From 9efecaa68b23b013e3bce54896f936136a5df603 Mon Sep 17 00:00:00 2001 From: Dominik Lindner Date: Thu, 16 Oct 2025 13:39:19 +0100 Subject: [PATCH 01/10] Add omero-zarr-pixel-buffer build --- .../OMERO-zarr-pixel-buffer-build/config.xml | 42 +++++++++++++++++ .../OMERO-zarr-pixel-buffer-push/config.xml | 47 +++++++++++++++++++ 2 files changed, 89 insertions(+) create mode 100644 home/jobs/OMERO-zarr-pixel-buffer-build/config.xml create mode 100644 home/jobs/OMERO-zarr-pixel-buffer-push/config.xml diff --git a/home/jobs/OMERO-zarr-pixel-buffer-build/config.xml b/home/jobs/OMERO-zarr-pixel-buffer-build/config.xml new file mode 100644 index 00000000..286e1832 --- /dev/null +++ b/home/jobs/OMERO-zarr-pixel-buffer-build/config.xml @@ -0,0 +1,42 @@ + + + + + false + + + testintegration + false + false + false + false + + false + + + rm -rf zarr-java +git clone https://github.com/zarr-developers/zarr-java.git +cd zarr-java +mvn clean install -DskipTests -Dgpg.skip=true +cd .. + +rm -rf omero-zarr-pixel-buffer +git clone -b $MERGE_PUSH_BRANCH https://github.com/$SPACE_USER/omero-zarr-pixel-buffer.git +cd omero-zarr-pixel-buffer +./gradlew publishToMavenLocal + + + + + + **/build/libs/*.jar, **/target/*.jar + false + false + false + true + true + false + + + + \ No newline at end of file diff --git a/home/jobs/OMERO-zarr-pixel-buffer-push/config.xml b/home/jobs/OMERO-zarr-pixel-buffer-push/config.xml new file mode 100644 index 00000000..d6a71c8b --- /dev/null +++ b/home/jobs/OMERO-zarr-pixel-buffer-push/config.xml @@ -0,0 +1,47 @@ + + + + Run scc merge and bump versions on omero-zarr-pixel-buffer + false + + + + + STATUS + PR check status + + + success-only + no-error + none + + + + + MERGE_OPTIONS + scc merge options + -vvv --no-ask --reset --comment + false + + + + + + + true + + + false + \ No newline at end of file From ec42d7e522f76e4d13b22d03f3df0561074330c2 Mon Sep 17 00:00:00 2001 From: Dominik Lindner Date: Thu, 11 Dec 2025 14:35:51 +0000 Subject: [PATCH 02/10] Remove zarr-java build --- home/jobs/OMERO-zarr-pixel-buffer-build/config.xml | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/home/jobs/OMERO-zarr-pixel-buffer-build/config.xml b/home/jobs/OMERO-zarr-pixel-buffer-build/config.xml index 286e1832..fce8be4d 100644 --- a/home/jobs/OMERO-zarr-pixel-buffer-build/config.xml +++ b/home/jobs/OMERO-zarr-pixel-buffer-build/config.xml @@ -14,13 +14,7 @@ false - rm -rf zarr-java -git clone https://github.com/zarr-developers/zarr-java.git -cd zarr-java -mvn clean install -DskipTests -Dgpg.skip=true -cd .. - -rm -rf omero-zarr-pixel-buffer + rm -rf omero-zarr-pixel-buffer git clone -b $MERGE_PUSH_BRANCH https://github.com/$SPACE_USER/omero-zarr-pixel-buffer.git cd omero-zarr-pixel-buffer ./gradlew publishToMavenLocal @@ -39,4 +33,4 @@ cd omero-zarr-pixel-buffer - \ No newline at end of file + From e3be71493c9b5beb9800463de84db5ae0f6c0ac5 Mon Sep 17 00:00:00 2001 From: Dominik Lindner Date: Tue, 6 Jan 2026 18:40:56 +0000 Subject: [PATCH 03/10] Add zarr-pb to Trigger --- home/jobs/Trigger/config.xml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/home/jobs/Trigger/config.xml b/home/jobs/Trigger/config.xml index 93f10fef..e72627f4 100644 --- a/home/jobs/Trigger/config.xml +++ b/home/jobs/Trigger/config.xml @@ -126,6 +126,13 @@ build job: 'WEBSITE-push', wait: false } } + + stage('OMERO zarr-pixel-buffer') { + steps { + build job: 'OMERO-zarr-pixel-buffer-push' + build job: 'OMERO-zarr-pixel-buffer-build' + } + } } } true From 0b68e7bd88d6c64abf8aedd3712a7a38b576b211 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 13 Jan 2026 10:18:01 +0000 Subject: [PATCH 04/10] remove target --- home/jobs/OMERO-zarr-pixel-buffer-build/config.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/home/jobs/OMERO-zarr-pixel-buffer-build/config.xml b/home/jobs/OMERO-zarr-pixel-buffer-build/config.xml index fce8be4d..b73187d2 100644 --- a/home/jobs/OMERO-zarr-pixel-buffer-build/config.xml +++ b/home/jobs/OMERO-zarr-pixel-buffer-build/config.xml @@ -23,7 +23,7 @@ cd omero-zarr-pixel-buffer - **/build/libs/*.jar, **/target/*.jar + **/build/libs/*.jar false false false From 3388e1cdeeb15c613c45fca0ec31d89d5f496801 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 13 Jan 2026 10:40:16 +0000 Subject: [PATCH 05/10] Copy version from other plugins to get better overview --- home/jobs/OMERO-zarr-pixel-buffer-push/config.xml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/home/jobs/OMERO-zarr-pixel-buffer-push/config.xml b/home/jobs/OMERO-zarr-pixel-buffer-push/config.xml index d6a71c8b..6ed2ff65 100644 --- a/home/jobs/OMERO-zarr-pixel-buffer-push/config.xml +++ b/home/jobs/OMERO-zarr-pixel-buffer-push/config.xml @@ -37,7 +37,9 @@ repo: 'omero-zarr-pixel-buffer.git') recursiveMerge( - baseRepo: 'omero-zarr-pixel-buffer.git') + baseRepo: 'omero-zarr-pixel-buffer.git' + parentVersions: 'OMERO-plugins-push', + versionFile: 'build/version.tsv') } true From 4c0f4d642f53fd54541a2ddbaa3ed2b9694fe240 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 13 Jan 2026 11:04:40 +0000 Subject: [PATCH 06/10] Build omero-zarr-pixel-buffer earlier --- home/jobs/Trigger/config.xml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/home/jobs/Trigger/config.xml b/home/jobs/Trigger/config.xml index e72627f4..044c7de1 100644 --- a/home/jobs/Trigger/config.xml +++ b/home/jobs/Trigger/config.xml @@ -69,6 +69,13 @@ } } + stage('OMERO zarr-pixel-buffer') { + steps { + build job: 'OMERO-zarr-pixel-buffer-push' + build job: 'OMERO-zarr-pixel-buffer-build' + } + } + stage("OMERO Python") { steps { build job: 'OMERO-python-superbuild-push', parameters: [string(name: 'STATUS', value: "${params.STATUS}")] @@ -127,12 +134,6 @@ } } - stage('OMERO zarr-pixel-buffer') { - steps { - build job: 'OMERO-zarr-pixel-buffer-push' - build job: 'OMERO-zarr-pixel-buffer-build' - } - } } } true From 44eb41b87be69b23572b232033fe34ef01345a9e Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 13 Jan 2026 22:11:33 +0000 Subject: [PATCH 07/10] Install zarr-pixel-buffer and dependencies --- home/jobs/OMERO-server/config.xml | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/home/jobs/OMERO-server/config.xml b/home/jobs/OMERO-server/config.xml index 5cbe66ae..9048575e 100644 --- a/home/jobs/OMERO-server/config.xml +++ b/home/jobs/OMERO-server/config.xml @@ -95,6 +95,16 @@ rm -rf $WORKSPACE/* # Should leave .venv3 true false + + + OMERO-zarr-pixel-buffer-build + + + false + + + true + false @@ -121,6 +131,15 @@ unzip $ZIP rm -f $ZIP mv $WORKSPACE/$DIST $OMERO_DIST +# Install omero-zarr-pixel-buffer +wget -P $OMERO_DIST/lib/server https://repo.maven.apache.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar +wget -P $OMERO_DIST/lib/server https://repo.maven.apache.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar +wget -P $OMERO_DIST/lib/server https://repo.maven.apache.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar +wget -P $OMERO_DIST/lib/server https://repo.maven.apache.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar +for x in *.jar; do + mv $x $OMERO_DIST/lib/server +done + source $WORKSPACE/.venv3/bin/activate pip install -U pip From 74d30fffabf87ad4c69b5579d49d7d31595f3633 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 14 Jan 2026 09:31:42 +0000 Subject: [PATCH 08/10] Add comment --- home/jobs/OMERO-server/config.xml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/home/jobs/OMERO-server/config.xml b/home/jobs/OMERO-server/config.xml index 9048575e..27b0ac3c 100644 --- a/home/jobs/OMERO-server/config.xml +++ b/home/jobs/OMERO-server/config.xml @@ -136,6 +136,8 @@ wget -P $OMERO_DIST/lib/server https://repo.maven.apache.org/maven2/com/github/b wget -P $OMERO_DIST/lib/server https://repo.maven.apache.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar wget -P $OMERO_DIST/lib/server https://repo.maven.apache.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar wget -P $OMERO_DIST/lib/server https://repo.maven.apache.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar + +# Install the jar from OMERO-zarr-pixel-buffer-build job for x in *.jar; do mv $x $OMERO_DIST/lib/server done From d32dd7a0cc11d921d674b53bd425f9296bcf9eb9 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 14 Jan 2026 11:37:37 +0000 Subject: [PATCH 09/10] remove version from previous build --- home/jobs/OMERO-zarr-pixel-buffer-push/config.xml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/home/jobs/OMERO-zarr-pixel-buffer-push/config.xml b/home/jobs/OMERO-zarr-pixel-buffer-push/config.xml index 6ed2ff65..d6a71c8b 100644 --- a/home/jobs/OMERO-zarr-pixel-buffer-push/config.xml +++ b/home/jobs/OMERO-zarr-pixel-buffer-push/config.xml @@ -37,9 +37,7 @@ repo: 'omero-zarr-pixel-buffer.git') recursiveMerge( - baseRepo: 'omero-zarr-pixel-buffer.git' - parentVersions: 'OMERO-plugins-push', - versionFile: 'build/version.tsv') + baseRepo: 'omero-zarr-pixel-buffer.git') } true From 806319318812ded3fac41f97e463d675a983e7dd Mon Sep 17 00:00:00 2001 From: Dominik Lindner Date: Wed, 14 Jan 2026 20:02:25 +0000 Subject: [PATCH 10/10] Add aws-java-sdk-core jar download to server/config.xml --- home/jobs/OMERO-server/config.xml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/home/jobs/OMERO-server/config.xml b/home/jobs/OMERO-server/config.xml index 27b0ac3c..c52c157a 100644 --- a/home/jobs/OMERO-server/config.xml +++ b/home/jobs/OMERO-server/config.xml @@ -136,7 +136,8 @@ wget -P $OMERO_DIST/lib/server https://repo.maven.apache.org/maven2/com/github/b wget -P $OMERO_DIST/lib/server https://repo.maven.apache.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar wget -P $OMERO_DIST/lib/server https://repo.maven.apache.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar wget -P $OMERO_DIST/lib/server https://repo.maven.apache.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar - +wget -P $OMERO_DIST/lib/server https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-core/1.12.659/aws-java-sdk-core-1.12.659.jar + # Install the jar from OMERO-zarr-pixel-buffer-build job for x in *.jar; do mv $x $OMERO_DIST/lib/server @@ -208,4 +209,4 @@ deactivate - \ No newline at end of file +