From 7fd8720f6aefe6afad5823426c31dd24f16b874e Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 12 Jan 2026 16:28:23 +0000 Subject: [PATCH 1/8] New perf profile --- .../perf_files/armadillo_hp-laptop-quay_perf-profile.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/perf_files/armadillo_hp-laptop-quay_perf-profile.csv b/tests/testthat/perf_files/armadillo_hp-laptop-quay_perf-profile.csv index 9ac69853..010650f1 100644 --- a/tests/testthat/perf_files/armadillo_hp-laptop-quay_perf-profile.csv +++ b/tests/testthat/perf_files/armadillo_hp-laptop-quay_perf-profile.csv @@ -6,7 +6,7 @@ "ds.asNumeric::perf:0","1.354","0.5","2" "ds.assign::perf::0","2.745","0.5","2" "ds.class::perf::combine:0","3.261","0.5","2" -"ds.colnames::perf:0","2.404","0.5","2" +"ds.colnames::perf:0","8.566","0.5","2" "ds.exists::perf::combine:0","6.342","0.5","2" "ds.length::perf::combine:0","7.835","0.5","2" "ds.mean::perf::combine:0","8.127","0.5","2" From 46b02ac15a13f3e93d0344efce28f2c2cbba0d80 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Wed, 14 Jan 2026 09:17:15 +0000 Subject: [PATCH 2/8] Switch to 'molgenis-rock-base' --- docker-compose_armadillo.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docker-compose_armadillo.yml b/docker-compose_armadillo.yml index 4461b24f..97b9bab5 100644 --- a/docker-compose_armadillo.yml +++ b/docker-compose_armadillo.yml @@ -16,6 +16,7 @@ services: default: hostname: default - image: datashield/rock-quebrada-lamda-permissive:latest +# image: datashield/rock-quebrada-lamda-permissive:latest + image: datashield/datashield/molgenis-rock-base-permissive:1.0.0 environment: DEBUG: "FALSE" From 245e5b3bc20c56a8d6b17469a3a306ec473e59d6 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Wed, 14 Jan 2026 12:29:58 +0000 Subject: [PATCH 3/8] Fix docker image typo --- docker-compose_armadillo.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose_armadillo.yml b/docker-compose_armadillo.yml index 97b9bab5..55f8129d 100644 --- a/docker-compose_armadillo.yml +++ b/docker-compose_armadillo.yml @@ -17,6 +17,6 @@ services: default: hostname: default # image: datashield/rock-quebrada-lamda-permissive:latest - image: datashield/datashield/molgenis-rock-base-permissive:1.0.0 + image: datashield/molgenis-rock-base-permissive:1.0.0 environment: DEBUG: "FALSE" From d4dca23b851b97dce63d3740b6964110a80048dd Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Fri, 16 Jan 2026 12:21:36 +0000 Subject: [PATCH 4/8] Update version of mongo --- docker-compose_opal.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose_opal.yml b/docker-compose_opal.yml index a62dec67..ff7b6085 100644 --- a/docker-compose_opal.yml +++ b/docker-compose_opal.yml @@ -15,7 +15,7 @@ services: - ROCK_HOSTS=rock:8085 - ROCK_ADMINISTRATOR_PASSWORD=foobar mongo: - image: mongo:4.4.15 + image: mongo:6.0.27 environment: - MONGO_INITDB_ROOT_USERNAME=root - MONGO_INITDB_ROOT_PASSWORD=foobar From 2847b6e5e78a7070f0d40df26b04e30192a7100b Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Fri, 6 Feb 2026 17:09:32 +0000 Subject: [PATCH 5/8] Switch to 'rio-lamba' profile --- docker-compose_opal.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose_opal.yml b/docker-compose_opal.yml index ff7b6085..828f068e 100644 --- a/docker-compose_opal.yml +++ b/docker-compose_opal.yml @@ -20,6 +20,6 @@ services: - MONGO_INITDB_ROOT_USERNAME=root - MONGO_INITDB_ROOT_PASSWORD=foobar rock: - image: datashield/rock-quebrada-lamda-permissive:latest + image: datashield/rock-rio-lamda-permissive:latest environment: DEBUG: "FALSE" From 2ef108206a6cfd88b47aa2098f444d510f0cd1c9 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 9 Feb 2026 11:58:32 +0000 Subject: [PATCH 6/8] Switched profile based on Rock 2.2.0 --- docker-compose_armadillo.yml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/docker-compose_armadillo.yml b/docker-compose_armadillo.yml index 55f8129d..0b03b80a 100644 --- a/docker-compose_armadillo.yml +++ b/docker-compose_armadillo.yml @@ -3,11 +3,13 @@ services: hostname: armadillo ports: - 8080:8080 - image: datashield/armadillo_citest:5.12.2 + image: datashield/armadillo_citest:latest +# image: datashield/armadillo_devel:latest environment: LOGGING_CONFIG: 'classpath:logback-file.xml' AUDIT_LOG_PATH: '/app/logs/audit.log' SPRING_SECURITY_USER_PASSWORD: 'admin' + DEBUG: "FALSE" volumes: - ./tests/docker/armadillo/standard/logs:/logs - ./tests/docker/armadillo/standard/data:/data @@ -16,7 +18,8 @@ services: default: hostname: default -# image: datashield/rock-quebrada-lamda-permissive:latest - image: datashield/molgenis-rock-base-permissive:1.0.0 + image: datashield/molgenis-rock-base-permissive:2.0.0 +# image: datashield/rserver-citest:latest +# image: datashield/rserver-devel:latest environment: DEBUG: "FALSE" From d41f142390455b1119828d44d672466aea524a20 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Wed, 11 Feb 2026 13:11:23 +0000 Subject: [PATCH 7/8] Rework image names --- docker-compose_armadillo.yml | 5 +---- docker-compose_opal.yml | 2 +- tests/docker/armadillo/standard/config/application.yml | 3 ++- 3 files changed, 4 insertions(+), 6 deletions(-) diff --git a/docker-compose_armadillo.yml b/docker-compose_armadillo.yml index 0b03b80a..4751e3b2 100644 --- a/docker-compose_armadillo.yml +++ b/docker-compose_armadillo.yml @@ -4,7 +4,6 @@ services: ports: - 8080:8080 image: datashield/armadillo_citest:latest -# image: datashield/armadillo_devel:latest environment: LOGGING_CONFIG: 'classpath:logback-file.xml' AUDIT_LOG_PATH: '/app/logs/audit.log' @@ -18,8 +17,6 @@ services: default: hostname: default - image: datashield/molgenis-rock-base-permissive:2.0.0 -# image: datashield/rserver-citest:latest -# image: datashield/rserver-devel:latest + image: datashield/rock-citest-permissive:latest environment: DEBUG: "FALSE" diff --git a/docker-compose_opal.yml b/docker-compose_opal.yml index 828f068e..a7db7fb3 100644 --- a/docker-compose_opal.yml +++ b/docker-compose_opal.yml @@ -20,6 +20,6 @@ services: - MONGO_INITDB_ROOT_USERNAME=root - MONGO_INITDB_ROOT_PASSWORD=foobar rock: - image: datashield/rock-rio-lamda-permissive:latest + image: datashield/rock-citest-permissive:latest environment: DEBUG: "FALSE" diff --git a/tests/docker/armadillo/standard/config/application.yml b/tests/docker/armadillo/standard/config/application.yml index 54e90c36..8a0e3da5 100644 --- a/tests/docker/armadillo/standard/config/application.yml +++ b/tests/docker/armadillo/standard/config/application.yml @@ -14,11 +14,12 @@ armadillo: # oidc-admin-user: user@yourdomain.org profiles: - name: default - image: datashield/rock-quebrada-lamda-permissive:latest + image: datashield/rock-citest-permissive:latest port: 8085 host: default package-whitelist: # Packages for 'permissive' - dsBase + - dsTidyverse - resourcer function-blacklist: [ ] options: From 29e869736e61e59cc81832e3ea8a8ff11e2623f0 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Wed, 11 Feb 2026 17:02:15 +0000 Subject: [PATCH 8/8] Fixed image name typo --- docker-compose_armadillo.yml | 2 +- docker-compose_opal.yml | 2 +- tests/docker/armadillo/standard/config/application.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docker-compose_armadillo.yml b/docker-compose_armadillo.yml index 4751e3b2..dba71daf 100644 --- a/docker-compose_armadillo.yml +++ b/docker-compose_armadillo.yml @@ -17,6 +17,6 @@ services: default: hostname: default - image: datashield/rock-citest-permissive:latest + image: datashield/rock_citest-permissive:latest environment: DEBUG: "FALSE" diff --git a/docker-compose_opal.yml b/docker-compose_opal.yml index a7db7fb3..d1566d20 100644 --- a/docker-compose_opal.yml +++ b/docker-compose_opal.yml @@ -20,6 +20,6 @@ services: - MONGO_INITDB_ROOT_USERNAME=root - MONGO_INITDB_ROOT_PASSWORD=foobar rock: - image: datashield/rock-citest-permissive:latest + image: datashield/rock_citest-permissive:latest environment: DEBUG: "FALSE" diff --git a/tests/docker/armadillo/standard/config/application.yml b/tests/docker/armadillo/standard/config/application.yml index 8a0e3da5..243160a3 100644 --- a/tests/docker/armadillo/standard/config/application.yml +++ b/tests/docker/armadillo/standard/config/application.yml @@ -14,7 +14,7 @@ armadillo: # oidc-admin-user: user@yourdomain.org profiles: - name: default - image: datashield/rock-citest-permissive:latest + image: datashield/rock_citest-permissive:latest port: 8085 host: default package-whitelist: # Packages for 'permissive'