orth"=>'duże'],
+                ["token_id"=>8, "report_id"=>$report_id, "from"=>25, "to"=>25, "eos"=>1, "orth_id"=>5, "orth"=>'.']
+            );
+
+		return $tokens;
+
+	} // generateTokensTestData()
+
+    private function generateCclTestData() {
+
+        // $report parameter
+        $report = $this->generateReportTestData();
+		// $tokens parameter
+		$tokens = $this->generateTokensTestData();
+		// $tags_by_tokens parameter
+		$tags_by_tokens = array();
+
+        $ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
+        return $ccl;
+    
+    } // generateCclTestData()
+
+    private function generateFullTestData() {
+
+        $this->report_id = 1234;
+
+        // $file_path_without_ext parameter
+        $this->file_path_without_ext = $this->virtualDir->url()."/test";
+
+        // $ccl parameter
+        $this->ccl = $this->generateCclTestData();
+
+
+    } // generateFullTestData()
+
+// tests
+
+    public function testEmptyReportMakesEmptyDataToWrite() {
+
+        // args for call
+            $report = array(); 
+            $tokens = array();
+            $tags_by_tokens = array();
+        $ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
+        $tokens = array();
+        $relations = array();
+        $annotations = array();
+        $tokens_ids = array();
+        $annotations_by_id = array();
+    
+        // invoke protected method
+        $protectedMethod = new ReflectionMethod('ConllAndJsonFactory','makeConllAndJsonExportData');
+        $protectedMethod->setAccessible(True);
+        list($conll,$json_builder) = $protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+        
+        // check results
+        $expectedConll = "ORDER_ID\tTOKEN_ID\tORTH\tCTAG\tFROM\tTO\tANN_TAGS\tANN_IDS\tREL_IDS\tREL_TARGET_ANN_IDS\n";
+        $this->assertEquals($expectedConll,$conll);
+
+        $expectedJson = array(
+            "chunks" => array(
+                array()
+            ),
+            "relations" => array(),
+            "annotations" => array()
+        );
+        $this->assertEquals($expectedJson,$json_builder);
+
+    } // testEmptyReportMakesEmptyDataToWrite()
+
+    public function testAllDataPlacesToDataConllAndJsonStructures() {
+
+        // args for call
+        $tokens = array();
+    
+        // DbToken::getTokenByReportId($report_id, null, true);
+        $relations = array();
+        $annotations = array();
+        $tokens_ids = array();
+        $annotations_by_id = array();
+
+        // invoke protected method
+        $protectedMethod = new ReflectionMethod('ConllAndJsonFactory','makeConllAndJsonExportData');
+        $protectedMethod->setAccessible(True);
+        list($conll,$json_builder) = $protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+
+        // check results
+        $expectedConll = "ORDER_ID\tTOKEN_ID\tORTH\tCTAG\tFROM\tTO\tANN_TAGS\tANN_IDS\tREL_IDS\tREL_TARGET_ANN_IDS\n";
+        $expectedConll .=   "0\t0\tTo\t\t0\t1\tO\t_\t_\t_\n".
+                            "1\t1\tjest\t\t2\t5\tO\t_\t_\t_\n".
+                            "2\t2\tduże\t\t6\t9\tO\t_\t_\t_\n".
+                            "3\t3\tokno\t\t10\t13\tO\t_\t_\t_\n".
+                            "4\t4\t.\t\t14\t14\tO\t_\t_\t_\n".
+                            "\n".
+                            "5\t0\tBardzo\t\t15\t20\tO\t_\t_\t_\n".
+                            "6\t1\tduże\t\t21\t24\tO\t_\t_\t_\n".
+                            "7\t2\t.\t\t25\t25\tO\t_\t_\t_\n".
+                            "\n";
+		$this->assertEquals($expectedConll,$conll);
+
+        $expectedJson = array(
+            "chunks" => array(
+                array(
+                    array(
+                        array('order_id' => 0,'token_id' => 0,'orth' => 'To','ctag' => null,'from' => 0,'to' => 1,'annotations' => array(),'relations' => array()),
+                        array('order_id' => 1,'token_id' => 1,'orth' => 'jest','ctag' => null,'from' => 2,'to' => 5,'annotations' => array(),'relations' => array()),
+                        array('order_id' => 2,'token_id' => 2,'orth' => 'duże','ctag' => null,'from' => 6,'to' => 9,'annotations' => array(),'relations' => array()),
+                        array('order_id' => 3,'token_id' => 3,'orth' => 'okno','ctag' => null,'from' => 10,'to' => 13,'annotations' => array(),'relations' => array()),
+                        array('order_id' => 4,'token_id' => 4,'orth' => '.','ctag' => null,'from' => 14,'to' => 14,'annotations' => array(),'relations' => array())
+                    ),
+                    array(
+                        array('order_id' => 5,'token_id' => 0,'orth' => 'Bardzo','ctag' => null,'from' => 15,'to' => 20,'annotations' => array(),'relations' => array()),
+                        array('order_id' => 6,'token_id' => 1,'orth' => 'duże','ctag' => null,'from' => 21,'to' => 24,'annotations' => array(),'relations' => array()),
+                        array('order_id' => 7,'token_id' => 2,'orth' => '.','ctag' => null,'from' => 25,'to' => 25,'annotations' => array(),'relations' => array())
+                    )
+                )
+            ),
+            "relations" => array(),
+            "annotations" => array()
+        );
+        $this->assertEquals($expectedJson,$json_builder);
+
+    } // testAllDataPlacesToDataConllAndJsonStructures() 
+
+/* class ConllAndJsonFactory has only 1 function
+    function exportToConllAndJson($file_path_without_ext, $ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id)
+*/
+
+	public function testDeliveredDataAreWrittenToFiles() {
+
+        $conll = "jakiś text";
+        $json_builder = array("a"=>1);
+
+        // this values doesn't matter
+            $report = array();
+            $tokens = array();
+            $tags_by_tokens = array();
+        $ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
+        $tokens = array();
+        $relations = array();
+        $annotations = array();
+        $tokens_ids = array();
+        $annotations_by_id = array();
+
+        // self-mocking another method
+        $mockedMethodNamesList = array('makeConllAndJsonExportData');
+        $mockedResult = array($conll,$json_builder);
+        $mock = $this->getMockBuilder(ConllAndJsonFactory::class)
+            -> setMethods($mockedMethodNamesList) // ustawia je na null
+            -> getMock();
+        $mock    // i mockuje na zwracanie określonego rezultatu
+            -> method('makeConllAndJsonExportData')
+            -> will($this->returnValue($mockedResult));
+        
+		// metoda exportToConllAndJson() powinna zachować obsługę oryginalną
+        $mock->exportToConllAndJson($this->file_path_without_ext,$this->ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+
+        $expectedConll = $conll;
+        $conllFileName = $this->file_path_without_ext.".conll";
+        $resultConll = file_get_contents($conllFileName);
+        $this->assertEquals($expectedConll,$resultConll);
+        $expectedJson = 
+'{
+    "a": 1
+}';
+        $jsonFileName = $this->file_path_without_ext.".json";
+        $resultJson = file_get_contents($jsonFileName);
+        $this->assertEquals($expectedJson,$resultJson);
+
+	} // testDeliveredDataAreWrittenToFiles
+
+} // ConllAndJsonFactoryTest class
+
+?>

From e49806ff8f82fd1a4c95625dd486daf1a1e8b40c Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Wed, 4 Oct 2023 12:57:06 +0200
Subject: [PATCH 113/154] unit tests with tokens, annotations, relations,
 lemmas and attributes

---
 .../export/ConllAndJsonFactoryTest.php        | 310 ++++++++++++++----
 1 file changed, 254 insertions(+), 56 deletions(-)

diff --git a/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php b/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
index 3e333577..d312a7aa 100644
--- a/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
+++ b/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
@@ -8,18 +8,29 @@ class ConllAndJsonFactoryTest extends PHPUnit_Framework_TestCase {
     private $virtualDir = null;
     // data for test
     private $report_id = null;
+	private $ccl = null;
+	private $tokens = null;
+	private $tokens_ids = null;
     // data for class method
     private $file_path_without_ext = null;
+	// reflection to protected method in tested class
+	private $protectedMethod = null;
 
     protected function setUp() {
 
         $this->virtualDir = org\bovigo\vfs\vfsStream::setup('root',null,[]);
         $this->generateFullTestData();
+        // protected method to invoke in all tests
+        $this->protectedMethod = new ReflectionMethod('ConllAndJsonFactory','makeConllAndJsonExportData');
+        $this->protectedMethod->setAccessible(True);
 
     } // setUp()
 
-    private function generateReportTestData() {
+    private function generateReportTestData($report_id=1234) {
 
+		if(!$this->report_id) {
+			$this->report_id = $report_id;
+		}
 		// $report = DbReport::getReportById($report_id);
 		//          "SELECT * FROM reports WHERE id = $report_id"
 		//          id,corpora,date,title,source,author,content,type,
@@ -38,8 +49,12 @@ private function generateReportTestData() {
 
     } // generateReportTestData()
 
-	private function generateTokensTestData() {
+	private function generateTokensTestData($report_id=1234) {
 
+        if(!$this->report_id) {
+            $this->report_id = $report_id;
+        }
+ 
 		$report_id = $this->report_id;
 		// $tokens = DbToken::getTokenByReportId($report_id, null, true);
 		//          "SELECT * FROM tokens LEFT JOIN orths USING (orth_id) WHERE report_id = ? ORDER BY `from`"
@@ -59,12 +74,127 @@ private function generateTokensTestData() {
 
 	} // generateTokensTestData()
 
-    private function generateCclTestData() {
+    private function getExpectedConllHeader() {
+        // static header for all CONLL files
+        return "ORDER_ID\tTOKEN_ID\tORTH\tCTAG\tFROM\tTO\tANN_TAGS\tANN_IDS\tREL_IDS\tREL_TARGET_ANN_IDS\n";
+    } //
+
+    private function getExpectedConll() {
+        // expected Conll pattern for our data and not annotations
+        $expectedConll = $this->getExpectedConllHeader();
+        $expectedConll .=   "0\t0\tTo\t\t0\t1\tO\t_\t_\t_\n".
+                            "1\t1\tjest\t\t2\t5\tO\t_\t_\t_\n".
+                            "2\t2\tduże\t\t6\t9\tO\t_\t_\t_\n".
+                            //"2\t2\tduże\t\t6\t9\tB-\t1\t_\t_\n".
+                            //"2\t2\tduże\t\t6\t9\tB-nam_adj\t1\t_\t_\n".
+                            "3\t3\tokno\t\t10\t13\tO\t_\t_\t_\n".
+                            "4\t4\t.\t\t14\t14\tO\t_\t_\t_\n".
+                            "\n".
+                            "5\t0\tBardzo\t\t15\t20\tO\t_\t_\t_\n".
+                            "6\t1\tduże\t\t21\t24\tO\t_\t_\t_\n".
+                            "7\t2\t.\t\t25\t25\tO\t_\t_\t_\n".
+                            "\n";
+		return $expectedConll; 
+    } // getExpectedConll()
+
+	private function getExpectedEmptyJson() {
+
+        return 	array(
+            		"chunks" => array(
+                			array()
+            		),
+            		"relations" => array(),
+            		"annotations" => array()
+        		);
+
+	} // getExpectedEmptyJson()
+
+    private function getExpectedChunks() {
+        // returns "chunks" section in expected table for JSON
+        // for our data without annotations
+        $chunks = array(
+                array(
+                    array(
+                        array('order_id' => 0,'token_id' => 0,'orth' => 'To','ctag' => null,'from' => 0,'to' => 1,'annotations' => array(),'relations' => array()),
+                        array('order_id' => 1,'token_id' => 1,'orth' => 'jest','ctag' => null,'from' => 2,'to' => 5,'annotations' => array(),'relations' => array()),
+                        array('order_id' => 2,'token_id' => 2,'orth' => 'duże','ctag' => null,'from' => 6,'to' => 9,'annotations' => array(),'relations' => array()),
+                        array('order_id' => 3,'token_id' => 3,'orth' => 'okno','ctag' => null,'from' => 10,'to' => 13,'annotations' => array(),'relations' => array()),
+                        array('order_id' => 4,'token_id' => 4,'orth' => '.','ctag' => null,'from' => 14,'to' => 14,'annotations' => array(),'relations' => array())
+                    ),
+                    array(
+                        array('order_id' => 5,'token_id' => 0,'orth' => 'Bardzo','ctag' => null,'from' => 15,'to' => 20,'annotations' => array(),'relations' => array()),
+                        array('order_id' => 6,'token_id' => 1,'orth' => 'duże','ctag' => null,'from' => 21,'to' => 24,'annotations' => array(),'relations' => array()),
+                        array('order_id' => 7,'token_id' => 2,'orth' => '.','ctag' => null,'from' => 25,'to' => 25,'annotations' => array(),'relations' => array())
+                    )
+                )
+            );
+        return $chunks;
+    } // getExpectedChunks
+
+    private function generateAnnotation_By_IdTestData(
+                        $annotationExtractorFields=true,
+                        $annotationsWithLemmaField=true,
+                        $annotationsWithTypeAttributte=true
+                    ) {
+
+        $annotation_id = 1;
+        // index must match 'id' field
+        $annotations_by_id = array(
+            $annotation_id  =>  array(  'id'=>$annotation_id, 
+                        // fields, that always exists
+                        //  only 'to' changes business logic
+                        'report_id'=>1,'type_id'=>360,'from'=>6,'to'=>9,'text'=>'duże','user_id'=>1,'creation_time'=>'2022-10-03 08:07:37','stage'=>'final','source'=>'user','annotation_subset_id'=>'52',
+                        // this are always, but from different tables
+                        'type'=>'nam_adj','group_id'=>1, 
+                    )
+
+        );
+        if($annotationExtractorFields) {
+            // fields, that exists for extractor 'annotation' only
+            $annotations_by_id[$annotation_id]['login']='admin';
+            $annotations_by_id[$annotation_id]['screename']='Inforex Admin';
+            if($annotationsWithLemmaField){
+                $annotations_by_id[$annotation_id]['lemma']='lemat dodany do duże';
+            } else {
+                $annotations_by_id[$annotation_id]['lemma']=null;
+            }
+        } else {
+            // fields, that exists for extractors 'annotation_id' 
+            //   and 'annotation_subset_id' only
+            $annotations_by_id[$annotation_id]['group']=1;
+            $annotations_by_id[$annotation_id]['name']='nam_adj';
+            $annotations_by_id[$annotation_id]['description']='Przymiotnik utworzony od nazwy własnej';
+            $annotations_by_id[$annotation_id]['css']='background: lightgreen;';
+            $annotations_by_id[$annotation_id]['cross_sentence']='0';
+            $annotations_by_id[$annotation_id]['shortlist']='0';
+            // this section only for simple extractor with attribute in DB
+            if($annotationsWithTypeAttributte) {
+                $annotations_by_id[$annotation_id]['annotation_id']=$annotation_id;
+                $annotations_by_id[$annotation_id]['annotation_attribute_id']=1;
+                $annotations_by_id[$annotation_id]['value']='valueAtrTypu';
+                $annotations_by_id[$annotation_id]['prop']='valueAtrTypu';
+            }
+        }
+
+        return $annotations_by_id;
+
+    } // generateAnnotation_By_IdTestData()
+
+    private function generateAnnotationsFromAnnotations_By_Id(array $annotations_by_id) {
+        return array_values($annotations_by_id);
+
+    } // generateAnnotationsFromAnnotations_By_Id
+
+    private function generateCclTestData($report=null,$tokens=null) {
 
         // $report parameter
-        $report = $this->generateReportTestData();
+		if($report==null){
+        	$report = $this->generateReportTestData();
+		}
 		// $tokens parameter
-		$tokens = $this->generateTokensTestData();
+		if($tokens==null){
+			$tokens = $this->generateTokensTestData();
+		}
 		// $tags_by_tokens parameter
 		$tags_by_tokens = array();
 
@@ -80,8 +210,16 @@ private function generateFullTestData() {
         // $file_path_without_ext parameter
         $this->file_path_without_ext = $this->virtualDir->url()."/test";
 
+		// $report parameter, local for CCL only
+		$report = $this->generateReportTestData();
+
+		// $tokens parameter
+		$this->tokens = $this->generateTokensTestData($this->report_id);
+        // tak jest ustawiane zawsze w CorpusExporter
+        $this->tokens_ids = array_column($this->tokens, 'token_id');
+
         // $ccl parameter
-        $this->ccl = $this->generateCclTestData();
+        $this->ccl = $this->generateCclTestData($report,$this->tokens);
 
 
     } // generateFullTestData()
@@ -90,6 +228,7 @@ private function generateFullTestData() {
 
     public function testEmptyReportMakesEmptyDataToWrite() {
 
+		// all empty input data generates minimal export output
         // args for call
             $report = array(); 
             $tokens = array();
@@ -101,80 +240,139 @@ public function testEmptyReportMakesEmptyDataToWrite() {
         $tokens_ids = array();
         $annotations_by_id = array();
     
-        // invoke protected method
-        $protectedMethod = new ReflectionMethod('ConllAndJsonFactory','makeConllAndJsonExportData');
-        $protectedMethod->setAccessible(True);
-        list($conll,$json_builder) = $protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+        // invoke tested method
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
         
         // check results
-        $expectedConll = "ORDER_ID\tTOKEN_ID\tORTH\tCTAG\tFROM\tTO\tANN_TAGS\tANN_IDS\tREL_IDS\tREL_TARGET_ANN_IDS\n";
-        $this->assertEquals($expectedConll,$conll);
-
-        $expectedJson = array(
-            "chunks" => array(
-                array()
-            ),
-            "relations" => array(),
-            "annotations" => array()
-        );
-        $this->assertEquals($expectedJson,$json_builder);
+		$this->assertEquals($this->getExpectedConllHeader(),$conll);
+        $this->assertEquals($this->getExpectedEmptyJson(),$json_builder);
 
     } // testEmptyReportMakesEmptyDataToWrite()
 
-    public function testAllDataPlacesToDataConllAndJsonStructures() {
+	public function testReportArrayFieldsMakesEmptyDataToWrite() {
+
+		// any content of $report array doesn't generate nonempty output
 
         // args for call
         $tokens = array();
-    
-        // DbToken::getTokenByReportId($report_id, null, true);
+		$tags_by_tokens = array();
         $relations = array();
         $annotations = array();
         $tokens_ids = array();
         $annotations_by_id = array();
 
-        // invoke protected method
-        $protectedMethod = new ReflectionMethod('ConllAndJsonFactory','makeConllAndJsonExportData');
-        $protectedMethod->setAccessible(True);
-        list($conll,$json_builder) = $protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+		// test only 'id' field
+        $report = array('id'=>1234);
+        $ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
+		list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id); 
+        $this->assertEquals($this->getExpectedConllHeader(),$conll);
+        $this->assertEquals($this->getExpectedEmptyJson(),$json_builder);
+
+        // test only 'content' field
+        $report = array('content'=>'jakiś tekst');
+        $ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
+
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+        $this->assertEquals($this->getExpectedConllHeader(),$conll);
+        $this->assertEquals($this->getExpectedEmptyJson(),$json_builder);
+
+		// test any other field in $report
+		$report = array('id'=>1234,
+						'content'=>'jakiś tekst',
+                    	'other_report_field'=>'other field text');
+        $ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+        $this->assertEquals($this->getExpectedConllHeader(),$conll);
+        $this->assertEquals($this->getExpectedEmptyJson(),$json_builder);
+		
+	} // testReportArrayFieldsMakesEmptyDataToWrite()
+
+    public function testAllDataPlacesToDataConllAndJsonStructures() {
+
+        // args for call
+        $relations = array();
+        $annotations_by_id = $this->generateAnnotation_By_IdTestData(False,True);
+        $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
+
+		// invoke tested method
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
 
         // check results
-        $expectedConll = "ORDER_ID\tTOKEN_ID\tORTH\tCTAG\tFROM\tTO\tANN_TAGS\tANN_IDS\tREL_IDS\tREL_TARGET_ANN_IDS\n";
-        $expectedConll .=   "0\t0\tTo\t\t0\t1\tO\t_\t_\t_\n".
-                            "1\t1\tjest\t\t2\t5\tO\t_\t_\t_\n".
-                            "2\t2\tduże\t\t6\t9\tO\t_\t_\t_\n".
-                            "3\t3\tokno\t\t10\t13\tO\t_\t_\t_\n".
-                            "4\t4\t.\t\t14\t14\tO\t_\t_\t_\n".
-                            "\n".
-                            "5\t0\tBardzo\t\t15\t20\tO\t_\t_\t_\n".
-                            "6\t1\tduże\t\t21\t24\tO\t_\t_\t_\n".
-                            "7\t2\t.\t\t25\t25\tO\t_\t_\t_\n".
-                            "\n";
+		$expectedConll = $this->getExpectedConll();
+        $expectedConll = str_replace(
+                            "2\t2\tduże\t\t6\t9\tO\t_\t_\t_\n",
+                            "2\t2\tduże\t\t6\t9\tB-nam_adj\t1\t_\t_\n",
+                            $expectedConll);
 		$this->assertEquals($expectedConll,$conll);
 
+        $expectedChunks = $this->getExpectedChunks();
+        // annotation_id to 'annotations' list in 3-rd chunk
+        $expectedChunks[0][0][2]['annotations'][] = 1;
         $expectedJson = array(
-            "chunks" => array(
-                array(
-                    array(
-                        array('order_id' => 0,'token_id' => 0,'orth' => 'To','ctag' => null,'from' => 0,'to' => 1,'annotations' => array(),'relations' => array()),
-                        array('order_id' => 1,'token_id' => 1,'orth' => 'jest','ctag' => null,'from' => 2,'to' => 5,'annotations' => array(),'relations' => array()),
-                        array('order_id' => 2,'token_id' => 2,'orth' => 'duże','ctag' => null,'from' => 6,'to' => 9,'annotations' => array(),'relations' => array()),
-                        array('order_id' => 3,'token_id' => 3,'orth' => 'okno','ctag' => null,'from' => 10,'to' => 13,'annotations' => array(),'relations' => array()),
-                        array('order_id' => 4,'token_id' => 4,'orth' => '.','ctag' => null,'from' => 14,'to' => 14,'annotations' => array(),'relations' => array())
-                    ),
-                    array(
-                        array('order_id' => 5,'token_id' => 0,'orth' => 'Bardzo','ctag' => null,'from' => 15,'to' => 20,'annotations' => array(),'relations' => array()),
-                        array('order_id' => 6,'token_id' => 1,'orth' => 'duże','ctag' => null,'from' => 21,'to' => 24,'annotations' => array(),'relations' => array()),
-                        array('order_id' => 7,'token_id' => 2,'orth' => '.','ctag' => null,'from' => 25,'to' => 25,'annotations' => array(),'relations' => array())
-                    )
-                )
-            ),
+            "chunks" => $expectedChunks,
             "relations" => array(),
-            "annotations" => array()
+            "annotations" => array(
+                array('id'=>1,'report_id'=>1,'type_id'=>360,'from'=>6,'to'=>9,
+                    'text' => 'duże','user_id' => 1,
+                    'creation_time' => '2022-10-03 08:07:37','stage' => 'final',
+                    'source' => 'user','annotation_subset_id' => '52',
+                    'type'=>'nam_adj','group_id'=>1,
+/*
+                    'login' => 'admin','screename' => 'Inforex Admin',
+                    'lemma' => 'lemat dodany do duże',
+*/
+                    'group' => 1,'description' => 'Przymiotnik utworzony od nazwy własnej','css' => 'background: lightgreen;','cross_sentence' => '0','shortlist' => '0',
+                    'name'=>'nam_adj', 
+                    // tylko jeśli istnieje atrybut
+                    'annotation_id' => 1,'annotation_attribute_id' => 1,'value' => 'valueAtrTypu','prop' => 'valueAtrTypu'
+                ),
+            )
         );
         $this->assertEquals($expectedJson,$json_builder);
 
     } // testAllDataPlacesToDataConllAndJsonStructures() 
 
+    public function testDocumentWithoutTokenizationPlaceDataToJsonAndConllArray() {
+		// CCL is self-tokenized by constructor
+        // args for call
+		$tokens = array();
+        // tak jest ustawiane zawsze w CorpusExporter
+        $tokens_ids = array_column($tokens, 'token_id');
+		$ccl = $this->generateCclTestData(
+				$this->generateReportTestData(),$tokens);
+        $relations = array();
+        $annotations = array();
+        $annotations_by_id = array();
+
+		// invoke tested method
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+
+        // check results
+        $this->assertEquals($this->getExpectedConll(),$conll);
+
+		$expectedJson = $this->getExpectedEmptyJson();
+		$expectedJson["chunks"] = $this->getExpectedChunks();
+		$this->assertEquals($expectedJson,$json_builder);
+
+		// with tokens without annotations there are all the same as above
+
+		// invoke tested method
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+
+		$this->assertEquals($this->getExpectedConll(),$conll);
+		$this->assertEquals($expectedJson,$json_builder);
+ 
+    } // testDocumentWithoutTokenizationPlaceDataToJsonAndConllArray() 
+
+    public function testGeneralAnnotationFieldsPlacedToJsonAndConllArray() {
+
+        // are all fields which always should be present in annotation 
+        // record placed correctly to JSON and CONLL structures
+
+        $this->assertTrue(True);
+
+    } // testGeneralAnnotationFieldsPlacedToJsonAndConllArray
+
 /* class ConllAndJsonFactory has only 1 function
     function exportToConllAndJson($file_path_without_ext, $ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id)
 */

From 15a5e7149fdaf957e0b4d760b71106044aeb7427 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Sat, 7 Oct 2023 18:54:46 +0200
Subject: [PATCH 114/154] mocked all Ccl input clases for tests

---
 .../export/ConllAndJsonFactoryTest.php        | 111 +++++++-----------
 1 file changed, 43 insertions(+), 68 deletions(-)

diff --git a/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php b/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
index d312a7aa..61cc6240 100644
--- a/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
+++ b/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
@@ -185,24 +185,6 @@ private function generateAnnotationsFromAnnotations_By_Id(array $annotations_by_
 
     } // generateAnnotationsFromAnnotations_By_Id
 
-    private function generateCclTestData($report=null,$tokens=null) {
-
-        // $report parameter
-		if($report==null){
-        	$report = $this->generateReportTestData();
-		}
-		// $tokens parameter
-		if($tokens==null){
-			$tokens = $this->generateTokensTestData();
-		}
-		// $tags_by_tokens parameter
-		$tags_by_tokens = array();
-
-        $ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
-        return $ccl;
-    
-    } // generateCclTestData()
-
     private function generateFullTestData() {
 
         $this->report_id = 1234;
@@ -210,35 +192,68 @@ private function generateFullTestData() {
         // $file_path_without_ext parameter
         $this->file_path_without_ext = $this->virtualDir->url()."/test";
 
-		// $report parameter, local for CCL only
-		$report = $this->generateReportTestData();
-
 		// $tokens parameter
 		$this->tokens = $this->generateTokensTestData($this->report_id);
         // tak jest ustawiane zawsze w CorpusExporter
         $this->tokens_ids = array_column($this->tokens, 'token_id');
 
         // $ccl parameter
-        $this->ccl = $this->generateCclTestData($report,$this->tokens);
-
+		$this->ccl = $this->generateFullCclData();
 
     } // generateFullTestData()
 
+	private function makeMockToken($id,$orth,$lexemes,$from,$to) {
+
+		$mockToken = $this->getMockBuilder(CclToken::class)->getMock();
+        $mockToken->id = $id; 
+		$mockToken->orth = $orth; 
+		$mockToken->lexemes = $lexemes; 
+		$mockToken->from = $from; 
+		$mockToken->to = $to;
+		return $mockToken;
+
+	} // makeMockToken
+
+    private function generateFullCclData() {
+
+        // mocked $ccl argument for empty report
+		$mockToken11 = $this->makeMockToken(0,"To",array(),0,1);
+		$mockToken12 = $this->makeMockToken(1,"jest",array(),2,5);
+		$mockToken13 = $this->makeMockToken(2,"duże",array(),6,9);
+		$mockToken14 = $this->makeMockToken(3,"okno",array(),10,13);
+		$mockToken15 = $this->makeMockToken(4,".",array(),14,14);
+        $mockSentence1 = $this->getMockBuilder(CclSentence::class)->getMock();
+        $mockSentence1->tokens = array($mockToken11,$mockToken12,$mockToken13,$mockToken14,$mockToken15);
+		$mockToken21 = $this->makeMockToken(5,"Bardzo",array(),15,20);
+		$mockToken22 = $this->makeMockToken(6,"duże",array(),21,24);
+		$mockToken23 = $this->makeMockToken(7,".",array(),25,25);
+		$mockSentence2 = $this->getMockBuilder(CclSentence::class)->getMock();
+        $mockSentence2->tokens = array($mockToken21,$mockToken22,$mockToken23);
+        $mockChunk = $this->getMockBuilder(CclChunk::class)->getMock();
+        $mockChunk->sentences = array($mockSentence1,$mockSentence2);
+        $mockCclDocument = $this->getMockBuilder(CclDocument::class)->getMock();
+        $mockCclDocument->chunks = array($mockChunk);
+        return  $mockCclDocument;
+
+    } // generateFullCclData()
+
 // tests
 
     public function testEmptyReportMakesEmptyDataToWrite() {
 
 		// all empty input data generates minimal export output
         // args for call
-            $report = array(); 
-            $tokens = array();
-            $tags_by_tokens = array();
-        $ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
         $tokens = array();
         $relations = array();
         $annotations = array();
         $tokens_ids = array();
         $annotations_by_id = array();
+		// mocked $ccl argument for empty report
+        $mockChunk = $this->getMockBuilder(CclChunk::class)->getMock();
+        $mockChunk->sentences = array();
+        $mockCclDocument = $this->getMockBuilder(CclDocument::class)->getMock();
+        $mockCclDocument->chunks = array($mockChunk);
+        $ccl = $mockCclDocument;
     
         // invoke tested method
         list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
@@ -249,44 +264,6 @@ public function testEmptyReportMakesEmptyDataToWrite() {
 
     } // testEmptyReportMakesEmptyDataToWrite()
 
-	public function testReportArrayFieldsMakesEmptyDataToWrite() {
-
-		// any content of $report array doesn't generate nonempty output
-
-        // args for call
-        $tokens = array();
-		$tags_by_tokens = array();
-        $relations = array();
-        $annotations = array();
-        $tokens_ids = array();
-        $annotations_by_id = array();
-
-		// test only 'id' field
-        $report = array('id'=>1234);
-        $ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
-		list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id); 
-        $this->assertEquals($this->getExpectedConllHeader(),$conll);
-        $this->assertEquals($this->getExpectedEmptyJson(),$json_builder);
-
-        // test only 'content' field
-        $report = array('content'=>'jakiś tekst');
-        $ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
-
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
-        $this->assertEquals($this->getExpectedConllHeader(),$conll);
-        $this->assertEquals($this->getExpectedEmptyJson(),$json_builder);
-
-		// test any other field in $report
-		$report = array('id'=>1234,
-						'content'=>'jakiś tekst',
-                    	'other_report_field'=>'other field text');
-        $ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
-        $this->assertEquals($this->getExpectedConllHeader(),$conll);
-        $this->assertEquals($this->getExpectedEmptyJson(),$json_builder);
-		
-	} // testReportArrayFieldsMakesEmptyDataToWrite()
-
     public function testAllDataPlacesToDataConllAndJsonStructures() {
 
         // args for call
@@ -338,14 +315,12 @@ public function testDocumentWithoutTokenizationPlaceDataToJsonAndConllArray() {
 		$tokens = array();
         // tak jest ustawiane zawsze w CorpusExporter
         $tokens_ids = array_column($tokens, 'token_id');
-		$ccl = $this->generateCclTestData(
-				$this->generateReportTestData(),$tokens);
         $relations = array();
         $annotations = array();
         $annotations_by_id = array();
 
 		// invoke tested method
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
 
         // check results
         $this->assertEquals($this->getExpectedConll(),$conll);

From 0f56fd7e69f217ef5b653ae1a0337292c264a825 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Mon, 9 Oct 2023 19:01:59 +0200
Subject: [PATCH 115/154] export unit tests for elementary Ccl elements

---
 .../export/ConllAndJsonFactoryTest.php        | 110 ++++++++++++++++++
 1 file changed, 110 insertions(+)

diff --git a/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php b/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
index 61cc6240..2af10178 100644
--- a/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
+++ b/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
@@ -264,6 +264,116 @@ public function testEmptyReportMakesEmptyDataToWrite() {
 
     } // testEmptyReportMakesEmptyDataToWrite()
 
+    public function testOneEmptySentenceCclReportMakesLinesWithNoData() {
+
+        // only 1 empty sentence in 1 chunk in Ccl
+        // args for call
+        $tokens = array();
+        $relations = array();
+        $annotations = array();
+        $tokens_ids = array();
+        $annotations_by_id = array();
+        // mocked $ccl argument for empty report
+        $mockSentence = $this->getMockBuilder(CclSentence::class)->getMock();
+        $mockSentence->tokens = array();
+        $mockChunk = $this->getMockBuilder(CclChunk::class)->getMock();
+        $mockChunk->sentences = array($mockSentence);
+        $mockCclDocument = $this->getMockBuilder(CclDocument::class)->getMock();
+        $mockCclDocument->chunks = array($mockChunk);
+        $ccl = $mockCclDocument;
+
+        // invoke tested method
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+
+        // check results
+        //  empty sentence generates one empty line in export CONLL
+        $expectedConll = $this->getExpectedConllHeader()."\n";
+        $this->assertEquals($expectedConll,$conll);
+        $expectedJson = $this->getExpectedEmptyJson();
+        //  empty sentence generates one empty array in export JSON      
+        $expectedJson['chunks'][0][] = array();
+        $this->assertEquals($expectedJson,$json_builder);
+
+    } // testOneEmptySentenceCclReportMakesLinesWithNoData()
+ 
+    public function testOneEmptyTokenCclReportMakesTokenWithEmptyData() {
+
+        // only 1 sentence with 1 empty token in 1 chunk in Ccl
+        // args for call
+        $tokens = array();
+        $relations = array();
+        $annotations = array();
+        $tokens_ids = array();
+        $annotations_by_id = array();
+        // mocked $ccl argument for empty report
+        $mockToken = $this->getMockBuilder(CclToken::class)->getMock();
+        $mockSentence = $this->getMockBuilder(CclSentence::class)->getMock();
+        $mockSentence->tokens = array($mockToken);
+        $mockChunk = $this->getMockBuilder(CclChunk::class)->getMock();
+        $mockChunk->sentences = array($mockSentence);
+        $mockCclDocument = $this->getMockBuilder(CclDocument::class)->getMock();
+        $mockCclDocument->chunks = array($mockChunk);
+        $ccl = $mockCclDocument;
+
+        // invoke tested method
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+
+        // check results
+        //  empty token generates row with empty data in export CONLL
+        $expectedConll = $this->getExpectedConllHeader()
+			."\t0\t\t\t\t\tO\t_\t_\t_\n"
+			."\n";
+        $this->assertEquals($expectedConll,$conll);
+        //  empty token generates one token array in sentence with export
+		//  dummy data in JSON & also creates annotations and relations arrays
+		$emptyTokenData = array('order_id' => null,'token_id' => 0,'orth' => null,'ctag' => null,'from' => null,'to' => null,'annotations' => Array (),'relations' => Array ());
+        $expectedJson['chunks'][0][] = array($emptyTokenData);
+		// 	if any token exist, must be annotations & relations tables in JSON
+		$expectedJson["annotations"] 	= array();
+		$expectedJson["relations"] 		= array();
+        $this->assertEquals($expectedJson,$json_builder);
+
+    } // testOneEmptyTokenCclReportMakesTokenWithEmptyData()
+ 
+    public function testOneTokenCclMakesNonemptyDataToWrite() {
+
+        // minimal set - 1 sentence with 1 normal token in 1 chunk in Ccl
+        // args for call
+        $tokens = array();
+        $relations = array();
+        $annotations = array();
+        $tokens_ids = array();
+        $annotations_by_id = array();
+        // mocked $ccl argument for empty report
+        $mockToken = $this->makeMockToken(0,"To",array(),0,1);
+        $mockSentence = $this->getMockBuilder(CclSentence::class)->getMock();
+        $mockSentence->tokens = array($mockToken);
+        $mockChunk = $this->getMockBuilder(CclChunk::class)->getMock();
+        $mockChunk->sentences = array($mockSentence);
+        $mockCclDocument = $this->getMockBuilder(CclDocument::class)->getMock();
+        $mockCclDocument->chunks = array($mockChunk);
+        $ccl = $mockCclDocument;
+
+        // invoke tested method
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+
+        // check results
+        //  simple token generates row with its data in export CONLL
+        $expectedConll = $this->getExpectedConllHeader()
+            ."0\t0\tTo\t\t0\t1\tO\t_\t_\t_\n"
+            ."\n";
+        $this->assertEquals($expectedConll,$conll);
+        //  one token generates token array with data in sentence array
+		//  & also creates annotations and relations arrays in export JSON
+        $emptyTokenData = array('order_id' => 0,'token_id' => 0,'orth' => 'To','ctag' => null,'from' => 0,'to' => 1,'annotations' => Array (),'relations' => Array ());
+        $expectedJson['chunks'][0][] = array($emptyTokenData);
+        //  if any token exist, must be annotations & relations tables in JSON
+        $expectedJson["annotations"]    = array();
+        $expectedJson["relations"]      = array();
+        $this->assertEquals($expectedJson,$json_builder);
+ 
+    } // testOneTokenCclMakesNonemptyDataToWrite
+
     public function testAllDataPlacesToDataConllAndJsonStructures() {
 
         // args for call

From 6da0801786ea251f3e681aa8bb4e46857b0424d7 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@frakoterm.pl>
Date: Thu, 12 Oct 2023 08:17:19 +0200
Subject: [PATCH 116/154] unit test for export with relation

---
 .../export/ConllAndJsonFactoryTest.php        | 24 +++++++++++++------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php b/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
index 2af10178..b0460fef 100644
--- a/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
+++ b/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
@@ -372,12 +372,23 @@ public function testOneTokenCclMakesNonemptyDataToWrite() {
         $expectedJson["relations"]      = array();
         $this->assertEquals($expectedJson,$json_builder);
  
-    } // testOneTokenCclMakesNonemptyDataToWrite
+    } // testOneTokenCclMakesNonemptyDataToWrite()
 
     public function testAllDataPlacesToDataConllAndJsonStructures() {
 
         // args for call
         $relations = array();
+		$relationData = array(
+    		'report_id' => '1',
+    		'id' => '1',
+    		'relation_type_id' => '1',
+    		'source_id' => '1',
+    		'target_id' => '2',
+    		'relation_set_id' => '1',
+    		'name' => 'test',
+    		'rsname' => 'test',
+        );
+		$relations = array( $relationData );
         $annotations_by_id = $this->generateAnnotation_By_IdTestData(False,True);
         $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
 
@@ -388,16 +399,19 @@ public function testAllDataPlacesToDataConllAndJsonStructures() {
 		$expectedConll = $this->getExpectedConll();
         $expectedConll = str_replace(
                             "2\t2\tduże\t\t6\t9\tO\t_\t_\t_\n",
-                            "2\t2\tduże\t\t6\t9\tB-nam_adj\t1\t_\t_\n",
+                            "2\t2\tduże\t\t6\t9\tB-nam_adj\t1\t1\t2\n",
                             $expectedConll);
 		$this->assertEquals($expectedConll,$conll);
 
         $expectedChunks = $this->getExpectedChunks();
         // annotation_id to 'annotations' list in 3-rd chunk
         $expectedChunks[0][0][2]['annotations'][] = 1;
+		$expectedChunks[0][0][2]['relations'][0] = 1;
         $expectedJson = array(
             "chunks" => $expectedChunks,
-            "relations" => array(),
+            "relations" => array(
+				$relationData
+			),
             "annotations" => array(
                 array('id'=>1,'report_id'=>1,'type_id'=>360,'from'=>6,'to'=>9,
                     'text' => 'duże','user_id' => 1,
@@ -468,10 +482,6 @@ public function testDeliveredDataAreWrittenToFiles() {
         $json_builder = array("a"=>1);
 
         // this values doesn't matter
-            $report = array();
-            $tokens = array();
-            $tags_by_tokens = array();
-        $ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
         $tokens = array();
         $relations = array();
         $annotations = array();

From 88eddcf78c681974b3a9a201b4c799122e53579d Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Fri, 20 Oct 2023 17:51:18 +0200
Subject: [PATCH 117/154] synchro with relation export startegy change

---
 engine/include/database/CDbCorpusRelation.php | 36 ++++++++-----------
 engine/include/export/CorpusExporter.php      | 16 +++++++--
 engine/include/export/ExportManager.php       |  2 +-
 engine/templates/page_corpus_export.tpl       |  1 +
 .../export/CorpusExporter_part0_Test.php      |  4 +--
 public_html/js/c_widget_annotation_panel.js   |  4 +--
 6 files changed, 34 insertions(+), 29 deletions(-)

diff --git a/engine/include/database/CDbCorpusRelation.php b/engine/include/database/CDbCorpusRelation.php
index 8f281e8c..28f99854 100644
--- a/engine/include/database/CDbCorpusRelation.php
+++ b/engine/include/database/CDbCorpusRelation.php
@@ -163,28 +163,20 @@ static function getRelationsByRelationSetIds($relation_set_ids){
 		return $db->fetch_rows($sql);		
 	}
 	
-	//TODO to delete
-	static function getRelationsBySets($report_ids, $relation_type_ids){
-		global $db;
-	    $sql = "SELECT reports_annotations.report_id as report_id, rel.id, rel.relation_type_id, rel.source_id, rel.target_id, relation_types.name " .
-	            "FROM " .
-	                "(SELECT * " .
-	                "FROM relations " .
-	                "WHERE source_id IN " .
-	                    "(SELECT id " .
-	                    "FROM reports_annotations " .
-	                    "WHERE report_id IN('" . implode("','",$report_ids) . "')) " .
-	                "AND relation_type_id " .
-	                "IN (".implode(",",$relation_type_ids).")) rel " .
-	            "LEFT JOIN relation_types " .
-	            "ON rel.relation_type_id=relation_types.id " .
-	            "LEFT JOIN reports_annotations " .
-	            "ON rel.source_id=reports_annotations.id ";
-		return $db->fetch_rows($sql);		            				
-	}
-	
-	static function getRelationsBySets2($report_ids=null, $relation_set_ids=null, $relation_type_ids=null, $stage_ids=null, $user_ids=null){
+	static function getRelationsBySets($report_ids=null, $relation_set_ids=null, $relation_type_ids=null, $stage_ids=null, $user_ids=null, $relation_stages=array()){
 		global $db;
+
+        // if $relation_stages not set is equal $stage_ids - stages of
+        // relation are identical as stages of annotations
+        if( is_array($relation_stages) && (count($relation_stages)==0)) {
+            $relation_stages = $stage_ids;
+        } // if not set
+
+        if (is_array($relation_stages) && (count($relation_stages)>0)) {
+            $relationStages = "stage IN('".implode("','",$relation_stages)."') AND";
+        } else { // if $relation_stages==null default is 'final'
+            $relationStages = "stage = 'final' AND"; 
+        }
 	    $sql = "SELECT reports_annotations.report_id as report_id, " .
 	    		"      rel.id, " .
 	    		"      rel.relation_type_id, " .
@@ -196,7 +188,7 @@ static function getRelationsBySets2($report_ids=null, $relation_set_ids=null, $r
 	            "FROM " .
 	                "(SELECT * " .
 	                "FROM relations " .
-	                "WHERE stage = 'final' AND source_id IN " .
+	                "WHERE ".$relationStages." source_id IN " .
 	                    "(SELECT id " .
 	                    "FROM reports_annotations " .
 	                    "WHERE report_id IN('0','" . implode("','",$report_ids) . "')) " .
diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index d465e18e..92fdf8fd 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -109,6 +109,7 @@ protected function parse_extractor($description){
                 $params['attributes_annotation_subset_ids'] = null;
                 $params['relation_set_ids'] = null;
 				$params['stages'] = null;
+                $params['relation_stages'] = array(); // internally expanded
 
 				foreach ( explode(";", $parts[1]) as $part ){
 					$name_value = explode("#", $part);
@@ -126,6 +127,17 @@ protected function parse_extractor($description){
 					}
 				}
 
+                // hint for selecting annotation in stage final and relation
+                // in stage agreement
+                if( is_array($params["stages"])) {
+                    foreach($params["stages"] as &$stage) {
+                        if($stage=='relationagreement') {
+                            $stage = 'final';    // for annotations
+                            $params["relation_stages"] = array('agreement'); // for relations
+                        } // if 'relationagreement'
+                    } // foreach "stages"
+                } // is_array('stages')
+
 				$extractor["params"] = $params;
 				$extractor["extractor"] = function($report_id, $params, &$elements){
 					// $params -- annotations_set_ids, $stages
@@ -163,7 +175,7 @@ protected function parse_extractor($description){
                     }
                     if(is_array($params['relation_set_ids']) && count($params['relation_set_ids'])>0) {
                         // add custom relation
-						$relations = DbCorpusRelation::getRelationsBySets2(array($report_id), $params['relation_set_ids'], null, $params["stages"],$params["user_ids"]);
+						$relations = DbCorpusRelation::getRelationsBySets(array($report_id), $params['relation_set_ids'], null, $params["stages"],$params["user_ids"],$params["relation_stages"]);
 						if ( is_array($relations) ) {
                         	$elements['relations'] = array_merge($elements['relations'], $relations);
                     	}
@@ -188,7 +200,7 @@ protected function parse_extractor($description){
 				$extractor["params"] = explode(",", $parts[1]);
 				$extractor["extractor"] = function($report_id, $params, &$elements){
 					// $params -- set of annotation_set_id
-					$relations = DbCorpusRelation::getRelationsBySets2(array($report_id), $params);
+					$relations = DbCorpusRelation::getRelationsBySets(array($report_id), $params);
 					if ( is_array($relations) ) {
 						$elements['relations'] = array_merge($elements['relations'], $relations);
 					}
diff --git a/engine/include/export/ExportManager.php b/engine/include/export/ExportManager.php
index 80a27532..8960f190 100644
--- a/engine/include/export/ExportManager.php
+++ b/engine/include/export/ExportManager.php
@@ -298,7 +298,7 @@ function readContent(){
 		}
 		
 		$this->log(" e) reading relations ...");
-		$relations = DbCorpusRelation::getRelationsBySets2($this->report_ids, 
+		$relations = DbCorpusRelation::getRelationsBySets($this->report_ids, 
 							$this->relation_set_ids, $this->relation_type_ids);
 		foreach ($relations as &$relation){
 			$report_id = $relation['report_id'];			
diff --git a/engine/templates/page_corpus_export.tpl b/engine/templates/page_corpus_export.tpl
index 2c3fb395..a928d070 100644
--- a/engine/templates/page_corpus_export.tpl
+++ b/engine/templates/page_corpus_export.tpl
@@ -109,6 +109,7 @@
                                                     <select class = "annotation_stage_select">
                                                         <option value = "final">final</option>
                                                         <option value = "agreement">agreement</option>
+                                                        <option value = "relationagreement">relation agreement</option>
                                                         <option value = "new">new</option>
                                                         <option value = "discarded">discarded</option>
 
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php
index 7b5a4d70..24ad207e 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php
@@ -84,7 +84,7 @@ public function test_parse_extractor()
 +    'annotation_set_ids' => Array (...)
 +    'annotation_subset_ids' => null
 +    'stages' => null
-                    )
++    'relation_stages' => array()
 +        'extractor' => Closure Object (...)
 */
         $this->assertTrue(is_array($result));
@@ -96,7 +96,7 @@ public function test_parse_extractor()
         $this->assertEquals(array(3),$result[0]["flag_ids"]);
         $this->assertEquals($extractorDescription,$result[0]["name"]);
         $this->assertTrue(is_array($result[0]['params']));
-        $this->assertEquals(9,count($result[0]['params']));
+        $this->assertEquals(10,count($result[0]['params']));
         $this->assertTrue(is_array($result[0]['params']['user_ids']));
         $this->assertEquals(array(70),$result[0]["params"]['user_ids']);
         $this->assertTrue(is_array($result[0]['params']['annotation_set_ids']));
diff --git a/public_html/js/c_widget_annotation_panel.js b/public_html/js/c_widget_annotation_panel.js
index e56cc0a5..7235ad4f 100644
--- a/public_html/js/c_widget_annotation_panel.js
+++ b/public_html/js/c_widget_annotation_panel.js
@@ -62,7 +62,7 @@ WidgetAnnotationPanel.prototype.createAnnotation = function(selection, type, ann
     var content_html = $.trim($(newNode).parents("div.content").html());
     content_html = content_html.replace(/<sup.*?<\/sup>/gi, '');
     content_html = content_html.replace(pattern, fromDelimiter+"$1"+toDelimiter);
-    content_no_html = content_html.replace(/<\/?[^>]+>/gi, '');
+    content_no_html = content_html.replace(/<\/?("[^"]*"|'[^']*'|[^>])*>/g,'');
     content_no_html = html_entity_decode(content_no_html);
 
     // Pobierz treść anotacji przed usunięciem białych znaków
@@ -147,4 +147,4 @@ WidgetAnnotationPanel.prototype.remove_temporal_add_annotation_tag_by_id = funct
             return $(this).contents();
         }
     );
-}
\ No newline at end of file
+}

From f209e0fec793881450f2872dd73c52ede82c6af7 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Sat, 21 Oct 2023 18:25:50 +0200
Subject: [PATCH 118/154] tests for lemmas and anntags exports

---
 .../export/ConllAndJsonFactoryTest.php        | 288 +++++++++++++++---
 1 file changed, 250 insertions(+), 38 deletions(-)

diff --git a/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php b/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
index b0460fef..c351d54e 100644
--- a/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
+++ b/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
@@ -97,6 +97,18 @@ private function getExpectedConll() {
 		return $expectedConll; 
     } // getExpectedConll()
 
+    private function extractAnntagsFromConllLines($conllStr,$lineNo) {
+
+        // divide to lines
+        $conllLines = explode("\n",$conllStr);
+        // line should looks like "2\t2\tduże\t\t6\t9\tO\t_\t_\t_"
+        $connLineForToken = $conllLines[$lineNo];
+        $columns = explode("\t",$connLineForToken);
+        $annTags = $columns[6];
+        return $annTags;
+
+    } // extractAnntagsFromConllLines()
+
 	private function getExpectedEmptyJson() {
 
         return 	array(
@@ -133,10 +145,23 @@ private function getExpectedChunks() {
 
     private function generateAnnotation_By_IdTestData(
                         $annotationExtractorFields=true,
+						$annotation_idExtractorFields=true,
                         $annotationsWithLemmaField=true,
                         $annotationsWithTypeAttributte=true
                     ) {
 
+		// Depends from extractor type, annotations row have different
+		// fields:
+		//  Common section: 
+		//		'id','report_id','type_id','from','to','text','user_id','creation_time','stage','source','annotation_subset_id','type','group_id'
+		//  Fields, that exists only for 'annotation' extractor: 
+		//		'login','screename','lemma'( exists always, but may be null if no lemma )
+		//  Fields that exist for extractors 'annotation_id' or 'annotation_subset_id' : 
+		//		'group','name','description','css','cross_sentence','shortlist'
+		//  Fields that exists only if type attribute is set : 
+		//		'annotation_id','annotation_attribute_id','value','prop'
+		
+
         $annotation_id = 1;
         // index must match 'id' field
         $annotations_by_id = array(
@@ -153,13 +178,9 @@ private function generateAnnotation_By_IdTestData(
             // fields, that exists for extractor 'annotation' only
             $annotations_by_id[$annotation_id]['login']='admin';
             $annotations_by_id[$annotation_id]['screename']='Inforex Admin';
-            if($annotationsWithLemmaField){
-                $annotations_by_id[$annotation_id]['lemma']='lemat dodany do duże';
-            } else {
-                $annotations_by_id[$annotation_id]['lemma']=null;
-            }
-        } else {
-            // fields, that exists for extractors 'annotation_id' 
+		}
+		if($annotation_idExtractorFields) {
+            // fields, that exists for extractors 'annotation_id'
             //   and 'annotation_subset_id' only
             $annotations_by_id[$annotation_id]['group']=1;
             $annotations_by_id[$annotation_id]['name']='nam_adj';
@@ -167,14 +188,18 @@ private function generateAnnotation_By_IdTestData(
             $annotations_by_id[$annotation_id]['css']='background: lightgreen;';
             $annotations_by_id[$annotation_id]['cross_sentence']='0';
             $annotations_by_id[$annotation_id]['shortlist']='0';
-            // this section only for simple extractor with attribute in DB
-            if($annotationsWithTypeAttributte) {
-                $annotations_by_id[$annotation_id]['annotation_id']=$annotation_id;
-                $annotations_by_id[$annotation_id]['annotation_attribute_id']=1;
-                $annotations_by_id[$annotation_id]['value']='valueAtrTypu';
-                $annotations_by_id[$annotation_id]['prop']='valueAtrTypu';
-            }
-        }
+		}
+     	if($annotationsWithLemmaField){
+         	$annotations_by_id[$annotation_id]['lemma']='lemat dodany do duże';
+      	} else {
+          	$annotations_by_id[$annotation_id]['lemma']=null;
+       	}
+    	if($annotationsWithTypeAttributte) {
+          	$annotations_by_id[$annotation_id]['annotation_id']=$annotation_id;
+           	$annotations_by_id[$annotation_id]['annotation_attribute_id']=1;
+           	$annotations_by_id[$annotation_id]['value']='valueAtrTypu';
+           	$annotations_by_id[$annotation_id]['prop']='valueAtrTypu';
+       	}
 
         return $annotations_by_id;
 
@@ -185,6 +210,23 @@ private function generateAnnotationsFromAnnotations_By_Id(array $annotations_by_
 
     } // generateAnnotationsFromAnnotations_By_Id
 
+    private function generateRelationsTestData() {
+
+        $relationData = array(
+            'report_id' => '1',
+            'id' => '1',
+            'relation_type_id' => '1',
+            'source_id' => '1',
+            'target_id' => '2',
+            'relation_set_id' => '1',
+            'name' => 'test',
+            'rsname' => 'test',
+        );
+        $relations = array( $relationData );
+        return $relations;
+
+    } // generateRelationsTestData()
+
     private function generateFullTestData() {
 
         $this->report_id = 1234;
@@ -377,20 +419,9 @@ public function testOneTokenCclMakesNonemptyDataToWrite() {
     public function testAllDataPlacesToDataConllAndJsonStructures() {
 
         // args for call
-        $relations = array();
-		$relationData = array(
-    		'report_id' => '1',
-    		'id' => '1',
-    		'relation_type_id' => '1',
-    		'source_id' => '1',
-    		'target_id' => '2',
-    		'relation_set_id' => '1',
-    		'name' => 'test',
-    		'rsname' => 'test',
-        );
-		$relations = array( $relationData );
-        $annotations_by_id = $this->generateAnnotation_By_IdTestData(False,True);
+        $annotations_by_id = $this->generateAnnotation_By_IdTestData(False,True,False,True);
         $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
+        $relations = $this->generateRelationsTestData();
 
 		// invoke tested method
         list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
@@ -409,23 +440,21 @@ public function testAllDataPlacesToDataConllAndJsonStructures() {
 		$expectedChunks[0][0][2]['relations'][0] = 1;
         $expectedJson = array(
             "chunks" => $expectedChunks,
-            "relations" => array(
-				$relationData
-			),
+            "relations" => $relations,
             "annotations" => array(
                 array('id'=>1,'report_id'=>1,'type_id'=>360,'from'=>6,'to'=>9,
                     'text' => 'duże','user_id' => 1,
                     'creation_time' => '2022-10-03 08:07:37','stage' => 'final',
                     'source' => 'user','annotation_subset_id' => '52',
                     'type'=>'nam_adj','group_id'=>1,
-/*
-                    'login' => 'admin','screename' => 'Inforex Admin',
-                    'lemma' => 'lemat dodany do duże',
-*/
+                    //'login' => 'admin','screename' => 'Inforex Admin',
+                    //'lemma' => 'lemat dodany do duże',
                     'group' => 1,'description' => 'Przymiotnik utworzony od nazwy własnej','css' => 'background: lightgreen;','cross_sentence' => '0','shortlist' => '0',
                     'name'=>'nam_adj', 
                     // tylko jeśli istnieje atrybut
-                    'annotation_id' => 1,'annotation_attribute_id' => 1,'value' => 'valueAtrTypu','prop' => 'valueAtrTypu'
+                    'annotation_id' => 1,'annotation_attribute_id' => 1,'value' => 'valueAtrTypu','prop' => 'valueAtrTypu',
+                    // puste lemma
+                    'lemma' => null
                 ),
             )
         );
@@ -466,12 +495,195 @@ public function testDocumentWithoutTokenizationPlaceDataToJsonAndConllArray() {
     public function testGeneralAnnotationFieldsPlacedToJsonAndConllArray() {
 
         // are all fields which always should be present in annotation 
-        // record placed correctly to JSON and CONLL structures
+        // record placed correctly to JSON and CONLL structures ?
+        // args for call without lemma
+        $annotations_by_id = $this->generateAnnotation_By_IdTestData(); // default annotation with: all extractors fields, lemma & type attribute
+        $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
+        $relations = $this->generateRelationsTestData();
 
-        $this->assertTrue(True);
+        // invoke tested method
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+
+        // check results
+        $expectedConll = $this->getExpectedConll();
+        $expectedConll = str_replace(
+                            "2\t2\tduże\t\t6\t9\tO\t_\t_\t_\n",
+                            "2\t2\tduże\t\t6\t9\tB-nam_adj\t1\t1\t2\n",
+                            $expectedConll);
+        $this->assertEquals($expectedConll,$conll);
+
+        $expectedChunks = $this->getExpectedChunks();
+        // annotation_id to 'annotations' list in 3-rd chunk
+        $expectedChunks[0][0][2]['annotations'][] = 1;
+        $expectedChunks[0][0][2]['relations'][0] = 1;
+        $expectedJson = array(
+            "chunks" => $expectedChunks,
+            "relations" => $relations,
+            "annotations" => array(
+                array('id'=>1,'report_id'=>1,'type_id'=>360,'from'=>6,'to'=>9,
+                    'text' => 'duże','user_id' => 1,
+                    'creation_time' => '2022-10-03 08:07:37','stage' => 'final',
+                    'source' => 'user','annotation_subset_id' => '52',
+                    'type'=>'nam_adj','group_id'=>1,
+					// 'annotation' extractor group
+                    'login' => 'admin','screename' => 'Inforex Admin',
+                    'lemma' => 'lemat dodany do duże',
+					// end of 'annotation' extractor group
+// these fields shows only for annotationExtractor = false
+                    'group' => 1,'description' => 'Przymiotnik utworzony od nazwy własnej','css' => 'background: lightgreen;','cross_sentence' => '0','shortlist' => '0',
+                    'name'=>'nam_adj',
+                    // tylko jeśli istnieje atrybut
+                    'annotation_id' => 1,'annotation_attribute_id' => 1,'value' => 'valueAtrTypu','prop' => 'valueAtrTypu'
+                ),
+            )
+        );
+		$this->assertEquals($expectedJson,$json_builder); 
 
     } // testGeneralAnnotationFieldsPlacedToJsonAndConllArray
 
+    public function testLemmaAdsNotChangesConll() {
+
+        $relations = $this->generateRelationsTestData();
+        // args for call without lemma
+		$LemmaExists = False;
+        $annotations_by_id = $this->generateAnnotation_By_IdTestData(True,True,$LemmaExists);
+        $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
+        // invoke tested method
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+
+        // args for call with lemma
+        $LemmaExists = True;
+        $annotations_by_id = $this->generateAnnotation_By_IdTestData(True,True,$LemmaExists);
+        $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
+        // invoke tested method
+        list($conll_wL,$json_builder_wL) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+
+		// conll not changed after add lemma:
+		$this->assertEquals($conll,$conll_wL);
+
+    } // testLemmaAdsNotChangesConll() 
+
+    public function testLemmaContentChangesNullInLemmaFieldInJson() {
+
+        $relations = $this->generateRelationsTestData();
+        // args for call without lemma
+        $LemmaExists = False;
+        $annotations_by_id = $this->generateAnnotation_By_IdTestData(True,False,$LemmaExists);
+        $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
+        // invoke tested method
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+
+        // args for call with lemma
+        $LemmaExists = True;
+        $annotations_by_id = $this->generateAnnotation_By_IdTestData(True,False,$LemmaExists);
+        $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
+        // invoke tested method
+        list($conll_wL,$json_builder_wL) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+
+        // json results after add lemma:
+		//   field 'lemma' changes from null to lemma text
+        $expectedJsonWithLemma = $json_builder;
+ 		$expectedJsonWithLemma['annotations'][0]['lemma'] = $annotations[0]['lemma'];
+        $this->assertEquals($expectedJsonWithLemma,$json_builder_wL);
+
+    } // testLemmaContentChangesNullInLemmaFieldInJson()
+
+    public function testTokensWithoutAnnotationHasOAnntag() {
+
+		// args for call w/o annotations
+        $relations = array();
+        $annotations_by_id = array();
+        $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
+        // invoke tested method
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+		
+        $expectedAnnTags = "O";
+		$fromLine = 3;
+		$annTags = $this->extractAnntagsFromConllLines($conll,$fromLine); 
+		$this->assertEquals($expectedAnnTags,$annTags);
+
+    } // testTokensWithoutAnnotationHasOAnntag()
+
+    public function testFirstTokenIntoAnnotationHasBAnntag() {
+
+		$annotationTokenLine = 3;
+		$relations = array();
+        // call args for annotations without "name" field
+  		$fieldsForAnnotationIdExtractorExists = False;
+        $annotations_by_id = $this->generateAnnotation_By_IdTestData(True,$fieldsForAnnotationIdExtractorExists);
+        $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
+        // invoke tested method
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+
+        $expectedAnnTags = "B-";
+        $annTags = $this->extractAnntagsFromConllLines($conll,$annotationTokenLine);
+        $this->assertEquals($expectedAnnTags,$annTags);
+
+        // call args for annotations with "name" field
+        $fieldsForAnnotationIdExtractorExists = True;
+        $annotations_by_id = $this->generateAnnotation_By_IdTestData(True,$fieldsForAnnotationIdExtractorExists);
+        $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
+        // invoke tested method
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+
+        $expectedAnnTags = "B-".'nam_adj'; // annotation type glued
+        $annTags = $this->extractAnntagsFromConllLines($conll,$annotationTokenLine);
+        $this->assertEquals($expectedAnnTags,$annTags);
+
+    } // testFirstTokenIntoAnnotationHasBAnntag()
+
+	public function testNextTokensIntoAnnotationHasIAnntag() {
+
+        $relations = array();
+        // call args for annotations without "name" field
+        $fieldsForAnnotationIdExtractorExists = False;
+        $annotations_by_id = $this->generateAnnotation_By_IdTestData(True,$fieldsForAnnotationIdExtractorExists);
+		// expand annotation 1 to charpos 20 includes 2 next tokens
+		$annotations_by_id[1]['to']=14;
+        $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
+        // invoke tested method
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+
+		$expectedAnnTags = "I-";
+		// for tokens in lines 4 and 5
+        $this->assertEquals($expectedAnnTags,$this->extractAnntagsFromConllLines($conll,4));
+		$this->assertEquals($expectedAnnTags,$this->extractAnntagsFromConllLines($conll,5));
+		
+        // call args for annotations with "name" field
+        $fieldsForAnnotationIdExtractorExists = True;
+        $annotations_by_id = $this->generateAnnotation_By_IdTestData(True,$fieldsForAnnotationIdExtractorExists);
+        // expand annotation 1 to charpos 20 includes 2 next tokens
+        $annotations_by_id[1]['to']=14;
+        $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
+        // invoke tested method
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+
+        $expectedAnnTags = "I-nam_adj";
+        // for tokens in lines 4 and 5
+        $this->assertEquals($expectedAnnTags,$this->extractAnntagsFromConllLines($conll,4));
+        $this->assertEquals($expectedAnnTags,$this->extractAnntagsFromConllLines($conll,5));
+
+	} // testNextTokensIntoAnnotationHasIAnntag()
+
+	public function testTokenInto2AnnotationsHasJoinedAnntags() {
+
+		$relations = array(); // no relations
+        // call args for two annotations on this same token
+        $annotations_by_id = $this->generateAnnotation_By_IdTestData();
+		// copy 1 anntotation to second one on this same <from,to>
+		$annotations_by_id[2] = $annotations_by_id[1];
+		$annotations_by_id[2]['id'] = 2; // correct annotation id 
+		$annotations_by_id[2]['name'] = '2nd'; // change ann type name 
+        $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
+        // invoke tested method
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+
+        // token in line 3 should have two annTags
+		$expectedAnnTags = "B-nam_adj:B-2nd";
+        $this->assertEquals($expectedAnnTags,$this->extractAnntagsFromConllLines($conll,3));
+ 
+	} // testTokenInto2AnnotationsHasJoinedAnntags() 
+
 /* class ConllAndJsonFactory has only 1 function
     function exportToConllAndJson($file_path_without_ext, $ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id)
 */

From 42aac8a460574941b36778ab22d9e038373c9ff5 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Fri, 27 Oct 2023 12:09:05 +0200
Subject: [PATCH 119/154] XML export output full tests

---
 engine/include/export/CorpusExporter.php      |   6 +-
 engine/include/export/XmlFactory.php          |  25 +
 engine/include/writers/CCclWriter.php         |  26 +-
 .../engine/include/writers/CCclWriterTest.php | 579 ++++++++++++++++++
 4 files changed, 624 insertions(+), 12 deletions(-)
 create mode 100644 engine/include/export/XmlFactory.php
 create mode 100644 phpunit/tests/engine/include/writers/CCclWriterTest.php

diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index 92fdf8fd..48397226 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -583,11 +583,7 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
 		(new ConllAndJsonFactory())->exportToConllAndJson($file_path_without_ext, $ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id);
 
         /* Wygeneruj xml i rel.xml */
-        CclFactory::setAnnotationsAndRelations($ccl, $annotations, $relations);
-        CclFactory::setAnnotationLemmas($ccl, $lemmas);
-        CclFactory::setAnnotationProperties($ccl, $attributes);
-		CclWriter::write($ccl, $output_folder . "/" . $ccl->getFileName() . ".xml", CclWriter::$CCL);
-		CclWriter::write($ccl, $output_folder . "/" . $ccl->getFileName() . ".rel.xml", CclWriter::$REL);
+        (new XmlFactory())->exportToXmlAndRelxml($file_path_without_ext,$ccl,$annotations,$relations,$lemmas,$attributes);
 
 		/* Eksport metadanych */
 		$report = DbReport::getReportById($report_id);
diff --git a/engine/include/export/XmlFactory.php b/engine/include/export/XmlFactory.php
new file mode 100644
index 00000000..9badd232
--- /dev/null
+++ b/engine/include/export/XmlFactory.php
@@ -0,0 +1,25 @@
+<?php
+
+class XmlFactory {
+
+    private function setDataToExport(&$ccl,&$annotations,&$relations,&$lemmas,&$attributes) {
+
+        CclFactory::setAnnotationsAndRelations($ccl, $annotations, $relations);
+        CclFactory::setAnnotationLemmas($ccl, $lemmas);
+        CclFactory::setAnnotationProperties($ccl, $attributes);
+ 
+        // returns modified $ccl by reference
+
+    } // 
+
+    public function exportToXmlAndRelxml($filePathWithoutExt,&$ccl,&$annotations,&$relations,&$lemmas,&$attributes) {
+
+        // set all other data to ccl structure
+        $this->setDataToExport($ccl,$annotations,$relations,$lemmas,$attributes); 
+        // export from $ccl to files
+        CclWriter::write($ccl, $filePathWithoutExt.".xml", CclWriter::$CCL);
+        CclWriter::write($ccl, $filePathWithoutExt.".rel.xml", CclWriter::$REL);
+
+    } // exportToXmlAndRelxml()
+
+} // XmlFormatExport class
diff --git a/engine/include/writers/CCclWriter.php b/engine/include/writers/CCclWriter.php
index 42329bf5..fc6823c2 100644
--- a/engine/include/writers/CCclWriter.php
+++ b/engine/include/writers/CCclWriter.php
@@ -11,8 +11,16 @@ class CclWriter{
 	public static $CCL    = 2;
 	public static $REL    = 3;
 	
+    private function writeTextToFile($fileName,$text) {
+
+        $handle = fopen($fileName, "w");
+        fwrite($handle, $text);
+        fclose($handle);
+
+    } // writeTextToFile()
 	
-	static function write($ccl, $filename, $mode){
+    private function makeXmlData($ccl,$mode) {
+
 		$xml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
 		$xml .= "<!DOCTYPE chunkList SYSTEM \"ccl.dtd\">\n";
 		
@@ -73,12 +81,16 @@ static function write($ccl, $filename, $mode){
 		}
 		if ($mode==self::$CCL || $mode==self::$CCLREL)
 			$xml .= "</chunkList>\n";		
-		$handle = fopen($filename, "w");
-		fwrite($handle, $xml);
-		fclose($handle);		
-	}
-	
-	
+
+        return $xml;
+
+    } // makeXmlData()
+ 
+   static function write($ccl, $filename, $mode){
+ 
+        self::writeTextToFile($filename,self::makeXmlData($ccl,$mode));
+
+	} // write()
 	
 }
 
diff --git a/phpunit/tests/engine/include/writers/CCclWriterTest.php b/phpunit/tests/engine/include/writers/CCclWriterTest.php
new file mode 100644
index 00000000..8fd413de
--- /dev/null
+++ b/phpunit/tests/engine/include/writers/CCclWriterTest.php
@@ -0,0 +1,579 @@
+<?php
+
+mb_internal_encoding("UTF-8");
+//use org\bovigo\vfs\vfsStream; // for vfsStream
+
+class CclWriterTest extends PHPUnit_Framework_TestCase {
+
+    private $virtualDir = null;
+    private $fileName = null;
+
+    private function xml2Dom($xml) {
+        // converts plain xml text to compressed DOM array without
+        // meaningless white chars. Will be used to compare xml export results.
+        $xml = preg_replace("/\n\s*/","",$xml); // all beutyfier go out
+        $dom = simplexml_load_string($xml,"SimpleXMLElement");
+        if($dom===false){ // string is not "dom"-able
+            return "String data are not in proper XML format !!!";
+        } else {
+            return $dom;
+        }
+    } // xml2Dom
+
+    private function assertXmls($expectedXml,$resultXml) {
+        // compare and assert two xml export results
+        $this->assertEquals($this->xml2Dom($expectedXml),
+                            $this->xml2Dom($resultXml));
+
+    } // assertXmls()
+
+    private function getXmlElement($xmlStr,$elementName){
+        // return xml export DOM element
+        return $this->xml2Dom($xmlStr)->{$elementName};
+    } // getXmlElement()
+    
+    private function getXmlAttribute($xmlElement,$attributeName){
+        // return attribute of SimpleXmlElement
+        return $xmlElement->attributes()->{$attributeName};
+    } // getXmlAttribute()
+
+    private function getXmlElementAttribute($xmlStr,$elementName,$attributeName) {
+        // return xml export DOM element atributte
+        $element = $this->getXmlElement($xmlStr,$elementName);
+        $attribute = $this->getXmlAttribute($element,$attributeName);
+        return $attribute;
+    } // getXmlElementAttribute()
+
+	private function getExpectedXmlProlog() {
+
+		return 
+        '<?xml version="1.0" encoding="UTF-8"?>'."\n".
+        '<!DOCTYPE chunkList SYSTEM "ccl.dtd">'."\n";
+
+	} // getExpectedXmlProlog()
+
+    private function getExpectedEmptyChunkList() {
+
+        return $this->getExpectedXmlProlog()
+                .'<chunkList>'."\n".'</chunkList>'."\n";
+
+    } // getExpectedEmptyChunkList()
+
+    private function getExpectedEmptyRelationList() {
+
+        return $this->getExpectedXmlProlog()
+                .'<relations>'."\n".'</relations>'."\n";
+
+    } // getExpectedEmptyRelationList()
+
+        // mocked data for simple tests
+
+    private function createMockLexeme($disamb,$base,$ctag){
+
+        $mockLexeme = $this->getMockBuilder(CclLexeme::class)
+            -> setMethods(['getDisamb','getBase','getCtag'])
+            -> getMock();
+        $mockLexeme->method('getDisamb')->will($this->returnValue($disamb));
+        $mockLexeme->method('getBase')->will($this->returnValue($base));
+        $mockLexeme->method('getCtag')->will($this->returnValue($ctag));
+        return $mockLexeme;
+
+    } // createMockLexeme()
+
+    private function createMockToken($orth,$ns=false,$prop=null,$lexemes=array(),$channels=array()){
+        // 'from', 'to' property aren't used in XML export
+        $mockToken = $this->getMockBuilder(CclToken::class)
+            -> setMethods(['getOrth','getChannels','getLexemes'])
+            -> getMock();
+        //$mockToken->prop = array($tokenPropKey=>$tokenPropValue);
+        $mockToken->prop = $prop; // should be array($key=>$val,...)
+        $mockToken->ns = $ns;
+        $mockToken->method('getOrth')->will($this->returnValue($orth));
+        $mockToken->method('getChannels')->will($this->returnValue($channels));
+        $mockToken->method('getLexemes')->will($this->returnValue($lexemes));
+        return $mockToken;
+
+    } // createMockToken()
+
+    private function createMockSentence($id,$tokens=array()) {
+
+        $mockSentence = $this->getMockBuilder(CclSentence::class)
+            -> setMethods(['getId','getTokens'])
+            -> getMock();
+        $mockSentence->method('getId')->will($this->returnValue($id));
+        $mockSentence->method('getTokens')->will($this->returnValue($tokens));
+        return $mockSentence;
+
+    } // createMockSentence()
+
+    private function createMockChunk($id,$type,$sentences=array()) {
+
+        $mockChunk = $this->getMockBuilder(CclChunk::class)
+            -> setMethods(['getId','getType','getSentences'])
+            -> getMock();
+        $mockChunk->method('getId')->will($this->returnValue($id));
+        $mockChunk->method('getType')->will($this->returnValue($type));
+        $mockChunk->method('getSentences')->will($this->returnValue($sentences));
+        return $mockChunk;
+
+    } // createMockChunk()
+
+    private function createMockCclRelation($name,$set,$fromSentence,$fromType,$fromChannel,$toSentence,$toType,$toChannel) {
+
+        $mockRelation = $this->getMockBuilder(CclRelation::class)
+            -> setMethods(array('getName','getSet','getFromSentence',
+                                'getFromType','getFromChannel',
+                                'getToSentence','getToType','getToChannel'))
+            -> getMock();
+        $mockRelation->method('getName')->will($this->returnValue($name));
+        $mockRelation->method('getSet')->will($this->returnValue($set));
+        $mockRelation->method('getFromSentence')->will($this->returnValue($fromSentence));
+        $mockRelation->method('getFromType')->will($this->returnValue($fromType));
+        $mockRelation->method('getFromChannel')->will($this->returnValue($fromChannel));
+        $mockRelation->method('getToSentence')->will($this->returnValue($toSentence));
+        $mockRelation->method('getToType')->will($this->returnValue($toType));
+        $mockRelation->method('getToChannel')->will($this->returnValue($toChannel));
+        return $mockRelation;
+
+    } // createMockCclRelation()
+
+    private function createMockCclDocument($chunks=array(),$relations=array()) {
+
+        $mockCclDocument = $this->getMockBuilder(CclDocument::class)
+            // wszystkie pozostałe metody są oryginalne
+            -> setMethods(array('getChunks','getRelations'))
+            -> getMock();
+        $mockCclDocument->method('getChunks')->will($this->returnValue($chunks));
+        $mockCclDocument->method('getRelations')->will($this->returnValue($relations));
+        return $mockCclDocument;
+
+    } // createMockCclDocument()
+
+    private function generateFullCclData() {
+
+		$mockChunk = $this->createMockChunk("1","TYP",array(
+			$this->createMockSentence("1",array(
+            	$this->createMockToken("To"),
+            	$this->createMockToken("jest"),
+            	$this->createMockToken("duże"),
+            	$this->createMockToken("okno"),
+            	$this->createMockToken(".",true)  // true sets ns in Token
+            	)),
+			$this->createMockSentence("2",array(
+            	$this->createMockToken("Bardzo"),
+            	$this->createMockToken("duże"),
+            	$this->createMockToken(".",true) // true sets ns in Token    
+            	))
+			));
+		$relations = array(
+				$this->createMockCclRelation(
+					'relName','relSet',
+					'fromSentence','fromType','fromChannel',
+					'toSentence','toType','toChannel') 
+			);
+        return $this->createMockCclDocument(
+							array($mockChunk),
+							$relations
+						);
+
+    } // generateFullCclData()
+
+    private function generateExpectedXMLForFullCclData() {
+
+        $expectedXml = $this->getExpectedXmlProlog()
+            .'<chunkList>'."\n"
+            .' <chunk id="1" type="TYP">'."\n"
+            .'  <sentence id="1">'."\n"
+            .'   <tok>'."\n"
+            .'    <orth>To</orth>'."\n"
+            .'   </tok>'."\n"
+            .'   <tok>'."\n"
+            .'    <orth>jest</orth>'."\n"
+            .'   </tok>'."\n"
+            .'   <tok>'."\n"
+            .'    <orth>duże</orth>'."\n"
+            .'   </tok>'."\n"
+            .'   <tok>'."\n"
+            .'    <orth>okno</orth>'."\n"
+            .'   </tok>'."\n"
+            .'   <tok>'."\n"
+            .'    <orth>.</orth>'."\n"
+            .'   </tok>'."\n"
+			.'   <ns/>'."\n"
+            .'  </sentence>'."\n"
+            .'  <sentence id="2">'."\n"
+            .'   <tok>'."\n"
+            .'    <orth>Bardzo</orth>'."\n"
+            .'   </tok>'."\n"
+            .'   <tok>'."\n"
+            .'    <orth>duże</orth>'."\n"
+            .'   </tok>'."\n"
+            .'   <tok>'."\n"
+            .'    <orth>.</orth>'."\n"
+            .'   </tok>'."\n"
+			.'   <ns/>'."\n"
+            .'  </sentence>'."\n"
+            .' </chunk>'."\n"
+			.' <relations>'."\n"
+			.'  <rel name="relname" set="relSet">'."\n"
+			.'    <from sent="fromSentence" chan="fromType">fromChannel</from>'."\n"
+			.'    <to sent="toSentence" chan="toType">toChannel</to>'."\n"
+			.'   </rel>'."\n"
+			.' </relations>'."\n"
+            .'</chunkList>'."\n";
+        ;
+        return $expectedXml;
+
+    } // generateExpectedXMLForFullCclData() 
+
+    protected function setUp() {
+
+        $this->virtualDir = org\bovigo\vfs\vfsStream::setup('root',null,[]);
+        $this->fileName = $this->virtualDir->url()."/test.txt";
+
+    } // setUp()
+
+    public function testOutputTextIsWrittenToFile() {
+
+        $text = "jnduie773nd n";
+
+        // private method need reflection to tests
+        $privateMethod = new ReflectionMethod('CclWriter','writeTextToFile');
+        $privateMethod->setAccessible(True);
+        $privateMethod->invoke(new CclWriter(),$this->fileName,$text);
+        $result = file_get_contents($this->fileName);
+        $this->assertEquals($text,$result);
+
+    } // testOutputTextIsWrittenToFile()
+
+    // static function write($ccl, $filename, $mode){...}
+ 
+    // private function makeXmlData($ccl,$mode) {...}
+
+    public function testCleanCclMakesOnlyXmlSkeleton() {
+
+        // empty $ccl data generates PHP Fatal Error
+        /*
+        $ccl = null;
+        $mode = CclWriter::$CCL;
+        CclWriter::write($ccl, $this->filename, $mode);
+        */
+
+        $ccl = new CclDocument();
+ 
+        // private method need reflection to tests
+        $privateMethod = new ReflectionMethod('CclWriter','makeXmlData');
+        $privateMethod->setAccessible(True);
+        
+        $mode = CclWriter::$CCL;
+        $expectedXml = $this->getExpectedEmptyChunkList();
+        $result = $privateMethod->invoke(new CclWriter(),$ccl,$mode);
+        $this->assertEquals($expectedXml,$result);
+
+        $mode = CclWriter::$CCLREL;
+        $result = $privateMethod->invoke(new CclWriter(),$ccl,$mode);
+        $this->assertEquals($expectedXml,$result);
+
+        $mode = CclWriter::$REL;
+        $expectedXml = $this->getExpectedEmptyRelationList();
+        $result = $privateMethod->invoke(new CclWriter(),$ccl,$mode);
+        $this->assertEquals($expectedXml,$result);
+
+    } // testCleanCclMakesOnlyXmlSkeleton()
+
+    public function testCclWithEmptyChunkMakesOnlyXmlSkeletonWithAttributes() {
+
+        $chunkId = '15';
+        $chunkType = 'ChType';
+        $mockChunk = $this->createMockChunk($chunkId,$chunkType);
+        $ccl = $this->createMockCclDocument(array($mockChunk));
+
+        // private method need reflection to tests
+        $privateMethod = new ReflectionMethod('CclWriter','makeXmlData');
+        $privateMethod->setAccessible(True);
+
+        $mode = CclWriter::$CCL;
+        /*
+        $expectedXml = $this->getExpectedXmlProlog()
+            .'<chunkList>'."\n"
+            .' <chunk id="'.$chunkId.'" type="'.$chunkType.'">'."\n"
+            .' </chunk>'."\n"
+            .'</chunkList>'."\n";
+        */
+        $expectedXml = $this->getExpectedXmlProlog().'<chunkList><chunk id="'.$chunkId.'" type="'.$chunkType.'"></chunk></chunkList>';
+        $result = $privateMethod->invoke(new CclWriter(),$ccl,$mode);
+        $this->assertXmls($expectedXml,$result);
+        $this->assertEquals($this->getXmlElement('<chunkList><chunk id="'.$chunkId.'" type="'.$chunkType.'"></chunk></chunkList>','chunk'),$this->getXmlElement($result,'chunk'));
+        $this->assertEquals($this->getXmlElement($expectedXml,'chunk'),$this->getXmlElement($result,'chunk'));
+        // element <chunk> is empty & has attributes properly set
+        $this->assertEquals('',$this->getXmlElement($result,'chunk'));
+        $this->assertEquals($chunkId,$this->getXmlElementAttribute($result,'chunk','id'));
+        $this->assertEquals($chunkType,$this->getXmlElementAttribute($result,'chunk','type'));
+
+        $mode = CclWriter::$CCLREL;
+        $result = $privateMethod->invoke(new CclWriter(),$ccl,$mode);
+        $this->assertXmls($expectedXml,$result);
+        // element <chunk> is empty & has attributes properly set
+        $this->assertEquals('',$this->getXmlElement($result,'chunk'));
+        $this->assertEquals($chunkId,$this->getXmlElementAttribute($result,'chunk','id'));
+        $this->assertEquals($chunkType,$this->getXmlElementAttribute($result,'chunk','type'));
+
+        $mode = CclWriter::$REL;
+        $expectedXml = $this->getExpectedEmptyRelationList();
+        $result = $privateMethod->invoke(new CclWriter(),$ccl,$mode);
+        $this->assertEquals($expectedXml,$result);
+
+    } // testCclWithEmptyChunkMakesOnlyXmlSkeletonWithAttributes()
+
+    public function testCclWithEmptySentenceMakesSentenceSkeletonWithId() {
+
+        $chunkId = '15';
+        $chunkType = 'ChType';
+		$sentenceId = '234';
+        $mockSentence = $this->createMockSentence($sentenceId);
+        $mockChunk = $this->createMockChunk($chunkId,$chunkType,array($mockSentence));
+        $ccl = $this->createMockCclDocument(array($mockChunk));
+
+        // private method need reflection to tests
+        $privateMethod = new ReflectionMethod('CclWriter','makeXmlData');
+        $privateMethod->setAccessible(True);
+
+        $mode = CclWriter::$CCL;
+        $result = $privateMethod->invoke(new CclWriter(),$ccl,$mode);
+        // element <chunk> has one sentence
+        $this->assertEquals(1,count($this->getXmlElement($result,'chunk')->children()));
+        $this->assertEquals('sentence',$this->getXmlElement($result,'chunk')->children()[0]->getName());
+        // element <sentence> is empty & has attributes properly set
+        $sentence = $this->getXmlElement($result,'chunk')->{'sentence'};
+        $this->assertEquals('',$sentence);
+        $this->assertEquals($sentenceId,$this->getXmlAttribute($sentence,'id'));
+
+        $mode = CclWriter::$CCLREL;
+        $result = $privateMethod->invoke(new CclWriter(),$ccl,$mode);
+        // element <chunk> has one sentence
+        $this->assertEquals(1,count($this->getXmlElement($result,'chunk')->children()));
+        $this->assertEquals('sentence',$this->getXmlElement($result,'chunk')->children()[0]->getName());
+        // element <sentence> is empty & has attributes properly set
+        $sentence = $this->getXmlElement($result,'chunk')->{'sentence'};
+        $this->assertEquals('',$sentence);
+        $this->assertEquals($sentenceId,$this->getXmlAttribute($sentence,'id'));
+
+        $mode = CclWriter::$REL;
+        $expectedXml = $this->getExpectedEmptyRelationList();
+        $result = $privateMethod->invoke(new CclWriter(),$ccl,$mode);
+        $this->assertEquals($expectedXml,$result);
+
+ 	} // testCclWithEmptySentenceMakesSentenceSkeletonWithId()
+
+    public function testCclInCclModeExportsAllTokensFields() {
+
+		$mode = CclWriter::$CCL;
+        $chunkId = '15';
+        $chunkType = 'ChType';
+        $sentenceId = '234';
+		$tokenOrth	= 'token orth';
+		$tokenPropKey  = 'token prop key';
+        $tokenPropValue  = 'token prop value';   
+        $tokenProp = array($tokenPropKey=>$tokenPropValue);
+		$lexDisamb = true;
+		$lexBase = 'base';
+		$lexCtag = 'ctag';
+		$channelType = 'chType';
+		$channelNumber = 'chNumber';
+		$tokenChannel = array($channelType=>$channelNumber);
+        $mockLexeme = $this->createMockLexeme($lexDisamb,$lexBase,$lexCtag);
+        $mockToken = $this->createMockToken($tokenOrth,false,$tokenProp,array($mockLexeme),$tokenChannel);
+        $mockSentence = $this->createMockSentence($sentenceId,array($mockToken));
+        $mockChunk = $this->createMockChunk($chunkId,$chunkType,array($mockSentence));
+        $ccl = $this->createMockCclDocument(array($mockChunk));
+        
+        // private method need reflection to tests
+        $privateMethod = new ReflectionMethod('CclWriter','makeXmlData');
+        $privateMethod->setAccessible(True);
+ 
+        $result = $privateMethod->invoke(new CclWriter(),$ccl,$mode);
+        // element <sentence> has one token element
+        //  and one ns selftag <ns/> if property ns inside token is set
+        $this->assertEquals(1,count($this->getXmlElement($result,'chunk')->{'sentence'}->children()));
+        $this->assertEquals('tok',$this->getXmlElement($result,'chunk')->{'sentence'}->children()[0]->getName());
+        // element <tok> has elements orth and array prop set
+        $tok = $this->getXmlElement($result,'chunk')->{'sentence'}->{'tok'};
+        $this->assertEquals('',$tok);
+		// orth <orth>token orth</orth>
+        $this->assertEquals($tokenOrth,$tok->{'orth'});
+		// prop <prop key="token prop key">token prop value</prop>
+        $prop = $tok->{'prop'};
+        $this->assertEquals($tokenPropKey,$this->getXmlAttribute($prop,'key'));
+        $this->assertEquals($tokenPropValue,$prop);
+		// lexeme <lex disamb="1"><base>base</base><ctag>ctag</ctag></lex>
+		$lexeme = $tok->{'lex'};
+		$this->assertEquals('',$lex);
+		$this->assertEquals('1',$this->getXmlAttribute($lexeme,'disamb'));
+		$this->assertEquals($lexBase,$lexeme->{'base'});
+		$this->assertEquals($lexCtag,$lexeme->{'ctag'});
+		// channel <ann chan="chType">chNumber</ann>
+		$this->assertEquals($channelType,$this->getXmlAttribute($tok->{'ann'},'chan'));
+		$this->assertEquals($channelNumber,$tok->{'ann'});
+
+        // if token->ns is true extra element after token is set
+        $mockToken->ns = true;
+        $result = $privateMethod->invoke(new CclWriter(),$ccl,$mode);
+        $this->assertEquals(2,count($this->getXmlElement($result,'chunk')->{'sentence'}->children()));
+        $this->assertEquals('ns',$this->getXmlElement($result,'chunk')->{'sentence'}->children()[1]->getName());
+
+	} // testCclInCclModeExportsAllTokensFields()
+
+    public function testCclInCclrelModeExportsAllTokensAndRelationsFields() {
+
+        $mode = CclWriter::$CCLREL;
+        $chunkId = '15';
+        $chunkType = 'ChType';
+        $sentenceId = '234';
+        $tokenOrth  = 'token orth';
+        $tokenPropKey  = 'token prop key';
+        $tokenPropValue  = 'token prop value';
+        $tokenProp = array($tokenPropKey=>$tokenPropValue);
+        $lexDisamb = true;
+        $lexBase = 'base';
+        $lexCtag = 'ctag';
+        $channelType = 'chType';
+        $channelNumber = 'chNumber';
+        $tokenChannel = array($channelType=>$channelNumber);
+        $relName = 'relation name';
+        $relSet = 'relation Set';
+        $relFromSentence = 'from sentence';
+        $relFromType = 'from type';
+        $relFromChannel = 'from channel';
+        $relToSentence = 'to sentence';
+        $relToType = 'to type';
+        $relToChannel = 'to channel';
+        $mockLexeme = $this->createMockLexeme($lexDisamb,$lexBase,$lexCtag);
+        $mockToken = $this->createMockToken($tokenOrth,false,$tokenProp,array($mockLexeme),$tokenChannel);
+        $mockSentence = $this->createMockSentence($sentenceId,array($mockToken));
+        $mockChunk = $this->createMockChunk($chunkId,$chunkType,array($mockSentence));
+        $mockRelation = $this->createMockCclRelation($relName,$relSet,$relFromSentence,$relFromType,$relFromChannel,$relToSentence,$relToType,$relToChannel);
+        $ccl = $this->createMockCclDocument(array($mockChunk),array($mockRelation));
+
+        // private method need reflection to tests
+        $privateMethod = new ReflectionMethod('CclWriter','makeXmlData');
+        $privateMethod->setAccessible(True);
+
+        $result = $privateMethod->invoke(new CclWriter(),$ccl,$mode);
+        // element <sentence> has one token element
+        //  and one ns selftag <ns/> if property ns inside token is set
+        $this->assertEquals(1,count($this->getXmlElement($result,'chunk')->{'sentence'}->children()));
+        $this->assertEquals('tok',$this->getXmlElement($result,'chunk')->{'sentence'}->children()[0]->getName());
+        // element <tok> has elements orth and array prop set
+        $tok = $this->getXmlElement($result,'chunk')->{'sentence'}->{'tok'};
+        $this->assertEquals('',$tok);
+        // orth <orth>token orth</orth>
+        $this->assertEquals($tokenOrth,$tok->{'orth'});
+        // prop <prop key="token prop key">token prop value</prop>
+        $prop = $tok->{'prop'};
+        $this->assertEquals($tokenPropKey,$this->getXmlAttribute($prop,'key'));
+        $this->assertEquals($tokenPropValue,$prop);
+        // lexeme <lex disamb="1"><base>base</base><ctag>ctag</ctag></lex>
+        $lexeme = $tok->{'lex'};
+        $this->assertEquals('',$lex);
+        $this->assertEquals('1',$this->getXmlAttribute($lexeme,'disamb'));
+        $this->assertEquals($lexBase,$lexeme->{'base'});
+        $this->assertEquals($lexCtag,$lexeme->{'ctag'});
+        // channel <ann chan="chType">chNumber</ann>
+        $this->assertEquals($channelType,$this->getXmlAttribute($tok->{'ann'},'chan'));
+        $this->assertEquals($channelNumber,$tok->{'ann'});
+        // relations data
+        // element <relations> has one rel element
+        $this->assertEquals(1,count($this->getXmlElement($result,'relations')));
+        // <rel> has two attributes and two children
+        $rel = $this->getXmlElement($result,'relations')->{'rel'};
+        $this->assertEquals($relName,$this->getXmlAttribute($rel,'name'));
+        $this->assertEquals($relSet,$this->getXmlAttribute($rel,'set'));
+        $this->assertEquals(2,count($rel->children()));
+        $this->assertEquals('from',$rel->children()[0]->getName());
+        $this->assertEquals('to',$rel->children()[1]->getName());
+        // <from> has 2 attributes and value
+        $from = $rel->{'from'};
+        $this->assertEquals($relFromSentence,$this->getXmlAttribute($from,'sent'));
+        $this->assertEquals($relFromType,$this->getXmlAttribute($from,'chan'));
+        $this->assertEquals($relFromChannel,$from);
+        // <to> has 2 attributes and value
+        $to = $rel->{'to'};
+        $this->assertEquals($relToSentence,$this->getXmlAttribute($to,'sent'));
+        $this->assertEquals($relToType,$this->getXmlAttribute($to,'chan'));
+        $this->assertEquals($relToChannel,$to);
+
+
+        // if token->ns is true extra element after token is set
+        $mockToken->ns = true;
+        $result = $privateMethod->invoke(new CclWriter(),$ccl,$mode);
+        $this->assertEquals(2,count($this->getXmlElement($result,'chunk')->{'sentence'}->children()));
+        $this->assertEquals('ns',$this->getXmlElement($result,'chunk')->{'sentence'}->children()[1]->getName());
+ 
+ 	} // testCclInCclrelModeExportsAllTokensAndRelationsFields() 
+
+    public function testCclInRelModeExportsAllRelationsFields() {
+
+        $mode = CclWriter::$REL;
+
+        $relName = 'relation name';
+        $relSet = 'relation Set';
+        $relFromSentence = 'from sentence';
+        $relFromType = 'from type';
+        $relFromChannel = 'from channel';
+        $relToSentence = 'to sentence';
+        $relToType = 'to type';
+        $relToChannel = 'to channel';
+        $mockRelation = $this->createMockCclRelation($relName,$relSet,$relFromSentence,$relFromType,$relFromChannel,$relToSentence,$relToType,$relToChannel);
+        $ccl = $this->createMockCclDocument(array(),array($mockRelation));
+
+        // private method need reflection to tests
+        $privateMethod = new ReflectionMethod('CclWriter','makeXmlData');
+        $privateMethod->setAccessible(True);
+
+        $result = $privateMethod->invoke(new CclWriter(),$ccl,$mode);
+		// <relations>
+		// <rel name="relation name" set="relation Set">
+		//   <from sent="from sentence" chan="from type">from channel</from>
+		//   <to sent="to sentence" chan="to type">to channel</to>
+		//  </rel>
+		// </relations>
+		// element <relations> has one rel element
+        $this->assertEquals(1,count($this->getXmlElement($result,'rel')));
+		// <rel> has two attributes and two children
+		$rel = $this->getXmlElement($result,'rel');
+		$this->assertEquals($relName,$this->getXmlAttribute($rel,'name'));
+		$this->assertEquals($relSet,$this->getXmlAttribute($rel,'set'));
+		$this->assertEquals(2,count($rel->children()));
+        $this->assertEquals('from',$rel->children()[0]->getName());
+		$this->assertEquals('to',$rel->children()[1]->getName());
+		// <from> has 2 attributes and value
+		$from = $rel->{'from'};
+		$this->assertEquals($relFromSentence,$this->getXmlAttribute($from,'sent'));
+		$this->assertEquals($relFromType,$this->getXmlAttribute($from,'chan'));
+		$this->assertEquals($relFromChannel,$from);
+        // <to> has 2 attributes and value
+        $to = $rel->{'to'};
+        $this->assertEquals($relToSentence,$this->getXmlAttribute($to,'sent'));
+        $this->assertEquals($relToType,$this->getXmlAttribute($to,'chan'));
+        $this->assertEquals($relToChannel,$to);
+ 
+	} // testCclInRelModeExportsAllRelationsFields()
+
+    public function testFullCclDataProperlyFormatsAsXml() {
+
+        $ccl = $this->generateFullCclData();
+
+        // private method need reflection to tests
+        $privateMethod = new ReflectionMethod('CclWriter','makeXmlData');
+        $privateMethod->setAccessible(True);
+
+        $mode = CclWriter::$CCLREL;  // for $CCLREL are both sections
+        $expectedXml = $this->generateExpectedXMLForFullCclData();
+        $result = $privateMethod->invoke(new CclWriter(),$ccl,$mode);
+        $this->assertEquals($expectedXml,$result);
+
+    } // testFullCclDataProperlyFormatsAsXml()
+
+} // CclWriterTest class
+
+?>

From b43b39f17eb17653a63707920a87618223e9682c Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Sat, 28 Oct 2023 18:21:45 +0200
Subject: [PATCH 120/154] more tests and drop unused code

---
 engine/include/export/CCclFactory.php         |   2 +-
 engine/include/structs/CclStruct.php          |   2 -
 .../engine/include/export/CclFactoryTest.php  |  40 +++-
 .../structs/CclStruct_CclDocumentTest.php     | 212 ++++++++++++++++++
 .../structs/CclStruct_CclTokenTest.php        |  72 ++++++
 5 files changed, 324 insertions(+), 4 deletions(-)

diff --git a/engine/include/export/CCclFactory.php b/engine/include/export/CCclFactory.php
index 130412b7..de59d5b4 100644
--- a/engine/include/export/CCclFactory.php
+++ b/engine/include/export/CCclFactory.php
@@ -115,7 +115,7 @@ function createFromReportAndTokens(&$report, &$tokens, &$tags){
 	}
 	
 
-	function setAnnotationLemmas(&$ccl, &$annotation_lemmas){
+	function setAnnotationLemmas(&$ccl, $annotation_lemmas){
 		if (empty($annotation_lemmas)){
 			return false;
 		}
diff --git a/engine/include/structs/CclStruct.php b/engine/include/structs/CclStruct.php
index 11d95472..ebf10ff3 100644
--- a/engine/include/structs/CclStruct.php
+++ b/engine/include/structs/CclStruct.php
@@ -97,7 +97,6 @@ function getRelations(){
 	}
 	
 	function setAnnotationLemma($annotation_lemma){
-		$type = $annotation_lemma['type'];
 
 		if ( !isset($this->char2token[$annotation_lemma['from']])){
 			$e = new CclError();
@@ -134,7 +133,6 @@ function setAnnotationLemma($annotation_lemma){
 	}
 
     function setAnnotationProperty($annotation_property){
-        $type = $annotation_property['type'];
 
         if ( !isset($this->char2token[$annotation_property['from']])){
             $e = new CclError();
diff --git a/phpunit/tests/engine/include/export/CclFactoryTest.php b/phpunit/tests/engine/include/export/CclFactoryTest.php
index 9cef01cc..ddb027a7 100644
--- a/phpunit/tests/engine/include/export/CclFactoryTest.php
+++ b/phpunit/tests/engine/include/export/CclFactoryTest.php
@@ -136,6 +136,44 @@ public function test_setAnnotationProperties_setPropTableInDocumentToken() {
 
     } // test_setAnnotationProperties_setPropTableInDocumentToken()
 
-} // class
+// function setAnnotationLemmas(&$ccl, &$annotation_lemmas)
+    
+    public function testEmptyLemmasCallsNoAction() {
+
+        $mockCcl = $this->getMockBuilder(CclDocument::class)->getMock();
+        // for empty $lemmas there are no internal call
+        $annotation_lemmas = array();
+        $mockCcl->expects($this->never())->method('setAnnotationLemma');
+        // result is returned in $ccl changes
+        (new CclFactory())->setAnnotationLemmas($mockCcl,$annotation_lemmas);
+
+    } // testEmptyLemmasCallsNoAction()     
+
+	public function testLemmaIsPassedToCclSetMethod() {
+
+		$mockCcl = $this->getMockBuilder(CclDocument::class)->getMock();
+        // $ccl->setAnnotationLemma should be call for each item from
+        // $lemmas array
+        $annotation_lemmas = array('element');
+        $mockCcl->expects($this->once())->method('setAnnotationLemma')->with('element');
+        (new CclFactory())->setAnnotationLemmas($mockCcl,$annotation_lemmas);		
+	} // testLemmaIsPassedToCclSetMethod()
+
+    public function testAddingLemmaToCclIsRepeatedForEachLemma() {
+
+        $mockCcl = $this->getMockBuilder(CclDocument::class)->getMock();
+        // $ccl->setAnnotationLemma should be call for each item from
+        // $lemmas array
+        $annotation_lemmas = array('raz','dwa','trzy');
+		//$mockCcl->expects($this->at(0))->method('setAnnotationLemma')->with('raz');
+		//$mockCcl->expects($this->at(1))->method('setAnnotationLemma')->with('dwa');
+		//$mockCcl->expects($this->at(2))->method('setAnnotationLemma')->with('trzy');
+		// zachowanie kolejności nie jest tu istotne
+        $mockCcl->expects($this->exactly(3))->method('setAnnotationLemma');
+        (new CclFactory())->setAnnotationLemmas($mockCcl,$annotation_lemmas);
+
+    } // testAddingLemmaToCclIsRepeatedForEachLemma()
+
+} // CclFactoryTest class
 
 ?>
diff --git a/phpunit/tests/engine/include/structs/CclStruct_CclDocumentTest.php b/phpunit/tests/engine/include/structs/CclStruct_CclDocumentTest.php
index f4a568d1..4206772c 100644
--- a/phpunit/tests/engine/include/structs/CclStruct_CclDocumentTest.php
+++ b/phpunit/tests/engine/include/structs/CclStruct_CclDocumentTest.php
@@ -88,6 +88,218 @@ public function test_setAnnotationProperty() {
 
     } // test_setAnnotationProperty_setInternalErrorOnEmptyArray()
 
+//  function setAnnotationLemma($annotation_lemma){...}
+
+    public function testAddLemmaWithNullParameterSetsError() {
+
+        $annotation_lemma = null;
+        $ccl = new CclDocument();
+        $ccl->setAnnotationLemma($annotation_lemma);
+        $this->assertEquals(1,count($ccl->errors)); // is sth in errors table
+        $this->assertInstanceOf('CclError',$ccl->errors[0]); // is this object
+        // verify message content
+        $expectedErrorMsg = array("Annotation out of range (annotation.from > document.char_count)");
+        $this->assertEquals($expectedErrorMsg,$ccl->errors[0]->comments);
+
+	} // testAddLemmaWithNullParameterSetsError()
+
+    public function testAddLemmaWithEmptyParameterSetsError() {
+
+        $annotation_lemma = array(); // should have 'from' and 'to' field
+        $ccl = new CclDocument();
+        $ccl->setAnnotationLemma($annotation_lemma);
+        $this->assertEquals(1,count($ccl->errors)); // is sth in errors table
+        $this->assertInstanceOf('CclError',$ccl->errors[0]); // is this object
+        // verify message content
+        $expectedErrorMsg = array("Annotation out of range (annotation.from > document.char_count)");
+        $this->assertEquals($expectedErrorMsg,$ccl->errors[0]->comments);
+
+    } // testAddLemmaWithEmptyParameterSetsError()
+
+    public function testLemmaWithoutFromSetsError() {
+
+        $from = 1; $to = 3;
+        $annotation_lemma = array('to'=>$to,'type'=>'TYP');
+
+        $mockToken = $this->getMockBuilder(CclToken::class)
+            -> setMethods(['setAnnotationLemma'])                                           -> getMock();
+        // $token->setAnnotationLemma will not be called in this case
+        $mockToken->expects($this->never())->method('setAnnotationLemma');
+        // this methods are originally, sets token range
+        $mockToken->setFrom($from); $mockToken->setTo($to);
+
+        $ccl = new CclDocument();
+        $ccl->addToken($mockToken);
+        $ccl->setAnnotationLemma($annotation_lemma);
+        $this->assertEquals(1,count($ccl->errors)); // is sth in errors table
+        $this->assertInstanceOf('CclError',$ccl->errors[0]); // is this object
+        // verify message content
+        $expectedErrorMsg = array("Annotation out of range (annotation.from > document.char_count)");
+        $this->assertEquals($expectedErrorMsg,$ccl->errors[0]->comments);
+
+	} // testLemmaWithoutFromSetsError()
+
+    public function testLemmaWithoutFromMatchesAnyTokenSetsError() {
+
+        $from = 1; $to = 3;
+        $annotation_lemma = array('from'=>$from-1,'to'=>$to,'type'=>'TYP');
+
+        $mockToken = $this->getMockBuilder(CclToken::class)
+            -> setMethods(['setAnnotationLemma'])
+            -> getMock();
+        // $token->setAnnotationLemma will not be called in this case
+        $mockToken->expects($this->never())->method('setAnnotationLemma');
+        // this methods are originally, sets token range
+        $mockToken->setFrom($from); $mockToken->setTo($to);
+
+        $ccl = new CclDocument();
+        $ccl->addToken($mockToken);
+        $ccl->setAnnotationLemma($annotation_lemma);
+        $this->assertEquals(1,count($ccl->errors)); // is sth in errors table
+        $this->assertInstanceOf('CclError',$ccl->errors[0]); // is this object
+        // verify message content
+        $expectedErrorMsg = array("Annotation out of range (annotation.from > document.char_count)");
+        $this->assertEquals($expectedErrorMsg,$ccl->errors[0]->comments);
+
+	} // testLemmaWithoutFromMatchesAnyTokenSetsError() 
+
+    public function testLemmaWithoutToSetsError() {
+
+        $from = 1; $to = 3;
+        $annotation_lemma = array('from'=>$from,'type'=>'TYP');
+
+        $mockToken = $this->getMockBuilder(CclToken::class)
+            -> setMethods(['setAnnotationLemma'])
+            -> getMock();
+        // $token->setAnnotationLemma will not be called in this case
+        $mockToken->expects($this->never())->method('setAnnotationLemma');
+        // this methods are originally, sets token range
+        $mockToken->setFrom($from); $mockToken->setTo($to);
+
+        $ccl = new CclDocument();
+        $ccl->addToken($mockToken);
+        $ccl->setAnnotationLemma($annotation_lemma);
+        $this->assertEquals(1,count($ccl->errors)); // is sth in errors table
+        $this->assertInstanceOf('CclError',$ccl->errors[0]); // is this object
+        // verify message content
+        $expectedErrorMsg = array("Annotation out of range (annotation.to > document.char_count)");
+        $this->assertEquals($expectedErrorMsg,$ccl->errors[0]->comments);
+
+	} // testLemmaWithoutToSetsError
+
+    public function testLemmaWithoutToMatchesAnyTokenSetsError() {
+
+        $from = 1; $to = 3;
+        $annotation_lemma = array('from'=>$from,'to'=>$to+1,'type'=>'TYP');
+
+        $mockToken = $this->getMockBuilder(CclToken::class)
+            -> setMethods(['setAnnotationLemma'])
+            -> getMock();
+        // $token->setAnnotationLemma will not be called in this case
+        $mockToken->expects($this->never())->method('setAnnotationLemma');
+        // this methods are originally, sets token range
+        $mockToken->setFrom($from); $mockToken->setTo($to);
+
+        $ccl = new CclDocument();
+        $ccl->addToken($mockToken);
+        $ccl->setAnnotationLemma($annotation_lemma);
+        $this->assertEquals(1,count($ccl->errors)); // is sth in errors table
+        $this->assertInstanceOf('CclError',$ccl->errors[0]); // is this object
+        // verify message content
+        $expectedErrorMsg = array("Annotation out of range (annotation.to > document.char_count)");
+        $this->assertEquals($expectedErrorMsg,$ccl->errors[0]->comments);
+
+    } // testLemmaWithoutToMatchesAnyTokenSetsError()
+
+    public function testLemmaWithoutTypeCallTokenSetLemmaMethodProperly() {
+
+        $from = 1; $to = 3;
+        $annotation_lemma = array('from'=>$from,'to'=>$to);
+
+        $mockToken = $this->getMockBuilder(CclToken::class)
+            -> setMethods(['setAnnotationLemma'])
+            -> getMock();
+        // $token->setAnnotationLemma will be called exactly once
+        $mockToken->expects($this->once())->will($this->returnValue(True))->method('setAnnotationLemma');
+        // this methods are originally, sets token range
+        $mockToken->setFrom($from); $mockToken->setTo($to);
+
+        $ccl = new CclDocument();
+        $ccl->addToken($mockToken);
+        $ccl->setAnnotationLemma($annotation_lemma);
+        $this->assertEquals(0,count($ccl->errors)); // no errors
+
+    } // testLemmaWithoutTypeCallTokenSetLemmaMethodProperly()
+
+    public function testSetAnnotationLemmaCallTokenSetLemmaMethod() {
+
+		$from = 1; $to = 3;
+		$annotation_lemma = array('from'=>$from,'to'=>$to,'type'=>'TYP');
+ 
+        $mockToken = $this->getMockBuilder(CclToken::class)
+            -> setMethods(['setAnnotationLemma'])
+            -> getMock();
+        // $token->setAnnotationLemma will be called exactly once
+        $mockToken->expects($this->once())->will($this->returnValue(True))->method('setAnnotationLemma');
+        // this methods are originally, sets token range
+        $mockToken->setFrom($from); $mockToken->setTo($to);
+
+        $ccl = new CclDocument();
+        $ccl->addToken($mockToken);
+		$ccl->setAnnotationLemma($annotation_lemma);
+        $this->assertEquals(0,count($ccl->errors)); // no errors 
+
+    } // testSetAnnotationLemmaCallTokenSetLemmaMethod()
+
+    public function testTokenSetLemmaReturnFalseSetsError() {
+
+        $from = 1; $to = 3;
+        $annotation_lemma = array('from'=>$from,'to'=>$to,'type'=>'TYP');
+
+        $mockToken = $this->getMockBuilder(CclToken::class)
+            -> setMethods(['setAnnotationLemma'])
+            -> getMock();
+        // $token->setAnnotationLemma will be called exactly once
+        $mockToken->expects($this->once())->will($this->returnValue(False))->method('setAnnotationLemma');
+        // this methods are originally, sets token range
+        $mockToken->setFrom($from); $mockToken->setTo($to);
+
+        $ccl = new CclDocument();
+        $ccl->addToken($mockToken);
+        $ccl->setAnnotationLemma($annotation_lemma);
+        $this->assertEquals(1,count($ccl->errors)); // is sth in errors table
+        $this->assertInstanceOf('CclError',$ccl->errors[0]); // is this object
+        // verify message content
+        $expectedErrorMsg = array("000 cannot set annotation lemma to specific token");
+        $this->assertEquals($expectedErrorMsg,$ccl->errors[0]->comments);
+
+    } // testTokenSetLemmaReturnFalseSetsError()
+
+    public function testLemmaOverMultiTokensCallSetLemmaForFirstOneOnly() {
+
+        $from = 1; $to = 5;
+        $annotation_lemma = array('from'=>$from,'to'=>$to,'type'=>'TYP');
+
+        $mockToken1 = $this->getMockBuilder(CclToken::class)
+            -> setMethods(['setAnnotationLemma'])
+            -> getMock();
+        // $token->setAnnotationLemma this should will be called exactly once
+        $mockToken1->expects($this->once())->will($this->returnValue(True))->method('setAnnotationLemma');
+        $mockToken1->setFrom($from); $mockToken1->setTo(3);
+        $mockToken2 = $this->getMockBuilder(CclToken::class)
+            -> setMethods(['setAnnotationLemma'])
+            -> getMock();
+        // $token->setAnnotationLemma this shouldn't never be called
+        $mockToken2->expects($this->never())->method('setAnnotationLemma');
+        $mockToken2->setFrom(4); $mockToken2->setTo($to);
+
+
+        $ccl = new CclDocument();
+        $ccl->addToken($mockToken1); $ccl->addToken($mockToken2);
+        $ccl->setAnnotationLemma($annotation_lemma);
+        $this->assertEquals(0,count($ccl->errors)); // no errors
+
+    } // testLemmaOverMultiTokensCallSetLemmaForFirstOneOnly()
 
 
 } // class
diff --git a/phpunit/tests/engine/include/structs/CclStruct_CclTokenTest.php b/phpunit/tests/engine/include/structs/CclStruct_CclTokenTest.php
index 9602aea1..41db4cc5 100644
--- a/phpunit/tests/engine/include/structs/CclStruct_CclTokenTest.php
+++ b/phpunit/tests/engine/include/structs/CclStruct_CclTokenTest.php
@@ -62,4 +62,76 @@ public function test_setAnnotationProperty() {
  
     }
 
+// function setAnnotationLemma($annotation_lemma){...}
+
+    public function testNullLemmaSetsPropForLemmaSuffixToNull() {
+
+        $annotation_lemma = null;
+
+        $token = new CclToken();
+        $result = $token->setAnnotationLemma($annotation_lemma);
+
+        $this->assertTrue($result); // always returns True
+        $expectedPropKey = ":lemma";
+        $this->assertNull($token->prop[$expectedPropKey]);
+
+    } // testEmptyLemmaSetsPropForLemmaSuffixToNull()
+
+    public function testEmptyLemmaSetsPropForLemmaSuffixToNull() {
+
+        $annotation_lemma = array();
+
+        $token = new CclToken();
+        $result = $token->setAnnotationLemma($annotation_lemma);
+
+        $this->assertTrue($result); // always returns True
+        $expectedPropKey = ":lemma";
+        $this->assertNull($token->prop[$expectedPropKey]);
+
+    } // testEmptyLemmaSetsPropForLemmaSuffixToNull()
+
+    public function testLemmaWithoutTypeSetsPropForLemmaSuffix() {
+
+        $lemmaText = "LEMMA";
+        $annotation_lemma = array( 'lemma'=>$lemmaText );
+
+        $token = new CclToken();
+        $result = $token->setAnnotationLemma($annotation_lemma);
+
+        $this->assertTrue($result); // always returns True
+        $expectedPropKey = ":lemma";
+        $expectedLemma = $lemmaText;
+        $this->assertEquals($expectedLemma,$token->prop[$expectedPropKey]);
+
+    } // testLemmaWithoutTypeSetsPropForLemmaSuffix()
+
+    public function testLemmaWithoutLemmaTextSetsPropWithLemmaToNull() {
+
+        $lemmaType = "TYP"; 
+        $annotation_lemma = array( 'type'=>$lemmaType );
+
+        $token = new CclToken();
+        $result = $token->setAnnotationLemma($annotation_lemma);
+
+        $this->assertTrue($result); // always returns True
+        $expectedPropKey = $lemmaType.":lemma";
+        $this->assertNull($token->prop[$expectedPropKey]);
+
+    } // testLemmaWithoutLemmaTextSetsPropWithLemmaToNull()
+
+    public function testSetAnnotationLemmaSetsPropWithLemmaSuffix() {
+
+        $lemmaType = "TYP"; $lemmaText = "LEMMA";
+        $annotation_lemma = array( 'type'=>$lemmaType, 'lemma'=>$lemmaText );
+        
+        $token = new CclToken();
+        $result = $token->setAnnotationLemma($annotation_lemma);
+
+        $this->assertTrue($result); // always returns True
+        $expectedPropKey = $lemmaType.":lemma";
+        $expectedLemma = $lemmaText;
+        $this->assertEquals($expectedLemma,$token->prop[$expectedPropKey]);
+
+    } // testSetAnnotationLemmaSetsPropWithLemmaSuffix()
+
 } // class

From bcdb0021fbb070f8de38acdf962ec847d1c5b276 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Tue, 31 Oct 2023 21:40:57 +0100
Subject: [PATCH 121/154] tests for token setAnnotation

---
 engine/include/structs/CclStruct.php          |  11 +-
 .../engine/include/export/CclFactoryTest.php  |  38 +++++
 .../structs/CclStruct_CclDocumentTest.php     |  37 +++++
 .../structs/CclStruct_CclTokenTest.php        | 150 ++++++++++++++++++
 4 files changed, 229 insertions(+), 7 deletions(-)

diff --git a/engine/include/structs/CclStruct.php b/engine/include/structs/CclStruct.php
index ebf10ff3..c90a50b4 100644
--- a/engine/include/structs/CclStruct.php
+++ b/engine/include/structs/CclStruct.php
@@ -563,7 +563,7 @@ function setAnnotationProperty($annotation_property){
         return true;
     }
 	
-	function setAnnotation($annotation,$parentChannels = null){
+	public function setAnnotation($annotation,$parentChannels = null){
 
 		$type = $annotation['type'];
 		if ($type=="sense"){
@@ -584,8 +584,6 @@ function setAnnotation($annotation,$parentChannels = null){
 			else if (!$this->prop || (count($this->prop) < count($annotation['value'])) ){
 				$this->prop = $annotation['value'];	
 			}			
-
-            $this->channels[$type] = $annotation['id'];
 		}
         else {
 			if (array_key_exists($type, $this->channels) && $this->channels[$type]!=0 ){
@@ -595,12 +593,11 @@ function setAnnotation($annotation,$parentChannels = null){
             if (is_array($parentChannels) && !array_key_exists($type, $parentChannels)  ){
 				return false;
 			}
-
-            $this->channels[$type] = $annotation['id'];
 		}
-		
+        // add to typed channel and return true if not exited earlier
+        $this->channels[$type] = $annotation['id'];
 		return true;
-	}
+	} // setAnnotation()
 	
 	function setContinuousAnnotation2($type,$parentChannels = null){
 
diff --git a/phpunit/tests/engine/include/export/CclFactoryTest.php b/phpunit/tests/engine/include/export/CclFactoryTest.php
index ddb027a7..299a9f1b 100644
--- a/phpunit/tests/engine/include/export/CclFactoryTest.php
+++ b/phpunit/tests/engine/include/export/CclFactoryTest.php
@@ -174,6 +174,44 @@ public function testAddingLemmaToCclIsRepeatedForEachLemma() {
 
     } // testAddingLemmaToCclIsRepeatedForEachLemma()
 
+// function setAnnotationsAndRelations(&$ccl, &$annotations, &$relations){...}
+
+    public function testCorrectDataForSetAnnotationAndRelationCallsCclMethods() {
+        $relations = array(
+            // continuous type==1
+            array( 'relation_type_id'=>1,'source_id'=>1,'target_id'=>2 ),
+            // normal
+            array( 'relation_type_id'=>2,'source_id'=>3,'target_id'=>4 )
+        );
+        $annotations = array( // ids includes all source and targets from above
+            array( 'id'=>1 ), array( 'id'=>2 ), array( 'id'=>3 ),
+            array( 'id'=>4 )
+        );
+
+        $mockCcl = $this->getMockBuilder(CclDocument::class)
+            -> setMethods(['setAnnotation', 'setContinuousAnnotation2',
+                            'addError','setRelation'])
+            -> getMock();
+        // call setAnnotation() 2 times for noncontinuous annotations
+        $mockCcl->expects($this->exactly(2))->method('setAnnotation'); 
+        $mockCcl->expects($this->at(0))->method('setAnnotation')->with($annotations[2]);
+        $mockCcl->expects($this->at(1))->method('setAnnotation')->with($annotations[3]);
+        // call setContinuousAnnotation2() once for continuous annotations pair
+        $mockCcl->expects($this->once())->method('setContinuousAnnotation2')->with($annotations[0],$annotations[1]);
+		// call setRelation() once for noncontinuous relation only
+		//  parametres are: source and target annotations record
+        $mockCcl->expects($this->once())->method('setRelation')->with($annotations[2],$annotations[3],$relations[1]);
+        // no error set is called
+        $mockCcl->expects($this->never())->method('addError');
+
+        $result = (new CclFactory())->setAnnotationsAndRelations($mockCcl,$annotations,$relations);
+
+        // returns true
+        $this->assertTrue($result); 
+
+    } // testCorrectDataForSetAnnotationAndRelationCallsCclMethods()
+
+
 } // CclFactoryTest class
 
 ?>
diff --git a/phpunit/tests/engine/include/structs/CclStruct_CclDocumentTest.php b/phpunit/tests/engine/include/structs/CclStruct_CclDocumentTest.php
index 4206772c..421f81e0 100644
--- a/phpunit/tests/engine/include/structs/CclStruct_CclDocumentTest.php
+++ b/phpunit/tests/engine/include/structs/CclStruct_CclDocumentTest.php
@@ -301,5 +301,42 @@ public function testLemmaOverMultiTokensCallSetLemmaForFirstOneOnly() {
 
     } // testLemmaOverMultiTokensCallSetLemmaForFirstOneOnly()
 
+// function setAnnotation($annotation)
+
+    public function testSetannotationForProperDataCallsTokensSetannotation() {
+
+        $from = 1; $to = 3;
+		$annotation = array( 'type'=>"TYP", 'from'=>1, 'to'=>3, 'value'=>'VALUE', 'name'=>'NAME' );
+
+        $mockToken = $this->getMockBuilder(CclToken::class)
+            -> setMethods(['setAnnotation'])
+            -> getMock();
+        // $token->setAnnotation will be called exactly once returns True
+        $mockToken->expects($this->once())->will($this->returnValue(True))->method('setAnnotation');
+        // this methods are originally, sets token range
+        $mockToken->setFrom($from); $mockToken->setTo($to);
+		$mockSentence = $this->getMockBuilder(CclSentence::class)
+            -> setMethods(['incChannel','fillChannel'])
+            -> getMock();
+        // incChannel() should be called once on argument $annotation['type']
+        $mockSentence->expects($this->once())->method('incChannel')->with($annotation['type']);
+        // fillChannel() should be called once on argument $annotation['type']
+        $mockSentence->expects($this->once())->method('fillChannel')->with($annotation['type']);
+		$mockSentence->channels = array();
+		$mockDocument = $this->getMockBuilder(CclDocument::class)
+            -> setMethods(['getSentenceByToken'])
+            -> getMock();
+        $mockDocument->expects($this->exactly(2))->will($this->returnValue($mockSentence))->method('getSentenceByToken');
+        $mockDocument->addToken($mockToken);
+
+        $expectedTokenProp = array(
+            "sense:".$annotation["name"]=>$annotation['value']
+        );
+        $mockDocument->setAnnotation($annotation);
+        $this->assertEquals(0,count($ccl->errors)); // no errors
+        // annotation.value is direct set to prop table in token
+        $this->assertEquals($expectedTokenProp,$mockToken->prop);
+
+    } // testSetannotationForProperDataCallsTokensSetannotation()
 
 } // class
diff --git a/phpunit/tests/engine/include/structs/CclStruct_CclTokenTest.php b/phpunit/tests/engine/include/structs/CclStruct_CclTokenTest.php
index 41db4cc5..586c58a0 100644
--- a/phpunit/tests/engine/include/structs/CclStruct_CclTokenTest.php
+++ b/phpunit/tests/engine/include/structs/CclStruct_CclTokenTest.php
@@ -134,4 +134,154 @@ public function testSetAnnotationLemmaSetsPropWithLemmaSuffix() {
 
     } // testSetAnnotationLemmaSetsPropWithLemmaSuffix()
 
+// function setAnnotation($annotation,$parentChannels = null)
+
+    public function testSetannotationWithoutTypeFieldWorksAsNonSense() {
+
+        $id=10;
+        $annotation = array( 'id'=>$id, 'value'=>array(1,2,3));
+        $parentChannels = null;
+
+        $token = new CclToken();
+        $result = $token->setAnnotation($annotation,$parentChannels);
+        // should return True
+        $this->assertTrue($result);
+        // in tabel token.channels key "" should be used if type not exist
+        $expectedTypeChannel = $id; 
+        $this->assertEquals($expectedTypeChannel,$token->channels[""]);
+        // for other types than 'sense' there are not prop attribute
+        $this->assertNull($token->prop);
+
+    } // testSetannotationWithoutTypeFieldWorksAsNonSense()
+
+    public function testSetannotationIfChannelForTypeExistsPreserveExistingAndReturnsFalse() {
+
+        $type = 'TYP'; $id=10; $existingIdForChannel = 17;
+        $annotation = array('type'=>$type, 'id'=>$id, 'value'=>array(1,2,3));
+        $parentChannels = null;
+
+        $token = new CclToken();
+		$token->channels[$type] = $existingIdForChannel;
+        $result = $token->setAnnotation($annotation,$parentChannels);
+        // should return False in this case
+        $this->assertFalse($result);
+        // in tabel token.channels should be [$type]=>$annotation.id
+        $expectedTypeChannel = $existingIdForChannel; // preserve existing
+        $this->assertEquals($expectedTypeChannel,$token->channels[$type]);
+        // for other types than 'sense' there are not prop attribute
+        $this->assertNull($token->prop);
+
+    } // testSetannotationIfChannelForTypeExistsPreserveExistingAndReturnsFalse() 
+
+    public function testParentChannelsWithoutTypeKeyBlocksAdding() {
+
+        $type = 'TYP'; $id=10;
+        $annotation = array('type'=>$type, 'id'=>$id, 'value'=>array(1,2,3));
+        $parentChannels = array( );
+
+        $token = new CclToken();
+        $result = $token->setAnnotation($annotation,$parentChannels);
+        // should return False if parent channels for type doesn't exists
+        $this->assertFalse($result);
+        // table token.channels remains empty
+        $this->assertEquals(array(),$token->channels);
+        // for other types than 'sense' there are not prop attribute
+        $this->assertNull($token->prop);
+
+    } // testParentChannelsWithoutTypeKeyBlocksAdding()
+
+    public function testParentChannelsWithTypeKeyAddsAnnotationLocally() {
+
+        $type = 'TYP'; $id=10;
+        $annotation = array('type'=>$type, 'id'=>$id, 'value'=>array(1,2,3));
+        $parentChannels = array( $type=>0 );
+
+        $token = new CclToken();
+        $result = $token->setAnnotation($annotation,$parentChannels);
+        // should return True if add locally
+        $this->assertTrue($result);
+        // in tabel token.channels should be [$type]=>$annotation.id
+        $expectedTypeChannel = $id;
+        $this->assertEquals($expectedTypeChannel,$token->channels[$type]);
+        // for other types than 'sense' there are not prop attribute
+        $this->assertNull($token->prop);
+
+    } // testParentChannelsWithTypeKeyAddsAnnotationLocally()
+
+    public function testSenseTypeWhenExistsValueWithSameCountReturnsFalse() {
+
+        $type = 'sense'; $id=10;
+        $annotation = array('type'=>$type, 'id'=>$id, 'value'=>array(1,2,3));
+        $parentChannels = null;
+		$existingProp = array(1,1,1); // 3 times as in 'value'
+
+        $token = new CclToken();
+		$token->prop = $existingProp;
+        $result = $token->setAnnotation($annotation,$parentChannels);
+        // should returs False for this case
+        $this->assertFalse($result);
+        // table token.channels remains empty
+        $this->assertEquals(array(),$token->channels);
+        // token.prop remains as was
+        $this->assertEquals($existingProp,$token->prop);
+
+    } // testSenseTypeWhenExistsValueWithSameCountReturnsFalse() 
+
+    public function testSenseTypeWhenExistsValueWithLessCountReplaceProp() {
+
+        $type = 'sense'; $id=10;
+        $annotation = array('type'=>$type, 'id'=>$id, 'value'=>array(1,2,3));
+        $parentChannels = null;
+		$existingProp = array(1,1); // 2 times less as in 'value'
+
+        $token = new CclToken();
+		$token->prop = $existingProp;
+        $result = $token->setAnnotation($annotation,$parentChannels);
+        // should return True
+        $this->assertTrue($result);
+        // in tabel token.channels should be [$type]=>$annotation.id
+        $expectedTypeChannel = $id;
+        $this->assertEquals($expectedTypeChannel,$token->channels[$type]);
+        // for 'sense' type prop is set to value
+        $this->assertEquals($annotation['value'],$token->prop);
+
+    } // testSenseTypeWhenExistsValueWithLessCountReplaceProp()
+
+
+    public function testSetannotationWithFullDataSetsChannels() {
+
+        $type = 'TYP'; $id=10;
+        $annotation = array('type'=>$type, 'id'=>$id, 'value'=>array(1,2,3));
+        $parentChannels = null;
+
+        $token = new CclToken();
+        $result = $token->setAnnotation($annotation,$parentChannels);
+        // should return True
+        $this->assertTrue($result);
+        // in tabel token.channels should be [$type]=>$annotation.id 
+        $expectedTypeChannel = $id;
+        $this->assertEquals($expectedTypeChannel,$token->channels[$type]);
+        // for other types than 'sense' there are not prop attribute
+        $this->assertNull($token->prop);
+
+    } // testSetannotationWithFullDataSetsChannels()
+
+    public function testSetannotationWithSenseTypeSetsPropTable() {
+
+        $type = 'sense'; $id=10;
+        $annotation = array('type'=>$type, 'id'=>$id, 'value'=>array(1,2,3));
+        $parentChannels = null;
+
+        $token = new CclToken();
+        $result = $token->setAnnotation($annotation,$parentChannels);
+        // should return True
+        $this->assertTrue($result);
+        // in tabel token.channels should be [$type]=>$annotation.id
+        $expectedTypeChannel = $id;
+        $this->assertEquals($expectedTypeChannel,$token->channels[$type]);
+        // for 'sense' type prop is set to value
+        $this->assertEquals($annotation['value'],$token->prop);
+
+    } // testSetannotationWithSenseTypeSetsPropTable()
+
 } // class

From 723adf2499bab4087493c0087a7a3e75ba2b9bb5 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Wed, 8 Nov 2023 20:10:12 +0100
Subject: [PATCH 122/154] tests for .txt file generation

---
 engine/include/export/CorpusExporter.php      |  38 ++++-
 .../export/CorpusExporter_part10_Test.php     | 135 ++++++++++++++++++
 2 files changed, 166 insertions(+), 7 deletions(-)
 create mode 100644 phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php

diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index 48397226..ed49afd4 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -9,7 +9,7 @@
  *
  */
 class CorpusExporter{
-	private $export_errors = array();
+	protected $export_errors = array();
 
     /**
      * Returns array given as param, without all items with value null
@@ -355,7 +355,7 @@ private function makeAssocArray($arr, $key, $disamb_only=false){
         return $ret;
     }
 
-	private function getReportTagsByTokens($report_id, $tokens_ids, $disamb_only=true, $tagging='tagger'){
+	protected function getReportTagsByTokens($report_id, $tokens_ids, $disamb_only=true, $tagging='tagger'){
 		$tags = array();
         $tags_by_tokens = array();
 
@@ -447,6 +447,30 @@ private function getReportTagsByTokens($report_id, $tokens_ids, $disamb_only=tru
 		return $tags_by_tokens;
 	}
 
+    protected function getFlagsByReportId($report_id) {
+
+        return DbReportFlag::getReportFlags($report_id);
+
+    } // getFlagsByReportId()
+
+    protected function getTokenByReportId($report_id){
+        
+        return DbToken::getTokenByReportId($report_id, null, true);
+
+    } // getTokenByReportId()
+
+    protected function getReportById($report_id){
+
+        return DbReport::getReportById($report_id);
+
+    } // getReportById()
+
+    protected function getReportExtById($report_id){
+
+        return DbReport::getReportExtById($report_id);
+
+    } // getReportExtById()
+
 	/**
 	 * Eksport dokumentu o wskazanym identyfikatorze
 	 * @param $report_id Identyfikator dokumentu do eksportu
@@ -456,7 +480,7 @@ private function getReportTagsByTokens($report_id, $tokens_ids, $disamb_only=tru
 	 * @param $tagging_method String tagging method from ['tagger', 'final', 'final_or_tagger', 'user:{id}']
 	 */
 	protected function export_document($report_id, $extractors, $disamb_only, &$extractor_stats, &$lists, $output_folder, $subcorpora, $tagging_method){
-		$flags = DbReportFlag::getReportFlags($report_id);
+		$flags = $this->getFlagsByReportId($report_id);
 		$elements = array("annotations"=>array(), "relations"=>array(), "lemmas"=>array(), "attributes"=>array());
 
 		// Wykonaj extraktor w zależności od ustalonej flagi
@@ -490,12 +514,12 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
 			}
 		}
 
-		$tokens = DbToken::getTokenByReportId($report_id, null, true);
+		$tokens = $this->getTokenByReportId($report_id);
 		$tokens_ids = array_column($tokens, 'token_id');
 
 		$tags_by_tokens = $this->getReportTagsByTokens($report_id, $tokens_ids, $disamb_only, $tagging_method);
 
-		$report = DbReport::getReportById($report_id);
+		$report = $this->getReportById($report_id);
 		try{
 			$ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
 		}
@@ -586,8 +610,8 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
         (new XmlFactory())->exportToXmlAndRelxml($file_path_without_ext,$ccl,$annotations,$relations,$lemmas,$attributes);
 
 		/* Eksport metadanych */
-		$report = DbReport::getReportById($report_id);
-		$ext = DbReport::getReportExtById($report_id);
+		$report = $this->getReportById($report_id);
+		$ext = $this->getReportExtById($report_id);
 
 		$basic = array("id", "date", "title", "source", "author", "tokenization", "subcorpus");
 		$lines = array();
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
new file mode 100644
index 00000000..65fdcbd0
--- /dev/null
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
@@ -0,0 +1,135 @@
+<?php
+
+use org\bovigo\vfs\vfsStream; // for vfsStream
+mb_internal_encoding("UTF-8");
+
+class CorpusExporter_part10_Test extends PHPUnit_Framework_TestCase
+{
+    private $virtualDir = null;
+
+    protected function setUp() {
+
+        $this->virtualDir = vfsStream::setup('root',null,[]);
+
+    } // setUp()
+
+//    protected function export_document($report_id, $extractors, $disamb_only, &$extractor_stats, &$lists, $output_folder, $subcorpora, $tagging_method){
+ 
+    public function testExport_documentExportsDocumentContentToTxtFile()
+    {
+        // export_document() dumb parameters
+        $report_id = 1;
+        $extractors = array();
+        $disamb_only = true;
+        $extractor_stats = array();
+        $lists = array();
+        $output_folder = $this->virtualDir->url();
+        $subcorpora = '';
+        $tagging_method = 'tagger';
+
+        // results returned by mocking methods
+        $reportContent = "tekst dokumentu raportu";
+        //$reportContent = str_repeat('s',300000);
+        $reportFlags = array('flagnamelowercase'=>array(-1)); 
+        $reportTokens = array();
+        $reportTags = array();
+        $report = array( 'id'=>$report_id, 'content'=>$reportContent );
+        $reportExt = null;
+
+        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
+            -> disableArgumentCloning()
+            -> setMethods(array('getFlagsByReportId','getTokenByReportId',
+                            'getReportTagsByTokens','getReportById',
+                            'getReportExtById')) 
+            -> getMock();
+        $mockCorpusExporter -> method('getFlagsByReportId')
+            -> will($this->returnValue($reportFlags));
+        $mockCorpusExporter -> method('getTokenByReportId')
+            -> will($this->returnValue($reportTokens));
+        $mockCorpusExporter -> method('getReportTagsByTokens')
+            -> will($this->returnValue($reportTags));
+        $mockCorpusExporter -> method('getReportById')
+            -> will($this->returnValue($report));
+        $mockCorpusExporter -> method('getReportExtById')
+            -> will($this->returnValue($reportExt));
+ 
+        // reflection for acces to private elements
+        $protectedMethod = new ReflectionMethod($mockCorpusExporter,'export_document');
+        $protectedMethod->setAccessible(True);
+        $export_errorsPrivateProperty = new ReflectionProperty($mockCorpusExporter,'export_errors');
+        $export_errorsPrivateProperty->setAccessible(True); 
+
+        // tested call
+        $protectedMethod->invokeArgs($mockCorpusExporter,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
+
+        // no errors check
+        $expectedErrors = array();
+        $this->assertEquals($expectedErrors,
+            $export_errorsPrivateProperty->getValue($mockCorpusExporter)
+            );
+        //check TxtFile
+        $expectedBaseFileName = $output_folder.'/'.str_pad($report_id,8,'0',STR_PAD_LEFT);
+        $expectedTxtContent = $reportContent;
+        $resultTxtFile = file_get_contents($expectedBaseFileName.'.txt');
+        $this->assertEquals($expectedTxtContent,$resultTxtFile);
+
+    } // testExport_documentExportsDocumentContentToTxtFile()
+
+    public function testExport_ErrorneusContentSetInternalError()
+    {
+        // export_document() dumb parameters
+        $report_id = 1;
+        $extractors = array();
+        $disamb_only = true;
+        $extractor_stats = array();
+        $lists = array();
+        $output_folder = $this->virtualDir->url();
+        $subcorpora = '';
+        $tagging_method = 'tagger';
+
+        // results returned by mocking methods
+        $reportContent = str_repeat('s',300000); // content too long
+        $reportFlags = array('flagnamelowercase'=>array(-1));
+        $reportTokens = array();
+        $reportTags = array();
+        $report = array( 'id'=>$report_id, 'content'=>$reportContent );
+        $reportExt = null;
+
+        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
+            -> disableArgumentCloning()
+            -> setMethods(array('getFlagsByReportId','getTokenByReportId',
+                            'getReportTagsByTokens','getReportById',
+                            'getReportExtById'))
+            -> getMock();
+        $mockCorpusExporter -> method('getFlagsByReportId')
+            -> will($this->returnValue($reportFlags));
+        $mockCorpusExporter -> method('getTokenByReportId')
+            -> will($this->returnValue($reportTokens));
+        $mockCorpusExporter -> method('getReportTagsByTokens')
+            -> will($this->returnValue($reportTags));
+        $mockCorpusExporter -> method('getReportById')
+            -> will($this->returnValue($report));
+        $mockCorpusExporter -> method('getReportExtById')
+            -> will($this->returnValue($reportExt));
+
+        // reflection for acces to private elements
+        $protectedMethod = new ReflectionMethod($mockCorpusExporter,'export_document');
+        $protectedMethod->setAccessible(True);
+        $export_errorsPrivateProperty = new ReflectionProperty($mockCorpusExporter,'export_errors');
+        $export_errorsPrivateProperty->setAccessible(True);
+
+        // tested call
+        $protectedMethod->invokeArgs($mockCorpusExporter,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
+
+        // internal errors table
+		$internalErrorsTable = $export_errorsPrivateProperty->getValue($mockCorpusExporter);
+		$expectedErrorsCount = 1;
+		$this->assertEquals($expectedErrorsCount,count($internalErrorsTable)); 
+        $expectedErrorsKey = "Text too long to display (over 50k characters)";
+        $this->assertEquals(1,$internalErrorsTable[2]['details']['error'][$expectedErrorsKey]);
+
+    } // testExport_ErrorneusContentSetInternalError()
+
+} // CorpusExporter_part10_Test class
+
+?>

From 614d2ed5b67e610ff78699ee3b9852ba1a4e1a62 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Mon, 13 Nov 2023 21:55:39 +0100
Subject: [PATCH 123/154] extract method for .txt file generation

---
 engine/include/export/CorpusExporter.php      |  39 ++++---
 .../export/CorpusExporter_part10_Test.php     | 103 +++++++++---------
 2 files changed, 73 insertions(+), 69 deletions(-)

diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index ed49afd4..09fda393 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -471,6 +471,27 @@ protected function getReportExtById($report_id){
 
     } // getReportExtById()
 
+    protected function exportReportContent($report,$file_path_without_ext) {
+
+        try {
+            $html = ReportContent::getHtmlStr($report);
+        } catch(Exception $ex){
+            $errorMsg = "Problem z eksportem zawartości HTML dokumentu";
+            $exceptionMsg = $ex->getMessage();
+            $error_params = array(
+                'message' => $errorMsg,
+                'error' => $exceptionMsg
+            );
+            $this->log_error(__FILE__, __LINE__, $report_id,
+                $errorMsg.": ".$exceptionMsg, 8, $error_params);
+            return False;
+        } // catch()
+        $content = $html->getContent();
+        file_put_contents($file_path_without_ext .".txt", $content);
+        return True;
+
+    } // exportReportContent()
+
 	/**
 	 * Eksport dokumentu o wskazanym identyfikatorze
 	 * @param $report_id Identyfikator dokumentu do eksportu
@@ -643,23 +664,9 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
 				}
 			}
 		}
-        try {
-            $html = ReportContent::getHtmlStr($report);
-        } catch(Exception $ex){
-            $errorMsg = "Problem z eksportem zawartości HTML dokumentu";
-            $exceptionMsg = $ex->getMessage();
-            $error_params = array(
-                'message' => $errorMsg,
-                'error' => $exceptionMsg
-            );
-            $this->log_error(__FILE__, __LINE__, $report_id, 
-                $errorMsg.": ".$exceptionMsg, 8, $error_params);
-            return;
-        } // catch()
-        $content = $html->getContent();
-		file_put_contents($output_folder . "/" . $ccl->getFileName() . ".txt", $content);
+        $this->exportReportContent($report,$file_path_without_ext);
 
-	}
+	} // export_document()
 
 	/**
 	 * Wykonuje eksport korpusu zgodnie z określonymi parametrami (selektory, ekstraktory i indeksy).
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
index 65fdcbd0..b82eaaf2 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
@@ -15,7 +15,7 @@ protected function setUp() {
 
 //    protected function export_document($report_id, $extractors, $disamb_only, &$extractor_stats, &$lists, $output_folder, $subcorpora, $tagging_method){
  
-    public function testExport_documentExportsDocumentContentToTxtFile()
+    public function testExport_documentCallsExportreportcontentMethod ()
     {
         // export_document() dumb parameters
         $report_id = 1;
@@ -29,7 +29,6 @@ public function testExport_documentExportsDocumentContentToTxtFile()
 
         // results returned by mocking methods
         $reportContent = "tekst dokumentu raportu";
-        //$reportContent = str_repeat('s',300000);
         $reportFlags = array('flagnamelowercase'=>array(-1)); 
         $reportTokens = array();
         $reportTags = array();
@@ -40,7 +39,7 @@ public function testExport_documentExportsDocumentContentToTxtFile()
             -> disableArgumentCloning()
             -> setMethods(array('getFlagsByReportId','getTokenByReportId',
                             'getReportTagsByTokens','getReportById',
-                            'getReportExtById')) 
+                            'getReportExtById','exportReportContent')) 
             -> getMock();
         $mockCorpusExporter -> method('getFlagsByReportId')
             -> will($this->returnValue($reportFlags));
@@ -52,83 +51,81 @@ public function testExport_documentExportsDocumentContentToTxtFile()
             -> will($this->returnValue($report));
         $mockCorpusExporter -> method('getReportExtById')
             -> will($this->returnValue($reportExt));
+
+        // method exportReportContent called exactly once with proper args:
+        $expectedReportArg = $report;
+        $expectedReportArg['subcorpus'] = ''; // this one is added
+        $expectedBaseFileName = $output_folder.'/'.str_pad($report_id,8,'0',STR_PAD_LEFT);
+        $mockCorpusExporter -> expects($this->once())
+            ->method('exportReportContent')
+            ->with($expectedReportArg,$expectedBaseFileName);
  
         // reflection for acces to private elements
         $protectedMethod = new ReflectionMethod($mockCorpusExporter,'export_document');
         $protectedMethod->setAccessible(True);
-        $export_errorsPrivateProperty = new ReflectionProperty($mockCorpusExporter,'export_errors');
-        $export_errorsPrivateProperty->setAccessible(True); 
 
         // tested call
         $protectedMethod->invokeArgs($mockCorpusExporter,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
 
-        // no errors check
+    } // testExport_documentCallsExportreportcontentMethod()
+
+// protected function exportReportContent($report,$file_path_without_ext){...}
+
+    public function testExportreportcontentsExportsDocumentContentToTxtFile() {
+
+		$report_id = 1;
+		$reportContent = "tekst dokumentu raportu";
+		$file_path_without_ext = $this->virtualDir->url().'/testname'; 
+		$report = array( 'id'=>$report_id, 'content'=>$reportContent );
+
+        // reflection for acces to private elements
+        $protectedMethod = new ReflectionMethod('CorpusExporter','exportReportContent');
+        $protectedMethod->setAccessible(True);
+        $ce = new CorpusExporter();
+        $export_errorsPrivateProperty = new ReflectionProperty($ce,'export_errors');
+        $export_errorsPrivateProperty->setAccessible(True);
+
+		$result=$protectedMethod->invokeArgs($ce,array($report,$file_path_without_ext));
+
+        // returns True
+        $this->assertTrue($result);
+        // no errors collected
         $expectedErrors = array();
         $this->assertEquals($expectedErrors,
-            $export_errorsPrivateProperty->getValue($mockCorpusExporter)
+            $export_errorsPrivateProperty->getValue($ce)
             );
         //check TxtFile
-        $expectedBaseFileName = $output_folder.'/'.str_pad($report_id,8,'0',STR_PAD_LEFT);
         $expectedTxtContent = $reportContent;
-        $resultTxtFile = file_get_contents($expectedBaseFileName.'.txt');
+        $resultTxtFile = file_get_contents($file_path_without_ext.'.txt');
         $this->assertEquals($expectedTxtContent,$resultTxtFile);
 
-    } // testExport_documentExportsDocumentContentToTxtFile()
+    } // testExportreportcontentsExportsDocumentContentToTxtFile()
 
-    public function testExport_ErrorneusContentSetInternalError()
-    {
-        // export_document() dumb parameters
+    public function testExportreportcontentsWithOversizedDocumentSetInternalError() {
         $report_id = 1;
-        $extractors = array();
-        $disamb_only = true;
-        $extractor_stats = array();
-        $lists = array();
-        $output_folder = $this->virtualDir->url();
-        $subcorpora = '';
-        $tagging_method = 'tagger';
-
-        // results returned by mocking methods
-        $reportContent = str_repeat('s',300000); // content too long
-        $reportFlags = array('flagnamelowercase'=>array(-1));
-        $reportTokens = array();
-        $reportTags = array();
+		$reportContent = str_repeat('s',300000); // content too long
+        $file_path_without_ext = $this->virtualDir->url().'/testname';
         $report = array( 'id'=>$report_id, 'content'=>$reportContent );
-        $reportExt = null;
-
-        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
-            -> disableArgumentCloning()
-            -> setMethods(array('getFlagsByReportId','getTokenByReportId',
-                            'getReportTagsByTokens','getReportById',
-                            'getReportExtById'))
-            -> getMock();
-        $mockCorpusExporter -> method('getFlagsByReportId')
-            -> will($this->returnValue($reportFlags));
-        $mockCorpusExporter -> method('getTokenByReportId')
-            -> will($this->returnValue($reportTokens));
-        $mockCorpusExporter -> method('getReportTagsByTokens')
-            -> will($this->returnValue($reportTags));
-        $mockCorpusExporter -> method('getReportById')
-            -> will($this->returnValue($report));
-        $mockCorpusExporter -> method('getReportExtById')
-            -> will($this->returnValue($reportExt));
 
         // reflection for acces to private elements
-        $protectedMethod = new ReflectionMethod($mockCorpusExporter,'export_document');
+        $protectedMethod = new ReflectionMethod('CorpusExporter','exportReportContent');
         $protectedMethod->setAccessible(True);
-        $export_errorsPrivateProperty = new ReflectionProperty($mockCorpusExporter,'export_errors');
+        $ce = new CorpusExporter();
+        $export_errorsPrivateProperty = new ReflectionProperty($ce,'export_errors');
         $export_errorsPrivateProperty->setAccessible(True);
 
-        // tested call
-        $protectedMethod->invokeArgs($mockCorpusExporter,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
+        $result=$protectedMethod->invokeArgs($ce,array($report,$file_path_without_ext));
 
+        // returns False
+        $this->assertFalse($result);
         // internal errors table
-		$internalErrorsTable = $export_errorsPrivateProperty->getValue($mockCorpusExporter);
-		$expectedErrorsCount = 1;
-		$this->assertEquals($expectedErrorsCount,count($internalErrorsTable)); 
+        $internalErrorsTable = $export_errorsPrivateProperty->getValue($ce);
+        $expectedErrorsCount = 1;
+        $this->assertEquals($expectedErrorsCount,count($internalErrorsTable));
         $expectedErrorsKey = "Text too long to display (over 50k characters)";
-        $this->assertEquals(1,$internalErrorsTable[2]['details']['error'][$expectedErrorsKey]);
+        $this->assertEquals(1,$internalErrorsTable[8]['details']['errors'][$expectedErrorsKey]);
 
-    } // testExport_ErrorneusContentSetInternalError()
+    } // testExportreportcontentsWithOversizedDocumentSetInternalError() 
 
 } // CorpusExporter_part10_Test class
 

From 7428fbc76d9e5972d08a8c00de2ed98d53ffcc2d Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Tue, 14 Nov 2023 18:35:32 +0100
Subject: [PATCH 124/154] extract method for .txt file generation

---
 engine/include/export/CorpusExporter.php      |  74 +++---
 .../export/CorpusExporter_part10_Test.php     | 249 +++++++++++++++++-
 2 files changed, 288 insertions(+), 35 deletions(-)

diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index 09fda393..bfb93a8d 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -492,6 +492,48 @@ protected function exportReportContent($report,$file_path_without_ext) {
 
     } // exportReportContent()
 
+    protected function updateLists($flags,$reportFileName,&$lists) {
+
+        /* Przypisanie dokumentu do list */
+        foreach ( $lists as $ix=>$list){
+            foreach ( $list['flags'] as $flag){
+                $flag_name = $flag["flag_name"];
+                $flag_ids = $flag["flag_ids"];
+                if ( isset($flags[$flag_name]) && in_array($flags[$flag_name], $flag_ids) ){
+                    $lists[$ix]["document_names"][$reportFileName.".xml"] = 1;
+                }
+            }
+        }
+ 		// returns changes in $lists array from params
+
+    } // updateLists()
+
+    protected function createIniFile($report,$subcorpora,$file_path_without_ext) {
+
+        $ext = $this->getReportExtById($report_id);
+
+        $basic = array("id", "date", "title", "source", "author", "tokenization", "subcorpus");
+        $lines = array();
+        $lines[] = "[document]";
+        $report["subcorpus"] = $subcorpora[$report['subcorpus_id']];
+
+        foreach ($basic as $name){
+            $lines[] = sprintf("%s = %s", $name, $report[$name]);
+        }
+        if ( count($ext) > 0 ){
+            $lines[] = "";
+            $lines[] = "[metadata]";
+            foreach ($ext as $key=>$val){
+                if ($key != "id"){
+                    $key = preg_replace("/[^\p{L}|\p{N}]+/u", "_", $key);
+                    $lines[] = sprintf("%s = %s", $key, $val);
+                }
+            }
+        }
+        file_put_contents($file_path_without_ext.".ini", implode("\n", $lines));
+
+    } // createIniFile()
+
 	/**
 	 * Eksport dokumentu o wskazanym identyfikatorze
 	 * @param $report_id Identyfikator dokumentu do eksportu
@@ -632,38 +674,10 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
 
 		/* Eksport metadanych */
 		$report = $this->getReportById($report_id);
-		$ext = $this->getReportExtById($report_id);
-
-		$basic = array("id", "date", "title", "source", "author", "tokenization", "subcorpus");
-		$lines = array();
-		$lines[] = "[document]";
-		$report["subcorpus"] = $subcorpora[$report['subcorpus_id']];
-
-		foreach ($basic as $name){
-			$lines[] = sprintf("%s = %s", $name, $report[$name]);
-		}
-		if ( count($ext) > 0 ){
-			$lines[] = "";
-			$lines[] = "[metadata]";
-			foreach ($ext as $key=>$val){
-				if ($key != "id"){
-					$key = preg_replace("/[^\p{L}|\p{N}]+/u", "_", $key);
-					$lines[] = sprintf("%s = %s", $key, $val);
-				}
-			}
-		}
-		file_put_contents($output_folder . "/" . $ccl->getFileName() . ".ini", implode("\n", $lines));
+        $this->createIniFile($report,$subcorpora,$file_path_without_ext);
 
 		/* Przypisanie dokumentu do list */
-		foreach ( $lists as $ix=>$list){
-			foreach ( $list['flags'] as $flag){
-				$flag_name = $flag["flag_name"];
-				$flag_ids = $flag["flag_ids"];
-				if ( isset($flags[$flag_name]) && in_array($flags[$flag_name], $flag_ids) ){
-					$lists[$ix]["document_names"][$ccl->getFileName() . ".xml"] = 1;
-				}
-			}
-		}
+		$this->updateLists($flags,$ccl->getFileName(),$lists);
         $this->exportReportContent($report,$file_path_without_ext);
 
 	} // export_document()
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
index b82eaaf2..6b28287c 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
@@ -15,6 +15,107 @@ protected function setUp() {
 
 //    protected function export_document($report_id, $extractors, $disamb_only, &$extractor_stats, &$lists, $output_folder, $subcorpora, $tagging_method){
  
+    public function testExport_documentCallsCreateinifileMethod()                     {
+        // export_document() dumb parameters
+        $report_id = 1;
+        $extractors = array();
+        $disamb_only = true;
+        $extractor_stats = array();
+        $lists = array();
+        $output_folder = $this->virtualDir->url();
+        $subcorpora = '';
+        $tagging_method = 'tagger';
+
+        // results returned by mocking methods
+        $reportContent = "tekst dokumentu raportu";
+        $reportFlags = array('flagnamelowercase'=>array(-1));
+        $reportTokens = array();
+        $reportTags = array();
+        $report = array( 'id'=>$report_id, 'content'=>$reportContent );
+
+        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
+            -> disableArgumentCloning()
+            -> setMethods(array('getFlagsByReportId','getTokenByReportId',
+                            'getReportTagsByTokens','getReportById',
+                            'getReportExtById','exportReportContent',
+                            'updateLists','createIniFile'))
+            -> getMock();
+        $mockCorpusExporter -> method('getFlagsByReportId')
+            -> will($this->returnValue($reportFlags));
+        $mockCorpusExporter -> method('getTokenByReportId')
+            -> will($this->returnValue($reportTokens));
+        $mockCorpusExporter -> method('getReportTagsByTokens')
+            -> will($this->returnValue($reportTags));
+        $mockCorpusExporter -> method('getReportById')
+            -> will($this->returnValue($report));
+
+        // method createIniFile called exactly once with proper args:
+        $expectedReportArg = $report;
+        $expectedBaseFileName = $output_folder.'/'.str_pad($report_id,8,'0',STR_PAD_LEFT);
+        $mockCorpusExporter -> expects($this->once())
+            ->method('createIniFile')
+            ->with($expectedReportArg,$subcorpora,$expectedBaseFileName);
+
+        // reflection for acces to private elements
+        $protectedMethod = new ReflectionMethod($mockCorpusExporter,'export_document');
+        $protectedMethod->setAccessible(True);
+
+        // tested call
+        $protectedMethod->invokeArgs($mockCorpusExporter,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
+
+    } // testExport_documentCallsCreateinifileMethod()      
+
+    public function testExport_documentCallsUpdatelistsMethod()
+    {
+        // export_document() dumb parameters
+        $report_id = 1;
+        $extractors = array();
+        $disamb_only = true;
+        $extractor_stats = array();
+        $lists = array();
+        $output_folder = $this->virtualDir->url();
+        $subcorpora = '';
+        $tagging_method = 'tagger';
+
+        // results returned by mocking methods
+        $reportContent = "tekst dokumentu raportu";
+        $reportFlags = array('flagnamelowercase'=>array(-1));
+        $reportTokens = array();
+        $reportTags = array();
+        $report = array( 'id'=>$report_id, 'content'=>$reportContent );
+
+        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
+            -> disableArgumentCloning()
+            -> setMethods(array('getFlagsByReportId','getTokenByReportId',
+                            'getReportTagsByTokens','getReportById',
+                            'getReportExtById','exportReportContent',
+							'updateLists','createIniFile'))
+            -> getMock();
+        $mockCorpusExporter -> method('getFlagsByReportId')
+            -> will($this->returnValue($reportFlags));
+        $mockCorpusExporter -> method('getTokenByReportId')
+            -> will($this->returnValue($reportTokens));
+        $mockCorpusExporter -> method('getReportTagsByTokens')
+            -> will($this->returnValue($reportTags));
+        $mockCorpusExporter -> method('getReportById')
+            -> will($this->returnValue($report));
+
+        // method updateLists called exactly once with proper args:
+		$expectedFlags = $reportFlags;
+        $expectedFileNameWithoutExt = str_pad($report_id,8,'0',STR_PAD_LEFT);
+        $mockCorpusExporter -> expects($this->once())
+            ->method('updateLists')
+			->with($expectedFlags,$expectedFileNameWithoutExt,$lists);
+
+        // reflection for acces to private elements
+        $protectedMethod = new ReflectionMethod($mockCorpusExporter,'export_document');
+        $protectedMethod->setAccessible(True);
+
+        // tested call
+        $protectedMethod->invokeArgs($mockCorpusExporter,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
+
+    } // testExport_documentCallsUpdatelistsMethod()
+
     public function testExport_documentCallsExportreportcontentMethod ()
     {
         // export_document() dumb parameters
@@ -33,13 +134,13 @@ public function testExport_documentCallsExportreportcontentMethod ()
         $reportTokens = array();
         $reportTags = array();
         $report = array( 'id'=>$report_id, 'content'=>$reportContent );
-        $reportExt = null;
 
         $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
             -> disableArgumentCloning()
             -> setMethods(array('getFlagsByReportId','getTokenByReportId',
                             'getReportTagsByTokens','getReportById',
-                            'getReportExtById','exportReportContent')) 
+                            'getReportExtById','exportReportContent',
+							'createIniFile')) 
             -> getMock();
         $mockCorpusExporter -> method('getFlagsByReportId')
             -> will($this->returnValue($reportFlags));
@@ -49,12 +150,9 @@ public function testExport_documentCallsExportreportcontentMethod ()
             -> will($this->returnValue($reportTags));
         $mockCorpusExporter -> method('getReportById')
             -> will($this->returnValue($report));
-        $mockCorpusExporter -> method('getReportExtById')
-            -> will($this->returnValue($reportExt));
 
         // method exportReportContent called exactly once with proper args:
         $expectedReportArg = $report;
-        $expectedReportArg['subcorpus'] = ''; // this one is added
         $expectedBaseFileName = $output_folder.'/'.str_pad($report_id,8,'0',STR_PAD_LEFT);
         $mockCorpusExporter -> expects($this->once())
             ->method('exportReportContent')
@@ -127,6 +225,147 @@ public function testExportreportcontentsWithOversizedDocumentSetInternalError()
 
     } // testExportreportcontentsWithOversizedDocumentSetInternalError() 
 
+// protected function updateLists($flags,$reportFileName,&$lists) {...}
+
+    public function testUpdatelistsEmptyCallDoNothing() {
+
+		$flags = array();
+		$file_name_without_ext = 'reportFileName';
+		$lists = array();
+
+        // reflection for acces to private elements
+        $protectedMethod = new ReflectionMethod('CorpusExporter','updateLists');
+        $protectedMethod->setAccessible(True);
+
+        $ce = new CorpusExporter();
+		$protectedMethod->invokeArgs($ce,array($flags,$file_name_without_ext,&$lists));
+
+		// check results
+		$expectedLists = array();
+		$this->assertEquals($expectedLists,$lists); 
+
+    } // testUpdatelistsEmptyCallDoNothing()
+
+    public function testUpdatelistsOnEmptyListsDoNothing() {
+
+        $testFlagName = 'TFN';
+        $testFlagId = 123;
+        $listName = 'ix';
+
+        $flags = array(
+            $testFlagName => $testFlagId
+        );
+        $file_name_without_ext = 'reportFileName';
+        $lists = array();
+
+        // reflection for acces to private elements
+        $protectedMethod = new ReflectionMethod('CorpusExporter','updateLists');
+        $protectedMethod->setAccessible(True);
+
+        $ce = new CorpusExporter();
+        $listsBeforeCall = $lists;
+        $protectedMethod->invokeArgs($ce,array($flags,$file_name_without_ext,&$lists));
+
+        // check results
+        $expectedLists = $listsBeforeCall;
+        $this->assertEquals($expectedLists,$lists);
+
+    } // testUpdatelistsOnEmptyListsDoNothing() 
+
+    public function testUpdatelistsSetsDocument_namesToLists() {
+
+        $testFlagName = 'TFN';
+        $testFlagId = 123;
+        $listName = 'ix';
+
+        $flags = array(
+            $testFlagName => $testFlagId
+        );
+        $file_name_without_ext = 'reportFileName';
+        $lists = array(
+				$listName => array(
+                    "flags" => array(  
+                        array( "flag_name"=>'flagName', 
+                                "flag_ids"=> array(1,2)),
+                        array( "flag_name"=>$testFlagName,                                                      "flag_ids"=> array(1,$testFlagId)),
+                    )
+                )
+			);
+
+        // reflection for acces to private elements
+        $protectedMethod = new ReflectionMethod('CorpusExporter','updateLists');
+        $protectedMethod->setAccessible(True);
+
+        $ce = new CorpusExporter();
+        $listsBeforeCall = $lists;
+        $protectedMethod->invokeArgs($ce,array($flags,$file_name_without_ext,&$lists));
+
+        // check results
+        $expectedLists = $listsBeforeCall;
+        $expectedLists[$listName]["document_names"][$file_name_without_ext.".xml"] = 1;
+        $this->assertEquals($expectedLists,$lists);
+
+    } // testUpdatelistsSetsDocument_namesToLists()
+
+// protected function createIniFile($report,$file_path_without_ext) {...}
+
+    public function testCreateinifileExportsReportMetadataToIniFile() {
+
+        $report_id = 1;
+        $reportContent = "tekst dokumentu raportu";
+		$reportDate = '23/12/2023';
+		$reportTitle = 'TYTUŁ RAPORTU';
+		$reportSource = 'ŹRÓDŁO RAPORTU';
+		$reportAuthor = 'AUTOR RAPORTU';
+		$reportTokenization = 'TOKENIZACJA';
+		$reportNonidExtKey = 'nonid';
+		$reportNonidExtValue = 13;
+        $reportNonLNKey = ' klucz ze spacjami';
+        $reportNonLNKey_converted = '_klucz_ze_spacjami';
+        $reportNonLNValue = 48;
+		$subcorpusKey = 341;
+		$subcorpusName = 'SUBCORPUS NAME';
+		$subcorpora = array( $subcorpusKey => $subcorpusName );
+        $file_path_without_ext = $this->virtualDir->url().'/testname';
+        $report = array( 'id'=>$report_id, 'subcorpus_id'=>$subcorpusKey,
+						'date' => $reportDate, 'title' => $reportTitle,
+						'source' => $reportSource, 'author' => $reportAuthor,
+						'tokenization' => $reportTokenization );
+		$reportExt = array( 'id' => 12,  // id is excluded from .ini
+                            $reportNonLNKey => $reportNonLNValue,
+							$reportNonidExtKey => $reportNonidExtValue );
+
+        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
+            -> disableArgumentCloning()
+            -> setMethods(array('getReportExtById'))
+            -> getMock();
+        $mockCorpusExporter -> method('getReportExtById')                                      -> will($this->returnValue($reportExt));
+
+        // reflection for acces to private elements
+        $protectedMethod = new ReflectionMethod('CorpusExporter','createIniFile');
+        $protectedMethod->setAccessible(True);
+
+        $result=$protectedMethod->invokeArgs($mockCorpusExporter,array($report,$subcorpora,$file_path_without_ext));
+
+        //check Ini File
+        $expectedIniContent = 
+"[document]
+id = 1
+date = $reportDate
+title = $reportTitle
+source = $reportSource
+author = $reportAuthor
+tokenization = $reportTokenization
+subcorpus = $subcorpusName
+
+[metadata]
+$reportNonLNKey_converted = $reportNonLNValue
+$reportNonidExtKey = $reportNonidExtValue";
+        $resultIniFile = file_get_contents($file_path_without_ext.'.ini');
+        $this->assertEquals($expectedIniContent,$resultIniFile);
+
+    } // testCreateinifileExportsReportMetadataToIniFile()
+ 
 } // CorpusExporter_part10_Test class
 
 ?>

From 58dd9cec64fa03f979067846f0822a808de4ad3c Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Tue, 14 Nov 2023 21:30:51 +0100
Subject: [PATCH 125/154] extract lemma checker

---
 engine/include/export/CorpusExporter.php      |  31 +++--
 .../export/CorpusExporter_part10_Test.php     | 108 ++++++++++++++++++
 2 files changed, 128 insertions(+), 11 deletions(-)

diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index bfb93a8d..afa106b9 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -534,6 +534,25 @@ protected function createIniFile($report,$subcorpora,$file_path_without_ext) {
 
     } // createIniFile()
 
+    protected function checkIfAnnotationForLemmaExists($lemmas,$annotations_by_id) {
+
+		$allLemmasCorrect = True;
+        foreach ($lemmas as $an){
+            $anid = intval($an['id']);
+            if ( !isset($annotations_by_id[$anid]) ){
+                $error_params = array(
+                    'message' => "Brak warstwy anotacji dla lematu.",
+                    'group_id' => $an['group_id'],
+                    'lemma' => $an['name']
+                );
+                $this->log_error(__FILE__, __LINE__, $report_id, "brak anotacji $anid dla lematu ({$an["name"]}) -- brakuje warstwy anotacji?", 6, $error_params);
+				$allLemmasCorrect = False;
+            }
+        }
+		return $allLemmasCorrect;
+
+    } // checkIfAnnotationForLemmaExists()
+
 	/**
 	 * Eksport dokumentu o wskazanym identyfikatorze
 	 * @param $report_id Identyfikator dokumentu do eksportu
@@ -652,17 +671,7 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
 		}
 
 		/* Sprawdzenie lematów */
-		foreach ($lemmas as $an){
-			$anid = intval($an['id']);
-			if ( !isset($annotations_by_id[$anid]) ){
-                $error_params = array(
-                    'message' => "Brak warstwy anotacji dla lematu.",
-                    'group_id' => $an['group_id'],
-                    'lemma' => $an['name']
-                );
-                $this->log_error(__FILE__, __LINE__, $report_id, "brak anotacji $anid dla lematu ({$an["name"]}) -- brakuje warstwy anotacji?", 6, $error_params);
-			}
-		}
+		$this->checkIfAnnotationForLemmaExists($lemmas,$annotations_by_id);
 
         $file_path_without_ext = $output_folder . "/" . $ccl->getFileName();
 
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
index 6b28287c..faad63db 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
@@ -15,6 +15,57 @@ protected function setUp() {
 
 //    protected function export_document($report_id, $extractors, $disamb_only, &$extractor_stats, &$lists, $output_folder, $subcorpora, $tagging_method){
  
+    public function testExport_documentCallsCheckifannotationforlemmaexistsMethod() {
+        // export_document() dumb parameters
+        $report_id = 1;
+        $extractors = array();
+        $disamb_only = true;
+        $extractor_stats = array();
+        $lists = array();
+        $output_folder = $this->virtualDir->url();
+        $subcorpora = '';
+        $tagging_method = 'tagger';
+
+        // results returned by mocking methods
+        $reportContent = "tekst dokumentu raportu";
+        $reportFlags = array('flagnamelowercase'=>array(-1));
+        $reportTokens = array();
+        $reportTags = array();
+        $report = array( 'id'=>$report_id, 'content'=>$reportContent );
+
+        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
+            -> disableArgumentCloning()
+            -> setMethods(array('getFlagsByReportId','getTokenByReportId',
+                            'getReportTagsByTokens','getReportById',
+                            'getReportExtById','exportReportContent',
+                            'updateLists','createIniFile',
+							'checkIfAnnotationForLemmaExists'))
+            -> getMock();
+        $mockCorpusExporter -> method('getFlagsByReportId')
+            -> will($this->returnValue($reportFlags));
+        $mockCorpusExporter -> method('getTokenByReportId')
+            -> will($this->returnValue($reportTokens));
+        $mockCorpusExporter -> method('getReportTagsByTokens')
+            -> will($this->returnValue($reportTags));
+        $mockCorpusExporter -> method('getReportById')
+            -> will($this->returnValue($report));
+
+        // method checkIfAnnotationForLemmaExists called exactly once with proper args:
+        $expectedLemmas = array();
+        $expectedAnnotationsById = array();;
+        $mockCorpusExporter -> expects($this->once())
+            ->method('checkIfAnnotationForLemmaExists')
+            ->with($expectedLemmas,$expectedAnnotationsById);
+
+        // reflection for acces to private elements
+        $protectedMethod = new ReflectionMethod($mockCorpusExporter,'export_document');
+        $protectedMethod->setAccessible(True);
+
+        // tested call
+        $protectedMethod->invokeArgs($mockCorpusExporter,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
+
+    } // testExport_documentCallsCheckifannotationforlemmaexistsMethod() 
+  
     public function testExport_documentCallsCreateinifileMethod()                     {
         // export_document() dumb parameters
         $report_id = 1;
@@ -366,6 +417,63 @@ public function testCreateinifileExportsReportMetadataToIniFile() {
 
     } // testCreateinifileExportsReportMetadataToIniFile()
  
+// protected function checkIfAnnotationForLemmaExists($lemmas,$annotations_by_id) {...}
+
+    public function testCheckifannotationforlemmaexistsReturnsTrueIfAllLemmasMatched() {
+		$annoId1 = 10;  $annoId2 = 20;
+        $lemmas = array(
+			array( "id"=>$annoId1 ),
+			array( "id"=>$annoId2 )
+		);
+		$annotationsById = array( $annoId1 => True, $annoId2 => True );
+
+        // reflection for acces to private elements
+        $protectedMethod = new ReflectionMethod('CorpusExporter','checkIfAnnotationForLemmaExists');
+        $protectedMethod->setAccessible(True);
+        $ce = new CorpusExporter();
+        $export_errorsPrivateProperty = new ReflectionProperty($ce,'export_errors');
+        $export_errorsPrivateProperty->setAccessible(True);
+
+        $result=$protectedMethod->invokeArgs($ce,array($lemmas,$annotationsById));
+        // returns True
+        $this->assertTrue($result);
+
+        // internal errors table is empty
+        $internalErrorsTable = $export_errorsPrivateProperty->getValue($ce);
+		$this->assertEquals(0,count($internalErrorsTable));
+
+    } // testCheckifannotationforlemmaexistsReturnsTrueIfAllLemmasMatched() 
+ 
+    public function testCheckifannotationforlemmaexistsSetInternalError() {
+
+        $annoId1 = 10;  $annoId2 = 20;
+        $lemmas = array(
+            array( "id"=>$annoId1 ),
+            array( "id"=>$annoId2 )
+        );
+        $annotationsById = array( $annoId1 => True );
+
+        // reflection for acces to private elements
+        $protectedMethod = new ReflectionMethod('CorpusExporter','checkIfAnnotationForLemmaExists');
+        $protectedMethod->setAccessible(True);
+        $ce = new CorpusExporter();
+        $export_errorsPrivateProperty = new ReflectionProperty($ce,'export_errors');
+        $export_errorsPrivateProperty->setAccessible(True);
+
+        $result=$protectedMethod->invokeArgs($ce,array($lemmas,$annotationisById));
+
+        // returns False
+        $this->assertFalse($result);
+
+        // internal errors table
+        $internalErrorsTable = $export_errorsPrivateProperty->getValue($ce);
+        $expectedErrorsCount = 1;
+        $this->assertEquals($expectedErrorsCount,count($internalErrorsTable));
+        $expectedErrorsKey = "Brak warstwy anotacji dla lematu.";
+        $this->assertEquals($expectedErrorsKey,$internalErrorsTable[6]['message']);
+
+    } // testCheckifannotationforlemmaexistsSetInternalError()
+
 } // CorpusExporter_part10_Test class
 
 ?>

From 5ef619bba15707764488525bf4f85f0a72af7c6d Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Wed, 15 Nov 2023 13:52:10 +0100
Subject: [PATCH 126/154] extract relations checker

---
 engine/include/export/CorpusExporter.php      | 50 ++++++++-----
 .../export/CorpusExporter_part10_Test.php     | 75 ++++++++++++++++++-
 2 files changed, 102 insertions(+), 23 deletions(-)

diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index afa106b9..7d58ddf3 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -553,6 +553,35 @@ protected function checkIfAnnotationForLemmaExists($lemmas,$annotations_by_id) {
 
     } // checkIfAnnotationForLemmaExists()
 
+    protected function checkIfAnnotationForRelationExists($relations,$annotations_by_id) {
+		/* Sprawdzenie, anotacji źródłowych i docelowych dla relacji */
+		$allRelationsCorrect = True;
+        foreach ( $relations as $rel ){
+            $source_id = $rel["source_id"];
+            $target_id = $rel["target_id"];
+            if ( !isset($annotations_by_id[$source_id]) ){
+                $error_params = array(
+                    'message' => "Brak anotacji źródłowej dla relacji.",
+                    'source_id' => $source_id,
+                    'relation' => $rel["name"]
+                );
+                $this->log_error(__FILE__, __LINE__, $report_id, "brak anotacji źródłowej o identyfikatorze $source_id ({$rel["name"]}) -- brakuje warstwy anotacji?", 4, $error_params);
+				$allRelationsCorrect = False;
+            }
+            if ( !isset($annotations_by_id[$target_id]) ){
+                $error_params = array(
+                    'message' => "Brak anotacji docelowej dla relacji.",
+                    'target_id' => $target_id,
+                    'relation' => $rel["name"]
+                );
+                $this->log_error(__FILE__, __LINE__, $report_id, "brak anotacji źródłowej o identyfikatorze $target_id ({$rel["name"]}) -- brakuje warsty anotacji?", 5, $error_params);
+				$allRelationsCorrect = False;
+            }
+        }
+		return $allRelationsCorrect;
+ 
+    } // checkIfAnnotationForRelationExists()
+
 	/**
 	 * Eksport dokumentu o wskazanym identyfikatorze
 	 * @param $report_id Identyfikator dokumentu do eksportu
@@ -649,26 +678,7 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
 		$annotations = array_values($annotations_by_id);
 
 		/* Sprawdzenie, anotacji źródłowych i docelowych dla relacji */
-		foreach ( $relations as $rel ){
-			$source_id = $rel["source_id"];
-			$target_id = $rel["target_id"];
-			if ( !isset($annotations_by_id[$source_id]) ){
-				$error_params = array(
-					'message' => "Brak anotacji źródłowej dla relacji.",
-					'source_id' => $source_id,
-					'relation' => $rel["name"]
-				);
-				$this->log_error(__FILE__, __LINE__, $report_id, "brak anotacji źródłowej o identyfikatorze $source_id ({$rel["name"]}) -- brakuje warstwy anotacji?", 4, $error_params);
-			}
-			if ( !isset($annotations_by_id[$target_id]) ){
-                $error_params = array(
-                    'message' => "Brak anotacji docelowej dla relacji.",
-                    'target_id' => $target_id,
-                    'relation' => $rel["name"]
-                );
-                $this->log_error(__FILE__, __LINE__, $report_id, "brak anotacji źródłowej o identyfikatorze $target_id ({$rel["name"]}) -- brakuje warsty anotacji?", 5, $error_params);
-			}
-		}
+		$this->checkIfAnnotationForRelationExists($relations,$annotations_by_id);
 
 		/* Sprawdzenie lematów */
 		$this->checkIfAnnotationForLemmaExists($lemmas,$annotations_by_id);
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
index faad63db..b24e2023 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
@@ -15,7 +15,7 @@ protected function setUp() {
 
 //    protected function export_document($report_id, $extractors, $disamb_only, &$extractor_stats, &$lists, $output_folder, $subcorpora, $tagging_method){
  
-    public function testExport_documentCallsCheckifannotationforlemmaexistsMethod() {
+    public function testExport_documentCallsCheckingForLemmaAndRelationExistsMethod() {
         // export_document() dumb parameters
         $report_id = 1;
         $extractors = array();
@@ -39,7 +39,8 @@ public function testExport_documentCallsCheckifannotationforlemmaexistsMethod()
                             'getReportTagsByTokens','getReportById',
                             'getReportExtById','exportReportContent',
                             'updateLists','createIniFile',
-							'checkIfAnnotationForLemmaExists'))
+							'checkIfAnnotationForLemmaExists',
+                            'checkIfAnnotationForRelationExists'))
             -> getMock();
         $mockCorpusExporter -> method('getFlagsByReportId')
             -> will($this->returnValue($reportFlags));
@@ -56,6 +57,11 @@ public function testExport_documentCallsCheckifannotationforlemmaexistsMethod()
         $mockCorpusExporter -> expects($this->once())
             ->method('checkIfAnnotationForLemmaExists')
             ->with($expectedLemmas,$expectedAnnotationsById);
+        $expectedRelations = array();
+        $mockCorpusExporter -> expects($this->once())
+            ->method('checkIfAnnotationForRelationExists')
+            ->with($expectedRelations,$expectedAnnotationsById);
+
 
         // reflection for acces to private elements
         $protectedMethod = new ReflectionMethod($mockCorpusExporter,'export_document');
@@ -64,7 +70,7 @@ public function testExport_documentCallsCheckifannotationforlemmaexistsMethod()
         // tested call
         $protectedMethod->invokeArgs($mockCorpusExporter,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
 
-    } // testExport_documentCallsCheckifannotationforlemmaexistsMethod() 
+    } // testExport_documentCallsCheckingForLemmaAndRelationExistsMethod() 
   
     public function testExport_documentCallsCreateinifileMethod()                     {
         // export_document() dumb parameters
@@ -474,6 +480,69 @@ public function testCheckifannotationforlemmaexistsSetInternalError() {
 
     } // testCheckifannotationforlemmaexistsSetInternalError()
 
+// protected function checkIfAnnotationForRelationExists($relations,$annotations_by_id) {
+
+    public function testCheckifannotationforrelationsexistsReturnsTrueIfAllRelationsMatched() {
+        $sourceId1 = 10; $targetId1 = 13;  
+		$sourceId2 = 20; $targetId2 = 27;
+        $relations = array(
+            array( "source_id"=>$sourceId1, "target_id"=>$targetId1 ),
+            array( "source_id"=>$sourceId2, "target_id"=>$targetId2 )
+        );
+        $annotationsById = array( $sourceId1 => True, $targetId1 => True,
+								  $sourceId2 => True, $targetId2 => True  );
+
+        // reflection for acces to private elements
+        $protectedMethod = new ReflectionMethod('CorpusExporter','checkIfAnnotationForRelationExists');
+        $protectedMethod->setAccessible(True);
+        $ce = new CorpusExporter();
+        $export_errorsPrivateProperty = new ReflectionProperty($ce,'export_errors');
+        $export_errorsPrivateProperty->setAccessible(True);
+
+        $result=$protectedMethod->invokeArgs($ce,array($relations,$annotationsById));
+        // returns True
+        $this->assertTrue($result);
+
+        // internal errors table is empty
+        $internalErrorsTable = $export_errorsPrivateProperty->getValue($ce);
+        $this->assertEquals(0,count($internalErrorsTable));
+
+    } // testCheckifannotationforrelationsexistsReturnsTrueIfAllRelationsMatched() 
+
+    public function testCheckifannotationforrelationsexistsSetInternalError() {
+        $sourceId1 = 10; $targetId1 = 13;
+        $sourceId2 = 20; $targetId2 = 27;
+        $relations = array(
+            array( "source_id"=>$sourceId1, "target_id"=>$targetId1 ),
+            array( "source_id"=>$sourceId2, "target_id"=>$targetId2 )
+        );
+        $annotationsById = array( $targetId1 => True,
+                                  $sourceId2 => True  );
+
+        // reflection for acces to private elements
+        $protectedMethod = new ReflectionMethod('CorpusExporter','checkIfAnnotationForRelationExists');
+        $protectedMethod->setAccessible(True);
+        $ce = new CorpusExporter();
+        $export_errorsPrivateProperty = new ReflectionProperty($ce,'export_errors');
+        $export_errorsPrivateProperty->setAccessible(True);
+
+        $result=$protectedMethod->invokeArgs($ce,array($relations,$annotationsById));
+        // returns False
+        $this->assertFalse($result);
+
+        // internal errors table
+        $internalErrorsTable = $export_errorsPrivateProperty->getValue($ce);
+        $expectedErrorsCount = 2;
+        $this->assertEquals($expectedErrorsCount,count($internalErrorsTable));
+        $expectedErrorsKey = "Brak anotacji źródłowej dla relacji.";
+        $this->assertEquals($expectedErrorsKey,$internalErrorsTable[4]['message']);
+        $expectedErrorsKey = "Brak anotacji docelowej dla relacji.";
+        $this->assertEquals($expectedErrorsKey,$internalErrorsTable[5]['message']);
+
+
+    } // testCheckifannotationforrelationsexistsSetInternalError()
+
+
 } // CorpusExporter_part10_Test class
 
 ?>

From 8b3f77ce1416a3c1cfd4c49fbe49c18de6f387f8 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Wed, 15 Nov 2023 18:54:18 +0100
Subject: [PATCH 127/154] extract method for unique sorting annotations array

---
 engine/include/export/CorpusExporter.php      |  34 ++-
 .../export/CorpusExporter_part10_Test.php     | 222 ++++++------------
 2 files changed, 91 insertions(+), 165 deletions(-)

diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index 7d58ddf3..2e6e9b85 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -582,6 +582,26 @@ protected function checkIfAnnotationForRelationExists($relations,$annotations_by
  
     } // checkIfAnnotationForRelationExists()
 
+	protected function sortUniqueAnnotationsById($annotations) {
+
+        /* Usunięcie zduplikowanych anotacji */
+        $annotations_by_id = array();
+        foreach ($annotations as $an){
+            $anid = intval($an['id']);
+            if ( $anid > 0 ){
+                $annotations_by_id[$anid] = $an;
+            }
+            else{
+                $error_params = array(
+                    'message' => "Brak identyfikatora anotacji."
+                );
+                $this->log_error(__FILE__, __LINE__, $report_id, "brak identyfikatora anotacji", 3, $error_params);
+            }
+        }
+		return $annotations_by_id;
+
+	} // sortUniqueAnnotationsById()
+
 	/**
 	 * Eksport dokumentu o wskazanym identyfikatorze
 	 * @param $report_id Identyfikator dokumentu do eksportu
@@ -662,19 +682,7 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
         }
 
 		/* Usunięcie zduplikowanych anotacji */
-		$annotations_by_id = array();
-		foreach ($annotations as $an){
-			$anid = intval($an['id']);
-			if ( $anid > 0 ){
-				$annotations_by_id[$anid] = $an;
-			}
-			else{
-				$error_params = array(
-					'message' => "Brak identyfikatora anotacji."
-				);
-				$this->log_error(__FILE__, __LINE__, $report_id, "brak identyfikatora anotacji", 3, $error_params);
-			}
-		}
+		$annotations_by_id = $this->sortUniqueAnnotationsById($annotations);
 		$annotations = array_values($annotations_by_id);
 
 		/* Sprawdzenie, anotacji źródłowych i docelowych dla relacji */
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
index b24e2023..52889207 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
@@ -15,7 +15,7 @@ protected function setUp() {
 
 //    protected function export_document($report_id, $extractors, $disamb_only, &$extractor_stats, &$lists, $output_folder, $subcorpora, $tagging_method){
  
-    public function testExport_documentCallsCheckingForLemmaAndRelationExistsMethod() {
+    public function testExport_documentCallsAllProcessingMethods() {
         // export_document() dumb parameters
         $report_id = 1;
         $extractors = array();
@@ -40,7 +40,8 @@ public function testExport_documentCallsCheckingForLemmaAndRelationExistsMethod(
                             'getReportExtById','exportReportContent',
                             'updateLists','createIniFile',
 							'checkIfAnnotationForLemmaExists',
-                            'checkIfAnnotationForRelationExists'))
+                            'checkIfAnnotationForRelationExists',
+							'sortUniqueAnnotationsById'))
             -> getMock();
         $mockCorpusExporter -> method('getFlagsByReportId')
             -> will($this->returnValue($reportFlags));
@@ -51,170 +52,37 @@ public function testExport_documentCallsCheckingForLemmaAndRelationExistsMethod(
         $mockCorpusExporter -> method('getReportById')
             -> will($this->returnValue($report));
 
-        // method checkIfAnnotationForLemmaExists called exactly once with proper args:
-        $expectedLemmas = array();
-        $expectedAnnotationsById = array();;
+        // tested methods called exactly once with proper args:
+		$expectedAnnotations = array();
+		$expectedAnnotationsById = array();;
         $mockCorpusExporter -> expects($this->once())
-            ->method('checkIfAnnotationForLemmaExists')
-            ->with($expectedLemmas,$expectedAnnotationsById);
+            ->method('sortUniqueAnnotationsById')
+            ->with($expectedAnnotations)
+			-> will($this->returnValue($expectedAnnotationsById));
         $expectedRelations = array();
         $mockCorpusExporter -> expects($this->once())
             ->method('checkIfAnnotationForRelationExists')
             ->with($expectedRelations,$expectedAnnotationsById);
-
-
-        // reflection for acces to private elements
-        $protectedMethod = new ReflectionMethod($mockCorpusExporter,'export_document');
-        $protectedMethod->setAccessible(True);
-
-        // tested call
-        $protectedMethod->invokeArgs($mockCorpusExporter,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
-
-    } // testExport_documentCallsCheckingForLemmaAndRelationExistsMethod() 
-  
-    public function testExport_documentCallsCreateinifileMethod()                     {
-        // export_document() dumb parameters
-        $report_id = 1;
-        $extractors = array();
-        $disamb_only = true;
-        $extractor_stats = array();
-        $lists = array();
-        $output_folder = $this->virtualDir->url();
-        $subcorpora = '';
-        $tagging_method = 'tagger';
-
-        // results returned by mocking methods
-        $reportContent = "tekst dokumentu raportu";
-        $reportFlags = array('flagnamelowercase'=>array(-1));
-        $reportTokens = array();
-        $reportTags = array();
-        $report = array( 'id'=>$report_id, 'content'=>$reportContent );
-
-        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
-            -> disableArgumentCloning()
-            -> setMethods(array('getFlagsByReportId','getTokenByReportId',
-                            'getReportTagsByTokens','getReportById',
-                            'getReportExtById','exportReportContent',
-                            'updateLists','createIniFile'))
-            -> getMock();
-        $mockCorpusExporter -> method('getFlagsByReportId')
-            -> will($this->returnValue($reportFlags));
-        $mockCorpusExporter -> method('getTokenByReportId')
-            -> will($this->returnValue($reportTokens));
-        $mockCorpusExporter -> method('getReportTagsByTokens')
-            -> will($this->returnValue($reportTags));
-        $mockCorpusExporter -> method('getReportById')
-            -> will($this->returnValue($report));
-
-        // method createIniFile called exactly once with proper args:
+        $expectedLemmas = array();
+        $mockCorpusExporter -> expects($this->once())
+            ->method('checkIfAnnotationForLemmaExists')
+            ->with($expectedLemmas,$expectedAnnotationsById);
         $expectedReportArg = $report;
         $expectedBaseFileName = $output_folder.'/'.str_pad($report_id,8,'0',STR_PAD_LEFT);
         $mockCorpusExporter -> expects($this->once())
             ->method('createIniFile')
             ->with($expectedReportArg,$subcorpora,$expectedBaseFileName);
-
-        // reflection for acces to private elements
-        $protectedMethod = new ReflectionMethod($mockCorpusExporter,'export_document');
-        $protectedMethod->setAccessible(True);
-
-        // tested call
-        $protectedMethod->invokeArgs($mockCorpusExporter,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
-
-    } // testExport_documentCallsCreateinifileMethod()      
-
-    public function testExport_documentCallsUpdatelistsMethod()
-    {
-        // export_document() dumb parameters
-        $report_id = 1;
-        $extractors = array();
-        $disamb_only = true;
-        $extractor_stats = array();
-        $lists = array();
-        $output_folder = $this->virtualDir->url();
-        $subcorpora = '';
-        $tagging_method = 'tagger';
-
-        // results returned by mocking methods
-        $reportContent = "tekst dokumentu raportu";
-        $reportFlags = array('flagnamelowercase'=>array(-1));
-        $reportTokens = array();
-        $reportTags = array();
-        $report = array( 'id'=>$report_id, 'content'=>$reportContent );
-
-        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
-            -> disableArgumentCloning()
-            -> setMethods(array('getFlagsByReportId','getTokenByReportId',
-                            'getReportTagsByTokens','getReportById',
-                            'getReportExtById','exportReportContent',
-							'updateLists','createIniFile'))
-            -> getMock();
-        $mockCorpusExporter -> method('getFlagsByReportId')
-            -> will($this->returnValue($reportFlags));
-        $mockCorpusExporter -> method('getTokenByReportId')
-            -> will($this->returnValue($reportTokens));
-        $mockCorpusExporter -> method('getReportTagsByTokens')
-            -> will($this->returnValue($reportTags));
-        $mockCorpusExporter -> method('getReportById')
-            -> will($this->returnValue($report));
-
-        // method updateLists called exactly once with proper args:
-		$expectedFlags = $reportFlags;
+        $expectedFlags = $reportFlags;
         $expectedFileNameWithoutExt = str_pad($report_id,8,'0',STR_PAD_LEFT);
         $mockCorpusExporter -> expects($this->once())
             ->method('updateLists')
-			->with($expectedFlags,$expectedFileNameWithoutExt,$lists);
-
-        // reflection for acces to private elements
-        $protectedMethod = new ReflectionMethod($mockCorpusExporter,'export_document');
-        $protectedMethod->setAccessible(True);
-
-        // tested call
-        $protectedMethod->invokeArgs($mockCorpusExporter,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
-
-    } // testExport_documentCallsUpdatelistsMethod()
-
-    public function testExport_documentCallsExportreportcontentMethod ()
-    {
-        // export_document() dumb parameters
-        $report_id = 1;
-        $extractors = array();
-        $disamb_only = true;
-        $extractor_stats = array();
-        $lists = array();
-        $output_folder = $this->virtualDir->url();
-        $subcorpora = '';
-        $tagging_method = 'tagger';
-
-        // results returned by mocking methods
-        $reportContent = "tekst dokumentu raportu";
-        $reportFlags = array('flagnamelowercase'=>array(-1)); 
-        $reportTokens = array();
-        $reportTags = array();
-        $report = array( 'id'=>$report_id, 'content'=>$reportContent );
-
-        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
-            -> disableArgumentCloning()
-            -> setMethods(array('getFlagsByReportId','getTokenByReportId',
-                            'getReportTagsByTokens','getReportById',
-                            'getReportExtById','exportReportContent',
-							'createIniFile')) 
-            -> getMock();
-        $mockCorpusExporter -> method('getFlagsByReportId')
-            -> will($this->returnValue($reportFlags));
-        $mockCorpusExporter -> method('getTokenByReportId')
-            -> will($this->returnValue($reportTokens));
-        $mockCorpusExporter -> method('getReportTagsByTokens')
-            -> will($this->returnValue($reportTags));
-        $mockCorpusExporter -> method('getReportById')
-            -> will($this->returnValue($report));
-
-        // method exportReportContent called exactly once with proper args:
+            ->with($expectedFlags,$expectedFileNameWithoutExt,$lists);
         $expectedReportArg = $report;
-        $expectedBaseFileName = $output_folder.'/'.str_pad($report_id,8,'0',STR_PAD_LEFT);
         $mockCorpusExporter -> expects($this->once())
             ->method('exportReportContent')
             ->with($expectedReportArg,$expectedBaseFileName);
- 
+
+
         // reflection for acces to private elements
         $protectedMethod = new ReflectionMethod($mockCorpusExporter,'export_document');
         $protectedMethod->setAccessible(True);
@@ -222,8 +90,8 @@ public function testExport_documentCallsExportreportcontentMethod ()
         // tested call
         $protectedMethod->invokeArgs($mockCorpusExporter,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
 
-    } // testExport_documentCallsExportreportcontentMethod()
-
+    } // testExport_documentCallsAllProcessingMethods
+  
 // protected function exportReportContent($report,$file_path_without_ext){...}
 
     public function testExportreportcontentsExportsDocumentContentToTxtFile() {
@@ -539,9 +407,59 @@ public function testCheckifannotationforrelationsexistsSetInternalError() {
         $expectedErrorsKey = "Brak anotacji docelowej dla relacji.";
         $this->assertEquals($expectedErrorsKey,$internalErrorsTable[5]['message']);
 
-
     } // testCheckifannotationforrelationsexistsSetInternalError()
 
+// protected function sortUniqueAnnotationsById($annotations) {...}
+
+    public function testSortuniqueannotationsbyidReturnsIndexedArray() {
+
+		$anno1 = array( "id"=>1 ); $anno2 = array( "id"=>2 );
+		$annotations = array( $anno1,$anno2,$anno2 );
+
+        // reflection for acces to private elements
+        $protectedMethod = new ReflectionMethod('CorpusExporter','sortUniqueAnnotationsById');
+        $protectedMethod->setAccessible(True);
+        $ce = new CorpusExporter();
+        $export_errorsPrivateProperty = new ReflectionProperty($ce,'export_errors');
+        $export_errorsPrivateProperty->setAccessible(True);
+
+        $result=$protectedMethod->invokeArgs($ce,array($annotations));
+
+		$expectedAnnotationById = array(
+			1 => $anno1,
+			2 => $anno2
+		);
+ 		$this->assertEquals($expectedAnnotationById,$result);
+
+    } // testSortuniqueannotationsbyidReturnsIndexedArray() 
+
+    public function testSortuniqueannotationsbyidSetInternalError() {
+
+        $annoWoId = array( "name"=>1 ); $anno2 = array( "id"=>2 );
+        $annotations = array( $annoWoId,$anno2,$anno2 );
+
+        // reflection for acces to private elements
+        $protectedMethod = new ReflectionMethod('CorpusExporter','sortUniqueAnnotationsById');
+        $protectedMethod->setAccessible(True);
+        $ce = new CorpusExporter();
+        $export_errorsPrivateProperty = new ReflectionProperty($ce,'export_errors');
+        $export_errorsPrivateProperty->setAccessible(True);
+
+        $result=$protectedMethod->invokeArgs($ce,array($annotations));
+
+        $expectedAnnotationById = array(
+            2 => $anno2
+        );
+        $this->assertEquals($expectedAnnotationById,$result);
+
+        // internal errors table
+        $internalErrorsTable = $export_errorsPrivateProperty->getValue($ce);
+        $expectedErrorsCount = 1;
+        $this->assertEquals($expectedErrorsCount,count($internalErrorsTable));
+        $expectedErrorsKey = "Brak identyfikatora anotacji.";
+        $this->assertEquals($expectedErrorsKey,$internalErrorsTable[3]['message']);
+
+    } // testSortuniqueannotationsbyidSetInternalError()
 
 } // CorpusExporter_part10_Test class
 

From b2c0129f0fa3812278818e5e7f7617f7d72d17a8 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Wed, 15 Nov 2023 19:44:07 +0100
Subject: [PATCH 128/154] extract method for dispatch elements table

---
 engine/include/export/CorpusExporter.php      | 40 +++++++++-------
 .../export/CorpusExporter_part10_Test.php     | 47 +++++++++++++++++--
 2 files changed, 66 insertions(+), 21 deletions(-)

diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index 2e6e9b85..b0c19cb9 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -602,6 +602,29 @@ protected function sortUniqueAnnotationsById($annotations) {
 
 	} // sortUniqueAnnotationsById()
 
+    protected function dispatchElements($elements) {
+
+        $annotations = array();
+        $relations = array();
+        $lemmas = array();
+        $attributes = array();
+        if ( isset($elements["annotations"]) && count($elements["annotations"]) ){
+            $annotations = $elements["annotations"];
+        }
+        if ( isset($elements["relations"]) && count($elements["relations"]) ){
+            $relations = $elements["relations"];
+        }
+        if ( isset($elements["lemmas"]) && count($elements["lemmas"]) ){
+            $lemmas = $elements["lemmas"];
+        }
+
+        if ( isset($elements["attributes"]) && count($elements["attributes"]) ){
+            $attributes = $elements["attributes"];
+        }
+		return [$annotations,$relations,$lemmas,$attributes];
+
+    } // dispatchElements()
+
 	/**
 	 * Eksport dokumentu o wskazanym identyfikatorze
 	 * @param $report_id Identyfikator dokumentu do eksportu
@@ -663,23 +686,8 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
 			$this->log_error(__FILE__, __LINE__, $report_id, "Problem z utworzeniem ccl: " . $error, 2, $error_params);
 			return;
 		}
-		$annotations = array();
-		$relations = array();
-		$lemmas = array();
-        $attributes = array();
-		if ( isset($elements["annotations"]) && count($elements["annotations"]) ){
-			$annotations = $elements["annotations"];
-		}
-		if ( isset($elements["relations"]) && count($elements["relations"]) ){
-			$relations = $elements["relations"];
-		}
-		if ( isset($elements["lemmas"]) && count($elements["lemmas"]) ){
-			$lemmas = $elements["lemmas"];
-		}
 
-        if ( isset($elements["attributes"]) && count($elements["attributes"]) ){
-            $attributes = $elements["attributes"];
-        }
+		list($annotations,$relations,$lemmas,$attributes) = $this->dispatchElements($elements);
 
 		/* Usunięcie zduplikowanych anotacji */
 		$annotations_by_id = $this->sortUniqueAnnotationsById($annotations);
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
index 52889207..0b2992d1 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
@@ -41,7 +41,8 @@ public function testExport_documentCallsAllProcessingMethods() {
                             'updateLists','createIniFile',
 							'checkIfAnnotationForLemmaExists',
                             'checkIfAnnotationForRelationExists',
-							'sortUniqueAnnotationsById'))
+							'sortUniqueAnnotationsById',
+							'dispatchElements'))
             -> getMock();
         $mockCorpusExporter -> method('getFlagsByReportId')
             -> will($this->returnValue($reportFlags));
@@ -53,20 +54,26 @@ public function testExport_documentCallsAllProcessingMethods() {
             -> will($this->returnValue($report));
 
         // tested methods called exactly once with proper args:
+		$expectedElements = array("annotations"=>array(), "relations"=>array(), "lemmas"=>array(), "attributes"=>array());
+		$returnedTableList = [array(),array(),array(),array()];
+        $mockCorpusExporter -> expects($this->once())
+            ->method('dispatchElements')
+            ->with($expectedElements)
+            -> will($this->returnValue($returnedTableList));
 		$expectedAnnotations = array();
-		$expectedAnnotationsById = array();;
+		$returnedAnnotationsById = array();
         $mockCorpusExporter -> expects($this->once())
             ->method('sortUniqueAnnotationsById')
             ->with($expectedAnnotations)
-			-> will($this->returnValue($expectedAnnotationsById));
+			-> will($this->returnValue($returnedAnnotationsById));
         $expectedRelations = array();
         $mockCorpusExporter -> expects($this->once())
             ->method('checkIfAnnotationForRelationExists')
-            ->with($expectedRelations,$expectedAnnotationsById);
+            ->with($expectedRelations,$returnedAnnotationsById);
         $expectedLemmas = array();
         $mockCorpusExporter -> expects($this->once())
             ->method('checkIfAnnotationForLemmaExists')
-            ->with($expectedLemmas,$expectedAnnotationsById);
+            ->with($expectedLemmas,$returnedAnnotationsById);
         $expectedReportArg = $report;
         $expectedBaseFileName = $output_folder.'/'.str_pad($report_id,8,'0',STR_PAD_LEFT);
         $mockCorpusExporter -> expects($this->once())
@@ -461,6 +468,36 @@ public function testSortuniqueannotationsbyidSetInternalError() {
 
     } // testSortuniqueannotationsbyidSetInternalError()
 
+// protected function dispatchElements($elements) 
+
+    public function testDispatchelementsGeneratesTableList() {
+
+		$annotations = array( 'tableName' => 'annotations' );
+		$relations = array( 'tableName' => 'relations' );
+		$lemmas = array( 'tableName' => 'lemmas' );
+		$attributes = array( 'tableName' => 'attributes' );
+		$elements = array(
+			"annotations" => $annotations,
+			"relations" => $relations,
+			"lemmas" => $lemmas,
+			"attributes" => $attributes
+		);
+
+        // reflection for access to private elements
+        $protectedMethod = new ReflectionMethod('CorpusExporter','dispatchElements');
+        $protectedMethod->setAccessible(True);
+        $ce = new CorpusExporter();
+        $export_errorsPrivateProperty = new ReflectionProperty($ce,'export_errors');
+        $export_errorsPrivateProperty->setAccessible(True);
+
+        $result=$protectedMethod->invokeArgs($ce,array($elements));
+
+		$expectedTableList = [$annotations,$relations,$lemmas,$attributes];
+		$this->assertEquals($expectedTableList,$result);
+
+    } // testDispatchelementsGeneratesTableList()
+
+
 } // CorpusExporter_part10_Test class
 
 ?>

From 7c0e5024f3f345ebf9347d850d18804eee810354 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Thu, 16 Nov 2023 10:35:38 +0100
Subject: [PATCH 129/154] extract method for generateCcl for export

---
 engine/include/export/CorpusExporter.php      | 31 +++++++-
 .../export/CorpusExporter_part10_Test.php     | 73 ++++++++++++++++++-
 2 files changed, 102 insertions(+), 2 deletions(-)

diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index b0c19cb9..a382514e 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -625,6 +625,31 @@ protected function dispatchElements($elements) {
 
     } // dispatchElements()
 
+    protected function callCclCreator($report,$tokens,$tags_by_tokens) {
+
+        // call static method which may throw exception
+        return CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
+
+    } // callCclCreator()
+
+	protected function generateCcl($report,$tokens,$tags_by_tokens) {
+
+        try{
+            $ccl = $this->callCclCreator($report, $tokens, $tags_by_tokens);
+        }
+        catch(Exception $ex){
+            $error = $ex->getMessage();
+            $error_params = array(
+                'message' => "Problem z utworzeniem CCL",
+                'error' => $error
+            );
+            $this->log_error(__FILE__, __LINE__, $report_id, "Problem z utworzeniem ccl: " . $error, 2, $error_params);
+            return False; // error is collected
+        }
+		return $ccl; // all ok
+
+	} // generateCcl() 
+
 	/**
 	 * Eksport dokumentu o wskazanym identyfikatorze
 	 * @param $report_id Identyfikator dokumentu do eksportu
@@ -674,6 +699,10 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
 		$tags_by_tokens = $this->getReportTagsByTokens($report_id, $tokens_ids, $disamb_only, $tagging_method);
 
 		$report = $this->getReportById($report_id);
+
+		$ccl = $this->generateCcl($report,$tokens,$tags_by_tokens);
+		if($ccl===False) { return; }
+/* 
 		try{
 			$ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
 		}
@@ -685,7 +714,7 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
 			);
 			$this->log_error(__FILE__, __LINE__, $report_id, "Problem z utworzeniem ccl: " . $error, 2, $error_params);
 			return;
-		}
+		}*/
 
 		list($annotations,$relations,$lemmas,$attributes) = $this->dispatchElements($elements);
 
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
index 0b2992d1..e2acae58 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
@@ -7,6 +7,15 @@ class CorpusExporter_part10_Test extends PHPUnit_Framework_TestCase
 {
     private $virtualDir = null;
 
+    private function createAccessToProtectedMethodOfClassObject($classObject,$method) {
+
+        // reflection for access to private method
+        $protectedMethod = new ReflectionMethod($classObject,$method);
+        $protectedMethod->setAccessible(True);
+		return $protectedMethod;
+		
+    } // createAccessToProtectedMethodOfClassObject() 
+
     protected function setUp() {
 
         $this->virtualDir = vfsStream::setup('root',null,[]);
@@ -42,7 +51,7 @@ public function testExport_documentCallsAllProcessingMethods() {
 							'checkIfAnnotationForLemmaExists',
                             'checkIfAnnotationForRelationExists',
 							'sortUniqueAnnotationsById',
-							'dispatchElements'))
+							'dispatchElements','generateCcl'))
             -> getMock();
         $mockCorpusExporter -> method('getFlagsByReportId')
             -> will($this->returnValue($reportFlags));
@@ -54,6 +63,16 @@ public function testExport_documentCallsAllProcessingMethods() {
             -> will($this->returnValue($report));
 
         // tested methods called exactly once with proper args:
+        $expectedReport = $report;
+        $expectedTokens = $reportTokens;
+        $expectedTagsByTokens = array();
+		$fileName = str_pad($report_id,8,'0',STR_PAD_LEFT);
+		$returnedCcl = new CclDocument(); 
+        $returnedCcl -> setFileName($fileName); 
+        $mockCorpusExporter -> expects($this->once())
+            ->method('generateCcl')
+            ->with($expectedReport,$expectedTokens,$expectedTagsByTokens)
+            -> will($this->returnValue($returnedCcl));
 		$expectedElements = array("annotations"=>array(), "relations"=>array(), "lemmas"=>array(), "attributes"=>array());
 		$returnedTableList = [array(),array(),array(),array()];
         $mockCorpusExporter -> expects($this->once())
@@ -497,6 +516,58 @@ public function testDispatchelementsGeneratesTableList() {
 
     } // testDispatchelementsGeneratesTableList()
 
+// protected function generateCcl($report,$tokens,$tags_by_tokens) 
+
+    public function testGeneratecclReturnsObjectofCclDocumentClass() {
+
+		$report_id = 12;
+		$report = array( 'id'=>$report_id );
+		$tokens = array();
+		$tags_by_tokens = array();
+	
+		$ce = new CorpusExporter();
+		$protectedMethod = $this->createAccessToProtectedMethodOfClassObject($ce,'generateCcl');
+		$result=$protectedMethod->invokeArgs($ce,array($report,$tokens,$tags_by_tokens));
+
+		// result is object of CclDocument class
+		$this->assertInstanceOf('CclDocument',$result);
+		// Ccl->fileName is set to name coresponding to report_id
+		$expectedFileName = str_pad($report_id,8,'0',STR_PAD_LEFT);
+		$this->assertEquals($expectedFileName,$result->getFilename());
+
+    } // testGeneratecclReturnsObjectofCclDocumentClass() 
+
+    public function testGeneratecclOnExceptionReturnsFalse() {
+
+        $report_id = 13; 
+        $report = array();
+        $tokens = array();
+        $tags_by_tokens = array();
+
+		// mocking for throw exception emulate
+        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
+            -> disableArgumentCloning()
+            -> setMethods(array('callCclCreator'))
+            -> getMock();
+        $mockCorpusExporter -> method('callCclCreator')
+			-> will($this->throwException(new Exception()));         
+
+        $protectedMethod = $this->createAccessToProtectedMethodOfClassObject($mockCorpusExporter,'generateCcl');
+        $export_errorsPrivateProperty = new ReflectionProperty($mockCorpusExporter,'export_errors');
+        $export_errorsPrivateProperty->setAccessible(True);
+
+        $result=$protectedMethod->invokeArgs($mockCorpusExporter,array($report,$tokens,$tags_by_tokens));
+
+        // result should be false
+        $this->assertFalse($result);
+        // internal errors table
+        $internalErrorsTable = $export_errorsPrivateProperty->getValue($mockCorpusExporter);
+        $expectedErrorsCount = 1;
+        $this->assertEquals($expectedErrorsCount,count($internalErrorsTable));
+        $expectedErrorsKey = "Problem z utworzeniem CCL";
+        $this->assertEquals($expectedErrorsKey,$internalErrorsTable[2]['message']);
+
+    } // testGeneratecclOnBadDataReturnsFalse()
 
 } // CorpusExporter_part10_Test class
 

From 656c9470c34b2ad05ada1298d60a8fa7184542bb Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Thu, 16 Nov 2023 13:06:07 +0100
Subject: [PATCH 130/154] extract updateExtractorStats method

---
 engine/include/export/CorpusExporter.php      | 46 +++++++++----------
 .../export/CorpusExporter_part10_Test.php     | 34 ++++++++++++++
 2 files changed, 55 insertions(+), 25 deletions(-)

diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index a382514e..2c63ffee 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -650,6 +650,26 @@ protected function generateCcl($report,$tokens,$tags_by_tokens) {
 
 	} // generateCcl() 
 
+    protected function updateExtractorStats($extractorName,$extractor_stats,$extractor_elements) {
+
+		// update $extractor_stats table, for index $extractorName 
+		//  	with counter from $extractor_elements results
+		// Returns updated stats table
+		$name = $extractorName;
+		if ( !isset($extractor_stats[$name]) ){
+			$extractor_stats[$name] = array();
+		}
+		foreach ( $extractor_elements as $type=>$items ){
+			if ( !isset($extractor_stats[$name][$type]) ){
+				$extractor_stats[$name][$type] = count($items);
+			} else {
+				$extractor_stats[$name][$type] += count($items);
+			}
+		}
+		return $extractor_stats;
+
+    } // updateExtractorStats()
+
 	/**
 	 * Eksport dokumentu o wskazanym identyfikatorze
 	 * @param $report_id Identyfikator dokumentu do eksportu
@@ -678,18 +698,7 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
 					$elements[$key] = array_merge($elements[$key], $extractor_elements[$key]);
 				}
 				// Zapisz statystyki
-				$name = $extractor["name"];
-				if ( !isset($extractor_stats[$name]) ){
-					$extractor_stats[$name] = array();
-				}
-				foreach ( $extractor_elements as $type=>$items ){
-					if ( !isset($extractor_stats[$name][$type]) ){
-						$extractor_stats[$name][$type] = count($items);
-					}
-					else{
-						$extractor_stats[$name][$type] += count($items);
-					}
-				}
+				$extractor_stats = $this->updateExtractorStats($extractor["name"],$extractor_stats,$extractor_elements); 
 			}
 		}
 
@@ -702,19 +711,6 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
 
 		$ccl = $this->generateCcl($report,$tokens,$tags_by_tokens);
 		if($ccl===False) { return; }
-/* 
-		try{
-			$ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
-		}
-		catch(Exception $ex){
-			$error = $ex->getMessage();
-			$error_params = array(
-				'message' => "Problem z utworzeniem CCL",
-				'error' => $error
-			);
-			$this->log_error(__FILE__, __LINE__, $report_id, "Problem z utworzeniem ccl: " . $error, 2, $error_params);
-			return;
-		}*/
 
 		list($annotations,$relations,$lemmas,$attributes) = $this->dispatchElements($elements);
 
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
index e2acae58..3d8ee07f 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
@@ -63,6 +63,7 @@ public function testExport_documentCallsAllProcessingMethods() {
             -> will($this->returnValue($report));
 
         // tested methods called exactly once with proper args:
+		$extractorName = 'nazwa_extraktora';
         $expectedReport = $report;
         $expectedTokens = $reportTokens;
         $expectedTagsByTokens = array();
@@ -569,6 +570,39 @@ public function testGeneratecclOnExceptionReturnsFalse() {
 
     } // testGeneratecclOnBadDataReturnsFalse()
 
+// protected function updateExtractorStats($extractorName,$extractor_stats,$extractor_elements) 
+
+	public function testUpdateextractorstatsUpdatesStatsTable() {
+
+        $extractorName = 'nazwa_extraktora';
+		$existentType 	= 'typ istniejący';
+		$existentCount	= 219;
+        $newType    = 'niestniejacy typ';
+        $arrWith2Items = array( 3,4 );
+		$extractor_stats = array(
+            $extractorName => array(
+			    $existentType => $existentCount 
+            )
+		);
+		$extractor_elements = array(
+	        $newType => $arrWith2Items,
+            $existentType => $arrWith2Items
+		);	
+
+        $ce = new CorpusExporter();
+        $protectedMethod = $this->createAccessToProtectedMethodOfClassObject($ce,'updateExtractorStats');
+        $result=$protectedMethod->invokeArgs($ce,array($extractorName,$extractor_stats,$extractor_elements));
+
+		$expectedStats = array(
+			$extractorName => array(
+                $existentType => $existentCount + 2,
+                $newType => 2 // count of $arrWith2Items 
+            )
+		);
+		$this->assertEquals($expectedStats,$result);
+
+	} // testUpdateextractorstatsUpdatesStatsTable()
+
 } // CorpusExporter_part10_Test class
 
 ?>

From ba0de59ffa37051e4a52555cd44e272e090422c2 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Thu, 16 Nov 2023 19:36:07 +0100
Subject: [PATCH 131/154] extract runExtractor method

---
 engine/include/export/CorpusExporter.php      | 44 ++++++----
 .../export/CorpusExporter_part10_Test.php     | 82 ++++++++++++++++++-
 2 files changed, 106 insertions(+), 20 deletions(-)

diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index 2c63ffee..180eeb2b 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -670,6 +670,31 @@ protected function updateExtractorStats($extractorName,$extractor_stats,$extract
 
     } // updateExtractorStats()
 
+    protected function runExtractor($flags,$report_id,$extractor,&$elements,&$extractor_stats) {
+
+		// Wykonaj extraktor w zależności od ustalonej flagi
+		$func = $extractor["extractor"];
+      	$params = $extractor["params"];
+      	$flag_name = $extractor["flag_name"];
+      	$flag_ids = $extractor["flag_ids"];
+     	if ( isset($flags[$flag_name]) && in_array($flags[$flag_name], $flag_ids) ){
+   			$extractor_elements = array();
+       		foreach (array_keys($elements) as $key){
+				$extractor_elements[$key] = array();
+			}
+
+			$func($report_id, $params, $extractor_elements);
+
+			foreach (array_keys($extractor_elements) as $key){
+     			$elements[$key] = array_merge($elements[$key], $extractor_elements[$key]);
+     		}
+
+   			// Zapisz statystyki
+			$extractor_stats = $this->updateExtractorStats($extractor["name"],$extractor_stats,$extractor_elements);
+		} // if flags is set
+ 
+    } // runExtractorFunction()
+
 	/**
 	 * Eksport dokumentu o wskazanym identyfikatorze
 	 * @param $report_id Identyfikator dokumentu do eksportu
@@ -682,24 +707,9 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
 		$flags = $this->getFlagsByReportId($report_id);
 		$elements = array("annotations"=>array(), "relations"=>array(), "lemmas"=>array(), "attributes"=>array());
 
-		// Wykonaj extraktor w zależności od ustalonej flagi
+		// Wykonaj extraktory w zależności od ustalonej flagi
 		foreach ( $extractors as $extractor ){
-			$func = $extractor["extractor"];
-			$params = $extractor["params"];
-			$flag_name = $extractor["flag_name"];
-			$flag_ids = $extractor["flag_ids"];
-			if ( isset($flags[$flag_name]) && in_array($flags[$flag_name], $flag_ids) ){
-				$extractor_elements = array();
-				foreach (array_keys($elements) as $key){
-					$extractor_elements[$key] = array();
-				}
-				$func($report_id, $params, $extractor_elements);
-				foreach (array_keys($extractor_elements) as $key){
-					$elements[$key] = array_merge($elements[$key], $extractor_elements[$key]);
-				}
-				// Zapisz statystyki
-				$extractor_stats = $this->updateExtractorStats($extractor["name"],$extractor_stats,$extractor_elements); 
-			}
+			$this->runExtractor($flags,$report_id,$extractor,$elements,$extractor_stats);
 		}
 
 		$tokens = $this->getTokenByReportId($report_id);
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
index 3d8ee07f..855408ba 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
@@ -27,7 +27,8 @@ protected function setUp() {
     public function testExport_documentCallsAllProcessingMethods() {
         // export_document() dumb parameters
         $report_id = 1;
-        $extractors = array();
+        $fakeExtractor = array();
+        $extractors = array( $fakeExtractor );
         $disamb_only = true;
         $extractor_stats = array();
         $lists = array();
@@ -51,7 +52,8 @@ public function testExport_documentCallsAllProcessingMethods() {
 							'checkIfAnnotationForLemmaExists',
                             'checkIfAnnotationForRelationExists',
 							'sortUniqueAnnotationsById',
-							'dispatchElements','generateCcl'))
+							'dispatchElements','generateCcl',
+                            'runExtractor'))
             -> getMock();
         $mockCorpusExporter -> method('getFlagsByReportId')
             -> will($this->returnValue($reportFlags));
@@ -63,7 +65,18 @@ public function testExport_documentCallsAllProcessingMethods() {
             -> will($this->returnValue($report));
 
         // tested methods called exactly once with proper args:
-		$extractorName = 'nazwa_extraktora';
+        $expectedFlags = $reportFlags;
+        $expectedExtractor = $fakeExtractor;
+        $expectedElements = array(
+            'annotations' => array(),
+            'relations' => array(),
+            'lemmas' => array(),
+            'attributes' => array()
+        );
+        $expectedExtractorStats = $extractor_stats;
+        $mockCorpusExporter -> expects($this->once())
+            ->method('runExtractor')
+            ->with($expectedFlags,$report_id,$expectedExtractor,$expectedElements,$expectedExtractorStats);
         $expectedReport = $report;
         $expectedTokens = $reportTokens;
         $expectedTagsByTokens = array();
@@ -603,6 +616,69 @@ public function testUpdateextractorstatsUpdatesStatsTable() {
 
 	} // testUpdateextractorstatsUpdatesStatsTable()
 
+// protected function runExtractor($flags,$report_id,$extractor,&$elements,&$extractor_stats) 
+
+    public function testRunextractorsReturnsChangedElementsAndStats() {
+
+        $report_id = 13;
+        $annotation1 = array( "id"=>17, "other_field"=>"sth" );
+        $flagId = -1;
+        $flagName = 'xxx'; $flagIds = [$flagId,0,1];
+        $flags = array( $flagName=>$flagId );
+        $extractorName = "exName";
+        $extractorFunc = function ($report_id, $params, &$elements) {
+                $elements["annotations"]=array(
+                    array( "id"=>17, "other_field"=>"sth" )  // $annotation1
+                );
+        };
+        $extractor = array( 
+            "name"      =>  $extractorName,
+            "flag_name" =>  $flagName,
+            "flag_ids"  =>  $flagIds,
+            "extractor" =>  $extractorFunc,
+            "params"    => array()
+        ); 
+        $elements = array(
+            "annotations"   => array(),
+            "relations"     => array(),
+            "lemmas"        => array(),
+            "attributes"    => array(),
+        );
+        $extractor_stats = array();
+
+        // mocking for throw exception emulate
+        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
+            -> disableArgumentCloning()
+            -> setMethods(array('updateExtractorStats'))
+            -> getMock();
+        $expectedName = $extractorName;
+        $expectedStats = array();
+        $expectedElements = array(
+            "annotations"   => array($annotation1),
+            "relations"     => array(),
+            "lemmas"        => array(),
+            "attributes"    => array(),
+        );
+        $returnedStats = array(
+            $extractorName  => array("annotations"=>1,"relations"=>0,"lemmas"=>0,"attributes"=>0)
+        );
+
+        $mockCorpusExporter -> expects($this->once())
+			-> method('updateExtractorStats')
+            -> with($expectedName,$expectedStats,$expectedElements)
+            -> will($this->returnValue($returnedStats));
+
+        $protectedMethod = $this->createAccessToProtectedMethodOfClassObject($mockCorpusExporter,'runExtractor');
+
+        $protectedMethod->invokeArgs($mockCorpusExporter,array($flags,$report_id,$extractor,&$elements,&$extractor_stats));
+
+        $expectedAnnotationsElements = array($annotation1);
+        $this->assertEquals($expectedAnnotationsElements,$elements["annotations"]);
+        $expectedStats = $returnedStats;
+        $this->assertEquals($expectedStats,$extractor_stats);
+
+    } // testRunextractorsReturnsChangedElementsAndStats()
+    
 } // CorpusExporter_part10_Test class
 
 ?>

From fabaf83dc0b023ca459ec3cd523e2606a33178df Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Mon, 27 Nov 2023 10:01:47 +0100
Subject: [PATCH 132/154] more reflection methods in tests

---
 engine/include/writers/CCclWriter.php         |  32 ++-
 phpunit/classes/CorpusExporter_mock.php       |  25 --
 phpunit/classes/TestAccessTools.php           |  15 ++
 .../export/CorpusExporter_part0_Test.php      |  25 +-
 .../export/CorpusExporter_part10_Test.php     |  17 +-
 .../export/CorpusExporter_part11_Test.php     | 230 ++++++++++++++++++
 .../export/CorpusExporter_part1_Test.php      |   6 +-
 .../export/CorpusExporter_part2_Test.php      |   5 +-
 .../export/CorpusExporter_part3_Test.php      |   5 +-
 .../export/CorpusExporter_part4_Test.php      |   5 +-
 .../export/CorpusExporter_part5_Test.php      |   5 +-
 .../export/CorpusExporter_part6_Test.php      |   5 +-
 .../export/CorpusExporter_part7_Test.php      |   5 +-
 .../export/CorpusExporter_part8_Test.php      |   5 +-
 .../export/CorpusExporter_part_Test.php       |   5 +-
 .../engine/include/writers/CCclWriterTest.php |  77 ++++++
 16 files changed, 389 insertions(+), 78 deletions(-)
 delete mode 100644 phpunit/classes/CorpusExporter_mock.php
 create mode 100644 phpunit/classes/TestAccessTools.php
 create mode 100644 phpunit/tests/engine/include/export/CorpusExporter_part11_Test.php

diff --git a/engine/include/writers/CCclWriter.php b/engine/include/writers/CCclWriter.php
index fc6823c2..29adf105 100644
--- a/engine/include/writers/CCclWriter.php
+++ b/engine/include/writers/CCclWriter.php
@@ -18,8 +18,26 @@ private function writeTextToFile($fileName,$text) {
         fclose($handle);
 
     } // writeTextToFile()
+
+    protected function formatPropToXML($propTable) {
+
+        $xml = ""; // for no data
+        if (($propTable) && is_array($propTable)) {
+            foreach ($propTable as $key=>$val) {
+                if (strpos($val, ';;') !== FALSE){
+                    $values = explode(";;", $val);
+                    $xml .= sprintf("    <prop key=\"%s\">%s</prop>\n", htmlspecialchars(str_replace("lemma", "lval", $key)), htmlspecialchars($values[0]));
+                    $xml .= sprintf("    <prop key=\"%s\">%s</prop>\n", htmlspecialchars(str_replace("lemma", "val", $key)), htmlspecialchars($values[1]));
+                } else {
+                    $xml .= sprintf("    <prop key=\"%s\">%s</prop>\n", htmlspecialchars($key), htmlspecialchars($val));
+                }
+            } // foreach
+        } // if is_array
+        return $xml; 
+
+    } // formatPropToXML()
 	
-    private function makeXmlData($ccl,$mode) {
+    private static function makeXmlData($ccl,$mode) {
 
 		$xml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
 		$xml .= "<!DOCTYPE chunkList SYSTEM \"ccl.dtd\">\n";
@@ -46,17 +64,7 @@ private function makeXmlData($ccl,$mode) {
 						}
 						foreach ($channels as $type=>$number)
 							$xml .= "    <ann chan=\"{$type}\">{$number}</ann>\n";
-						if ($token->prop){
-							foreach ($token->prop as $key=>$val){
-								if (strpos($val, ';;') !== FALSE){
-									$values = explode(";;", $val);
-									$xml .= sprintf("    <prop key=\"%s\">%s</prop>\n", htmlspecialchars(str_replace("lemma", "lval", $key)), htmlspecialchars($values[0]));
-									$xml .= sprintf("    <prop key=\"%s\">%s</prop>\n", htmlspecialchars(str_replace("lemma", "val", $key)), htmlspecialchars($values[1]));
-								}
-								else
-									$xml .= sprintf("    <prop key=\"%s\">%s</prop>\n", htmlspecialchars($key), htmlspecialchars($val));
-							}
-						}
+                        $xml.= self::formatPropToXML($token->prop);
 						$xml .= $token->ns ? "   </tok>\n   <ns/>\n" : "   </tok>\n";
 					}
 					$xml .= "  </sentence>\n";
diff --git a/phpunit/classes/CorpusExporter_mock.php b/phpunit/classes/CorpusExporter_mock.php
deleted file mode 100644
index 56234c22..00000000
--- a/phpunit/classes/CorpusExporter_mock.php
+++ /dev/null
@@ -1,25 +0,0 @@
-<?php
-
-class CorpusExporter_mock extends CorpusExporter {
-
-    // access to protected method in CorpusExporter:
-    //   parse_extractor($description)
-    // which are not needed for rest of application. Should be
-    // private in future
-
-    public function mock_parse_extractor($description){
-
-        return $this->parse_extractor($description);
-
-    } // mock_parse_extractor()
-
-    public function mock_export_document($report_id, $extractors, $disamb_only, &$extractor_stats, &$lists, $output_folder, $subcorpora, $tagging_method){
-
-        // returns void
-        $this->export_document($report_id, $extractors, $disamb_only, $extractor_stats, $lists, $output_folder, $subcorpora, $tagging_method);
-
-    } // mock_export_document()
-
-} // CorpusExporter_mock class
-
-?>
diff --git a/phpunit/classes/TestAccessTools.php b/phpunit/classes/TestAccessTools.php
new file mode 100644
index 00000000..6df3455c
--- /dev/null
+++ b/phpunit/classes/TestAccessTools.php
@@ -0,0 +1,15 @@
+<?php
+
+class TestAccessTools {
+
+    static function createAccessToProtectedMethodOfClassObject($classObject,$method) {
+        // reflection for access to private method
+        $protectedMethod = new ReflectionMethod($classObject,$method);
+        $protectedMethod->setAccessible(True);
+        return $protectedMethod;
+
+    } // createAccessToProtectedMethodOfClassObject()
+
+} // TestAccessTools()
+
+?>
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php
index 24ad207e..90d60107 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php
@@ -10,10 +10,11 @@ class CorpusExporter_part0_Test extends CorpusExporterTest
     public function test_parse_extractor_throwsException_on_emptyText(){
 
         $emptyData = '';
-        $ce = new CorpusExporter_mock();
+        $ce = new CorpusExporter();
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'parse_extractor');
 
         try {
-            $result = $ce->mock_parse_extractor($emptyData);
+            $result = $protectedMethod->invokeArgs($ce,array($emptyData));
         } catch(Exception $e) {
             // expected Exception "Niepoprawny opis ekstraktora "
             $this->assertInstanceOf(\Exception::class,$e);
@@ -28,10 +29,11 @@ public function test_parse_extractor_throwsException_on_emptyText(){
     public function test_parse_extractor_throwsException_on_ambigousText(){
 
         $syntacticallyImproperData = 'jakieś bzdury';
-        $ce = new CorpusExporter_mock();
+        $ce = new CorpusExporter();
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'parse_extractor');
 
         try {
-            $result = $ce->mock_parse_extractor($syntacticallyImproperData);
+            $result = $protectedMethod->invokeArgs($ce,array($syntacticallyImproperData));
         } catch(Exception $e) {
             // expected Exception "Niepoprawny opis ekstraktora "
             $this->assertInstanceOf(\Exception::class,$e);
@@ -46,10 +48,11 @@ public function test_parse_extractor_throwsException_on_ambigousText(){
     public function test_parse_extractor_throwsException_on_nonText(){
 
         $nonTextData = array();
-        $ce = new CorpusExporter_mock();
+        $ce = new CorpusExporter();
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'parse_extractor');
 
         try {
-            $result = $ce->mock_parse_extractor($emptyData);
+            $result = $result = $protectedMethod->invokeArgs($ce,array($emptyData));
         } catch(Exception $e) {
             // expected Exception "Niepoprawny opis ekstraktora "
             $this->assertInstanceOf(\Exception::class,$e);
@@ -73,8 +76,9 @@ public function test_parse_extractor()
 		// zamieniamy nazwę flagi na duże litery, aby stestować lowercasing
 		$extractorDescriptionwithUC = str_replace('dg','DG',$extractorDescription);
 
-        $ce = new CorpusExporter_mock();
-        $result = $ce->mock_parse_extractor($extractorDescriptionwithUC);
+        $ce = new CorpusExporter();
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'parse_extractor');
+        $result = $protectedMethod->invokeArgs($ce,array($extractorDescriptionwithUC));
 /*
 +        'flag_name' => '1_key_dg'
 +        'flag_ids' => Array (...)
@@ -210,8 +214,9 @@ public function test_parse_extractor()
 
 
 
-        $ce = new CorpusExporter_mock();
-        $result = $ce->mock_parse_extractor($extractorDescription);
+        $ce = new CorpusExporter();
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'parse_extractor');
+        $result = $protectedMethod->invokeArgs($ce,array($extractorDescription));
 /*
         var_dump($result);
   [0]=> array(5) {
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
index 855408ba..e5a766a6 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
@@ -7,15 +7,6 @@ class CorpusExporter_part10_Test extends PHPUnit_Framework_TestCase
 {
     private $virtualDir = null;
 
-    private function createAccessToProtectedMethodOfClassObject($classObject,$method) {
-
-        // reflection for access to private method
-        $protectedMethod = new ReflectionMethod($classObject,$method);
-        $protectedMethod->setAccessible(True);
-		return $protectedMethod;
-		
-    } // createAccessToProtectedMethodOfClassObject() 
-
     protected function setUp() {
 
         $this->virtualDir = vfsStream::setup('root',null,[]);
@@ -540,7 +531,7 @@ public function testGeneratecclReturnsObjectofCclDocumentClass() {
 		$tags_by_tokens = array();
 	
 		$ce = new CorpusExporter();
-		$protectedMethod = $this->createAccessToProtectedMethodOfClassObject($ce,'generateCcl');
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'generateCcl');
 		$result=$protectedMethod->invokeArgs($ce,array($report,$tokens,$tags_by_tokens));
 
 		// result is object of CclDocument class
@@ -566,7 +557,7 @@ public function testGeneratecclOnExceptionReturnsFalse() {
         $mockCorpusExporter -> method('callCclCreator')
 			-> will($this->throwException(new Exception()));         
 
-        $protectedMethod = $this->createAccessToProtectedMethodOfClassObject($mockCorpusExporter,'generateCcl');
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($mockCorpusExporter,'generateCcl');
         $export_errorsPrivateProperty = new ReflectionProperty($mockCorpusExporter,'export_errors');
         $export_errorsPrivateProperty->setAccessible(True);
 
@@ -603,7 +594,7 @@ public function testUpdateextractorstatsUpdatesStatsTable() {
 		);	
 
         $ce = new CorpusExporter();
-        $protectedMethod = $this->createAccessToProtectedMethodOfClassObject($ce,'updateExtractorStats');
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'updateExtractorStats');
         $result=$protectedMethod->invokeArgs($ce,array($extractorName,$extractor_stats,$extractor_elements));
 
 		$expectedStats = array(
@@ -668,7 +659,7 @@ public function testRunextractorsReturnsChangedElementsAndStats() {
             -> with($expectedName,$expectedStats,$expectedElements)
             -> will($this->returnValue($returnedStats));
 
-        $protectedMethod = $this->createAccessToProtectedMethodOfClassObject($mockCorpusExporter,'runExtractor');
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($mockCorpusExporter,'runExtractor');
 
         $protectedMethod->invokeArgs($mockCorpusExporter,array($flags,$report_id,$extractor,&$elements,&$extractor_stats));
 
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part11_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part11_Test.php
new file mode 100644
index 00000000..6a0f221a
--- /dev/null
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part11_Test.php
@@ -0,0 +1,230 @@
+<?php
+
+use org\bovigo\vfs\vfsStream; // for vfsStream
+mb_internal_encoding("UTF-8");
+
+class CorpusExporter_part11_Test extends PHPUnit_Framework_TestCase
+{
+    // tests with lemma fields sets    
+
+    private $virtualDir = null;
+
+// protected function runExtractor($flags,$report_id,$extractor,&$elements,&$extractor_stats) 
+
+    // 2a
+    public function testRunextractorsForExtractorCustomAnnotationsSetsLemmaFieldsInElementsAnnotationsSection() {
+
+        $report_id = 13;
+        // annotacja z pustym lematem, z wykonania LEFT JOIN
+        $annotation1 = array( "id"=>1, "orth"=>"nam_adj", "lemma"=>NULL );
+        // annotacja z niepustym lematem
+        $annotation2 = array( "id"=>2, "orth"=>"nam_orth", "lemma"=>"lemat1" );
+        $flagId = -1;
+        $flagName = 'xxx'; $flagIds = [$flagId,0,1];
+        $flags = array( $flagName=>$flagId );
+        $extractorName = "exName";
+        $extractorFunc = function ($report_id, $params, &$elements) {
+                $elements["annotations"]=array(
+                    // annotation 1
+                    array( "id"=>1, "orth"=>"nam_adj", "lemma"=>NULL ),
+                    // annotation 2
+                    array( "id"=>2, "orth"=>"nam_orth", "lemma"=>"lemat1" )
+                );
+        };
+        $extractor = array( 
+            "name"      =>  $extractorName,
+            "flag_name" =>  $flagName,
+            "flag_ids"  =>  $flagIds,
+            "extractor" =>  $extractorFunc,
+            "params"    => array()
+        ); 
+        $elements = array(
+            "annotations"   => array(),
+            "relations"     => array(),
+            "lemmas"        => array(),
+            "attributes"    => array(),
+        );
+        $extractor_stats = array();
+
+        // mocking for throw exception emulate
+        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
+            -> disableArgumentCloning()
+            -> setMethods(array('updateExtractorStats'))
+            -> getMock();
+        $expectedName = $extractorName;
+        $expectedStats = array();
+        $expectedElements = array(
+            "annotations"   => array($annotation1,$annotation2),
+            "relations"     => array(),
+            "lemmas"        => array(),
+            "attributes"    => array(),
+        );
+        $returnedStats = array(
+            $extractorName  => array("annotations"=>2,"relations"=>0,"lemmas"=>0,"attributes"=>0)
+        );
+
+        $mockCorpusExporter -> expects($this->once())
+			-> method('updateExtractorStats')
+            -> with($expectedName,$expectedStats,$expectedElements)
+            -> will($this->returnValue($returnedStats));
+
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($mockCorpusExporter,'runExtractor');
+        $protectedMethod->invokeArgs($mockCorpusExporter,array($flags,$report_id,$extractor,&$elements,&$extractor_stats));
+
+        $expectedElements = array(
+            "annotations" => array( $annotation1, $annotation2 ),
+            "relations"=>[], "lemmas"=>[], "attributes"=>[]
+        );
+        $this->assertEquals($expectedElements,$elements);
+        $expectedStats = $returnedStats;
+        $this->assertEquals($expectedStats,$extractor_stats);
+
+    } // testRunextractorsForExtractorCustomAnnotationsSetsLemmaFieldsInElementsAnnotationsSection()
+    
+    // 2b
+    public function testRunextractorsForExtractorCustomLemmasSetsLemmaFieldsInElementsAnnotationsAndLemmasSection() {
+
+        $report_id = 13;
+        // annotacja z pustym lematem, z wykonania LEFT JOIN
+        $annotation1 = array( "id"=>1, "orth"=>"nam_adj", "lemma"=>NULL );
+        // annotacja z niepustym lematem
+        $annotation2 = array( "id"=>2, "orth"=>"nam_orth", "lemma"=>"lemat1" );
+        $lemma2 = array( "report_annotation_id" => "2", "lemma" => "lemat1", "id"=>2 );
+        $flagId = -1;
+        $flagName = 'xxx'; $flagIds = [$flagId,0,1];
+        $flags = array( $flagName=>$flagId );
+        $extractorName = "exName";
+        $extractorFunc = function ($report_id, $params, &$elements) {
+                $elements["annotations"]=array(
+                    // annotation 1
+                    array( "id"=>1, "orth"=>"nam_adj", "lemma"=>NULL ),
+                    // annotation 2
+                    array( "id"=>2, "orth"=>"nam_orth", "lemma"=>"lemat1" )
+                );
+                $elements["lemmas"]=array(
+                    // lemma2
+                    array( "report_annotation_id" => "2", "lemma" => "lemat1", "id"=>2 )
+                );
+        };
+        $extractor = array(
+            "name"      =>  $extractorName,
+            "flag_name" =>  $flagName,
+            "flag_ids"  =>  $flagIds,
+            "extractor" =>  $extractorFunc,
+            "params"    => array()
+        );
+        $elements = array(
+            "annotations"   => array(),
+            "relations"     => array(),
+            "lemmas"        => array(),
+            "attributes"    => array(),
+        );
+        $extractor_stats = array();
+ 
+        // mocking for throw exception emulate
+        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
+            -> disableArgumentCloning()
+            -> setMethods(array('updateExtractorStats'))
+            -> getMock();
+        $expectedName = $extractorName;
+        $expectedStats = array();
+        $expectedElements = array(
+            "annotations"   => array($annotation1,$annotation2),
+            "relations"     => array(),
+            "lemmas"        => array($lemma2),
+            "attributes"    => array(),
+        );
+        $returnedStats = array(
+            $extractorName  => array("annotations"=>2,"relations"=>0,"lemmas"=>1,"attributes"=>0)
+        );
+
+        $mockCorpusExporter -> expects($this->once())
+            -> method('updateExtractorStats')
+            -> with($expectedName,$expectedStats,$expectedElements)
+            -> will($this->returnValue($returnedStats));
+
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($mockCorpusExporter,'runExtractor');
+        $protectedMethod->invokeArgs($mockCorpusExporter,array($flags,$report_id,$extractor,&$elements,&$extractor_stats));
+
+        $expectedElements = array(
+            "annotations" => array( $annotation1, $annotation2 ),
+            "relations"=>[], 
+			"lemmas"=>array($lemma2), 
+			"attributes"=>[]
+        );
+        $this->assertEquals($expectedElements,$elements);
+        $expectedStats = $returnedStats;
+        $this->assertEquals($expectedStats,$extractor_stats);
+
+    } // testRunextractorsForExtractorCustomLemmasSetsLemmaFieldsInElementsAnnotationsAndLemmasSection() 
+
+    // 3
+    public function testRunextractorsForExtractorStandardLemmasSetsLemmaFieldsInElementsLemmasSection() {
+
+        $report_id = 13;
+        $lemma2 = array( "report_annotation_id" => "2", "lemma" => "lemat1", "id"=>2 );
+        $flagId = -1;
+        $flagName = 'xxx'; $flagIds = [$flagId,0,1];
+        $flags = array( $flagName=>$flagId );
+        $extractorName = "exName";
+        $extractorFunc = function ($report_id, $params, &$elements) {
+                $elements["lemmas"]=array(
+                    // lemma2
+                    array( "report_annotation_id" => "2", "lemma" => "lemat1", "id"=>2 )
+                );
+        };
+        $extractor = array(
+            "name"      =>  $extractorName,
+            "flag_name" =>  $flagName,
+            "flag_ids"  =>  $flagIds,
+            "extractor" =>  $extractorFunc,
+            "params"    => array()
+        );
+        $elements = array(
+            "annotations"   => array(),
+            "relations"     => array(),
+            "lemmas"        => array(),
+            "attributes"    => array(),
+        );
+        $extractor_stats = array();
+
+        // mocking for throw exception emulate
+        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
+            -> disableArgumentCloning()
+            -> setMethods(array('updateExtractorStats'))
+            -> getMock();
+        $expectedName = $extractorName;
+        $expectedStats = array();
+        $expectedElements = array(
+            "annotations"   => array(),
+            "relations"     => array(),
+            "lemmas"        => array($lemma2),
+            "attributes"    => array(),
+        );
+        $returnedStats = array(
+            $extractorName  => array("annotations"=>0,"relations"=>0,"lemmas"=>1,"attributes"=>0)
+        );
+
+        $mockCorpusExporter -> expects($this->once())
+            -> method('updateExtractorStats')
+            -> with($expectedName,$expectedStats,$expectedElements)
+            -> will($this->returnValue($returnedStats));
+
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($mockCorpusExporter,'runExtractor');
+        $protectedMethod->invokeArgs($mockCorpusExporter,array($flags,$report_id,$extractor,&$elements,&$extractor_stats));
+
+        $expectedElements = array(
+            "annotations" => [],
+            "relations"=>[],
+            "lemmas"=>array($lemma2),
+            "attributes"=>[]
+        );
+        $this->assertEquals($expectedElements,$elements);
+        $expectedStats = $returnedStats;
+        $this->assertEquals($expectedStats,$extractor_stats);
+
+    } // testRunextractorsForExtractorStandardLemmasSetsLemmaFieldsInElementsLemmasSection() 
+
+} // CorpusExporter_part11_Test class
+
+?>
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part1_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part1_Test.php
index a5247975..459d60aa 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part1_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part1_Test.php
@@ -96,13 +96,15 @@ private function export_document($disamb_only,$tagging_method)
         global $db;
         $db = $dbEmu;
 
-        $ce = new CorpusExporter_mock();
+        $ce = new CorpusExporter();
+
         $extractor_stats = array(); // this will change
         // $extractors is var parameter, but shouldn't change
         $extractors = $extractorObj->getExtractorsTable();
         $expectedExtractors = $extractors;
 
-        $ce->mock_export_document($report_id,$extractors,$disamb_only,$extractor_stats,$lists,$this->virtualDir->url(),$subcorpora,$tagging_method);
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'export_document');
+        $protectedMethod->invokeArgs($ce,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$this->virtualDir->url(),$subcorpora,$tagging_method));
             
         // check results in variables and files
         $this->assertEquals($expectedExtractors,$extractors);
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part2_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part2_Test.php
index 8647e138..818d67b6 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part2_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part2_Test.php
@@ -93,13 +93,14 @@ private function export_document($disamb_only,$tagging_method)
         global $db;
         $db = $dbEmu;
 
-        $ce = new CorpusExporter_mock();
+        $ce = new CorpusExporter();
         $extractor_stats = array(); // this will change
         // $extractors is var parameter, but shouldn't change
         $extractors = $extractorObj->getExtractorsTable();
         $expectedExtractors = $extractors;
 
-        $ce->mock_export_document($report_id,$extractors,$disamb_only,$extractor_stats,$lists,$this->virtualDir->url(),$subcorpora,$tagging_method);
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'export_document');
+        $protectedMethod->invokeArgs($ce,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$this->virtualDir->url(),$subcorpora,$tagging_method));
             
         // check results in variables and files
         $this->assertEquals($expectedExtractors,$extractors);
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part3_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part3_Test.php
index c788a00c..4fd12862 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part3_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part3_Test.php
@@ -96,14 +96,15 @@ private function export_document($disamb_only,$tagging_method)
         global $db;
         $db = $dbEmu;
 
-        $ce = new CorpusExporter_mock();
+        $ce = new CorpusExporter();
         $output_folder = $this->virtualDir->url();
         $extractor_stats = array(); // this will change
         // $extractors is var parameter, but shouldn't change
         $extractors = $extractorObj->getExtractorsTable();
         $expectedExtractors = $extractors;
 
-        $ce->mock_export_document($report_id,$extractors,$disamb_only,$extractor_stats,$lists,$output_folder,$subcorpora,$tagging_method);
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'export_document');
+        $protectedMethod->invokeArgs($ce,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
             
         // check results in variables and files
         $this->assertEquals($expectedExtractors,$extractors);
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part4_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part4_Test.php
index d952ff73..941ac7f9 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part4_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part4_Test.php
@@ -96,14 +96,15 @@ private function export_document($disamb_only,$tagging_method)
         global $db;
         $db = $dbEmu;
 
-        $ce = new CorpusExporter_mock();
+        $ce = new CorpusExporter();
         $output_folder = $this->virtualDir->url();
         $extractor_stats = array(); // this will change
         // $extractors is var parameter, but shouldn't change
         $extractors = $extractorObj->getExtractorsTable();
         $expectedExtractors = $extractors;
 
-        $ce->mock_export_document($report_id,$extractors,$disamb_only,$extractor_stats,$lists,$output_folder,$subcorpora,$tagging_method);
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'export_document');
+        $protectedMethod->invokeArgs($ce,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
             
         // check results in variables and files
         $this->assertEquals($expectedExtractors,$extractors);
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part5_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part5_Test.php
index 3eea0511..7b98b979 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part5_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part5_Test.php
@@ -96,14 +96,15 @@ private function export_document($disamb_only,$tagging_method)
         global $db;
         $db = $dbEmu;
 
-        $ce = new CorpusExporter_mock();
+        $ce = new CorpusExporter();
         $output_folder = $this->virtualDir->url();
         $extractor_stats = array(); // this will change
         // $extractors is var parameter, but shouldn't change
         $extractors = $extractorObj->getExtractorsTable();
         $expectedExtractors = $extractors;
 
-        $ce->mock_export_document($report_id,$extractors,$disamb_only,$extractor_stats,$lists,$output_folder,$subcorpora,$tagging_method);
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'export_document');
+        $protectedMethod->invokeArgs($ce,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
             
         // check results in variables and files
         $this->assertEquals($expectedExtractors,$extractors);
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part6_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part6_Test.php
index 986ef957..f8c16232 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part6_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part6_Test.php
@@ -96,14 +96,15 @@ private function export_document($disamb_only,$tagging_method)
         global $db;
         $db = $dbEmu;
 
-        $ce = new CorpusExporter_mock();
+        $ce = new CorpusExporter();
         $output_folder = $this->virtualDir->url();
         $extractor_stats = array(); // this will change
         // $extractors is var parameter, but shouldn't change
         $extractors = $extractorObj->getExtractorsTable();
         $expectedExtractors = $extractors;
 
-        $ce->mock_export_document($report_id,$extractors,$disamb_only,$extractor_stats,$lists,$output_folder,$subcorpora,$tagging_method);
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'export_document');
+        $protectedMethod->invokeArgs($ce,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
             
         // check results in variables and files
         $this->assertEquals($expectedExtractors,$extractors);
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part7_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part7_Test.php
index 247edd0d..cbcee6fc 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part7_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part7_Test.php
@@ -96,14 +96,15 @@ private function export_document($disamb_only,$tagging_method)
         global $db;
         $db = $dbEmu;
 
-        $ce = new CorpusExporter_mock();
+        $ce = new CorpusExporter();
         $output_folder = $this->virtualDir->url();
         $extractor_stats = array(); // this will change
         // $extractors is var parameter, but shouldn't change
         $extractors = $extractorObj->getExtractorsTable();
         $expectedExtractors = $extractors;
 
-        $ce->mock_export_document($report_id,$extractors,$disamb_only,$extractor_stats,$lists,$output_folder,$subcorpora,$tagging_method);
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'export_document');
+        $protectedMethod->invokeArgs($ce,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
             
         // check results in variables and files
         $this->assertEquals($expectedExtractors,$extractors);
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part8_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part8_Test.php
index 39d8b927..c43b1096 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part8_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part8_Test.php
@@ -96,14 +96,15 @@ private function export_document($disamb_only,$tagging_method)
         global $db;
         $db = $dbEmu;
 
-        $ce = new CorpusExporter_mock();
         $output_folder = $this->virtualDir->url();
         $extractor_stats = array(); // this will change
         // $extractors is var parameter, but shouldn't change
         $extractors = $extractorObj->getExtractorsTable();
         $expectedExtractors = $extractors;
 
-        $ce->mock_export_document($report_id,$extractors,$disamb_only,$extractor_stats,$lists,$output_folder,$subcorpora,$tagging_method);
+        $ce = new CorpusExporter();
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'export_document');
+        $protectedMethod->invokeArgs($ce,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
             
         // check results in variables and files
         $this->assertEquals($expectedExtractors,$extractors);
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part_Test.php
index 9a49e583..ba05f917 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part_Test.php
@@ -95,10 +95,11 @@ public function test_export_document()
         global $db;
         $db = $dbEmu;
 
-        $ce = new CorpusExporter_mock();
+        $ce = new CorpusExporter();
         // $extractors is var parameter, but shouldn't change
         $expectedExtractors = $extractors;
-        $ce->mock_export_document($report_id,$extractors,$disamb_only,$extractor_stats,$lists,$this->virtualDir->url(),$subcorpora,$tagging_method);
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'export_document');
+        $protectedMethod->invokeArgs($ce,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$this->virtualDir->url(),$subcorpora,$tagging_method));
         // check results in variables and files
         $this->assertEquals($expectedExtractors,$extractors);
         $expectedLists = array();
diff --git a/phpunit/tests/engine/include/writers/CCclWriterTest.php b/phpunit/tests/engine/include/writers/CCclWriterTest.php
index 8fd413de..0d5d8ad8 100644
--- a/phpunit/tests/engine/include/writers/CCclWriterTest.php
+++ b/phpunit/tests/engine/include/writers/CCclWriterTest.php
@@ -574,6 +574,83 @@ public function testFullCclDataProperlyFormatsAsXml() {
 
     } // testFullCclDataProperlyFormatsAsXml()
 
+    public function testLemmaDataGeneratesPropXml() {
+
+		$annotation_lemma = array (
+			"type" => "annotation_type",
+			"lemma" => "annotation_lemma"
+			);
+		$token = new CclToken();
+		$token->setAnnotationLemma($annotation_lemma);
+		$sentence = new CclSentence();
+		$sentence->addToken($token);
+		$chunk = new CclChunk();
+		$chunk->addSentence($sentence);
+		$ccl = new CclDocument();
+		$ccl->addChunk($chunk);
+
+        // private method need reflection to tests
+        $privateMethod = new ReflectionMethod('CclWriter','makeXmlData');
+        $privateMethod->setAccessible(True);
+
+        $mode = CclWriter::$CCLREL;  // for $CCLREL are both sections
+        $expectedXmlLine = 
+			 "@"	// regexp delimiter
+			.'    <prop key="annotation_type:lemma">annotation_lemma</prop>'."\n"
+			."@";
+
+        $result = $privateMethod->invoke(new CclWriter(),$ccl,$mode);
+		// test if is above line in result
+        $this->assertRegexp($expectedXmlLine,$result);
+
+	} // testLemmaDataGeneratesPropXml()
+
+// protected function formatPropToXML($propTable) {...}
+
+    public function testInValidPropGenerateEmptyXml() {
+
+        // private method need reflection to tests
+        $privateMethod = new ReflectionMethod('CclWriter','formatPropToXML');
+        $privateMethod->setAccessible(True);
+
+        $expectedEmptyXml = "";
+        $result = $privateMethod->invoke(new CclWriter(),null);
+        $this->assertEquals($expectedEmptyXml,$result);
+	
+        $result = $privateMethod->invoke(new CclWriter(),array());
+        $this->assertEquals($expectedEmptyXml,$result);
+
+    } // testInValidPropGenerateEmptyXml()
+
+    public function testValidPropGeneratePropXmlTagElements() {
+
+        // private method need reflection to tests
+        $privateMethod = new ReflectionMethod('CclWriter','formatPropToXML');
+        $privateMethod->setAccessible(True);
+
+		// single property
+		$prop = array( "key" => "value" );
+        $expectedXml = '    <prop key="key">value</prop>'."\n";
+        $result = $privateMethod->invoke(new CclWriter(),$prop);
+        $this->assertEquals($expectedXml,$result);
+
+		// 2 props in one line - ;; is separator
+        $prop = array( "key" => "val1;;val2" );
+        $expectedXml = '    <prop key="key">val1</prop>'."\n"
+					  .'    <prop key="key">val2</prop>'."\n";
+        $result = $privateMethod->invoke(new CclWriter(),$prop);
+        $this->assertEquals($expectedXml,$result);
+
+		// more than 2 values are throwed silently
+        $prop = array( "key" => "val1;;val2;;val3" );
+        $expectedXml = '    <prop key="key">val1</prop>'."\n"
+                      .'    <prop key="key">val2</prop>'."\n";
+        $result = $privateMethod->invoke(new CclWriter(),$prop);
+        $this->assertEquals($expectedXml,$result);
+
+    } // testValidPropGeneratePropXmlTagElements()
+
+
 } // CclWriterTest class
 
 ?>

From 66f940096ce9eb55b3b93ccf96397e9dfaa26bef Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Tue, 28 Nov 2023 09:41:05 +0100
Subject: [PATCH 133/154] decomposition CclStruct.php to class files

---
 engine/include/export/XmlFactory.php          |   4 +-
 engine/include/structs/CclChunk.php           |  63 +++
 .../{CclStruct.php => CclDocument.php}        | 477 +-----------------
 engine/include/structs/CclError.php           |  92 ++++
 engine/include/structs/CclLexeme.php          |  40 ++
 engine/include/structs/CclRelation.php        |  85 ++++
 engine/include/structs/CclSentence.php        |  75 +++
 engine/include/structs/CclStruct2.php         | 124 -----
 engine/include/structs/CclToken.php           | 189 +++++++
 ...clDocumentTest.php => CclDocumentTest.php} |   4 +-
 ...ruct_CclTokenTest.php => CclTokenTest.php} |   4 +-
 11 files changed, 553 insertions(+), 604 deletions(-)
 create mode 100644 engine/include/structs/CclChunk.php
 rename engine/include/structs/{CclStruct.php => CclDocument.php} (56%)
 create mode 100644 engine/include/structs/CclError.php
 create mode 100644 engine/include/structs/CclLexeme.php
 create mode 100644 engine/include/structs/CclRelation.php
 create mode 100644 engine/include/structs/CclSentence.php
 delete mode 100644 engine/include/structs/CclStruct2.php
 create mode 100644 engine/include/structs/CclToken.php
 rename phpunit/tests/engine/include/structs/{CclStruct_CclDocumentTest.php => CclDocumentTest.php} (99%)
 rename phpunit/tests/engine/include/structs/{CclStruct_CclTokenTest.php => CclTokenTest.php} (99%)

diff --git a/engine/include/export/XmlFactory.php b/engine/include/export/XmlFactory.php
index 9badd232..1cde7c24 100644
--- a/engine/include/export/XmlFactory.php
+++ b/engine/include/export/XmlFactory.php
@@ -2,7 +2,7 @@
 
 class XmlFactory {
 
-    private function setDataToExport(&$ccl,&$annotations,&$relations,&$lemmas,&$attributes) {
+    protected function setDataToExport(&$ccl,&$annotations,&$relations,&$lemmas,&$attributes) {
 
         CclFactory::setAnnotationsAndRelations($ccl, $annotations, $relations);
         CclFactory::setAnnotationLemmas($ccl, $lemmas);
@@ -10,7 +10,7 @@ private function setDataToExport(&$ccl,&$annotations,&$relations,&$lemmas,&$attr
  
         // returns modified $ccl by reference
 
-    } // 
+    } // setDataToExport()
 
     public function exportToXmlAndRelxml($filePathWithoutExt,&$ccl,&$annotations,&$relations,&$lemmas,&$attributes) {
 
diff --git a/engine/include/structs/CclChunk.php b/engine/include/structs/CclChunk.php
new file mode 100644
index 00000000..4bd9be47
--- /dev/null
+++ b/engine/include/structs/CclChunk.php
@@ -0,0 +1,63 @@
+<?php
+/**
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ * See LICENCE 
+ */
+ 
+/**
+ * Document contains a set of chunks and set of relations. Chunk contains
+ * sentenes. Sentence contains token. Token contains channels. Values in 
+ * channels represent annotation numbers.
+ */
+
+class CclChunk{
+	var $id; // optional
+	var $type; //required
+	var $sentences = array();	
+	
+	function addSentence($sentence){
+		assert('$sentence instanceof CclSentence');
+        $sentence->setSentenceIndexInTokens(count($this->sentences));
+		$this->sentences[] = $sentence;
+	}
+	
+	function setType($type){
+		$this->type = $type;
+	}
+	
+	function setId($id){
+		$this->id = $id;
+	}
+	
+	function getSentences(){
+		return $this->sentences;
+	}
+	
+	function getId(){
+		return $this->id;
+	}
+	
+	function getType(){
+		return $this->type;
+	}	
+
+    public function setChunkIndexInTokens($chunkIndex) {
+        foreach($this->sentences as $sentence) {
+            $sentence->setChunkIndexInTokens($chunkIndex);
+        }
+    } // setParentIndexesInTokens
+	
+    public function getSentenceByIndex($sentenceIndex){
+        // sentenceIndex may be digit 0
+        if( is_numeric($sentenceIndex) and ($sentenceIndex < count($this->sentences)) ) {
+            return $this->sentences[$sentenceIndex];
+        } else {
+            return null;
+        }
+    } // getSentenceByIndex
+
+} // CclChunk class
+
+?>
diff --git a/engine/include/structs/CclStruct.php b/engine/include/structs/CclDocument.php
similarity index 56%
rename from engine/include/structs/CclStruct.php
rename to engine/include/structs/CclDocument.php
index c90a50b4..e3ad164f 100644
--- a/engine/include/structs/CclStruct.php
+++ b/engine/include/structs/CclDocument.php
@@ -122,6 +122,8 @@ function setAnnotationLemma($annotation_lemma){
 		$token = & $this->tokens[$i];
 			
 		if (! $token->setAnnotationLemma($annotation_lemma)){
+            // 'dead code' - actually CclToken->setAnnotationLemma()
+            // returns always true. For invalid data too.
 			$e = new CclError();
 			$e->setClassName("CclDocument");
 			$e->setFunctionName("setAnnotationLemma");
@@ -408,480 +410,7 @@ protected function getSentenceByToken($token){
             return null;
 
     } // getSentenceByToken
-}
 
-class CclChunk{
-	var $id; // optional
-	var $type; //required
-	var $sentences = array();	
-	
-	function addSentence($sentence){
-		assert('$sentence instanceof CclSentence');
-        $sentence->setSentenceIndexInTokens(count($this->sentences));
-		$this->sentences[] = $sentence;
-	}
-	
-	function setType($type){
-		$this->type = $type;
-	}
-	
-	function setId($id){
-		$this->id = $id;
-	}
-	
-	function getSentences(){
-		return $this->sentences;
-	}
-	
-	function getId(){
-		return $this->id;
-	}
-	
-	function getType(){
-		return $this->type;
-	}	
-
-    public function setChunkIndexInTokens($chunkIndex) {
-        foreach($this->sentences as $sentence) {
-            $sentence->setChunkIndexInTokens($chunkIndex);
-        }
-    } // setParentIndexesInTokens
-	
-    public function getSentenceByIndex($sentenceIndex){
-        // sentenceIndex may be digit 0
-        if( is_numeric($sentenceIndex) and ($sentenceIndex < count($this->sentences)) ) {
-            return $this->sentences[$sentenceIndex];
-        } else {
-            return null;
-        }
-    } // getSentenceByIndex
-
-}
-
-class CclSentence{
-	var $id; // optional	
-	var $tokens = array();
-	var $channels = array(); //key: annotation_type, value: last channel number
-	
-	
-	function setId($id){
-		$this->id = $id;
-	}
-	
-	function addToken($token){
-		assert('$token instanceof CclToken');
-		$this->tokens[] = $token;		
-	}
-	
-	function getTokens(){
-		return $this->tokens;
-	}
-	
-	function getId(){
-		return $this->id;
-	}	
-	
-	function setChannel($type, $value){
-		$this->channels[$type] = $value;
-	}
-	
-	function incChannel($type){
-		if (!array_key_exists($type, $this->channels))
-			$this->channels[$type]=1;
-		else $this->channels[$type]++;
-	}
-	
-	function fillChannel($type){
-		foreach ($this->tokens as $token){
-			$token->fillChannel($type);
-		}
-	}
-	
-	function getChannel($type){
-		if ($type == null) return 0;
-		if (!array_key_exists($type, $this->channels))
-			return 0;
-		else return $this->channels[$type];
-	}
-	
-    public function setSentenceIndexInTokens($sentenceIndex) {
-        foreach($this->tokens as $token) {
-            $token->setParentSentenceIndex($sentenceIndex);
-        }
-    }   // setSentenceIndexInTokens
-
-    public function setChunkIndexInTokens($chunkIndex) {
-        foreach($this->tokens as $token) {
-            $token->setParentChunkIndex($chunkIndex);
-        }
-    }   // setChunkIndexInTokens
-
-}
-
-class CclToken{
-	var $id = null;
-	var $orth = null;
-	// If token is preceded by a white space
-	var $ns = false;	
-	var $lexemes = array();
-	var $from = null;
-	var $to = null;
-    private $parentSentenceIndex = null; 
-        // parent sentence index in chunk sentences[] array
-    private $parentChunkIndex = null;
-        // parent chunk index in document chunks[] array
-	var $channels = array(); //same as in sentence, but with unique according number
-	var $prop = null;
-	
-	function setOrth($orth){
-		$this->orth = $orth;
-	}	
-	
-	function setNs($ns){
-		$this->ns = $ns;
-	}
-	
-	function setId($id){
-		$this->id = $id;
-	}
-	
-	function setFrom($from){
-		$this->from = $from;
-	}
-	
-	function setTo($to){
-		$this->to = $to;
-	}
-	
-	function setAnnotationLemma($annotation_lemma){
-		$this->prop[$annotation_lemma["type"].":lemma"] = $annotation_lemma["lemma"];
-		return true;
-	}
-
-    function setAnnotationProperty($annotation_property){
-        $this->prop[$annotation_property["type"].":".$annotation_property["name"]] = $annotation_property["value"];
-        return true;
-    }
-	
-	public function setAnnotation($annotation,$parentChannels = null){
-
-		$type = $annotation['type'];
-		if ($type=="sense"){
-			/*
-			 * Caution! Now WSD annotations are not part of any relations
-			 * and all instances (even having more than 1 name in db) can 
-			 * be renumbered in 'sense' channel, e.g.
-			 * [metrów] as wsd_m got number 6, but in db this instance
-			 * was described also as wsd_metr (#3767), so there will be next 
-			 * assignment of channel number from parent sentence, which will be 7. 
-			 */
-
-			//if more than 1 annotation with the same name length covers one token (#3767):
-			if ($this->prop && (count($this->prop) == count($annotation['value'])) ){
-				return false;
-			}
-			
-			else if (!$this->prop || (count($this->prop) < count($annotation['value'])) ){
-				$this->prop = $annotation['value'];	
-			}			
-		}
-        else {
-			if (array_key_exists($type, $this->channels) && $this->channels[$type]!=0 ){
-				return false;
-			}		
-			
-            if (is_array($parentChannels) && !array_key_exists($type, $parentChannels)  ){
-				return false;
-			}
-		}
-        // add to typed channel and return true if not exited earlier
-        $this->channels[$type] = $annotation['id'];
-		return true;
-	} // setAnnotation()
-	
-	function setContinuousAnnotation2($type,$parentChannels = null){
-
-        // $parentChannels may be null or sth
-        if(!is_array($parentChannels))
-            return false;
-		//annotation might exist in more than one sentence
-		if (!array_key_exists($type, $parentChannels)  )
-			return false;
-		$this->channels[$type] = $parentChannels[$type];
-		return true;
-	}		
-	
-	function fillChannel($type){
-		if (!array_key_exists($type, $this->channels))
-			$this->channels[$type]=0;		
-	}
-	
-	function addLexeme($lexeme){
-		$this->lexemes[] = $lexeme;
-	}
-
-	function getOrth(){
-		return $this->orth;
-	}
-	
-	function getNs(){
-		return $this->ns;
-	}
-	
-	function getLexemes(){
-		return $this->lexemes;
-	}
-	
-	function getChannels(){
-		return $this->channels;
-	}
-	
-	function getChannel($type){
-		if (!array_key_exists($type, $this->channels))
-			return 0;
-		return $this->channels[$type];
-	}
-	
-	function getId(){
-		return $this->id;
-	}
-	
-	function getFrom(){
-		return $this->from;
-	}
-	
-	function getTo(){
-		return $this->to;
-	}
-	
-	function isIn($annotation){
-		return ($this->from >= $annotation['from'] && $this->to <= $annotation['to']);
-	}
-	
-	/**
-	 * Return base for first disamb lexem.
-	 * If no dismb lexems is found then the base of a first lexem is returned.
-	 */
-	function getBase(){	
-		foreach ($this->lexemes as $lexem){
-			if ($lexem->getDisamb()){
-				return $lexem->getBase();
-			}
-		}
-		if ( count($this->lexemes) > 0){
-			return $this->lexemes[0]->getBase();
-		}
-		return null;
-	}
-
-    public function setParentSentenceIndex($parentSentenceIndex) {
-        $this->parentSentenceIndex = $parentSentenceIndex;
-    } // setParentSentenceIndex
-
-    public function getParentSentenceIndex() {
-        return $this->parentSentenceIndex;
-    } // getParentSentenceIndex
-	
-    public function setParentChunkIndex($parentChunkIndex) {
-        $this->parentChunkIndex = $parentChunkIndex;
-    } // setParentChunkIndex
-
-    public function getParentChunkIndex() {
-        return $this->parentChunkIndex;
-    } // getParentChunkIndex
-
-}
-
-class CclLexeme{
-	var $disamb = null;
-	var $base = null;
-	var $ctag = null;	
-	
-	function setDisamb($disamb){
-		$this->disamb = $disamb;
-	}
-	
-	function setBase($base){
-		$this->base = $base;
-	}
-	
-	function setCtag($ctag){
-		$this->ctag = $ctag;
-	}
-	
-	function getDisamb(){
-		return $this->disamb;
-	}
-	
-	function getBase(){
-		return $this->base;
-	}
-	
-	function getCtag(){
-		return $this->ctag;
-	}
-	
-}
-
-class CclRelation{
-	var $name = null;
-	var $set = null;
-	var $fromSentence = null;
-	var $fromChannel = null;
-	var $toSentence = null;
-	var $toChannel = null;	
-	var $fromType = null;
-	var $toType = null;
-
-	function getName(){
-		return $this->name;
-	}
-	
-	function getSet(){
-		return $this->set;
-	}
-	
-	function getFromSentence(){
-		return $this->fromSentence;
-	}
-	
-	function getToSentence(){
-		return $this->toSentence;
-	}
-	
-	function getFromChannel(){
-		return $this->fromChannel;
-	}
-	
-	function getToChannel(){
-		return $this->toChannel;
-	}
-	
-	function getFromType(){
-		return $this->fromType;
-	}	
-
-	function getToType(){
-		return $this->toType;
-	}
-
-	function setName($name){
-		$this->name = $name;
-	}
-	
-	function setSet($set){
-		$this->set = $set;
-	}
-	
-	function setFromSentence($fromSentence){
-		$this->fromSentence = $fromSentence;
-	}
-	
-	function setToSentence($toSentence){
-		$this->toSentence = $toSentence;
-	}
-	
-	function setFromChannel($fromChannel){
-		$this->fromChannel = $fromChannel;
-	}
-	
-	function setToChannel($toChannel){
-		$this->toChannel = $toChannel;
-	}
-	
-	function setFromType($fromType){
-		$this->fromType = $fromType;
-	}	
-
-	function setToType($toType){
-		$this->toType = $toType;
-	}		
-	
-}
-
-class CclError{
-	var $className = null;
-	var $functionName = null;
-	var $objects = array();
-	var $comments = array();
-	
-	
-	function setClassName($className){
-		$this->className = $className;
-	}
-	
-	function setFunctionName($functionName){
-		$this->functionName = $functionName;
-	}
-	
-	function addObject($key, $value){
-		$this->objects[$key] = $value;
-	}
-	
-	function addComment($value){
-		$this->comments[] = $value;
-	}
-	
-	
-	function getClassName(){
-		return $this->className;
-	}
-	
-	function getFunctionName(){
-		return $this->functionName;
-	}
-	
-	function getObjects(){
-		return $this->objects;
-	}
-	
-	function getComments(){
-		return $this->comments;
-	}	
-	
-	
-	function __toString(){
-		$str =  "---------------------ERROR-------------------------\n";
-		$str .= "class:    {$this->className}\n";
-		$str .= "function: {$this->functionName}\n";
-		$str .= "comments: \n";
-		foreach ($this->comments as $comment)
-			$str .= "  $comment\n";
-		$str .= "objects: \n";		
-		
-		foreach ($this->objects as $key=>$obj){
-			if ($key=="token"){
-				$str .= "  Token:\n";
-				$str .= "    Orth: {$obj->getOrth()}\n"; 
-				$str .= "    From: {$obj->getFrom()}\n";
-				$str .= "    To  : {$obj->getTo()}\n";
-			}
-			elseif (strpos($key, "annotation") === 0){
-				$str .= "  Annotation:\n";
-				$str .= "    Key : $key \n";
-				$str .= "    Type: {$obj['type']}\n"; 
-				$str .= "    From: {$obj['from']}\n"; 
-				$str .= "    To  : {$obj['to']}\n";
-				$str .= "    Text: {$obj['text']}\n"; 
-			}
-			elseif ($key=="relation"){
-				$str .= "  Relation:\n";
-				$str .= "    Source id: {$obj['source_id']}\n"; 
-				$str .= "    Target id: {$obj['target_id']}\n"; 
-			}
-			elseif ($key=="message"){
-				$str .= "message: $obj";
-			}			
-			else {
-				$str .= "  $key\n";
-				$str .= "    build your own user-friendly dump\n";
-			}			
-		}		
-		return $str;
-	}
-	
-	
-	
-}
+} // CclDocument
 
 ?>
diff --git a/engine/include/structs/CclError.php b/engine/include/structs/CclError.php
new file mode 100644
index 00000000..fac4713b
--- /dev/null
+++ b/engine/include/structs/CclError.php
@@ -0,0 +1,92 @@
+<?php
+/**
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ * See LICENCE 
+ */
+ 
+class CclError{
+	var $className = null;
+	var $functionName = null;
+	var $objects = array();
+	var $comments = array();
+	
+	
+	function setClassName($className){
+		$this->className = $className;
+	}
+	
+	function setFunctionName($functionName){
+		$this->functionName = $functionName;
+	}
+	
+	function addObject($key, $value){
+		$this->objects[$key] = $value;
+	}
+	
+	function addComment($value){
+		$this->comments[] = $value;
+	}
+	
+	
+	function getClassName(){
+		return $this->className;
+	}
+	
+	function getFunctionName(){
+		return $this->functionName;
+	}
+	
+	function getObjects(){
+		return $this->objects;
+	}
+	
+	function getComments(){
+		return $this->comments;
+	}	
+	
+	
+	function __toString(){
+		$str =  "---------------------ERROR-------------------------\n";
+		$str .= "class:    {$this->className}\n";
+		$str .= "function: {$this->functionName}\n";
+		$str .= "comments: \n";
+		foreach ($this->comments as $comment)
+			$str .= "  $comment\n";
+		$str .= "objects: \n";		
+		
+		foreach ($this->objects as $key=>$obj){
+			if ($key=="token"){
+				$str .= "  Token:\n";
+				$str .= "    Orth: {$obj->getOrth()}\n"; 
+				$str .= "    From: {$obj->getFrom()}\n";
+				$str .= "    To  : {$obj->getTo()}\n";
+			}
+			elseif (strpos($key, "annotation") === 0){
+				$str .= "  Annotation:\n";
+				$str .= "    Key : $key \n";
+				$str .= "    Type: {$obj['type']}\n"; 
+				$str .= "    From: {$obj['from']}\n"; 
+				$str .= "    To  : {$obj['to']}\n";
+				$str .= "    Text: {$obj['text']}\n"; 
+			}
+			elseif ($key=="relation"){
+				$str .= "  Relation:\n";
+				$str .= "    Source id: {$obj['source_id']}\n"; 
+				$str .= "    Target id: {$obj['target_id']}\n"; 
+			}
+			elseif ($key=="message"){
+				$str .= "message: $obj";
+			}			
+			else {
+				$str .= "  $key\n";
+				$str .= "    build your own user-friendly dump\n";
+			}			
+		}		
+		return $str;
+	}
+	
+} // CclError class
+
+?>
diff --git a/engine/include/structs/CclLexeme.php b/engine/include/structs/CclLexeme.php
new file mode 100644
index 00000000..95c5f5b2
--- /dev/null
+++ b/engine/include/structs/CclLexeme.php
@@ -0,0 +1,40 @@
+<?php
+/**
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ * See LICENCE 
+ */
+ 
+class CclLexeme{
+	var $disamb = null;
+	var $base = null;
+	var $ctag = null;	
+	
+	function setDisamb($disamb){
+		$this->disamb = $disamb;
+	}
+	
+	function setBase($base){
+		$this->base = $base;
+	}
+	
+	function setCtag($ctag){
+		$this->ctag = $ctag;
+	}
+	
+	function getDisamb(){
+		return $this->disamb;
+	}
+	
+	function getBase(){
+		return $this->base;
+	}
+	
+	function getCtag(){
+		return $this->ctag;
+	}
+	
+} // CclLexeme class
+
+?>
diff --git a/engine/include/structs/CclRelation.php b/engine/include/structs/CclRelation.php
new file mode 100644
index 00000000..e587c9b9
--- /dev/null
+++ b/engine/include/structs/CclRelation.php
@@ -0,0 +1,85 @@
+<?php
+/**
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ * See LICENCE 
+ */
+ 
+class CclRelation{
+	var $name = null;
+	var $set = null;
+	var $fromSentence = null;
+	var $fromChannel = null;
+	var $toSentence = null;
+	var $toChannel = null;	
+	var $fromType = null;
+	var $toType = null;
+
+	function getName(){
+		return $this->name;
+	}
+	
+	function getSet(){
+		return $this->set;
+	}
+	
+	function getFromSentence(){
+		return $this->fromSentence;
+	}
+	
+	function getToSentence(){
+		return $this->toSentence;
+	}
+	
+	function getFromChannel(){
+		return $this->fromChannel;
+	}
+	
+	function getToChannel(){
+		return $this->toChannel;
+	}
+	
+	function getFromType(){
+		return $this->fromType;
+	}	
+
+	function getToType(){
+		return $this->toType;
+	}
+
+	function setName($name){
+		$this->name = $name;
+	}
+	
+	function setSet($set){
+		$this->set = $set;
+	}
+	
+	function setFromSentence($fromSentence){
+		$this->fromSentence = $fromSentence;
+	}
+	
+	function setToSentence($toSentence){
+		$this->toSentence = $toSentence;
+	}
+	
+	function setFromChannel($fromChannel){
+		$this->fromChannel = $fromChannel;
+	}
+	
+	function setToChannel($toChannel){
+		$this->toChannel = $toChannel;
+	}
+	
+	function setFromType($fromType){
+		$this->fromType = $fromType;
+	}	
+
+	function setToType($toType){
+		$this->toType = $toType;
+	}		
+	
+} // CclRelation class
+	
+?>
diff --git a/engine/include/structs/CclSentence.php b/engine/include/structs/CclSentence.php
new file mode 100644
index 00000000..cfce19db
--- /dev/null
+++ b/engine/include/structs/CclSentence.php
@@ -0,0 +1,75 @@
+<?php
+/**
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ * See LICENCE 
+ */
+ 
+/**
+ * Document contains a set of chunks and set of relations. Chunk contains
+ * sentenes. Sentence contains token. Token contains channels. Values in 
+ * channels represent annotation numbers.
+ */
+
+class CclSentence{
+	var $id; // optional	
+	var $tokens = array();
+	var $channels = array(); //key: annotation_type, value: last channel number
+	
+	
+	function setId($id){
+		$this->id = $id;
+	}
+	
+	function addToken($token){
+		assert('$token instanceof CclToken');
+		$this->tokens[] = $token;		
+	}
+	
+	function getTokens(){
+		return $this->tokens;
+	}
+	
+	function getId(){
+		return $this->id;
+	}	
+	
+	function setChannel($type, $value){
+		$this->channels[$type] = $value;
+	}
+	
+	function incChannel($type){
+		if (!array_key_exists($type, $this->channels))
+			$this->channels[$type]=1;
+		else $this->channels[$type]++;
+	}
+	
+	function fillChannel($type){
+		foreach ($this->tokens as $token){
+			$token->fillChannel($type);
+		}
+	}
+	
+	function getChannel($type){
+		if ($type == null) return 0;
+		if (!array_key_exists($type, $this->channels))
+			return 0;
+		else return $this->channels[$type];
+	}
+	
+    public function setSentenceIndexInTokens($sentenceIndex) {
+        foreach($this->tokens as $token) {
+            $token->setParentSentenceIndex($sentenceIndex);
+        }
+    }   // setSentenceIndexInTokens
+
+    public function setChunkIndexInTokens($chunkIndex) {
+        foreach($this->tokens as $token) {
+            $token->setParentChunkIndex($chunkIndex);
+        }
+    }   // setChunkIndexInTokens
+
+} // CclSentence class
+
+?>
diff --git a/engine/include/structs/CclStruct2.php b/engine/include/structs/CclStruct2.php
deleted file mode 100644
index ffe213d0..00000000
--- a/engine/include/structs/CclStruct2.php
+++ /dev/null
@@ -1,124 +0,0 @@
-<?php
-/**
- * Part of the Inforex project
- * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
- * Wrocław University of Technology
- * See LICENCE 
- */
- 
-class CclChannel {
-	public $name = null; 
-	public $value = null;
-	
-	function __construct($name, $value){
-		$this->name = $name;
-		$this->value = $value;
-	}
-	
-	function getXml(){
-		return "    <ann chan=\"{$this->name}\">{$this->value}</ann>\n";		
-	}
-}
-
-class CclLexem {
-	public $disamb = null;
-	public $base = null;
-	public $ctag = null;	
-	function __construct($disamb, $base, $ctag){
-		$this->disamb = $disamb;
-		$this->base = htmlspecialchars($base);
-		$this->ctag = $ctag;
-	}
-	
-	function getXml(){
-        //return "";
-		$xml = $this->disamb ? "    <lex disamb=\"1\">\n" : "    <lex>\n";
-		$xml .= "     <base>{$this->base}</base>\n";
-		$xml .= "     <ctag>{$this->ctag}</ctag>\n";
-		return $xml . "    </lex> \n";
-	}
-}
-
-class CclToken {
-	public $orth = null;
-	public $lexemes = null;
-	public $channels = null;
-	public $ns = null;
-	
-	function __construct($orth){
-		$this->orth = htmlspecialchars($orth);
-		$this->lexemes = array();
-		$this->channels = array();
-		$this->ns = false;
-	}
-	
-	function getXml($channelTypes){
-		$xml =  "   <tok>\n";
-		$xml .= "    <orth>{$this->orth}</orth>\n";
-		foreach ($this->lexemes as $lexeme)
-			$xml .= $lexeme->getXml();
-		
-		foreach ($channelTypes as $annType)
-			$xml .= $this->channels[$annType]->getXml();
-		if ($this->ns) return $xml . "   </tok>\n   <ns/>\n";	
-		return $xml . "   </tok>\n";		
-			
-	}
-}
-
-class CclSentence {
-	public $tokens = null;
-	public $channelTypes = null;
-	public $id = null;
-	
-	function __construct($id){
-		$this->tokens = array();
-		$this->channelTypes = array();
-		$this->id = $id;
-	}
-		
-	function getXml(){
-		$usedTypes = array_keys($this->channelTypes);
-		$xml = "  <sentence id=\"s{$this->id}\">\n";
-		foreach ($this->tokens as $token)
-			$xml .= $token->getXml($usedTypes);
-		return $xml . "  </sentence>\n";
-	}
-}
-
-class CclChunk {
-	public $id = null;
-	public $sentences = null;
-	function __construct($id){
-		$this->id = $id;
-		$this->sentences = array();
-	}
-	
-	function getXml(){
-		$xml = " <chunk id=\"{$this->id}\">\n";
-		foreach ($this->sentences as $sentence)
-			$xml .= $sentence->getXml();		
-		return $xml . " </chunk>\n";
-	}
-} 
-
-class CclDocument {
-	public $chunks = null;
-	
-	function __construct(){
-		$this->chunks = array();
-	}
-	
-	function getXml(){
-		$xml = "<chunkList>\n";
-		foreach ($this->chunks as $chunk)
-			$xml .= $chunk->getXml();
-		return $xml . "</chunkList>\n";
-		
-	}
-	
-}
-
-
-
-?>
diff --git a/engine/include/structs/CclToken.php b/engine/include/structs/CclToken.php
new file mode 100644
index 00000000..d8e97712
--- /dev/null
+++ b/engine/include/structs/CclToken.php
@@ -0,0 +1,189 @@
+<?php
+/**
+ * Part of the Inforex project
+ * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
+ * Wrocław University of Technology
+ * See LICENCE 
+ */
+ 
+/**
+ * Document contains a set of chunks and set of relations. Chunk contains
+ * sentenes. Sentence contains token. Token contains channels. Values in 
+ * channels represent annotation numbers.
+ */
+
+class CclToken{
+	var $id = null;
+	var $orth = null;
+	// If token is preceded by a white space
+	var $ns = false;	
+	var $lexemes = array();
+	var $from = null;
+	var $to = null;
+    private $parentSentenceIndex = null; 
+        // parent sentence index in chunk sentences[] array
+    private $parentChunkIndex = null;
+        // parent chunk index in document chunks[] array
+	var $channels = array(); //same as in sentence, but with unique according number
+	var $prop = null;
+	
+	function setOrth($orth){
+		$this->orth = $orth;
+	}	
+	
+	function setNs($ns){
+		$this->ns = $ns;
+	}
+	
+	function setId($id){
+		$this->id = $id;
+	}
+	
+	function setFrom($from){
+		$this->from = $from;
+	}
+	
+	function setTo($to){
+		$this->to = $to;
+	}
+	
+	function setAnnotationLemma($annotation_lemma){
+		$this->prop[$annotation_lemma["type"].":lemma"] = $annotation_lemma["lemma"];
+		return true;
+	}
+
+    function setAnnotationProperty($annotation_property){
+        $this->prop[$annotation_property["type"].":".$annotation_property["name"]] = $annotation_property["value"];
+        return true;
+    }
+	
+	public function setAnnotation($annotation,$parentChannels = null){
+
+		$type = $annotation['type'];
+		if ($type=="sense"){
+			/*
+			 * Caution! Now WSD annotations are not part of any relations
+			 * and all instances (even having more than 1 name in db) can 
+			 * be renumbered in 'sense' channel, e.g.
+			 * [metrów] as wsd_m got number 6, but in db this instance
+			 * was described also as wsd_metr (#3767), so there will be next 
+			 * assignment of channel number from parent sentence, which will be 7. 
+			 */
+
+			//if more than 1 annotation with the same name length covers one token (#3767):
+			if ($this->prop && (count($this->prop) == count($annotation['value'])) ){
+				return false;
+			}
+			
+			else if (!$this->prop || (count($this->prop) < count($annotation['value'])) ){
+				$this->prop = $annotation['value'];	
+			}			
+		}
+        else {
+			if (array_key_exists($type, $this->channels) && $this->channels[$type]!=0 ){
+				return false;
+			}		
+			
+            if (is_array($parentChannels) && !array_key_exists($type, $parentChannels)  ){
+				return false;
+			}
+		}
+        // add to typed channel and return true if not exited earlier
+        $this->channels[$type] = $annotation['id'];
+		return true;
+	} // setAnnotation()
+	
+	function setContinuousAnnotation2($type,$parentChannels = null){
+
+        // $parentChannels may be null or sth
+        if(!is_array($parentChannels))
+            return false;
+		//annotation might exist in more than one sentence
+		if (!array_key_exists($type, $parentChannels)  )
+			return false;
+		$this->channels[$type] = $parentChannels[$type];
+		return true;
+	}		
+	
+	function fillChannel($type){
+		if (!array_key_exists($type, $this->channels))
+			$this->channels[$type]=0;		
+	}
+	
+	function addLexeme($lexeme){
+		$this->lexemes[] = $lexeme;
+	}
+
+	function getOrth(){
+		return $this->orth;
+	}
+	
+	function getNs(){
+		return $this->ns;
+	}
+	
+	function getLexemes(){
+		return $this->lexemes;
+	}
+	
+	function getChannels(){
+		return $this->channels;
+	}
+	
+	function getChannel($type){
+		if (!array_key_exists($type, $this->channels))
+			return 0;
+		return $this->channels[$type];
+	}
+	
+	function getId(){
+		return $this->id;
+	}
+	
+	function getFrom(){
+		return $this->from;
+	}
+	
+	function getTo(){
+		return $this->to;
+	}
+	
+	function isIn($annotation){
+		return ($this->from >= $annotation['from'] && $this->to <= $annotation['to']);
+	}
+	
+	/**
+	 * Return base for first disamb lexem.
+	 * If no dismb lexems is found then the base of a first lexem is returned.
+	 */
+	function getBase(){	
+		foreach ($this->lexemes as $lexem){
+			if ($lexem->getDisamb()){
+				return $lexem->getBase();
+			}
+		}
+		if ( count($this->lexemes) > 0){
+			return $this->lexemes[0]->getBase();
+		}
+		return null;
+	}
+
+    public function setParentSentenceIndex($parentSentenceIndex) {
+        $this->parentSentenceIndex = $parentSentenceIndex;
+    } // setParentSentenceIndex
+
+    public function getParentSentenceIndex() {
+        return $this->parentSentenceIndex;
+    } // getParentSentenceIndex
+	
+    public function setParentChunkIndex($parentChunkIndex) {
+        $this->parentChunkIndex = $parentChunkIndex;
+    } // setParentChunkIndex
+
+    public function getParentChunkIndex() {
+        return $this->parentChunkIndex;
+    } // getParentChunkIndex
+
+} // CclToken class
+
+?>
diff --git a/phpunit/tests/engine/include/structs/CclStruct_CclDocumentTest.php b/phpunit/tests/engine/include/structs/CclDocumentTest.php
similarity index 99%
rename from phpunit/tests/engine/include/structs/CclStruct_CclDocumentTest.php
rename to phpunit/tests/engine/include/structs/CclDocumentTest.php
index 421f81e0..9b03d707 100644
--- a/phpunit/tests/engine/include/structs/CclStruct_CclDocumentTest.php
+++ b/phpunit/tests/engine/include/structs/CclDocumentTest.php
@@ -2,7 +2,7 @@
 
 mb_internal_encoding("UTF-8");
 
-class CclDocument_Test extends PHPUnit_Framework_TestCase
+class CclDocumentTest extends PHPUnit_Framework_TestCase
 {
 
     public function test_addToken_set_char2token_array() {
@@ -339,4 +339,4 @@ public function testSetannotationForProperDataCallsTokensSetannotation() {
 
     } // testSetannotationForProperDataCallsTokensSetannotation()
 
-} // class
+} // CclDocumentTest class
diff --git a/phpunit/tests/engine/include/structs/CclStruct_CclTokenTest.php b/phpunit/tests/engine/include/structs/CclTokenTest.php
similarity index 99%
rename from phpunit/tests/engine/include/structs/CclStruct_CclTokenTest.php
rename to phpunit/tests/engine/include/structs/CclTokenTest.php
index 586c58a0..c24a77f2 100644
--- a/phpunit/tests/engine/include/structs/CclStruct_CclTokenTest.php
+++ b/phpunit/tests/engine/include/structs/CclTokenTest.php
@@ -2,7 +2,7 @@
 
 mb_internal_encoding("UTF-8");
 
-class CclToken_Test extends PHPUnit_Framework_TestCase
+class CclTokenTest extends PHPUnit_Framework_TestCase
 {
 
     public function test_createObjectOfCclTokenClass() {
@@ -284,4 +284,4 @@ public function testSetannotationWithSenseTypeSetsPropTable() {
 
     } // testSetannotationWithSenseTypeSetsPropTable()
 
-} // class
+} // CclTokenTest class

From 5fd2b2fa6de83198188729cb025df0eae797e8c9 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Thu, 30 Nov 2023 08:23:31 +0100
Subject: [PATCH 134/154] duplicate tokens in test ccl on main level & on tree
 inside

---
 .../engine/include/export/CclFactoryTest.php  | 42 +++++++++-
 .../engine/include/export/XmlFactoryTest.php  | 77 ++++++++++++++++++
 .../include/structs/CclDocumentTest.php       | 80 ++++++++++++++++++-
 .../engine/include/writers/CCclWriterTest.php | 12 ++-
 4 files changed, 204 insertions(+), 7 deletions(-)
 create mode 100644 phpunit/tests/engine/include/export/XmlFactoryTest.php

diff --git a/phpunit/tests/engine/include/export/CclFactoryTest.php b/phpunit/tests/engine/include/export/CclFactoryTest.php
index 299a9f1b..b85c4d67 100644
--- a/phpunit/tests/engine/include/export/CclFactoryTest.php
+++ b/phpunit/tests/engine/include/export/CclFactoryTest.php
@@ -4,10 +4,8 @@
 
 class CclFactoryTest extends PHPUnit_Framework_TestCase
 {
-/*
-    function createFromReportAndTokens(&$report, &$tokens, &$tags){
-   returns object of CclDocument class
-*/
+//    function createFromReportAndTokens(&$report, &$tokens, &$tags){
+//   returns object of CclDocument class
 
     public function test_createFromReportAndTokens_createsValidCclDocumentFromNullParameters() {
 
@@ -175,6 +173,7 @@ public function testAddingLemmaToCclIsRepeatedForEachLemma() {
     } // testAddingLemmaToCclIsRepeatedForEachLemma()
 
 // function setAnnotationsAndRelations(&$ccl, &$annotations, &$relations){...}
+//   modifies $ccl and returns boolean as operation result
 
     public function testCorrectDataForSetAnnotationAndRelationCallsCclMethods() {
         $relations = array(
@@ -208,9 +207,44 @@ public function testCorrectDataForSetAnnotationAndRelationCallsCclMethods() {
 
         // returns true
         $this->assertTrue($result); 
+        // no errors in $ccl
+        $this->assertEquals(0,count($ccl->errors));
 
     } // testCorrectDataForSetAnnotationAndRelationCallsCclMethods()
 
+    public function testSetannotationsandrelationsOnEmptyAnnotationsReturnsFalse() {
+
+        $ccl = new CclDocument;
+        $annotations = array();
+        $relations = array(array("key"=>"value"));
+        $result = (new CclFactory())->setAnnotationsAndRelations($ccl,$annotations,$relations);
+        $this->assertFalse($result);
+        // no errors in $ccl
+        $this->assertEquals(0,count($ccl->errors));
+
+    } // testSetannotationsandrelationsOnEmptyAnnotationsReturnsFalse() 
+
+    public function testSetannotationsandrelationsOnAnnotationsWithNoRelationsCallCclsetannotation() {
+
+        $annotation1 = array( "annotation_id"=>1 );
+        $annotations = array( $annotation1 );
+        $relations = array();
+
+        $mockCcl = $this->getMockBuilder(CclDocument::class)
+            -> setMethods(['setAnnotation'])
+            -> getMock();
+        $mockCcl->expects($this->once())
+            ->method('setAnnotation')
+            -> with($annotation1);
+
+        $result = (new CclFactory())->setAnnotationsAndRelations($mockCcl,$annotations,$relations);
+
+        $this->assertTrue($result);
+        // no errors in $ccl
+        $this->assertEquals(0,count($ccl->errors));
+
+    } // testSetannotationsandrelationsOnAnnotationsWithNoRelationsCallCclsetannotation() 
+
 
 } // CclFactoryTest class
 
diff --git a/phpunit/tests/engine/include/export/XmlFactoryTest.php b/phpunit/tests/engine/include/export/XmlFactoryTest.php
new file mode 100644
index 00000000..6c7f831b
--- /dev/null
+++ b/phpunit/tests/engine/include/export/XmlFactoryTest.php
@@ -0,0 +1,77 @@
+<?php
+
+use org\bovigo\vfs\vfsStream; // for vfsStream
+mb_internal_encoding("UTF-8");
+
+class XmlFactoryTest extends PHPUnit_Framework_TestCase
+{
+
+// public function exportToXmlAndRelxml($filePathWithoutExt,&$ccl,&$annotations,&$relations,&$lemmas,&$attributes) 
+
+    public function testExporttoxmlandrelxmlCallSetdatatoexportMethod() {
+
+        $filePathWithoutExt = '';
+        $ccl = new CclDocument();
+        $annotations = array();
+        $relations = array();
+        $lemmas = array();
+        $attributes = array();
+
+        $mockXmlFactory = $this->getMockBuilder(XmlFactory::class)
+            -> disableArgumentCloning()
+            -> setMethods(array('setDataToExport'))
+            -> getMock();
+        // call setDataToExport with params            
+        $mockXmlFactory -> expects($this->once())
+            ->method('setDataToExport')
+            ->with($ccl,$annotations,$relations,$lemmas,$attributes);
+            // returns modified $ccl by reference
+           
+        $mockXmlFactory->exportToXmlAndRelxml($filePathWithoutExt,$ccl,$annotations,$relations,$lemmas,$attributes);
+
+    } // testExporttoxmlandrelxmlCallSetdatatoexportMethod()
+
+// protected function setDataToExport(&$ccl,&$annotations,&$relations,&$lemmas,&$attributes) 
+
+
+    public function testSetdatatoexportPutsLemmaIntoCcl() {
+
+        $annotations = array();
+        $relations = array();
+        $lemmas = array(
+                array($lemma1key => $lemma1data)
+            );
+        $attributes = array();
+
+        $token = new CclToken();
+        $token->from = $annotation_from; $token->to = $annotation_to;
+        $sentence = new CclSentence();
+        $sentence->addToken($token);
+        $chunk = new CclChunk();
+        $chunk->addSentence($sentence);
+        $ccl = new CclDocument();
+        $ccl->addChunk($chunk);
+        $ccl->addToken($token);
+        //var_dump($ccl->tokens);
+        
+        $xf = new XmlFactory();    
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($xf,'setDataToExport');
+        $protectedMethod->invokeArgs($xf,array(&$ccl,&$annotations,&$relations,&$lemmas,&$attributes));
+
+        // returns modified $ccl by reference
+        // no errors
+        $expectedErrors = array();
+        //var_dump($ccl->errors);
+        //$this->assertEquals($expectedErrors,$ccl->errors);
+
+        //var_dump($ccl->char2token);
+        //var_dump($ccl->tokens);
+
+
+    } // 
+
+
+
+} // XmlFactoryTest class
+
+?>
diff --git a/phpunit/tests/engine/include/structs/CclDocumentTest.php b/phpunit/tests/engine/include/structs/CclDocumentTest.php
index 9b03d707..adb00c08 100644
--- a/phpunit/tests/engine/include/structs/CclDocumentTest.php
+++ b/phpunit/tests/engine/include/structs/CclDocumentTest.php
@@ -293,7 +293,6 @@ public function testLemmaOverMultiTokensCallSetLemmaForFirstOneOnly() {
         $mockToken2->expects($this->never())->method('setAnnotationLemma');
         $mockToken2->setFrom(4); $mockToken2->setTo($to);
 
-
         $ccl = new CclDocument();
         $ccl->addToken($mockToken1); $ccl->addToken($mockToken2);
         $ccl->setAnnotationLemma($annotation_lemma);
@@ -303,6 +302,56 @@ public function testLemmaOverMultiTokensCallSetLemmaForFirstOneOnly() {
 
 // function setAnnotation($annotation)
 
+	private function generateProperCclToSetAnnotationTests($from,$to) {
+
+		// token on chars from $from to $to
+		$token = new cclToken();
+		$token->setFrom($from); $token->setTo($to);
+		// add token to tree structure
+		$sentence = new CclSentence();
+		$sentence->addToken($token);
+		$chunk = new CclChunk();
+		$chunk->addSentence($sentence);
+		$ccl = new CclDocument();
+		// set token to $ccl->tokens at pos. 0 
+		// and fill 3 first places at char2token to this index
+		$ccl->addToken($token);
+		// set chunk->sentence->token object tree also
+		$ccl->addChunk($chunk);
+
+		return $ccl;
+
+	} // generateProperCclToSetAnnotationTests
+
+    public function testSetannotationWithNullParameterSetsError() {
+
+        $annotation = null;
+		// must be token in $ccl
+        $ccl = $this->generateProperCclToSetAnnotationTests(1,3);
+
+        $ccl->setAnnotation($annotation);
+
+        $this->assertEquals(1,count($ccl->errors)); // is sth in errors table
+        $this->assertInstanceOf('CclError',$ccl->errors[0]); // is this object
+        $expectedErrorMsg = array("Annotation out of range (annotation.from > document.char_count)");
+        $this->assertEquals($expectedErrorMsg,$ccl->errors[0]->comments);
+
+    } // testSetannotationWithNullParameterSetsError()
+
+    public function testSetannotationWithAnnotationWithoutFromSetsError() {
+
+        $annotation = array('type'=>"TYP", 'to'=>3, 'value'=>'VALUE', 'name'=>'NAME' );
+		// must be token in $ccl
+		$ccl = $this->generateProperCclToSetAnnotationTests(1,3);
+
+        $ccl->setAnnotation($annotation);
+        $this->assertEquals(1,count($ccl->errors)); // is sth in errors table
+        $this->assertInstanceOf('CclError',$ccl->errors[0]); // is this object
+        $expectedErrorMsg = array("Annotation out of range (annotation.from > document.char_count)");
+        $this->assertEquals($expectedErrorMsg,$ccl->errors[0]->comments);
+
+    } // testSetannotationWithEmptyAnnotationSetsError()
+ 
     public function testSetannotationForProperDataCallsTokensSetannotation() {
 
         $from = 1; $to = 3;
@@ -333,10 +382,37 @@ public function testSetannotationForProperDataCallsTokensSetannotation() {
             "sense:".$annotation["name"]=>$annotation['value']
         );
         $mockDocument->setAnnotation($annotation);
-        $this->assertEquals(0,count($ccl->errors)); // no errors
+        $this->assertEquals(0,count($mockDocument->errors)); // no errors
         // annotation.value is direct set to prop table in token
         $this->assertEquals($expectedTokenProp,$mockToken->prop);
+		// in token in main ccl table
+		$this->assertEquals($expectedTokenProp,$mockDocument->tokens[0]->prop);
+		//var_dump($mockDocument->chunks);
 
     } // testSetannotationForProperDataCallsTokensSetannotation()
 
+	public function testSetannotationForProperDataSetPropInTokenAndTypeInChannels() {
+
+        $from = 1; $to = 3;
+        $annotation = array( 'type'=>"TYP", 'from'=>1, 'to'=>3, 'value'=>'VALUE', 'name'=>'NAME' );
+        // must be token in proper range in $ccl
+        $ccl = $this->generateProperCclToSetAnnotationTests($from,$to);
+
+        $ccl->setAnnotation($annotation);
+
+        $this->assertEquals(0,count($ccl->errors)); // no errors
+        // annotation.value is direct set to prop table in token
+        $expectedTokenProp = array(
+            "sense:".$annotation["name"]=>$annotation['value']
+        );
+        // in token in main ccl table
+        $this->assertEquals($expectedTokenProp,$ccl->tokens[0]->prop);
+        // and in chunks->sentence->tokens tree
+        $this->assertEquals($expectedTokenProp,$ccl->chunks[0]->sentences[0]->tokens[0]->prop);
+		// set channel in sentence
+		$expectedSentenceChannels = array( $annotation["type"]=>1 );
+		$this->assertEquals($expectedSentenceChannels,$ccl->chunks[0]->sentences[0]->channels);
+
+	} // testSetannotationForProperDataSetPropInTokenAndTypeInChannels() 
+
 } // CclDocumentTest class
diff --git a/phpunit/tests/engine/include/writers/CCclWriterTest.php b/phpunit/tests/engine/include/writers/CCclWriterTest.php
index 0d5d8ad8..39f2758c 100644
--- a/phpunit/tests/engine/include/writers/CCclWriterTest.php
+++ b/phpunit/tests/engine/include/writers/CCclWriterTest.php
@@ -171,10 +171,19 @@ private function generateFullCclData() {
 					'fromSentence','fromType','fromChannel',
 					'toSentence','toType','toChannel') 
 			);
-        return $this->createMockCclDocument(
+        $ccl = $this->createMockCclDocument(
 							array($mockChunk),
 							$relations
 						);
+        // duplicate tokens on main $ccl level
+        foreach($ccl->chunks as $chunk) {
+            foreach($chunk->sentences as $sentence) {
+                foreach($sentence->tokens as $token) {
+                    $ccl->addToken($token);
+                } // tokens
+            } // sentences
+        } // chunks
+        return $ccl;
 
     } // generateFullCclData()
 
@@ -588,6 +597,7 @@ public function testLemmaDataGeneratesPropXml() {
 		$chunk->addSentence($sentence);
 		$ccl = new CclDocument();
 		$ccl->addChunk($chunk);
+        $ccl->addToken($token);
 
         // private method need reflection to tests
         $privateMethod = new ReflectionMethod('CclWriter','makeXmlData');

From c9ec2e051a8b38a9fa7361e75e2c40509f2f09f1 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Fri, 1 Dec 2023 09:58:27 +0100
Subject: [PATCH 135/154] test lemma in XML with emulated Ccl

---
 .../export/CorpusExporter_part12_Test.php     | 295 ++++++++++++++++++
 1 file changed, 295 insertions(+)
 create mode 100644 phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php

diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
new file mode 100644
index 00000000..d3ae3203
--- /dev/null
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
@@ -0,0 +1,295 @@
+<?php
+
+use org\bovigo\vfs\vfsStream; // for vfsStream
+mb_internal_encoding("UTF-8");
+
+class CorpusExporter_part12_Test extends PHPUnit_Framework_TestCase
+{
+    // tests with lemma fields sets    
+
+    private $virtualDir = null;
+
+    protected function setUp() {
+
+        $this->virtualDir = vfsStream::setup('root',null,[]);
+
+    } // setUp()
+
+    private function emptyExtractorData() {
+
+        return array("annotations"=>array(), "relations"=>array(), "lemmas"=>array(), "attributes"=>array());
+
+    } // emptyExtractorData
+
+    private function lemmaData() {
+
+        return array ( 'report_annotation_id' => '2', 'lemma' => 'lemat dodany do okno', 'id' => '2', 'report_id' => '1', 'type_id' => '119', 'type' => 'nam_oth', 'group' => '1', 'from' => '10', 'to' => '13', 'text' => 'okno', 'user_id' => NULL, 'creation_time' => '2022-10-03 08:34:21', 'stage' => 'final', 'source' => 'user', 'annotation_type_id' => '119', 'name' => 'nam_oth', 'description' => 'Nazwy własne niezaklasyfikowane do pozostałych grup (w przypadku braku bardziej szczegółowego typu anotacji w obrębie nam_oth).', 'group_id' => '1', 'annotation_subset_id' => '8', 'level' => '0', 'short_description' => '', 'css' => 'background: lightgreen; border: 1px dashed red; border-bottom: 2px solid red;', 'cross_sentence' => '0', 'shortlist' => '0', 'annotation_id' => NULL, 'annotation_attribute_id' => NULL, 'value' => NULL );
+
+    } // lemmaData()
+
+    private function annotationWithLemmaData() {
+
+        return array ( 'id' => '2', 'report_id' => '1', 'type_id' => '119', 'from' => '10', 'to' => '13', 'text' => 'okno', 'user_id' => '1', 'creation_time' => '2022-10-03 08:34:21', 'stage' => 'final', 'source' => 'user', 'type' => 'nam_oth', 'group_id' => '1', 'annotation_subset_id' => '8', 'lemma' => 'lemat dodany do okno', 'login' => 'admin', 'screename' => 'Inforex Admin' );
+
+    } // annotationWithLemmaData()
+
+    private function annotationWoLemmaData() {
+
+        return array ( 'id' => '1', 'report_id' => '1', 'type_id' => '360', 'from' => '6', 'to' => '9', 'text' => 'duże', 'user_id' => '1', 'creation_time' => '2022-10-03 08:07:37', 'stage' => 'final', 'source' => 'user', 'type' => 'nam_adj', 'group_id' => '1', 'annotation_subset_id' => '52', 'lemma' => NULL, 'login' => 'admin', 'screename' => 'Inforex Admin' );
+
+    } // annotationWoLemmaData() 
+
+	private function addTokenToCcl(&$ccl,$from,$to,$orth,$ns=false) {
+
+		// create and add token with properties: $from,$to,$orth,$ns
+		// to existing CclDocument object, in main table and as chunk tree
+        $token = new CclToken(); $token->setFrom($from); $token->setTo($to);
+            $token->setOrth($orth); $token->setNs($ns);
+        $sentence = new CclSentence(); $sentence->addToken($token);
+        $chunk = new CclChunk(); $chunk->addSentence($sentence);
+        $ccl->addChunk($chunk); $ccl->addToken($token);
+		return $ccl;
+
+	} // addTokenToCcl()
+
+	private function flagsData() {
+
+		// emulate data returned by getFlagsByReportId($report_id)
+		//   rekordy typu:
+		// 		strtolower($f['short']) => $f['flag_id']
+		// 'short','flag_id' z tabel DB, $f['flag_id'] = INT(-1,...,5) 
+		$flagData = array(
+			'flag_short_name' => 1
+		);
+		return $flagData;
+
+	} // flagsData()
+
+    public function test_LemmaInAnnotationsTable() {
+
+        // export_document() dumb parameters
+        $report_id = 1;
+        $fakeExtractor = array();
+        $extractors = array( $fakeExtractor );
+        $disamb_only = true;
+        $extractor_stats = array();
+        $lists = array();
+        $output_folder = $this->virtualDir->url();
+        $subcorpora = '';
+        $tagging_method = 'tagger';
+
+
+
+        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
+            -> disableArgumentCloning()
+			-> setMethods(array('getFlagsByReportId','getTokenByReportId',
+							'getReportTagsByTokens','getReportById',
+                            'getReportExtById','exportReportContent',
+                            'updateLists','createIniFile',
+                            'checkIfAnnotationForLemmaExists',
+                            'checkIfAnnotationForRelationExists',
+                            //'sortUniqueAnnotationsById',
+                            'dispatchElements','generateCcl',
+                            'runExtractor'))
+            -> getMock();
+
+		$reportFlags = array('flagnamelowercase'=>array(-1));
+        $mockCorpusExporter -> method('getFlagsByReportId')
+            -> will($this->returnValue($reportFlags));
+        $annotations = array();
+        $returnedTableList = [$annotations,array(),array(),array()];
+        $mockCorpusExporter -> expects($this->once())
+            ->method('dispatchElements')
+            -> will($this->returnValue($returnedTableList));
+		$reportTokens = array();
+        $mockCorpusExporter -> method('getTokenByReportId')
+            -> will($this->returnValue($reportTokens));
+		$reportTags = array();
+        $mockCorpusExporter -> method('getReportTagsByTokens')
+            -> will($this->returnValue($reportTags));
+        $reportContent = "tekst dokumentu raportu";
+        $report = array( 'id'=>$report_id, 'content'=>$reportContent );
+        $mockCorpusExporter -> method('getReportById')
+            -> will($this->returnValue($report));
+        $fileName = str_pad($report_id,8,'0',STR_PAD_LEFT);
+        $returnedCcl = new CclDocument();
+        $returnedCcl -> setFileName($fileName);
+        $mockCorpusExporter -> expects($this->once())
+            ->method('generateCcl')
+            ->with($report,$reportTokens,$reportTags)
+            -> will($this->returnValue($returnedCcl));
+
+		// reflection for acces to private elements
+		$protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($mockCorpusExporter,'export_document');
+
+        // tested call
+        $protectedMethod->invokeArgs($mockCorpusExporter,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
+
+		// returned results in $extractor_stats, $lists and export files
+
+
+    } // test_LemmaInAnnotationsTable()
+
+// =====
+
+    public function testMinimalParameterForExampleExecution() {
+    // minimal setting for proper execution of mock export_document 
+
+        // var_dump(file_get_contents('.xml')); // zwraca zawartość ?
+        $report_id = 1;
+        $fakeExtractor = array();
+        $extractors = array( $fakeExtractor );
+        $disamb_only = true;
+        $extractor_stats = array();
+        $lists = array();
+        $output_folder = $this->virtualDir->url();
+        $subcorpora = '';
+        $tagging_method = 'tagger';
+        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
+            -> disableArgumentCloning()
+            -> setMethods(array(
+                'getFlagsByReportId', // block fetch() error
+                'getTokenByReportId', // block fetch() error
+                'getReportTagsByTokens', // block fetch() error
+                'getReportById', // block fetch() error
+                'getReportExtById', // block fetch() error
+                'generateCcl', // for proper filename generation
+                ))
+                            -> getMock();
+        $mockCorpusExporter -> method('getTokenByReportId')
+            -> will($this->returnValue(array())); // block array_column error
+        // for create proper filename for output files:
+        $fileName = str_pad($report_id,8,'0',STR_PAD_LEFT);
+        $ccl = new CclDocument(); $ccl -> setFileName($fileName);
+        $mockCorpusExporter -> expects($this->once())
+            ->method('generateCcl')
+            // ->with(null,array(),null) - it works
+            -> will($this->returnValue($ccl));
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($mockCorpusExporter,'export_document');
+        $protectedMethod->invokeArgs($mockCorpusExporter,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
+        
+        // possible outputs 
+        $this->assertEquals(array(),$lists);    // lists array
+        $this->assertEquals(array(),$extractor_stats); // extractor_stats array
+        // 6 files should be created
+        $file_path_without_ext = $output_folder."/".$fileName;
+        //  INI file
+        $this->assertTrue(file_exists($file_path_without_ext.'.ini'));
+        //  TXT file 
+        $this->assertTrue(file_exists($file_path_without_ext.'.txt'));
+        //  XML file 
+        $this->assertTrue(file_exists($file_path_without_ext.'.xml'));
+        //  REL.XML file 
+        $this->assertTrue(file_exists($file_path_without_ext.'.rel.xml'));
+        //  JSON file 
+        $this->assertTrue(file_exists($file_path_without_ext.'.json'));
+        //  CONLL file 
+        $this->assertTrue(file_exists($file_path_without_ext.'.conll'));
+ 
+        //$resultFileContent = file_get_contents($file_path_without_ext.'.xml');
+
+    } // testMinimalParameterForExampleExecution() 
+
+    public function testMainFlowForXMLLemmaExport() {
+
+        $report_id = 1;
+        $fakeExtractor = array( 'name' => 'extractorNAME' );
+        $extractors = array( $fakeExtractor );
+        $disamb_only = true;
+        $extractor_stats = array();
+        $lists = array();
+        $output_folder = $this->virtualDir->url();
+        $subcorpora = '';
+        $tagging_method = 'tagger';
+		// emulowane dane z bazy danych
+		$annotations = array(
+			$this->annotationWoLemmaData(),
+			$this->annotationWithLemmaData()
+		);
+		$relations = array();
+		$lemmas = array( $this->lemmaData() );
+		$attributes = array();
+ 
+        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
+            -> disableArgumentCloning()
+            -> setMethods(array(
+                'getFlagsByReportId', // block fetch() error
+                'getTokenByReportId', // block fetch() error
+                'getReportTagsByTokens', // block fetch() error
+                'getReportById', // block fetch() error
+                'getReportExtById', // block fetch() error
+                 'generateCcl', // for proper filename generation
+				'dispatchElements',
+/*							'exportReportContent',
+                            'updateLists','createIniFile',
+                            'checkIfAnnotationForLemmaExists',
+                            'checkIfAnnotationForRelationExists',
+                            'sortUniqueAnnotationsById',
+                            'dispatchElements', 'runExtractor' */
+                )) -> getMock();
+        $mockCorpusExporter -> expects($this->once())
+			-> method('getTokenByReportId')
+			-> with($report_id)
+            -> will($this->returnValue(array())); // block array_column error
+		//  === dodane do generowania lematów
+		// wygenerowne flagi - używane tylko w ekstraktorze
+		$returnedFlags = $this->flagsData();
+		$mockCorpusExporter -> expects($this->once())
+			-> method('getFlagsByReportId')
+			-> with($report_id)
+			-> will($this->returnValue($returnedFlags));
+		//  emulate $ccl structure
+        // also for create proper filename for output files:
+        $fileName = str_pad($report_id,8,'0',STR_PAD_LEFT);
+        $ccl = new CclDocument(); $ccl -> setFileName($fileName);
+        $this->addTokenToCcl($ccl,6,9,"duże"); // token from=6,to=9,orth="duże"
+        $this->addTokenToCcl($ccl,10,13,"okno",true); // token (10,13,"okno")
+        $mockCorpusExporter -> expects($this->once())
+            ->method('generateCcl')
+            ->with(null,array(),null)
+            -> will($this->returnValue($ccl));
+		// emulacja wyników z ekstraktora - w $elements
+		$returnedExtractorData = array($annotations,$relations,$lemmas,$attributes); 
+		$mockCorpusExporter -> expects($this->once())
+			-> method('dispatchElements')
+			-> will($this->returnValue($returnedExtractorData));
+		;
+
+
+		// powyższe nie ustawia extractor_stats, trzeba to zrobić osobno,
+		// jeśli wyeliminowaliśmy runExtractor() z generowania wyniku
+		$protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($mockCorpusExporter,'updateExtractorStats');
+		$extractor_stats = $protectedMethod->invokeArgs($mockCorpusExporter,array($fakeExtractor["name"],$extractor_stats,$returnedExtractorData));
+ 
+        // reflection for acces to private elements
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($mockCorpusExporter,'export_document');
+
+        // tested call
+        $protectedMethod->invokeArgs($mockCorpusExporter,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
+
+		// check results in XML file
+		$resultFileName = $output_folder.'/'.$fileName.".xml";
+		$resultFileContent = file_get_contents($resultFileName);
+		//var_dump($resultFileContent);
+		// prefix for proper XML
+		$expectedXmlContentPrefix = '<?xml version="1.0" encoding="UTF-8"?';
+		$this->assertRegexp('@'.$expectedXmlContentPrefix."@",$resultFileContent);
+		// annotacja bez lematu ( lemma=NULL )
+		$expectedAnnWithoutLemmaLine = '<ann chan="nam_adj">1</ann>';
+		$this->assertRegexp('@'.$expectedAnnWithoutLemmaLine.'@m',$resultFileContent);
+		// annotacja towarzysząca lematowi
+		$expectedAnnWithLemmaLine = '<ann chan="nam_oth">2</ann>';
+        $this->assertRegexp('@'.$expectedAnnWithLemmaLine.'@m',$resultFileContent);
+		// lemat - z pozycji w $lemmas
+		$expectedLemmaLine = '<prop key="nam_oth:lemma">lemat dodany do okno</prop>';
+		$this->assertRegexp('@'.$expectedLemmaLine.'@m',$resultFileContent);
+		// lemma line after anno line in export XML 
+        $expectedAnnWithLemmaLines = 
+'<ann chan="nam_oth">2</ann>'.'\s*'.'<prop key="nam_oth:lemma">lemat dodany do okno</prop>';
+        $this->assertRegexp('@'.$expectedAnnWithLemmaLines.'@m',$resultFileContent);
+
+	 }//
+
+} // CorpusExporter_part12_Test class
+
+?>

From a1402d7f4945b837aed794e41517b96e1d29c784 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Fri, 1 Dec 2023 13:42:09 +0100
Subject: [PATCH 136/154] all modules real test for XML export

---
 .../export/CorpusExporter_part12_Test.php     | 97 ++++++++-----------
 1 file changed, 43 insertions(+), 54 deletions(-)

diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
index d3ae3203..4a5e69e0 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
@@ -39,32 +39,6 @@ private function annotationWoLemmaData() {
 
     } // annotationWoLemmaData() 
 
-	private function addTokenToCcl(&$ccl,$from,$to,$orth,$ns=false) {
-
-		// create and add token with properties: $from,$to,$orth,$ns
-		// to existing CclDocument object, in main table and as chunk tree
-        $token = new CclToken(); $token->setFrom($from); $token->setTo($to);
-            $token->setOrth($orth); $token->setNs($ns);
-        $sentence = new CclSentence(); $sentence->addToken($token);
-        $chunk = new CclChunk(); $chunk->addSentence($sentence);
-        $ccl->addChunk($chunk); $ccl->addToken($token);
-		return $ccl;
-
-	} // addTokenToCcl()
-
-	private function flagsData() {
-
-		// emulate data returned by getFlagsByReportId($report_id)
-		//   rekordy typu:
-		// 		strtolower($f['short']) => $f['flag_id']
-		// 'short','flag_id' z tabel DB, $f['flag_id'] = INT(-1,...,5) 
-		$flagData = array(
-			'flag_short_name' => 1
-		);
-		return $flagData;
-
-	} // flagsData()
-
     public function test_LemmaInAnnotationsTable() {
 
         // export_document() dumb parameters
@@ -193,7 +167,12 @@ public function testMinimalParameterForExampleExecution() {
     public function testMainFlowForXMLLemmaExport() {
 
         $report_id = 1;
-        $fakeExtractor = array( 'name' => 'extractorNAME' );
+        $flag_name = 'flag_short_name';
+        $flag_id = 1;   // -1,...,5
+        $fakeExtractor = array( 
+            'name' => 'extractorNAME', 
+            "flag_name" => $flag_name,
+            "flag_ids" => array($flag_id) );
         $extractors = array( $fakeExtractor );
         $disamb_only = true;
         $extractor_stats = array();
@@ -202,6 +181,15 @@ public function testMainFlowForXMLLemmaExport() {
         $subcorpora = '';
         $tagging_method = 'tagger';
 		// emulowane dane z bazy danych
+		$flags = array( $flag_name => $flag_id );
+		$report = array( "id"=>$report_id, "content"=>'To jest duże okno.' );
+		$tokens = array(
+			// all fields from DB, enough are "from","to","token_id" 
+			// from,to are offset in content without white chars and tags
+			array( "from"=>6, "to"=>9, "orth"=>'duże', "eos"=>false, "token_id"=>231, "report_id"=>$report_id ),
+			array( "from"=>10, "to"=>13, "orth"=>'okno', "eos"=>true, "token_id"=>2314, "report_id"=>$report_id  ),
+		);
+		$tags = array();
 		$annotations = array(
 			$this->annotationWoLemmaData(),
 			$this->annotationWithLemmaData()
@@ -209,6 +197,16 @@ public function testMainFlowForXMLLemmaExport() {
 		$relations = array();
 		$lemmas = array( $this->lemmaData() );
 		$attributes = array();
+        $extractors[0]["extractor"] = 
+            function($report_id, $params, &$extractor_elements) {
+                $extractor_elements=  array( 
+                    "relations"=>[], 
+                    "attributes"=>[],
+                    "annotations" => array(
+                        $this->annotationWoLemmaData(),
+                        $this->annotationWithLemmaData() ),
+                    "lemmas" => array( $this->lemmaData() ));
+            };
  
         $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
             -> disableArgumentCloning()
@@ -218,49 +216,39 @@ public function testMainFlowForXMLLemmaExport() {
                 'getReportTagsByTokens', // block fetch() error
                 'getReportById', // block fetch() error
                 'getReportExtById', // block fetch() error
-                 'generateCcl', // for proper filename generation
-				'dispatchElements',
+                //'generateCcl', // for proper filename generation
+				//'dispatchElements',
+                //'runExtractor',
 /*							'exportReportContent',
                             'updateLists','createIniFile',
                             'checkIfAnnotationForLemmaExists',
                             'checkIfAnnotationForRelationExists',
-                            'sortUniqueAnnotationsById',
-                            'dispatchElements', 'runExtractor' */
+                            'sortUniqueAnnotationsById', */
                 )) -> getMock();
         $mockCorpusExporter -> expects($this->once())
 			-> method('getTokenByReportId')
 			-> with($report_id)
-            -> will($this->returnValue(array())); // block array_column error
+            -> will($this->returnValue($tokens)); // block array_column error
 		//  === dodane do generowania lematów
 		// wygenerowne flagi - używane tylko w ekstraktorze
-		$returnedFlags = $this->flagsData();
 		$mockCorpusExporter -> expects($this->once())
 			-> method('getFlagsByReportId')
 			-> with($report_id)
-			-> will($this->returnValue($returnedFlags));
-		//  emulate $ccl structure
-        // also for create proper filename for output files:
-        $fileName = str_pad($report_id,8,'0',STR_PAD_LEFT);
-        $ccl = new CclDocument(); $ccl -> setFileName($fileName);
-        $this->addTokenToCcl($ccl,6,9,"duże"); // token from=6,to=9,orth="duże"
-        $this->addTokenToCcl($ccl,10,13,"okno",true); // token (10,13,"okno")
-        $mockCorpusExporter -> expects($this->once())
-            ->method('generateCcl')
-            ->with(null,array(),null)
-            -> will($this->returnValue($ccl));
-		// emulacja wyników z ekstraktora - w $elements
-		$returnedExtractorData = array($annotations,$relations,$lemmas,$attributes); 
+			-> will($this->returnValue($flags));
+        // emulacja getReportById - dla generateCcl
+        $mockCorpusExporter -> expects($this->exactly(2)) // call twice now !!!
+            -> method('getReportById')
+            -> with($report_id)
+            -> will($this->returnValue($report))
+        ;
+		// emulacja getReportTagsByTokens - dla generate Ccl
+		$token_ids = array(231,2314); // array_column($tokens, 'token_id')
 		$mockCorpusExporter -> expects($this->once())
-			-> method('dispatchElements')
-			-> will($this->returnValue($returnedExtractorData));
+            -> method('getReportTagsByTokens')
+			-> with($report_id,$token_ids,$disamb_only,$tagging_method)
+			-> will($this->returnValue($tags))
 		;
 
-
-		// powyższe nie ustawia extractor_stats, trzeba to zrobić osobno,
-		// jeśli wyeliminowaliśmy runExtractor() z generowania wyniku
-		$protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($mockCorpusExporter,'updateExtractorStats');
-		$extractor_stats = $protectedMethod->invokeArgs($mockCorpusExporter,array($fakeExtractor["name"],$extractor_stats,$returnedExtractorData));
- 
         // reflection for acces to private elements
         $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($mockCorpusExporter,'export_document');
 
@@ -268,6 +256,7 @@ public function testMainFlowForXMLLemmaExport() {
         $protectedMethod->invokeArgs($mockCorpusExporter,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
 
 		// check results in XML file
+		$fileName = str_pad($report_id,8,'0',STR_PAD_LEFT);
 		$resultFileName = $output_folder.'/'.$fileName.".xml";
 		$resultFileContent = file_get_contents($resultFileName);
 		//var_dump($resultFileContent);

From eb080ecf59f125c1f5b63519003f031935d395fa Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Thu, 7 Dec 2023 09:52:57 +0100
Subject: [PATCH 137/154] remove not really used ExportManager class

---
 engine/include/export/CorpusExporter.php      |   7 +-
 engine/include/export/ExportManager.php       | 644 ------------------
 local/ccl2iob.php                             |  12 +-
 phpunit/phpunit_full.warnings.xml             |   7 +
 .../export/CorpusExporter_part12_Test.php     |  38 +-
 5 files changed, 48 insertions(+), 660 deletions(-)
 delete mode 100644 engine/include/export/ExportManager.php
 create mode 100644 phpunit/phpunit_full.warnings.xml

diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index 180eeb2b..4066bc37 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -311,7 +311,8 @@ private function log_error($file_name, $line_no, $report_id, $message, $error_ty
                 break;
        		//Problem z utworzeniem CCL
 			case 2:
-                $this->export_errors[$error_type]['details']['names'][$error_params['name']] = 1;
+                if(isset($error_params['name']))  
+                    $this->export_errors[$error_type]['details']['names'][$error_params['name']] = 1;
                 $this->export_errors[$error_type]['details']['error'][$error_params['error']] = 1;
                 break;
 			//Brak anotacji źródłowej dla relacji
@@ -510,7 +511,7 @@ protected function updateLists($flags,$reportFileName,&$lists) {
 
     protected function createIniFile($report,$subcorpora,$file_path_without_ext) {
 
-        $ext = $this->getReportExtById($report_id);
+        $ext = $this->getReportExtById($report["id"]);
 
         $basic = array("id", "date", "title", "source", "author", "tokenization", "subcorpus");
         $lines = array();
@@ -643,7 +644,7 @@ protected function generateCcl($report,$tokens,$tags_by_tokens) {
                 'message' => "Problem z utworzeniem CCL",
                 'error' => $error
             );
-            $this->log_error(__FILE__, __LINE__, $report_id, "Problem z utworzeniem ccl: " . $error, 2, $error_params);
+            $this->log_error(__FILE__, __LINE__, $report["id"], "Problem z utworzeniem ccl: " . $error, 2, $error_params);
             return False; // error is collected
         }
 		return $ccl; // all ok
diff --git a/engine/include/export/ExportManager.php b/engine/include/export/ExportManager.php
deleted file mode 100644
index 8960f190..00000000
--- a/engine/include/export/ExportManager.php
+++ /dev/null
@@ -1,644 +0,0 @@
-<?php
-/**
- * Part of the Inforex project
- * Copyright (C) 2013 Michał Marcińczuk, Jan Kocoń, Marcin Ptak
- * Wrocław University of Technology
- * See LICENCE 
- */
- 
-class ExportManager { 
-	var $channelPriority = array(
-			"title_nam"=>7,
-			"software_nam"=>7,
-			"event_nam"=>6,
-			"road_nam"=>5,
-			"facility_nam"=>4, 
-			"company_nam"=>3,
-			"astronomical_nam"=>3,
-			"person_nam"=>2,
-			"city_nam"=>1);
-	var $cclDocuments = array();
-	//input parameters
-	var $db = null; 				//instance of Database 
-	var $corpus_ids = null; 		//array, value: id
-	var $subcorpus_ids = null; 		//array, value: id
-	var $document_ids = null; 		//array, value: id
-	var $flags = null; 				//array, key: flag name; value: array of flag values
-	var $annotation_layers = null; 	//array, value: id
-	var $annotation_names = null;	//array, value: type name
-	var $folder = null;				//string
-	var $relation_set_ids = null;
-	var $relation_type_ids = null;
-	var $index_flags = null;		//array, value: corpora_flags.corpora_flag_id or corpora_flags.short
-	var $index_flag_ids = array();  //array, value: corpora_flags.corpora_flag_id
-	var $index_flag_paths = array(); //array, key: corpora_flags.short(lowercase, "_" instead of " "), value: array of strings (paths)
-	var $report_flag_ids = array(); //array, key: report_id; value: array (value: corpora_flags.short)
-	
-	var $split_documents = false;
-	var $separate_relations = false;
-	
-	var $iob_file_name = false;	
-	
-	var $report_ids = array(); 		//array, value: id
-	var $reports = array();			//array, key: report id; value: report
-	var $metadata = array();
-	var $tokens = array();			//array, key: report id; value: token
-	var $tags = array();			//array, key: report id; value: array (key: token_id, value: tag)
-	var $annotations = array();		//array, key: report id; value: annotation
-	var $relations = array();
-	var $annotation_lemmas = array();
-    var $annotation_properties = array();
-
-	var $verbose = false;
-	var $no_disamb = false;
-	
-	function setCorpusIds($corpus_ids){
-		$this->corpus_ids = $corpus_ids;
-	}	
-	
-	function setSubcorpusIds($subcorpus_ids){
-		$this->subcorpus_ids = $subcorpus_ids;
-	}
-	
-	function setDocumentIds($document_ids){
-		$this->document_ids = $document_ids;
-	}
-	
-	function setFlags($flags){
-		$this->flags = $flags;
-	}
-	
-	function setAnnotationLayers($annotation_layers){
-		$this->annotation_layers = $annotation_layers;
-	}
-	
-	function setAnnotationNames($annotation_names){
-		$this->annotation_names = $annotation_names;
-	}
-	
-	function setRelationSetIds($relation_set_ids){
-		$this->relation_set_ids = $relation_set_ids;
-	}
-	
-	function setRelationTypeIds($relation_type_ids){
-		$this->relation_type_ids = $relation_type_ids;
-	}	
-	
-	function setIndexFlags($index_flags){
-		if ($index_flags){
-			$this->index_flags = array();
-			foreach($index_flags as $item){
-				$this->index_flags[] = mb_strtolower($item);
-			}
- 		}
-	}	
-	
-	function setDb($db){
-		assert('$db instanceof Database');
-		$this->db = $db;
-	}
-	
-	function setFolder($folder){
-		$this->folder = $folder;
-	}
-	
-	function setSplit($split_documents){
-		$this->split_documents = $split_documents;
-	}
-	
-	function setSeparateRelations($separate_relations){
-		$this->separate_relations = $separate_relations;
-	}
-	
-	function setIob($iob_file_name){
-		$this->iob_file_name = $iob_file_name;
-	}
-	
-	function log($text){
-		if ( $this->verbose )
-			echo date("\r[H:i:s]") . " $text\n";
-	}
-	
-	function setVerbose($verbose){
-		$this->verbose = $verbose;
-	}
-	
-	function setNoDisamb($no_disamb){
-		$this->no_disamb = $no_disamb;
-	}
-	
-	/**
-	 * Wczytuje dokumenty do eksportu na podstawie ustawionych filtrów.
-	 */
-	function readDocuments(){
-		$reports = DbReport::getReports($this->corpus_ids, $this->subcorpus_ids, 
-						$this->document_ids, $this->flags);
-
-		foreach ($reports as &$r)
-			$this->reports[$r['id']] = &$r;
-		$this->report_ids = array_keys($this->reports);
-		$this->log(sprintf("Number of documents to export: %d", count($this->report_ids)));
-		if ($this->index_flags){
-			$this->getIndexFlags();
-			if ($this->no_content){
-				$this->writeRawIndexes();
-			}
-		}
-	}
-	
-	function getIndexFlags(){
-		echo date("[H:i:s] ") . " - get index flags\n";
-		$index_flags = DbCorporaFlag::getCorporaFlagIds($this->index_flags);
-		
-		//check if all given flags exist in database
-		$flag_errors = array();
-		$flag_ids = array();
-		$flag_shorts_orig = array();
-		if (empty($index_flags)){
-			$e = new CclError();
-			$e->setClassName("CclSetFactory");
-			$e->setFunctionName("acquireData");
-			$e->addObject("message", "flag error");
-			$e->addComment("015 no given flag was found");		
-			$flag_errors[] = $e;	
-		}
-		else {
-			$flag_shorts = array();
-			foreach ($index_flags as $item){
-				$flag_ids[] = $item['corpora_flag_id'];	
-				$flag_lower = mb_strtolower($item['short']);;						
-				if (!in_array($flag_lower, $flag_shorts)){
-					$flag_shorts[] = $flag_lower;
-				}
-			}
-			foreach ($this->index_flags as $item){
-				if (! (in_array($item, $flag_ids) || in_array($item, $flag_shorts)) ){
-					$e = new CclError();
-					$e->setClassName("CclSetFactory");
-					$e->setFunctionName("acquireData");
-					$e->addObject("message", "flag error");
-					$e->addComment("016 flag \"$item\" not found");							
-					$flag_errors[] = $e;	
-				}
-			}
-		}
-		if ($flag_errors){
-			foreach ($flag_errors as $flag_error){
-				print (string)$flag_error . "\n";
-			}
-			exit("EXIT: flag error\n");
-		}
-		else {
-			$this->index_flag_ids = $flag_ids;
-			
-			$report_flag_ids = DBReportFlag::getReportFlagData($this->report_ids, $flag_ids);
-			foreach ($report_flag_ids as $item){
-				$report_id = $item['report_id'];
-				$short = $item['short'];
-				if (empty($this->report_flag_ids[$report_id]))					
-					$this->report_flag_ids[$report_id] = array();
-				$this->report_flag_ids[$report_id][] = mb_strtolower(str_replace(" ","_",$short));
-			}
-		}		
-	}
-	
-	/**
-	 * Przygotowuje indeksy do zapisu.
-	 */
-	function processIndexes(){
-		foreach ($this->report_flag_ids as $report_id=>$flag_shorts){
-			$path = "";
-			if ($this->split_documents)
-				$relativePath = preg_replace("/[^\p{L}|\p{N}]+/u","_",$this->reports[$report_id]['name']) . "/";
-			foreach ($flag_shorts as $short){
-				$path = $relativePath . str_pad($report_id,8,'0',STR_PAD_LEFT) . ".xml";	
-				if (empty($this->index_flag_paths[$short]))
-					$this->index_flag_paths[$short] = array();				
-				$this->index_flag_paths[$short][] = $path;
-			}
-		}		
-	}		
-
-	/**
-	 * Zapisuje indeksy dla flag.
-	 */
-	function writeIndexes(){
-		$subfolder = $this->folder . "/";
-		foreach($this->index_flag_paths as $index_name=>$paths){
-			$filename = "index_" . $index_name . ".txt";
-			$handle = fopen($subfolder . $filename, "w");
-			sort($paths);
-			foreach ($paths as $path)
-				fwrite($handle, $path . "\n");			
-			fclose($handle);
-			if ( $this->verbose )
-				echo sprintf(" - index: %4d in %s\n", count($paths), $filename);
-		}
-	}
-		
-	/**
-	 * Wczytuje dane o treści dokumentów, tokenizacji, anotacjach i relacjach
-	 * z bazy danych.
-	 */
-	function readContent(){
-		$this->log("Reading content ...");
-		$this->log(" a) reading tokens ...");
-		$tokens = DbToken::getTokensByReportIds($this->report_ids);
-		foreach ($tokens as &$token){
-			$report_id = $token['report_id'];
-			if (!array_key_exists($report_id, $this->tokens))
-				$this->tokens[$report_id] = array();
-			$this->tokens[$report_id][] = &$token; 
-		}
-		
-		$this->log(" b) reading tags ...");
-		$tags = DbTag::getTagsByReportIds($this->report_ids);
-						
-		$this->log(" c) assigning tags to tokens ...");
-		foreach ($tags as $tag){
-			$report_id = $tag['report_id'];
-			$token_id = $tag['token_id'];
-			if ( !isset($this->tags[$report_id]) )
-				$this->tags[$report_id] = array();
-			if ( !isset($this->tags[$report_id][$token_id]) )
-				$this->tags[$report_id][$token_id] = array();
-			$this->tags[$report_id][$token_id][] = $tag; 
-		}
-		
-		/** Reorganize tags */
-		foreach ($this->tags as $report_id=>$tokens){
-			foreach ($tokens as $token_id=>$tags){
-				$ign = null;
-				$other = array();
-				foreach ($tags as $i_tag=>$tag){
-					if ($this->no_disamb)
-						$this->tags[$report_id][$token_id][$i_tag]['disamb'] = 0;
-						
-					if ($tag['ctag'] == "ign")
-						$ign = $tag;
-					else
-						$other[] = $tag; 
-				}
-				/* Jeżeli jedną z interpretacji jest ign, to usuń pozostałe. */
-				if ($this->no_disamb && $ign)
-					$this->tags[$report_id][$token_id] = array($ign);
-				elseif ($ign)
-					$this->tags[$report_id][$token_id] = array_merge(array($ign), $other);
-			}				
-		}
-		
-		$this->log(" d) reading annotations ...");
-		$annotations = DbAnnotation::getAnnotationsBySets($this->report_ids, 
-							$this->annotation_layers, $this->annotation_names);												  
-		foreach ($annotations as &$annotation){
-			$report_id = $annotation['report_id'];
-			if (!array_key_exists($report_id, $this->annotations))
-				$this->annotations[$report_id] = array();
-			$this->annotations[$report_id][] = &$annotation; 
-		}
-		
-		$this->log(" e) reading relations ...");
-		$relations = DbCorpusRelation::getRelationsBySets($this->report_ids, 
-							$this->relation_set_ids, $this->relation_type_ids);
-		foreach ($relations as &$relation){
-			$report_id = $relation['report_id'];			
-			if (!array_key_exists($report_id, $this->relations)){
-				$this->relations[$report_id] = array();
-			}
-			$this->relations[$report_id][] = &$relation; 
-		}
-		
-		$this->log(" f) reading annotation lemmas ...");
-		//$this->annotation_lemmas = DbReportAnnotationLemma::getLemmasByReportsIds($this->report_ids);
-		$this->annotation_lemmas = DbReportAnnotationLemma::getLemmasBySets2($this->report_ids, $this->annotation_layers, $this->annotation_names);
-
-        $this->log(" f) reading annotation attributes ...");
-        $this->annotation_properties = DbReportAnnotationLemma::getPropertiesBySets2($this->report_ids, $this->annotation_layers, $this->annotation_names);
-
-
-        $this->log("Reading content is done.");
-	}
-	
-	/**
-	 * Read documents metadata from the database.
-	 */
-	function readMetadata(){
-		$corpora = array();
-		$cnt=0;
-		foreach ($this->report_ids as $report_id){
-			$cnt ++;
-			$report = $this->reports[$report_id];
-			$corpora[$report['corpora']][] = $report['id'];	
-		}
-		foreach ($corpora as $corpus_id => $report_ids){
-			$corpus = DbCorpus::getCorpusById($corpus_id);
-			$ext = $corpus['ext'];
-			if ($ext){
-				$exts = DbReport::getReportExtByIds($report_ids, $ext);
-				foreach ($exts as $ext){
-					$this->metadata[$ext['id']] = $ext;
-				}
-			}
-		}
-	} 
-	
-	/**
-	 * Read documents segmentation, annotation and relations from databse.
-	 */
-	function processContent(){
-		//$this->log("Processing content ...");
-		$allReports = count($this->report_ids);
-		$cnt = 0;
-		foreach ($this->report_ids as $report_id){
-			$cnt ++;
-			$report = $this->reports[$report_id];
-			
-			$tokens = array();
-			$tags = array();	
-			$annotations = array();
-			$relations = array();		
-			$annotation_lemmas = array();
-            $annotation_properties = array();
-
-			if (array_key_exists($report_id, $this->tokens))
-				$tokens = &$this->tokens[$report_id];
-								
-			if (array_key_exists($report_id, $this->tags))
-				$tags = &$this->tags[$report_id];
-				
-			if (array_key_exists($report_id, $this->annotations))
-				$annotations = &$this->annotations[$report_id];	
-						
-			if (array_key_exists($report_id, $this->relations))
-				$relations = &$this->relations[$report_id];			
-			
-			if (array_key_exists($report_id, $this->annotation_lemmas))
-				$annotation_lemmas = $this->annotation_lemmas[$report_id];
-            if (array_key_exists($report_id, $this->annotation_properties))
-                $annotation_properties = $this->annotation_properties[$report_id];
-
-			try{
-				$ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags);
-
-				if (count($tokens)==0){
-					$e = new CclError();
-					$e->setClassName("CclSetFactory");
-					$e->setFunctionName("create");
-					$e->addObject("report", $report);
-					$e->addComment("010 no tokenization in report");
-					$ccl->addError($e);
-				}
-				else {
-					$flags = DbReportFlag::getReportFlags($report_id);
-					$annotations = $this->filterAnnotationsByFlags($report_id, $flags, $annotations);
-					$relations = $this->filterRelationsByFlags($report_id, $flags, $relations);
-					CclFactory::setAnnotationsAndRelations($ccl, $annotations, $relations);
-					CclFactory::setAnnotationLemmas($ccl, $annotation_lemmas);
-                    CclFactory::setAnnotationProperties($ccl, $annotation_properties);
-				}
-
-				if (count($tags)==0){
-					$e = new CclError();
-					$e->setClassName("CclSetFactory");
-					$e->setFunctionName("create");
-					$e->addObject("report", $report);
-					$e->addComment("011 no tags in report");
-					$ccl->addError($e);
-				}
-
-				$this->cclDocuments[$report_id] = $ccl;
-			}
-			catch(Exception $ex){
-				print "!!!!! FIX ME report_id = $report_id\n";
-			}
-		}
-		//$this->log("Processing content ... done");
-	}
-	
-	/**
-	 * Write documents tokens, annotations and relations to files. 
-	 */
-	function writeContent(){
-		//$this->log("Writing content ... ");
-		if ($this->iob_file_name)
-			$this->_writeIob();	
-		else
-			$this->_writeCcl(); 		
-		//$this->log("Writing content ... done");
-	}
-
-	/**
-	 * 
-	 */
-	function _writeCcl(){
-		$subfolder = $this->folder . "/";
-		$relativePath = "";
-		$failed = array();
-		if (!is_dir($subfolder)) mkdir($subfolder, 0777);
-		foreach ($this->cclDocuments as $cclDocument){
-			if ($this->split_documents){
-				$relativePath = $cclDocument->getSubcorpus() . "/";
-				$subfolder = $this->folder . "/" . $relativePath;
-				if (!is_dir($subfolder)) mkdir($subfolder, 0777);
-			} 
-			
-			if (!$cclDocument->hasErrors()){
-				if ($this->separate_relations){
-					CclWriter::write($cclDocument, $subfolder . $cclDocument->getFileName() . ".xml", CclWriter::$CCL);
-					CclWriter::write($cclDocument, $subfolder . $cclDocument->getFileName() . ".rel.xml", CclWriter::$REL);
-				}
-				else 
-					CclWriter::write($cclDocument, $subfolder . $cclDocument->getFileName() . ".xml", CclWriter::$CCLREL);
-				if ($this->index_flags){
-					$report = $cclDocument->getReport();
-					$report_id = $report['id'];
-					if (!empty($this->report_flag_ids[$report_id])){
-						foreach ($this->report_flag_ids[$report_id] as $short){
-							if (empty($this->index_flag_paths[$short]))
-								$this->index_flag_paths[$short] = array();
-							$this->index_flag_paths[$short][] = $relativePath . $cclDocument->getFileName() . ".xml";
-						}						
-					}
-				}													
-			}
-			else {
-				echo "ERROR in " . $cclDocument->getFileName() . " \n";
-				$failed[] = $cclDocument->getFileName();
-				$errors = $cclDocument->getErrors(); 
-				foreach ($errors as $error){
-					print (string)$error . "\n";	
-				}
-			}			
-		}
-		
-		if ( count($failed) ){
-			$this->log("[ERROR] Following documents were not saved because of errors:");
-			foreach ($failed as $f)
-				$this->log(" - $f");
-		}
-	}	
-	
-	/**
-	 * Write tokens and annotations to a single IOB file.
-	 */
-	function _writeIob(){
-		$subfolder = $this->folder . "/";
-		if (!is_dir($subfolder)) mkdir($subfolder, 0777);
-		$filename = $subfolder . $this->iob_file_name;
-		$writer = new IobWriter($filename, $this->channelPriority);
-		$writer->writeAll($this->cclDocuments); 
-		$writer->close();
-		$writer->printStats();
-	}
-	
-	/**
-	 * Save documents metadata to files.
-	 */
-	function writeMetadata(){
-		$this->log("Writing medatada ...");
-		$subfolder = $this->folder . "/";			
-		foreach ($this->reports as $r){
-			$basic = array("id", "date", "title", "source", "author", "tokenization", "name:subcorpus");			
-			$lines = array();
-			$lines[] = "[document]";
-			
-			foreach ($basic as $b=>$br){
-				$parts = split(":", $br);
-				$name = $parts[0];
-				$name_target = $parts[1] ? $parts[1] : $name;
-				$lines[] = sprintf("%s = %s", $name_target, $r[$name]);
-			}				
-			
-			if (isset($this->metadata[$r['id']])){
-				$lines[] = "";
-				$lines[] = "[metadata]";
-				foreach ($this->metadata[$r['id']] as $key=>$val)
-					if ($key != "id"){
-						$key = preg_replace("/[^\p{L}|\p{N}]+/u", "_", $key);
-						$lines[] = sprintf("%s = %s", $key, $val);
-					}
-			}
-
-			if ($this->split_documents){
-				$subfolder = $this->folder . "/" . 
-								preg_replace("/[^\p{L}|\p{N}]+/u", "_", $r['name']) . "/";
-			}
-								
-			$filename = $subfolder . str_pad($r['id'], 8, "0", STR_PAD_LEFT) . ".ini";
-			$f = fopen($filename, "w");
-			fwrite($f, implode("\n", $lines));
-			fclose($f);
-		}
-	}
-		
-	/**
-	 * Removes annotations according to flags. If there is a flag
-	 * for fiven layer of annotations, the flag for document must be set to 3 or 4.
-	 * In other case the annotation is discarded.
-	 * 
-	 * @param $flags --- array of document flags and values.
-	 * @param $annotations --- array of annotations.
-	 */
-	function filterAnnotationsByFlags($report_id, $flags, $annotations){
-		$annotatons_filtered = array();
-		$skipped = array();
-		foreach ($annotations as $an){
-			$group_id = intval($an['group_id']);
-			$keep = false;
-			
-			switch ( $group_id ) {
-				case 1:
-					$keep = isset($flags[FLAG_NAMES])
-							&& $this->flagReady($flags[FLAG_NAMES]);
-					break;
-
-				case 2:
-					$keep = isset($flags[FLAG_WSD])
-							&& $this->flagReady($flags[FLAG_WSD]);										
-					break;
-					
-				case 7:				
-					$keep = isset($flags[FLAG_CHUNKS])
-							&& $this->flagReady($flags[FLAG_CHUNKS]);					
-					break;
-
-				default:
-				$keep = true;
-					break;
-			}
-			
-			if ($keep){
-				$annotatons_filtered[] = $an;
-			}
-			else{
-				$skipped[$an['name']] = 1;
-			}			
-		}
-		
-		if (count($skipped) && $this->verbose){
-			echo sprintf(">> [id=%d] Skipped annotations: %s\n", 
-					$report_id, implode(", ", array_keys($skipped)));
-		}
-		
-		return $annotatons_filtered;
-	}
-	
-	/**
-	 * 
-	 */
-	function filterRelationsByFlags($report_id, $flags, $relations){
-		$relations_filtered = array();
-		$skipped = array();
-		foreach ($relations as $rel){
-			$group_id = intval($rel['relation_set_id']);
-			$keep = false;
-
-			switch ( $group_id ) {
-				case 1: /* Chunks relations */
-					$keep = isset($flags[FLAG_CHUNKS_REL])
-							&& $this->flagReady($flags[FLAG_CHUNKS_REL]);			
-					break;
-					
-				case 2: /* Names relations */
-					$keep = isset($flags[FLAG_NAMES_REL])
-							&& $this->flagReady($flags[FLAG_NAMES_REL]);							
-					break;
-					
-				case 3: /* Coreference */
-					$keep = isset($flags[FLAG_COREF])
-							&& $this->flagReady($flags[FLAG_COREF]);				
-					break;					
-
-				default:
-					$keep = true;
-					break;
-			}			
-			
-			if ($keep){
-				$relations_filtered[] = $rel;
-			}
-			else{
-				$skipped[$rel['name']] = 1;
-			}
-		}
-		
-		if (count($skipped) && $this->verbose){
-			echo sprintf(">> [id=%d] Skipped relations: %s\n", 
-					$report_id, implode(", ", array_keys($skipped)));
-		}
-				
-		return $relations_filtered;
-	}
-	
-	/**
-	 * 
-	 */
-	function flagReady($value){
-		return in_array(intval($value), array(3,4));
-	}
-}
-
-
-
-
-?>
diff --git a/local/ccl2iob.php b/local/ccl2iob.php
index 1aee5ca3..58e4b8f3 100644
--- a/local/ccl2iob.php
+++ b/local/ccl2iob.php
@@ -44,8 +44,16 @@
 if (count($contains))
 	$contains = $contains[0];
 $cWcclDocuments = CclReader::readCclDocumentBatch($input, $ignChannels, $reverse, $contains);
-$exportManager = new ExportManager();
-$channelPriority = $exportManager->channelPriority;
+$channelPriority = array(
+            "title_nam"=>7,
+            "software_nam"=>7,
+            "event_nam"=>6,
+            "road_nam"=>5,
+            "facility_nam"=>4,
+            "company_nam"=>3,
+            "astronomical_nam"=>3,
+            "person_nam"=>2,
+            "city_nam"=>1);
 
 if ( !$opt->exists("separate") ){
 	$output = $opt->getRequired("output");
diff --git a/phpunit/phpunit_full.warnings.xml b/phpunit/phpunit_full.warnings.xml
new file mode 100644
index 00000000..e0513dd1
--- /dev/null
+++ b/phpunit/phpunit_full.warnings.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<phpunit>
+  <php>
+    <ini name="display_errors" value="On"/>
+    <ini name="error_reporting" value="-1"/>
+  </php>
+</phpunit>
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
index 4a5e69e0..cb91c4bf 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
@@ -111,7 +111,7 @@ public function testMinimalParameterForExampleExecution() {
 
         // var_dump(file_get_contents('.xml')); // zwraca zawartość ?
         $report_id = 1;
-        $fakeExtractor = array();
+        $fakeExtractor = array("extractor" => null, "params"=>array(), "flag_name"=>null, "flag_ids"=>array());
         $extractors = array( $fakeExtractor );
         $disamb_only = true;
         $extractor_stats = array();
@@ -172,7 +172,9 @@ public function testMainFlowForXMLLemmaExport() {
         $fakeExtractor = array( 
             'name' => 'extractorNAME', 
             "flag_name" => $flag_name,
-            "flag_ids" => array($flag_id) );
+            "flag_ids" => array($flag_id), 
+            "extractor" => null,
+            "params" => array() );
         $extractors = array( $fakeExtractor );
         $disamb_only = true;
         $extractor_stats = array();
@@ -216,14 +218,6 @@ function($report_id, $params, &$extractor_elements) {
                 'getReportTagsByTokens', // block fetch() error
                 'getReportById', // block fetch() error
                 'getReportExtById', // block fetch() error
-                //'generateCcl', // for proper filename generation
-				//'dispatchElements',
-                //'runExtractor',
-/*							'exportReportContent',
-                            'updateLists','createIniFile',
-                            'checkIfAnnotationForLemmaExists',
-                            'checkIfAnnotationForRelationExists',
-                            'sortUniqueAnnotationsById', */
                 )) -> getMock();
         $mockCorpusExporter -> expects($this->once())
 			-> method('getTokenByReportId')
@@ -258,6 +252,8 @@ function($report_id, $params, &$extractor_elements) {
 		// check results in XML file
 		$fileName = str_pad($report_id,8,'0',STR_PAD_LEFT);
 		$resultFileName = $output_folder.'/'.$fileName.".xml";
+        //var_dump($resultFileName);
+        $this->assertTrue(file_exists($resultFileName));
 		$resultFileContent = file_get_contents($resultFileName);
 		//var_dump($resultFileContent);
 		// prefix for proper XML
@@ -277,7 +273,27 @@ function($report_id, $params, &$extractor_elements) {
 '<ann chan="nam_oth">2</ann>'.'\s*'.'<prop key="nam_oth:lemma">lemat dodany do okno</prop>';
         $this->assertRegexp('@'.$expectedAnnWithLemmaLines.'@m',$resultFileContent);
 
-	 }//
+        // check results in JSON file
+        $resultFileName = $output_folder.'/'.$fileName.".json";
+        $resultFileContent = file_get_contents($resultFileName);
+        //var_dump($resultFileContent);
+        // annotacja bez lematu ( lemma=NULL )
+        $expectedAnnWithoutLemmaPattern = '@'
+            .'"annotations": '.'.+'        // w sekcji po słowie 'annotations'
+            .'\{.+"from": "6",.+"to": "9",[^\}]*' // w tokenie na poz. 6-9
+                .'"lemma": null,'   // jest wpis o lemacie
+            .'.*\}'.'@s';
+        $this->assertRegexp($expectedAnnWithoutLemmaPattern,$resultFileContent);
+        // annotacja z lematem ( "lemat dodany do okno" )
+        $expectedAnnWithLemmaPattern = '@'
+            .'"annotations": '.'.+'        // w sekcji po słowie 'annotations'
+            .'\{.+"from": "10",.+"to": "13",[^\}]*' // w tokenie na poz. 10-13
+                .'"lemma": "lemat dodany do okno",'   // jest wpis o lemacie
+            .'.*\}'.'@s';
+        $this->assertRegexp($expectedAnnWithLemmaPattern,$resultFileContent);
+       
+
+	 }// testMainFlowForXMLLemmaExport()
 
 } // CorpusExporter_part12_Test class
 

From e0f8a9ee3f71ec50f5db755dd2873556a9d45a1e Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Thu, 7 Dec 2023 13:57:43 +0100
Subject: [PATCH 138/154] Change CclFactory with extended ccl version

---
 ...{CCclFactory.php => CclExportDocument.php} |  55 ++--
 engine/include/export/CorpusExporter.php      |   4 +-
 engine/include/export/XmlFactory.php          |  16 +-
 .../include/export/CclExportDocumentTest.php  | 301 ++++++++++++++++++
 .../engine/include/export/CclFactoryTest.php  | 251 ---------------
 .../export/CorpusExporter_part10_Test.php     |   2 +-
 .../export/CorpusExporter_part12_Test.php     |  15 +-
 .../engine/include/export/XmlFactoryTest.php  |  72 ++---
 8 files changed, 368 insertions(+), 348 deletions(-)
 rename engine/include/export/{CCclFactory.php => CclExportDocument.php} (80%)
 create mode 100644 phpunit/tests/engine/include/export/CclExportDocumentTest.php
 delete mode 100644 phpunit/tests/engine/include/export/CclFactoryTest.php

diff --git a/engine/include/export/CCclFactory.php b/engine/include/export/CclExportDocument.php
similarity index 80%
rename from engine/include/export/CCclFactory.php
rename to engine/include/export/CclExportDocument.php
index de59d5b4..55b0bc10 100644
--- a/engine/include/export/CCclFactory.php
+++ b/engine/include/export/CclExportDocument.php
@@ -6,22 +6,21 @@
  * See LICENCE 
  */
 
-class CclFactory{
+class CclExportDocument extends CclDocument {
 	
 	/**
 	 * $report --- tablica asocjacyjna z atrybutami dokumentu (jak z tabeli reports)
 	 * $tokens --- tablica asocjacyjna z wartościami 'from', 'to' i 'eos'
 	 * $tags --- 
 	 * function creates ccl document using 'eos' token attributes to match end of sentence
-	 * see: createFromReportAndTokensSentence 
+	 * see: createFromReportAndTokensSentence, was createFromReportAndTokens()
 	 */	 
-	function createFromReportAndTokens(&$report, &$tokens, &$tags){
+	public function __construct(&$report, &$tokens, &$tags){
 		$fileName = str_pad($report['id'],8,'0',STR_PAD_LEFT);
 		
-		$ccl = new CclDocument();
-		$ccl->setFileName($fileName);
-		$ccl->setSubcorpus(preg_replace("/[^\p{L}|\p{N}]+/u","_",$report['name']));
-		$ccl->setReport($report);
+		$this->setFileName($fileName);
+		$this->setSubcorpus(preg_replace("/[^\p{L}|\p{N}]+/u","_",$report['name']));
+		$this->setReport($report);
 	
 		$chunkList = explode('<\\chunk>', $report['content']);
 
@@ -34,7 +33,10 @@ function createFromReportAndTokens(&$report, &$tokens, &$tags){
 			$chunk = str_replace(">","> ",$chunk);
 			preg_match_all($pattern, $chunk, $matches);
 			$type = "p";
-			if (is_array($matches) && array_key_exists(1, $matches))
+			if (is_array($matches) 
+                && array_key_exists(1, $matches)
+                && array_key_exists(0,$matches[1])
+            )
 				$type = $matches[1][0];					
 			$tmpStr = trim(preg_replace("/\s\s+/"," ",custom_html_entity_decode(strip_tags($chunk))));
 			$tmpStr2 = preg_replace("/\n+|\r+|\s+/","",$tmpStr);
@@ -93,7 +95,7 @@ function createFromReportAndTokens(&$report, &$tokens, &$tags){
 				}
 				
 				$s->addToken($t);
-				$ccl->addToken($t);
+				$this->addToken($t);
 				if ( $token['eos'] ){
 					$c->addSentence($s);
 					$s = new CclSentence();
@@ -108,37 +110,36 @@ function createFromReportAndTokens(&$report, &$tokens, &$tags){
 				else 
 					$sentenceIndex--;
 			}
-			$ccl->addChunk($c);
+			$this->addChunk($c);
 		}			
 		
-		return $ccl;
-	}
+	} // __construct()
 	
 
-	function setAnnotationLemmas(&$ccl, $annotation_lemmas){
+	protected function setAnnotationLemmas($annotation_lemmas){
 		if (empty($annotation_lemmas)){
 			return false;
 		}
 		
 		foreach($annotation_lemmas as $lemma){
-			$ccl->setAnnotationLemma($lemma);
+			$this->setAnnotationLemma($lemma);
 		}
 	}
 
-    function setAnnotationProperties(&$ccl, &$annotation_properties){
+    protected function setAnnotationProperties($annotation_properties){
         if (empty($annotation_properties)){
         	return false;
 		}
 
         foreach($annotation_properties as $property){
-            $ccl->setAnnotationProperty($property);
+            $this->setAnnotationProperty($property);
         }
     }
 
 	/**
 	 * 
 	 */	
-	function setAnnotationsAndRelations(&$ccl, &$annotations, &$relations){
+	protected function setAnnotationsAndRelations(&$annotations, &$relations){
 		if (empty($annotations)) return false;
 		$annotationsById = array();
 		$continuousAnnotationIds = array();
@@ -157,7 +158,7 @@ function setAnnotationsAndRelations(&$ccl, &$annotations, &$relations){
 		
 		foreach ($annotations as &$annotation){
 			if ( !in_array($annotation['id'], $continuousAnnotationIds)){
-				$ccl->setAnnotation($annotation);
+				$this->setAnnotation($annotation);
 			} else {
 				$continuousAnnotations[$annotation['id']] =& $annotation;
 			}
@@ -169,7 +170,7 @@ function setAnnotationsAndRelations(&$ccl, &$annotations, &$relations){
 			$target_id = $cRelation['target_id'];
 			if (array_key_exists($source_id, $annotationsById) && 
 				array_key_exists($target_id, $annotationsById)){
-				$ccl->setContinuousAnnotation2(
+				$this->setContinuousAnnotation2(
 					$continuousAnnotations[$source_id],
 					$continuousAnnotations[$target_id]);
 			} else if (array_key_exists($source_id, $annotationsById) ||
@@ -179,7 +180,7 @@ function setAnnotationsAndRelations(&$ccl, &$annotations, &$relations){
 				$e->setFunctionName("setAnnotationsAndRelations");
 				$e->addObject("relation", $cRelation);
 				$e->addComment("008 no source or target annotation in a continuous relation");
-				$ccl->addError($e);					
+				$this->addError($e);					
 			}
 		}
 		
@@ -188,7 +189,7 @@ function setAnnotationsAndRelations(&$ccl, &$annotations, &$relations){
 			$target_id = $nRelation['target_id'];
 			if (array_key_exists($source_id, $annotationsById) && 
 				array_key_exists($target_id, $annotationsById)){			
-				$ccl->setRelation(
+				$this->setRelation(
 					$annotationsById[$nRelation['source_id']],
 					$annotationsById[$nRelation['target_id']],
 					$nRelation);
@@ -198,10 +199,18 @@ function setAnnotationsAndRelations(&$ccl, &$annotations, &$relations){
 				$e->setFunctionName("setAnnotationsAndRelations");
 				$e->addObject("relation", $nRelation);
 				$e->addComment("009 no source or target annotation in a normal relation");
-				$ccl->addError($e);						
+				$this->addError($e);						
 			}
 		}
 		return true;
 	}
 	
-}
+    public function setCclProperties(&$annotations, &$relations, $lemmas, $attributes ) {
+
+        $this->setAnnotationsAndRelations($annotations, $relations);
+        $this->setAnnotationLemmas($lemmas);
+        $this->setAnnotationProperties($attributes);
+
+    } // setCclProperties()
+
+} // CclExportDocument class
diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index 4066bc37..88266abd 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -628,8 +628,8 @@ protected function dispatchElements($elements) {
 
     protected function callCclCreator($report,$tokens,$tags_by_tokens) {
 
-        // call static method which may throw exception
-        return CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
+        $ccl = new CclExportDocument($report, $tokens, $tags_by_tokens);
+        return $ccl;
 
     } // callCclCreator()
 
diff --git a/engine/include/export/XmlFactory.php b/engine/include/export/XmlFactory.php
index 1cde7c24..e35930fb 100644
--- a/engine/include/export/XmlFactory.php
+++ b/engine/include/export/XmlFactory.php
@@ -2,24 +2,14 @@
 
 class XmlFactory {
 
-    protected function setDataToExport(&$ccl,&$annotations,&$relations,&$lemmas,&$attributes) {
-
-        CclFactory::setAnnotationsAndRelations($ccl, $annotations, $relations);
-        CclFactory::setAnnotationLemmas($ccl, $lemmas);
-        CclFactory::setAnnotationProperties($ccl, $attributes);
- 
-        // returns modified $ccl by reference
-
-    } // setDataToExport()
-
-    public function exportToXmlAndRelxml($filePathWithoutExt,&$ccl,&$annotations,&$relations,&$lemmas,&$attributes) {
+    public function exportToXmlAndRelxml($filePathWithoutExt,CclExportDocument &$ccl,&$annotations,&$relations,&$lemmas,&$attributes) {
 
         // set all other data to ccl structure
-        $this->setDataToExport($ccl,$annotations,$relations,$lemmas,$attributes); 
+        $ccl->setCclProperties($annotations,$relations,$lemmas,$attributes);
         // export from $ccl to files
         CclWriter::write($ccl, $filePathWithoutExt.".xml", CclWriter::$CCL);
         CclWriter::write($ccl, $filePathWithoutExt.".rel.xml", CclWriter::$REL);
 
     } // exportToXmlAndRelxml()
 
-} // XmlFormatExport class
+} // XmlFactory class
diff --git a/phpunit/tests/engine/include/export/CclExportDocumentTest.php b/phpunit/tests/engine/include/export/CclExportDocumentTest.php
new file mode 100644
index 00000000..40374a09
--- /dev/null
+++ b/phpunit/tests/engine/include/export/CclExportDocumentTest.php
@@ -0,0 +1,301 @@
+<?php
+
+mb_internal_encoding("UTF-8");
+
+class CclExportDocumentTest extends PHPUnit_Framework_TestCase
+{
+    private $ccl = null;
+
+    protected function setUp() {
+
+        $report = null; $tokens = null; $tags_by_tokens = null;
+        $this->ccl = new CclExportDocument($report, $tokens, $tags_by_tokens);
+
+    } // setUp()
+
+//    function __construct(&$report, &$tokens, &$tags){
+
+    public function test_constructor_createsValidCclExportDocumentFromNullParameters() {
+
+        $this->assertInstanceOf('CclExportDocument',$this->ccl);
+
+    } // test_constructor_createsValidCclExportDocumentFromNullParameters() 
+
+//    function setAnnotationProperties(&$annotation_properties){
+
+    public function test_setAnnotationProperties_failsFor1stParameterIsNull() {
+
+        $annotation_properties = null;
+        // reflection test call for access to private elements
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($this->ccl,'setAnnotationProperties');
+        $result = $protectedMethod->invokeArgs($this->ccl,array(&$annotation_properties));
+        $this->assertFalse($result);
+
+        $annotation_properties = array();
+        // reflection test call for access to private elements
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($this->ccl,'setAnnotationProperties');
+        $result = $protectedMethod->invokeArgs($this->ccl,array(&$annotation_properties));
+        $this->assertFalse($result);
+
+        // this one for non-empty 2nd param calls method on null object...
+        $annotation_properties = array("id"=>1);
+        // reflection test call for access to private elements
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($this->ccl,'setAnnotationProperties');
+        $result = $protectedMethod->invokeArgs($this->ccl,array(&$annotation_properties));
+        //$this->assertFalse($result); 
+       
+    } // test_setAnnotationProperties_failsFor1stParameterIsNull() 
+
+
+    public function test_setAnnotationProperties_returnsFalseForEmpty2ndParameter() {
+        $annotation_properties = null;
+        // reflection test call for access to private elements
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($this->ccl,'setAnnotationProperties');
+        $result = $protectedMethod->invokeArgs($this->ccl,array(&$annotation_properties));
+        $this->assertFalse($result);
+
+        $report = null;
+        $tokens = null;
+        $tags_by_tokens = null;
+        // reflection test call for access to private elements
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($this->ccl,'setAnnotationProperties');
+        $result = $protectedMethod->invokeArgs($this->ccl,array(&$annotation_properties));
+        $this->assertFalse($result);
+
+        $annotation_properties = array(); // empty array as null
+        // reflection test call for access to private elements
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($this->ccl,'setAnnotationProperties');
+        $result = $protectedMethod->invokeArgs($this->ccl,array(&$annotation_properties));
+        $this->assertFalse($result);
+
+    } // test_setAnnotationProperties_returnsFalseForEmpty2ndParameter()  
+
+    public function test_setAnnotationProperties_silentlyDoNothingIfNoProperTokenInDocument() {
+
+        $type = 1;
+        $from = 1; $to = 3;
+        $name = 'nazwa własności';
+        $value = 'wartość własności';
+        $annotation_property = array( // must have this 5 fields
+            "type" => $type,
+            "from" => $from,
+            "to" => $to,
+            "name" => $name,
+            "value" => $value
+        );
+        $annotation_properties = array( $annotation_property );
+
+        // new document w/o tokens
+        // no tokens added to document - no action will be proceeded
+
+        // do test
+        // reflection test call for access to private elements
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($this->ccl,'setAnnotationProperties');
+        $result = $protectedMethod->invokeArgs($this->ccl,array(&$annotation_properties));
+        // returns null like for good results...
+        $this->assertNull($result);
+        // ...but no token with property added exists
+        $expectedTokensTable = array();
+        $this->assertEquals($expectedTokensTable,$this->ccl->tokens);
+
+    } // test_setAnnotationProperties_silentlyDoNothingIfNoProperTokenInDocument() 
+ 
+    public function test_setAnnotationProperties_setPropTableInDocumentToken() {
+
+        $type = 1;
+        $from = 1; $to = 3;
+        $name = 'nazwa własności';
+        $value = 'wartość własności';
+        $annotation_property = array( // must have this 5 fields
+            "type" => $type,
+            "from" => $from,
+            "to" => $to,
+            "name" => $name,
+            "value" => $value
+        );
+        $annotation_properties = array( $annotation_property );
+
+        // document must have valid cclToken for $from to $to chars
+        $t = new CclToken(); // $t->prop is null here
+        $t->setFrom($from); $t->setTo($to);
+        // must have valid document with this token added
+        // must set token to document to add property for this range
+        $this->ccl->addToken($t);
+ 
+        // do test
+        //$result = $this->ccl->setAnnotationProperties($annotation_properties);
+        // reflection test call for access to private elements
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($this->ccl,'setAnnotationProperties');
+        $result = $protectedMethod->invokeArgs($this->ccl,array(&$annotation_properties));
+        // returns null for good results...
+        $this->assertNull($result);
+        // added property should be written to token prop table as below
+        $expectedPropTable = array(
+            $type.':'.$name => $value
+        );
+        $this->assertEquals($expectedPropTable,$this->ccl->tokens[0]->prop);
+
+    } // test_setAnnotationProperties_setPropTableInDocumentToken()
+
+// function setAnnotationLemmas(&$annotation_lemmas)
+    
+    public function testEmptyLemmasCallsNoAction() {
+
+        $mockCcl = $this->getMockBuilder('CclExportDocument')
+            ->disableOriginalConstructor()
+            -> setMethods(['setAnnotationLemma'])
+            ->getMock();
+        // for empty $lemmas there are no internal call
+        $annotation_lemmas = array();
+        $mockCcl->expects($this->never())->method('setAnnotationLemma');
+        // result is returned in $mockCcl changes
+        // reflection test call for access to private elements
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($mockCcl,'setAnnotationLemmas');
+        $result = $protectedMethod->invokeArgs($mockCcl,array($annotation_lemmas));
+ 
+
+    } // testEmptyLemmasCallsNoAction()     
+
+	public function testLemmaIsPassedToCclSetMethod() {
+
+		$mockCcl = $this->getMockBuilder(CclExportDocument::class)
+            ->disableOriginalConstructor()
+            -> setMethods(['setAnnotationLemma'])
+            ->getMock();
+        // $mockCcl->setAnnotationLemma should be call for each item from
+        // $lemmas array
+        $annotation_lemmas = array('element');
+        $mockCcl->expects($this->once())->method('setAnnotationLemma')->with('element');
+        // reflection test call for access to private elements
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($mockCcl,'setAnnotationLemmas');
+        $result = $protectedMethod->invokeArgs($mockCcl,array($annotation_lemmas));
+
+	} // testLemmaIsPassedToCclSetMethod()
+
+    public function testAddingLemmaToCclIsRepeatedForEachLemma() {
+
+        $mockCcl = $this->getMockBuilder(CclExportDocument::class)
+            ->disableOriginalConstructor()
+            -> setMethods(['setAnnotationLemma'])
+            ->getMock();
+        // $mockCcl->setAnnotationLemma should be call for each item from
+        // $lemmas array
+        $annotation_lemmas = array('raz','dwa','trzy');
+		//$mockCcl->expects($this->at(0))->method('setAnnotationLemma')->with('raz');
+		//$mockCcl->expects($this->at(1))->method('setAnnotationLemma')->with('dwa');
+		//$mockCcl->expects($this->at(2))->method('setAnnotationLemma')->with('trzy');
+		// zachowanie kolejności nie jest tu istotne
+        $mockCcl->expects($this->exactly(3))->method('setAnnotationLemma');
+        // reflection test call for access to private elements
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($mockCcl,'setAnnotationLemmas');
+        $result = $protectedMethod->invokeArgs($mockCcl,array($annotation_lemmas));
+
+    } // testAddingLemmaToCclIsRepeatedForEachLemma()
+
+// function setAnnotationsAndRelations( &$annotations, &$relations){...}
+//   modifies $ccl and returns boolean as operation result
+
+    public function testCorrectDataForSetAnnotationAndRelationCallsCclMethods() {
+        $relations = array(
+            // continuous type==1
+            array( 'relation_type_id'=>1,'source_id'=>1,'target_id'=>2 ),
+            // normal
+            array( 'relation_type_id'=>2,'source_id'=>3,'target_id'=>4 )
+        );
+        $annotations = array( // ids includes all source and targets from above
+            array( 'id'=>1 ), array( 'id'=>2 ), array( 'id'=>3 ),
+            array( 'id'=>4 )
+        );
+
+        $mockCcl = $this->getMockBuilder(CclExportDocument::class)
+            ->disableOriginalConstructor()
+            -> setMethods(['setAnnotation', 'setContinuousAnnotation2',
+                            'addError','setRelation'])
+            -> getMock();
+        // call setAnnotation() 2 times for noncontinuous annotations
+        $mockCcl->expects($this->exactly(2))->method('setAnnotation'); 
+        $mockCcl->expects($this->at(0))->method('setAnnotation')->with($annotations[2]);
+        $mockCcl->expects($this->at(1))->method('setAnnotation')->with($annotations[3]);
+        // call setContinuousAnnotation2() once for continuous annotations pair
+        $mockCcl->expects($this->once())->method('setContinuousAnnotation2')->with($annotations[0],$annotations[1]);
+		// call setRelation() once for noncontinuous relation only
+		//  parametres are: source and target annotations record
+        $mockCcl->expects($this->once())->method('setRelation')->with($annotations[2],$annotations[3],$relations[1]);
+        // no error set is called
+        $mockCcl->expects($this->never())->method('addError');
+
+        // reflection test call for acces to private elements
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($mockCcl,'setAnnotationsAndRelations');
+        $result = $protectedMethod->invokeArgs($mockCcl,array(&$annotations,&$relations));
+
+        // returns true
+        $this->assertTrue($result); 
+        // no errors in $ccl
+        $this->assertEquals(0,count($this->ccl->errors));
+
+    } // testCorrectDataForSetAnnotationAndRelationCallsCclMethods()
+
+    public function testSetannotationsandrelationsOnEmptyAnnotationsReturnsFalse() {
+
+        $annotations = array();
+        $relations = array(array("key"=>"value"));
+        // reflection test call for acces to private elements
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($this->ccl,'setAnnotationsAndRelations');
+        $result = $protectedMethod->invokeArgs($this->ccl,array(&$annotations,&$relations));
+
+        $this->assertFalse($result);
+        // no errors in $ccl
+        $this->assertEquals(0,count($this->ccl->errors));
+
+    } // testSetannotationsandrelationsOnEmptyAnnotationsReturnsFalse() 
+
+    public function testSetannotationsandrelationsOnAnnotationsWithNoRelationsCallCclsetannotation() {
+
+        $annotation1 = array( "annotation_id"=>1 );
+        $annotations = array( $annotation1 );
+        $relations = array();
+
+        $mockCcl = $this->getMockBuilder(CclExportDocument::class)
+            ->disableOriginalConstructor()
+            -> setMethods(['setAnnotation'])
+            -> getMock();
+        $mockCcl->expects($this->once())
+            ->method('setAnnotation')
+            -> with($annotation1);
+
+        // reflection test call for acces to private elements
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($mockCcl,'setAnnotationsAndRelations');
+        $result = $protectedMethod->invokeArgs($mockCcl,array(&$annotations,&$relations));
+
+        $this->assertTrue($result);
+        // no errors in $ccl
+        $this->assertEquals(0,count($this->ccl->errors));
+
+    } // testSetannotationsandrelationsOnAnnotationsWithNoRelationsCallCclsetannotation() 
+
+// public function setCclProperties(&$annotations, &$relations, $lemmas, $attributes ) 
+
+    public function testSetcclpropertiesCallsAllPropertySetMethodsOnce() {
+
+        $annotations = array('annotacje');
+        $relations = array('relacje');
+        $lemmas = array('lematy');
+        $attributtes = array('atrybuty');
+        $mockCcl = $this->getMockBuilder(CclExportDocument::class)
+            ->disableOriginalConstructor()
+            -> setMethods(['setAnnotationsAndRelations','setAnnotationLemmas','setAnnotationProperties'])
+            -> getMock();
+        $mockCcl->expects($this->once())->method('setAnnotationsAndRelations')
+            -> with($annotations,$relations);
+        $mockCcl->expects($this->once())->method('setAnnotationLemmas')
+            -> with($lemmas);
+        $mockCcl->expects($this->once())->method('setAnnotationProperties')
+            -> with($attributes);
+ 
+        $mockCcl->setCclProperties($annotations, $relations, $lemmas, $attributes );
+
+    } // testSetcclpropertiesCallsAllPropertySetMethodsOnce() 
+
+} // CclExportDocumentTest class
+
+?>
diff --git a/phpunit/tests/engine/include/export/CclFactoryTest.php b/phpunit/tests/engine/include/export/CclFactoryTest.php
deleted file mode 100644
index b85c4d67..00000000
--- a/phpunit/tests/engine/include/export/CclFactoryTest.php
+++ /dev/null
@@ -1,251 +0,0 @@
-<?php
-
-mb_internal_encoding("UTF-8");
-
-class CclFactoryTest extends PHPUnit_Framework_TestCase
-{
-//    function createFromReportAndTokens(&$report, &$tokens, &$tags){
-//   returns object of CclDocument class
-
-    public function test_createFromReportAndTokens_createsValidCclDocumentFromNullParameters() {
-
-        $report = null;
-        $tokens = null;
-        $tags_by_tokens = null;
-        $ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
-        $this->assertInstanceOf('CclDocument',$ccl);
-
-    } // test_createFromReportAndTokens_createsValidCclDocumentFromNullParameters() 
-
-/*
-    function setAnnotationProperties(&$ccl, &$annotation_properties){
-*/
-
-    public function test_setAnnotationProperties_failsFor1stParameterIsNull() {
-        $ccl = null;
-
-        $annotation_properties = null;
-        $result = CclFactory::setAnnotationProperties($ccl,$annotation_properties);
-        $this->assertFalse($result);
-
-        $annotation_properties = array();
-        $result = CclFactory::setAnnotationProperties($ccl,$annotation_properties);
-        $this->assertFalse($result);
-
-        /* this one for non-empty 2nd param calls method on null object...
-        $annotation_properties = array("id"=>1);
-        $result = CclFactory::setAnnotationProperties($ccl,$annotation_properties);
-        $this->assertFalse($result); 
-        */
-       
-    } // test_setAnnotationProperties_failsFor1stParameterIsNull() 
-
-
-    public function test_setAnnotationProperties_returnsFalseForEmpty2ndParameter() {
-        $annotation_properties = null;
-
-        $ccl = null;
-        $result = CclFactory::setAnnotationProperties($ccl,$annotation_properties);
-        $this->assertFalse($result);
-
-        $report = null;
-        $tokens = null;
-        $tags_by_tokens = null;
-        $ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
-        $result = CclFactory::setAnnotationProperties($ccl,$annotation_properties);
-        $this->assertFalse($result);
-
-        $annotation_properties = array(); // empty array as null
-
-        $ccl = null;
-        $result = CclFactory::setAnnotationProperties($ccl,$annotation_properties);
-        $this->assertFalse($result);
-
-        $report = null;
-        $tokens = null;
-        $tags_by_tokens = null;
-        $ccl = CclFactory::createFromReportAndTokens($report, $tokens, $tags_by_tokens);
-        $result = CclFactory::setAnnotationProperties($ccl,$annotation_properties);
-        $this->assertFalse($result);
-
-    } // test_setAnnotationProperties_returnsFalseForEmpty2ndParameter()  
-
-    public function test_setAnnotationProperties_silentlyDoNothingIfNoProperTokenInDocument() {
-
-        $type = 1;
-        $from = 1; $to = 3;
-        $name = 'nazwa własności';
-        $value = 'wartość własności';
-        $annotation_property = array( // must have this 5 fields
-            "type" => $type,
-            "from" => $from,
-            "to" => $to,
-            "name" => $name,
-            "value" => $value
-        );
-        $annotation_properties = array( $annotation_property );
-
-        // new document w/o tokens
-        $ccl = new CclDocument();
-        // no tokens added to document - no action will be proceeded
-
-        // do test
-        $result = CclFactory::setAnnotationProperties($ccl,$annotation_properties);
-        // returns null like for good results...
-        $this->assertNull($result);
-        // ...but no token with property added exists
-        $expectedTokensTable = array();
-        $this->assertEquals($expectedTokensTable,$ccl->tokens);
-
-    } // test_setAnnotationProperties_silentlyDoNothingIfNoProperTokenInDocument() 
- 
-    public function test_setAnnotationProperties_setPropTableInDocumentToken() {
-
-        $type = 1;
-        $from = 1; $to = 3;
-        $name = 'nazwa własności';
-        $value = 'wartość własności';
-        $annotation_property = array( // must have this 5 fields
-            "type" => $type,
-            "from" => $from,
-            "to" => $to,
-            "name" => $name,
-            "value" => $value
-        );
-        $annotation_properties = array( $annotation_property );
-
-        // document must have valid cclToken for $from to $to chars
-        $t = new CclToken(); // $t->prop is null here
-        $t->setFrom($from); $t->setTo($to);
-        // must have valid document with this token added
-        $ccl = new CclDocument();
-        // must set token to document to add property for this range
-        $ccl->addToken($t);
- 
-        // do test
-        $result = CclFactory::setAnnotationProperties($ccl,$annotation_properties);
-        // returns null for good results...
-        $this->assertNull($result);
-        // added property should be written to token prop table as below
-        $expectedPropTable = array(
-            $type.':'.$name => $value
-        );
-        $this->assertEquals($expectedPropTable,$ccl->tokens[0]->prop);
-
-    } // test_setAnnotationProperties_setPropTableInDocumentToken()
-
-// function setAnnotationLemmas(&$ccl, &$annotation_lemmas)
-    
-    public function testEmptyLemmasCallsNoAction() {
-
-        $mockCcl = $this->getMockBuilder(CclDocument::class)->getMock();
-        // for empty $lemmas there are no internal call
-        $annotation_lemmas = array();
-        $mockCcl->expects($this->never())->method('setAnnotationLemma');
-        // result is returned in $ccl changes
-        (new CclFactory())->setAnnotationLemmas($mockCcl,$annotation_lemmas);
-
-    } // testEmptyLemmasCallsNoAction()     
-
-	public function testLemmaIsPassedToCclSetMethod() {
-
-		$mockCcl = $this->getMockBuilder(CclDocument::class)->getMock();
-        // $ccl->setAnnotationLemma should be call for each item from
-        // $lemmas array
-        $annotation_lemmas = array('element');
-        $mockCcl->expects($this->once())->method('setAnnotationLemma')->with('element');
-        (new CclFactory())->setAnnotationLemmas($mockCcl,$annotation_lemmas);		
-	} // testLemmaIsPassedToCclSetMethod()
-
-    public function testAddingLemmaToCclIsRepeatedForEachLemma() {
-
-        $mockCcl = $this->getMockBuilder(CclDocument::class)->getMock();
-        // $ccl->setAnnotationLemma should be call for each item from
-        // $lemmas array
-        $annotation_lemmas = array('raz','dwa','trzy');
-		//$mockCcl->expects($this->at(0))->method('setAnnotationLemma')->with('raz');
-		//$mockCcl->expects($this->at(1))->method('setAnnotationLemma')->with('dwa');
-		//$mockCcl->expects($this->at(2))->method('setAnnotationLemma')->with('trzy');
-		// zachowanie kolejności nie jest tu istotne
-        $mockCcl->expects($this->exactly(3))->method('setAnnotationLemma');
-        (new CclFactory())->setAnnotationLemmas($mockCcl,$annotation_lemmas);
-
-    } // testAddingLemmaToCclIsRepeatedForEachLemma()
-
-// function setAnnotationsAndRelations(&$ccl, &$annotations, &$relations){...}
-//   modifies $ccl and returns boolean as operation result
-
-    public function testCorrectDataForSetAnnotationAndRelationCallsCclMethods() {
-        $relations = array(
-            // continuous type==1
-            array( 'relation_type_id'=>1,'source_id'=>1,'target_id'=>2 ),
-            // normal
-            array( 'relation_type_id'=>2,'source_id'=>3,'target_id'=>4 )
-        );
-        $annotations = array( // ids includes all source and targets from above
-            array( 'id'=>1 ), array( 'id'=>2 ), array( 'id'=>3 ),
-            array( 'id'=>4 )
-        );
-
-        $mockCcl = $this->getMockBuilder(CclDocument::class)
-            -> setMethods(['setAnnotation', 'setContinuousAnnotation2',
-                            'addError','setRelation'])
-            -> getMock();
-        // call setAnnotation() 2 times for noncontinuous annotations
-        $mockCcl->expects($this->exactly(2))->method('setAnnotation'); 
-        $mockCcl->expects($this->at(0))->method('setAnnotation')->with($annotations[2]);
-        $mockCcl->expects($this->at(1))->method('setAnnotation')->with($annotations[3]);
-        // call setContinuousAnnotation2() once for continuous annotations pair
-        $mockCcl->expects($this->once())->method('setContinuousAnnotation2')->with($annotations[0],$annotations[1]);
-		// call setRelation() once for noncontinuous relation only
-		//  parametres are: source and target annotations record
-        $mockCcl->expects($this->once())->method('setRelation')->with($annotations[2],$annotations[3],$relations[1]);
-        // no error set is called
-        $mockCcl->expects($this->never())->method('addError');
-
-        $result = (new CclFactory())->setAnnotationsAndRelations($mockCcl,$annotations,$relations);
-
-        // returns true
-        $this->assertTrue($result); 
-        // no errors in $ccl
-        $this->assertEquals(0,count($ccl->errors));
-
-    } // testCorrectDataForSetAnnotationAndRelationCallsCclMethods()
-
-    public function testSetannotationsandrelationsOnEmptyAnnotationsReturnsFalse() {
-
-        $ccl = new CclDocument;
-        $annotations = array();
-        $relations = array(array("key"=>"value"));
-        $result = (new CclFactory())->setAnnotationsAndRelations($ccl,$annotations,$relations);
-        $this->assertFalse($result);
-        // no errors in $ccl
-        $this->assertEquals(0,count($ccl->errors));
-
-    } // testSetannotationsandrelationsOnEmptyAnnotationsReturnsFalse() 
-
-    public function testSetannotationsandrelationsOnAnnotationsWithNoRelationsCallCclsetannotation() {
-
-        $annotation1 = array( "annotation_id"=>1 );
-        $annotations = array( $annotation1 );
-        $relations = array();
-
-        $mockCcl = $this->getMockBuilder(CclDocument::class)
-            -> setMethods(['setAnnotation'])
-            -> getMock();
-        $mockCcl->expects($this->once())
-            ->method('setAnnotation')
-            -> with($annotation1);
-
-        $result = (new CclFactory())->setAnnotationsAndRelations($mockCcl,$annotations,$relations);
-
-        $this->assertTrue($result);
-        // no errors in $ccl
-        $this->assertEquals(0,count($ccl->errors));
-
-    } // testSetannotationsandrelationsOnAnnotationsWithNoRelationsCallCclsetannotation() 
-
-
-} // CclFactoryTest class
-
-?>
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
index e5a766a6..d2f53e2f 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
@@ -72,7 +72,7 @@ public function testExport_documentCallsAllProcessingMethods() {
         $expectedTokens = $reportTokens;
         $expectedTagsByTokens = array();
 		$fileName = str_pad($report_id,8,'0',STR_PAD_LEFT);
-		$returnedCcl = new CclDocument(); 
+		$returnedCcl = new CclExportDocument($expectedReport,$expectedTokens,$expectedTagsByTokens); 
         $returnedCcl -> setFileName($fileName); 
         $mockCorpusExporter -> expects($this->once())
             ->method('generateCcl')
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
index cb91c4bf..5e9844da 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
@@ -82,12 +82,13 @@ public function test_LemmaInAnnotationsTable() {
         $mockCorpusExporter -> method('getReportTagsByTokens')
             -> will($this->returnValue($reportTags));
         $reportContent = "tekst dokumentu raportu";
-        $report = array( 'id'=>$report_id, 'content'=>$reportContent );
+        $report = array( 'id'=>$report_id, 'content'=>$reportContent,
+                    'name'=>"report name must exists" );
         $mockCorpusExporter -> method('getReportById')
             -> will($this->returnValue($report));
         $fileName = str_pad($report_id,8,'0',STR_PAD_LEFT);
-        $returnedCcl = new CclDocument();
-        $returnedCcl -> setFileName($fileName);
+        $returnedCcl = new CclExportDocument($report,$reportTokens,$reportTags);
+        //$returnedCcl -> setFileName($fileName);
         $mockCorpusExporter -> expects($this->once())
             ->method('generateCcl')
             ->with($report,$reportTokens,$reportTags)
@@ -134,7 +135,12 @@ public function testMinimalParameterForExampleExecution() {
             -> will($this->returnValue(array())); // block array_column error
         // for create proper filename for output files:
         $fileName = str_pad($report_id,8,'0',STR_PAD_LEFT);
-        $ccl = new CclDocument(); $ccl -> setFileName($fileName);
+        $report = array('id'=>$report_id, 
+                        'content'=>'content must exists',
+                        'name'=>"report name must exists" ); 
+        $tokens = array(); $tags = array();
+        $ccl = new CclExportDocument($report,$tokens,$tags); 
+        $ccl -> setFileName($fileName);
         $mockCorpusExporter -> expects($this->once())
             ->method('generateCcl')
             // ->with(null,array(),null) - it works
@@ -252,7 +258,6 @@ function($report_id, $params, &$extractor_elements) {
 		// check results in XML file
 		$fileName = str_pad($report_id,8,'0',STR_PAD_LEFT);
 		$resultFileName = $output_folder.'/'.$fileName.".xml";
-        //var_dump($resultFileName);
         $this->assertTrue(file_exists($resultFileName));
 		$resultFileContent = file_get_contents($resultFileName);
 		//var_dump($resultFileContent);
diff --git a/phpunit/tests/engine/include/export/XmlFactoryTest.php b/phpunit/tests/engine/include/export/XmlFactoryTest.php
index 6c7f831b..6053c6f4 100644
--- a/phpunit/tests/engine/include/export/XmlFactoryTest.php
+++ b/phpunit/tests/engine/include/export/XmlFactoryTest.php
@@ -5,73 +5,39 @@
 
 class XmlFactoryTest extends PHPUnit_Framework_TestCase
 {
+    private $xmlFactory = null;
+
+    protected function setUp() {
+
+        $this->xmlFactory = new XmlFactory();
+
+    } // setUp()
 
 // public function exportToXmlAndRelxml($filePathWithoutExt,&$ccl,&$annotations,&$relations,&$lemmas,&$attributes) 
 
     public function testExporttoxmlandrelxmlCallSetdatatoexportMethod() {
 
         $filePathWithoutExt = '';
-        $ccl = new CclDocument();
-        $annotations = array();
-        $relations = array();
-        $lemmas = array();
-        $attributes = array();
+        $annotations = array('anotacje');
+        $relations = array('relacje');
+        $lemmas = array('lematy');
+        $attributes = array('atrybuty');
 
-        $mockXmlFactory = $this->getMockBuilder(XmlFactory::class)
+        $mockCcl = $this->getMockBuilder(CclExportDocument::class)
             -> disableArgumentCloning()
-            -> setMethods(array('setDataToExport'))
+            -> disableOriginalConstructor()
+            -> setMethods(array('setCclProperties'))
             -> getMock();
-        // call setDataToExport with params            
-        $mockXmlFactory -> expects($this->once())
-            ->method('setDataToExport')
-            ->with($ccl,$annotations,$relations,$lemmas,$attributes);
+        // call setCclProperties with params            
+        $mockCcl -> expects($this->once())
+            ->method('setCclProperties')
+            ->with($annotations,$relations,$lemmas,$attributes);
             // returns modified $ccl by reference
            
-        $mockXmlFactory->exportToXmlAndRelxml($filePathWithoutExt,$ccl,$annotations,$relations,$lemmas,$attributes);
+        $this->xmlFactory->exportToXmlAndRelxml($filePathWithoutExt,$mockCcl,$annotations,$relations,$lemmas,$attributes);
 
     } // testExporttoxmlandrelxmlCallSetdatatoexportMethod()
 
-// protected function setDataToExport(&$ccl,&$annotations,&$relations,&$lemmas,&$attributes) 
-
-
-    public function testSetdatatoexportPutsLemmaIntoCcl() {
-
-        $annotations = array();
-        $relations = array();
-        $lemmas = array(
-                array($lemma1key => $lemma1data)
-            );
-        $attributes = array();
-
-        $token = new CclToken();
-        $token->from = $annotation_from; $token->to = $annotation_to;
-        $sentence = new CclSentence();
-        $sentence->addToken($token);
-        $chunk = new CclChunk();
-        $chunk->addSentence($sentence);
-        $ccl = new CclDocument();
-        $ccl->addChunk($chunk);
-        $ccl->addToken($token);
-        //var_dump($ccl->tokens);
-        
-        $xf = new XmlFactory();    
-        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($xf,'setDataToExport');
-        $protectedMethod->invokeArgs($xf,array(&$ccl,&$annotations,&$relations,&$lemmas,&$attributes));
-
-        // returns modified $ccl by reference
-        // no errors
-        $expectedErrors = array();
-        //var_dump($ccl->errors);
-        //$this->assertEquals($expectedErrors,$ccl->errors);
-
-        //var_dump($ccl->char2token);
-        //var_dump($ccl->tokens);
-
-
-    } // 
-
-
-
 } // XmlFactoryTest class
 
 ?>

From 92e9c02c71085f6a872ac72895c7688ce1bd9088 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Thu, 7 Dec 2023 19:40:55 +0100
Subject: [PATCH 139/154] minor warnings that crashed execution

---
 engine/include/export/CorpusExporter.php      |  2 +-
 engine/include/export/XmlFactory.php          |  5 +++--
 engine/include/writers/CCclWriter.php         | 18 +++++-------------
 phpunit/classes/SimpleCcl.php                 |  2 +-
 .../export/CorpusExporter_part12_Test.php     | 19 +++++++++++++++----
 .../export/CorpusExporter_part_Test.php       |  2 +-
 .../engine/include/writers/CCclWriterTest.php | 13 -------------
 7 files changed, 26 insertions(+), 35 deletions(-)

diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index 88266abd..fb800ca3 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -483,7 +483,7 @@ protected function exportReportContent($report,$file_path_without_ext) {
                 'message' => $errorMsg,
                 'error' => $exceptionMsg
             );
-            $this->log_error(__FILE__, __LINE__, $report_id,
+            $this->log_error(__FILE__, __LINE__, $report["id"],
                 $errorMsg.": ".$exceptionMsg, 8, $error_params);
             return False;
         } // catch()
diff --git a/engine/include/export/XmlFactory.php b/engine/include/export/XmlFactory.php
index e35930fb..9d08818e 100644
--- a/engine/include/export/XmlFactory.php
+++ b/engine/include/export/XmlFactory.php
@@ -7,8 +7,9 @@ public function exportToXmlAndRelxml($filePathWithoutExt,CclExportDocument &$ccl
         // set all other data to ccl structure
         $ccl->setCclProperties($annotations,$relations,$lemmas,$attributes);
         // export from $ccl to files
-        CclWriter::write($ccl, $filePathWithoutExt.".xml", CclWriter::$CCL);
-        CclWriter::write($ccl, $filePathWithoutExt.".rel.xml", CclWriter::$REL);
+        $writer = new CclWriter();
+        $writer->write($ccl, $filePathWithoutExt.".xml", CclWriter::$CCL);
+        $writer->write($ccl, $filePathWithoutExt.".rel.xml", CclWriter::$REL);
 
     } // exportToXmlAndRelxml()
 
diff --git a/engine/include/writers/CCclWriter.php b/engine/include/writers/CCclWriter.php
index 29adf105..7a8d8083 100644
--- a/engine/include/writers/CCclWriter.php
+++ b/engine/include/writers/CCclWriter.php
@@ -11,14 +11,6 @@ class CclWriter{
 	public static $CCL    = 2;
 	public static $REL    = 3;
 	
-    private function writeTextToFile($fileName,$text) {
-
-        $handle = fopen($fileName, "w");
-        fwrite($handle, $text);
-        fclose($handle);
-
-    } // writeTextToFile()
-
     protected function formatPropToXML($propTable) {
 
         $xml = ""; // for no data
@@ -37,7 +29,7 @@ protected function formatPropToXML($propTable) {
 
     } // formatPropToXML()
 	
-    private static function makeXmlData($ccl,$mode) {
+    private function makeXmlData($ccl,$mode) {
 
 		$xml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
 		$xml .= "<!DOCTYPE chunkList SYSTEM \"ccl.dtd\">\n";
@@ -64,7 +56,7 @@ private static function makeXmlData($ccl,$mode) {
 						}
 						foreach ($channels as $type=>$number)
 							$xml .= "    <ann chan=\"{$type}\">{$number}</ann>\n";
-                        $xml.= self::formatPropToXML($token->prop);
+                        $xml.= $this->formatPropToXML($token->prop);
 						$xml .= $token->ns ? "   </tok>\n   <ns/>\n" : "   </tok>\n";
 					}
 					$xml .= "  </sentence>\n";
@@ -94,12 +86,12 @@ private static function makeXmlData($ccl,$mode) {
 
     } // makeXmlData()
  
-   static function write($ccl, $filename, $mode){
+   public function write($ccl, $filename, $mode){
  
-        self::writeTextToFile($filename,self::makeXmlData($ccl,$mode));
+        (new FileWriter()) -> writeTextToFile($filename,$this->makeXmlData($ccl,$mode));
 
 	} // write()
 	
-}
+} // CclWriter class
 
 ?>
diff --git a/phpunit/classes/SimpleCcl.php b/phpunit/classes/SimpleCcl.php
index 9e6fb5ff..faa81066 100644
--- a/phpunit/classes/SimpleCcl.php
+++ b/phpunit/classes/SimpleCcl.php
@@ -612,7 +612,7 @@ public function toXML() {
         $indent = 0;
         $xml = $this->spc($indent++)."<chunkList>"; 
         foreach($this->chunks as $chunk){
-            $xml .= "\n".$this->spc($indent++)."<chunk id=\"ch".$chunk["idx"]."\" type=\"\">";
+            $xml .= "\n".$this->spc($indent++)."<chunk id=\"ch".$chunk["idx"]."\" type=\"p\">";
             foreach($chunk["sentences"] as $sentence){
                 $xml .= "\n".$this->spc($indent++)."<sentence id=\"sent".$chunk["idx"]."\">"; 
                 foreach($sentence["tokens"] as $token){
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
index 5e9844da..b61743f0 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
@@ -118,7 +118,7 @@ public function testMinimalParameterForExampleExecution() {
         $extractor_stats = array();
         $lists = array();
         $output_folder = $this->virtualDir->url();
-        $subcorpora = '';
+        $subcorpora = array(1=>'must exists for report[subcorpus_id] index');
         $tagging_method = 'tagger';
         $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
             -> disableArgumentCloning()
@@ -137,13 +137,24 @@ public function testMinimalParameterForExampleExecution() {
         $fileName = str_pad($report_id,8,'0',STR_PAD_LEFT);
         $report = array('id'=>$report_id, 
                         'content'=>'content must exists',
-                        'name'=>"report name must exists" ); 
+                        'name'=>"report name must exists",
+                        'subcorpus_id'=>1,
+                        "date"=>'DATA', 
+                        "title"=>'TITLE', 
+                        "source"=>'SOURCE', 
+                        "author"=>'AUTHOR', 
+                        "tokenization"=>'TOKENIZATION'); 
         $tokens = array(); $tags = array();
         $ccl = new CclExportDocument($report,$tokens,$tags); 
         $ccl -> setFileName($fileName);
+        $mockCorpusExporter 
+            //-> expects($this->once())
+            -> method('getReportById')
+            -> with($report_id) 
+            -> will($this->returnValue($report));
         $mockCorpusExporter -> expects($this->once())
-            ->method('generateCcl')
-            // ->with(null,array(),null) - it works
+            -> method('generateCcl')
+            -> with($report,array(),null) 
             -> will($this->returnValue($ccl));
         $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($mockCorpusExporter,'export_document');
         $protectedMethod->invokeArgs($mockCorpusExporter,array($report_id,$extractors,$disamb_only,&$extractor_stats,&$lists,$output_folder,$subcorpora,$tagging_method));
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part_Test.php
index ba05f917..9ab57b8f 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part_Test.php
@@ -122,7 +122,7 @@ public function test_export_document()
         $expectedRelxmlContent = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<!DOCTYPE chunkList SYSTEM \"ccl.dtd\">\n<relations>\n</relations>\n";
         $resultRelxmlFile = file_get_contents($expectedBaseFileName.'.rel.xml');
         $this->assertEquals($expectedRelxmlContent,$resultRelxmlFile);
-        $expectedXmlContent = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<!DOCTYPE chunkList SYSTEM \"ccl.dtd\">\n<chunkList>\n <chunk id=\"ch1\" type=\"\">\n  <sentence id=\"sent1\">\n   <tok>\n    <orth>e</orth>\n   </tok>\n   <ns/>\n  </sentence>\n </chunk>\n</chunkList>\n";
+        $expectedXmlContent = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<!DOCTYPE chunkList SYSTEM \"ccl.dtd\">\n<chunkList>\n <chunk id=\"ch1\" type=\"p\">\n  <sentence id=\"sent1\">\n   <tok>\n    <orth>e</orth>\n   </tok>\n   <ns/>\n  </sentence>\n </chunk>\n</chunkList>\n";
         $resultXmlFile = file_get_contents($expectedBaseFileName.'.xml');
         $this->assertEquals($expectedXmlContent,$resultXmlFile);
 
diff --git a/phpunit/tests/engine/include/writers/CCclWriterTest.php b/phpunit/tests/engine/include/writers/CCclWriterTest.php
index 39f2758c..3dcf33ef 100644
--- a/phpunit/tests/engine/include/writers/CCclWriterTest.php
+++ b/phpunit/tests/engine/include/writers/CCclWriterTest.php
@@ -242,19 +242,6 @@ protected function setUp() {
 
     } // setUp()
 
-    public function testOutputTextIsWrittenToFile() {
-
-        $text = "jnduie773nd n";
-
-        // private method need reflection to tests
-        $privateMethod = new ReflectionMethod('CclWriter','writeTextToFile');
-        $privateMethod->setAccessible(True);
-        $privateMethod->invoke(new CclWriter(),$this->fileName,$text);
-        $result = file_get_contents($this->fileName);
-        $this->assertEquals($text,$result);
-
-    } // testOutputTextIsWrittenToFile()
-
     // static function write($ccl, $filename, $mode){...}
  
     // private function makeXmlData($ccl,$mode) {...}

From 6c5e9b51a37b4a7173498fafe5d2c1616646b7a6 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Sat, 9 Dec 2023 11:57:48 +0100
Subject: [PATCH 140/154] missing name field in DB annotation data changed to
 type

---
 engine/include/database/CDbAnnotation.php          |  2 +-
 engine/include/export/ConllAndJsonFactory.php      |  2 +-
 phpunit/classes/SimpleCcl.php                      | 14 +++++++++++++-
 .../include/export/ConllAndJsonFactoryTest.php     |  6 +++---
 .../include/export/CorpusExporter_part12_Test.php  | 14 ++++++++++++--
 5 files changed, 30 insertions(+), 8 deletions(-)

diff --git a/engine/include/database/CDbAnnotation.php b/engine/include/database/CDbAnnotation.php
index a11aa456..6f4eda07 100755
--- a/engine/include/database/CDbAnnotation.php
+++ b/engine/include/database/CDbAnnotation.php
@@ -203,7 +203,7 @@ static function getAnnotationsBySets($report_ids=null, $annotation_layers=null,
 	 */
 	static function getAnnotationsBySubsets($report_ids=null, $annotation_subset_ids=null){
 		global $db;
-		$sql = "SELECT *, ra.type, raa.`value` AS `prop` " .
+		$sql = "SELECT *, raa.`value` AS `prop` " .
 				" FROM reports_annotations ra" .
 				" LEFT JOIN annotation_types at ON (ra.type=at.name) " .
 				" LEFT JOIN reports_annotations_attributes raa ON (ra.id=raa.annotation_id) ";
diff --git a/engine/include/export/ConllAndJsonFactory.php b/engine/include/export/ConllAndJsonFactory.php
index dd516bec..7c5dba6d 100644
--- a/engine/include/export/ConllAndJsonFactory.php
+++ b/engine/include/export/ConllAndJsonFactory.php
@@ -101,7 +101,7 @@ protected function makeConllAndJsonExportData($ccl, $tokens, $relations, $annota
                             $iob = $annotations_from_cache["iob"];
 
                             $annotation = $annotations_by_id[$annotations_from_cache_id];
-                            $ann_tag[] = $iob . $annotation['name'];
+                            $ann_tag[] = $iob . $annotation['type'];
                             $ann_id[] = $annotation['id'];
 
                             if (array_key_exists($annotation['id'], $relations_cache)) {
diff --git a/phpunit/classes/SimpleCcl.php b/phpunit/classes/SimpleCcl.php
index faa81066..228985a3 100644
--- a/phpunit/classes/SimpleCcl.php
+++ b/phpunit/classes/SimpleCcl.php
@@ -375,6 +375,18 @@ private static function annotationIdsForToken($token,$withoutChannelAnnotations=
 
     } // annotationIdsForToken()
 
+    private static function annotationTypesForToken($token,$withoutChannelAnnotations=true){
+        // zwraca listę typów annotacji związanych z tokenem
+        // z uwzględnieniem lub nie, sztucznych annotacji z id=0
+        // utworzonych na potrzeby kanałów
+        $annTypesForToken = array();
+        foreach(self::annotationsForToken($token,$withoutChannelAnnotations) as $annotation) {
+            $annTypesForToken[] = $annotation["type"];
+        }
+        return $annTypesForToken;
+
+    } // annotationTypesForToken()
+
     public static function tagStrForToken($token) {
 
         //  tagi dla CONLL odpowiadajace annotacjom związanym 
@@ -382,7 +394,7 @@ public static function tagStrForToken($token) {
 
         $annotationCount = count(self::annotationIdsForToken($token,True));
         if($annotationCount>0) {
-            $tagStr = "B-";
+            $tagStr = "B-".join(":", self::annotationTypesForToken($token)) ;
             $tagStr .= str_repeat(":I-",$annotationCount-1);
         } else {
             $tagStr = 'O'; // brak annotacji pasujących do tokena
diff --git a/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php b/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
index c351d54e..e0498adf 100644
--- a/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
+++ b/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
@@ -615,7 +615,7 @@ public function testFirstTokenIntoAnnotationHasBAnntag() {
         // invoke tested method
         list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
 
-        $expectedAnnTags = "B-";
+        $expectedAnnTags = "B-".'nam_adj'; // annotation type glued
         $annTags = $this->extractAnntagsFromConllLines($conll,$annotationTokenLine);
         $this->assertEquals($expectedAnnTags,$annTags);
 
@@ -644,7 +644,7 @@ public function testNextTokensIntoAnnotationHasIAnntag() {
         // invoke tested method
         list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
 
-		$expectedAnnTags = "I-";
+		$expectedAnnTags = "I-".'nam_adj'; // annotation type glued
 		// for tokens in lines 4 and 5
         $this->assertEquals($expectedAnnTags,$this->extractAnntagsFromConllLines($conll,4));
 		$this->assertEquals($expectedAnnTags,$this->extractAnntagsFromConllLines($conll,5));
@@ -673,7 +673,7 @@ public function testTokenInto2AnnotationsHasJoinedAnntags() {
 		// copy 1 anntotation to second one on this same <from,to>
 		$annotations_by_id[2] = $annotations_by_id[1];
 		$annotations_by_id[2]['id'] = 2; // correct annotation id 
-		$annotations_by_id[2]['name'] = '2nd'; // change ann type name 
+		$annotations_by_id[2]['type'] = '2nd'; // change ann type name 
         $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
         // invoke tested method
         list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
index b61743f0..0ce349e7 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
@@ -143,7 +143,8 @@ public function testMinimalParameterForExampleExecution() {
                         "title"=>'TITLE', 
                         "source"=>'SOURCE', 
                         "author"=>'AUTHOR', 
-                        "tokenization"=>'TOKENIZATION'); 
+                        "tokenization"=>'TOKENIZATION',
+                        "format"=>'FORMAT'); 
         $tokens = array(); $tags = array();
         $ccl = new CclExportDocument($report,$tokens,$tags); 
         $ccl -> setFileName($fileName);
@@ -201,7 +202,16 @@ public function testMainFlowForXMLLemmaExport() {
         $tagging_method = 'tagger';
 		// emulowane dane z bazy danych
 		$flags = array( $flag_name => $flag_id );
-		$report = array( "id"=>$report_id, "content"=>'To jest duże okno.' );
+        $report = array('id'=>$report_id,
+                        "content"=>'To jest duże okno.',
+                        'name'=>"report name must exists",
+                        'subcorpus_id'=>1,
+                        "date"=>'DATA',
+                        "title"=>'TITLE',
+                        "source"=>'SOURCE',
+                        "author"=>'AUTHOR',
+                        "tokenization"=>'TOKENIZATION',
+                        "format"=>'FORMAT');
 		$tokens = array(
 			// all fields from DB, enough are "from","to","token_id" 
 			// from,to are offset in content without white chars and tags

From b3149a713853461cbdcb89fe8500f89928c9319f Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Sat, 9 Dec 2023 17:16:22 +0100
Subject: [PATCH 141/154] correct read from DB obscured by attr user annotation
 user_id data

---
 engine/include/database/CDbAnnotation.php                    | 4 ++--
 phpunit/tests/engine/include/database/CDbAnnotationTest.php  | 5 ++---
 .../engine/include/export/CorpusExporter_part0_Test.php      | 2 +-
 3 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/engine/include/database/CDbAnnotation.php b/engine/include/database/CDbAnnotation.php
index 6f4eda07..5d58a9f9 100755
--- a/engine/include/database/CDbAnnotation.php
+++ b/engine/include/database/CDbAnnotation.php
@@ -166,7 +166,7 @@ static function getAnnotationTypesBySets($report_ids, $relation_ids){
 
 	static function getAnnotationsBySets($report_ids=null, $annotation_layers=null, $annotation_names=null, $stage = null){
 		global $db;
-		$sql = "SELECT *, raa.`value` AS `prop` " .
+		$sql = "SELECT ra.*, at.*, raa.annotation_id, raa.annotation_attribute_id, raa.`user_id` AS `attr_user_id`, raa.`value` AS `prop` " .
 				" FROM reports_annotations ra" .
 				" LEFT JOIN annotation_types at ON (ra.type=at.name) " .
 				" LEFT JOIN reports_annotations_attributes raa ON (ra.id=raa.annotation_id) ";
@@ -203,7 +203,7 @@ static function getAnnotationsBySets($report_ids=null, $annotation_layers=null,
 	 */
 	static function getAnnotationsBySubsets($report_ids=null, $annotation_subset_ids=null){
 		global $db;
-		$sql = "SELECT *, raa.`value` AS `prop` " .
+		$sql = "SELECT ra.*, at.*, raa.annotation_id, raa.annotation_attribute_id, raa.`user_id` AS `attr_user_id`, raa.`value` AS `prop` " .
 				" FROM reports_annotations ra" .
 				" LEFT JOIN annotation_types at ON (ra.type=at.name) " .
 				" LEFT JOIN reports_annotations_attributes raa ON (ra.id=raa.annotation_id) ";
diff --git a/phpunit/tests/engine/include/database/CDbAnnotationTest.php b/phpunit/tests/engine/include/database/CDbAnnotationTest.php
index e7999c79..c39c6e8a 100644
--- a/phpunit/tests/engine/include/database/CDbAnnotationTest.php
+++ b/phpunit/tests/engine/include/database/CDbAnnotationTest.php
@@ -103,8 +103,7 @@ public function test_getAnnotationsBySets()
  // all fields from reports_annotations_attributes 
  "annotation_id"			=>null,
  "annotation_attribute_id"	=>null,
- "value"					=>null,
- "user_id"					=>null,
+ "attr_user_id"				=>null,
 
  "prop"						=>null			// raa.value as prop
                                     );
@@ -112,7 +111,7 @@ public function test_getAnnotationsBySets()
             $oneRowOptimizedAnnotationData
         );
         $dbEmu->setResponse("fetch_rows",
-"SELECT *, raa.`value` AS `prop`  FROM reports_annotations ra LEFT JOIN annotation_types at ON (ra.type=at.name)  LEFT JOIN reports_annotations_attributes raa ON (ra.id=raa.annotation_id)  WHERE ( ra.stage = 'final'  AND report_id IN (1))   GROUP BY ra.id ORDER BY `from`",
+"SELECT ra.*, at.*, raa.annotation_id, raa.annotation_attribute_id, raa.`user_id` AS `attr_user_id`, raa.`value` AS `prop`  FROM reports_annotations ra LEFT JOIN annotation_types at ON (ra.type=at.name)  LEFT JOIN reports_annotations_attributes raa ON (ra.id=raa.annotation_id)  WHERE ( ra.stage = 'final'  AND report_id IN (1))   GROUP BY ra.id ORDER BY `from`",
                             $allOptimizedAnnotationData
         );
 
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php
index 90d60107..9ce28781 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php
@@ -209,7 +209,7 @@ public function test_parse_extractor()
         $ReturnedDataRow = array( "id"=>1, "report_id"=>$report_id, "type_id"=>$type, "type"=>'typ annotacji', "group"=>1, "from"=>$from, "to"=>$to, "text"=>$text, "user_id"=>$user_id, "creation_time"=>'2022-12-21 18:16:58', "stage"=>'final', "source"=>'auto', "prop"=>$value);
         $allReturnedDataRows = array( $ReturnedDataRow );
         $dbEmu->setResponse("fetch_rows",
-"SELECT *, raa.`value` AS `prop`  FROM reports_annotations ra LEFT JOIN annotation_types at ON (ra.type=at.name)  LEFT JOIN reports_annotations_attributes raa ON (ra.id=raa.annotation_id)  WHERE ( ra.stage = 'final'  AND report_id IN ($report_id))   GROUP BY ra.id ORDER BY `from`",
+"SELECT ra.*, at.*, raa.annotation_id, raa.annotation_attribute_id, raa.`user_id` AS `attr_user_id`, raa.`value` AS `prop`  FROM reports_annotations ra LEFT JOIN annotation_types at ON (ra.type=at.name)  LEFT JOIN reports_annotations_attributes raa ON (ra.id=raa.annotation_id)  WHERE ( ra.stage = 'final'  AND report_id IN ($report_id))   GROUP BY ra.id ORDER BY `from`",
             $allReturnedDataRows );
 
 

From baa9a435a7225530bf5affc6cd157786148b4a6c Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Mon, 11 Dec 2023 18:36:27 +0100
Subject: [PATCH 142/154] fix tags export

---
 engine/include/export/ConllAndJsonFactory.php          |  5 +++--
 .../include/export/CorpusExporter_part12_Test.php      | 10 ++++++++--
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/engine/include/export/ConllAndJsonFactory.php b/engine/include/export/ConllAndJsonFactory.php
index 7c5dba6d..6735d75f 100644
--- a/engine/include/export/ConllAndJsonFactory.php
+++ b/engine/include/export/ConllAndJsonFactory.php
@@ -116,11 +116,12 @@ protected function makeConllAndJsonExportData($ccl, $tokens, $relations, $annota
                         }
                     }
                     $token_id = $id++;
+                    $ctag = isset($token->lexemes[0]->ctag) ? $token->lexemes[0]->ctag :'';
                     $json_sentence[] = array(
                         "order_id" => $token->id,
                         "token_id" => $token_id,
                         "orth" => $token->orth,
-                        "ctag" => $token->lexemes[0]->ctag,
+                        "ctag" => $ctag,
                         "from" => $token->from,
                         "to"  => $token->to,
                         "annotations" => $ann_id,
@@ -137,7 +138,7 @@ protected function makeConllAndJsonExportData($ccl, $tokens, $relations, $annota
                             $array_to_check += ["_"];
                         }
                     }
-                    $conll .= $token->id . "\t" . $token_id . "\t" . $token->orth . "\t" . $token->lexemes[0]->ctag . "\t" . $token->from . "\t" .
+                    $conll .= $token->id . "\t" . $token_id . "\t" . $token->orth . "\t" . $ctag . "\t" . $token->from . "\t" .
                         $token->to . "\t" . join(":", $ann_tag) . "\t" . join(":", $ann_id) . "\t" .
                         join(":", $rel_id) . "\t" . join(":", $rel_target_id) . "\n";
 
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
index 0ce349e7..a8d6496a 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
@@ -218,7 +218,13 @@ public function testMainFlowForXMLLemmaExport() {
 			array( "from"=>6, "to"=>9, "orth"=>'duże', "eos"=>false, "token_id"=>231, "report_id"=>$report_id ),
 			array( "from"=>10, "to"=>13, "orth"=>'okno', "eos"=>true, "token_id"=>2314, "report_id"=>$report_id  ),
 		);
-		$tags = array();
+        // records for tokens id's above
+		$tags_by_tokens = array( 
+            231 => array (
+                    // must have "disamb","ctag","base_text" 
+                    [ "token_tag_id" => "30","token_id"=>"231","disamb"=>"1","ctag_id"=>"25","ctag"=>"CTAG","tagset_id"=>1,"base_id"=>7,"base_text"=>"BASE" ]
+                )
+            );
 		$annotations = array(
 			$this->annotationWoLemmaData(),
 			$this->annotationWithLemmaData()
@@ -267,7 +273,7 @@ function($report_id, $params, &$extractor_elements) {
 		$mockCorpusExporter -> expects($this->once())
             -> method('getReportTagsByTokens')
 			-> with($report_id,$token_ids,$disamb_only,$tagging_method)
-			-> will($this->returnValue($tags))
+			-> will($this->returnValue($tags_by_tokens))
 		;
 
         // reflection for acces to private elements

From c1c3a8016d2bedcdc6a86cfbdbf8693cd6212ffa Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Mon, 11 Dec 2023 18:45:01 +0100
Subject: [PATCH 143/154] in custom export value annotation field is not
 obligatory

---
 engine/include/structs/CclDocument.php | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/engine/include/structs/CclDocument.php b/engine/include/structs/CclDocument.php
index e3ad164f..f519d1fc 100644
--- a/engine/include/structs/CclDocument.php
+++ b/engine/include/structs/CclDocument.php
@@ -205,8 +205,8 @@ function setAnnotation($annotation){
 				}
 				$found = true;
 			}	
-			if ( $annotation['value'] ){
-				$prop_name = sprintf("sense:%s", $annotation['name']);
+			if ( isset($annotation['value']) && $annotation['value'] ){
+				$prop_name = sprintf("sense:%s", $annotation['type']);
 				$token->prop[$prop_name] = $annotation['value'];
 			}
 			if (! $token->setAnnotation($annotation,$this->getSentenceByToken($token)->channels)){					

From 9944b9ac9b88e0c77ba33f664aa3f29c26641de6 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Mon, 11 Dec 2023 19:01:05 +0100
Subject: [PATCH 144/154] subcorpora_id in record may be NULL

---
 engine/include/export/CorpusExporter.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index fb800ca3..e9f248e2 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -516,7 +516,7 @@ protected function createIniFile($report,$subcorpora,$file_path_without_ext) {
         $basic = array("id", "date", "title", "source", "author", "tokenization", "subcorpus");
         $lines = array();
         $lines[] = "[document]";
-        $report["subcorpus"] = $subcorpora[$report['subcorpus_id']];
+        $report["subcorpus"] = isset($subcorpora[$report['subcorpus_id']]) ? $subcorpora[$report['subcorpus_id']] : "";
 
         foreach ($basic as $name){
             $lines[] = sprintf("%s = %s", $name, $report[$name]);

From 293722a1a089b379bdb5636e2fdd8719aee32c51 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Thu, 14 Dec 2023 19:30:36 +0100
Subject: [PATCH 145/154] fix usage of unexisting in DB fields

---
 engine/include/export/CclExportDocument.php   |  7 +-
 engine/include/export/ConllAndJsonFactory.php |  2 +-
 engine/include/export/CorpusExporter.php      | 64 +++++++++++++------
 .../DocumentExportDatabaseEmulator.php        | 24 +++++--
 phpunit/classes/MockedExtractor.php           |  5 +-
 phpunit/classes/SimpleCcl.php                 | 49 ++++++++++++--
 .../include/export/CclExportDocumentTest.php  |  4 +-
 .../include/export/CorpusExporterTest.php     | 48 ++++++++++++--
 .../export/CorpusExporter_part0_Test.php      | 19 +++---
 .../export/CorpusExporter_part10_Test.php     | 37 ++++++-----
 .../export/CorpusExporter_part1_Test.php      |  2 +-
 .../export/CorpusExporter_part5_Test.php      |  5 +-
 .../export/CorpusExporter_part6_Test.php      |  5 +-
 .../export/CorpusExporter_part_Test.php       | 17 +++--
 .../include/structs/CclDocumentTest.php       | 16 ++---
 .../engine/include/structs/CclTokenTest.php   |  8 +--
 .../include/utils/CReportContentTest.php      |  4 +-
 .../engine/include/writers/CCclWriterTest.php |  4 +-
 18 files changed, 223 insertions(+), 97 deletions(-)

diff --git a/engine/include/export/CclExportDocument.php b/engine/include/export/CclExportDocument.php
index 55b0bc10..4dbf5294 100644
--- a/engine/include/export/CclExportDocument.php
+++ b/engine/include/export/CclExportDocument.php
@@ -19,7 +19,12 @@ public function __construct(&$report, &$tokens, &$tags){
 		$fileName = str_pad($report['id'],8,'0',STR_PAD_LEFT);
 		
 		$this->setFileName($fileName);
-		$this->setSubcorpus(preg_replace("/[^\p{L}|\p{N}]+/u","_",$report['name']));
+		$this->setSubcorpus(
+            // SW ?? there are not 'name' column  in DB table reports 
+            isset($report['name'])
+            ? preg_replace("/[^\p{L}|\p{N}]+/u","_",$report['name'])
+            : ""
+        );
 		$this->setReport($report);
 	
 		$chunkList = explode('<\\chunk>', $report['content']);
diff --git a/engine/include/export/ConllAndJsonFactory.php b/engine/include/export/ConllAndJsonFactory.php
index 6735d75f..127d70d6 100644
--- a/engine/include/export/ConllAndJsonFactory.php
+++ b/engine/include/export/ConllAndJsonFactory.php
@@ -89,7 +89,7 @@ protected function makeConllAndJsonExportData($ccl, $tokens, $relations, $annota
                 $json_sentence = [];
                 $id = 0;
                 foreach ($sentence->tokens as $token) {
-                    $original_id = $tokens_ids[$it++];
+                    $original_id = isset($tokens_ids[$it]) ? $tokens_ids[$it++] : null;
                     $ann_tag = [];
                     $ann_id = [];
                     $rel_id = [];
diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index e9f248e2..5f937155 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -61,7 +61,11 @@ public static function arrayRemoveNullElements(array $arr) {
 	 */
 	protected function parse_extractor($description){
 		$extractors = array();
-		$parts = explode(":", $description);
+        try {
+		    $parts = explode(":", $description);
+        } catch(Exception $ex){
+            throw new Exception("Niepoprawny opis ekstraktora ");
+        } // catch()
 		if ( count($parts) !== 2 ){
 			throw new Exception("Niepoprawny opis ekstraktora " . $description);
 		}
@@ -475,6 +479,15 @@ protected function getReportExtById($report_id){
     protected function exportReportContent($report,$file_path_without_ext) {
 
         try {
+            // getHtmlStr() need $report['format'] field, which isn't
+            // exists in `reports` DB now. We must create it from
+            // $reports['format_id']. Its not elegant here, but works...
+            if(!isset($report['format'])){
+                $report['format'] =
+                    isset($report['format_id']) && $report['format_id']
+                    ? DbReport::formatName($report['format_id'])
+                    : '' ;
+            }
             $html = ReportContent::getHtmlStr($report);
         } catch(Exception $ex){
             $errorMsg = "Problem z eksportem zawartości HTML dokumentu";
@@ -535,7 +548,7 @@ protected function createIniFile($report,$subcorpora,$file_path_without_ext) {
 
     } // createIniFile()
 
-    protected function checkIfAnnotationForLemmaExists($lemmas,$annotations_by_id) {
+    protected function checkIfAnnotationForLemmaExists($report_id,$lemmas,$annotations_by_id) {
 
 		$allLemmasCorrect = True;
         foreach ($lemmas as $an){
@@ -554,7 +567,7 @@ protected function checkIfAnnotationForLemmaExists($lemmas,$annotations_by_id) {
 
     } // checkIfAnnotationForLemmaExists()
 
-    protected function checkIfAnnotationForRelationExists($relations,$annotations_by_id) {
+    protected function checkIfAnnotationForRelationExists($report_id,$relations,$annotations_by_id) {
 		/* Sprawdzenie, anotacji źródłowych i docelowych dla relacji */
 		$allRelationsCorrect = True;
         foreach ( $relations as $rel ){
@@ -583,12 +596,12 @@ protected function checkIfAnnotationForRelationExists($relations,$annotations_by
  
     } // checkIfAnnotationForRelationExists()
 
-	protected function sortUniqueAnnotationsById($annotations) {
+	protected function sortUniqueAnnotationsById($report_id,$annotations) {
 
         /* Usunięcie zduplikowanych anotacji */
         $annotations_by_id = array();
         foreach ($annotations as $an){
-            $anid = intval($an['id']);
+            $anid = isset($an['id']) ? intval($an['id']) : 0;
             if ( $anid > 0 ){
                 $annotations_by_id[$anid] = $an;
             }
@@ -726,14 +739,14 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
 		list($annotations,$relations,$lemmas,$attributes) = $this->dispatchElements($elements);
 
 		/* Usunięcie zduplikowanych anotacji */
-		$annotations_by_id = $this->sortUniqueAnnotationsById($annotations);
+		$annotations_by_id = $this->sortUniqueAnnotationsById($report_id,$annotations);
 		$annotations = array_values($annotations_by_id);
 
 		/* Sprawdzenie, anotacji źródłowych i docelowych dla relacji */
-		$this->checkIfAnnotationForRelationExists($relations,$annotations_by_id);
+		$this->checkIfAnnotationForRelationExists($report_id,$relations,$annotations_by_id);
 
 		/* Sprawdzenie lematów */
-		$this->checkIfAnnotationForLemmaExists($lemmas,$annotations_by_id);
+		$this->checkIfAnnotationForLemmaExists($report_id,$lemmas,$annotations_by_id);
 
         $file_path_without_ext = $output_folder . "/" . $ccl->getFileName();
 
@@ -753,6 +766,26 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
 
 	} // export_document()
 
+    protected function getSubcorporaList() {
+
+        /* Przygotuj listę podkorpusów w postaci tablicy id=>nazwa*/
+        $subcorpora_assoc = DbCorpus::getSubcorpora();
+        $subcorpora = array();
+        foreach ( $subcorpora_assoc as $sub ){
+            $subcorpora[$sub['subcorpus_id']] = $sub['name'];
+        }
+		return $subcorpora;
+
+    } // getSubcorporaList()
+
+    protected function writeConsoleMessage($msg) {
+
+        $isCLI = (php_sapi_name() == 'cli');
+        if($isCLI)
+            echo($msg);
+
+    } // writeConsoleMessage()
+
 	/**
 	 * Wykonuje eksport korpusu zgodnie z określonymi parametrami (selektory, ekstraktory i indeksy).
 	 * @param $output Ścieżka do katalogu wyjściowego
@@ -768,13 +801,8 @@ public function exportToCcl($output_folder, $selectors_description, $extractors_
 			mkdir("$output_folder/documents", 0777, true);
 		}
 
-
 		/* Przygotuj listę podkorpusów w postaci tablicy id=>nazwa*/
-		$subcorpora_assoc = DbCorpus::getSubcorpora();
-		$subcorpora = array();
-		foreach ( $subcorpora_assoc as $sub ){
-			$subcorpora[$sub['subcorpus_id']] = $sub['name'];
-		}
+		$subcorpora = $this->getSubcorporaList();
 
 		$extractors = array();
 		foreach ( $extractors_description as $extractor ){
@@ -794,7 +822,7 @@ public function exportToCcl($output_folder, $selectors_description, $extractors_
 		}
 
 		$document_ids = array_keys($document_ids);
-		echo "Liczba dokumentów do eksportu: " . count($document_ids) . "\n";
+		$this->writeConsoleMessage("Liczba dokumentów do eksportu: " . count($document_ids) . "\n");
 
 		$extractor_stats = array();
 	    $number_of_docs = count($document_ids);
@@ -808,11 +836,11 @@ public function exportToCcl($output_folder, $selectors_description, $extractors_
             if($percent_done > $progress){
                 $progress = $percent_done;
                 DbExport::updateExportProgress($export_id, $progress);
-                echo intval($progress) . "%" . "\n";
+                $this->writeConsoleMessage(intval($progress) . "%" . "\n");
             }
 		}
 		foreach ($lists as $list){
-			echo sprintf("%4d %s\n", count(array_keys($list["document_names"])), $list["name"]);
+			$this->writeConsoleMessage(sprintf("%4d %s\n", count(array_keys($list["document_names"])), $list["name"]));
 			$lines = array();
 			foreach ( array_keys($list["document_names"]) as $document_name ){
 				$lines[] = "./documents/" . $document_name;
@@ -829,7 +857,7 @@ public function exportToCcl($output_folder, $selectors_description, $extractors_
 				$types[$type] = 1;
 			}
 		}
-        echo "\n";
+        $this->writeConsoleMessage("\n");
 
         $stats_str = str_repeat(" ", $max_len_name);
         foreach ( array_keys($types) as $type ){
diff --git a/phpunit/classes/DocumentExportDatabaseEmulator.php b/phpunit/classes/DocumentExportDatabaseEmulator.php
index 884ef94f..b8bd43a2 100644
--- a/phpunit/classes/DocumentExportDatabaseEmulator.php
+++ b/phpunit/classes/DocumentExportDatabaseEmulator.php
@@ -3,7 +3,7 @@
 
 class DocumentExportDatabaseEmulator extends DatabaseEmulator {
 
-    private function addReportCorporaExtDB($report_id){
+    private function addReportCorporaExtDB($report_id, $corpora_ext=null){
 
         //  DbReport::getReportExtById($report_id)
         //
@@ -12,12 +12,14 @@ private function addReportCorporaExtDB($report_id){
         // zawsze sprawdza rekord korpusu wskazywany przez
         // reports[$report_id]["corpora"] wywołaniem:
         //  DbCorpora::getCorporaById() która 1 wiersz lub null
-        // aby ustalić wartość ext dla tego korpusu
+        // aby ustalić wartość ext dla tego korpusu ( to pole musi być )
 
-        $emptyDataRows = array();
+        $corporaRows = array(
+                            array( 'ext'=>$corpora_ext )
+                        );
         $this->setResponse("fetch_rows",
             'SELECT * FROM corpora WHERE id = ?',
-            $emptyDataRows );
+            $corporaRows );
 
     } // addReportCorporaExtDB()
 
@@ -53,7 +55,8 @@ private function addTagsDB($report_id, $token_ids, $tagsData ) {
         $tags = array();
         foreach($tagsData as $tagRow) {
             // tylko bez ustawionego user_id
-            if($tagRow["user_id"]==null) {
+            if( !isset($tagRow["user_id"])
+                || $tagRow["user_id"]==null) {
                 $tags[] = array( 'token_tag_id' => $id, 'token_id' => $token_id, 'disamb' => $tagRow["disamb"], 'tto.ctag_id' => $tto_ctag_id, 'ctag_id' => $ctag_id, 'ctag'=>$tagRow["ctag"], 'tagset_id' => $tagset_id, 'base_id' => $base_id, 'base_text' => $tagRow["base_text"] );
                 $id++;
             }
@@ -69,7 +72,8 @@ private function addTagsDB($report_id, $token_ids, $tagsData ) {
         foreach($tagsData as $tagRow) {
             // tylko ze stage='final'
             if($tagRow["stage"]=='final') {
-                $tags[] = array( 'token_tag_id' => $id, 'token_id' => $token_id, 'disamb' => $tagRow["disamb"], 'tto.ctag_id' => $tto_ctag_id, 'ctag_id' => $ctag_id, 'ctag'=>$tagRow["ctag"], 'tagset_id' => $tagset_id, 'base_id' => $base_id, 'base_text' => $tagRow["base_text"], 'user_id' => $tagRow["user_id"] );
+                $tags[] = array( 'token_tag_id' => $id, 'token_id' => $token_id, 'disamb' => $tagRow["disamb"], 'tto.ctag_id' => $tto_ctag_id, 'ctag_id' => $ctag_id, 'ctag'=>$tagRow["ctag"], 'tagset_id' => $tagset_id, 'base_id' => $base_id, 'base_text' => $tagRow["base_text"], 
+    'user_id' => isset($tagRow["user_id"]) ? $tagRow["user_id"] : '' );
                 $id++;
             }
         }
@@ -123,7 +127,7 @@ private function addTokenDB($report_id, $tokensDBData) {
 
         $this->addTagsDB($report_id, $token_ids, $tagsData);
 
-    } // setTokenDB
+    } // addTokenDB()
 
     public function addReportsDB($report_id, $documentDBData ) {
 
@@ -155,6 +159,12 @@ public function addReportsDB($report_id, $documentDBData ) {
             'SELECT * FROM reports WHERE id = ?',
             $allReturnedDataRows );
 
+        $formatName = 'xml'; // for format_id=1
+        $this->setResponse("fetch_one",
+            'SELECT format FROM reports_formats WHERE id = ?',
+            $formatName   // fetch_one - only string without array packing
+            );
+
         $this->addReportFlagDB( $report_id, $documentDBData['flags'] );
         $this->addTokenDB( $report_id, $documentDBData['tokens'] );
         $this->addReportCorporaExtDB( $report_id, $corpora_ext );
diff --git a/phpunit/classes/MockedExtractor.php b/phpunit/classes/MockedExtractor.php
index a61c1fda..d8b0bb5c 100644
--- a/phpunit/classes/MockedExtractor.php
+++ b/phpunit/classes/MockedExtractor.php
@@ -5,7 +5,7 @@ class MockedExtractor {
     private $flagName = '';                 // ex. 'f'
     private $flagIds  = array();            // ex. array(3,4)
     private $extractorName = '';            // ex. "annotation_subset_id"    
-    private $extractorParams = array();     // ex. array(1)
+    private $extractorParams = array("user_ids"=>null,'annotation_set_ids'=>null,'annotation_subset_ids'=>null,'stages'=>null,'lemma_set_ids'=>null,'lemma_subset_ids'=>null,'attributes_annotation_set_ids'=>null,'attributes_annotation_subset_ids'=>null,'relation_set_ids'=>null);     // ex. array(1)
 
     private $extractorReturnedData = array();
 
@@ -31,7 +31,8 @@ public function getExtractorsTable() {
  function($report_id, $params, &$elements) {
     foreach( ['annotations','lemmas','attributes','relations'] as $n ) {
         $elements[$n] = array();
-        if($data = $this->extractorReturnedData[$n]) {
+        if( isset($this->extractorReturnedData[$n])
+            && $data = $this->extractorReturnedData[$n]) {
             foreach($this->extractorReturnedData[$n] as $data) {
                 $elements[$n][] = $data;
             }
diff --git a/phpunit/classes/SimpleCcl.php b/phpunit/classes/SimpleCcl.php
index 228985a3..c421ab15 100644
--- a/phpunit/classes/SimpleCcl.php
+++ b/phpunit/classes/SimpleCcl.php
@@ -99,7 +99,9 @@ private function recognizeSentence($sentence,&$chunk) {
         if(isset($sentence["to"])) {
             // sentencja niepusta - uzupełnij tekst
             $sentence["text"] = $this->getText($sentence["from"],$sentence["to"]);
-            $sentence["idx"] = count($chunk["sentences"])+1;
+            $sentence["idx"] = isset($chunk["sentences"]) 
+                                ? count($chunk["sentences"])+1
+                                : 1;
             // dopisz do chunka nadrzędnego
             $chunk["sentences"][] = $sentence;
         }
@@ -126,7 +128,7 @@ private function parse($contentText) {
         //  jest jeden chunk, chyba, że są w tekście elementy rozdzielające
         // <\chunk>
         //$chunkList = explode('<\\chunk>', $contentText);
-        $chunkList = explode(self::CHUNK_SEPARATOR, $contentText);
+        //$chunkList = explode(self::CHUNK_SEPARATOR, $contentText);
 
         $chunks = array(); $sentences = array(); $tokens = array();
         $contentLength = mb_strlen($contentText);
@@ -224,6 +226,35 @@ public function addAnnotation($annotation) {
 
     } // addAnnotation()
 
+    public function addLemmas($lemmasList) {
+
+        foreach($lemmasList as $lemma) {
+            $this->addLemma($lemma);
+        }
+
+    } // addLemmas()
+
+    public function addLemma($lemma) {
+
+        $from = $lemma["from"];
+        // atrybut jest dodawana do tokenów zaczynających się od
+		// pozycji podanej w $lemma["from"] liczonym bez spacji
+        foreach($this->chunks as &$chunk){
+            foreach($chunk["sentences"] as &$sentence){
+            	foreach($sentence["tokens"] as &$token){
+                        if($from == $token["nsiFrom"]) {
+							// dodaję do atrybutów odpowiednio sformatowane 
+							// dla wydruku XML
+							$token["attributes"][] = array('type'=>$lemma["type"], 'name'=>"lemma", 'value'=>$lemma["lemma"]);
+							//$token[$lemma["type"].":lemma"] = $lemma["lemma"];
+                        }
+                }
+            }
+        }
+
+    } // addLemma()
+ 
+
     public function addAttributes($annotationsList) {
 
         if(!is_array($annotationsList))
@@ -334,7 +365,8 @@ private function removeNonUserAndMaskedTags($Tags,$tagging_method){
         // i nie są maskowane identycznym tagiem 'final'
         $selected = array();
         foreach($Tags as $tag){
-            if($tag["user_id"]==$userId) {
+            if(isset($tag["user_id"])
+                && ($tag["user_id"]==$userId)) {
                 if(!$this->isTagMaskedByFinal($tag,$Tags)) {
                     $selected[] = $tag;
                 }
@@ -435,7 +467,7 @@ public function addTagsForTokens($tokensData,$tagging_method,$disambOnly){
                 $tags = $this->removeNonUserAndMaskedTags($token["tags"],$tagging_method);
                 foreach($tags as $tag){
                     if( (!$disambOnly) || ($tag["disamb"]) ) {
-                        $this->addTag($token["from"],$token["to"],$tag["disamb"],$tag["base_text"],$tag[ctag],
+                        $this->addTag($token["from"],$token["to"],$tag["disamb"],$tag["base_text"],$tag["ctag"],
                         isset($tag["stage"]) ? $tag["stage"] : null,
                         isset($tag["user_id"]) ? $tag["user_id"] : null);
                     }
@@ -573,12 +605,14 @@ public function toJSON($annotations = null, $relations = null) {
             $from = $token["nsiFrom"];
             $to = $token["nsiTo"];
             $text = $token["text"];
-            $annId = $extractorData[$extractorIndex]["id"];
+            if( isset($extractorData[$extractorIndex])
+                && isset($extractorData[$extractorIndex]["id"]))
+                $annId = $extractorData[$extractorIndex]["id"];
             // ctag jest wybierany tylko z pierwszego wiersza z tagami dla
             // danego tokena, przy czym jeśli $disamb_only jest true liczą
             // się tylko wiersze z "disamb"=1. Jeśli żadnego takiego wiersza
             // nie ma jest pustym napisem
-            $ctag = count($token["tags"])>0 ? '"'.$token["tags"][0]["ctag"].'"' : 'null';
+            $ctag = count($token["tags"])>0 ? '"'.$token["tags"][0]["ctag"].'"' : '""';
 
             $tokenAnnotationStr =   isset($annId)
                                     ? "[".$spc20."    ".$annId.$spc20."]"
@@ -643,7 +677,8 @@ public function toXML() {
                         $xml .= "\n".$this->spc($indent)."<ann chan=\"".$type."\">".$annIdsStr."</ann>";    
                     }
                     // attributes 4 token
-                    if(is_array($token["attributes"])) {
+                    if(isset($token["attributes"]) 
+                        && is_array($token["attributes"])) {
                         foreach($token["attributes"] as $attr) {
                             $xml .= "\n".$this->spc($indent)."<prop key=\"".$attr["type"].":".$attr["name"]."\">".$attr["value"]."</prop>";
                         }       
diff --git a/phpunit/tests/engine/include/export/CclExportDocumentTest.php b/phpunit/tests/engine/include/export/CclExportDocumentTest.php
index 40374a09..b5044242 100644
--- a/phpunit/tests/engine/include/export/CclExportDocumentTest.php
+++ b/phpunit/tests/engine/include/export/CclExportDocumentTest.php
@@ -251,7 +251,7 @@ public function testSetannotationsandrelationsOnEmptyAnnotationsReturnsFalse() {
 
     public function testSetannotationsandrelationsOnAnnotationsWithNoRelationsCallCclsetannotation() {
 
-        $annotation1 = array( "annotation_id"=>1 );
+        $annotation1 = array( "id"=>1, "annotation_id"=>1 );
         $annotations = array( $annotation1 );
         $relations = array();
 
@@ -280,7 +280,7 @@ public function testSetcclpropertiesCallsAllPropertySetMethodsOnce() {
         $annotations = array('annotacje');
         $relations = array('relacje');
         $lemmas = array('lematy');
-        $attributtes = array('atrybuty');
+        $attributes = array('atrybuty');
         $mockCcl = $this->getMockBuilder(CclExportDocument::class)
             ->disableOriginalConstructor()
             -> setMethods(['setAnnotationsAndRelations','setAnnotationLemmas','setAnnotationProperties'])
diff --git a/phpunit/tests/engine/include/export/CorpusExporterTest.php b/phpunit/tests/engine/include/export/CorpusExporterTest.php
index 71c8e0d1..3d453d58 100644
--- a/phpunit/tests/engine/include/export/CorpusExporterTest.php
+++ b/phpunit/tests/engine/include/export/CorpusExporterTest.php
@@ -1,23 +1,59 @@
 <?php
 
+use org\bovigo\vfs\vfsStream; // for vfsStream
 mb_internal_encoding("UTF-8");
 
 class CorpusExporterTest extends PHPUnit_Framework_TestCase
 {
+
+    private $virtualDir = null;
+
+    protected function setUp() {
+
+        $this->virtualDir = vfsStream::setup('root',null,[]);
+
+    } // setUp()
+
     public function test_exportToCcl_createOutput()
     {
+        $output_folder = $this->virtualDir->url(); 
+        $selectors_description = array();
+        $extractors_description = array(); // array of strings 
+        $lists_description = array();
 
         $table =    array(
                         '1' => 'jeden'
                     );
 
-        $dbcorpus = $this->getMockBuilder('DbCorpus')->getMock();
-        $dbcorpus->method('getSubcorpora')
+        $mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
+            -> disableArgumentCloning()
+            -> setMethods(array(
+                'parse_extractor',
+                'parse_lists',
+                'getSubcorporaList',
+                'export_document',
+                'writeConsoleMessage'
+                )) -> getMock();
+        // przygotowuje listę wszystkich podkorpusów w postaci id=>nazwa
+        // i ładuje do zmiennej $subcorpora
+        $mockCorpusExporter -> expects($this->once())
+            -> method('getSubcorporaList')
             ->will($this->returnValue($table));
-
-        $ce = new CorpusExporter($dbcorpus);
-        //$result = $ce->exportToCcl('','','','');
-        $this->assertEquals('',$result);
+        $mockCorpusExporter -> expects($this->never())
+            -> method('parse_extractor');
+        $mockCorpusExporter -> expects($this->never())
+            -> method('parse_lists');
+        $mockCorpusExporter -> expects($this->never())
+            -> method('export_document');
+        // write console msgs
+        $mockCorpusExporter -> expects($this->at(1))
+            -> method('writeConsoleMessage')
+            -> with("Liczba dokumentów do eksportu: 0\n");
+        $mockCorpusExporter -> expects($this->at(2))
+            -> method('writeConsoleMessage')
+            -> with("\n");
+
+        $mockCorpusExporter->exportToCcl($output_folder,$selectors_description,$extractors_description,$lists_description);
 
     }
 
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php
index 9ce28781..4809620a 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php
@@ -1,9 +1,8 @@
 <?php
 
 mb_internal_encoding("UTF-8");
-require_once("CorpusExporterTest.php");
 
-class CorpusExporter_part0_Test extends CorpusExporterTest
+class CorpusExporter_part0_Test extends PHPUnit_Framework_TestCase
 {
 // function parse_extractor($description){
 
@@ -50,13 +49,15 @@ public function test_parse_extractor_throwsException_on_nonText(){
         $nonTextData = array();
         $ce = new CorpusExporter();
         $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'parse_extractor');
+        //$result = $protectedMethod->invokeArgs($ce,array($nonTextData));
 
         try {
-            $result = $result = $protectedMethod->invokeArgs($ce,array($emptyData));
+            $result = $protectedMethod->invokeArgs($ce,array($nonTextData));
         } catch(Exception $e) {
             // expected Exception "Niepoprawny opis ekstraktora "
             $this->assertInstanceOf(\Exception::class,$e);
-            $this->assertEquals("Niepoprawny opis ekstraktora ",$e->getMessage());
+            $this->assertEquals("Niepoprawny opis ekstraktora ",
+                                $e->getMessage());
             return;
         }
         // no exception throwed on empty data
@@ -150,7 +151,7 @@ public function test_parse_extractor()
 'SELECT a.*, at.name as type, at.group_id, at.annotation_subset_id, l.lemma, u.login, u.screename FROM reports_annotations_optimized a LEFT JOIN reports_annotations_lemma l ON (a.id = l.report_annotation_id) JOIN annotation_types at ON (a.type_id = at.annotation_type_id) LEFT JOIN users u ON (u.user_id = a.user_id) WHERE a.report_id = ?',
                             $allOptimizedAnnotationData 
         );
-        $params = array(); // empty
+        $params = array("user_ids"=>null,'annotation_set_ids'=>null,'annotation_subset_ids'=>null,'stages'=>null,'lemma_set_ids'=>null,'lemma_subset_ids'=>null,'attributes_annotation_set_ids'=>null,'attributes_annotation_subset_ids'=>null,'relation_set_ids'=>null); // empty
         $funcResult = array('annotations'=>array(),"relations"=>array(),"lemmas"=>array(),"attributes"=>array()); // empty answer template
         $extractorFunc($report_id,$params,$funcResult);
         $expectedResult = array('annotations'=>$allOptimizedAnnotationData,"relations"=>array(),"lemmas"=>array(),"attributes"=>array());
@@ -164,7 +165,7 @@ public function test_parse_extractor()
         $this->assertEquals($expectedResult,$funcResult);
 
         // with params set - all fields must exists, all must be arrays
-        $params = array("user_ids"=>array(70),"annotation_set_ids"=>array(12),"annotation_subset_ids"=>array(3),"stages"=>array('final')); 
+        $params = array("user_ids"=>array(70),"annotation_set_ids"=>array(12),"annotation_subset_ids"=>array(3),"stages"=>array('final'),'lemma_set_ids'=>null,'lemma_subset_ids'=>null,'attributes_annotation_set_ids'=>null,'attributes_annotation_subset_ids'=>null,'relation_set_ids'=>null); 
         $dbEmu->setResponse("fetch_rows",
 "SELECT a.*, at.name as type, at.group_id, at.annotation_subset_id, l.lemma, u.login, u.screename FROM reports_annotations_optimized a LEFT JOIN reports_annotations_lemma l ON (a.id = l.report_annotation_id) JOIN annotation_types at ON (a.type_id = at.annotation_type_id) LEFT JOIN users u ON (u.user_id = a.user_id) WHERE a.report_id = ? AND at.group_id IN (12) AND at.annotation_subset_id IN (3) AND a.user_id IN (70) AND a.stage IN ('final')",
                             $allOptimizedAnnotationData
@@ -175,7 +176,7 @@ public function test_parse_extractor()
         $this->assertEquals($expectedResult,$funcResult);
 
         // some of the params field may be empty array
-        $params = array("user_ids"=>array(70),"annotation_set_ids"=>array(12),"annotation_subset_ids"=>array(),"stages"=>array('final'));
+        $params = array("user_ids"=>array(70),"annotation_set_ids"=>array(12),"annotation_subset_ids"=>array(),"stages"=>array('final'),'lemma_set_ids'=>null,'lemma_subset_ids'=>null,'attributes_annotation_set_ids'=>null,'attributes_annotation_subset_ids'=>null,'relation_set_ids'=>null);
         $dbEmu->setResponse("fetch_rows",
 "SELECT a.*, at.name as type, at.group_id, at.annotation_subset_id, l.lemma, u.login, u.screename FROM reports_annotations_optimized a LEFT JOIN reports_annotations_lemma l ON (a.id = l.report_annotation_id) JOIN annotation_types at ON (a.type_id = at.annotation_type_id) LEFT JOIN users u ON (u.user_id = a.user_id) WHERE a.report_id = ? AND at.group_id IN (12) AND at.annotation_subset_id IN () AND a.user_id IN (70) AND a.stage IN ('final')",
                             $allOptimizedAnnotationData
@@ -185,7 +186,7 @@ public function test_parse_extractor()
         $expectedResult = array('annotations'=>$allOptimizedAnnotationData,"relations"=>array(),"lemmas"=>array(),"attributes"=>array());
         $this->assertEquals($expectedResult,$funcResult);
         // some of the params field may be null
-        $params = array("user_ids"=>array(70),"annotation_set_ids"=>array(12),"annotation_subset_ids"=>null,"stages"=>array('final'));
+        $params = array("user_ids"=>array(70),"annotation_set_ids"=>array(12),"annotation_subset_ids"=>null,"stages"=>array('final'),'lemma_set_ids'=>null,'lemma_subset_ids'=>null,'attributes_annotation_set_ids'=>null,'attributes_annotation_subset_ids'=>null,'relation_set_ids'=>null);
         $dbEmu->setResponse("fetch_rows",
 "SELECT a.*, at.name as type, at.group_id, at.annotation_subset_id, l.lemma, u.login, u.screename FROM reports_annotations_optimized a LEFT JOIN reports_annotations_lemma l ON (a.id = l.report_annotation_id) JOIN annotation_types at ON (a.type_id = at.annotation_type_id) LEFT JOIN users u ON (u.user_id = a.user_id) WHERE a.report_id = ? AND at.group_id IN (12) AND a.user_id IN (70) AND a.stage IN ('final')",
                             $allOptimizedAnnotationData
@@ -212,8 +213,6 @@ public function test_parse_extractor()
 "SELECT ra.*, at.*, raa.annotation_id, raa.annotation_attribute_id, raa.`user_id` AS `attr_user_id`, raa.`value` AS `prop`  FROM reports_annotations ra LEFT JOIN annotation_types at ON (ra.type=at.name)  LEFT JOIN reports_annotations_attributes raa ON (ra.id=raa.annotation_id)  WHERE ( ra.stage = 'final'  AND report_id IN ($report_id))   GROUP BY ra.id ORDER BY `from`",
             $allReturnedDataRows );
 
-
-
         $ce = new CorpusExporter();
         $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($ce,'parse_extractor');
         $result = $protectedMethod->invokeArgs($ce,array($extractorDescription));
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
index d2f53e2f..809a9ca9 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part10_Test.php
@@ -88,16 +88,16 @@ public function testExport_documentCallsAllProcessingMethods() {
 		$returnedAnnotationsById = array();
         $mockCorpusExporter -> expects($this->once())
             ->method('sortUniqueAnnotationsById')
-            ->with($expectedAnnotations)
+            ->with($report_id,$expectedAnnotations)
 			-> will($this->returnValue($returnedAnnotationsById));
         $expectedRelations = array();
         $mockCorpusExporter -> expects($this->once())
             ->method('checkIfAnnotationForRelationExists')
-            ->with($expectedRelations,$returnedAnnotationsById);
+            ->with($report_id,$expectedRelations,$returnedAnnotationsById);
         $expectedLemmas = array();
         $mockCorpusExporter -> expects($this->once())
             ->method('checkIfAnnotationForLemmaExists')
-            ->with($expectedLemmas,$returnedAnnotationsById);
+            ->with($report_id,$expectedLemmas,$returnedAnnotationsById);
         $expectedReportArg = $report;
         $expectedBaseFileName = $output_folder.'/'.str_pad($report_id,8,'0',STR_PAD_LEFT);
         $mockCorpusExporter -> expects($this->once())
@@ -325,6 +325,7 @@ public function testCreateinifileExportsReportMetadataToIniFile() {
 // protected function checkIfAnnotationForLemmaExists($lemmas,$annotations_by_id) {...}
 
     public function testCheckifannotationforlemmaexistsReturnsTrueIfAllLemmasMatched() {
+        $report_id = 1; // needed only for error reporting text
 		$annoId1 = 10;  $annoId2 = 20;
         $lemmas = array(
 			array( "id"=>$annoId1 ),
@@ -339,7 +340,7 @@ public function testCheckifannotationforlemmaexistsReturnsTrueIfAllLemmasMatched
         $export_errorsPrivateProperty = new ReflectionProperty($ce,'export_errors');
         $export_errorsPrivateProperty->setAccessible(True);
 
-        $result=$protectedMethod->invokeArgs($ce,array($lemmas,$annotationsById));
+        $result=$protectedMethod->invokeArgs($ce,array($report_id,$lemmas,$annotationsById));
         // returns True
         $this->assertTrue($result);
 
@@ -351,10 +352,11 @@ public function testCheckifannotationforlemmaexistsReturnsTrueIfAllLemmasMatched
  
     public function testCheckifannotationforlemmaexistsSetInternalError() {
 
+        $report_id = 1; // needed only for error reporting text
         $annoId1 = 10;  $annoId2 = 20;
         $lemmas = array(
-            array( "id"=>$annoId1 ),
-            array( "id"=>$annoId2 )
+            array( "id"=>$annoId1, "lemma"=>'lemma annotacji 1', "group_id"=>1, "name"=>'NAME', "from"=>0, "to"=>4, "type"=>'TYPE'  ),
+            array( "id"=>$annoId2, "lemma"=>'lemma annotacji 2', "group_id"=>1, "name"=>'NAME', "from"=>5, "to"=>13, "type"=>'TYPE'  )
         );
         $annotationsById = array( $annoId1 => True );
 
@@ -365,7 +367,7 @@ public function testCheckifannotationforlemmaexistsSetInternalError() {
         $export_errorsPrivateProperty = new ReflectionProperty($ce,'export_errors');
         $export_errorsPrivateProperty->setAccessible(True);
 
-        $result=$protectedMethod->invokeArgs($ce,array($lemmas,$annotationisById));
+        $result=$protectedMethod->invokeArgs($ce,array($report_id,$lemmas,$annotationsById));
 
         // returns False
         $this->assertFalse($result);
@@ -382,6 +384,7 @@ public function testCheckifannotationforlemmaexistsSetInternalError() {
 // protected function checkIfAnnotationForRelationExists($relations,$annotations_by_id) {
 
     public function testCheckifannotationforrelationsexistsReturnsTrueIfAllRelationsMatched() {
+        $report_id = 1; // needed only for error reporting text
         $sourceId1 = 10; $targetId1 = 13;  
 		$sourceId2 = 20; $targetId2 = 27;
         $relations = array(
@@ -398,7 +401,7 @@ public function testCheckifannotationforrelationsexistsReturnsTrueIfAllRelations
         $export_errorsPrivateProperty = new ReflectionProperty($ce,'export_errors');
         $export_errorsPrivateProperty->setAccessible(True);
 
-        $result=$protectedMethod->invokeArgs($ce,array($relations,$annotationsById));
+        $result=$protectedMethod->invokeArgs($ce,array($report_id,$relations,$annotationsById));
         // returns True
         $this->assertTrue($result);
 
@@ -409,11 +412,12 @@ public function testCheckifannotationforrelationsexistsReturnsTrueIfAllRelations
     } // testCheckifannotationforrelationsexistsReturnsTrueIfAllRelationsMatched() 
 
     public function testCheckifannotationforrelationsexistsSetInternalError() {
+        $report_id = 1; // needed only for error reporting text
         $sourceId1 = 10; $targetId1 = 13;
         $sourceId2 = 20; $targetId2 = 27;
         $relations = array(
-            array( "source_id"=>$sourceId1, "target_id"=>$targetId1 ),
-            array( "source_id"=>$sourceId2, "target_id"=>$targetId2 )
+            array( "source_id"=>$sourceId1, "target_id"=>$targetId1, "name"=>'NAME' ),
+            array( "source_id"=>$sourceId2, "target_id"=>$targetId2, "name"=>'NAME' )
         );
         $annotationsById = array( $targetId1 => True,
                                   $sourceId2 => True  );
@@ -425,7 +429,7 @@ public function testCheckifannotationforrelationsexistsSetInternalError() {
         $export_errorsPrivateProperty = new ReflectionProperty($ce,'export_errors');
         $export_errorsPrivateProperty->setAccessible(True);
 
-        $result=$protectedMethod->invokeArgs($ce,array($relations,$annotationsById));
+        $result=$protectedMethod->invokeArgs($ce,array($report_id,$relations,$annotationsById));
         // returns False
         $this->assertFalse($result);
 
@@ -443,7 +447,7 @@ public function testCheckifannotationforrelationsexistsSetInternalError() {
 // protected function sortUniqueAnnotationsById($annotations) {...}
 
     public function testSortuniqueannotationsbyidReturnsIndexedArray() {
-
+        $report_id = 1; // needed only for error reporting text
 		$anno1 = array( "id"=>1 ); $anno2 = array( "id"=>2 );
 		$annotations = array( $anno1,$anno2,$anno2 );
 
@@ -454,7 +458,7 @@ public function testSortuniqueannotationsbyidReturnsIndexedArray() {
         $export_errorsPrivateProperty = new ReflectionProperty($ce,'export_errors');
         $export_errorsPrivateProperty->setAccessible(True);
 
-        $result=$protectedMethod->invokeArgs($ce,array($annotations));
+        $result=$protectedMethod->invokeArgs($ce,array($report_id,$annotations));
 
 		$expectedAnnotationById = array(
 			1 => $anno1,
@@ -466,6 +470,7 @@ public function testSortuniqueannotationsbyidReturnsIndexedArray() {
 
     public function testSortuniqueannotationsbyidSetInternalError() {
 
+        $report_id = 1; // needed only for error reporting text
         $annoWoId = array( "name"=>1 ); $anno2 = array( "id"=>2 );
         $annotations = array( $annoWoId,$anno2,$anno2 );
 
@@ -476,7 +481,7 @@ public function testSortuniqueannotationsbyidSetInternalError() {
         $export_errorsPrivateProperty = new ReflectionProperty($ce,'export_errors');
         $export_errorsPrivateProperty->setAccessible(True);
 
-        $result=$protectedMethod->invokeArgs($ce,array($annotations));
+        $result=$protectedMethod->invokeArgs($ce,array($report_id,$annotations));
 
         $expectedAnnotationById = array(
             2 => $anno2
@@ -526,7 +531,7 @@ public function testDispatchelementsGeneratesTableList() {
     public function testGeneratecclReturnsObjectofCclDocumentClass() {
 
 		$report_id = 12;
-		$report = array( 'id'=>$report_id );
+		$report = array( 'id'=>$report_id, 'content'=>'' );
 		$tokens = array();
 		$tags_by_tokens = array();
 	
@@ -545,7 +550,7 @@ public function testGeneratecclReturnsObjectofCclDocumentClass() {
     public function testGeneratecclOnExceptionReturnsFalse() {
 
         $report_id = 13; 
-        $report = array();
+        $report = array( 'id'=>null );
         $tokens = array();
         $tags_by_tokens = array();
 
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part1_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part1_Test.php
index 459d60aa..2842f505 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part1_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part1_Test.php
@@ -90,7 +90,7 @@ private function export_document($disamb_only,$tagging_method)
  
             ) // tokens
         );
-        $dbEmu->addReportsDB($report_id,$documentDBData); 
+        $dbEmu->addReportsDB($report_id,$documentDBData);
 
         // do test...
         global $db;
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part5_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part5_Test.php
index 7b98b979..4a4ad544 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part5_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part5_Test.php
@@ -50,8 +50,8 @@ private function export_document($disamb_only,$tagging_method)
         $extractorObj = new MockedExtractor($extractorParameters["FlagName"],$extractorParameters["FlagValues"],$extractorParameters["Name"],$extractorParameters["Parameters"]);
         // $lemmas = DbReportAnnotationLemma::getLemmasBySets(array($report_id), $params);
         $extractorData = array(
-            array( "reports_annotation_id"=>1, "lemma"=>'lemma annotacji 1' ),
-            array( "reports_annotation_id"=>100, "lemma"=>'lemma annotacji 100'),
+            array( "reports_annotation_id"=>1, "lemma"=>'lemma annotacji 1', "id"=>12345, "group_id"=>1, "name"=>'NAME', "from"=>0, "to"=>4, "type"=>'TYPE' ),
+            array( "reports_annotation_id"=>100, "lemma"=>'lemma annotacji 100', "id"=>12346, "group_id"=>1, "name"=>'NAME', "from"=>5, "to"=>13, "type"=>'TYPE' ),
         );
         $extractorObj->setExtractorReturnedData('lemmas',$extractorData);
 
@@ -128,6 +128,7 @@ private function checkFiles($report_id,$disambOnly,$tagging_method,$reportData,$
 
         $expectedBaseFileName = $this->virtualDir->url().'/'.str_pad($report_id,8,'0',STR_PAD_LEFT);
         $scl=new SimpleCcl($reportData,$tagging_method,$disambOnly);
+        $scl->addLemmas($extractorData);
 
         //checkConllFile
         $expectedContent = $scl->toCONLL();
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part6_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part6_Test.php
index f8c16232..a7aa7439 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part6_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part6_Test.php
@@ -50,8 +50,8 @@ private function export_document($disamb_only,$tagging_method)
         $extractorObj = new MockedExtractor($extractorParameters["FlagName"],$extractorParameters["FlagValues"],$extractorParameters["Name"],$extractorParameters["Parameters"]);
         // $lemmas = DbReportAnnotationLemma::getLemmasBySubsets(array($report_id), $params);
         $extractorData = array(
-            array( "reports_annotation_id"=>1, "lemma"=>'lemma annotacji 1' ),
-            array( "reports_annotation_id"=>100, "lemma"=>'lemma annotacji 100'),
+            array( "reports_annotation_id"=>1, "lemma"=>'lemma annotacji 1', "id"=>12345, "group_id"=>1, "name"=>'NAME', "from"=>0, "to"=>4, "type"=>'TYPE' ),
+            array( "reports_annotation_id"=>100, "lemma"=>'lemma annotacji 100', "id"=>12346, "group_id"=>1, "name"=>'NAME', "from"=>5, "to"=>13, "type"=>'TYPE' ),
         );
         $extractorObj->setExtractorReturnedData('lemmas',$extractorData);
 
@@ -128,6 +128,7 @@ private function checkFiles($report_id,$disambOnly,$tagging_method,$reportData,$
 
         $expectedBaseFileName = $this->virtualDir->url().'/'.str_pad($report_id,8,'0',STR_PAD_LEFT);
         $scl=new SimpleCcl($reportData,$tagging_method,$disambOnly);
+        $scl->addLemmas($extractorData);
 
         //checkConllFile
         $expectedContent = $scl->toCONLL();
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part_Test.php
index 9ab57b8f..c47613ed 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part_Test.php
@@ -2,9 +2,8 @@
 
 use org\bovigo\vfs\vfsStream; // for vfsStream
 mb_internal_encoding("UTF-8");
-require_once("CorpusExporterTest.php");
 
-class CorpusExporter_part_Test extends CorpusExporterTest {
+class CorpusExporter_part_Test extends PHPUnit_Framework_TestCase {
 
     private $virtualDir = null;
 
@@ -25,7 +24,7 @@ public function test_export_document()
         $lists = array();
         $subcorpora = array();
         //String tagging method from ['tagger', 'final', 'final_or_tagger', 'user:{id}']
-        $tagging_method = '';
+        $tagging_method = 'tagger';
 
         
         $dbEmu = new DatabaseEmulator();
@@ -87,10 +86,16 @@ public function test_export_document()
             'SELECT * FROM reports WHERE id = ?',
             $allReturnedDataRows );
 
-        $emptyDataRows = array();
+        $emptyCorpora = array( 'ext'=>NULL ); // must have 'ext' field
         $dbEmu->setResponse("fetch_rows",
             'SELECT * FROM corpora WHERE id = ?',
-            $emptyDataRows );
+            array($emptyCorpora)
+            );
+        $formatName = 'xml'; // for format_id=1
+        $dbEmu->setResponse("fetch_one",
+            'SELECT format FROM reports_formats WHERE id = ?',
+            $formatName   // fetch_one - only string without array packing
+            );
 
         global $db;
         $db = $dbEmu;
@@ -113,7 +118,7 @@ public function test_export_document()
         $expectedIniContent = "[document]\nid = 1\ndate = 2022-12-16\ntitle = tytuł\nsource = source\nauthor = author\ntokenization = tokenization\nsubcorpus = ";
         $resultIniFile = file_get_contents($expectedBaseFileName.'.ini');
         $this->assertEquals($expectedIniContent,$resultIniFile);
-        $expectedJsonContent = "{\n    \"chunks\": [\n        [\n            [\n                {\n                    \"order_id\": 0,\n                    \"token_id\": 0,\n                    \"orth\": \"e\",\n                    \"ctag\": null,\n                    \"from\": 1,\n                    \"to\": 1,\n                    \"annotations\": [],\n                    \"relations\": []\n                }\n            ]\n        ]\n    ],\n    \"relations\": [],\n    \"annotations\": []\n}";
+        $expectedJsonContent = "{\n    \"chunks\": [\n        [\n            [\n                {\n                    \"order_id\": 0,\n                    \"token_id\": 0,\n                    \"orth\": \"e\",\n                    \"ctag\": \"\",\n                    \"from\": 1,\n                    \"to\": 1,\n                    \"annotations\": [],\n                    \"relations\": []\n                }\n            ]\n        ]\n    ],\n    \"relations\": [],\n    \"annotations\": []\n}";
         $resultJsonFile = file_get_contents($expectedBaseFileName.'.json');
         $this->assertEquals($expectedJsonContent,$resultJsonFile);
         $expectedTxtContent = $content;
diff --git a/phpunit/tests/engine/include/structs/CclDocumentTest.php b/phpunit/tests/engine/include/structs/CclDocumentTest.php
index adb00c08..d589b549 100644
--- a/phpunit/tests/engine/include/structs/CclDocumentTest.php
+++ b/phpunit/tests/engine/include/structs/CclDocumentTest.php
@@ -43,7 +43,7 @@ public function test_setAnnotationProperty_setInternalErrorOnNull() {
 
     public function test_setAnnotationProperty_setInternalErrorOnEmptyArray() {
 
-        $annotation_property = array();
+        $annotation_property = array("from"=>null);
 
         $cclDocument = new CclDocument();
         $cclDocument->setAnnotationProperty($annotation_property);
@@ -105,7 +105,7 @@ public function testAddLemmaWithNullParameterSetsError() {
 
     public function testAddLemmaWithEmptyParameterSetsError() {
 
-        $annotation_lemma = array(); // should have 'from' and 'to' field
+        $annotation_lemma = array('from'=>null); // should have 'from' and 'to' field
         $ccl = new CclDocument();
         $ccl->setAnnotationLemma($annotation_lemma);
         $this->assertEquals(1,count($ccl->errors)); // is sth in errors table
@@ -119,7 +119,7 @@ public function testAddLemmaWithEmptyParameterSetsError() {
     public function testLemmaWithoutFromSetsError() {
 
         $from = 1; $to = 3;
-        $annotation_lemma = array('to'=>$to,'type'=>'TYP');
+        $annotation_lemma = array('to'=>$to,'type'=>'TYP', 'from'=>null);
 
         $mockToken = $this->getMockBuilder(CclToken::class)
             -> setMethods(['setAnnotationLemma'])                                           -> getMock();
@@ -166,7 +166,7 @@ public function testLemmaWithoutFromMatchesAnyTokenSetsError() {
     public function testLemmaWithoutToSetsError() {
 
         $from = 1; $to = 3;
-        $annotation_lemma = array('from'=>$from,'type'=>'TYP');
+        $annotation_lemma = array('from'=>$from,'type'=>'TYP', 'to'=>null);
 
         $mockToken = $this->getMockBuilder(CclToken::class)
             -> setMethods(['setAnnotationLemma'])
@@ -340,7 +340,7 @@ public function testSetannotationWithNullParameterSetsError() {
 
     public function testSetannotationWithAnnotationWithoutFromSetsError() {
 
-        $annotation = array('type'=>"TYP", 'to'=>3, 'value'=>'VALUE', 'name'=>'NAME' );
+        $annotation = array('type'=>"TYP", 'to'=>3, 'value'=>'VALUE', 'name'=>'NAME', 'from'=>null );
 		// must be token in $ccl
 		$ccl = $this->generateProperCclToSetAnnotationTests(1,3);
 
@@ -379,7 +379,7 @@ public function testSetannotationForProperDataCallsTokensSetannotation() {
         $mockDocument->addToken($mockToken);
 
         $expectedTokenProp = array(
-            "sense:".$annotation["name"]=>$annotation['value']
+            "sense:".$annotation["type"]=>$annotation['value']
         );
         $mockDocument->setAnnotation($annotation);
         $this->assertEquals(0,count($mockDocument->errors)); // no errors
@@ -394,7 +394,7 @@ public function testSetannotationForProperDataCallsTokensSetannotation() {
 	public function testSetannotationForProperDataSetPropInTokenAndTypeInChannels() {
 
         $from = 1; $to = 3;
-        $annotation = array( 'type'=>"TYP", 'from'=>1, 'to'=>3, 'value'=>'VALUE', 'name'=>'NAME' );
+        $annotation = array( 'type'=>"TYP", 'from'=>1, 'to'=>3, 'value'=>'VALUE', 'name'=>'NAME', 'id'=>'ID' );
         // must be token in proper range in $ccl
         $ccl = $this->generateProperCclToSetAnnotationTests($from,$to);
 
@@ -403,7 +403,7 @@ public function testSetannotationForProperDataSetPropInTokenAndTypeInChannels()
         $this->assertEquals(0,count($ccl->errors)); // no errors
         // annotation.value is direct set to prop table in token
         $expectedTokenProp = array(
-            "sense:".$annotation["name"]=>$annotation['value']
+            "sense:".$annotation["type"]=>$annotation['value']
         );
         // in token in main ccl table
         $this->assertEquals($expectedTokenProp,$ccl->tokens[0]->prop);
diff --git a/phpunit/tests/engine/include/structs/CclTokenTest.php b/phpunit/tests/engine/include/structs/CclTokenTest.php
index c24a77f2..b58288c1 100644
--- a/phpunit/tests/engine/include/structs/CclTokenTest.php
+++ b/phpunit/tests/engine/include/structs/CclTokenTest.php
@@ -79,7 +79,7 @@ public function testNullLemmaSetsPropForLemmaSuffixToNull() {
 
     public function testEmptyLemmaSetsPropForLemmaSuffixToNull() {
 
-        $annotation_lemma = array();
+        $annotation_lemma = array("type"=>null, "lemma"=>null);
 
         $token = new CclToken();
         $result = $token->setAnnotationLemma($annotation_lemma);
@@ -93,7 +93,7 @@ public function testEmptyLemmaSetsPropForLemmaSuffixToNull() {
     public function testLemmaWithoutTypeSetsPropForLemmaSuffix() {
 
         $lemmaText = "LEMMA";
-        $annotation_lemma = array( 'lemma'=>$lemmaText );
+        $annotation_lemma = array( 'lemma'=>$lemmaText, "type"=>null );
 
         $token = new CclToken();
         $result = $token->setAnnotationLemma($annotation_lemma);
@@ -108,7 +108,7 @@ public function testLemmaWithoutTypeSetsPropForLemmaSuffix() {
     public function testLemmaWithoutLemmaTextSetsPropWithLemmaToNull() {
 
         $lemmaType = "TYP"; 
-        $annotation_lemma = array( 'type'=>$lemmaType );
+        $annotation_lemma = array( 'type'=>$lemmaType, "lemma"=>null );
 
         $token = new CclToken();
         $result = $token->setAnnotationLemma($annotation_lemma);
@@ -139,7 +139,7 @@ public function testSetAnnotationLemmaSetsPropWithLemmaSuffix() {
     public function testSetannotationWithoutTypeFieldWorksAsNonSense() {
 
         $id=10;
-        $annotation = array( 'id'=>$id, 'value'=>array(1,2,3));
+        $annotation = array( 'id'=>$id, 'value'=>array(1,2,3), "type"=>null );
         $parentChannels = null;
 
         $token = new CclToken();
diff --git a/phpunit/tests/engine/include/utils/CReportContentTest.php b/phpunit/tests/engine/include/utils/CReportContentTest.php
index 906c2e31..3ef8c16b 100644
--- a/phpunit/tests/engine/include/utils/CReportContentTest.php
+++ b/phpunit/tests/engine/include/utils/CReportContentTest.php
@@ -8,7 +8,7 @@ class CReportContentTest extends PHPUnit_Framework_TestCase
 
     public function test_getHtmlStr_returnsHtmlStr2Object_onEmptyArray() {
 
-        $testReport = array();
+        $testReport = array('content'=>null, 'format'=>null);
         $result = ReportContent::getHtmlStr($testReport);
         $this->assertInstanceOf('HtmlStr2',$result);
         
@@ -16,7 +16,7 @@ public function test_getHtmlStr_returnsHtmlStr2Object_onEmptyArray() {
 
     public function test_getHtmlStr_returnsHtmlStr2Object_onArrayWoFormat() {
 
-        $testReport = array("content"=>$this->testContent);       
+        $testReport = array("content"=>$this->testContent, 'format'=>null);       
         $result = ReportContent::getHtmlStr($testReport);
         $this->assertInstanceOf('HtmlStr2',$result);
 
diff --git a/phpunit/tests/engine/include/writers/CCclWriterTest.php b/phpunit/tests/engine/include/writers/CCclWriterTest.php
index 3dcf33ef..b57258e7 100644
--- a/phpunit/tests/engine/include/writers/CCclWriterTest.php
+++ b/phpunit/tests/engine/include/writers/CCclWriterTest.php
@@ -403,7 +403,7 @@ public function testCclInCclModeExportsAllTokensFields() {
         $this->assertEquals($tokenPropValue,$prop);
 		// lexeme <lex disamb="1"><base>base</base><ctag>ctag</ctag></lex>
 		$lexeme = $tok->{'lex'};
-		$this->assertEquals('',$lex);
+        $this->assertEquals('',$lexeme);
 		$this->assertEquals('1',$this->getXmlAttribute($lexeme,'disamb'));
 		$this->assertEquals($lexBase,$lexeme->{'base'});
 		$this->assertEquals($lexCtag,$lexeme->{'ctag'});
@@ -470,7 +470,7 @@ public function testCclInCclrelModeExportsAllTokensAndRelationsFields() {
         $this->assertEquals($tokenPropValue,$prop);
         // lexeme <lex disamb="1"><base>base</base><ctag>ctag</ctag></lex>
         $lexeme = $tok->{'lex'};
-        $this->assertEquals('',$lex);
+        $this->assertEquals('',$lexeme);
         $this->assertEquals('1',$this->getXmlAttribute($lexeme,'disamb'));
         $this->assertEquals($lexBase,$lexeme->{'base'});
         $this->assertEquals($lexCtag,$lexeme->{'ctag'});

From 0b6ab5914e8af8c326c45a1858683687567d44ce Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Sat, 16 Dec 2023 11:52:39 +0100
Subject: [PATCH 146/154] getReport call twice in document_export - one call
 removed

---
 engine/include/export/CorpusExporter.php              | 11 ++++++++---
 .../include/export/CorpusExporter_part12_Test.php     |  4 ++--
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index 5f937155..c80ef8c9 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -476,6 +476,12 @@ protected function getReportExtById($report_id){
 
     } // getReportExtById()
 
+    protected function getFormatName($format_id) {
+
+        return DbReport::formatName($format_id);
+
+    } // getFormatName()
+
     protected function exportReportContent($report,$file_path_without_ext) {
 
         try {
@@ -485,8 +491,8 @@ protected function exportReportContent($report,$file_path_without_ext) {
             if(!isset($report['format'])){
                 $report['format'] =
                     isset($report['format_id']) && $report['format_id']
-                    ? DbReport::formatName($report['format_id'])
-                    : '' ;
+                    ? $this->getFormatName($report['format_id'])
+                    : 'xml' ;  // default for default format_id=1
             }
             $html = ReportContent::getHtmlStr($report);
         } catch(Exception $ex){
@@ -757,7 +763,6 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
         (new XmlFactory())->exportToXmlAndRelxml($file_path_without_ext,$ccl,$annotations,$relations,$lemmas,$attributes);
 
 		/* Eksport metadanych */
-		$report = $this->getReportById($report_id);
         $this->createIniFile($report,$subcorpora,$file_path_without_ext);
 
 		/* Przypisanie dokumentu do list */
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
index a8d6496a..523280e1 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part12_Test.php
@@ -149,7 +149,7 @@ public function testMinimalParameterForExampleExecution() {
         $ccl = new CclExportDocument($report,$tokens,$tags); 
         $ccl -> setFileName($fileName);
         $mockCorpusExporter 
-            //-> expects($this->once())
+            -> expects($this->once())
             -> method('getReportById')
             -> with($report_id) 
             -> will($this->returnValue($report));
@@ -263,7 +263,7 @@ function($report_id, $params, &$extractor_elements) {
 			-> with($report_id)
 			-> will($this->returnValue($flags));
         // emulacja getReportById - dla generateCcl
-        $mockCorpusExporter -> expects($this->exactly(2)) // call twice now !!!
+        $mockCorpusExporter -> expects($this->once())
             -> method('getReportById')
             -> with($report_id)
             -> will($this->returnValue($report))

From 62a6d4b302cb018ba5e7dcebbc792f8fd0b1c52d Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Sat, 16 Dec 2023 12:37:20 +0100
Subject: [PATCH 147/154] change behavior of export lemma from annotation
 records

---
 engine/include/export/CorpusExporter.php      | 20 +++++++++++++++++++
 .../export/CorpusExporter_part0_Test.php      |  2 +-
 2 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index c80ef8c9..b3ab6d16 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -32,6 +32,24 @@ public static function arrayRemoveNullElements(array $arr) {
         return $arr;
     } // arrayRemoveNullElements()
 
+    /**
+     * Parameter array should be list of subarrays with field <key>=><value> 
+     * We remove all fileds with <key>=='lemma'
+     *
+     * @param $ann - list of associative arrays
+     *
+     * @returns - array given w/o 'lemma' fields
+     */ 
+    private function RemoveLemmaFieldFromAnnotationsList(array $anns) {
+
+        foreach($anns as &$ann) {
+            if(array_key_exists('lemma',$ann))
+                unset($ann['lemma']);
+        }
+        return $anns;
+
+    } // RemoveLemmaFieldFromAnnotationsList()
+
 	/**
 	 * Funkcja parsuje opis ekstraktora danych
      *
@@ -147,6 +165,8 @@ protected function parse_extractor($description){
 					// $params -- annotations_set_ids, $stages
 					$annotations = DbAnnotation::getReportAnnotations($report_id,
 							$params["user_ids"], $params["annotation_set_ids"], $params["annotation_subset_ids"], null, $params["stages"]);
+                    // we don't want lemma field in full annotation records
+                    $annotations = $this->RemoveLemmaFieldFromAnnotationsList($annotations);
 					if ( is_array($annotations) ) {
 						$elements['annotations'] = array_merge($elements['annotations'], $annotations);
 					}
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php
index 4809620a..42780d2a 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part0_Test.php
@@ -140,7 +140,7 @@ public function test_parse_extractor()
  "type"                     =>'chunk_np',
  "group_id"                 =>7,
  "annotation_subset_id"     =>22,
- "lemma"                    =>null,
+ //"lemma"                    =>null, - this is removed by custom extractor
  "login"                    =>'anna.j.koch',
  "screename"                =>'anna.j.koch'
                                     );

From 8311b9306d2678528cfa3026fc11d609a92a2059 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Mon, 18 Dec 2023 10:54:54 +0100
Subject: [PATCH 148/154] add lemmas param do JSON generate method

---
 engine/include/export/ConllAndJsonFactory.php | 41 ++++++++-
 engine/include/export/CorpusExporter.php      |  2 +-
 .../export/ConllAndJsonFactoryTest.php        | 90 ++++++++++++++-----
 3 files changed, 109 insertions(+), 24 deletions(-)

diff --git a/engine/include/export/ConllAndJsonFactory.php b/engine/include/export/ConllAndJsonFactory.php
index 127d70d6..6cbd7038 100644
--- a/engine/include/export/ConllAndJsonFactory.php
+++ b/engine/include/export/ConllAndJsonFactory.php
@@ -2,7 +2,42 @@
 
 class ConllAndJsonFactory {
 
-    protected function makeConllAndJsonExportData($ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id) {
+    /**
+     * make index of $lemma list by 'report_annotation_id' field
+     * field 'lemma' is added if exists
+     *
+     * @param $lemma - list of lemma records
+     *
+     * @return associative array of
+     *      <report_annotation_id> => [ 'idx'=>.., 'lemma'=>.. ]
+     **/
+    protected function makeLemmaCache(array $lemma) {
+
+        $lemmaCache = array();
+        for($i=0;$i<count($lemma);$i++) {
+            if(isset($lemma[$i]['report_annotation_id'])) {
+                $lemmaCache[$lemma[$i]['report_annotation_id']] =
+                    array(  'idx'=>$i, 
+                            'lemma'=> isset($lemma[$i]['lemma']) 
+                                        ? $lemma[$i]['lemma'] 
+                                        : null // lemma record with no 'lemma' field
+                    );
+            }
+        } 
+        return $lemmaCache;
+
+    } // makeLemmaCache()
+
+    protected function makeConllAndJsonExportData($ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id, $lemmas) {
+
+        // create index for $lemmas
+        $lemmas_by_annotation_id = $this->makeLemmaCache($lemmas);
+        // add only lemmas pointed by extractor to proper annotations
+        foreach($annotations as &$ann) {
+            if(array_key_exists($ann['id'],$lemmas_by_annotation_id)) {
+                $ann['lemma']=$lemmas_by_annotation_id[$ann['id']]['lemma'];
+            }
+        }
 
         /**
          * Create a cache for 'token from' to boost processing
@@ -153,9 +188,9 @@ protected function makeConllAndJsonExportData($ccl, $tokens, $relations, $annota
 
     } // makeConllAndJsonExportData()
 
-    public function exportToConllAndJson($file_path_without_ext, $ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id)
+    public function exportToConllAndJson($file_path_without_ext, $ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id, $lemmas)
     {
-        list($conll,$json_builder) = $this->makeConllAndJsonExportData($ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id);
+        list($conll,$json_builder) = $this->makeConllAndJsonExportData($ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id, $lemmas);
         $fw = new FileWriter();
         $fw->writeTextToFile($file_path_without_ext . ".conll",$conll);
         $fw->writeJSONToFile($file_path_without_ext . ".json",$json_builder);
diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index b3ab6d16..f1a6e641 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -777,7 +777,7 @@ protected function export_document($report_id, $extractors, $disamb_only, &$extr
         $file_path_without_ext = $output_folder . "/" . $ccl->getFileName();
 
         /* Wygeneruj CONLL i JSON */
-		(new ConllAndJsonFactory())->exportToConllAndJson($file_path_without_ext, $ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id);
+		(new ConllAndJsonFactory())->exportToConllAndJson($file_path_without_ext, $ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id, $lemmas);
 
         /* Wygeneruj xml i rel.xml */
         (new XmlFactory())->exportToXmlAndRelxml($file_path_without_ext,$ccl,$annotations,$relations,$lemmas,$attributes);
diff --git a/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php b/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
index e0498adf..3e1f2762 100644
--- a/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
+++ b/phpunit/tests/engine/include/export/ConllAndJsonFactoryTest.php
@@ -290,6 +290,7 @@ public function testEmptyReportMakesEmptyDataToWrite() {
         $annotations = array();
         $tokens_ids = array();
         $annotations_by_id = array();
+        $lemmas = array();
 		// mocked $ccl argument for empty report
         $mockChunk = $this->getMockBuilder(CclChunk::class)->getMock();
         $mockChunk->sentences = array();
@@ -298,7 +299,7 @@ public function testEmptyReportMakesEmptyDataToWrite() {
         $ccl = $mockCclDocument;
     
         // invoke tested method
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id,$lemmas);
         
         // check results
 		$this->assertEquals($this->getExpectedConllHeader(),$conll);
@@ -315,6 +316,7 @@ public function testOneEmptySentenceCclReportMakesLinesWithNoData() {
         $annotations = array();
         $tokens_ids = array();
         $annotations_by_id = array();
+        $lemmas = array();
         // mocked $ccl argument for empty report
         $mockSentence = $this->getMockBuilder(CclSentence::class)->getMock();
         $mockSentence->tokens = array();
@@ -325,7 +327,7 @@ public function testOneEmptySentenceCclReportMakesLinesWithNoData() {
         $ccl = $mockCclDocument;
 
         // invoke tested method
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id,$lemmas);
 
         // check results
         //  empty sentence generates one empty line in export CONLL
@@ -347,6 +349,7 @@ public function testOneEmptyTokenCclReportMakesTokenWithEmptyData() {
         $annotations = array();
         $tokens_ids = array();
         $annotations_by_id = array();
+        $lemmas = array();
         // mocked $ccl argument for empty report
         $mockToken = $this->getMockBuilder(CclToken::class)->getMock();
         $mockSentence = $this->getMockBuilder(CclSentence::class)->getMock();
@@ -358,7 +361,7 @@ public function testOneEmptyTokenCclReportMakesTokenWithEmptyData() {
         $ccl = $mockCclDocument;
 
         // invoke tested method
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id,$lemmas);
 
         // check results
         //  empty token generates row with empty data in export CONLL
@@ -386,6 +389,7 @@ public function testOneTokenCclMakesNonemptyDataToWrite() {
         $annotations = array();
         $tokens_ids = array();
         $annotations_by_id = array();
+        $lemmas = array();
         // mocked $ccl argument for empty report
         $mockToken = $this->makeMockToken(0,"To",array(),0,1);
         $mockSentence = $this->getMockBuilder(CclSentence::class)->getMock();
@@ -397,7 +401,7 @@ public function testOneTokenCclMakesNonemptyDataToWrite() {
         $ccl = $mockCclDocument;
 
         // invoke tested method
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id,$lemmas);
 
         // check results
         //  simple token generates row with its data in export CONLL
@@ -422,9 +426,10 @@ public function testAllDataPlacesToDataConllAndJsonStructures() {
         $annotations_by_id = $this->generateAnnotation_By_IdTestData(False,True,False,True);
         $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
         $relations = $this->generateRelationsTestData();
+        $lemmas = array();
 
 		// invoke tested method
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id,$lemmas);
 
         // check results
 		$expectedConll = $this->getExpectedConll();
@@ -471,9 +476,10 @@ public function testDocumentWithoutTokenizationPlaceDataToJsonAndConllArray() {
         $relations = array();
         $annotations = array();
         $annotations_by_id = array();
+        $lemmas = array();
 
 		// invoke tested method
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id,$lemmas);
 
         // check results
         $this->assertEquals($this->getExpectedConll(),$conll);
@@ -485,7 +491,7 @@ public function testDocumentWithoutTokenizationPlaceDataToJsonAndConllArray() {
 		// with tokens without annotations there are all the same as above
 
 		// invoke tested method
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id,$lemmas);
 
 		$this->assertEquals($this->getExpectedConll(),$conll);
 		$this->assertEquals($expectedJson,$json_builder);
@@ -500,9 +506,10 @@ public function testGeneralAnnotationFieldsPlacedToJsonAndConllArray() {
         $annotations_by_id = $this->generateAnnotation_By_IdTestData(); // default annotation with: all extractors fields, lemma & type attribute
         $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
         $relations = $this->generateRelationsTestData();
+        $lemmas = array();
 
         // invoke tested method
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id,$lemmas);
 
         // check results
         $expectedConll = $this->getExpectedConll();
@@ -544,19 +551,20 @@ public function testGeneralAnnotationFieldsPlacedToJsonAndConllArray() {
     public function testLemmaAdsNotChangesConll() {
 
         $relations = $this->generateRelationsTestData();
+        $lemmas = array();
         // args for call without lemma
 		$LemmaExists = False;
         $annotations_by_id = $this->generateAnnotation_By_IdTestData(True,True,$LemmaExists);
         $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
         // invoke tested method
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id,$lemmas);
 
         // args for call with lemma
         $LemmaExists = True;
         $annotations_by_id = $this->generateAnnotation_By_IdTestData(True,True,$LemmaExists);
         $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
         // invoke tested method
-        list($conll_wL,$json_builder_wL) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+        list($conll_wL,$json_builder_wL) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id,$lemmas);
 
 		// conll not changed after add lemma:
 		$this->assertEquals($conll,$conll_wL);
@@ -566,19 +574,20 @@ public function testLemmaAdsNotChangesConll() {
     public function testLemmaContentChangesNullInLemmaFieldInJson() {
 
         $relations = $this->generateRelationsTestData();
+        $lemmas = array();
         // args for call without lemma
         $LemmaExists = False;
         $annotations_by_id = $this->generateAnnotation_By_IdTestData(True,False,$LemmaExists);
         $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
         // invoke tested method
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id,$lemmas);
 
         // args for call with lemma
         $LemmaExists = True;
         $annotations_by_id = $this->generateAnnotation_By_IdTestData(True,False,$LemmaExists);
         $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
         // invoke tested method
-        list($conll_wL,$json_builder_wL) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+        list($conll_wL,$json_builder_wL) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id,$lemmas);
 
         // json results after add lemma:
 		//   field 'lemma' changes from null to lemma text
@@ -592,10 +601,11 @@ public function testTokensWithoutAnnotationHasOAnntag() {
 
 		// args for call w/o annotations
         $relations = array();
+        $lemmas = array();
         $annotations_by_id = array();
         $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
         // invoke tested method
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id,$lemmas);
 		
         $expectedAnnTags = "O";
 		$fromLine = 3;
@@ -608,12 +618,13 @@ public function testFirstTokenIntoAnnotationHasBAnntag() {
 
 		$annotationTokenLine = 3;
 		$relations = array();
+        $lemmas = array();
         // call args for annotations without "name" field
   		$fieldsForAnnotationIdExtractorExists = False;
         $annotations_by_id = $this->generateAnnotation_By_IdTestData(True,$fieldsForAnnotationIdExtractorExists);
         $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
         // invoke tested method
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id,$lemmas);
 
         $expectedAnnTags = "B-".'nam_adj'; // annotation type glued
         $annTags = $this->extractAnntagsFromConllLines($conll,$annotationTokenLine);
@@ -624,7 +635,7 @@ public function testFirstTokenIntoAnnotationHasBAnntag() {
         $annotations_by_id = $this->generateAnnotation_By_IdTestData(True,$fieldsForAnnotationIdExtractorExists);
         $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
         // invoke tested method
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id,$lemmas);
 
         $expectedAnnTags = "B-".'nam_adj'; // annotation type glued
         $annTags = $this->extractAnntagsFromConllLines($conll,$annotationTokenLine);
@@ -635,6 +646,7 @@ public function testFirstTokenIntoAnnotationHasBAnntag() {
 	public function testNextTokensIntoAnnotationHasIAnntag() {
 
         $relations = array();
+        $lemmas = array();
         // call args for annotations without "name" field
         $fieldsForAnnotationIdExtractorExists = False;
         $annotations_by_id = $this->generateAnnotation_By_IdTestData(True,$fieldsForAnnotationIdExtractorExists);
@@ -642,7 +654,7 @@ public function testNextTokensIntoAnnotationHasIAnntag() {
 		$annotations_by_id[1]['to']=14;
         $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
         // invoke tested method
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id, $lemmas);
 
 		$expectedAnnTags = "I-".'nam_adj'; // annotation type glued
 		// for tokens in lines 4 and 5
@@ -656,7 +668,7 @@ public function testNextTokensIntoAnnotationHasIAnntag() {
         $annotations_by_id[1]['to']=14;
         $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
         // invoke tested method
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id,$lemmas);
 
         $expectedAnnTags = "I-nam_adj";
         // for tokens in lines 4 and 5
@@ -668,6 +680,7 @@ public function testNextTokensIntoAnnotationHasIAnntag() {
 	public function testTokenInto2AnnotationsHasJoinedAnntags() {
 
 		$relations = array(); // no relations
+        $lemmas = array(); // no lemmas
         // call args for two annotations on this same token
         $annotations_by_id = $this->generateAnnotation_By_IdTestData();
 		// copy 1 anntotation to second one on this same <from,to>
@@ -676,7 +689,7 @@ public function testTokenInto2AnnotationsHasJoinedAnntags() {
 		$annotations_by_id[2]['type'] = '2nd'; // change ann type name 
         $annotations = $this->generateAnnotationsFromAnnotations_By_Id($annotations_by_id);
         // invoke tested method
-        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id);
+        list($conll,$json_builder) = $this->protectedMethod->invoke(new ConllAndJsonFactory(),$this->ccl,$this->tokens,$relations,$annotations,$this->tokens_ids,$annotations_by_id,$lemmas);
 
         // token in line 3 should have two annTags
 		$expectedAnnTags = "B-nam_adj:B-2nd";
@@ -685,7 +698,7 @@ public function testTokenInto2AnnotationsHasJoinedAnntags() {
 	} // testTokenInto2AnnotationsHasJoinedAnntags() 
 
 /* class ConllAndJsonFactory has only 1 function
-    function exportToConllAndJson($file_path_without_ext, $ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id)
+    function exportToConllAndJson($file_path_without_ext, $ccl, $tokens, $relations, $annotations, $tokens_ids, $annotations_by_id, $lemmas)
 */
 
 	public function testDeliveredDataAreWrittenToFiles() {
@@ -699,6 +712,7 @@ public function testDeliveredDataAreWrittenToFiles() {
         $annotations = array();
         $tokens_ids = array();
         $annotations_by_id = array();
+        $lemmas = array();
 
         // self-mocking another method
         $mockedMethodNamesList = array('makeConllAndJsonExportData');
@@ -711,7 +725,7 @@ public function testDeliveredDataAreWrittenToFiles() {
             -> will($this->returnValue($mockedResult));
         
 		// metoda exportToConllAndJson() powinna zachować obsługę oryginalną
-        $mock->exportToConllAndJson($this->file_path_without_ext,$this->ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id);
+        $mock->exportToConllAndJson($this->file_path_without_ext,$this->ccl,$tokens,$relations,$annotations,$tokens_ids,$annotations_by_id,$lemmas);
 
         $expectedConll = $conll;
         $conllFileName = $this->file_path_without_ext.".conll";
@@ -727,6 +741,42 @@ public function testDeliveredDataAreWrittenToFiles() {
 
 	} // testDeliveredDataAreWrittenToFiles
 
+// protected function makeLemmaCache(array $lemma) 
+
+    public function testMakelemmacacheReturnsEmptyIndexOnEmptyArray() {
+
+        $lemmas = array();
+
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject(ConllAndJsonFactory::class,'makeLemmaCache');
+
+        $result = $protectedMethod->invokeArgs(new ConllAndJsonFactory(),array($lemmas));
+
+        $this->assertEquals(array(),$result);
+
+    } // testMakelemmacacheReturnsEmptyIndexOnEmptyArray() 
+
+    public function testMakelemmacacheOnFullDataMakesIndexArray() {
+
+        $lemmas = array(
+                ['report_annotation_id'=>5, 'lemma'=>'lemma5'], // [0]
+                ['report_annotation_id'=>2, 'lemma'=>'lemma2'], // [1]
+                [ 'lemma'=>'lemma_no_ann_id'], // no annotation id field
+                ['report_annotation_id'=>7, ], // [3] no lemma field
+            );
+
+        $protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject(ConllAndJsonFactory::class,'makeLemmaCache');
+
+        $result = $protectedMethod->invokeArgs(new ConllAndJsonFactory(),array($lemmas));
+
+        $expectedResult = array(
+            2=>['idx'=>1, 'lemma'=>'lemma2'],
+            5=>['idx'=>0, 'lemma'=>'lemma5'],
+            7=>['idx'=>3, 'lemma'=>null],
+        );
+        $this->assertEquals($expectedResult,$result);
+
+    } // testMakelemmacacheOnFullDataMakesIndexArray()
+
 } // ConllAndJsonFactoryTest class
 
 ?>

From 753d4df524bcd4478db2e4139d464714742a3def Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Mon, 18 Dec 2023 11:38:32 +0100
Subject: [PATCH 149/154] no lemma export if coresponding annotations doesn't
 exists

---
 engine/include/export/CclExportDocument.php   |   5 +-
 .../export/CorpusExporter_part13_Test.php     | 449 ++++++++++++++++++
 .../export/CorpusExporter_part5_Test.php      |   3 +-
 .../export/CorpusExporter_part6_Test.php      |   3 +-
 4 files changed, 457 insertions(+), 3 deletions(-)
 create mode 100644 phpunit/tests/engine/include/export/CorpusExporter_part13_Test.php

diff --git a/engine/include/export/CclExportDocument.php b/engine/include/export/CclExportDocument.php
index 4dbf5294..cd492fd0 100644
--- a/engine/include/export/CclExportDocument.php
+++ b/engine/include/export/CclExportDocument.php
@@ -213,7 +213,10 @@ protected function setAnnotationsAndRelations(&$annotations, &$relations){
     public function setCclProperties(&$annotations, &$relations, $lemmas, $attributes ) {
 
         $this->setAnnotationsAndRelations($annotations, $relations);
-        $this->setAnnotationLemmas($lemmas);
+        // Lemmas will be added only if annotations are too
+        if(is_array($annotations) && (count($annotations)>0)) {
+            $this->setAnnotationLemmas($lemmas);
+        }
         $this->setAnnotationProperties($attributes);
 
     } // setCclProperties()
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part13_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part13_Test.php
new file mode 100644
index 00000000..4d12489d
--- /dev/null
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part13_Test.php
@@ -0,0 +1,449 @@
+<?php
+
+use org\bovigo\vfs\vfsStream; // for vfsStream
+mb_internal_encoding("UTF-8");
+
+class CorpusExporter_part13_Test extends PHPUnit_Framework_TestCase
+{
+    // tests with lemma fields sets    
+
+    private $virtualDir = null;
+
+    protected function setUp() {
+
+        $this->virtualDir = vfsStream::setup('root',null,[]);
+        $this->commonDataSetup();
+
+    } // setUp()
+
+    private function emptyExtractorData() {
+
+        return array("annotations"=>array(), "relations"=>array(), "lemmas"=>array(), "attributes"=>array());
+
+    } // emptyExtractorData
+
+    private function reportData($report_id=1) {
+
+        // full filled record
+        return array( "id"=>$report_id,"corpora"=>1,"date"=>'DATA',"title"=>'TITLE',"source"=>'SOURCE',"author"=>'AUTHOR',"content"=>'To jest duże okno.',"type"=>1,"status"=>1,"user_id"=>1,"subcorpus_id"=>1,"tokenization"=>'TOKENIZATION',"format_id"=>'',"lang"=>'LANG',"filename"=>'FILENAME',"parent_report_id"=>1,"deleted"=>0);
+    // "format"='' generate as default format_id=1 format = 'xml'
+
+    } // reportData()
+
+    private function lemmaData() {
+
+        return array ( 'report_annotation_id' => '2', 'lemma' => 'lemat dodany do okno', 'id' => '2', 'report_id' => '1', 'type_id' => '119', 'type' => 'nam_oth', 'group' => '1', 'from' => '10', 'to' => '13', 'text' => 'okno', 'user_id' => NULL, 'creation_time' => '2022-10-03 08:34:21', 'stage' => 'final', 'source' => 'user', 'annotation_type_id' => '119', 'name' => 'nam_oth', 'description' => 'Nazwy własne niezaklasyfikowane do pozostałych grup (w przypadku braku bardziej szczegółowego typu anotacji w obrębie nam_oth).', 'group_id' => '1', 'annotation_subset_id' => '8', 'level' => '0', 'short_description' => '', 'css' => 'background: lightgreen; border: 1px dashed red; border-bottom: 2px solid red;', 'cross_sentence' => '0', 'shortlist' => '0', 'annotation_id' => NULL, 'annotation_attribute_id' => NULL, 'value' => NULL );
+
+    } // lemmaData()
+
+    private function annotationStandardExtractorRecord($report_id=1,$annotation_id=1,$from=6,$to=9,$type='nam_adj') {
+
+        // fullfilled
+        // as generated by annotation_set_id or annotation_subset_id
+        // extractor ( all fields from reports_annotations, 
+        // annotation_types and annotation_id, annotation_attribute_id,
+        // attr_user_id( cast from user_id), prop(cast from value )
+        // from report_annotations_attributes
+        return array( 'id' => $annotation_id, 'report_id' => $report_id, 'type_id' => '360', 'type'=>$type, 'group'=>'1', 'from' => $from, 'to' => $to, 'text' => 'duże', 'user_id' => '1', 'creation_time' => '2022-10-03 08:07:37', 'stage' => 'final', 'source' => 'user', 'annotation_type_id'=>'360', 'name'=>$type, 'description'=>'DESCRIPTION', 'group_id' => '1', 'annotation_subset_id' => '52', 'level'=>0, 'short_description'=>'SHORT_DESCRIPTION', 'css'=>'CSS', 'cross_sentence'=>'CROSS_SENTENCE', 'shortlist'=>'SHORTLIST', 'annotation_id'=>$annotation_id, 'annotation_attribute_id'=>721, 'attr_user_id'=>'1', 'prop'=>'ATRYBUT'
+        );
+
+    } // annotationStandardRecord
+
+    private function annotationCustomExtractorRecord($report_id=1,$annotation_id=1,$from=6,$to=9,$type='nam_adj',$lemma='LEMMA') {
+
+        // fullfilled
+        // as generated by "annotation=" extractor ( all fields from
+        // reports_annotations_optimized, from annotation_types only
+        // type( cast from name ), group_id, annotation_subset_id, 
+        // lemma from reports_annotations_lemma, from users only
+        // login and screename  
+        return array( 'id' => $annotation_id, 'report_id' => $report_id, 'type_id' => '360', 'from' => $from, 'to' => $to, 'text' => 'duże', 'user_id' => '1', 'creation_time' => '2022-10-03 08:07:37', 'stage' => 'final', 'source' => 'user', 'type'=>$type, 'group_id' => '1', 'annotation_subset_id' => '52', 
+        // 'lemma'=>$lemma, - 'lemma' field is now removed by ekstractor
+        'login'=>'LOGIN', 'screename'=>'SCREENAME'); 
+
+    } // annotationCustomExtractorRecord() 
+
+    private function getMinimalExtractorData($flag_name='flag_short_name',$flag_id=1) {
+            return array( 'name' => 'extractorNAME', "flag_name" => $flag_name, "flag_ids" => array($flag_id), "extractor" => null, "params" => array() );
+
+    } // getMinimalExtractorData()
+
+    private function getTokenData($report_id=1,$token_id=231,$from=6,$to=9) {
+
+        return array( "from"=>$from, "to"=>$to, "orth"=>'duże', "eos"=>false, "token_id"=>$token_id, "report_id"=>$report_id );
+
+    } // getTokenData()
+
+    private function getTagsData($token_id) {
+
+        return array ( "token_tag_id" => "30","token_id"=>$token_id,"disamb"=>"1","ctag_id"=>"25","ctag"=>"CTAG","tagset_id"=>1,"base_id"=>7,"base_text"=>"BASE" );
+
+    } // getTokenData()
+
+    private function commonDataSetup($report_id=1) {
+
+        $this->report_id = $report_id;
+        $flag_name = 'flag_short_name';
+        $flag_id = 1;   // -1,...,5
+        $this->extractors = array( $this->getMinimalExtractorData($flag_name,$flag_id) );
+        $this->disamb_only = true;
+        $this->extractor_stats = array();
+        $this->lists = array();
+        $this->output_folder = $this->virtualDir->url();
+        $this->subcorpora = '';
+        $this->tagging_method = 'tagger';
+        // emulowane dane z bazy danych
+        $flags = array( $flag_name => $flag_id );
+        $report = $this->reportData($report_id);
+        $tokens = array(
+            $this->getTokenData($report_id,231,6,9), $this->getTokenData($report_id,2314,10,13)
+        );
+        $tags_by_tokens = array( 231 => array ( $this->getTagsData(231) ) );          
+
+        $this->mockCorpusExporter = $this->getMockBuilder(CorpusExporter::class)
+            -> disableArgumentCloning()
+            -> setMethods(array(
+                'getFlagsByReportId', // block fetch() error
+                'getTokenByReportId', // block fetch() error
+                'getReportTagsByTokens', // block fetch() error
+                'getReportById', // block fetch() error
+                'getReportExtById', // block fetch() error
+                )) -> getMock();
+        $this->mockCorpusExporter -> expects($this->once())
+            -> method('getTokenByReportId')
+            -> with($report_id)
+            -> will($this->returnValue($tokens)); // block array_column error
+        //  === dodane do generowania lematów
+        // wygenerowne flagi - używane tylko w ekstraktorze
+        $this->mockCorpusExporter -> expects($this->once())
+            -> method('getFlagsByReportId')
+            -> with($report_id)
+            -> will($this->returnValue($flags));
+        // emulacja getReportById - dla generateCcl
+        $this->mockCorpusExporter -> expects($this->once()) 
+            -> method('getReportById')
+            -> with($report_id)
+            -> will($this->returnValue($report))
+        ;
+        // emulacja getReportTagsByTokens - dla generate Ccl
+        $token_ids = array(231,2314); // array_column($tokens, 'token_id')
+        $this->mockCorpusExporter -> expects($this->once())
+            -> method('getReportTagsByTokens')
+            -> with($report_id,$token_ids,$this->disamb_only,$this->tagging_method)
+            -> will($this->returnValue($tags_by_tokens))
+        ;
+  
+        // reflection for acces to private elements
+        $this->protectedMethod = TestAccessTools::createAccessToProtectedMethodOfClassObject($this->mockCorpusExporter,'export_document');
+
+		$this->fileName = str_pad($report_id,8,'0',STR_PAD_LEFT);
+
+    } // commonDataSetup()
+
+// =====
+
+    public function testStandardLemmaExtractorOnlyWritesNoLemmaInExportOutputs()  {
+
+		// Standard extractor lemma_annotation_set_id 
+		//		or lemma_annotation_subset_id only
+        $this->extractors[0]["extractor"] = // set extractor function()
+            function($report_id, $params, &$extractor_elements) {
+                $extractor_elements=  array(
+                    "relations"=>[],
+                    "attributes"=>[],
+                    "annotations" => array(),
+                    "lemmas" => array( $this->lemmaData() ));
+            };
+
+        // tested call
+        $this->protectedMethod->invokeArgs($this->mockCorpusExporter,array($this->report_id,$this->extractors,$this->disamb_only,&$this->extractor_stats,&$this->lists,$this->output_folder,$this->subcorpora,$this->tagging_method));
+
+        // check results in XML file
+        $resultFileName = $this->output_folder.'/'.$this->fileName.".xml";
+        $this->assertTrue(file_exists($resultFileName));
+        $resultFileContent = file_get_contents($resultFileName);
+        // no lemma phrase in export output
+        $lemmaPattern = '@lemma@s';
+        $this->assertEquals(0,preg_match($lemmaPattern,$resultFileContent));
+
+        // check results in JSON file
+        $resultFileName = $this->output_folder.'/'.$this->fileName.".json";
+		$this->assertTrue(file_exists($resultFileName));
+        $resultFileContent = file_get_contents($resultFileName);
+        // no lemma phrase in export output
+        $lemmaPattern = '@lemma@s';
+        $this->assertEquals(0,preg_match($lemmaPattern,$resultFileContent));
+
+     } // testStandardLemmaExtractorOnlyWritesNoLemmaInExportOutputs()
+
+    public function testStandardAnnotationAndLemmaExtractorWritesLemmaInExportOutputs()  {
+
+        // Standard extractor lemma_annotation_set_id         
+        //      or lemma_annotation_subset_id only
+		//		with coresponding annotation
+        $this->extractors[0]["extractor"] = // set extractor function()
+            function($report_id, $params, &$extractor_elements) {
+                $extractor_elements=  array(
+                    "relations"=>[],
+                    "attributes"=>[],
+                    "annotations" => array(
+                        $this->annotationStandardExtractorRecord($report_id,2,10,13,'nam_oth')
+                        ),
+                    "lemmas" => array( $this->lemmaData() ));
+            };
+
+        // tested call
+        $this->protectedMethod->invokeArgs($this->mockCorpusExporter,array($this->report_id,$this->extractors,$this->disamb_only,&$this->extractor_stats,&$this->lists,$this->output_folder,$this->subcorpora,$this->tagging_method));
+
+        // check results in XML file
+        $resultFileName = $this->output_folder.'/'.$this->fileName.".xml";
+        $this->assertTrue(file_exists($resultFileName));
+        $resultFileContent = file_get_contents($resultFileName);
+        // lemat - w pozycji tokenu ( "lemat dodany do okno" )
+        $expectedLemmaLine = '<prop key="nam_oth:lemma">lemat dodany do okno</prop>';
+        $this->assertRegexp('@'.$expectedLemmaLine.'@m',$resultFileContent);
+        // lemat wpisany w tag odpowiadajacej annotacji
+        $expectedAnnWithLemmaLines =
+'<ann chan="nam_oth">2</ann>'.'\s*'.'<prop key="nam_oth:lemma">lemat dodany do okno</prop>';
+        $this->assertRegexp('@'.$expectedAnnWithLemmaLines.'@m',$resultFileContent);
+
+        // check results in JSON file
+        $resultFileName = $this->output_folder.'/'.$this->fileName.".json";
+        $this->assertTrue(file_exists($resultFileName));
+        $resultFileContent = file_get_contents($resultFileName);
+            // in .json format there are not lemma in chunks
+            // only link to annotation
+        // lemat w tabeli annotacji ( "lemat dodany do okno" )
+        $expectedAnnWithLemmaPattern = '@'
+            .'"annotations": '.'.+'        // w sekcji po słowie 'annotations'
+            .'\{.+"from": 10,.+"to": 13,[^\}]*' // w tokenie na poz. 10-13
+                .'"lemma": "lemat dodany do okno"'   // jest wpis o lemacie
+            .'.*\}'.'@s';
+        $this->assertRegexp($expectedAnnWithLemmaPattern,$resultFileContent);
+
+     } // testStandardAnnotationAndLemmaExtractorWritesLemmaInExportOutputs() 
+
+    public function testStandardAnnotationExtractorWritesNoLemmaInExportOutputs() {
+
+        // Standard extractor annotation_set_id or annotation_subset_id only
+        $this->extractors[0]["extractor"] = // set extractor function()
+            function($report_id, $params, &$extractor_elements) {
+                $extractor_elements=  array(
+                    "relations"=>[],
+                    "attributes"=>[],
+                    "annotations" => array(
+                        // standard annotation exports has no lemma fields
+                        $this->annotationStandardExtractorRecord($report_id,1,6,9,'nam_adj'),
+                        $this->annotationStandardExtractorRecord($report_id,2,10,13,'nam_oth')
+                        ),
+                    "lemmas" => array()
+                    //"lemmas" => array( $this->lemmaData() )
+                    );
+            };
+
+        // tested call
+        $this->protectedMethod->invokeArgs($this->mockCorpusExporter,array($this->report_id,$this->extractors,$this->disamb_only,&$this->extractor_stats,&$this->lists,$this->output_folder,$this->subcorpora,$this->tagging_method));
+
+        // check results in XML file
+        $resultFileName = $this->output_folder.'/'.$this->fileName.".xml";
+        $this->assertTrue(file_exists($resultFileName));
+        $resultFileContent = file_get_contents($resultFileName);
+        // no lemma phrase in export output
+        $lemmaPattern = '@lemma@s';
+        $this->assertEquals(0,preg_match($lemmaPattern,$resultFileContent));
+
+        // check results in JSON file
+        $resultFileName = $this->output_folder.'/'.$this->fileName.".json";
+        $this->assertTrue(file_exists($resultFileName));
+        $resultFileContent = file_get_contents($resultFileName);
+        // no lemma phrase in export output
+        $lemmaPattern = '@lemma@s';
+        $this->assertEquals(0,preg_match($lemmaPattern,$resultFileContent));
+
+     }// testStandardAnnotationExtractorWritesNoLemmaInExportOutputs()
+
+    public function testCustomLemmaExtractorOnlyWritesNoLemmaInExportOutputs()  {
+
+        // Custom extractor annotation=lemma_set_id 
+        //      or annotation=lemma_subset_id only
+        $this->extractors[0]["extractor"] = // set extractor function()
+
+            function($report_id, $params, &$extractor_elements) {
+                $extractor_elements=  array(
+                    "relations"=>[],
+                    "attributes"=>[],
+                    "annotations" => array(),
+                    "lemmas" => array( $this->lemmaData() ));
+            };
+
+        // tested call
+        $this->protectedMethod->invokeArgs($this->mockCorpusExporter,array($this->report_id,$this->extractors,$this->disamb_only,&$this->extractor_stats,&$this->lists,$this->output_folder,$this->subcorpora,$this->tagging_method));
+
+        // check results in XML file
+        $resultFileName = $this->output_folder.'/'.$this->fileName.".xml";
+        $this->assertTrue(file_exists($resultFileName));
+        $resultFileContent = file_get_contents($resultFileName);
+        // no lemma phrase in export output
+        $lemmaPattern = '@lemma@s';
+        $this->assertEquals(0,preg_match($lemmaPattern,$resultFileContent));
+
+        // check results in JSON file
+        $resultFileName = $this->output_folder.'/'.$this->fileName.".json";
+        $this->assertTrue(file_exists($resultFileName));
+        $resultFileContent = file_get_contents($resultFileName);
+        // no lemma phrase in export output
+        $lemmaPattern = '@lemma@s';
+        $this->assertEquals(0,preg_match($lemmaPattern,$resultFileContent));
+
+     }// testCustomLemmaExtractorOnlyWritesNoLemmaInExportOutputs
+
+    public function testCustomAnnotationAndLemmaExtractorWritesLemmaInExportOutputs()  {
+
+        // Custom extractor annotation=annotation_set_id;lemma__set_id
+        //      or annotation=annotation_subset_id;lemma_subset_id 
+        //      with coresponding annotation
+        $this->extractors[0]["extractor"] = // set extractor function()
+            function($report_id, $params, &$extractor_elements) {
+                $extractor_elements=  array(
+                    "relations"=>[],
+                    "attributes"=>[],
+                    "annotations" => array(
+                        $this->annotationCustomExtractorRecord($report_id,2,10,13,'nam_oth',"lemat dodany do okno")
+                        ),
+                    "lemmas" => array( $this->lemmaData() ));
+            };
+
+        // tested call
+        $this->protectedMethod->invokeArgs($this->mockCorpusExporter,array($this->report_id,$this->extractors,$this->disamb_only,&$this->extractor_stats,&$this->lists,$this->output_folder,$this->subcorpora,$this->tagging_method));
+
+        // check results in XML file
+        $resultFileName = $this->output_folder.'/'.$this->fileName.".xml";
+        $this->assertTrue(file_exists($resultFileName));
+        $resultFileContent = file_get_contents($resultFileName);
+        // lemat - w pozycji tokenu ( "lemat dodany do okno" )
+        $expectedLemmaLine = '<prop key="nam_oth:lemma">lemat dodany do okno</prop>';
+        $this->assertRegexp('@'.$expectedLemmaLine.'@m',$resultFileContent);
+
+        // lemat wpisany w tag odpowiadajacej annotacji
+        $expectedAnnWithLemmaLines =
+'<ann chan="nam_oth">2</ann>'.'\s*'.'<prop key="nam_oth:lemma">lemat dodany do okno</prop>';
+        $this->assertRegexp('@'.$expectedAnnWithLemmaLines.'@m',$resultFileContent);
+
+        // check results in JSON file
+        $resultFileName = $this->output_folder.'/'.$this->fileName.".json";
+        $this->assertTrue(file_exists($resultFileName));
+        $resultFileContent = file_get_contents($resultFileName);
+        // lemat w pozycji tokena w chunks[]
+            // in .json format there are not lemma in chunks
+            // only link to annotation
+        // lemat w tabeli annotacji ( "lemat dodany do okno" )
+        $expectedAnnWithLemmaPattern = '@'
+            .'"annotations": '.'.+'        // w sekcji po słowie 'annotations'
+            .'\{.+"from": 10,.+"to": 13,[^\}]*' // w tokenie na poz. 10-13
+                .'"lemma": "lemat dodany do okno"'   // jest wpis o lemacie
+            .'.*\}'.'@s';
+        $this->assertRegexp($expectedAnnWithLemmaPattern,$resultFileContent);
+
+     } // testCustomAnnotationAndLemmaExtractorWritesLemmaInExportOutputs() 
+
+    public function testCustomAnnotationExtractorWritesNoLemmaInExportOutputs() {
+
+        // Custom extractor annotation=annotation_set_id 
+		//		or annotation=annotation_subset_id only
+        $this->extractors[0]["extractor"] = // set extractor function()
+            function($report_id, $params, &$extractor_elements) {
+                $extractor_elements=  array(
+                    "relations"=>[],
+                    "attributes"=>[],
+                    "annotations" => array(
+                        // standard annotation exports has no lemma fields
+                        $this->annotationCustomExtractorRecord($report_id,1,6,9,'nam_adj',null),
+                        $this->annotationCustomExtractorRecord($report_id,2,10,13,'nam_oth',"lemat dodany do okno")
+                        ),
+                    "lemmas" => array()
+                    );
+            };
+
+        // tested call
+        $this->protectedMethod->invokeArgs($this->mockCorpusExporter,array($this->report_id,$this->extractors,$this->disamb_only,&$this->extractor_stats,&$this->lists,$this->output_folder,$this->subcorpora,$this->tagging_method));
+
+        // check results in XML file
+        $resultFileName = $this->output_folder.'/'.$this->fileName.".xml";
+        $this->assertTrue(file_exists($resultFileName));
+        $resultFileContent = file_get_contents($resultFileName);
+        // no lemma phrase in export output
+        $lemmaPattern = '@lemma@s';
+        $this->assertEquals(0,preg_match($lemmaPattern,$resultFileContent));
+
+        // check results in JSON file
+        $resultFileName = $this->output_folder.'/'.$this->fileName.".json";
+        $this->assertTrue(file_exists($resultFileName));
+        $resultFileContent = file_get_contents($resultFileName);
+        // no lemma phrase in export output
+        $lemmaPattern = '@lemma@s';
+        $this->assertEquals(0,preg_match($lemmaPattern,$resultFileContent));
+
+     } // testCustomAnnotationExtractorWritesNoLemmaInExportOutputs() 
+ 
+    public function testCustomExportManuallyModifiedWorksAsOldVersion() {
+
+        $this->extractors[0]["extractor"] = // set extractor function()
+            function($report_id, $params, &$extractor_elements) {
+                $anno1 = $this->annotationCustomExtractorRecord($report_id,1,6,9,'nam_adj',null);
+                $anno1['lemma'] = null;   // lemma must be add manually now
+                $anno2 = $this->annotationCustomExtractorRecord($report_id,2,10,13,'nam_oth',"lemat dodany do okno");
+                $anno2['lemma'] = "lemat dodany do okno"; // lemma must be add manually now
+                $extractor_elements=  array( 
+                    "relations"=>[], 
+                    "attributes"=>[],
+                    "annotations" => array( $anno1,$anno2 ),
+                    "lemmas" => array( $this->lemmaData() ));
+            };
+
+        // tested call
+        $this->protectedMethod->invokeArgs($this->mockCorpusExporter,array($this->report_id,$this->extractors,$this->disamb_only,&$this->extractor_stats,&$this->lists,$this->output_folder,$this->subcorpora,$this->tagging_method));
+
+		// check results in XML file
+		$resultFileName = $this->output_folder.'/'.$this->fileName.".xml";
+        $this->assertTrue(file_exists($resultFileName));
+		$resultFileContent = file_get_contents($resultFileName);
+		// prefix for proper XML
+		$expectedXmlContentPrefix = '<?xml version="1.0" encoding="UTF-8"?';
+		$this->assertRegexp('@'.$expectedXmlContentPrefix."@",$resultFileContent);
+		// annotacja bez lematu ( lemma=NULL )
+		$expectedAnnWithoutLemmaLine = '<ann chan="nam_adj">1</ann>';
+		$this->assertRegexp('@'.$expectedAnnWithoutLemmaLine.'@m',$resultFileContent);
+		// annotacja towarzysząca lematowi
+		$expectedAnnWithLemmaLine = '<ann chan="nam_oth">2</ann>';
+        $this->assertRegexp('@'.$expectedAnnWithLemmaLine.'@m',$resultFileContent);
+		// lemat - z pozycji w $lemmas
+		$expectedLemmaLine = '<prop key="nam_oth:lemma">lemat dodany do okno</prop>';
+		$this->assertRegexp('@'.$expectedLemmaLine.'@m',$resultFileContent);
+		// lemma line after anno line in export XML 
+        $expectedAnnWithLemmaLines = 
+'<ann chan="nam_oth">2</ann>'.'\s*'.'<prop key="nam_oth:lemma">lemat dodany do okno</prop>';
+        $this->assertRegexp('@'.$expectedAnnWithLemmaLines.'@m',$resultFileContent);
+
+        // check results in JSON file
+        $resultFileName = $this->output_folder.'/'.$this->fileName.".json";
+        $resultFileContent = file_get_contents($resultFileName);
+        // annotacja bez lematu ( lemma=NULL )
+        $expectedAnnWithoutLemmaPattern = '@'
+            .'"annotations": '.'.+'        // w sekcji po słowie 'annotations'
+            .'\{.+"from": 6,.+"to": 9,[^\}]*' // w tokenie na poz. 6-9
+                .'"lemma": null'   // jest wpis o lemacie
+            .'.*\}'.'@s';
+        $this->assertRegexp($expectedAnnWithoutLemmaPattern,$resultFileContent);
+        // annotacja z lematem ( "lemat dodany do okno" )
+        $expectedAnnWithLemmaPattern = '@'
+            .'"annotations": '.'.+'        // w sekcji po słowie 'annotations'
+            .'\{.+"from": 10,.+"to": 13,[^\}]*' // w tokenie na poz. 10-13
+                .'"lemma": "lemat dodany do okno"'   // jest wpis o lemacie
+            .'.*\}'.'@s';
+        $this->assertRegexp($expectedAnnWithLemmaPattern,$resultFileContent);
+
+	 }// testCustomExport()
+
+} // CorpusExporter_part13_Test class
+
+?>
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part5_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part5_Test.php
index 4a4ad544..5e83d34b 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part5_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part5_Test.php
@@ -128,7 +128,8 @@ private function checkFiles($report_id,$disambOnly,$tagging_method,$reportData,$
 
         $expectedBaseFileName = $this->virtualDir->url().'/'.str_pad($report_id,8,'0',STR_PAD_LEFT);
         $scl=new SimpleCcl($reportData,$tagging_method,$disambOnly);
-        $scl->addLemmas($extractorData);
+        // if no annotations, there are no lemmas
+        //$scl->addLemmas($extractorData);
 
         //checkConllFile
         $expectedContent = $scl->toCONLL();
diff --git a/phpunit/tests/engine/include/export/CorpusExporter_part6_Test.php b/phpunit/tests/engine/include/export/CorpusExporter_part6_Test.php
index a7aa7439..e28bc8c6 100644
--- a/phpunit/tests/engine/include/export/CorpusExporter_part6_Test.php
+++ b/phpunit/tests/engine/include/export/CorpusExporter_part6_Test.php
@@ -128,7 +128,8 @@ private function checkFiles($report_id,$disambOnly,$tagging_method,$reportData,$
 
         $expectedBaseFileName = $this->virtualDir->url().'/'.str_pad($report_id,8,'0',STR_PAD_LEFT);
         $scl=new SimpleCcl($reportData,$tagging_method,$disambOnly);
-        $scl->addLemmas($extractorData);
+        // if no annotations, there are not lemmas
+        //$scl->addLemmas($extractorData);
 
         //checkConllFile
         $expectedContent = $scl->toCONLL();

From 2ce1052de2c0c093a322e6c1071e8952f1a23386 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Fri, 22 Dec 2023 10:59:39 +0100
Subject: [PATCH 150/154] checking subsets lemma or attributes, forces
 annotation column check in extraction form

---
 public_html/js/page_corpus_export.js | 61 +++++++++++++++++++++++-----
 1 file changed, 51 insertions(+), 10 deletions(-)

diff --git a/public_html/js/page_corpus_export.js b/public_html/js/page_corpus_export.js
index 1497604a..a9fc6efd 100644
--- a/public_html/js/page_corpus_export.js
+++ b/public_html/js/page_corpus_export.js
@@ -187,28 +187,43 @@ function setStateForValue(element,value,on=true){
 } // setStateForValue()
 
 /**
- *  set all annotations for value id to checked state
+ *  set all annotations set for value id to checked state
  *
  *  @param form - extractor form object
  *  @param value - value of "value" attr, checked annotations
  *
  **/
-function setAnnotationsForValue(form,value) {
+function setAnnotationsSetForValue(form,value) {
 
 	$("input[type=checkbox].group_cb",form).each(function(index,element){
 		setStateForValue(element,value,true);
 	}); 
 	
-} // setAnnotationsForValue()
+} // setAnnotationsSetForValue()
 
 /**
- *  set all lemmas and attributes for value id to unchecked state
+ *  set all annotations subsets for value id to checked state
+ *
+ *  @param form - extractor form object
+ *  @param value - value of "value" attr, checked annotations
+ *
+ **/
+function setAnnotationsSubsetForValue(form,value) {
+
+        $("input[type=checkbox].subset_cb",form).each(function(index,element){
+                setStateForValue(element,value,true);
+        });
+
+} // setAnnotationsSubsetForValue()
+
+/**
+ *  set all lemmas and attributes sets for value id to unchecked state
  *
  *  @param form - extractor form object
  *  @param value - value of "value" attr, unchecked lemmas & attributtes
  *
  **/
-function unsetLemmasAndAttributesForValue(form,value) {
+function unsetLemmasAndAttributesSetsForValue(form,value) {
 
         $("input[type=checkbox].lemma_group_cb",form).each(function(index,element){
                 setStateForValue(element,value,false);
@@ -217,7 +232,25 @@ function unsetLemmasAndAttributesForValue(form,value) {
                 setStateForValue(element,value,false);
         });
 
-} // unsetLemmasAndAttributesForValue()
+} // unsetLemmasAndAttributesSetsForValue()
+
+/**
+ *  set all lemmas and attributes subsets for value id to unchecked state
+ *
+ *  @param form - extractor form object
+ *  @param value - value of "value" attr, unchecked lemmas & attributtes
+ *
+ **/
+function unsetLemmasAndAttributesSubsetsForValue(form,value) {
+
+        $("input[type=checkbox].lemma_subset_cb",form).each(function(index,element){
+                setStateForValue(element,value,false);
+        });
+        $("input[type=checkbox].attribute_subset_cb",form).each(function(index,element){
+                setStateForValue(element,value,false);
+        });
+
+} // unsetLemmasAndAttributesSubsetsForValue()
 
 /**
  *  set action to dynamically created extractor form, binding to input 
@@ -234,15 +267,23 @@ function setActionToFollowAnnotationAfterLemmaAndAttrs(extractorForm){
 
 	if(!extractorForm) return;
 	extractorForm.on('click',"input[type=checkbox]:checked.lemma_group_cb",function(){
-		setAnnotationsForValue(extractorForm,$(this).attr("value"));
+		setAnnotationsSetForValue(extractorForm,$(this).attr("value"));
 	});
 	extractorForm.on('click',"input[type=checkbox]:checked.attribute_group_cb",function(){
-		setAnnotationsForValue(extractorForm,$(this).attr("value"));
+		setAnnotationsSetForValue(extractorForm,$(this).attr("value"));
 	});
         extractorForm.on('click',"input[type=checkbox]:unchecked.group_cb",function(){
-                unsetLemmasAndAttributesForValue(extractorForm,$(this).attr("value"));
+                unsetLemmasAndAttributesSetsForValue(extractorForm,$(this).attr("value"));
+        });
+	extractorForm.on('click',"input[type=checkbox]:checked.lemma_subset_cb",function(){
+                setAnnotationsSubsetForValue(extractorForm,$(this).attr("value"));
+        });
+        extractorForm.on('click',"input[type=checkbox]:checked.attribute_subset_cb",function(){
+                setAnnotationsSubsetForValue(extractorForm,$(this).attr("value"));
+        });
+        extractorForm.on('click',"input[type=checkbox]:unchecked.subset_cb",function(){
+                unsetLemmasAndAttributesSubsetsForValue(extractorForm,$(this).attr("value"));
         });
-
 
 } // setActionToFollowAnnotationAfterLemmaAndAttrs()
 

From d3d1ef137e41d3de12bfaeb58cab3416f4246b13 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Wed, 27 Dec 2023 09:05:19 +0100
Subject: [PATCH 151/154] merging bugs fixed

---
 engine/include/database/CDbAnnotation.php     | 44 ++++++++++---------
 engine/include/export/CorpusExporter.php      |  2 +-
 engine/settings.php                           |  6 +++
 .../include/database/CDbAnnotationTest.php    |  6 ++-
 .../include/export/CclExportDocumentTest.php  |  2 +-
 5 files changed, 36 insertions(+), 24 deletions(-)

diff --git a/engine/include/database/CDbAnnotation.php b/engine/include/database/CDbAnnotation.php
index f5ddd423..d2097af6 100755
--- a/engine/include/database/CDbAnnotation.php
+++ b/engine/include/database/CDbAnnotation.php
@@ -778,32 +778,34 @@ static private function annotationStructureFromDBToArrayTree($dbResult,$limited
         $annotation_sets = array();
         foreach($dbResult as $at){
             $set_id = $at['set_id'];
-            $subset_id = $at['subset_id'];
+            $subset_id = $at['subset_id']; // may be null
             if (!isset($annotation_sets[$set_id])){
                 $annotation_sets[$set_id] = array('name' => $at['set_name']);
             }
-            if (!isset($annotation_sets[$set_id][$subset_id])){
-                $annotation_sets[$set_id][$subset_id] = array('name' => $at['subset_name']);
-            }
-
-            if($limited){
-                // counts types for set,subset
-                $typesCountForSetSubset[$set_id][$subset_id] = 1 +
-                    ( isset($typesCountForSetSubset[$set_id][$subset_id])
-                        ? $typesCountForSetSubset[$set_id][$subset_id] : 0 );
-                // test threshold
-                if($typesCountForSetSubset[$set_id][$subset_id]
-                    == $maxTypesLimitThreshold ) {
-                    $annotation_sets[$set_id][$subset_id][MAX_TYPES_LABEL_INDEX] = MAX_TYPES_NAME_LABEL;
+            if(isset($subset_id)) {
+                if (!isset($annotation_sets[$set_id][$subset_id])){
+                    $annotation_sets[$set_id][$subset_id] = array('name' => $at['subset_name']);
                 }
-                if($typesCountForSetSubset[$set_id][$subset_id]
-                    < $maxTypesLimitThreshold ) {
+
+                if($limited){
+                    // counts types for set,subset
+                    $typesCountForSetSubset[$set_id][$subset_id] = 1 +
+                        ( isset($typesCountForSetSubset[$set_id][$subset_id])
+                            ? $typesCountForSetSubset[$set_id][$subset_id] : 0 );
+                    // test threshold
+                    if($typesCountForSetSubset[$set_id][$subset_id]
+                        == $maxTypesLimitThreshold ) {
+                        $annotation_sets[$set_id][$subset_id][MAX_TYPES_LABEL_INDEX] = MAX_TYPES_NAME_LABEL;
+                    }
+                    if($typesCountForSetSubset[$set_id][$subset_id]
+                        < $maxTypesLimitThreshold ) {
+                        $annotation_sets[$set_id][$subset_id][$at['type_id']] = $at['type_name'];
+                    }
+                } else {
+                    // old method generating very big html structure
                     $annotation_sets[$set_id][$subset_id][$at['type_id']] = $at['type_name'];
-                }
-            } else {
-                // old method generating very big html structure
-                $annotation_sets[$set_id][$subset_id][$at['type_id']] = $at['type_name'];
-            } // if !limited
+                } // if !limited
+            } // $subset_id!=null
 
         } // foreach()
 
diff --git a/engine/include/export/CorpusExporter.php b/engine/include/export/CorpusExporter.php
index f1a6e641..3224dd67 100644
--- a/engine/include/export/CorpusExporter.php
+++ b/engine/include/export/CorpusExporter.php
@@ -560,7 +560,7 @@ protected function createIniFile($report,$subcorpora,$file_path_without_ext) {
         foreach ($basic as $name){
             $lines[] = sprintf("%s = %s", $name, $report[$name]);
         }
-        if ( count($ext) > 0 ){
+        if ( is_array($ext) && (count($ext) > 0) ){
             $lines[] = "";
             $lines[] = "[metadata]";
             foreach ($ext as $key=>$val){
diff --git a/engine/settings.php b/engine/settings.php
index 5aed2ff0..c0d70137 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -15,6 +15,12 @@
 ini_set("output_buffering", 0);
 ini_set("short_open_tag",1);
 setlocale(LC_CTYPE, "en_US.UTF-8");
+
+// threshold of count types for one set/subset combination
+define('MAX_TYPES_LIMIT_THRESHOLD',300);
+define('MAX_TYPES_LABEL_INDEX',999999999999); // over autoincrement id
+define('MAX_TYPES_NAME_LABEL','...');
+
 set_error_handler("ErrorService::errorHandler");
 if(! PHPUnitTools::isPHPUnitRunning()) {
 	// under PHPUnit this one not works
diff --git a/phpunit/tests/engine/include/database/CDbAnnotationTest.php b/phpunit/tests/engine/include/database/CDbAnnotationTest.php
index c39c6e8a..cf4f8455 100644
--- a/phpunit/tests/engine/include/database/CDbAnnotationTest.php
+++ b/phpunit/tests/engine/include/database/CDbAnnotationTest.php
@@ -1,6 +1,10 @@
 <?php
 
 mb_internal_encoding("UTF-8");
+// from settings.php
+define('MAX_TYPES_LIMIT_THRESHOLD',300);
+define('MAX_TYPES_LABEL_INDEX',999999999999); // over autoincrement id
+define('MAX_TYPES_NAME_LABEL','...');
 
 class CDbAnnotationTest extends PHPUnit_Framework_TestCase
 {
@@ -150,7 +154,7 @@ public function test_getAnnotationStructureByCorpora()
 "SELECT ans.annotation_set_id AS set_id, ans.name AS set_name, ansub.annotation_subset_id AS subset_id, ansub.name AS subset_name, at.name AS type_name, at.annotation_type_id AS type_id FROM annotation_types at LEFT JOIN annotation_subsets ansub ON ansub.annotation_subset_id=at.annotation_subset_id LEFT JOIN annotation_sets ans ON ans.annotation_set_id=at.group_id LEFT JOIN annotation_sets_corpora ac ON ac.annotation_set_id=ans.annotation_set_id WHERE ac.corpus_id = ?",
                             $allReturnedRows
         );
-        $result = DbAnnotation::getAnnotationStructureByCorpora($corpus_id);
+        $result = DbAnnotation::getAnnotationStructureByCorpora($corpus_id,True);
 
         $this->assertTrue(is_array($result));
         // returns raw DB response
diff --git a/phpunit/tests/engine/include/export/CclExportDocumentTest.php b/phpunit/tests/engine/include/export/CclExportDocumentTest.php
index b5044242..d64bb043 100644
--- a/phpunit/tests/engine/include/export/CclExportDocumentTest.php
+++ b/phpunit/tests/engine/include/export/CclExportDocumentTest.php
@@ -8,7 +8,7 @@ class CclExportDocumentTest extends PHPUnit_Framework_TestCase
 
     protected function setUp() {
 
-        $report = null; $tokens = null; $tags_by_tokens = null;
+        $report = null; $tokens = array(); $tags_by_tokens = null;
         $this->ccl = new CclExportDocument($report, $tokens, $tags_by_tokens);
 
     } // setUp()

From f8b66e86afdcbae993f891474da9843c06c5cc58 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Wed, 27 Dec 2023 12:04:38 +0100
Subject: [PATCH 152/154] fix duplicate constructor name

---
 docker/www/sample.config.local.php            |   8 +-
 engine/Config/Config.php                      |  13 +-
 engine/actions/a_document_image_upload.php    |   6 +-
 engine/actions/a_upload.php                   |   2 +-
 engine/ajax/ajax_dspace_import.php            |   2 +-
 engine/ajax/ajax_lps_get_corr_tags.php        |   2 +-
 engine/ajax/ajax_lps_get_interp.php           |   2 +-
 engine/ajax/ajax_lps_get_tag_docs.php         |   2 +-
 engine/ajax/ajax_lps_validate_xml.php         |   2 +-
 engine/ajax/ajax_ner_process.php              |   4 +-
 engine/ajax/ajax_nextcloud_import.php         |   2 +-
 .../ajax_report_autoextension_ner_process.php |   6 +-
 .../ajax/ajax_report_tokenization_process.php |   2 +-
 engine/ajax/ajax_semquel_get_result.php       |   2 +-
 engine/ajax/ajax_semquel_get_sql.php          |   2 +-
 engine/ajax/ajax_semquel_run.php              |   6 +-
 engine/ajax/ajax_task_check_status.php        |   2 +-
 engine/ajax/ajax_test_wccl_rules.php          |   8 +-
 .../ajax/ajax_wccl_match_get_reports_id.php   |   2 +-
 engine/ajax/ajax_wccl_match_run.php           |   8 +-
 engine/include/CInforexWeb.php                |  22 +--
 engine/include/CPage.php                      |  10 +-
 engine/include/CUserAuthorize.php             |   4 +-
 engine/include/class/TableReport.php          |   2 +-
 engine/include/database/CDbAnnotation.php     |   2 +-
 engine/include/database/CDbImage.php          |   2 +-
 .../diagnostics/CPageAjaxDiagnostic.php       |   8 +-
 engine/include/integrity/CCclIntegrity.php    |   2 +-
 engine/include/utils/CHelperBootstrap.php     |   2 +-
 engine/include/utils/CHelperTokenize.php      |  12 +-
 engine/include/utils/CWcclImport.php          |   4 +-
 .../page_administration_diagnostic_access.php |   4 +-
 engine/page/page_corpus_export.php            |   2 +-
 engine/page/page_corpus_settings.php          |   6 +-
 engine/page/page_export_download.php          |   2 +-
 engine/page/page_ner.php                      |   2 +-
 engine/page/page_report.php                   |   6 +-
 engine/page/page_wccl_match_tester.php        |   2 +-
 engine/settings.php                           |   5 -
 engine/templates/inc_footer.tpl               |   2 +-
 engine/templates/inc_header.tpl               |   2 +-
 local/agreement.php                           |   4 +-
 local/ccl2iob.php                             |   4 +-
 local/cli-import-corpus-annotations.php       |   8 +-
 local/cli-liner2-nlprest2.php                 |   6 +-
 local/cli-restore-corpus.php                  |   6 +-
 local/cli-tokenize-from-ccl.php               |  10 +-
 local/cli-upload-txt.php                      |   4 +-
 local/daemon-cleanup.php                      |   8 +-
 local/daemon-export.php                       |  10 +-
 local/daemon-grab.php                         |  14 +-
 local/daemon-tasks.php                        |  12 +-
 local/daemon-upload.php                       |  20 +--
 local/export-corpus.php                       |   4 +-
 local/flags.php                               |   4 +-
 local/import-corpus-cli.php                   |   8 +-
 local/import-sherlock.php                     |   6 +-
 local/import-wsd-annotations.php              |   6 +-
 local/liner2.php                              |  18 +--
 local/slavicner2019-annotate.php              |   4 +-
 local/slavicner2019.php                       |   4 +-
 local/tokenize-update.php                     |  34 ++--
 local/tokenize.php                            |  34 ++--
 local/upload.php                              |   4 +-
 local/wsd-annotate.php                        |   4 +-
 phpunit/tests/engine/Config/ConfigTest.php    | 146 ++++++++++++++++++
 phpunit/tests/engine/Config/SingletonTest.php |  32 ++++
 .../include/database/CDbAnnotationTest.php    |   4 -
 .../engine/include/export/FileWriterTest.php  |   1 -
 public_html/css.php                           |   6 +-
 public_html/image.php                         |   8 +-
 public_html/index.php                         |  16 +-
 72 files changed, 405 insertions(+), 230 deletions(-)
 create mode 100644 phpunit/tests/engine/Config/ConfigTest.php
 create mode 100644 phpunit/tests/engine/Config/SingletonTest.php

diff --git a/docker/www/sample.config.local.php b/docker/www/sample.config.local.php
index 8a06e3fd..a8b2d7d0 100644
--- a/docker/www/sample.config.local.php
+++ b/docker/www/sample.config.local.php
@@ -1,8 +1,8 @@
 <?php
-Config::Config()->put_path_engine('/home/inforex/engine');
-Config::Config()->put_path_www('/home/inforex/public_html');
-Config::Config()->put_path_secured_data('/home/inforex/secured_data');
-Config::Config()->put_dsn(array(
+Config::Cfg()->put_path_engine('/home/inforex/engine');
+Config::Cfg()->put_path_www('/home/inforex/public_html');
+Config::Cfg()->put_path_secured_data('/home/inforex/secured_data');
+Config::Cfg()->put_dsn(array(
     'phptype'  => 'mysqli',
     'username' => 'inforex', 
     'port' => '3306', 
diff --git a/engine/Config/Config.php b/engine/Config/Config.php
index 2a5c7c7d..2787b9fd 100644
--- a/engine/Config/Config.php
+++ b/engine/Config/Config.php
@@ -6,6 +6,11 @@
  * See LICENCE 
  */
 
+// threshold of count types for one set/subset combination
+define('MAX_TYPES_LIMIT_THRESHOLD',300);
+define('MAX_TYPES_LABEL_INDEX',999999999999); // over autoincrement id
+define('MAX_TYPES_NAME_LABEL','...');
+
 class Phantom {
 
     public function __call($name, $arguments)
@@ -91,11 +96,11 @@ class Config extends Singleton\Singleton{
 	);
 		
 	// for more friendly call only...
-    final public static function Config(){
+    final public static function Cfg(){
 
         return self::getInstance();
 
-    } // Config()
+    } // Cfg()
 		
 	// constructor - default values of some parameters 	
 	final protected function __construct(){
@@ -151,7 +156,9 @@ function __call($method,$arguments){
             }
         } 
 		else
-			call_user_func_array(array($this,"_".$method),$arguments);		
+            if (method_exists($this,$method)) {       
+			    call_user_func_array(array($this,"_".$method),$arguments);
+            }		
 	}
 	
     private function loadOldLocalConfig($pathname) {
diff --git a/engine/actions/a_document_image_upload.php b/engine/actions/a_document_image_upload.php
index 9819dc80..ce4a3b4a 100644
--- a/engine/actions/a_document_image_upload.php
+++ b/engine/actions/a_document_image_upload.php
@@ -37,11 +37,11 @@ function execute(){
 		$image->setHashName($hashname);
 		$image->save();
 				
-		$path = Config::Config()->get_path_secured_data() . "/images" . "/" . $image->getServerFileName();
+		$path = Config::Cfg()->get_path_secured_data() . "/images" . "/" . $image->getServerFileName();
 		DbImage::addImageToReport($report_id, $image->id);
 
-        if ( !file_exists(Config::Config()->get_path_secured_data() . "/images") ){
-            mkdir(Config::Config()->get_path_secured_data() . "/images", 0755, true);
+        if ( !file_exists(Config::Cfg()->get_path_secured_data() . "/images") ){
+            mkdir(Config::Cfg()->get_path_secured_data() . "/images", 0755, true);
         }
 
 		if (move_uploaded_file($_FILES['image']['tmp_name'], $path)) {
diff --git a/engine/actions/a_upload.php b/engine/actions/a_upload.php
index 7a0e976f..b72a2211 100644
--- a/engine/actions/a_upload.php
+++ b/engine/actions/a_upload.php
@@ -36,7 +36,7 @@ function execute()
             return null;
         }
 
-        $newPath = tempnam(Config::Config()->get_path_secured_data(). "/import", "upload_zip_");
+        $newPath = tempnam(Config::Cfg()->get_path_secured_data(). "/import", "upload_zip_");
         move_uploaded_file($path, $newPath);
         chmod($newPath, 0755);
         $params["path"] = $newPath;
diff --git a/engine/ajax/ajax_dspace_import.php b/engine/ajax/ajax_dspace_import.php
index ec389e03..5a7949d8 100644
--- a/engine/ajax/ajax_dspace_import.php
+++ b/engine/ajax/ajax_dspace_import.php
@@ -61,7 +61,7 @@ function execute(){
 		$task->status = "new";
 		$task->save();
 		
-		$url = sprintf("%s?page=tasks&corpus=%d&task_id=%d",Config::Config()->get_url(), $corpus->id, $task->task_id);
+		$url = sprintf("%s?page=tasks&corpus=%d&task_id=%d",Config::Cfg()->get_url(), $corpus->id, $task->task_id);
 		 		
 		//print(json_encode(array("redirect"=>$url))); 
 		//return;
diff --git a/engine/ajax/ajax_lps_get_corr_tags.php b/engine/ajax/ajax_lps_get_corr_tags.php
index 467d8a7d..b54234c1 100644
--- a/engine/ajax/ajax_lps_get_corr_tags.php
+++ b/engine/ajax/ajax_lps_get_corr_tags.php
@@ -7,7 +7,7 @@
  */
 
 // ToDo: Move common methods to an external file
-require_once(Config::Config()->get_path_engine() . "/page/page_lps_stats.php");
+require_once(Config::Cfg()->get_path_engine() . "/page/page_lps_stats.php");
 
 /**
  */
diff --git a/engine/ajax/ajax_lps_get_interp.php b/engine/ajax/ajax_lps_get_interp.php
index 10f38acf..51dced1f 100644
--- a/engine/ajax/ajax_lps_get_interp.php
+++ b/engine/ajax/ajax_lps_get_interp.php
@@ -7,7 +7,7 @@
  */
 
 // ToDo: Move common methods to an external file
-require_once(Config::Config()->get_path_engine() . "/page/page_lps_stats.php");
+require_once(Config::Cfg()->get_path_engine() . "/page/page_lps_stats.php");
 
 /**
  */
diff --git a/engine/ajax/ajax_lps_get_tag_docs.php b/engine/ajax/ajax_lps_get_tag_docs.php
index bbcc248b..d0171a96 100644
--- a/engine/ajax/ajax_lps_get_tag_docs.php
+++ b/engine/ajax/ajax_lps_get_tag_docs.php
@@ -7,7 +7,7 @@
  */
 
 // ToDo: Move common methods to an external file
-require_once(Config::Config()->get_path_engine() . "/page/page_lps_stats.php");
+require_once(Config::Cfg()->get_path_engine() . "/page/page_lps_stats.php");
 
 /**
  */
diff --git a/engine/ajax/ajax_lps_validate_xml.php b/engine/ajax/ajax_lps_validate_xml.php
index bb943daa..485be401 100644
--- a/engine/ajax/ajax_lps_validate_xml.php
+++ b/engine/ajax/ajax_lps_validate_xml.php
@@ -29,7 +29,7 @@ function execute(){
 
 		$c = new MyDOMDocument();
 		$c->loadXML($content);
-		$c->schemaValidate(Config::Config()->get_path_engine()."/resources/lps/lps.xsd");
+		$c->schemaValidate(Config::Cfg()->get_path_engine()."/resources/lps/lps.xsd");
 
 		return array("errors"=>$c->errors );
 	}
diff --git a/engine/ajax/ajax_ner_process.php b/engine/ajax/ajax_ner_process.php
index f75891a2..6f6a456a 100644
--- a/engine/ajax/ajax_ner_process.php
+++ b/engine/ajax/ajax_ner_process.php
@@ -7,7 +7,7 @@
  */
 
 // ToDo: Move common methods to an external file
-require_once(Config::Config()->get_path_engine()."/page/page_ner.php");
+require_once(Config::Cfg()->get_path_engine()."/page/page_ner.php");
 
 /**
  */
@@ -28,7 +28,7 @@ function execute(){
 		$annotation_types = null;
 		$api = null;
 		
-		foreach (Config::Config()->get_liner2_api() as $m){
+		foreach (Config::Cfg()->get_liner2_api() as $m){
 			if ($m['wsdl'] == $wsdl && $m['model'] == $model){
 				if ( isset($m['annotations'] )){
 					$annotation_types = $m['annotations'];
diff --git a/engine/ajax/ajax_nextcloud_import.php b/engine/ajax/ajax_nextcloud_import.php
index d0c4e0f8..f46dc5d5 100644
--- a/engine/ajax/ajax_nextcloud_import.php
+++ b/engine/ajax/ajax_nextcloud_import.php
@@ -67,7 +67,7 @@ function execute(){
 		$task->status = "new";
 		$task->save();
 		
-		$url = sprintf("%s?page=tasks&corpus=%d&task_id=%d", Config::Config()->get_url(), $corpus->id, $task->task_id);
+		$url = sprintf("%s?page=tasks&corpus=%d&task_id=%d", Config::Cfg()->get_url(), $corpus->id, $task->task_id);
 		 		
 		print(json_encode(array("redirect"=>$url)));
 		return;
diff --git a/engine/ajax/ajax_report_autoextension_ner_process.php b/engine/ajax/ajax_report_autoextension_ner_process.php
index 35d82359..5ff1390b 100644
--- a/engine/ajax/ajax_report_autoextension_ner_process.php
+++ b/engine/ajax/ajax_report_autoextension_ner_process.php
@@ -7,7 +7,7 @@
  */
 
 // ToDo: Move common methods to an external file
-require_once(Config::Config()->get_path_engine()."/page/page_ner.php");
+require_once(Config::Cfg()->get_path_engine()."/page/page_ner.php");
 
 /**
  */
@@ -27,7 +27,7 @@ function execute(){
 		
 		$models = PerspectiveAutoExtension::getModels();
 
-		$tagger = new WSTagger(Config::Config()->get_takipi_wsdl());
+		$tagger = new WSTagger(Config::Cfg()->get_takipi_wsdl());
 		$tagger->tag($text);
 		$sentences = $tagger->getIOB();
 		
@@ -39,7 +39,7 @@ function execute(){
 	  	}	  	
 		$text = $takipiText;
 		
-		$chunker = new Liner(Config::Config()->get_path_python(), Config::Config()->get_path_liner(), Config::Config()->get_path_liner()."/models/" . $models[$model]['file']);
+		$chunker = new Liner(Config::Cfg()->get_path_python(), Config::Cfg()->get_path_liner(), Config::Cfg()->get_path_liner()."/models/" . $models[$model]['file']);
 
 		$htmlStr = new HtmlStr($text, true);
 		$offset = 0;
diff --git a/engine/ajax/ajax_report_tokenization_process.php b/engine/ajax/ajax_report_tokenization_process.php
index 246b432f..c0e56d08 100644
--- a/engine/ajax/ajax_report_tokenization_process.php
+++ b/engine/ajax/ajax_report_tokenization_process.php
@@ -8,7 +8,7 @@
 
 // ToDo: Move common methods to an external file
 //  loaded earlier by composer classmap mechanism
-//require_once(Config::Config()->get_path_engine()."/page/page_ner.php");
+//require_once(Config::Cfg()->get_path_engine()."/page/page_ner.php");
 
 /**
  */
diff --git a/engine/ajax/ajax_semquel_get_result.php b/engine/ajax/ajax_semquel_get_result.php
index c0becb4e..13d0af53 100644
--- a/engine/ajax/ajax_semquel_get_result.php
+++ b/engine/ajax/ajax_semquel_get_result.php
@@ -11,7 +11,7 @@ class Ajax_semquel_get_result extends CPage {
 	function execute(){
 	
 		$ids = $_POST['id_list'];		
-		$db2 = new Database(Config::Config()->get_relation_marks_db());
+		$db2 = new Database(Config::Cfg()->get_relation_marks_db());
 	
 		$sql = " SELECT ans.begin as source_begin, " .
 				" ans.end as source_end, " .
diff --git a/engine/ajax/ajax_semquel_get_sql.php b/engine/ajax/ajax_semquel_get_sql.php
index 8272b345..db51bc31 100644
--- a/engine/ajax/ajax_semquel_get_sql.php
+++ b/engine/ajax/ajax_semquel_get_sql.php
@@ -12,7 +12,7 @@ class Ajax_semquel_get_sql extends CPage {
 	function execute(){
 	
 		$sql = $_POST['semquel'];
-		$db2 = new Database(Config::Config()->get_relation_marks_db());
+		$db2 = new Database(Config::Cfg()->get_relation_marks_db());
 		
 		return $db2->fetch_rows($sql);
 	}	
diff --git a/engine/ajax/ajax_semquel_run.php b/engine/ajax/ajax_semquel_run.php
index 9ee9ce93..110d997f 100644
--- a/engine/ajax/ajax_semquel_run.php
+++ b/engine/ajax/ajax_semquel_run.php
@@ -13,7 +13,7 @@ function execute(){
 		$question = $_POST['question'];
 		$ip = strval($_SERVER['REMOTE_ADDR']);
 		
-		$db_serel = new Database(Config::Config()->get_dsn_questions(), true);
+		$db_serel = new Database(Config::Cfg()->get_dsn_questions(), true);
 		$db_serel->execute("INSERT INTO questions (question, ip)" .
 				" VALUES(?, ?)", array($question, $ip));
 		
@@ -24,9 +24,9 @@ function execute(){
 		$ccl = $liner->chunk($question, "plain:wcrft", "ccl");
 		
 		$wccl = new Wccl();
-		$ccl = $wccl->run($ccl, Config::Config()->get_file_with_rules());
+		$ccl = $wccl->run($ccl, Config::Cfg()->get_file_with_rules());
 
-		$semql = new Semql(Config::Config()->get_path_semql());
+		$semql = new Semql(Config::Cfg()->get_path_semql());
 		$json = $semql->analyze($ccl);
 		
 		$json = str_replace('\t\t\t', "", $json);
diff --git a/engine/ajax/ajax_task_check_status.php b/engine/ajax/ajax_task_check_status.php
index 619a5b45..30f360c2 100644
--- a/engine/ajax/ajax_task_check_status.php
+++ b/engine/ajax/ajax_task_check_status.php
@@ -39,7 +39,7 @@ function execute(){
 		$data['documents_status'] = $documents_status;
 		
 		if ($task['type'] == "grab"){
-			$task_status_path = Config::Config()->get_path_secured_data()."/grab/{$task_id}/status.txt";
+			$task_status_path = Config::Cfg()->get_path_secured_data()."/grab/{$task_id}/status.txt";
 			if (file_exists($task_status_path)){
 				$task_status_file = fopen($task_status_path, "r");
 				$data['grab_status'] = intval(fgets($task_status_file));
diff --git a/engine/ajax/ajax_test_wccl_rules.php b/engine/ajax/ajax_test_wccl_rules.php
index ef57413d..21514a85 100644
--- a/engine/ajax/ajax_test_wccl_rules.php
+++ b/engine/ajax/ajax_test_wccl_rules.php
@@ -8,9 +8,9 @@ function execute(){
 		$offset = intval($_POST['offset']);
 		$rules = strval($_POST['wccl_rules']);
 		$corpus = intval($_POST['corpus']);
-		$corpus_path = Config::Config()->get_wccl_match_tester_corpora()[$corpus]["path"];
+		$corpus_path = Config::Cfg()->get_wccl_match_tester_corpora()[$corpus]["path"];
 
-		$cmd = "python ".Config::Config()->get_wccl_match_tester_script()." -s %d -o %d -r %s -c %s 2>&1";
+		$cmd = "python ".Config::Cfg()->get_wccl_match_tester_script()." -s %d -o %d -r %s -c %s 2>&1";
 		$cmd = sprintf($cmd, $start, $offset, escapeshellarg($rules), $corpus_path);
 
 		$output = array();
@@ -18,8 +18,8 @@ function execute(){
 		
 		$errors = array();
 
-		if (!file_exists(Config::Config()->get_wccl_match_tester_script()))
-			$errors[] = "Błąd konfiguracji: plik nie istnieje {Config::Config()->get_wccl_match_script()}";
+		if (!file_exists(Config::Cfg()->get_wccl_match_tester_script()))
+			$errors[] = "Błąd konfiguracji: plik nie istnieje {Config::Cfg()->get_wccl_match_script()}";
 
 		if (count($output) > 1){
 			$output_joined = implode($output);
diff --git a/engine/ajax/ajax_wccl_match_get_reports_id.php b/engine/ajax/ajax_wccl_match_get_reports_id.php
index 7578536c..57c8a688 100644
--- a/engine/ajax/ajax_wccl_match_get_reports_id.php
+++ b/engine/ajax/ajax_wccl_match_get_reports_id.php
@@ -12,7 +12,7 @@ function execute(){
 
 		$reports_id = array();
 		
-		$ccl_folder = sprintf("%s/ccls/corpus%04d", Config::Config()->get_path_secured_data(), $corpus['id']);
+		$ccl_folder = sprintf("%s/ccls/corpus%04d", Config::Cfg()->get_path_secured_data(), $corpus['id']);
 		
 		if ( file_exists($ccl_folder) ){
 			$files = scandir($ccl_folder);
diff --git a/engine/ajax/ajax_wccl_match_run.php b/engine/ajax/ajax_wccl_match_run.php
index 791de0ad..7b82ac0d 100644
--- a/engine/ajax/ajax_wccl_match_run.php
+++ b/engine/ajax/ajax_wccl_match_run.php
@@ -14,9 +14,9 @@ function execute(){
 		$annotations = strval($_POST['annotations']);
 		$report_id = intval($_POST['report_id']);
 
-		$cmd = "python ".Config::Config()->get_wccl_match_script()." -r %s -f %s -a %s 2>&1";
+		$cmd = "python ".Config::Cfg()->get_wccl_match_script()." -r %s -f %s -a %s 2>&1";
 		
-		$file_path = sprintf("%s/ccls/corpus%04d/%08d.xml", Config::Config()->get_path_secured_data(), $corpus['id'], $report_id);
+		$file_path = sprintf("%s/ccls/corpus%04d/%08d.xml", Config::Cfg()->get_path_secured_data(), $corpus['id'], $report_id);
 		
 		$cmd = sprintf($cmd, escapeshellarg($rules), $file_path, escapeshellarg($annotations));
 		fb($cmd);
@@ -26,8 +26,8 @@ function execute(){
 		
 		$errors = array();
 
-		if (!file_exists(Config::Config()->get_wccl_match_script()))
-			$errors[] = "Błąd konfiguracji: plik nie istnieje ".Config::Config()->get_wccl_match_script();
+		if (!file_exists(Config::Cfg()->get_wccl_match_script()))
+			$errors[] = "Błąd konfiguracji: plik nie istnieje ".Config::Cfg()->get_wccl_match_script();
 
 		if (count($output) > 1){
 			$output_joined = implode($output);
diff --git a/engine/include/CInforexWeb.php b/engine/include/CInforexWeb.php
index 902e2454..46f5e2d7 100644
--- a/engine/include/CInforexWeb.php
+++ b/engine/include/CInforexWeb.php
@@ -33,8 +33,8 @@ function __construct()
          * Rozpocznij sesję
          */
         HTTP_Session2::useCookies(true);
-        HTTP_Session2::start(Config::Config()->get_sid());
-        HTTP_Session2::setExpire(time() + Config::Config()->get_session_time());
+        HTTP_Session2::start(Config::Cfg()->get_sid());
+        HTTP_Session2::setExpire(time() + Config::Cfg()->get_session_time());
     }
 
     /**
@@ -87,7 +87,7 @@ function doAction($action, &$variables)
     {
         global $user, $corpus;
 
-        include(Config::Config()->get_path_engine() . "/actions/a_{$action}.php");
+        include(Config::Cfg()->get_path_engine() . "/actions/a_{$action}.php");
         $class_name = "Action_{$action}";
         $o = new $class_name();
 
@@ -122,7 +122,7 @@ function doAjax($ajax, &$variables)
         header('Content-Type: application/json; charset=utf-8');
 
         /** Process an ajax request */
-        $filename = Config::Config()->get_path_engine() . "/ajax/ajax_{$ajax}.php";
+        $filename = Config::Cfg()->get_path_engine() . "/ajax/ajax_{$ajax}.php";
         if (!file_exists($filename)) {
             echo $this->ajaxError("ERROR_APPLICATION", "Ajax not found: " . $filename);
             return;
@@ -162,7 +162,7 @@ function doPage($page, &$variables)
         $page = $page ? $page : 'home';
 
         // If the required module does not exist, change it silently to the default.
-        $pageFile = Config::Config()->get_path_engine() . "/page/page_{$page}.php";
+        $pageFile = Config::Cfg()->get_path_engine() . "/page/page_{$page}.php";
         if (!file_exists($pageFile)) {
             return $this->doPage("home", $variables);
         }
@@ -182,7 +182,7 @@ function doPage($page, &$variables)
         $o->set('page', $page);
         $o->set('corpus', $corpus);
         $o->set('release', defined("RELEASE") ? RELEASE : "RELEASE" );
-        $o->set('config', Config::Config());
+        $o->set('config', Config::Cfg());
         $o->set('rev', $this->getRevisionKey());
 
         $access = $o->hasAccess($user, $corpus);
@@ -197,10 +197,10 @@ function doPage($page, &$variables)
             $o->set('warnings', $o->getWarnings());
             $o->set('exceptions', $variables['exceptions']);
             $o->set('Config', array(
-                "log_sql" => Config::Config()->get_log_sql(),
-                "url" => Config::Config()->get_url(),
-                "wccl_match_enable" => Config::Config()->get_wccl_match_enable(),
-                "federationLoginUrl" => Config::Config()->get_federationLoginUrl()
+                "log_sql" => Config::Cfg()->get_log_sql(),
+                "url" => Config::Cfg()->get_url(),
+                "wccl_match_enable" => Config::Cfg()->get_wccl_match_enable(),
+                "federationLoginUrl" => Config::Cfg()->get_federationLoginUrl()
             ));
             foreach ($variables as $k => $v) {
                 $o->set($k, $v);
@@ -256,7 +256,7 @@ function execute()
         $activity_page['datetime'] = date("Y-m-d H:i:s");
 
         try {
-            if ($action && file_exists(Config::Config()->get_path_engine() . "/actions/a_{$action}.php")) {
+            if ($action && file_exists(Config::Cfg()->get_path_engine() . "/actions/a_{$action}.php")) {
                 $page = $this->doAction($action, $variables);
                 $activity_page['activity_type_id'] = $db->get_entry_key("activity_types", "activity_type_id", array("name" => $action, "category" => "action"));
                 $activity_page['execution_time'] = time() - $stamp_start;
diff --git a/engine/include/CPage.php b/engine/include/CPage.php
index d7183bd3..5181a3ff 100644
--- a/engine/include/CPage.php
+++ b/engine/include/CPage.php
@@ -77,7 +77,7 @@ function __construct($name=null,$description=null){
 		$this->name = $name;
 		$this->description = $description;
 		$this->template = new Smarty();
-		$this->template->compile_dir = Config::Config()->get_path_engine() . "/templates_c";
+		$this->template->compile_dir = Config::Cfg()->get_path_engine() . "/templates_c";
 		$this->set('RELEASE', defined('RELEASE') ? RELEASE : "RELEASE");
 
 		/**
@@ -92,13 +92,13 @@ function __construct($name=null,$description=null){
 		if ( substr($className, 0, 5) == "Page_"){
 			$this->includeJs("js/page.js");				
 			$page = str_replace("Page_", "", $className);
-			if (file_exists(Config::Config()->get_path_www() . "/js/page_{$page}.js")){
+			if (file_exists(Config::Cfg()->get_path_www() . "/js/page_{$page}.js")){
 				$this->includeJs("js/page_{$page}.js");
 			}
-			if (file_exists(Config::Config()->get_path_www() . "/js/page_{$page}_resize.js")){
+			if (file_exists(Config::Cfg()->get_path_www() . "/js/page_{$page}_resize.js")){
 				$this->includeJs("js/page_{$page}_resize.js");
 			}
-			if (file_exists(Config::Config()->get_path_www() . "/css/page_{$page}.css")){
+			if (file_exists(Config::Cfg()->get_path_www() . "/css/page_{$page}.css")){
 				$this->includeCss("css/page_{$page}.css");
 			}
 		}
@@ -265,7 +265,7 @@ function execute(){}
 	 */
 	function display($template_name){
 		$this->set("include_files", $this->include_files);
-		$this->template->display(Config::Config()->get_path_engine() . "/templates/page_{$template_name}.tpl");
+		$this->template->display(Config::Cfg()->get_path_engine() . "/templates/page_{$template_name}.tpl");
 	}
 		
 	/**
diff --git a/engine/include/CUserAuthorize.php b/engine/include/CUserAuthorize.php
index abcf35e1..bea975f4 100644
--- a/engine/include/CUserAuthorize.php
+++ b/engine/include/CUserAuthorize.php
@@ -52,7 +52,7 @@ function getUserData(){
 	}
 
 	function redirectToClarinLogin(){
-        header('Location: '.Config::Config()->get_federationLoginUrl()."http://".$_SERVER["HTTP_HOST"].$_SERVER["REQUEST_URI"]);
+        header('Location: '.Config::Cfg()->get_federationLoginUrl()."http://".$_SERVER["HTTP_HOST"].$_SERVER["REQUEST_URI"]);
     }
 
     function logInClarinUser($userClarin){
@@ -87,7 +87,7 @@ private function getClarinUserByToken($token){
 
         // using system curl command
         // sudo apt-get install php5-curl
-        $curl = curl_init(Config::Config()->get_federationValidateTokenUrl() . $token);
+        $curl = curl_init(Config::Cfg()->get_federationValidateTokenUrl() . $token);
 
         curl_setopt($curl, CURLOPT_POST, true);
         curl_setopt($curl, CURLOPT_POSTFIELDS, '');
diff --git a/engine/include/class/TableReport.php b/engine/include/class/TableReport.php
index b607bede..23d8d88e 100644
--- a/engine/include/class/TableReport.php
+++ b/engine/include/class/TableReport.php
@@ -64,7 +64,7 @@ public function validateSchema(){
 				$parse = HtmlParser::parseXml($this->content);
 				break;
 			case "premorph":
-				$parse = HtmlParser::validateXmlWithXsd($this->content, Config::Config()->get_path_engine()."/resources/synat/premorph.xsd");
+				$parse = HtmlParser::validateXmlWithXsd($this->content, Config::Cfg()->get_path_engine()."/resources/synat/premorph.xsd");
 				break;
 			default:
 				$parse = array();
diff --git a/engine/include/database/CDbAnnotation.php b/engine/include/database/CDbAnnotation.php
index 4691fa1c..c16e12cf 100755
--- a/engine/include/database/CDbAnnotation.php
+++ b/engine/include/database/CDbAnnotation.php
@@ -772,7 +772,7 @@ static private function annotationStructureFromDBToArrayTree($dbResult,$limited
         if($limited){
             // key for this array is [set_id,subset_id]
             $typesCountForSetSubset = array();
-            $maxTypesLimitThreshold = Config::Config()->get_max_types_limit_threshold();
+            $maxTypesLimitThreshold = Config::Cfg()->get_max_types_limit_threshold();
         }
 
         $annotation_sets = array();
diff --git a/engine/include/database/CDbImage.php b/engine/include/database/CDbImage.php
index a7d22993..cc1fec2c 100644
--- a/engine/include/database/CDbImage.php
+++ b/engine/include/database/CDbImage.php
@@ -41,7 +41,7 @@ static function deleteImage($image_id, $image_name){
         $sql = "DELETE FROM images WHERE id = ?";
         $db->execute($sql, array($image_id));
 
-        $image_path = Config::Config()->get_path_www() . "/images/" . $image_id . "_" . $image_name;
+        $image_path = Config::Cfg()->get_path_www() . "/images/" . $image_id . "_" . $image_name;
         if (file_exists($image_path)) {
             unlink($image_path);
         }
diff --git a/engine/include/diagnostics/CPageAjaxDiagnostic.php b/engine/include/diagnostics/CPageAjaxDiagnostic.php
index b3b94ec1..8a0910b9 100644
--- a/engine/include/diagnostics/CPageAjaxDiagnostic.php
+++ b/engine/include/diagnostics/CPageAjaxDiagnostic.php
@@ -2,7 +2,7 @@
 class PageAjaxDiagnostic{
 
     static function findAjaxUsage($file_keywords){
-        $js_folder = Config::Config()->get_path_www() . "/js";
+        $js_folder = Config::Cfg()->get_path_www() . "/js";
         $files = scandir($js_folder);
         $regex_pattern = "/doAjax(.+|)[(]('|\")([^'\"]+)('|\")/";
         $ajax_list = array();
@@ -41,7 +41,7 @@ static function findAjaxUsage($file_keywords){
     }
 
     private static function getAjaxUsedOnPages($ajaxClassName){
-        $filename = Config::Config()->get_path_engine() . "/ajax/" . strtolower($ajaxClassName) . ".php";
+        $filename = Config::Cfg()->get_path_engine() . "/ajax/" . strtolower($ajaxClassName) . ".php";
         if ( file_exists($filename) ){
             require_once($filename);
             $p = new $ajaxClassName();
@@ -52,7 +52,7 @@ private static function getAjaxUsedOnPages($ajaxClassName){
     }
 
     private function getAjaxAccessInfo($ajax_list){
-        $validatorAjax = new PageAccessValidator(Config::Config()->get_path_engine(), "ajax");
+        $validatorAjax = new PageAccessValidator(Config::Cfg()->get_path_engine(), "ajax");
         $validatorAjax->process();
         $ajax_access = $validatorAjax->items;
 
@@ -166,7 +166,7 @@ private function hasAccessConflict($ajax){
      */
     private function getPageAccessInfoByFilename(){
 
-        $validatorPage = new PageAccessValidator(Config::Config()->get_path_engine(), "page");
+        $validatorPage = new PageAccessValidator(Config::Cfg()->get_path_engine(), "page");
         $validatorPage->process();
         $pages = $validatorPage->items;
         $pages_ordered = array();
diff --git a/engine/include/integrity/CCclIntegrity.php b/engine/include/integrity/CCclIntegrity.php
index 24eca50d..5fcc4857 100644
--- a/engine/include/integrity/CCclIntegrity.php
+++ b/engine/include/integrity/CCclIntegrity.php
@@ -50,7 +50,7 @@ static function checkXSDContent($content){
 		$content = preg_replace('/xlink:href="[^"]*"/', "", $content);
 		$c = new MyDOMDocument();
 		$c->loadXML($content);
-		$c->schemaValidate(Config::Config()->get_path_engine()."/resources/synat/premorph.xsd");
+		$c->schemaValidate(Config::Cfg()->get_path_engine()."/resources/synat/premorph.xsd");
 		
 		return array("count"=> count($c->errors),"data"=>$c->errors);
 	}
diff --git a/engine/include/utils/CHelperBootstrap.php b/engine/include/utils/CHelperBootstrap.php
index ceebb64c..813331c6 100644
--- a/engine/include/utils/CHelperBootstrap.php
+++ b/engine/include/utils/CHelperBootstrap.php
@@ -70,7 +70,7 @@ static function transformCclToAnnotations($ccl){
 
 	// TODO: to remove
 	static function chunkWithLiner2($text, $model){
-		$liner2 = Config::Config()->get_path_liner2()."/liner2.sh";
+		$liner2 = Config::Cfg()->get_path_liner2()."/liner2.sh";
 		$liner2 = "liner2";
 		
 		$tmp_in = "/tmp/inforex_liner2_input.txt";
diff --git a/engine/include/utils/CHelperTokenize.php b/engine/include/utils/CHelperTokenize.php
index c54328dc..f5987791 100644
--- a/engine/include/utils/CHelperTokenize.php
+++ b/engine/include/utils/CHelperTokenize.php
@@ -26,7 +26,7 @@ static function xcesToCcl($text){
 
 	static function tagWithTakipiWs($text, $guesser){
 		$text = preg_replace("/<!DOCTYPE [^>]+>/", "", $text);
-		$tagger = new WSTagger(Config::Config()->get_takipi_wsdl());
+		$tagger = new WSTagger(Config::Cfg()->get_takipi_wsdl());
 		$tagger->tag($text, $guesser);
 		$text_tagged = "<doc>".$tagger->tagged."</doc>"; 
 		return $text_tagged;		
@@ -44,7 +44,7 @@ static function tagPremorphWithWcrft2($text, $sentences=false){
 		$tmp = ".inforex_tokenize.tmp";
 		file_put_contents($tmp, $text);
 		$cmd_template = 'cat %s | maca-analyse -qs morfeusz-nkjp -i %s -o ccl | wcrft-app %s -i ccl -o ccl - 2>/dev/null';
-		$cmd = sprintf($cmd_template, $tmp, $input, Config::Config()->get_wcrft2_config());
+		$cmd = sprintf($cmd_template, $tmp, $input, Config::Cfg()->get_wcrft2_config());
 		echo $cmd;
 		$text_tagged = shell_exec($cmd);
 		if (file_exists($tmp)) unlink($tmp);
@@ -56,7 +56,7 @@ static function tagPremorphWithWcrft2Working($text, $sentences=false){
 		$tmp = ".inforex_tokenize.tmp";
 		file_put_contents($tmp, $text);
 		$cmd_template = 'cat %s | wcrft-app %s -i premorph -o ccl - 2>/dev/null';
-		$cmd = sprintf($cmd_template, $tmp, Config::Config()->get_wcrft2_config());
+		$cmd = sprintf($cmd_template, $tmp, Config::Cfg()->get_wcrft2_config());
 		echo $cmd;
 		$text_tagged = shell_exec($cmd);
 		if (file_exists($tmp)) unlink($tmp);
@@ -68,7 +68,7 @@ static function tagPlainWithWcrft2($text){
 		$tmp = ".inforex_tokenize.tmp";
 		file_put_contents($tmp, $text);
 		$cmd_template = 'cat %s | maca-analyse -qs morfeusz-nkjp-official -i %s -o ccl | wcrft-app %s -i ccl -o ccl -A - 2>/dev/null';
-		$cmd = sprintf($cmd_template, $tmp, $input, Config::Config()->get_wcrft2_config());
+		$cmd = sprintf($cmd_template, $tmp, $input, Config::Cfg()->get_wcrft2_config());
 		$text_tagged = shell_exec($cmd);
 		if (file_exists($tmp)) unlink($tmp);
 		return $text_tagged;		
@@ -88,7 +88,7 @@ static function tagWithMaca($text, $format="xces"){
 	
 	static function tagPremorphWithMacaWcrft($text, $useSentencer=false){
 		$input = $useSentencer ? "premorph" : "premorph-stream-nosent";
-		$wmbt = sprintf("wcrft %s -d %s -i ccl -A -o ccl -", Config::Config()->get_wcrft_config(),Config::Config()->get_path_wcrft_model());
+		$wmbt = sprintf("wcrft %s -d %s -i ccl -A -o ccl -", Config::Cfg()->get_wcrft_config(),Config::Cfg()->get_path_wcrft_model());
 		$text = escapeshellarg($text);
 		$cmd = sprintf('echo %s | maca-analyse -qs morfeusz-nkjp -i %s -o ccl 2>/dev/null | %s 2>/dev/null', $text, $input, $wmbt);
 		ob_start();
@@ -98,7 +98,7 @@ static function tagPremorphWithMacaWcrft($text, $useSentencer=false){
 	}	
 	
 	static function tagPlainWithWcrft($text){
-		$wcrft = sprintf("wcrft %s -d %s -i ccl -o ccl -", Config::Config()->get_wcrft_config(), Config::Config()->get_path_wcrft_model());
+		$wcrft = sprintf("wcrft %s -d %s -i ccl -o ccl -", Config::Cfg()->get_wcrft_config(), Config::Cfg()->get_path_wcrft_model());
 		$cmd = sprintf('echo %s | maca-analyse -qs morfeusz-nkjp -i plain -o ccl | %s', escapeshellarg($text), $wcrft);
 		ob_start();
 		$text_tagged = shell_exec($cmd);
diff --git a/engine/include/utils/CWcclImport.php b/engine/include/utils/CWcclImport.php
index a3d92371..cbd9e854 100644
--- a/engine/include/utils/CWcclImport.php
+++ b/engine/include/utils/CWcclImport.php
@@ -185,8 +185,8 @@ function tag_document($ccl, $r){
 			}
 	
 			/** Sentences */
-			if( Config::Config()->get_insertSentenceTags() && $useSentencer )
-				Premorph::set_sentence_tag($report_id,Config::Config()->get_user());
+			if( Config::Cfg()->get_insertSentenceTags() && $useSentencer )
+				Premorph::set_sentence_tag($report_id,Config::Cfg()->get_user());
 				
 			$db->execute("COMMIT");
 				
diff --git a/engine/page/page_administration_diagnostic_access.php b/engine/page/page_administration_diagnostic_access.php
index 864eedab..ffb1aee2 100755
--- a/engine/page/page_administration_diagnostic_access.php
+++ b/engine/page/page_administration_diagnostic_access.php
@@ -21,11 +21,11 @@ function execute(){
 
 		$items = array();
 
-        $validatorAjax = new PageAccessValidator(Config::Config()->get_path_engine(), "ajax");
+        $validatorAjax = new PageAccessValidator(Config::Cfg()->get_path_engine(), "ajax");
         $validatorAjax->process();
         $items = array_merge($items, $validatorAjax->items);
 
-        $validatorPage = new PageAccessValidator(Config::Config()->get_path_engine(), "page");
+        $validatorPage = new PageAccessValidator(Config::Cfg()->get_path_engine(), "page");
         $validatorPage->process();
         $items = array_merge($items, $validatorPage->items);
 
diff --git a/engine/page/page_corpus_export.php b/engine/page/page_corpus_export.php
index 7dbe1bc3..e1c8b30e 100644
--- a/engine/page/page_corpus_export.php
+++ b/engine/page/page_corpus_export.php
@@ -88,7 +88,7 @@ function getExports($corpus_id){
 	}
 	
 	static function getExportFilePath($export_id){
-		return Config::Config()->get_path_exports().DIRECTORY_SEPARATOR.sprintf("inforex_export_%d.7z", $export_id);
+		return Config::Cfg()->get_path_exports().DIRECTORY_SEPARATOR.sprintf("inforex_export_%d.7z", $export_id);
 	}
 }
 ?>
diff --git a/engine/page/page_corpus_settings.php b/engine/page/page_corpus_settings.php
index 6e0abf58..9ebed989 100644
--- a/engine/page/page_corpus_settings.php
+++ b/engine/page/page_corpus_settings.php
@@ -32,13 +32,13 @@ function execute(){
          * js/page_report_{$subpage}_resize.js — kod JS odpowiedzialny za automatyczne dopasowanie okna do strony.
          * css/page_report_{$subpage}.css — style CSS występujące tylko w danej perspektywie.
          */
-        if (file_exists(Config::Config()->get_path_www() . "/js/page_corpus_{$subpage}.js")){
+        if (file_exists(Config::Cfg()->get_path_www() . "/js/page_corpus_{$subpage}.js")){
             $this->includeJs("js/page_corpus_{$subpage}.js");
         }
-        if (file_exists(Config::Config()->get_path_www() . "/js/page_corpus_{$subpage}_resize.js")){
+        if (file_exists(Config::Cfg()->get_path_www() . "/js/page_corpus_{$subpage}_resize.js")){
             $this->includeJs("js/page_corpus_{$subpage}_resize.js");
         }
-        if (file_exists(Config::Config()->get_path_www() . "/css/page_corpus_{$subpage}.css")){
+        if (file_exists(Config::Cfg()->get_path_www() . "/css/page_corpus_{$subpage}.css")){
             $this->includeCss("css/page_corpus_{$subpage}.css");
         }
 
diff --git a/engine/page/page_export_download.php b/engine/page/page_export_download.php
index 89383c05..a1ee490e 100644
--- a/engine/page/page_export_download.php
+++ b/engine/page/page_export_download.php
@@ -6,7 +6,7 @@
  * See LICENCE 
  */
  
-require_once(implode(DIRECTORY_SEPARATOR, array(Config::Config()->get_path_engine(), "page", "page_corpus_export.php")));
+require_once(implode(DIRECTORY_SEPARATOR, array(Config::Cfg()->get_path_engine(), "page", "page_corpus_export.php")));
 
 class Page_export_download extends CPage{
 
diff --git a/engine/page/page_ner.php b/engine/page/page_ner.php
index 655e8e91..9ea7d3c9 100644
--- a/engine/page/page_ner.php
+++ b/engine/page/page_ner.php
@@ -16,7 +16,7 @@ function __construct(){
 
     function execute(){
 
-		$this->set('models', Config::Config()->get_liner2_api());
+		$this->set('models', Config::Cfg()->get_liner2_api());
 	}
 	
 }
diff --git a/engine/page/page_report.php b/engine/page/page_report.php
index 7153df92..1a4d45b6 100755
--- a/engine/page/page_report.php
+++ b/engine/page/page_report.php
@@ -163,13 +163,13 @@ function execute(){
 		 * js/page_report_{$subpage}_resize.js — kod JS odpowiedzialny za automatyczne dopasowanie okna do strony.
 		 * css/page_report_{$subpage}.css — style CSS występujące tylko w danej perspektywie.
 		 */
-		if (file_exists(Config::Config()->get_path_www() . "/js/page_report_{$subpage}.js")){
+		if (file_exists(Config::Cfg()->get_path_www() . "/js/page_report_{$subpage}.js")){
 			$this->includeJs("js/page_report_{$subpage}.js");
 		}
-		if (file_exists(Config::Config()->get_path_www() . "/js/page_report_{$subpage}_resize.js")){
+		if (file_exists(Config::Cfg()->get_path_www() . "/js/page_report_{$subpage}_resize.js")){
 			$this->includeJs("js/page_report_{$subpage}_resize.js");
 		}
-		if (file_exists(Config::Config()->get_path_www() . "/css/page_report_{$subpage}.css")){
+		if (file_exists(Config::Cfg()->get_path_www() . "/css/page_report_{$subpage}.css")){
 			$this->includeCss("css/page_report_{$subpage}.css");
 		}
 		
diff --git a/engine/page/page_wccl_match_tester.php b/engine/page/page_wccl_match_tester.php
index 94b36222..9b501c49 100644
--- a/engine/page/page_wccl_match_tester.php
+++ b/engine/page/page_wccl_match_tester.php
@@ -23,7 +23,7 @@ function execute(){
 		$annotation_types[] = "t3_set";
 		$annotation_types[] = "t3_range";
 						
-		$this->set('corpora', Config::Config()->wccl_match_tester_corpora);
+		$this->set('corpora', Config::Cfg()->wccl_match_tester_corpora);
 		$this->set('annotation_types', $annotation_types);
 	}
 }
diff --git a/engine/settings.php b/engine/settings.php
index 66073885..98f37f53 100644
--- a/engine/settings.php
+++ b/engine/settings.php
@@ -16,11 +16,6 @@
 ini_set("short_open_tag",1);
 setlocale(LC_CTYPE, "en_US.UTF-8");
 
-// threshold of count types for one set/subset combination
-define('MAX_TYPES_LIMIT_THRESHOLD',300);
-define('MAX_TYPES_LABEL_INDEX',999999999999); // over autoincrement id
-define('MAX_TYPES_NAME_LABEL','...');
-
 require_once(__DIR__ . DIRECTORY_SEPARATOR . 'include.php');
 
 set_error_handler("ErrorService::errorHandler");
diff --git a/engine/templates/inc_footer.tpl b/engine/templates/inc_footer.tpl
index 7b6c84e6..60b2de84 100644
--- a/engine/templates/inc_footer.tpl
+++ b/engine/templates/inc_footer.tpl
@@ -43,7 +43,7 @@
 
 			<span>
 		    {if $Config.log_sql}
-				<div style="text-align: left; background: red; color: white; padding: 3px;"><b>Warning:</b> SQL logging is ON. To disable it set <em style="color: yellow">Config::Config()->put_log_sql(false);</em> in <em style="color: yellow">config.local.php</em>.</div>
+				<div style="text-align: left; background: red; color: white; padding: 3px;"><b>Warning:</b> SQL logging is ON. To disable it set <em style="color: yellow">Config::Cfg()->put_log_sql(false);</em> in <em style="color: yellow">config.local.php</em>.</div>
 			{/if}
 			</span>
      </div>  <!-- id="page" -->
diff --git a/engine/templates/inc_header.tpl b/engine/templates/inc_header.tpl
index e6d2936b..11e159a1 100644
--- a/engine/templates/inc_header.tpl
+++ b/engine/templates/inc_header.tpl
@@ -161,7 +161,7 @@
 	{/if}
 
 	<div id="logo">
-		<a href="{Config::Config()->get_url()}"><img src="gfx/inforex_logo_small.jpg" style="margin: 4px" title="Inforex home page"/></a>
+		<a href="{Config::Cfg()->get_url()}"><img src="gfx/inforex_logo_small.jpg" style="margin: 4px" title="Inforex home page"/></a>
 	</div>
 
 	<div style="float: right; margin-right: 10px; line-height: 30px;">
diff --git a/local/agreement.php b/local/agreement.php
index 655a6087..ff62cbc7 100644
--- a/local/agreement.php
+++ b/local/agreement.php
@@ -8,8 +8,8 @@
  
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 
diff --git a/local/ccl2iob.php b/local/ccl2iob.php
index 467b1ee3..db86c6f4 100644
--- a/local/ccl2iob.php
+++ b/local/ccl2iob.php
@@ -8,8 +8,8 @@
  
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 
diff --git a/local/cli-import-corpus-annotations.php b/local/cli-import-corpus-annotations.php
index 9ba4d344..f49472ce 100644
--- a/local/cli-import-corpus-annotations.php
+++ b/local/cli-import-corpus-annotations.php
@@ -2,8 +2,8 @@
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath . DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath . DIRECTORY_SEPARATOR . 'include.php');
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/") . DIRECTORY_SEPARATOR . "config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/") . DIRECTORY_SEPARATOR . "config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
@@ -42,7 +42,7 @@ function assertContains($needle, $stack)
 try {
     $opt->parseCli($argv);
 
-    Config::Config()->put_dsn(array(
+    Config::Cfg()->put_dsn(array(
         'phptype' => 'mysql',
         'username' => 'inforex',
         'password' => 'password',
@@ -63,7 +63,7 @@ function assertContains($needle, $stack)
     $ignore_duplicates = $opt->exists("ignore-duplicates");
     $ignore_unknown_types = $opt->exists("ignore-unknown-types");
 
-    $cliImporter = new CliAnnotationImporter(Config::Config()->get_dsn(), $verbose);
+    $cliImporter = new CliAnnotationImporter(Config::Cfg()->get_dsn(), $verbose);
     $cliImporter->import_annotations_dir($corpusDir,
         $corpusId,
         $userIds,
diff --git a/local/cli-liner2-nlprest2.php b/local/cli-liner2-nlprest2.php
index 1343d77f..0b139cf6 100644
--- a/local/cli-liner2-nlprest2.php
+++ b/local/cli-liner2-nlprest2.php
@@ -8,8 +8,8 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
@@ -39,7 +39,7 @@
 
     $modelsAnnotationSets = array("n82"=>1, "timex4"=>15);
 
-    $dsn = CliOptCommon::parseDbParameters($opt, Config::Config()->get_dsn());
+    $dsn = CliOptCommon::parseDbParameters($opt, Config::Cfg()->get_dsn());
     $subcorpusIds = $opt->getParameters(PARAM_SUBCORPUS);
     $documentIds = $opt->getParameters(PARAM_DOCUMENT);
     $ownerUserId = $opt->getRequired(PARAM_USER);
diff --git a/local/cli-restore-corpus.php b/local/cli-restore-corpus.php
index 65788193..bb558a76 100644
--- a/local/cli-restore-corpus.php
+++ b/local/cli-restore-corpus.php
@@ -8,8 +8,8 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
@@ -28,7 +28,7 @@
 try{
     /** Parse cli parameters */
 	$opt->parseCli(isset($argv) ? $argv : null);
-    $dsn = CliOptCommon::parseDbParameters($opt, Config::Config()->get_dsn());
+    $dsn = CliOptCommon::parseDbParameters($opt, Config::Cfg()->get_dsn());
 	$corpusId = $opt->getRequired("corpus");
 	$output = $opt->getOptional("output", null);
 
diff --git a/local/cli-tokenize-from-ccl.php b/local/cli-tokenize-from-ccl.php
index af7e33b4..6e9ebb0b 100644
--- a/local/cli-tokenize-from-ccl.php
+++ b/local/cli-tokenize-from-ccl.php
@@ -9,8 +9,8 @@
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath . DIRECTORY_SEPARATOR . "settings.php");
 require_once($enginePath . DIRECTORY_SEPARATOR . 'include.php');
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/") . DIRECTORY_SEPARATOR . "config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/") . DIRECTORY_SEPARATOR . "config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
@@ -43,7 +43,7 @@
             $dbHost = $m[3];
             $dbPort = $m[4];
             $dbName = $m[5];
-            Config::Config()->put_dsn(array(
+            Config::Cfg()->put_dsn(array(
                 'phptype' => 'mysql',
                 'username' => $dbUser,
                 'password' => $dbPass,
@@ -54,7 +54,7 @@
             throw new Exception("DB URI is incorrect. Given '$uri', but expected 'user:pass@host:port/name'");
         }
     }
-    Config::Config()->put_verbose($opt->exists("verbose"));
+    Config::Cfg()->put_verbose($opt->exists("verbose"));
 } catch (Exception $ex) {
     print "!! " . $ex->getMessage() . " !!\n\n";
     $opt->printHelp();
@@ -62,7 +62,7 @@
 }
 
 try {
-    $loader = new CclLoader(Config::Config()->get_dsn(), Config::Config()->get_verbose());
+    $loader = new CclLoader(Config::Cfg()->get_dsn(), Config::Cfg()->get_verbose());
     $dir = new DirectoryIterator(dirname($path));
 
     foreach (new DirectoryIterator($path) as $fileInfo) {
diff --git a/local/cli-upload-txt.php b/local/cli-upload-txt.php
index bd879f2e..107ab145 100644
--- a/local/cli-upload-txt.php
+++ b/local/cli-upload-txt.php
@@ -8,8 +8,8 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
diff --git a/local/daemon-cleanup.php b/local/daemon-cleanup.php
index 874a3f27..11876b61 100644
--- a/local/daemon-cleanup.php
+++ b/local/daemon-cleanup.php
@@ -8,8 +8,8 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
@@ -22,7 +22,7 @@
 
 try{
 	$opt->parseCli(isset($argv) ? $argv : null);
-	Config::Config()->put_dsn(CliOptCommon::parseDbParameters($opt, Config::Config()->get_dsn()));
+	Config::Cfg()->put_dsn(CliOptCommon::parseDbParameters($opt, Config::Cfg()->get_dsn()));
 }catch(Exception $ex){
 	print "!! ". $ex->getMessage() . " !!\n\n";
 	$opt->printHelp();
@@ -31,7 +31,7 @@
 }
 
 try{
-	$daemon = new TaskDaemon(Config::Config()->get_dsn());
+	$daemon = new TaskDaemon(Config::Cfg()->get_dsn());
 	$daemon->tick();
 	sleep(2);
 }
diff --git a/local/daemon-export.php b/local/daemon-export.php
index 4bc8a583..3b15dd8d 100644
--- a/local/daemon-export.php
+++ b/local/daemon-export.php
@@ -8,8 +8,8 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
@@ -58,9 +58,9 @@
 		$dsn['password'] = $dbPass;
 		$dsn['hostspec'] = $dbHost . ":" . $dbPort;
 		$dsn['database'] = $dbName;
-		Config::Config()->put_dsn($dsn);
+		Config::Cfg()->put_dsn($dsn);
 	}
-	Config::Config()->put_verbose($opt->exists("verbose"));
+	Config::Cfg()->put_verbose($opt->exists("verbose"));
 		
 }catch(Exception $ex){
 	print "!! ". $ex->getMessage() . " !!\n\n";
@@ -70,7 +70,7 @@
 }
 
 try{
-	$daemon = new TaskExport(Config::Config());
+	$daemon = new TaskExport(Config::Cfg());
 	$daemon->tick();
 }
 catch(Exception $ex){
diff --git a/local/daemon-grab.php b/local/daemon-grab.php
index ed17eb6b..bf1f2610 100644
--- a/local/daemon-grab.php
+++ b/local/daemon-grab.php
@@ -8,8 +8,8 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 
@@ -51,9 +51,9 @@
 		$dsn['password'] = $dbPass;
 		$dsn['hostspec'] = $dbHost . ":" . $dbPort;
 		$dsn['database'] = $dbName;
-		Config::Config()->put_dsn($dsn);
+		Config::Cfg()->put_dsn($dsn);
 	}
-	Config::Config()->put_verbose($opt->exists("verbose"));
+	Config::Cfg()->put_verbose($opt->exists("verbose"));
 		
 }catch(Exception $ex){
 	print "!! ". $ex->getMessage() . " !!\n\n";
@@ -62,13 +62,13 @@
 	return;
 }
 
-if (!file_exists(Config::Config()->get_path_secured_data()."/grab"))
-	mkdir(Config::Config()->get_path_secured_data()."/grab");
+if (!file_exists(Config::Cfg()->get_path_secured_data()."/grab"))
+	mkdir(Config::Cfg()->get_path_secured_data()."/grab");
 
 // Główna pętla sprawdzająca żądania w kolejce.
 //while (true){
 	try{
-		$daemon = new TaskGrabDaemon(Config::Config());
+		$daemon = new TaskGrabDaemon(Config::Cfg());
 		$daemon->tick();
 		//while ($daemon->tick()){
 		//};
diff --git a/local/daemon-tasks.php b/local/daemon-tasks.php
index 51e22cf8..7dfc5a63 100644
--- a/local/daemon-tasks.php
+++ b/local/daemon-tasks.php
@@ -8,8 +8,8 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
@@ -49,7 +49,7 @@
 			$dbHost = $m[3];
 			$dbPort = $m[4];
 			$dbName = $m[5];
-			Config::Config()->put_dsn(array(
+			Config::Cfg()->put_dsn(array(
 				'phptype' => 'mysqli',
 				'username' => $dbUser,
 				'password' => $dbPass,
@@ -61,7 +61,7 @@
 		}
 	}
 	
-	Config::Config()->put_verbose($opt->exists("verbose"));
+	Config::Cfg()->put_verbose($opt->exists("verbose"));
 			
 }catch(Exception $ex){
 	print "!! ". $ex->getMessage() . " !!\n\n";
@@ -70,7 +70,7 @@
 }
 
 try{
-	$daemon = new TaskDaemon(Config::Config()->get_dsn(), Config::Config()->get_verbose());
+	$daemon = new TaskDaemon(Config::Cfg()->get_dsn(), Config::Cfg()->get_verbose());
 	while ($daemon->tick()){};
 }
 catch(Exception $ex){
@@ -458,7 +458,7 @@ function processUpdateCcl($report_id){
         $nlp = new NlpRest2('wcrft2({"guesser":"false","morfeusz2":"false"})');
         $ccl = $nlp->processSync($content);
 
-		$corpus_dir = sprintf("%s/ccls/corpus%04d", Config::Config()->get_path_secured_data(), $corpus_id);
+		$corpus_dir = sprintf("%s/ccls/corpus%04d", Config::Cfg()->get_path_secured_data(), $corpus_id);
 		if ( !file_exists($corpus_dir) ){
 			$this->info("Create folder: $corpus_dir");
 			mkdir($corpus_dir);
diff --git a/local/daemon-upload.php b/local/daemon-upload.php
index 2b91b2ad..26800739 100644
--- a/local/daemon-upload.php
+++ b/local/daemon-upload.php
@@ -8,8 +8,8 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 
@@ -53,9 +53,9 @@
 		$dsn['password'] = $dbPass;
 		$dsn['hostspec'] = $dbHost . ":" . $dbPort;
 		$dsn['database'] = $dbName;
-		Config::Config()->put_dsn($dsn);
+		Config::Cfg()->put_dsn($dsn);
 	}
-	Config::Config()->put_verbose($opt->exists("verbose"));
+	Config::Cfg()->put_verbose($opt->exists("verbose"));
 		
 }catch(Exception $ex){
 	print "!! ". $ex->getMessage() . " !!\n\n";
@@ -64,15 +64,15 @@
 	return;
 }
 
-if (!file_exists(Config::Config()->get_path_secured_data()."/import"))
-	mkdir(Config::Config()->get_path_secured_data()."/import");
-if (!file_exists(Config::Config()->get_path_secured_data()."/import/corpora"))
-	mkdir(Config::Config()->get_path_secured_data()."/import/corpora");
+if (!file_exists(Config::Cfg()->get_path_secured_data()."/import"))
+	mkdir(Config::Cfg()->get_path_secured_data()."/import");
+if (!file_exists(Config::Cfg()->get_path_secured_data()."/import/corpora"))
+	mkdir(Config::Cfg()->get_path_secured_data()."/import/corpora");
 
 // Główna pętla sprawdzająca żądania w kolejce.
 //while (true){
 	try{
-		$daemon = new TaskUploadDaemon(Config::Config());
+		$daemon = new TaskUploadDaemon(Config::Cfg());
 		$daemon->tick();
 		$daemon = null;
 	}
@@ -169,7 +169,7 @@ function process($task){
 		$user_id = $task['user_id'];
 		
 		// Utwórz katalog na pliki ccl
-		$corpus_dir = sprintf("%s/ccls/corpus%04d", Config::Config()->get_path_secured_data(), $corpus_id);
+		$corpus_dir = sprintf("%s/ccls/corpus%04d", Config::Cfg()->get_path_secured_data(), $corpus_id);
 		if ( !file_exists($corpus_dir) ){
 			$this->info("Create folder: $corpus_dir");
 			// for recursive call, umask guarantee all created
diff --git a/local/export-corpus.php b/local/export-corpus.php
index c28dd69e..19ae205e 100644
--- a/local/export-corpus.php
+++ b/local/export-corpus.php
@@ -33,8 +33,8 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 
diff --git a/local/flags.php b/local/flags.php
index 18cec00a..e8f54cb0 100644
--- a/local/flags.php
+++ b/local/flags.php
@@ -8,8 +8,8 @@
  
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" ). DIRECTORY_SEPARATOR ."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config" ). DIRECTORY_SEPARATOR ."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 
diff --git a/local/import-corpus-cli.php b/local/import-corpus-cli.php
index e002b2eb..da152173 100644
--- a/local/import-corpus-cli.php
+++ b/local/import-corpus-cli.php
@@ -2,8 +2,8 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
 
@@ -28,13 +28,13 @@
 
 try {
     $opt->parseCli(isset($argv) ? $argv : null);
-    $dsn = CliOptCommon::parseDbParameters($opt, Config::Config()->get_dsn());
+    $dsn = CliOptCommon::parseDbParameters($opt, Config::Cfg()->get_dsn());
     $verbose = $opt->exists("verbose");
     $corpusDir = $opt->getRequired("corpus-directory");
     $corpusName = $opt->getRequired("corpus-name");
     $corpusDesc = $opt->getRequired("corpus-description");
     $userId = intval($opt->getRequired("user-id"));
-    Config::Config()->put_user($userId);
+    Config::Cfg()->put_user($userId);
     $annotationSetsIds = array_map('intval', explode(',', $opt->getRequired("annotation-sets")));
 
     gc_disable(); 
diff --git a/local/import-sherlock.php b/local/import-sherlock.php
index d0e335c3..cf9d876a 100644
--- a/local/import-sherlock.php
+++ b/local/import-sherlock.php
@@ -2,8 +2,8 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
@@ -23,7 +23,7 @@
 
 try{
     $opt->parseCli(isset($argv) ? $argv : null);
-    $dsn = CliOptCommon::parseDbParameters($opt, Config::Config()->get_dsn());
+    $dsn = CliOptCommon::parseDbParameters($opt, Config::Cfg()->get_dsn());
     $verbose = $opt->exists("verbose");
     $jsonPath = $opt->getRequired("json");
     $annotationSetId = $opt->getRequired("annotation-set");
diff --git a/local/import-wsd-annotations.php b/local/import-wsd-annotations.php
index 9e50e004..72ccc286 100644
--- a/local/import-wsd-annotations.php
+++ b/local/import-wsd-annotations.php
@@ -2,8 +2,8 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
@@ -24,7 +24,7 @@
 try {
     ini_set('memory_limit', '1024M');
     $opt->parseCli(isset($argv) ? $argv : null);
-    $dsn = CliOptCommon::parseDbParameters($opt, Config::Config()->get_dsn());
+    $dsn = CliOptCommon::parseDbParameters($opt, Config::Cfg()->get_dsn());
     $verbose = $opt->exists("verbose");
     $jsonPath = $opt->getRequired("json");
     $annotationSetId = $opt->getRequired("annotation-set");
diff --git a/local/liner2.php b/local/liner2.php
index c0d3a25e..eb049787 100644
--- a/local/liner2.php
+++ b/local/liner2.php
@@ -8,8 +8,8 @@
  
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath. DIRECTORY_SEPARATOR . ".." . DIRECTORY_SEPARATOR . "config") . DIRECTORY_SEPARATOR ."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 
@@ -42,22 +42,22 @@
 		}
 	}
 	
-	Config::Config()->put_dsn(array(
+	Config::Cfg()->put_dsn(array(
 	    			'phptype'  => 'mysqli',
 	    			'username' => isset($dbUser) ? $dbUser : "",
 	    			'password' => isset($dbPass) ? $dbPass : "",
 	    			'hostspec' => isset($dbHost) ? $dbHost : "localhost",
 	    			'database' => isset($dbName) ? $dbName : ""));	
-	$db = new Database(Config::Config()->get_dsn());
+	$db = new Database(Config::Cfg()->get_dsn());
 	$db->set_encoding('utf8'); 	
 	// SET CHARACTER SET sets only subset of SET NAMES params
 	// which is set in Databse constructor
 	//$db->execute("SET CHARACTER SET utf8");
 
-	Config::Config()->put_corpus($opt->getParameters("corpus"));
-	Config::Config()->put_subcorpus($opt->getParameters("subcorpus"));
-	Config::Config()->put_documents($opt->getParameters("document"));
-	Config::Config()->put_ini($opt->getRequired("ini"));
+	Config::Cfg()->put_corpus($opt->getParameters("corpus"));
+	Config::Cfg()->put_subcorpus($opt->getParameters("subcorpus"));
+	Config::Cfg()->put_documents($opt->getParameters("document"));
+	Config::Cfg()->put_ini($opt->getRequired("ini"));
 	
 }catch(Exception $ex){
 	print "!! ". $ex->getMessage() . " !!\n\n";
@@ -112,5 +112,5 @@ function main ($config){
 } 
 
 /******************** main invoke         *********************************************/
-main(Config::Config());
+main(Config::Cfg());
 ?>
diff --git a/local/slavicner2019-annotate.php b/local/slavicner2019-annotate.php
index 2081ec00..b337909c 100644
--- a/local/slavicner2019-annotate.php
+++ b/local/slavicner2019-annotate.php
@@ -2,8 +2,8 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
diff --git a/local/slavicner2019.php b/local/slavicner2019.php
index 468c3503..c02cf109 100644
--- a/local/slavicner2019.php
+++ b/local/slavicner2019.php
@@ -1,8 +1,8 @@
 <?php
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 require_once($enginePath . "/clioptcommon.php");
diff --git a/local/tokenize-update.php b/local/tokenize-update.php
index 02a4b36c..6ca96764 100644
--- a/local/tokenize-update.php
+++ b/local/tokenize-update.php
@@ -8,8 +8,8 @@
 
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 
@@ -56,7 +56,7 @@
 		}
 	}
 
-    Config::Config()->put_tagsetName('nkjp');
+    Config::Cfg()->put_tagsetName('nkjp');
 
 	$dsn = array();
 	$dsn['phptype'] = 'mysqli';
@@ -64,20 +64,20 @@
 	$dsn['password'] = $dbPass;
 	$dsn['hostspec'] = $dbHost . ":" . $dbPort;
 	$dsn['database'] = $dbName;
-	Config::Config()->put_dsn($dsn);
+	Config::Cfg()->put_dsn($dsn);
 	
-	Config::Config()->put_discardSentenceTags($opt->exists("discard-sentence-tags"));
-	Config::Config()->put_insertSentenceTags($opt->exists("insert-sentence-tags"));
-	Config::Config()->put_analyzer($opt->getRequired("analyzer"));
-	Config::Config()->put_corpus($opt->getParameters("corpus"));
-	Config::Config()->put_documents($opt->getParameters("document"));
-	Config::Config()->put_flags(null);
-	Config::Config()->put_subcorpus($opt->getParameters("subcorpus"));
-	Config::Config()->put_user($opt->getOptional("user","1"));
+	Config::Cfg()->put_discardSentenceTags($opt->exists("discard-sentence-tags"));
+	Config::Cfg()->put_insertSentenceTags($opt->exists("insert-sentence-tags"));
+	Config::Cfg()->put_analyzer($opt->getRequired("analyzer"));
+	Config::Cfg()->put_corpus($opt->getParameters("corpus"));
+	Config::Cfg()->put_documents($opt->getParameters("document"));
+	Config::Cfg()->put_flags(null);
+	Config::Cfg()->put_subcorpus($opt->getParameters("subcorpus"));
+	Config::Cfg()->put_user($opt->getOptional("user","1"));
 	
-	if ( !in_array(Config::Config()->get_analyzer(), $tools))
-		throw new Exception("Unrecognized tool. ".Config::Config()->get_analyzer()." not in [".implode(", ", $tools)."]");
-	if (!Config::Config()->get_corpus() && !Config::Config()->get_subcorpus() && !Config::Config()->get_documents())
+	if ( !in_array(Config::Cfg()->get_analyzer(), $tools))
+		throw new Exception("Unrecognized tool. ".Config::Cfg()->get_analyzer()." not in [".implode(", ", $tools)."]");
+	if (!Config::Cfg()->get_corpus() && !Config::Cfg()->get_subcorpus() && !Config::Cfg()->get_documents())
 		throw new Exception("No corpus, subcorpus nor document id set");
 	
 	$flags = null;
@@ -98,7 +98,7 @@
 				throw new Exception("Flag is incorrect. Given '$flag', but exptected 'name=value'");
 			}	
 		}		
-		Config::Config()->put_flags($flags);
+		Config::Cfg()->put_flags($flags);
 	}		
 		
 }catch(Exception $ex){
@@ -307,5 +307,5 @@ function tag_documents($config, $db, $ids, $formats, $tagset_id ){
 }
 
 /******************** main invoke         *********************************************/
-main(Config::Config());
+main(Config::Cfg());
 ?>
diff --git a/local/tokenize.php b/local/tokenize.php
index fdb2b16d..6e5cbff7 100644
--- a/local/tokenize.php
+++ b/local/tokenize.php
@@ -8,8 +8,8 @@
  
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 
@@ -55,7 +55,7 @@
 		}
 	}
 
-    Config::Config()->put_tagsetName('nkjp');
+    Config::Cfg()->put_tagsetName('nkjp');
 
 	$dsn = array();
 	$dsn['phptype'] = 'mysqli';
@@ -63,20 +63,20 @@
 	$dsn['password'] = $dbPass;
 	$dsn['hostspec'] = $dbHost . ":" . $dbPort;
 	$dsn['database'] = $dbName;
-	Config::Config()->put_dsn($dsn);
+	Config::Cfg()->put_dsn($dsn);
 	
-	Config::Config()->put_discardSentenceTags($opt->exists("discard-sentence-tags"));
-	Config::Config()->put_insertSentenceTags($opt->exists("insert-sentence-tags"));
-	Config::Config()->put_analyzer($opt->getRequired("analyzer"));
-	Config::Config()->put_corpus($opt->getParameters("corpus"));
-	Config::Config()->put_documents($opt->getParameters("document"));
-	Config::Config()->put_flags(null);
-	Config::Config()->put_subcorpus($opt->getParameters("subcorpus"));
-	Config::Config()->put_user($opt->getOptional("user","1"));
+	Config::Cfg()->put_discardSentenceTags($opt->exists("discard-sentence-tags"));
+	Config::Cfg()->put_insertSentenceTags($opt->exists("insert-sentence-tags"));
+	Config::Cfg()->put_analyzer($opt->getRequired("analyzer"));
+	Config::Cfg()->put_corpus($opt->getParameters("corpus"));
+	Config::Cfg()->put_documents($opt->getParameters("document"));
+	Config::Cfg()->put_flags(null);
+	Config::Cfg()->put_subcorpus($opt->getParameters("subcorpus"));
+	Config::Cfg()->put_user($opt->getOptional("user","1"));
 	
-	if ( !in_array(Config::Config()->get_analyzer(), array("takipi", "maca", "wcrft", "wcrft2", "morphodita")))
-		throw new Exception("Unrecognized analyzer. ".Config::Config()->get_analyzer());
-	if (!Config::Config()->gut_corpus() && !Config::Config()->get_subcorpus() && !Config::Config()->get_documents())
+	if ( !in_array(Config::Cfg()->get_analyzer(), array("takipi", "maca", "wcrft", "wcrft2", "morphodita")))
+		throw new Exception("Unrecognized analyzer. ".Config::Cfg()->get_analyzer());
+	if (!Config::Cfg()->gut_corpus() && !Config::Cfg()->get_subcorpus() && !Config::Cfg()->get_documents())
 		throw new Exception("No corpus, subcorpus nor document id set");
 	
 	$flags = null;
@@ -97,7 +97,7 @@
 				throw new Exception("Flag is incorrect. Given '$flag', but exptected 'name=value'");
 			}	
 		}		
-		Config::Config()->put_flags($flags);
+		Config::Cfg()->put_flags($flags);
 	}		
 		
 }catch(Exception $ex){
@@ -401,5 +401,5 @@ function progress($act_num,$all){
 }
 
 /******************** main invoke         *********************************************/
-main(Config::Config());
+main(Config::Cfg());
 ?>
diff --git a/local/upload.php b/local/upload.php
index 03e2e21f..640c73c9 100644
--- a/local/upload.php
+++ b/local/upload.php
@@ -8,8 +8,8 @@
  
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 
diff --git a/local/wsd-annotate.php b/local/wsd-annotate.php
index 3dd3cd1a..6a15834e 100644
--- a/local/wsd-annotate.php
+++ b/local/wsd-annotate.php
@@ -6,8 +6,8 @@
  
 $enginePath = realpath(implode(DIRECTORY_SEPARATOR, array(dirname(__FILE__), "..", "engine")));
 require_once($enginePath. DIRECTORY_SEPARATOR . "settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 require_once($enginePath . "/cliopt.php");
 
diff --git a/phpunit/tests/engine/Config/ConfigTest.php b/phpunit/tests/engine/Config/ConfigTest.php
new file mode 100644
index 00000000..e2d87d21
--- /dev/null
+++ b/phpunit/tests/engine/Config/ConfigTest.php
@@ -0,0 +1,146 @@
+<?php
+
+use engine\Config\Singleton as Singleton;
+
+class ConfigTest extends PHPUnit_Framework_TestCase {
+
+    public function test_instanceOf() {
+
+		$obj = Config::Cfg();
+		$classname = "Config";	
+		$msg = "creating of ".$classname." class instance failed.";
+		$this->assertInstanceOf($classname, $obj, $msg);
+
+    } // test_instanceOf()
+
+	public function test_reinstance() {
+
+		$this->obj = Config::Cfg();
+		$magicToken = "ghghdsah";
+		$this->obj->property=$magicToken;
+		$localobj = Config::Cfg();
+		$msg = "Config class doesn't preserve static property. May be is not the same instance...";
+		$this->assertSame($localobj->property,$magicToken,$msg);
+
+	} // test_reinstance()
+
+	public function test_get() {
+
+		$expectedValue = "gpw";
+		$result = Config::Cfg()->get_sid();
+		$msg = "Cannot read sid property from config";
+		$this->assertSame($expectedValue,$result,$msg);
+
+		// odczyt parametru o wartości null
+		$expectedValue = null;
+        $result = Config::Cfg()->get_federationLoginUrl();
+        $msg = "Cannot read federationLoginUrl as null from config";
+        $this->assertSame($expectedValue,$result,$msg);
+
+		// odczyt nieistniejącego parametru
+		$propertyName = "jakasnieistniejacanazwaparametru";
+		try {
+			$commandName = "get_".$propertyName;
+			$result = Config::Cfg()->$commandName();
+			// tu dojdzie jeśli nie zrzuci wyjątku
+			$this->fail("Didn't generate exception on read unexistent property ".$propertyName."from Config");
+		} catch ( ConfigException $e ) {
+			$expectedMessage = "Parameter '".$propertyName."' not defined in the configuration file.";
+			$msg = "Unproper message for exception in Config get_".$propertyName."()";
+			$this->assertSame($e->getMessage(),$expectedMessage,$msg);
+		}
+
+	} // test_get()
+
+	public function test_put() {
+	
+		$expectedValue = "cośtam";
+		$propertyName = "takanazwacojejjeszczeniema";
+		$commandName = "put_".$propertyName;
+		Config::Cfg()->$commandName($expectedValue);
+		$commandName = "get_".$propertyName;
+		$result = Config::Cfg()->$commandName();
+        $msg = "Cannot write ".$propertyName." property to config";
+        $this->assertSame($expectedValue,$result,$msg);
+
+		// test zapisu parametru o wartości null
+        $expectedValue = null;
+        $propertyName = "zmiennaowartoscinull";
+        $commandName = "put_".$propertyName;
+        Config::Cfg()->$commandName($expectedValue);
+        $commandName = "get_".$propertyName;
+        $result = Config::Cfg()->$commandName();
+        $msg = "Cannot write ".$propertyName." property as null to config";
+        $this->assertSame($expectedValue,$result,$msg);
+
+	} // test_put()
+
+    public function test_update() {
+
+        $expectedValue = "cośtam";
+        $propertyName = "takanazwacojejjeszczeniema";
+        $commandName = "put_".$propertyName;
+        Config::Cfg()->$commandName("firstvalue");
+		// teraz aktualizacja wartości istniejącego parametru
+		Config::Cfg()->$commandName($expectedValue);
+		// i odczyt tego co tam jest aktualnie
+        $commandName = "get_".$propertyName;
+        $result = Config::Cfg()->$commandName();
+        $msg = "Cannot write ".$propertyName." property from config";
+        $this->assertSame($expectedValue,$result,$msg);
+
+    } // test_update()
+
+	public function test_loadConfigFromFile() {
+
+        $virtualDir = org\bovigo\vfs\vfsStream::setup('root',null,[]);
+		$expectedValue = "cośtam";
+        $propertyName = "takanazwacojejjeszczeniema";
+        $commandName = "get_".$propertyName;
+
+		// najpierw wg. starego stylu configa
+		// generate test file
+		$fileName = $virtualDir->url()."/oldConfigTest.php";
+		$configLine = "<?php ".'$config'."->".$propertyName." = '".$expectedValue."'; ?>";
+		file_put_contents($fileName,$configLine);
+		
+		// loadOldLocalConfig jest funkcja prywatną klasy Config
+		// aby sprowokować jej wykonanie nalezy ustawić zmienną
+		// konfiguracyjną localConfigFilename, na nazwę pliku,
+		// i wtedy klasa Config próbuje załadować ten plik zaraz po
+		// ustawieniu zmiennej, najpierw wg. starego stylu, a jeśli
+		// to skończy się wyjątkiem, to według nowego:
+		Config::Cfg()->put_localConfigFilename($fileName);
+		// sprawdzamy, czy parametr został dodany prawidłowo
+		$result = Config::Cfg()->$commandName();
+        $msg = "Error reading old config file ".$fileName;
+        $this->assertSame($expectedValue,$result,$msg);
+
+		// teraz wg. nowej synataktyki pliku
+		$expectedValue = "cośinnego";
+		$configLine = "<?php ".'$config'."->put_".$propertyName."('".$expectedValue."'); ?>";
+        file_put_contents($fileName,$configLine);
+
+		// wymusza przeładowanie pliku configa
+		Config::Cfg()->put_localConfigFilename($fileName);
+        // sprawdzamy, czy parametr został dodany prawidłowo
+        $result = Config::Cfg()->$commandName();
+        $msg = "Error reading old config file ".$fileName;
+        $this->assertSame($expectedValue,$result,$msg);
+
+		// skasowanie pliku lokalnego configa po teście
+		//unlink($fileName);    // przy wirtualnym filesystemie niepotrzebne
+
+	} // test_loadConfigFromFile()
+
+	public function test_dumpConfigSets() {
+
+		$result=Config::Cfg()->dumpConfigSets();
+		//var_dump($result);
+		$msg = "dumpConfigSets doesn't return array";
+		$this->assertTrue(is_array($result),$msg);
+
+	} // test_dumpConfigSets()
+
+}
+?>
diff --git a/phpunit/tests/engine/Config/SingletonTest.php b/phpunit/tests/engine/Config/SingletonTest.php
new file mode 100644
index 00000000..32f10c54
--- /dev/null
+++ b/phpunit/tests/engine/Config/SingletonTest.php
@@ -0,0 +1,32 @@
+<?php
+
+use engine\Config\Singleton as Singleton;
+
+// klasy abstrakcyjnej nie da się testowac bezpośrednio, bo nie można
+// utworzyć jej instancji. Musimy zrobić identyczną klasę rzeczywistą
+class SingletonShadow extends Singleton\Singleton {};
+
+class SingletonTest extends PHPUnit_Framework_TestCase {
+
+    public function test_instanceOf() {
+
+		$classname = "SingletonShadow";
+		$this->obj = $classname::getInstance();
+		$msg = "creating of ".$classname." class instance failed.";
+		$this->assertTrue($this->obj instanceof Singleton\Singleton, $msg);
+
+    } // test_instanceOf()
+
+	public function test_reinstance() {
+
+		$this->obj = SingletonShadow::getInstance();
+		$magicToken = "ghghdsah";
+		$this->obj->property=$magicToken;
+		$localobj = SingletonShadow::getInstance();
+		$msg = "Singleton class doesn't preserve static property. May be is not the same instance...";
+		$this->assertSame($localobj->property,$magicToken,$msg);
+
+	} // test_reinstance()
+
+}
+?>
diff --git a/phpunit/tests/engine/include/database/CDbAnnotationTest.php b/phpunit/tests/engine/include/database/CDbAnnotationTest.php
index cf4f8455..be3af6d2 100644
--- a/phpunit/tests/engine/include/database/CDbAnnotationTest.php
+++ b/phpunit/tests/engine/include/database/CDbAnnotationTest.php
@@ -1,10 +1,6 @@
 <?php
 
 mb_internal_encoding("UTF-8");
-// from settings.php
-define('MAX_TYPES_LIMIT_THRESHOLD',300);
-define('MAX_TYPES_LABEL_INDEX',999999999999); // over autoincrement id
-define('MAX_TYPES_NAME_LABEL','...');
 
 class CDbAnnotationTest extends PHPUnit_Framework_TestCase
 {
diff --git a/phpunit/tests/engine/include/export/FileWriterTest.php b/phpunit/tests/engine/include/export/FileWriterTest.php
index 30a4748b..ce48b076 100644
--- a/phpunit/tests/engine/include/export/FileWriterTest.php
+++ b/phpunit/tests/engine/include/export/FileWriterTest.php
@@ -1,7 +1,6 @@
 <?php
 
 mb_internal_encoding("UTF-8");
-//use org\bovigo\vfs\vfsStream; // for vfsStream
 
 class FileWriterTest extends PHPUnit_Framework_TestCase {
 
diff --git a/public_html/css.php b/public_html/css.php
index 029ad30b..726cc586 100644
--- a/public_html/css.php
+++ b/public_html/css.php
@@ -8,13 +8,13 @@
 
 $enginePath = realpath(__DIR__ . "/../engine/");
 require_once($enginePath . "/settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 /********************************************************************8
  * Połączenie z bazą danych (nowy sposób)
  */
-$db = new Database(Config::Config()->get_dsn());
+$db = new Database(Config::Cfg()->get_dsn());
 $db->set_encoding('utf8');
 /********************************************************************/
 
diff --git a/public_html/image.php b/public_html/image.php
index e6b83a13..a02f8094 100644
--- a/public_html/image.php
+++ b/public_html/image.php
@@ -8,13 +8,13 @@
 
 $enginePath = realpath(__DIR__ . "/../engine/");
 require_once($enginePath."/settings.php");
-Config::Config()->put_path_engine($enginePath);
-Config::Config()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
+Config::Cfg()->put_path_engine($enginePath);
+Config::Cfg()->put_localConfigFilename(realpath($enginePath . "/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
 /********************************************************************8
  * Połączenie z bazą danych (nowy sposób)
  */
-$db=new Database(Config::Config()->get_dsn());
+$db=new Database(Config::Cfg()->get_dsn());
 $db->set_encoding('utf8');
 /********************************************************************/
 ob_start();
@@ -24,7 +24,7 @@
 $width = isset($_GET['width']) ? intval($_GET['width']) : 0;
 
 if ($row){
-	$filename = Config::Config()->get_path_secured_data() . "/images/" . $row['id']."_".$row['hash_name'];
+	$filename = Config::Cfg()->get_path_secured_data() . "/images/" . $row['id']."_".$row['hash_name'];
 	$ext = strtolower(pathinfo($filename, PATHINFO_EXTENSION));
 	
 	if ($ext == "png" )
diff --git a/public_html/index.php b/public_html/index.php
index 1919c668..256b9614 100644
--- a/public_html/index.php
+++ b/public_html/index.php
@@ -22,14 +22,14 @@
     CookieResetter::resetAllCookies();
     //DebugLogger::logAllDynamicVariables(); // log all dynamic HTTP variables
 
-	Config::Config()->put_path_engine($enginePath);
-	Config::Config()->put_localConfigFilename(realpath($enginePath."/../config/").DIRECTORY_SEPARATOR."config.local.php");
+	Config::Cfg()->put_path_engine($enginePath);
+	Config::Cfg()->put_localConfigFilename(realpath($enginePath."/../config/").DIRECTORY_SEPARATOR."config.local.php");
 
-	if ( !file_exists(Config::Config()->get_path_engine() . "/templates_c") ){
-		throw new Exception("Folder '" . Config::Config()->get_path_engine() . "/templates_c' does not exist");
+	if ( !file_exists(Config::Cfg()->get_path_engine() . "/templates_c") ){
+		throw new Exception("Folder '" . Config::Cfg()->get_path_engine() . "/templates_c' does not exist");
 	}
 
-	if ( Config::Config()->get_offline() ){
+	if ( Config::Cfg()->get_offline() ){
 		$variables = array();
 		$inforex = new InforexWeb();
 		$inforex->doPage("offline", $variables);
@@ -39,14 +39,14 @@
 	ob_clean();
 
 	$p = new InforexWeb();
-	$db = new Database(Config::Config()->get_dsn(), Config::Config()->get_log_sql(), Config::Config()->get_log_output(), Config::Config()->get_db_charset());
+	$db = new Database(Config::Cfg()->get_dsn(), Config::Cfg()->get_log_sql(), Config::Cfg()->get_log_output(), Config::Cfg()->get_db_charset());
 	
-	$auth = new UserAuthorize(Config::Config()->get_dsn());
+	$auth = new UserAuthorize(Config::Cfg()->get_dsn());
 	$auth->authorize(isset($_POST['logout']) && ($_POST['logout']=="1"));
 	$user = $auth->getUserData();
 
 	// federation login is enabled
-	if(Config::Config()->get_federationLoginUrl()){
+	if(Config::Cfg()->get_federationLoginUrl()){
 		$clarinUser = $auth->getClarinUser();
 
 		// try to connect to local account

From efb7004f5002e8f6ef13760cc3e72a420d021115 Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Wed, 27 Dec 2023 18:59:10 +0100
Subject: [PATCH 153/154] fix merging

---
 engine/include/export/CclExportDocument.php   | 10 +++--
 engine/include/functions/func_roles.php       |  6 ++-
 engine/include/structs/CclChunk.php           |  2 +-
 engine/include/structs/CclDocument.php        | 24 +++++++----
 engine/include/structs/CclSentence.php        |  2 +-
 engine/include/structs/CclToken.php           |  4 +-
 engine/include/utils/CCookieManager.php       | 14 ++++--
 engine/include/utils/CReportContent.php       |  7 +--
 .../PerspectiveAnnotator.php                  | 43 +++++++++++++------
 9 files changed, 77 insertions(+), 35 deletions(-)

diff --git a/engine/include/export/CclExportDocument.php b/engine/include/export/CclExportDocument.php
index cd492fd0..48bef54f 100644
--- a/engine/include/export/CclExportDocument.php
+++ b/engine/include/export/CclExportDocument.php
@@ -16,7 +16,11 @@ class CclExportDocument extends CclDocument {
 	 * see: createFromReportAndTokensSentence, was createFromReportAndTokens()
 	 */	 
 	public function __construct(&$report, &$tokens, &$tags){
-		$fileName = str_pad($report['id'],8,'0',STR_PAD_LEFT);
+
+        $reportIdStr = isset($report['id']) ? $report['id'] : '';
+        $reportContent = isset($report['content']) ? $report['content'] :'';
+
+		$fileName = str_pad($reportIdStr,8,'0',STR_PAD_LEFT);
 		
 		$this->setFileName($fileName);
 		$this->setSubcorpus(
@@ -27,7 +31,7 @@ public function __construct(&$report, &$tokens, &$tags){
         );
 		$this->setReport($report);
 	
-		$chunkList = explode('<\\chunk>', $report['content']);
+		$chunkList = explode('<\\chunk>', $reportContent);
 
 		$from = 0;
 		$to = 0;
@@ -56,7 +60,7 @@ public function __construct(&$report, &$tokens, &$tags){
 			$from = $to+1;		
 		}	
 		
-		$htmlStr = new HtmlStr2(strip_tags($report['content']), false);
+		$htmlStr = new HtmlStr2(strip_tags($reportContent), false);
 			
 		// Podziel tokeny miedzy chunkami
 		$tokenIndex = 0;
diff --git a/engine/include/functions/func_roles.php b/engine/include/functions/func_roles.php
index 9a4adee6..e02426a3 100644
--- a/engine/include/functions/func_roles.php
+++ b/engine/include/functions/func_roles.php
@@ -51,7 +51,11 @@ function hasRole($role){
  */
 function hasCorpusRole($role){
 	global $corpus, $user;
-	return isset($corpus['role'][$user['user_id']][$role]) || isCorpusOwner();
+    $defined =  isset($user['user_id'])
+                && isset($corpus['role'])
+                && isset($corpus['role'][$user['user_id']])
+                && isset($corpus['role'][$user['user_id']][$role]);
+	return $defined || isCorpusOwner();
 }
 
 /**
diff --git a/engine/include/structs/CclChunk.php b/engine/include/structs/CclChunk.php
index 4bd9be47..6b83ddfa 100644
--- a/engine/include/structs/CclChunk.php
+++ b/engine/include/structs/CclChunk.php
@@ -18,7 +18,7 @@ class CclChunk{
 	var $sentences = array();	
 	
 	function addSentence($sentence){
-		assert('$sentence instanceof CclSentence');
+		assert($sentence instanceof CclSentence);
         $sentence->setSentenceIndexInTokens(count($this->sentences));
 		$this->sentences[] = $sentence;
 	}
diff --git a/engine/include/structs/CclDocument.php b/engine/include/structs/CclDocument.php
index f519d1fc..a53b9500 100644
--- a/engine/include/structs/CclDocument.php
+++ b/engine/include/structs/CclDocument.php
@@ -25,7 +25,7 @@ class CclDocument{
 	var $char2token = array();
 	
 	function addError($error){
-		assert('$error instanceof CclError');
+		assert($error instanceof CclError);
 		$this->errors[] = $error;
 	}
 	
@@ -59,13 +59,13 @@ function setSubcorpus($subcorpus){
 	} 
 	
 	function addChunk($chunk){
-		assert('$chunk instanceof CclChunk');
+		assert($chunk instanceof CclChunk);
         $chunk->setChunkIndexInTokens(count($this->chunks)); 
 		$this->chunks[] = $chunk;
 	}
 	
 	function addToken($token){
-		assert('$token instanceof CclToken');
+		assert($token instanceof CclToken);
 		$index = count($this->tokens);
 		$this->tokens[] = $token;
 		for ( $i=$token->getFrom(); $i<=$token->getTo(); $i++)
@@ -98,7 +98,9 @@ function getRelations(){
 	
 	function setAnnotationLemma($annotation_lemma){
 
-		if ( !isset($this->char2token[$annotation_lemma['from']])){
+		if (   !isset($annotation_lemma['from'])
+            || !isset($this->char2token[$annotation_lemma['from']])
+            ){
 			$e = new CclError();
 			$e->setClassName("CclDocument");
 			$e->setFunctionName("setAnnotationLemma");
@@ -136,7 +138,9 @@ function setAnnotationLemma($annotation_lemma){
 
     function setAnnotationProperty($annotation_property){
 
-        if ( !isset($this->char2token[$annotation_property['from']])){
+        if (    !isset($annotation_property['from']) 
+             || !isset($this->char2token[$annotation_property['from']])
+            ){
             $e = new CclError();
             $e->setClassName("CclDocument");
             $e->setFunctionName("setAnnotation");
@@ -146,7 +150,9 @@ function setAnnotationProperty($annotation_property){
             return;
         }
 
-        if ( !isset($this->char2token[$annotation_property['to']])){
+        if (   !isset($annotation_property['to'])
+            || !isset($this->char2token[$annotation_property['to']])
+            ){
             $e = new CclError();
             $e->setClassName("CclDocument");
             $e->setFunctionName("setAnnotation");
@@ -174,9 +180,11 @@ function setAnnotationProperty($annotation_property){
 	function setAnnotation($annotation){
 		$found = false;
 		$sentence = null; //parent sentence 
-		$type = $annotation['type'];
+		$type = isset($annotation['type']) ? $annotation['type'] :'';
 
-		if ( !isset($this->char2token[$annotation['from']]) ){
+		if (   !isset($annotation['from'])
+            || !isset($this->char2token[$annotation['from']]) 
+            ){
 			$e = new CclError();
 			$e->setClassName("CclDocument");
 			$e->setFunctionName("setAnnotation");
diff --git a/engine/include/structs/CclSentence.php b/engine/include/structs/CclSentence.php
index cfce19db..e132527f 100644
--- a/engine/include/structs/CclSentence.php
+++ b/engine/include/structs/CclSentence.php
@@ -23,7 +23,7 @@ function setId($id){
 	}
 	
 	function addToken($token){
-		assert('$token instanceof CclToken');
+		assert($token instanceof CclToken);
 		$this->tokens[] = $token;		
 	}
 	
diff --git a/engine/include/structs/CclToken.php b/engine/include/structs/CclToken.php
index d8e97712..54803dac 100644
--- a/engine/include/structs/CclToken.php
+++ b/engine/include/structs/CclToken.php
@@ -48,7 +48,9 @@ function setTo($to){
 	}
 	
 	function setAnnotationLemma($annotation_lemma){
-		$this->prop[$annotation_lemma["type"].":lemma"] = $annotation_lemma["lemma"];
+        $type = (isset($annotation_lemma["type"]) && ($annotation_lemma["type"])) ? $annotation_lemma["type"] : '';
+        $lemma = (isset($annotation_lemma["lemma"]) && ($annotation_lemma["lemma"])) ? $annotation_lemma["lemma"] : null;
+		$this->prop[$type.":lemma"] = $lemma;
 		return true;
 	}
 
diff --git a/engine/include/utils/CCookieManager.php b/engine/include/utils/CCookieManager.php
index 8e3b4482..078af7f3 100644
--- a/engine/include/utils/CCookieManager.php
+++ b/engine/include/utils/CCookieManager.php
@@ -32,7 +32,10 @@ static function getAnnotatorWSDAnnotationSet(){
      * @return a list of annotation type identifiers
      */
     static function getAnnotationTypeTreeAnnotationTypes($corpusId){
-        $annotationTypesStr = trim(strval($_COOKIE[$corpusId . '_annotation_lemma_types']));
+        $annotationTypesStr = 
+            isset($_COOKIE[$corpusId . '_annotation_lemma_types'])
+            ? trim(strval($_COOKIE[$corpusId . '_annotation_lemma_types']))
+            : '';
         $annotationTypes = array();
         foreach ( explode(",", $annotationTypesStr) as $id ){
             $id = intval($id);
@@ -80,7 +83,9 @@ static function getRelationAgreementRelationTypes($corpusId){
     }
 
     static function getSelectedAnnotationTypeTreeAnnotationTypes($corpusId){
-        $annotationTypesStr = trim(strval($_COOKIE[$corpusId . '_annotation_lemma_layers']));
+        $annotationTypesStr = isset($_COOKIE[$corpusId . '_annotation_lemma_layers']) 
+            ? trim(strval($_COOKIE[$corpusId . '_annotation_lemma_layers']))
+            : '' ;
         $annotationTypes = array();
         foreach ( explode(",", $annotationTypesStr) as $id ){
             $id = intval($id);
@@ -97,7 +102,8 @@ static function getSelectedAnnotationTypeTreeAnnotationTypes($corpusId){
      * @return a list of relation set identifiers
      */
     static function getRelationSets($corpusId){
-        $relationSetsStr = trim(strval($_COOKIE[$corpusId . '_relation_sets']));
+        $relationSetsStr = isset($_COOKIE[$corpusId . '_relation_sets'])
+            ? trim(strval($_COOKIE[$corpusId . '_relation_sets'])) :'';
         $relationSets = array();
         foreach ( explode(",", $relationSetsStr) as $id ){
             $id = intval($id);
@@ -108,4 +114,4 @@ static function getRelationSets($corpusId){
         return $relationSets;
     }
 
-}
\ No newline at end of file
+}
diff --git a/engine/include/utils/CReportContent.php b/engine/include/utils/CReportContent.php
index 1e0321cb..3f727ad7 100644
--- a/engine/include/utils/CReportContent.php
+++ b/engine/include/utils/CReportContent.php
@@ -141,9 +141,10 @@ static function insertAnnotationsWithRelations(HtmlStr2 $htmlStr, $annotations,
      * @return HtmlStr2
      */
     static function getHtmlStr($report){
-        $content = $report['content'];
+        $content = isset($report['content']) ? $report['content'] :'';
+        $format = isset($report['format']) ? $report['format'] :'';
         // Escape html special characters for plain format
-        if ( $report['format'] == 'plain'){
+        if ( $format == 'plain'){
             $content = htmlspecialchars($content);
         }
         return new HtmlStr2($content, true);
@@ -157,4 +158,4 @@ static function getHtmlStrForReport($report){
         }
         return new HtmlStr2($content, true);
     }
-}
\ No newline at end of file
+}
diff --git a/engine/page/report_perspectives/PerspectiveAnnotator.php b/engine/page/report_perspectives/PerspectiveAnnotator.php
index cbc76011..362b6f12 100644
--- a/engine/page/report_perspectives/PerspectiveAnnotator.php
+++ b/engine/page/report_perspectives/PerspectiveAnnotator.php
@@ -35,11 +35,16 @@ function execute(){
 		$an_source = null;
 		$anUserIds = null;
 		$annotation_mode = 'final';
-        $report = $this->page->report;
-        $corpusId = $corpus['id'];
+        $report = isset($this->page->report) ? $this->page->report : null;
+        $pageCid = isset($this->page->cid) ? $this->page->cid : null;
+        $pageId = isset($this->page->id) ? $this->page->id : null;
+        $reportId = isset($report["id"]) ? $report["id"] : '';
+        $corpusId = isset($corpus['id']) ? $corpus['id'] : '';
 
 		// Init global tables
-		if (!is_array($this->annotationsClear)){
+		if (   !isset($this->annotationsClear) 
+            || !is_array($this->annotationsClear)
+            ){
 			$this->annotationsClear = array();
 		}
 		
@@ -89,10 +94,13 @@ function execute(){
 
         $htmlStr = ReportContent::getHtmlStr($report);
         $annotationTypes = CookieManager::getAnnotationTypeTreeAnnotationTypes($corpusId);
-        $annotations = DbAnnotation::getReportAnnotations($report['id'], $anUserIds, null, null, $annotationTypes, $anStages);
-        $relations = DbReportRelation::getReportRelations($this->page->cid, $this->page->id, $relationTypeIds, $annotationTypes, null,null, $annotation_mode);
+        $annotations = DbAnnotation::getReportAnnotations($reportId, $anUserIds, null, null, $annotationTypes, $anStages);
+        $relations = DbReportRelation::getReportRelations($pageCid, $pageId, $relationTypeIds, $annotationTypes, null,null, $annotation_mode);
         $htmlStr = ReportContent::insertAnnotationsWithRelations($htmlStr, $annotations, $relations);
-        $htmlStr = ReportContent::insertTokens($htmlStr, DbToken::getTokenByReportId($report[DB_COLUMN_REPORTS__REPORT_ID]));
+        $reportIdColumn = isset($report[DB_COLUMN_REPORTS__REPORT_ID])
+            ? $report[DB_COLUMN_REPORTS__REPORT_ID]
+            : '';
+        $htmlStr = ReportContent::insertTokens($htmlStr, DbToken::getTokenByReportId($reportIdColumn));
 
         $annotation_sets =  DbAnnotation::getAnnotationStructureByCorpora($corpusId);
 
@@ -108,7 +116,9 @@ function execute(){
 
         /* Setup active accordion panel */
         $accordions = array("collapseConfiguration", "collapsePad", "collapseAnnotations", "collapseRelations");
-        $activeAccordion = $_COOKIE['accordion_active'];
+        $activeAccordion = isset($_COOKIE['accordion_active']) 
+                            ? $_COOKIE['accordion_active']
+                            : '';
         if ( !in_array($activeAccordion, $accordions) ){
             $activeAccordion = $accordions[0];
         }
@@ -137,7 +147,7 @@ function set_panels(){
 	 *
 	 */
 	function set_annotation_menu(){
-		global $db, $user;
+		global $user;
 
 		//Find out which annotation types are selected in view configuration
 		$selected_annotation_types = CookieManager::getSelectedAnnotationTypeTreeAnnotationTypes($this->document['corpora']);
@@ -157,10 +167,13 @@ function set_annotation_menu(){
 				" LEFT JOIN annotation_subsets ss USING (annotation_subset_id)" .
 				" WHERE (c.corpus_id = {$this->document['corpora']} AND t.group_id IN ({$selected_types_string}))" .
 				" ORDER BY `set`, subset, t.name";
-		$annotation_types = $db->fetch_rows($sql);
+		$annotation_types = $this->page->getDb()->fetch_rows($sql);
 
         $sql = "SELECT * FROM annotation_types_shortlist ats WHERE ats.user_id = ?";
-        $user_preferences = $db->fetch_rows($sql, array($user['user_id']));
+        
+        $user_preferences = isset($user['user_id'])
+                ? $this->page->getDb()->fetch_rows($sql, array($user['user_id']))
+                : array() ;  // no preferences in DB
 
 
         //Find out if user changed the visibility of any annotations
@@ -210,7 +223,9 @@ function set_annotation_menu(){
 			$annotation_grouped[$set][$set_name][$subset][$an['name']] = $an;
 			$annotation_grouped[$set][$set_name][$subset]['notcommon'] |= !$an['common'];
 		}
-		if (!$_COOKIE['clearedLayer']){
+		if ( !isset($_COOKIE['clearedLayer'])
+            || !$_COOKIE['clearedLayer']
+            ){
 			setcookie('clearedLayer', '{"id'.implode('":1,"id', $this->annotationsClear).'":1}');
 			setcookie('clearedSublayer', '{"id'.implode('":1,"id', $annotationsSubsets).'":1}');
 		}
@@ -221,11 +236,13 @@ function set_annotation_menu(){
 	 */
 	function set_events(){
 		/*****obsluga zdarzeń********/
+        $pageCid = isset($this->page->cid) ? $this->page->cid : null;
+        $pageId = isset($this->page->id) ? $this->page->id : null;
 		//lista dostepnych grup zdarzen dla danego korpusu
 		$sql = "SELECT DISTINCT event_groups.event_group_id, event_groups.name " .
 				"FROM corpus_event_groups " .
 				"JOIN event_groups " .
-					"ON (corpus_event_groups.corpus_id={$this->page->cid} AND corpus_event_groups.event_group_id=event_groups.event_group_id) " .
+					"ON (corpus_event_groups.corpus_id={$pageCid} AND corpus_event_groups.event_group_id=event_groups.event_group_id) " .
 				"JOIN event_types " .
 					"ON (event_groups.event_group_id=event_types.event_group_id)";
 		$event_groups = $this->page->getDb()->fetch_rows($sql);
@@ -238,7 +255,7 @@ function set_events(){
 					  "count(reports_events_slots.report_event_slot_id) AS slots " .
 					  "FROM reports_events " .
 					  "JOIN reports " .
-					  	"ON (reports_events.report_id={$this->page->id} " .
+					  	"ON (reports_events.report_id={$pageId} " .
 					  	"AND reports_events.report_event_id=reports.id) " .
 				  	  "JOIN event_types " .
 				  	  	"ON (reports_events.event_type_id=event_types.event_type_id) " .

From db2bdba101556385147ab46bf73a782fdbf5bb5e Mon Sep 17 00:00:00 2001
From: Seweryn Walentynowicz <Seweryn.Walentynowicz@walor.torun.pl>
Date: Thu, 28 Dec 2023 09:45:07 +0100
Subject: [PATCH 154/154] describe HtmlParser2 problem with HTML comments
 recognize

---
 phpunit/data/document_testowy.010.html  | 547 ++++++++++++++++++++++++
 phpunit/dynamic/HtmlStrBigParseTest.php |  31 ++
 2 files changed, 578 insertions(+)
 create mode 100644 phpunit/data/document_testowy.010.html

diff --git a/phpunit/data/document_testowy.010.html b/phpunit/data/document_testowy.010.html
new file mode 100644
index 00000000..e7f75961
--- /dev/null
+++ b/phpunit/data/document_testowy.010.html
@@ -0,0 +1,547 @@
+<!DOCTYPE html>
+<html>
+    <head>
+        <meta charset="UTF-8" />
+        <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+        <title>Internal value representation in PHP 7 - Part 1</title>
+        <link rel="stylesheet" href="/asset/reset.css" />
+        <link rel="stylesheet" href="/asset/main.css" />
+        <link rel="stylesheet" href="/asset/highlight.css" />
+        <link rel="alternate" type="application/rss+xml" href="/rss.xml" />
+        <link rel="canonical" href="https://www.npopov.com/2015/05/05/Internal-value-representation-in-PHP-7-part-1.html" />
+        <!-- Google tag (gtag.js) -->
+        <script async src="https://www.googletagmanager.com/gtag/js?id=G-69DTLTFJ7P"></script>
+        <script>
+          window.dataLayer = window.dataLayer || [];
+          function gtag(){dataLayer.push(arguments);}
+          gtag('js', new Date());
+
+          gtag('config', 'G-69DTLTFJ7P');
+        </script>
+    </head>
+    <body>
+        <header>
+            Blog by <strong>nikic</strong>.
+            Find me on <a href="https://github.com/nikic">GitHub</a>,
+            <a href="https://stackoverflow.com/users/385378/nikic">StackOverflow</a>
+            and <a href="http://twitter.com/nikita_ppv">Twitter</a>.
+            Learn more <a href="/aboutMe.html">about me</a>.
+        </header>
+        <section>
+            <section class="post">
+    <header>
+        <a href="/" class="backLink">&laquo; Back to article overview.</a>
+        <h1>Internal value representation in PHP 7 - Part 1</h1>
+        <time datetime="2015-05-05" pubdate>
+            05. May 2015
+        </time>
+        
+    </header>
+    <section>
+        <p>My last article described the <a href="https://www.npopov.com/2014/12/22/PHPs-new-hashtable-implementation.html">improvements to the hashtable implementation</a> that were introduced in PHP 7. This
+followup will take a look at the new representation of PHP values in general.</p>
+
+<p>Due to the amount of material to cover, the article is split in two parts: This part will describe how the zval (Zend
+value) implementation differs between PHP 5 and PHP 7, and also discuss the implementation of references. The second
+part will investigate the realization of individual types like strings or objects in more detail.</p>
+
+<h2 id="zvals-in-php-5">Zvals in PHP 5</h2>
+
+<p>In PHP 5 the zval struct is defined as follows:</p>
+
+<figure class="highlight"><pre><code class="language-c" data-lang="c"><span class="k">typedef</span> <span class="k">struct</span> <span class="n">_zval_struct</span> <span class="p">{</span>
+    <span class="n">zvalue_value</span> <span class="n">value</span><span class="p">;</span>
+    <span class="n">zend_uint</span> <span class="n">refcount__gc</span><span class="p">;</span>
+    <span class="n">zend_uchar</span> <span class="n">type</span><span class="p">;</span>
+    <span class="n">zend_uchar</span> <span class="n">is_ref__gc</span><span class="p">;</span>
+<span class="p">}</span> <span class="n">zval</span><span class="p">;</span></code></pre></figure>
+
+<p>As you can see, a zval consists of a <code class="language-plaintext highlighter-rouge">value</code>, a <code class="language-plaintext highlighter-rouge">type</code> and some additional <code class="language-plaintext highlighter-rouge">__gc</code> information, which we’ll talk about in
+a moment. The <code class="language-plaintext highlighter-rouge">value</code> member is a union of different possible values that a zval can store:</p>
+
+<figure class="highlight"><pre><code class="language-c" data-lang="c"><span class="k">typedef</span> <span class="k">union</span> <span class="n">_zvalue_value</span> <span class="p">{</span>
+    <span class="kt">long</span> <span class="n">lval</span><span class="p">;</span>                 <span class="c1">// For booleans, integers and resources</span>
+    <span class="kt">double</span> <span class="n">dval</span><span class="p">;</span>               <span class="c1">// For floating point numbers</span>
+    <span class="k">struct</span> <span class="p">{</span>                   <span class="c1">// For strings</span>
+        <span class="kt">char</span> <span class="o">*</span><span class="n">val</span><span class="p">;</span>
+        <span class="kt">int</span> <span class="n">len</span><span class="p">;</span>
+    <span class="p">}</span> <span class="n">str</span><span class="p">;</span>
+    <span class="n">HashTable</span> <span class="o">*</span><span class="n">ht</span><span class="p">;</span>             <span class="c1">// For arrays</span>
+    <span class="n">zend_object_value</span> <span class="n">obj</span><span class="p">;</span>     <span class="c1">// For objects</span>
+    <span class="n">zend_ast</span> <span class="o">*</span><span class="n">ast</span><span class="p">;</span>             <span class="c1">// For constant expressions</span>
+<span class="p">}</span> <span class="n">zvalue_value</span><span class="p">;</span></code></pre></figure>
+
+<p>A C union is a structure in which only one member can be active at a time and those size matches the size of its largest
+member. All members of the union will be stored in the <em>same</em> place in memory and will be interpreted differently
+depending on which one you access. If you read the <code class="language-plaintext highlighter-rouge">lval</code> member of the above union, its value will be interpreted as a
+signed integer. If you read the <code class="language-plaintext highlighter-rouge">dval</code> member the value will be interpreted as a double-precision floating point
+number instead. And so on.</p>
+
+<p>To figure out which of these union members is currently in use, the <code class="language-plaintext highlighter-rouge">type</code> property of a zval stores a type tag, which
+is simply an integer:</p>
+
+<figure class="highlight"><pre><code class="language-c" data-lang="c"><span class="cp">#define IS_NULL     0      </span><span class="cm">/* Doesn't use value */</span><span class="cp">
+#define IS_LONG     1      </span><span class="cm">/* Uses lval */</span><span class="cp">
+#define IS_DOUBLE   2      </span><span class="cm">/* Uses dval */</span><span class="cp">
+#define IS_BOOL     3      </span><span class="cm">/* Uses lval with values 0 and 1 */</span><span class="cp">
+#define IS_ARRAY    4      </span><span class="cm">/* Uses ht */</span><span class="cp">
+#define IS_OBJECT   5      </span><span class="cm">/* Uses obj */</span><span class="cp">
+#define IS_STRING   6      </span><span class="cm">/* Uses str */</span><span class="cp">
+#define IS_RESOURCE 7      </span><span class="cm">/* Uses lval, which is the resource ID */</span><span class="cp">
+</span>
+<span class="cm">/* Special types used for late-binding of constants */</span>
+<span class="cp">#define IS_CONSTANT 8
+#define IS_CONSTANT_AST 9</span></code></pre></figure>
+
+<h2 id="reference-counting-in-php-5">Reference counting in PHP 5</h2>
+
+<p>Zvals in PHP 5 are (with a few exceptions) allocated on the heap and PHP needs some way to keep track which zvals are
+currently in use and which should be freed. For this purpose reference counting is employed: The <code class="language-plaintext highlighter-rouge">refcount__gc</code> member
+of the zval structure stores how often a zval is currently “referenced”. For example in <code class="language-plaintext highlighter-rouge">$a = $b = 42</code> the value <code class="language-plaintext highlighter-rouge">42</code>
+is referenced by two variables, so its refcount is 2. If the refcount reaches zero, it means a value is unused and can
+be freed.</p>
+
+<p>Note that the references that the refcount refers to (how many times a value is currently used) have nothing to do with
+PHP references (using <code class="language-plaintext highlighter-rouge">&amp;</code>). I will always using the terms “reference” and “PHP reference” to disambiguate both concepts
+in the following. For now we’ll ignore PHP references altogether.</p>
+
+<p>A concept that is closely related to reference counting is “copy on write”: A zval can only be shared between multiple
+users as long as it isn’t modified. In order to change a shared zval it needs to be duplicated (“separated”) and the
+modification will happen only on the duplicated zval.</p>
+
+<p>Lets look at an example that shows off both copy-on-write and zval destruction:</p>
+
+<div class="language-php highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="nv">$a</span> <span class="o">=</span> <span class="mi">42</span><span class="p">;</span>   <span class="c1">// $a         -&gt; zval_1(type=IS_LONG, value=42, refcount=1)</span>
+<span class="nv">$b</span> <span class="o">=</span> <span class="nv">$a</span><span class="p">;</span>   <span class="c1">// $a, $b     -&gt; zval_1(type=IS_LONG, value=42, refcount=2)</span>
+<span class="nv">$c</span> <span class="o">=</span> <span class="nv">$b</span><span class="p">;</span>   <span class="c1">// $a, $b, $c -&gt; zval_1(type=IS_LONG, value=42, refcount=3)</span>
+
+<span class="c1">// The following line causes a zval separation</span>
+<span class="nv">$a</span> <span class="o">+=</span> <span class="mi">1</span><span class="p">;</span>   <span class="c1">// $b, $c -&gt; zval_1(type=IS_LONG, value=42, refcount=2)</span>
+           <span class="c1">// $a     -&gt; zval_2(type=IS_LONG, value=43, refcount=1)</span>
+
+<span class="nb">unset</span><span class="p">(</span><span class="nv">$b</span><span class="p">);</span> <span class="c1">// $c -&gt; zval_1(type=IS_LONG, value=42, refcount=1)</span>
+           <span class="c1">// $a -&gt; zval_2(type=IS_LONG, value=43, refcount=1)</span>
+
+<span class="nb">unset</span><span class="p">(</span><span class="nv">$c</span><span class="p">);</span> <span class="c1">// zval_1 is destroyed, because refcount=0</span>
+           <span class="c1">// $a -&gt; zval_2(type=IS_LONG, value=43, refcount=1)</span>
+</code></pre></div></div>
+
+<p>Reference counting has one fatal flaw: It is not able to detect and release cyclic references. To handle this PHP uses
+an additional <a href="https://php.net/manual/en/features.gc.collecting-cycles.php">cycle collector</a>. Whenever the refcount of a zval is decremented and there is a chance that this
+zval is part of a cycle, the zval is written into a “root buffer”. Once this root buffer is full, potential cycles will
+be collected using a mark and sweep garbage collection.</p>
+
+<p>In order to support this additional cycle collector, the actually used zval structure is the following:</p>
+
+<figure class="highlight"><pre><code class="language-c" data-lang="c"><span class="k">typedef</span> <span class="k">struct</span> <span class="n">_zval_gc_info</span> <span class="p">{</span>
+    <span class="n">zval</span> <span class="n">z</span><span class="p">;</span>
+    <span class="k">union</span> <span class="p">{</span>
+        <span class="n">gc_root_buffer</span>       <span class="o">*</span><span class="n">buffered</span><span class="p">;</span>
+        <span class="k">struct</span> <span class="n">_zval_gc_info</span> <span class="o">*</span><span class="n">next</span><span class="p">;</span>
+    <span class="p">}</span> <span class="n">u</span><span class="p">;</span>
+<span class="p">}</span> <span class="n">zval_gc_info</span><span class="p">;</span></code></pre></figure>
+
+<p>The <code class="language-plaintext highlighter-rouge">zval_gc_info</code> structure embeds the normal zval, as well as one additional pointer - note that <code class="language-plaintext highlighter-rouge">u</code> is a union, so
+this is really just one pointer with two different types it may point to. The <code class="language-plaintext highlighter-rouge">buffered</code> pointer is used to store where
+in the root buffer this zval is referenced, so that it may be removed from it if it’s destroyed before the cycle
+collector runs (which is very likely). <code class="language-plaintext highlighter-rouge">next</code> is used when the collector destroys values, but I won’t go into that here.</p>
+
+<h2 id="motivation-for-change">Motivation for change</h2>
+
+<p>Let’s talk about sizes a bit (all sizes are for 64-bit systems): First of all, the <code class="language-plaintext highlighter-rouge">zvalue_value</code> union is 16 bytes
+large, because both the <code class="language-plaintext highlighter-rouge">str</code> and <code class="language-plaintext highlighter-rouge">obj</code> members have that size. The whole <code class="language-plaintext highlighter-rouge">zval</code> struct is 24 bytes (due to padding) and
+<code class="language-plaintext highlighter-rouge">zval_gc_info</code> is 32 bytes. On top of this, allocating the zval on the heap adds another 16 bytes of allocation
+overhead. So we end up using 48 bytes per zval - although this zval may be used by multiple places.</p>
+
+<p>At this point we can start thinking about the (many) ways in which this zval implementation is inefficient. Consider the
+simple case of a zval storing an integer, which by itself is 8 bytes. Additionally the type-tag needs to be stored in
+any case, which is a single byte by itself, but due to padding needs another 8 bytes.</p>
+
+<p>To these 16 bytes that we really “need” (in first approximation), we add another 16 bytes handling reference counting
+and cycle collection and another 16 bytes of allocation overhead. Not to mention that we actually have to perform that
+allocation and the subsequent free, both being quite expensive operations.</p>
+
+<p>This raises the question: Does a simple integer value <em>really</em> need to be stored as a reference-counted,
+cycle-collectible, heap-allocated value? The answer to this question is of course, no, this doesn’t make sense.</p>
+
+<p>Here is a summary of the primary problems with the PHP 5 zval implementation:</p>
+
+<ul>
+  <li>Zvals (nearly) always require a heap allocation.</li>
+  <li>Zvals are always reference counted and always have cycle collection information, even in cases where sharing the
+value is not worthwhile (an integer) and it can’t form cycles.</li>
+  <li>Directly refcounting the zvals leads to double refcounting in the case of objects and resources. The reasons behind
+this will be explained in the next part.</li>
+  <li>Some cases involve quite an awesome amount of indirection. For example to access the object stored in a variable, a
+total of four pointers need to be dereferenced (which means following a pointer chain of length four). Once again
+this will be discussed in the next part.</li>
+  <li>Directly refcounting the zvals also means that values can only be shared between zvals. For example it’s not possible
+to share a string between a zval and hashtable key (without storing the hashtable key as a zval as well).</li>
+</ul>
+
+<h2 id="zvals-in-php-7">Zvals in PHP 7</h2>
+
+<p>And this brings us to the new zval implementation in PHP 7. The fundamental change that was implemented, is that zvals
+are no longer individually heap-allocated and no longer store a refcount themselves. Instead any complex values they
+may point to (like strings, arrays or objects) will store the refcount themselves. This has the following advantages:</p>
+
+<ul>
+  <li>Simple values do not require allocation and don’t use refcounting.</li>
+  <li>There is no more double refcounting. In the object case, only the refcount in the object is used now.</li>
+  <li>Because the refcount is now stored in the value itself, the value can be shared independently of the zval structure.
+A string can be used both in a zval and a hashtable key.</li>
+  <li>There is a lot less indirection, i.e. the number of pointers you need to follow to get to a value is lower.</li>
+</ul>
+
+<p>Now lets take a look at how the new zval is defined:</p>
+
+<figure class="highlight"><pre><code class="language-c" data-lang="c"><span class="k">struct</span> <span class="n">_zval_struct</span> <span class="p">{</span>
+    <span class="n">zend_value</span> <span class="n">value</span><span class="p">;</span>
+    <span class="k">union</span> <span class="p">{</span>
+        <span class="k">struct</span> <span class="p">{</span>
+            <span class="n">ZEND_ENDIAN_LOHI_4</span><span class="p">(</span>
+                <span class="n">zend_uchar</span> <span class="n">type</span><span class="p">,</span>
+                <span class="n">zend_uchar</span> <span class="n">type_flags</span><span class="p">,</span>
+                <span class="n">zend_uchar</span> <span class="n">const_flags</span><span class="p">,</span>
+                <span class="n">zend_uchar</span> <span class="n">reserved</span><span class="p">)</span>
+        <span class="p">}</span> <span class="n">v</span><span class="p">;</span>
+        <span class="kt">uint32_t</span> <span class="n">type_info</span><span class="p">;</span>
+    <span class="p">}</span> <span class="n">u1</span><span class="p">;</span>
+    <span class="k">union</span> <span class="p">{</span>
+        <span class="kt">uint32_t</span> <span class="n">var_flags</span><span class="p">;</span>
+        <span class="kt">uint32_t</span> <span class="n">next</span><span class="p">;</span>                 <span class="c1">// hash collision chain</span>
+        <span class="kt">uint32_t</span> <span class="n">cache_slot</span><span class="p">;</span>           <span class="c1">// literal cache slot</span>
+        <span class="kt">uint32_t</span> <span class="n">lineno</span><span class="p">;</span>               <span class="c1">// line number (for ast nodes)</span>
+        <span class="kt">uint32_t</span> <span class="n">num_args</span><span class="p">;</span>             <span class="c1">// arguments number for EX(This)</span>
+        <span class="kt">uint32_t</span> <span class="n">fe_pos</span><span class="p">;</span>               <span class="c1">// foreach position</span>
+        <span class="kt">uint32_t</span> <span class="n">fe_iter_idx</span><span class="p">;</span>          <span class="c1">// foreach iterator index</span>
+    <span class="p">}</span> <span class="n">u2</span><span class="p">;</span>
+<span class="p">};</span></code></pre></figure>
+
+<p>The first member stays pretty similar, this is still a <code class="language-plaintext highlighter-rouge">value</code> union. The second member is an integer storing type
+information, which is further subdivided into individual bytes using a union (you can ignore the <code class="language-plaintext highlighter-rouge">ZEND_ENDIAN_LOHI_4</code>
+macro, which just ensures a consistent layout across platforms with different endianness). The important parts of this
+substructure are the <code class="language-plaintext highlighter-rouge">type</code> (which is similar to what it was before) and the <code class="language-plaintext highlighter-rouge">type_flags</code>, which I’ll explain in a
+moment.</p>
+
+<p>At this point there exists a small problem: The <code class="language-plaintext highlighter-rouge">value</code> member is 8 bytes large and due to struct padding adding even a
+single byte to that grows the zval size to 16 bytes. However we obviously don’t need 8 bytes just to store a type. This
+is why the zval contains the additional <code class="language-plaintext highlighter-rouge">u2</code> union, which remains unused by default, but can be repurposed by the
+surrounding code to store 4 bytes of data. The different union members correspond to different usages of this extra data
+slot.</p>
+
+<p>The <code class="language-plaintext highlighter-rouge">value</code> union looks slightly different in PHP 7:</p>
+
+<figure class="highlight"><pre><code class="language-c" data-lang="c"><span class="k">typedef</span> <span class="k">union</span> <span class="n">_zend_value</span> <span class="p">{</span>
+    <span class="n">zend_long</span>         <span class="n">lval</span><span class="p">;</span>
+    <span class="kt">double</span>            <span class="n">dval</span><span class="p">;</span>
+    <span class="n">zend_refcounted</span>  <span class="o">*</span><span class="n">counted</span><span class="p">;</span>
+    <span class="n">zend_string</span>      <span class="o">*</span><span class="n">str</span><span class="p">;</span>
+    <span class="n">zend_array</span>       <span class="o">*</span><span class="n">arr</span><span class="p">;</span>
+    <span class="n">zend_object</span>      <span class="o">*</span><span class="n">obj</span><span class="p">;</span>
+    <span class="n">zend_resource</span>    <span class="o">*</span><span class="n">res</span><span class="p">;</span>
+    <span class="n">zend_reference</span>   <span class="o">*</span><span class="n">ref</span><span class="p">;</span>
+    <span class="n">zend_ast_ref</span>     <span class="o">*</span><span class="n">ast</span><span class="p">;</span>
+
+    <span class="c1">// Ignore these for now, they are special</span>
+    <span class="n">zval</span>             <span class="o">*</span><span class="n">zv</span><span class="p">;</span>
+    <span class="kt">void</span>             <span class="o">*</span><span class="n">ptr</span><span class="p">;</span>
+    <span class="n">zend_class_entry</span> <span class="o">*</span><span class="n">ce</span><span class="p">;</span>
+    <span class="n">zend_function</span>    <span class="o">*</span><span class="n">func</span><span class="p">;</span>
+    <span class="k">struct</span> <span class="p">{</span>
+        <span class="n">ZEND_ENDIAN_LOHI</span><span class="p">(</span>
+            <span class="kt">uint32_t</span> <span class="n">w1</span><span class="p">,</span>
+            <span class="kt">uint32_t</span> <span class="n">w2</span><span class="p">)</span>
+    <span class="p">}</span> <span class="n">ww</span><span class="p">;</span>
+<span class="p">}</span> <span class="n">zend_value</span><span class="p">;</span></code></pre></figure>
+
+<p>First of all, note that the value union is now 8 bytes instead of 16. It will only store integers (<code class="language-plaintext highlighter-rouge">lval</code>) and doubles
+(<code class="language-plaintext highlighter-rouge">dval</code>) directly, everything else is a pointer. All the pointer types (apart from those marked as special above) use
+refcounting and have a common header defined by <code class="language-plaintext highlighter-rouge">zend_refcounted</code>:</p>
+
+<figure class="highlight"><pre><code class="language-c" data-lang="c"><span class="k">struct</span> <span class="n">_zend_refcounted</span> <span class="p">{</span>
+    <span class="kt">uint32_t</span> <span class="n">refcount</span><span class="p">;</span>
+    <span class="k">union</span> <span class="p">{</span>
+        <span class="k">struct</span> <span class="p">{</span>
+            <span class="n">ZEND_ENDIAN_LOHI_3</span><span class="p">(</span>
+                <span class="n">zend_uchar</span>    <span class="n">type</span><span class="p">,</span>
+                <span class="n">zend_uchar</span>    <span class="n">flags</span><span class="p">,</span>
+                <span class="kt">uint16_t</span>      <span class="n">gc_info</span><span class="p">)</span>
+        <span class="p">}</span> <span class="n">v</span><span class="p">;</span>
+        <span class="kt">uint32_t</span> <span class="n">type_info</span><span class="p">;</span>
+    <span class="p">}</span> <span class="n">u</span><span class="p">;</span>
+<span class="p">};</span></code></pre></figure>
+
+<p>Of course the structure contains a refcount. Additionally it contains a <code class="language-plaintext highlighter-rouge">type</code>, some <code class="language-plaintext highlighter-rouge">flags</code> and <code class="language-plaintext highlighter-rouge">gc_info</code>. The <code class="language-plaintext highlighter-rouge">type</code>
+just duplicates the zval type and allows the GC to distinguish different refcounted structures without storing a zval.
+The <code class="language-plaintext highlighter-rouge">flags</code> are used for different purposes with different types and will be explained for each type separately in the
+next part.</p>
+
+<p>The <code class="language-plaintext highlighter-rouge">gc_info</code> is the equivalent of the <code class="language-plaintext highlighter-rouge">buffered</code> entry in the old zvals. However instead of storing a pointer into the
+root buffer it now contains an index into it. Because the root buffer has a fixed size (10000 elements) it is enough to
+use a 16 bit number for this instead of a 64 bit pointer. The <code class="language-plaintext highlighter-rouge">gc_info</code> info also encodes the “color” of the node, which
+is used to mark nodes during collection.</p>
+
+<h2 id="zval-memory-management">Zval memory management</h2>
+
+<p>I’ve mentioned that zvals are no longer individually heap-allocated. However they obviously still need to be stored
+<em>somewhere</em>, so how does this work? While zvals are still mostly part of heap-allocated structures, they are directly
+embedded into them. E.g. a hashtable bucket will directly embed a <code class="language-plaintext highlighter-rouge">zval</code> instead of storing a pointer to a separate
+zval. The compiled variables table of a function or the property table of an object will be zval arrays that are
+allocated in one chunk, instead of storing pointers to separate zvals. As such zvals are now usually stored with one
+level of indirection less. What was previously a <code class="language-plaintext highlighter-rouge">zval*</code> is now a <code class="language-plaintext highlighter-rouge">zval</code>.</p>
+
+<p>When a zval is used in a new place, previously this meant copying a <code class="language-plaintext highlighter-rouge">zval*</code> and incrementing its refcount. Now it means
+copying the contents of a <code class="language-plaintext highlighter-rouge">zval</code> (ignoring <code class="language-plaintext highlighter-rouge">u2</code>) instead and <em>maybe</em> incrementing the refcount of the value it points
+to, if said value uses refcounting.</p>
+
+<p>How does PHP know whether a value is refcounted? This cannot be determined solely based on the type, because some types
+like strings and arrays are not always refcounted. Instead one bit of the zvals <code class="language-plaintext highlighter-rouge">type_info</code> member determines whether or
+not the zval is refcounted. There are a number of other bits encoding properties of the type:</p>
+
+<figure class="highlight"><pre><code class="language-c" data-lang="c"><span class="cp">#define IS_TYPE_CONSTANT            (1&lt;&lt;0)   </span><span class="cm">/* special */</span><span class="cp">
+#define IS_TYPE_IMMUTABLE           (1&lt;&lt;1)   </span><span class="cm">/* special */</span><span class="cp">
+#define IS_TYPE_REFCOUNTED          (1&lt;&lt;2)
+#define IS_TYPE_COLLECTABLE         (1&lt;&lt;3)
+#define IS_TYPE_COPYABLE            (1&lt;&lt;4)
+#define IS_TYPE_SYMBOLTABLE         (1&lt;&lt;5)   </span><span class="cm">/* special */</span></code></pre></figure>
+
+<p>The three primary properties a type can have are “refcounted”, “collectable” and “copyable”. You already know what
+refcounted means. Collectable means that the zval can participate in a cycle. E.g. strings are (often) refcounted, but
+there’s no way you can create a cycle with a string in it.</p>
+
+<p>Copyability determines whether the value needs to copied when a “duplication” is performed. A duplication is a hard
+copy, e.g. if you duplicate a zval that points to an array, this will not simply increase the refcount on the array.
+Instead a new and independent copy of the array will be created. However for some types like objects and resources even
+a duplication should only increment the refcount - such types are called non-copyable. This matches the passing
+semantics of objects and resources (which are, for the record, not passed by reference).</p>
+
+<p>The following table shows the different types and what type flags they use. “Simple types” refers to types like integers
+or booleans that don’t use a pointer to a separate structure. A column for the “immutable” flag is also present, which
+is used to mark immutable arrays and will be discussed in more detail in the next part.</p>
+
+<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>                | refcounted | collectable | copyable | immutable
+----------------+------------+-------------+----------+----------
+simple types    |            |             |          |
+string          |      x     |             |     x    |
+interned string |            |             |          |
+array           |      x     |      x      |     x    |
+immutable array |            |             |          |     x
+object          |      x     |      x      |          |
+resource        |      x     |             |          |
+reference       |      x     |             |          |
+</code></pre></div></div>
+
+<p>At this point, lets take a look at two examples of how the zval management works in practice. First, an example using
+integers based off the PHP 5 example from above:</p>
+
+<div class="language-php highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="nv">$a</span> <span class="o">=</span> <span class="mi">42</span><span class="p">;</span>   <span class="c1">// $a = zval_1(type=IS_LONG, value=42)</span>
+
+<span class="nv">$b</span> <span class="o">=</span> <span class="nv">$a</span><span class="p">;</span>   <span class="c1">// $a = zval_1(type=IS_LONG, value=42)</span>
+           <span class="c1">// $b = zval_2(type=IS_LONG, value=42)</span>
+
+<span class="nv">$a</span> <span class="o">+=</span> <span class="mi">1</span><span class="p">;</span>   <span class="c1">// $a = zval_1(type=IS_LONG, value=43)</span>
+           <span class="c1">// $b = zval_2(type=IS_LONG, value=42)</span>
+
+<span class="nb">unset</span><span class="p">(</span><span class="nv">$a</span><span class="p">);</span> <span class="c1">// $a = zval_1(type=IS_UNDEF)</span>
+           <span class="c1">// $b = zval_2(type=IS_LONG, value=42)</span>
+</code></pre></div></div>
+
+<p>This is pretty boring. As integers are no longer shared, both variables will use separate zvals. Don’t forget that these
+are now embedded rather than allocated, which I try to signify by writing <code class="language-plaintext highlighter-rouge">=</code> instead of a <code class="language-plaintext highlighter-rouge">-&gt;</code> pointer. Unsetting a
+variable will set the type of the corresponding zval to <code class="language-plaintext highlighter-rouge">IS_UNDEF</code>. Now consider a more interesting case where a complex
+value is involved:</p>
+
+<div class="language-php highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="nv">$a</span> <span class="o">=</span> <span class="p">[];</span>   <span class="c1">// $a = zval_1(type=IS_ARRAY) -&gt; zend_array_1(refcount=1, value=[])</span>
+
+<span class="nv">$b</span> <span class="o">=</span> <span class="nv">$a</span><span class="p">;</span>   <span class="c1">// $a = zval_1(type=IS_ARRAY) -&gt; zend_array_1(refcount=2, value=[])</span>
+           <span class="c1">// $b = zval_2(type=IS_ARRAY) ---^</span>
+
+<span class="c1">// Zval separation occurs here</span>
+<span class="nv">$a</span><span class="p">[]</span> <span class="o">=</span> <span class="mi">1</span>   <span class="c1">// $a = zval_1(type=IS_ARRAY) -&gt; zend_array_2(refcount=1, value=[1])</span>
+           <span class="c1">// $b = zval_2(type=IS_ARRAY) -&gt; zend_array_1(refcount=1, value=[])</span>
+
+<span class="nb">unset</span><span class="p">(</span><span class="nv">$a</span><span class="p">);</span> <span class="c1">// $a = zval_1(type=IS_UNDEF) and zend_array_2 is destroyed</span>
+           <span class="c1">// $b = zval_2(type=IS_ARRAY) -&gt; zend_array_1(refcount=1, value=[])</span>
+</code></pre></div></div>
+
+<p>Here each variable still has a separate (embedded) zval, but both zvals point to the same (refcounted) <code class="language-plaintext highlighter-rouge">zend_array</code>
+structure. Once a modification is done the array needs to be duplicated. This case is similar to how things work in PHP
+5.</p>
+
+<h2 id="types">Types</h2>
+
+<p>Lets take a closer look at what types are supported in PHP 7:</p>
+
+<figure class="highlight"><pre><code class="language-c" data-lang="c"><span class="c1">// regular data types</span>
+<span class="cp">#define IS_UNDEF                    0
+#define IS_NULL                     1
+#define IS_FALSE                    2
+#define IS_TRUE                     3
+#define IS_LONG                     4
+#define IS_DOUBLE                   5
+#define IS_STRING                   6
+#define IS_ARRAY                    7
+#define IS_OBJECT                   8
+#define IS_RESOURCE                 9
+#define IS_REFERENCE                10
+</span>
+<span class="c1">// constant expressions</span>
+<span class="cp">#define IS_CONSTANT                 11
+#define IS_CONSTANT_AST             12
+</span>
+<span class="c1">// internal types</span>
+<span class="cp">#define IS_INDIRECT                 15
+#define IS_PTR                      17</span></code></pre></figure>
+
+<p>This list is quite similar to what was used in PHP 5, however there are a few additions:</p>
+
+<ul>
+  <li>The <code class="language-plaintext highlighter-rouge">IS_UNDEF</code> type is used in places where previously a <code class="language-plaintext highlighter-rouge">NULL</code> zval pointer (not to be confused with an <code class="language-plaintext highlighter-rouge">IS_NULL</code>
+zval) was used. For example, in the refcounting examples above the <code class="language-plaintext highlighter-rouge">IS_UNDEF</code> type is set for variables that have
+been <code class="language-plaintext highlighter-rouge">unset</code>.</li>
+  <li>The <code class="language-plaintext highlighter-rouge">IS_BOOL</code> type has been split into <code class="language-plaintext highlighter-rouge">IS_FALSE</code> and <code class="language-plaintext highlighter-rouge">IS_TRUE</code>. As such the value of the boolean is now encoded in
+the type, which allows the optimization of a number of type-based checks. This change is transparent to userland,
+where this is still a single “boolean” type.</li>
+  <li>PHP references no longer use an <code class="language-plaintext highlighter-rouge">is_ref</code> flag on the zval and use a new <code class="language-plaintext highlighter-rouge">IS_REFERENCE</code> type instead. How this works
+will be described in the next section.</li>
+  <li>The <code class="language-plaintext highlighter-rouge">IS_INDIRECT</code> and <code class="language-plaintext highlighter-rouge">IS_PTR</code> types are special internal types.</li>
+</ul>
+
+<p>The <code class="language-plaintext highlighter-rouge">IS_LONG</code> type now uses a <code class="language-plaintext highlighter-rouge">zend_long</code> value instead of an ordinary C long. The reason behind this is that on 64-bit
+Windows (LLP64) a <code class="language-plaintext highlighter-rouge">long</code> is only 32-bit wide, so PHP 5 ended up always using 32-bit numbers on Windows. PHP 7 will allow
+you to use 64-bit numbers if you’re on an 64-bit operating system, even if that operating system is Windows.</p>
+
+<p>Details of the individual <code class="language-plaintext highlighter-rouge">zend_refcounted</code> types will be discussed in the next part. For now we’ll only look at the
+implementation of PHP references.</p>
+
+<h2 id="references">References</h2>
+
+<p>PHP 7 uses an entirely different approach to handling PHP <code class="language-plaintext highlighter-rouge">&amp;</code> references than PHP 5 (and I can tell you that this change
+is one of the largest source of bugs in PHP 7). Lets start by taking a look at how PHP references used to work in PHP 5:</p>
+
+<p>Normally, the copy-on-write principle says that before modifying a zval it needs to be separated, in order to make sure
+you don’t end up changing the value for every place sharing the zval. This matches by-value passing semantics.</p>
+
+<p>For PHP references this does not apply. If a value is a PHP reference, you <em>want</em> it to change for every user of the
+value. The <code class="language-plaintext highlighter-rouge">is_ref</code> flag that was part of PHP 5 zvals determined whether a value is a PHP reference and as such whether
+it required separation before modification. An example:</p>
+
+<div class="language-php highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="nv">$a</span> <span class="o">=</span> <span class="p">[];</span>  <span class="c1">// $a     -&gt; zval_1(type=IS_ARRAY, refcount=1, is_ref=0) -&gt; HashTable_1(value=[])</span>
+<span class="nv">$b</span> <span class="o">=&amp;</span> <span class="nv">$a</span><span class="p">;</span> <span class="c1">// $a, $b -&gt; zval_1(type=IS_ARRAY, refcount=2, is_ref=1) -&gt; HashTable_1(value=[])</span>
+
+<span class="nv">$b</span><span class="p">[]</span> <span class="o">=</span> <span class="mi">1</span><span class="p">;</span> <span class="c1">// $a = $b = zval_1(type=IS_ARRAY, refcount=2, is_ref=1) -&gt; HashTable_1(value=[1])</span>
+</code></pre></div></div>
+
+<p>One significant problem with this design is that it’s not possible to share a value between a variable that’s a PHP
+reference and one that isn’t. Consider the following example:</p>
+
+<div class="language-php highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="nv">$a</span> <span class="o">=</span> <span class="p">[];</span>  <span class="c1">// $a         -&gt; zval_1(type=IS_ARRAY, refcount=1, is_ref=0) -&gt; HashTable_1(value=[])</span>
+<span class="nv">$b</span> <span class="o">=</span> <span class="nv">$a</span><span class="p">;</span>  <span class="c1">// $a, $b     -&gt; zval_1(type=IS_ARRAY, refcount=2, is_ref=0) -&gt; HashTable_1(value=[])</span>
+<span class="nv">$c</span> <span class="o">=</span> <span class="nv">$b</span>   <span class="c1">// $a, $b, $c -&gt; zval_1(type=IS_ARRAY, refcount=3, is_ref=0) -&gt; HashTable_1(value=[])</span>
+
+<span class="nv">$d</span> <span class="o">=&amp;</span> <span class="nv">$c</span><span class="p">;</span> <span class="c1">// $a, $b -&gt; zval_1(type=IS_ARRAY, refcount=2, is_ref=0) -&gt; HashTable_1(value=[])</span>
+          <span class="c1">// $c, $d -&gt; zval_1(type=IS_ARRAY, refcount=2, is_ref=1) -&gt; HashTable_2(value=[])</span>
+          <span class="c1">// $d is a reference of $c, but *not* of $a and $b, so the zval needs to be copied</span>
+          <span class="c1">// here. Now we have the same zval once with is_ref=0 and once with is_ref=1.</span>
+
+<span class="nv">$d</span><span class="p">[]</span> <span class="o">=</span> <span class="mi">1</span><span class="p">;</span> <span class="c1">// $a, $b -&gt; zval_1(type=IS_ARRAY, refcount=2, is_ref=0) -&gt; HashTable_1(value=[])</span>
+          <span class="c1">// $c, $d -&gt; zval_1(type=IS_ARRAY, refcount=2, is_ref=1) -&gt; HashTable_2(value=[1])</span>
+          <span class="c1">// Because there are two separate zvals $d[] = 1 does not modify $a and $b.</span>
+</code></pre></div></div>
+
+<p>This behavior of references is one of the reasons why using references in PHP will usually end up being slower than
+using normal values. To give a less-contrived example where this is a problem:</p>
+
+<div class="language-php highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="nv">$array</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1000000</span><span class="p">);</span>
+<span class="nv">$ref</span> <span class="o">=&amp;</span> <span class="nv">$array</span><span class="p">;</span>
+<span class="nb">var_dump</span><span class="p">(</span><span class="nb">count</span><span class="p">(</span><span class="nv">$array</span><span class="p">));</span> <span class="c1">// &lt;-- separation occurs here</span>
+</code></pre></div></div>
+
+<p>Because <code class="language-plaintext highlighter-rouge">count()</code> accepts its value by-value, but <code class="language-plaintext highlighter-rouge">$array</code> is a PHP reference, a full copy of the array is done before
+passing it off to <code class="language-plaintext highlighter-rouge">count()</code>. If <code class="language-plaintext highlighter-rouge">$array</code> weren’t a reference, the value would be shared instead.</p>
+
+<p>Now, let’s switch to the PHP 7 implementation of PHP references. Because zvals are no longer individually allocated, it
+is not possible to use the same approach that PHP 5 used. Instead a new <code class="language-plaintext highlighter-rouge">IS_REFERENCE</code> type is added, which uses the
+<code class="language-plaintext highlighter-rouge">zend_reference</code> structure as its value:</p>
+
+<figure class="highlight"><pre><code class="language-c" data-lang="c"><span class="k">struct</span> <span class="n">_zend_reference</span> <span class="p">{</span>
+    <span class="n">zend_refcounted</span>   <span class="n">gc</span><span class="p">;</span>
+    <span class="n">zval</span>              <span class="n">val</span><span class="p">;</span>
+<span class="p">};</span></code></pre></figure>
+
+<p>So essentially a <code class="language-plaintext highlighter-rouge">zend_reference</code> is simply a refcounted zval. All variables in a reference set will store a zval with
+type <code class="language-plaintext highlighter-rouge">IS_REFERENCE</code> pointing to the same <code class="language-plaintext highlighter-rouge">zend_reference</code> instance. The <code class="language-plaintext highlighter-rouge">val</code> zval behaves like any other zval, in
+particular it is possible to share a complex value it points to. E.g. an array can be shared between a variable that is
+a reference and another that is a value.</p>
+
+<p>Lets go through the above code samples again, this time looking at the PHP 7 semantics. For the sake of brevity I will
+stop writing the individual zvals of the variables and only show what structure they point to.</p>
+
+<div class="language-php highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="nv">$a</span> <span class="o">=</span> <span class="p">[];</span>  <span class="c1">// $a                                     -&gt; zend_array_1(refcount=1, value=[])</span>
+<span class="nv">$b</span> <span class="o">=&amp;</span> <span class="nv">$a</span><span class="p">;</span> <span class="c1">// $a, $b -&gt; zend_reference_1(refcount=2) -&gt; zend_array_1(refcount=1, value=[])</span>
+
+<span class="nv">$b</span><span class="p">[]</span> <span class="o">=</span> <span class="mi">1</span><span class="p">;</span> <span class="c1">// $a, $b -&gt; zend_reference_1(refcount=2) -&gt; zend_array_1(refcount=1, value=[1])</span>
+</code></pre></div></div>
+
+<p>The by-reference assignment created a new <code class="language-plaintext highlighter-rouge">zend_reference</code>. Note that the refcount is 2 on the reference (because two
+variables are part of the PHP reference set), but the value itself only has a refcount of 1 (because one
+<code class="language-plaintext highlighter-rouge">zend_reference</code> structure points to it). Now consider the case where references and non-references are mixed:</p>
+
+<div class="language-php highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="nv">$a</span> <span class="o">=</span> <span class="p">[];</span>  <span class="c1">// $a         -&gt; zend_array_1(refcount=1, value=[])</span>
+<span class="nv">$b</span> <span class="o">=</span> <span class="nv">$a</span><span class="p">;</span>  <span class="c1">// $a, $b,    -&gt; zend_array_1(refcount=2, value=[])</span>
+<span class="nv">$c</span> <span class="o">=</span> <span class="nv">$b</span>   <span class="c1">// $a, $b, $c -&gt; zend_array_1(refcount=3, value=[])</span>
+
+<span class="nv">$d</span> <span class="o">=&amp;</span> <span class="nv">$c</span><span class="p">;</span> <span class="c1">// $a, $b                                 -&gt; zend_array_1(refcount=3, value=[])</span>
+          <span class="c1">// $c, $d -&gt; zend_reference_1(refcount=2) ---^</span>
+          <span class="c1">// Note that all variables share the same zend_array, even though some are</span>
+          <span class="c1">// PHP references and some aren't.</span>
+
+<span class="nv">$d</span><span class="p">[]</span> <span class="o">=</span> <span class="mi">1</span><span class="p">;</span> <span class="c1">// $a, $b                                 -&gt; zend_array_1(refcount=2, value=[])</span>
+          <span class="c1">// $c, $d -&gt; zend_reference_1(refcount=2) -&gt; zend_array_2(refcount=1, value=[1])</span>
+          <span class="c1">// Only at this point, once an assignment occurs, the zend_array is duplicated.</span>
+</code></pre></div></div>
+
+<p>The important difference to PHP 5 is that all variables were able to share the same array, even though some were PHP
+references and some weren’t. Only once some kind of modification is performed the array will be separated. This means
+that in PHP 7 it’s safe to pass a large, referenced array to <code class="language-plaintext highlighter-rouge">count()</code>, it is not going to be duplicated. References
+will still be slower than normal values, because they require allocation of the <code class="language-plaintext highlighter-rouge">zend_reference</code> structure (and
+indirection through it) and are usually not handled in the fast-path of engine code.</p>
+
+<h2 id="wrapping-up">Wrapping up</h2>
+
+<p>To summarize, the primary change that was implemented in PHP 7 is that zvals are no longer individually heap-allocated
+and no longer store a refcount themselves. Instead any complex values they may point to (like strings, array or objects)
+will store the refcount themselves. This usually leads to less allocations, less indirection and less memory usage.</p>
+
+<p>In the second part of this article the remaining complex types will be discussed.</p>
+
+
+    </section>
+    <footer>
+        <section class="followupActions">
+            If you liked this article, you may want to <a href="/">browse my other articles</a> or
+            <a href="https://twitter.com/nikita_ppv">follow me on Twitter</a>.
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+        <div id="disqus_thread"></div>
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+        <script src="/asset/anchor.js"></script>
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+            anchors.add('h2, h3');
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+</html>
diff --git a/phpunit/dynamic/HtmlStrBigParseTest.php b/phpunit/dynamic/HtmlStrBigParseTest.php
index f663abf3..076e7551 100644
--- a/phpunit/dynamic/HtmlStrBigParseTest.php
+++ b/phpunit/dynamic/HtmlStrBigParseTest.php
@@ -5,6 +5,17 @@
 final class HtmlStrBigParseTest extends PHPUnit_Framework_TestCase
 {
 
+/* this tests doesn't work because source HTML text include 
+ * HTML comment <!-- Google tag (gtag.js) -->
+ *   At now HtmlParser2 class doesn't recognize properly HTML comments
+ * and expects closed paired tag. 
+ *  We must decide how to process HTML comments and implement recognising
+ * this tags in parser.
+ *  Added test testCanBeCreatedFromValidLocalFileAfterCommentsRemoved()
+ * which self remove HTML comments in source text - should will be removed
+ * after solve problem. 
+ *  SW 20231228
+
     private static $testURL = "https://nikic.github.io/2015/05/05/Internal-value-representation-in-PHP-7-part-1.html";
 
     public function testCanBeCreatedFromValidUTF8Html()
@@ -21,5 +32,25 @@ public function testCanBeRestoredFromInternalRepresentation()
 
     } // testCanBeRestoredFromInternalRepresentation
 
+    public function testCanBeCreatedFromValidLocalFile()
+    {
+        $fileName = __DIR__."/../data/"."document_testowy.010.html";
+        $text = file_get_contents($fileName);
+        $obj = new HtmlStr2($text);
+        $this->assertInstanceOf("HtmlStr2",$obj);
+
+    } // testCanBeCreatedFromValidLocalFile()
+*/
+    public function testCanBeCreatedFromValidLocalFileAfterCommentsRemoved()
+    {
+        $fileName = __DIR__."/../data/"."document_testowy.010.html";
+        $text = file_get_contents($fileName);
+        // remove HTML comments
+        $text = preg_replace('/<!--.*-->/','',$text);
+        $obj = new HtmlStr2($text);
+        $this->assertInstanceOf("HtmlStr2",$obj);
+
+    } // testCanBeCreatedFromValidLocalFileAfterCommentsRemoved()
+
 }
 ?>