KPMP-6260: Check for missing slides after inserting to ensure we are …

data_management/services/dlu_management.py

@@ -101,11 +101,6 @@ def update_dlu_package(self, package_id: str, fields_values: dict):
             values = query_info["values"][0:] + (package_id,)
             query = "UPDATE data_manager_data_v SET " + query_info["set_clause"] + " WHERE dlu_package_id = %s"
             self.db.insert_data(query, values)
-
-    def get_missing_slides(self, redcap_id: str):
-        return self.db.get_data(
-            "select * from missing_slides_v where spectrack_redcap_record_id = %s", 
-            (redcap_id,)),
 
     def update_missing_slides(self, redcap_id: str):
         return self.db.get_data(
@@ -270,27 +265,34 @@ def get_slide_manifest_import_by_kit(self, kit_id, stain):
     def set_error_message_slide_scan_curation(self, error, image_id):
         self.db.insert_data("UPDATE slide_scan_curation set error_message = %s where image_id = %s",
                        (error, image_id,))
-
-    def set_error_message_slide_scan_curation_redcap_id(self, error, redcap_id):
-        self.db.insert_data_no_alert("UPDATE slide_scan_curation set error_message = %s where redcap_id = %s",
-                       (error, redcap_id,))
 
     def find_slide_scan_info_by_package_id(self, package_id):
-        self.db.get_data("SELECT * FROM slide_scan_v WHERE dlu_package_id = %s",
+        return self.db.get_data("SELECT * FROM slide_scan_v WHERE dlu_package_id = %s",
                          (package_id,))
 
     def is_package_missing_slides(self, package_id):
-        self.db.get_data("SELECT * FROM slide_scan_v WHERE dlu_package_id = %s and missing_slides = 1",
+        return self.db.get_data("SELECT * FROM slide_scan_v WHERE dlu_package_id = %s and missing_slides = 1",
                          (package_id,))
 
+    def slides_marked_missing_by_redcap_id(self, redcap_id: str):
+        return self.db.get_data("SELECT * FROM slide_scan_v WHERE redcap_id = %s AND missing_slides = 1",
+                         (redcap_id,))
+
+    def get_missing_slides_from_view(self, redcap_id: str):
+        return self.db.get_data("select * from missing_slides_v where spectrack_redcap_record_id = %s",
+                                (redcap_id,))
+
     def is_slides_in_error(self, package_id):
-        self.db.get_data("SELECT * FROM slide_scan_curation WHERE dlu_package_id = %s and error_message IS NOT NULL",
+        return self.db.get_data("SELECT * FROM slide_scan_curation WHERE dlu_package_id = %s and error_message IS NOT NULL",
                          (package_id,))
 
     def find_not_approved_filenames(self, package_id):
-        self.db.get_data("SELECT * FROM slide_scan_curation WHERE approve_file_name = 'yes' AND dlu_package_id = %s",
+        return self.db.get_data("SELECT * FROM slide_scan_curation WHERE approve_file_name = 'yes' AND dlu_package_id = %s",
                          (package_id,))
 
+    def update_missing_slide_flag(self, image_id):
+        return self.db.insert_data("UPDATE slide_scan_curation SET missing_slides = 0 WHERE image_id = %s",
+                                   (image_id,))
 
 if __name__ == "__main__":
     dlu_management = DluManagement()

data_management/services/slide_management.py

@@ -74,6 +74,7 @@ def __init__(self, db):
 
     def process_slide_manifest_imports(self):
         new_records = self.db.get_new_slide_manifest_import_rows()
+        redcap_ids_processed = []
         for record in new_records:
             record_in_error = False
             error_message = ""
@@ -84,7 +85,7 @@ def process_slide_manifest_imports(self):
                 error_message = "No redcap_id found for kit_id " + kit_id + "; "
                 logger.error(error_message)
                 continue
-                
+
             if record["accession"] is not None:
                 new_file_name = self.determine_new_slide_name(sample_id=record["accession"], kit_id=kit_id,
                                                               stain_info=record["stain"], block_id=record["block_id"])
@@ -108,23 +109,29 @@ def process_slide_manifest_imports(self):
                                     new_file_name=new_file_name, source_file_name=source_file_name,
                                     source_folder_name=source_folder_name)
             self.db.insert_into_slide_scan_curation(slide_scan.get_dmd_tuple())
-            check_missing_slides = self.db.get_missing_slides(redcap_id)
+
+            check_missing_slides = self.db.get_missing_slides_from_view(redcap_id)
+            redcap_ids_processed.append(redcap_id)
             if all(check_missing_slides):
-                if error_message != None: 
-
-                    error_message += "There are missing slide(s) for participant " + redcap_id + "; "
-                elif error_message is None:
-                    error_message = "There are missing slide(s) for participant " + redcap_id + "; "
-                logger.info(error_message)
                 self.db.update_missing_slides(redcap_id)
-
-                # Can't use record_in_error here because we can't set an error message for an image_id that doesn't exist
-                self.db.set_error_message_slide_scan_curation_redcap_id(error=error_message, redcap_id=redcap_id)
-
+
             if record_in_error:
                 self.db.set_error_message_slide_scan_curation(image_id=image_id, error=error_message)
         logger.info("Processed " + str(len(new_records)) + " new slide_manifest_import records.")
 
+        for redcap_id in redcap_ids_processed:
+            self.update_missing_slides(redcap_id)
+
+    def update_missing_slides(self, redcap_id: str):
+        # This MAY seem redundant, however this will ensure that we unmark any missing slides records that just got
+        # the missing one added
+        missing_slides = self.db.get_missing_slides_from_view(redcap_id)
+        if not missing_slides or len(missing_slides) ==0 :
+            slides_marked_missing = self.db.slides_marked_missing_by_redcap_id(redcap_id)
+            if slides_marked_missing and len(slides_marked_missing) > 0:
+                for slide in slides_marked_missing:
+                    self.db.update_missing_slide_flag(slide['image_id'])
+
     def determine_new_slide_name(self, sample_id: str, kit_id: str, stain_info: str, block_id: str):
         slides_for_kit = self.db.get_slide_manifest_import_by_kit(kit_id, stain_info)
 

data_management/watch_files.py

@@ -113,6 +113,7 @@ def move_packages_to_DLU(self, packages):
 
             self.dlu_state.set_package_state(package_id, PackageState.UPLOAD_SUCCEEDED)
             self.dlu_state.clear_cache()
+
     def fill_in_null_package_ids(self):
         self.slide_management.fill_in_package_ids()