From d11319bca614a21c5414cfc6b92b2c7825901f87 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 5 Mar 2024 11:42:38 +0100 Subject: [PATCH 001/107] Restore branch before the aborted release --- commons-datastore/commons-datastore-core/pom.xml | 2 +- commons-datastore/commons-datastore-mongodb/pom.xml | 3 ++- commons-datastore/commons-datastore-solr/pom.xml | 4 +++- commons-datastore/pom.xml | 2 +- commons-lib/pom.xml | 3 ++- pom.xml | 12 +++++------- 6 files changed, 14 insertions(+), 12 deletions(-) diff --git a/commons-datastore/commons-datastore-core/pom.xml b/commons-datastore/commons-datastore-core/pom.xml index aa880ed3..c78e2899 100644 --- a/commons-datastore/commons-datastore-core/pom.xml +++ b/commons-datastore/commons-datastore-core/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.0.0 + 4.12.0 ../pom.xml diff --git a/commons-datastore/commons-datastore-mongodb/pom.xml b/commons-datastore/commons-datastore-mongodb/pom.xml index 81b7ca56..ccfdf544 100644 --- a/commons-datastore/commons-datastore-mongodb/pom.xml +++ b/commons-datastore/commons-datastore-mongodb/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.0.0 + 4.12.0 ../pom.xml @@ -50,6 +50,7 @@ org.hamcrest hamcrest-core + test junit diff --git a/commons-datastore/commons-datastore-solr/pom.xml b/commons-datastore/commons-datastore-solr/pom.xml index d50e0ec6..c8928016 100644 --- a/commons-datastore/commons-datastore-solr/pom.xml +++ b/commons-datastore/commons-datastore-solr/pom.xml @@ -22,7 +22,7 @@ org.opencb.commons commons-datastore - 5.0.0 + 4.12.0 ../pom.xml @@ -34,6 +34,7 @@ org.opencb.commons commons-datastore-core + org.apache.solr solr-solrj @@ -51,4 +52,5 @@ slf4j-api + diff --git a/commons-datastore/pom.xml b/commons-datastore/pom.xml index 2519bb24..338658a6 100644 --- a/commons-datastore/pom.xml +++ b/commons-datastore/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.0.0 + 4.12.0 ../pom.xml diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index 7fbeb7c4..c28f2b56 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.0.0 + 4.12.0 ../pom.xml @@ -67,6 +67,7 @@ com.fasterxml.jackson.core jackson-databind + test diff --git a/pom.xml b/pom.xml index 50c9ed94..2d6414ba 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.0.0 + 4.12.0 pom OpenCB commons project @@ -20,9 +20,9 @@ - 2.14.3 - 3.14.0 - 1.7.36 + 2.11.4 + 3.12.0 + 1.7.32 1.7.7 4.8.2 8.8.2 @@ -32,6 +32,7 @@ 1.3 4.13.2 + opencb https://sonarcloud.io 1.8 @@ -296,9 +297,6 @@ * - - * - From 195503565003989345370d88dcd4eb83ff8a2733 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Mon, 3 Jun 2024 10:22:22 +0200 Subject: [PATCH 002/107] utils: add the method FileUtils.copyFile, #TASK-6297, #TASK-6255 On branch TASK-6255 Changes to be committed: modified: commons-lib/pom.xml modified: commons-lib/src/main/java/org/opencb/commons/utils/FileUtils.java --- commons-lib/pom.xml | 6 +++++ .../org/opencb/commons/utils/FileUtils.java | 22 +++++++++++++++++++ 2 files changed, 28 insertions(+) diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index dccbe7ec..0e057979 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -68,5 +68,11 @@ com.fasterxml.jackson.core jackson-databind + + commons-io + commons-io + 2.8.0 + compile + diff --git a/commons-lib/src/main/java/org/opencb/commons/utils/FileUtils.java b/commons-lib/src/main/java/org/opencb/commons/utils/FileUtils.java index 93fba0f0..1ae5ba87 100644 --- a/commons-lib/src/main/java/org/opencb/commons/utils/FileUtils.java +++ b/commons-lib/src/main/java/org/opencb/commons/utils/FileUtils.java @@ -18,6 +18,7 @@ import org.apache.commons.lang3.StringUtils; import org.opencb.commons.exec.Command; +import org.slf4j.LoggerFactory; import java.io.*; import java.nio.charset.Charset; @@ -188,6 +189,27 @@ public static String[] getUserAndGroup(Path path, boolean numericId) throws IOEx return new String[]{split[2], split[3]}; } + + public static void copyFile(File src, File dest) throws IOException { + try { + org.apache.commons.io.FileUtils.copyFile(src, dest); + } catch (IOException e) { + try { + if (src.length() == dest.length()) { + LoggerFactory.getLogger(FileUtils.class).warn(e.getMessage()); + return; + } + throw e; + } catch (Exception e1) { + throw e; + } + } + } + + //------------------------------------------------------------------------- + // P R I V A T E M E T H O D S + //------------------------------------------------------------------------- + private static String getLsOutput(Path path, boolean numericId) throws IOException { FileUtils.checkPath(path); From df70872e5d941c6a76327332103ebd9ac3044dc5 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 20 Jun 2024 12:07:42 +0200 Subject: [PATCH 003/107] test-xetabase-workflow.yml: New workflow to test xetabase on pullrequest approve of the libraries #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 93 ++++++++++++++++++++ 1 file changed, 93 insertions(+) create mode 100644 .github/workflows/test-xetabase-workflow.yml diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml new file mode 100644 index 00000000..49c4c2af --- /dev/null +++ b/.github/workflows/test-xetabase-workflow.yml @@ -0,0 +1,93 @@ +name: Pull request approve workflow + +on: + workflow_call: + inputs: + task: + type: string + required: true + branch: + type: string + required: true + +jobs: + test: + name: Execute JUnit and Jacoco tests + runs-on: ubuntu-22.04 + steps: + - name: Clone OpenCGA Enterprise branch '${{ github.event.inputs.branch }}' + uses: actions/checkout@v4 + with: + repository: zetta-genomics/opencga-enterprise + ref: ${{ github.event.inputs.branch }} + token: ${{ secrets.GH_PRIVATE_TOKEN }} + path: opencga-enterprise + fetch-depth: "10" + - id: get_opencga_branch + name: Get OpenCGA branch from 'pom.xml' property + run: | + pwd + chmod +x ./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh + opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh ${{ github.event.inputs.task }}) + echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT + - uses: actions/checkout@v4 + with: + repository: opencb/opencga + ref: ${{ steps.get_opencga_branch.outputs.opencga_branch }} + path: opencga + fetch-depth: '10' + - name: Set up JDK 8 + uses: actions/setup-java@v4 + with: + distribution: 'temurin' + java-version: '8' + cache: 'maven' + - name: Install Samtools + run: sudo apt-get install samtools python3-deeptools + - name: Start MongoDB v6.0 + uses: supercharge/mongodb-github-action@1.8.0 + with: + mongodb-version: 6.0 + mongodb-replica-set: rs-test + - name: K8s Tunnel MongoDB + run: | + wget https://dl.k8s.io/release/v1.28.2/bin/linux/amd64/kubectl + chmod +x ./kubectl + echo "${{ secrets.AZURE_KUBE_CONFIG }}" > admin.conf + ./kubectl -n cellbase-db port-forward services/cellbase-rs0-svc 27018:27017 --kubeconfig ./admin.conf & + - name: Install Azure AZCOPY + uses: kheiakiyama/install-azcopy-action@v1 + with: + version: 'v10' + - name: DockerHub login + uses: docker/login-action@v3 + with: + username: ${{ secrets.DOCKER_HUB_USER }} + password: ${{ secrets.DOCKER_HUB_PASSWORD }} + - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise + run: | + ln -s opencga opencga-enterprise/opencga-home + cd opencga-enterprise + ./build.sh -t -l runShortTests,runMediumTests,runLongTests -b -s -f -T ${{ github.event.inputs.task }} -c localhost:27018 -H hdp3.1 + - name: Upload reports results to Github + uses: actions/upload-artifact@v4 + with: + name: report-test + path: /home/runner/work/testing-environment/testing-environment/opencga-enterprise/reports/test + - name: Upload log + uses: actions/upload-artifact@v4 + with: + name: build-log + path: /home/runner/work/testing-environment/testing-environment/opencga-enterprise/build.log + - name: Upload junit reports to a remote scp server + uses: garygrossgarten/github-action-scp@release + with: + local: opencga-enterprise/reports/test + remote: /var/www/html/reports/xetabase/${{ github.event.inputs.task }}/ + host: ${{ secrets.SSH_TESTING_SERVER_HOST}} + port: ${{ secrets.SSH_TESTING_SERVER_PORT}} + username: ${{ secrets.SSH_TESTING_SERVER_USER }} + password: ${{ secrets.SSH_TESTING_SERVER_PASSWORD }} + concurrency: 2 + + From 3f2f4eb710dab9238ead39aee8d47a0a4213d652 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 20 Jun 2024 12:08:14 +0200 Subject: [PATCH 004/107] test-xetabase-workflow.yml: New workflow to test xetabase on pullrequest approve of the libraries #TASK-6399 --- .github/workflows/scripts/xetabase-branch.sh | 42 ++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 .github/workflows/scripts/xetabase-branch.sh diff --git a/.github/workflows/scripts/xetabase-branch.sh b/.github/workflows/scripts/xetabase-branch.sh new file mode 100644 index 00000000..af17f7f1 --- /dev/null +++ b/.github/workflows/scripts/xetabase-branch.sh @@ -0,0 +1,42 @@ +#!/bin/bash + +# Function to calculate the corresponding branch of Xetabase project +get_xetabase_branch() { + # Input parameter (branch name) + input_branch="$1" + + # Check if the branch name is "develop" in that case return the same branch name + if [[ "$input_branch" == "develop" ]]; then + echo "develop" + return 0 + fi + + # Check if the branch name starts with "release-" and follows the patterns "release-a.b.x" or "release-a.b.c.x" + if [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.x$ ]] || [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.([0-9]+)\.x$ ]]; then + # Extract the MAJOR part of the branch name + MAJOR=${BASH_REMATCH[1]} + # Calculate the XETABASE_MAJOR by subtracting 3 from MAJOR + XETABASE_MAJOR=$((MAJOR - 3)) + # Check if the XETABASE_MAJOR is negative + if (( XETABASE_MAJOR < 0 )); then + echo "Error: 'MAJOR' digit after subtraction results in a negative number." + return 1 + fi + # Construct and echo the new branch name + echo "release-$XETABASE_MAJOR.${input_branch#release-$MAJOR.}" + return 0 + fi + + # If the branch name does not match any of the expected patterns + echo "Error: The branch name is not correct." + return 1 +} + +# Check if the script receives exactly one argument +if [ "$#" -ne 1 ]; then + echo "Usage: $0 " + exit 1 +fi + +# Call the function with the input branch name +get_xetabase_branch "$1" From 37bfcd14022f33c5f23b6b449148709935f409bd Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 20 Jun 2024 12:09:42 +0200 Subject: [PATCH 005/107] test-xetabase-workflow.yml: Modify pull_request approve workflow to test all Xetabase instead only jcl #TASK-6399 --- .github/workflows/pull-request-approved.yml | 22 ++++++++++++++------- 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 329df1be..c20e61c9 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -5,11 +5,19 @@ on: types: [ submitted ] jobs: - build: - uses: ./.github/workflows/build-java-app-workflow.yml - test: - name: "Run all tests before merging" - uses: ./.github/workflows/test-analysis.yml - needs: build - secrets: inherit \ No newline at end of file + name: Execute JUnit and Jacoco tests + runs-on: ubuntu-22.04 + steps: + - id: get_xetabase_branch + name: Get current branch for Xetabase from 'pom.xml' property + run: | + chmod +x ./.github/workflows/scripts/xetabase-branch.sh + xetabase_branch=$(./.github/workflows/scripts/xetabase-branch.sh ${{ github.event.pull_request.base.ref }} + echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} + echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT + - name: "Run all tests before merging" + uses: ./.github/workflows/test-xetabase-workflow.yml + with: + branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }} + task: ${{ github.event.pull_request.head.ref }} \ No newline at end of file From f930213af02064275854e38a3665f4167f0644bf Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 20 Jun 2024 12:31:42 +0200 Subject: [PATCH 006/107] cicd:clone jcl to exec script in pull request approve #TASK-6399 --- .github/workflows/pull-request-approved.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index c20e61c9..ecc00780 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -9,6 +9,8 @@ jobs: name: Execute JUnit and Jacoco tests runs-on: ubuntu-22.04 steps: + - name: Clone java-common-libs + uses: actions/checkout@v4 - id: get_xetabase_branch name: Get current branch for Xetabase from 'pom.xml' property run: | From 9b2e5cf79cc6a5263e05a88da1235d0d0125420f Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 20 Jun 2024 12:34:25 +0200 Subject: [PATCH 007/107] cicd: fix parenthesi #TASK-6399 --- .github/workflows/pull-request-approved.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index ecc00780..7f80bfed 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -15,7 +15,7 @@ jobs: name: Get current branch for Xetabase from 'pom.xml' property run: | chmod +x ./.github/workflows/scripts/xetabase-branch.sh - xetabase_branch=$(./.github/workflows/scripts/xetabase-branch.sh ${{ github.event.pull_request.base.ref }} + xetabase_branch=$(./.github/workflows/scripts/xetabase-branch.sh ${{ github.event.pull_request.base.ref }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT - name: "Run all tests before merging" From b5149297841333bdab23748264999675dbf72df9 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 20 Jun 2024 13:00:11 +0200 Subject: [PATCH 008/107] cicd: debug ./.github/workflows/ #TASK-6399 --- .github/workflows/pull-request-approved.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 7f80bfed..36defafa 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -11,10 +11,14 @@ jobs: steps: - name: Clone java-common-libs uses: actions/checkout@v4 + with: + fetch-depth: '10' - id: get_xetabase_branch - name: Get current branch for Xetabase from 'pom.xml' property + name: "Get current branch for Xetabase from 'pom.xml' property" run: | chmod +x ./.github/workflows/scripts/xetabase-branch.sh + ls ./.github/workflows/scripts/ + ls ./.github/workflows/ xetabase_branch=$(./.github/workflows/scripts/xetabase-branch.sh ${{ github.event.pull_request.base.ref }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT From f8be19c4ec6154c7fe8ecc03394fb5acf9414531 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 25 Jun 2024 09:42:26 +0200 Subject: [PATCH 009/107] CICD: Added ZETTA_REPO_ACCESS_TOKEN to co xetabase #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 49c4c2af..fa78b2e2 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -1,4 +1,4 @@ -name: Pull request approve workflow +name: TEST Xetabase and publish report workflow on: workflow_call: @@ -20,7 +20,7 @@ jobs: with: repository: zetta-genomics/opencga-enterprise ref: ${{ github.event.inputs.branch }} - token: ${{ secrets.GH_PRIVATE_TOKEN }} + token: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }} path: opencga-enterprise fetch-depth: "10" - id: get_opencga_branch From 6cca2db321899bfe48e857b437de5b242a9d3a32 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 25 Jun 2024 09:57:54 +0200 Subject: [PATCH 010/107] cicd: Temporal workflow_dispatch for PR to tests #TASK-6399 --- .github/workflows/pull-request-approved.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 36defafa..de45af75 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -1,6 +1,7 @@ name: Pull request approve workflow on: + workflow_dispatch: pull_request_review: types: [ submitted ] From 1aa53aa3a12df7d065c2574b246e2b91db435ae7 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 25 Jun 2024 09:59:05 +0200 Subject: [PATCH 011/107] cicd: Delete Temporal workflow_dispatch for PR to tests #TASK-6399 --- .github/workflows/pull-request-approved.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index de45af75..36defafa 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -1,7 +1,6 @@ name: Pull request approve workflow on: - workflow_dispatch: pull_request_review: types: [ submitted ] From e29adf1e6c06ad520b56c947e4fa6308a84f822d Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 25 Jun 2024 10:07:45 +0200 Subject: [PATCH 012/107] cicd: Temporal call to TASK-6399 yml #TASK-6399 --- .github/workflows/pull-request-approved.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 36defafa..1ee5a141 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -23,7 +23,7 @@ jobs: echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT - name: "Run all tests before merging" - uses: ./.github/workflows/test-xetabase-workflow.yml + uses: ./.github/workflows/test-xetabase-workflow.yml@TASK-6399 with: branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }} task: ${{ github.event.pull_request.head.ref }} \ No newline at end of file From 55e0c2f25e0c418453b718a1e42e3de62a1f9919 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 25 Jun 2024 10:11:00 +0200 Subject: [PATCH 013/107] cicd: Temporal call to TASK-6399 yml #TASK-6399 --- .github/workflows/pull-request-approved.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 1ee5a141..4169383c 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -23,7 +23,7 @@ jobs: echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT - name: "Run all tests before merging" - uses: ./.github/workflows/test-xetabase-workflow.yml@TASK-6399 + uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@TASK-6399 with: branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }} task: ${{ github.event.pull_request.head.ref }} \ No newline at end of file From 2083020f3b2ed2035d264a8dcff845d6127b47a2 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 25 Jun 2024 10:43:16 +0200 Subject: [PATCH 014/107] create workflow in develop to test xetabase #TASK-6399 --- .github/workflows/pull-request-approved.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 4169383c..609bec4a 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -1,4 +1,5 @@ name: Pull request approve workflow +run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref }} -> ${{ github.event.pull_request.base.ref }} by @${{ github.actor }}' on: pull_request_review: From e0d260146f9c5f8e655d1c7be7c8151ccf190121 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 25 Jun 2024 10:52:58 +0200 Subject: [PATCH 015/107] Separate in two jobs to run the tests #TASK-6399 --- .github/workflows/pull-request-approved.yml | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 609bec4a..f5c6d8a6 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -6,7 +6,7 @@ on: types: [ submitted ] jobs: - test: + calculate-xetabase-branch: name: Execute JUnit and Jacoco tests runs-on: ubuntu-22.04 steps: @@ -15,7 +15,7 @@ jobs: with: fetch-depth: '10' - id: get_xetabase_branch - name: "Get current branch for Xetabase from 'pom.xml' property" + name: "Get current branch for Xetabase from target branch" run: | chmod +x ./.github/workflows/scripts/xetabase-branch.sh ls ./.github/workflows/scripts/ @@ -23,8 +23,11 @@ jobs: xetabase_branch=$(./.github/workflows/scripts/xetabase-branch.sh ${{ github.event.pull_request.base.ref }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT - - name: "Run all tests before merging" - uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@TASK-6399 - with: - branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }} - task: ${{ github.event.pull_request.head.ref }} \ No newline at end of file + + test: + name: "Run all tests before merging" + needs: calculate-xetabase-branch + uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@TASK-6399 + with: + branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }} + task: ${{ github.event.pull_request.head.ref }} \ No newline at end of file From 606b93ef03e0d71e161e07f80f8cc509ba18b6a1 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 25 Jun 2024 11:01:43 +0200 Subject: [PATCH 016/107] cicd secrets: inherit #TASK-6399 --- .github/workflows/pull-request-approved.yml | 3 ++- .github/workflows/test-xetabase-workflow.yml | 4 ++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index f5c6d8a6..e0260769 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -30,4 +30,5 @@ jobs: uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@TASK-6399 with: branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }} - task: ${{ github.event.pull_request.head.ref }} \ No newline at end of file + task: ${{ github.event.pull_request.head.ref }} + secrets: inherit \ No newline at end of file diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index fa78b2e2..12e8504a 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -15,6 +15,10 @@ jobs: name: Execute JUnit and Jacoco tests runs-on: ubuntu-22.04 steps: + - name: Log inputs + run: | + echo "__OpenCGA-enterprise branch:__ \"${{ github.event.inputs.branch }}\"" | tee -a $GITHUB_STEP_SUMMARY + echo "__Task to test:__ \"${{ github.event.inputs.task }}\"" | tee -a $GITHUB_STEP_SUMMARY - name: Clone OpenCGA Enterprise branch '${{ github.event.inputs.branch }}' uses: actions/checkout@v4 with: From 8014992836d93e82c259478a4c4301f2983627a6 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 25 Jun 2024 12:34:23 +0200 Subject: [PATCH 017/107] cicd create outputs #TASK-6399 --- .github/workflows/pull-request-approved.yml | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index e0260769..36baa148 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -4,11 +4,17 @@ run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref on: pull_request_review: types: [ submitted ] + outputs: + version: + description: "XetaBase branch to test" + value: ${{ jobs.calculate-xetabase-branch.outputs.xetabase_branch }} jobs: calculate-xetabase-branch: - name: Execute JUnit and Jacoco tests + name: Calculate Xetabase branch runs-on: ubuntu-22.04 + outputs: + xetabase_branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }} steps: - name: Clone java-common-libs uses: actions/checkout@v4 @@ -23,7 +29,7 @@ jobs: xetabase_branch=$(./.github/workflows/scripts/xetabase-branch.sh ${{ github.event.pull_request.base.ref }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT - + test: name: "Run all tests before merging" needs: calculate-xetabase-branch From 8c8cf8c95c09c06fbc93a0eeb521db94add3716c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 25 Jun 2024 12:38:14 +0200 Subject: [PATCH 018/107] cicd check bash --version #TASK-6399 --- .github/workflows/pull-request-approved.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 36baa148..8a32022f 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -26,6 +26,7 @@ jobs: chmod +x ./.github/workflows/scripts/xetabase-branch.sh ls ./.github/workflows/scripts/ ls ./.github/workflows/ + bash --version xetabase_branch=$(./.github/workflows/scripts/xetabase-branch.sh ${{ github.event.pull_request.base.ref }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT From f6719a7a5ff185936fbdbeb759c0c25f19b67683 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 25 Jun 2024 12:39:55 +0200 Subject: [PATCH 019/107] cicd check bash --version #TASK-6399 --- .github/workflows/pull-request-approved.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 8a32022f..93efbc86 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -4,10 +4,6 @@ run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref on: pull_request_review: types: [ submitted ] - outputs: - version: - description: "XetaBase branch to test" - value: ${{ jobs.calculate-xetabase-branch.outputs.xetabase_branch }} jobs: calculate-xetabase-branch: From 26914c71e137a412432514661fc15abde6291476 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 25 Jun 2024 13:25:31 +0200 Subject: [PATCH 020/107] cicd: remove github.event. in inputs #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 12e8504a..6fceeaa5 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -17,13 +17,13 @@ jobs: steps: - name: Log inputs run: | - echo "__OpenCGA-enterprise branch:__ \"${{ github.event.inputs.branch }}\"" | tee -a $GITHUB_STEP_SUMMARY - echo "__Task to test:__ \"${{ github.event.inputs.task }}\"" | tee -a $GITHUB_STEP_SUMMARY - - name: Clone OpenCGA Enterprise branch '${{ github.event.inputs.branch }}' + echo "__OpenCGA-enterprise branch:__ \"${{ inputs.branch }}\"" | tee -a $GITHUB_STEP_SUMMARY + echo "__Task to test:__ \"${{ inputs.task }}\"" | tee -a $GITHUB_STEP_SUMMARY + - name: Clone OpenCGA Enterprise branch '${{ inputs.branch }}' uses: actions/checkout@v4 with: repository: zetta-genomics/opencga-enterprise - ref: ${{ github.event.inputs.branch }} + ref: ${{ inputs.branch }} token: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }} path: opencga-enterprise fetch-depth: "10" @@ -32,7 +32,7 @@ jobs: run: | pwd chmod +x ./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh - opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh ${{ github.event.inputs.task }}) + opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh ${{ inputs.task }}) echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT - uses: actions/checkout@v4 with: @@ -72,7 +72,7 @@ jobs: run: | ln -s opencga opencga-enterprise/opencga-home cd opencga-enterprise - ./build.sh -t -l runShortTests,runMediumTests,runLongTests -b -s -f -T ${{ github.event.inputs.task }} -c localhost:27018 -H hdp3.1 + ./build.sh -t -l runShortTests,runMediumTests,runLongTests -b -s -f -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 - name: Upload reports results to Github uses: actions/upload-artifact@v4 with: @@ -87,7 +87,7 @@ jobs: uses: garygrossgarten/github-action-scp@release with: local: opencga-enterprise/reports/test - remote: /var/www/html/reports/xetabase/${{ github.event.inputs.task }}/ + remote: /var/www/html/reports/xetabase/${{ inputs.task }}/ host: ${{ secrets.SSH_TESTING_SERVER_HOST}} port: ${{ secrets.SSH_TESTING_SERVER_PORT}} username: ${{ secrets.SSH_TESTING_SERVER_USER }} From b4b7a47f23852753aa7e82559227091d232a6c8b Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 25 Jun 2024 13:41:16 +0200 Subject: [PATCH 021/107] cicd: workflow dispatch to test#TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 6fceeaa5..94782ae0 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -9,6 +9,16 @@ on: branch: type: string required: true + workflow_dispatch: + inputs: + task: + type: string + description: 'Task ID to be tested.' + required: true + branch: + type: string + description: 'Branch of opencga-enterprise to be tested and built.' + required: true jobs: test: From 39ec574b58d5b6b8d0023dd8fcea2ce499a33b3c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 25 Jun 2024 13:44:09 +0200 Subject: [PATCH 022/107] cicd: debug logs added #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 94782ae0..3cf69952 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -80,6 +80,11 @@ jobs: password: ${{ secrets.DOCKER_HUB_PASSWORD }} - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise run: | + pwd + ls -lrtha + echo "------------------------------------" + ls -lrtha /home/runner/work/java-common-libs/java-common-libs + echo "------------------------------------" ln -s opencga opencga-enterprise/opencga-home cd opencga-enterprise ./build.sh -t -l runShortTests,runMediumTests,runLongTests -b -s -f -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 From 3bea1075a79d7b0c305c3e6cb1212988282cc7b1 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 25 Jun 2024 13:49:39 +0200 Subject: [PATCH 023/107] cicd: debug logs added #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 3cf69952..7b14f482 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -83,10 +83,13 @@ jobs: pwd ls -lrtha echo "------------------------------------" - ls -lrtha /home/runner/work/java-common-libs/java-common-libs - echo "------------------------------------" - ln -s opencga opencga-enterprise/opencga-home cd opencga-enterprise + pwd + ls -lrtha + echo "------------------------------------" + ln -s ../opencga opencga-home + echo "------------------------------------" + ls -lrtha ./build.sh -t -l runShortTests,runMediumTests,runLongTests -b -s -f -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 - name: Upload reports results to Github uses: actions/upload-artifact@v4 From ae6267643cf5cc16b6e5fd4953f74af94b565e67 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 25 Jun 2024 13:53:17 +0200 Subject: [PATCH 024/107] cicd: debug logs added #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 7b14f482..54e684b5 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -9,16 +9,16 @@ on: branch: type: string required: true - workflow_dispatch: - inputs: - task: - type: string - description: 'Task ID to be tested.' - required: true - branch: - type: string - description: 'Branch of opencga-enterprise to be tested and built.' - required: true +# workflow_dispatch: +# inputs: +# task: +# type: string +# description: 'Task ID to be tested.' +# required: true +# branch: +# type: string +# description: 'Branch of opencga-enterprise to be tested and built.' +# required: true jobs: test: From 6a7eee58003057ef8f4658639533008cf15be168 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 28 Jun 2024 10:04:47 +0200 Subject: [PATCH 025/107] cicd: Test level short to fast test upload to report server #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 54e684b5..6f963631 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -90,7 +90,8 @@ jobs: ln -s ../opencga opencga-home echo "------------------------------------" ls -lrtha - ./build.sh -t -l runShortTests,runMediumTests,runLongTests -b -s -f -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 + #./build.sh -t -l runShortTests,runMediumTests,runLongTests -b -s -f -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 + ./build.sh -t -l runShortTests -b -s -f -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 - name: Upload reports results to Github uses: actions/upload-artifact@v4 with: From d5b4f38f6164c9684b87157149b972f304efffe3 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 28 Jun 2024 10:19:20 +0200 Subject: [PATCH 026/107] cicd: Uncomment workflow_dispatch Test level short to fast test upload to report server #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 6f963631..f0f56f3f 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -9,16 +9,16 @@ on: branch: type: string required: true -# workflow_dispatch: -# inputs: -# task: -# type: string -# description: 'Task ID to be tested.' -# required: true -# branch: -# type: string -# description: 'Branch of opencga-enterprise to be tested and built.' -# required: true + workflow_dispatch: + inputs: + task: + type: string + description: 'Task ID to be tested.' + required: true + branch: + type: string + description: 'Branch of opencga-enterprise to be tested and built.' + required: true jobs: test: From 5bb1d4c55600a2c0ccd564e3bbda50812c254036 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 28 Jun 2024 12:17:23 +0200 Subject: [PATCH 027/107] cicd: fix paths to upload artifacts #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index eab1f53e..f0e5ad1d 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -103,12 +103,12 @@ jobs: uses: actions/upload-artifact@v4 with: name: report-test - path: /home/runner/work/testing-environment/testing-environment/opencga-enterprise/reports/test + path: /home/runner/work/java-common-libs/java-common-libs/opencga-enterprise/reports/test - name: Upload log uses: actions/upload-artifact@v4 with: name: build-log - path: /home/runner/work/testing-environment/testing-environment/opencga-enterprise/build.log + path: /home/runner/work/java-common-libs/java-common-libs/opencga-enterprise/build.log - name: Upload junit reports to a remote scp server uses: garygrossgarten/github-action-scp@release with: From d4ebf31452cd2c8caf33a0acb28ed96f79a38c71 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 28 Jun 2024 12:45:13 +0200 Subject: [PATCH 028/107] Added keeper passwords #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 34 ++++++++++++++------ 1 file changed, 24 insertions(+), 10 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index f0e5ad1d..57294ee6 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -21,10 +21,7 @@ on: required: true env: - AZCOPY_SPA_CLIENT_SECRET: ${{ secrets.AZCOPY_SPA_CLIENT_SECRET }} AZCOPY_AUTO_LOGIN_TYPE: "SPN" - AZCOPY_SPA_APPLICATION_ID: ${{ secrets.AZCOPY_SPA_APPLICATION_ID }} - AZCOPY_TENANT_ID: ${{ secrets.AZCOPY_TENANT_ID }} jobs: @@ -32,6 +29,23 @@ jobs: name: Execute JUnit and Jacoco tests runs-on: ubuntu-22.04 steps: + - name: Retrieve secrets from Keeper + id: ksecrets + uses: Keeper-Security/ksm-action@master + with: + keeper-secret-config: ${{ secrets.KEEPER_SM_GH_OPENCB }} + secrets: | + AZCOPY_SPA_CLIENT_SECRET/field/Secret Value > env:AZCOPY_SPA_CLIENT_SECRET + AZCOPY_SPA_APPLICATION_ID/field/Secret Value > env:AZCOPY_SPA_APPLICATION_ID + AZCOPY_TENANT_ID/field/Secret Value > env:AZCOPY_TENANT_ID + #ZETTA_REPO_ACCESS_TOKEN/field/Secret Value > env:ZETTA_REPO_ACCESS_TOKEN + AZURE_KUBE_CONFIG/field/Secret Value > env:AZURE_KUBE_CONFIG + DOCKER_HUB_USER/field/Secret Value > env:DOCKER_HUB_USER + DOCKER_HUB_PASSWORD/field/Secret Value > env:DOCKER_HUB_PASSWORD + SSH_TESTING_SERVER_HOST/field/Secret Value > env:SSH_TESTING_SERVER_HOST + SSH_TESTING_SERVER_PORT/field/Secret Value > env:SSH_TESTING_SERVER_PORT + SSH_TESTING_SERVER_USER/field/Secret Value > env:SSH_TESTING_SERVER_USER + SSH_TESTING_SERVER_PASSWORD/field/Secret Value > env:SSH_TESTING_SERVER_PASSWORD - name: Log inputs run: | echo "__OpenCGA-enterprise branch:__ \"${{ inputs.branch }}\"" | tee -a $GITHUB_STEP_SUMMARY @@ -74,7 +88,7 @@ jobs: run: | wget https://dl.k8s.io/release/v1.28.2/bin/linux/amd64/kubectl chmod +x ./kubectl - echo "${{ secrets.AZURE_KUBE_CONFIG }}" > admin.conf + echo "${{ env.AZURE_KUBE_CONFIG }}" > admin.conf ./kubectl -n cellbase-db port-forward services/cellbase-rs0-svc 27018:27017 --kubeconfig ./admin.conf & - name: Install Azure AZCOPY uses: kheiakiyama/install-azcopy-action@v1 @@ -83,8 +97,8 @@ jobs: - name: DockerHub login uses: docker/login-action@v3 with: - username: ${{ secrets.DOCKER_HUB_USER }} - password: ${{ secrets.DOCKER_HUB_PASSWORD }} + username: ${{ env.DOCKER_HUB_USER }} + password: ${{ env.DOCKER_HUB_PASSWORD }} - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise run: | pwd @@ -114,10 +128,10 @@ jobs: with: local: opencga-enterprise/reports/test remote: /var/www/html/reports/xetabase/${{ inputs.task }}/ - host: ${{ secrets.SSH_TESTING_SERVER_HOST}} - port: ${{ secrets.SSH_TESTING_SERVER_PORT}} - username: ${{ secrets.SSH_TESTING_SERVER_USER }} - password: ${{ secrets.SSH_TESTING_SERVER_PASSWORD }} + host: ${{ env.SSH_TESTING_SERVER_HOST}} + port: ${{ env.SSH_TESTING_SERVER_PORT}} + username: ${{ env.SSH_TESTING_SERVER_USER }} + password: ${{ env.SSH_TESTING_SERVER_PASSWORD }} concurrency: 2 From df6f77b2ffe82780c8ccf33bdbf74fd128bc3676 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 28 Jun 2024 12:50:53 +0200 Subject: [PATCH 029/107] Added keeper passwords #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 57294ee6..afa04521 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -38,7 +38,6 @@ jobs: AZCOPY_SPA_CLIENT_SECRET/field/Secret Value > env:AZCOPY_SPA_CLIENT_SECRET AZCOPY_SPA_APPLICATION_ID/field/Secret Value > env:AZCOPY_SPA_APPLICATION_ID AZCOPY_TENANT_ID/field/Secret Value > env:AZCOPY_TENANT_ID - #ZETTA_REPO_ACCESS_TOKEN/field/Secret Value > env:ZETTA_REPO_ACCESS_TOKEN AZURE_KUBE_CONFIG/field/Secret Value > env:AZURE_KUBE_CONFIG DOCKER_HUB_USER/field/Secret Value > env:DOCKER_HUB_USER DOCKER_HUB_PASSWORD/field/Secret Value > env:DOCKER_HUB_PASSWORD From 8c9f95802cdcd658edcc091ef7146212db0f8237 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 1 Jul 2024 11:31:44 +0200 Subject: [PATCH 030/107] cicd: Remove absolute references in Path #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index afa04521..459768a6 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -116,12 +116,12 @@ jobs: uses: actions/upload-artifact@v4 with: name: report-test - path: /home/runner/work/java-common-libs/java-common-libs/opencga-enterprise/reports/test + path: ./opencga-enterprise/reports/test - name: Upload log uses: actions/upload-artifact@v4 with: name: build-log - path: /home/runner/work/java-common-libs/java-common-libs/opencga-enterprise/build.log + path: ./opencga-enterprise/build.log - name: Upload junit reports to a remote scp server uses: garygrossgarten/github-action-scp@release with: From 2b5ccecda260326ae715ad249f64dc244a1c4d08 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 1 Jul 2024 17:15:39 +0200 Subject: [PATCH 031/107] Added get-xetabase-branch.sh #TASK-6399 --- .github/workflows/pull-request-approved.yml | 2 +- .../workflows/scripts/get-opencga-branch.sh | 44 +++++++++++++++++++ ...abase-branch.sh => get-xetabase-branch.sh} | 8 ++++ .github/workflows/test-xetabase-workflow.yml | 5 ++- 4 files changed, 56 insertions(+), 3 deletions(-) create mode 100644 .github/workflows/scripts/get-opencga-branch.sh rename .github/workflows/scripts/{xetabase-branch.sh => get-xetabase-branch.sh} (82%) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 93efbc86..5fdf66da 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -23,7 +23,7 @@ jobs: ls ./.github/workflows/scripts/ ls ./.github/workflows/ bash --version - xetabase_branch=$(./.github/workflows/scripts/xetabase-branch.sh ${{ github.event.pull_request.base.ref }}) + xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.base.ref }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT diff --git a/.github/workflows/scripts/get-opencga-branch.sh b/.github/workflows/scripts/get-opencga-branch.sh new file mode 100644 index 00000000..29aa6871 --- /dev/null +++ b/.github/workflows/scripts/get-opencga-branch.sh @@ -0,0 +1,44 @@ +#!/bin/bash + +## Navigate to the root folder where the pom.xml is +cd "$(dirname "$0")"/../../../ || exit 2 + +## Use the first argument passed as the branch. If it is not passed, I exit +if [[ -n $1 ]]; then + GIT_BRANCH=$1 +else + exit 2 +fi + +# If the branch exists in the opencga repository, I return it +if [ "$(git ls-remote https://github.com/opencb/opencga.git "$GIT_BRANCH" )" ] ; then + echo "$GIT_BRANCH"; + exit 0; +fi + +## Read the opencga version from the pom.xml +BUILD_VERSION=$(mvn help:evaluate -Dexpression=opencga.version -q -DforceStdout) + +## We remove the -SNAPSHOT if it exists +CLEAN_BUILD_VERSION=$(echo "$BUILD_VERSION" | cut -d "-" -f 1) + +## Read the numbers separately to compose the name of the branch +MAJOR=$(echo "$CLEAN_BUILD_VERSION" | cut -d "." -f 1) +MINOR=$(echo "$CLEAN_BUILD_VERSION" | cut -d "." -f 2) +PATCH=$(echo "$CLEAN_BUILD_VERSION" | cut -d "." -f 3) + +## it's a HOTFIX. Count the number of points to know if it is a hotfix +COUNT=$(echo "$CLEAN_BUILD_VERSION" | grep -o '\.' | wc -l ) +if [ "$COUNT" -gt 2 ]; then + echo "release-$MAJOR.$MINOR.$PATCH.x" + exit 0 +fi + +## It's develop branch +if [[ "$PATCH" == "0" ]]; then + echo "develop" + exit 0 +else #Is release branch + echo "release-$MAJOR.$MINOR.x" + exit 0 +fi \ No newline at end of file diff --git a/.github/workflows/scripts/xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh similarity index 82% rename from .github/workflows/scripts/xetabase-branch.sh rename to .github/workflows/scripts/get-xetabase-branch.sh index af17f7f1..0be5cb32 100644 --- a/.github/workflows/scripts/xetabase-branch.sh +++ b/.github/workflows/scripts/get-xetabase-branch.sh @@ -5,6 +5,14 @@ get_xetabase_branch() { # Input parameter (branch name) input_branch="$1" + # If the branch begins with 'TASK' and exists in the opencga-enterprise repository, I return it + if [[ $input_branch == TASK* ]]; then + if [ "$(git ls-remote https://github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then + echo "$GIT_BRANCH"; + exit 0; + fi + fi + # Check if the branch name is "develop" in that case return the same branch name if [[ "$input_branch" == "develop" ]]; then echo "develop" diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 459768a6..d332ec40 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -62,9 +62,10 @@ jobs: run: | pwd chmod +x ./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh - opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh ${{ inputs.task }}) + opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-branch.sh ${{ inputs.task }}) echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT - - uses: actions/checkout@v4 + - name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}' + uses: actions/checkout@v4 with: repository: opencb/opencga ref: ${{ steps.get_opencga_branch.outputs.opencga_branch }} From 7d6d051929a10ab8306d52494d9b617bdd7e0ef3 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 1 Jul 2024 17:24:30 +0200 Subject: [PATCH 032/107] Added remove get-opencga-branch.sh #TASK-6399 --- .../workflows/scripts/get-opencga-branch.sh | 44 ------------------- .github/workflows/test-xetabase-workflow.yml | 4 +- 2 files changed, 2 insertions(+), 46 deletions(-) delete mode 100644 .github/workflows/scripts/get-opencga-branch.sh diff --git a/.github/workflows/scripts/get-opencga-branch.sh b/.github/workflows/scripts/get-opencga-branch.sh deleted file mode 100644 index 29aa6871..00000000 --- a/.github/workflows/scripts/get-opencga-branch.sh +++ /dev/null @@ -1,44 +0,0 @@ -#!/bin/bash - -## Navigate to the root folder where the pom.xml is -cd "$(dirname "$0")"/../../../ || exit 2 - -## Use the first argument passed as the branch. If it is not passed, I exit -if [[ -n $1 ]]; then - GIT_BRANCH=$1 -else - exit 2 -fi - -# If the branch exists in the opencga repository, I return it -if [ "$(git ls-remote https://github.com/opencb/opencga.git "$GIT_BRANCH" )" ] ; then - echo "$GIT_BRANCH"; - exit 0; -fi - -## Read the opencga version from the pom.xml -BUILD_VERSION=$(mvn help:evaluate -Dexpression=opencga.version -q -DforceStdout) - -## We remove the -SNAPSHOT if it exists -CLEAN_BUILD_VERSION=$(echo "$BUILD_VERSION" | cut -d "-" -f 1) - -## Read the numbers separately to compose the name of the branch -MAJOR=$(echo "$CLEAN_BUILD_VERSION" | cut -d "." -f 1) -MINOR=$(echo "$CLEAN_BUILD_VERSION" | cut -d "." -f 2) -PATCH=$(echo "$CLEAN_BUILD_VERSION" | cut -d "." -f 3) - -## it's a HOTFIX. Count the number of points to know if it is a hotfix -COUNT=$(echo "$CLEAN_BUILD_VERSION" | grep -o '\.' | wc -l ) -if [ "$COUNT" -gt 2 ]; then - echo "release-$MAJOR.$MINOR.$PATCH.x" - exit 0 -fi - -## It's develop branch -if [[ "$PATCH" == "0" ]]; then - echo "develop" - exit 0 -else #Is release branch - echo "release-$MAJOR.$MINOR.x" - exit 0 -fi \ No newline at end of file diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index d332ec40..411c0ee8 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -61,8 +61,8 @@ jobs: name: Get OpenCGA branch from 'pom.xml' property run: | pwd - chmod +x ./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh - opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-branch.sh ${{ inputs.task }}) + chmod +x ./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh + opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh false) echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT - name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}' uses: actions/checkout@v4 From 61b806a7df651eea18c891477ed97d5e4f3b83fd Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 1 Jul 2024 17:46:35 +0200 Subject: [PATCH 033/107] Added log summary step #TASK-6399 --- .github/workflows/pull-request-approved.yml | 5 +---- .github/workflows/test-xetabase-workflow.yml | 5 +++++ 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 5fdf66da..d96c9562 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -19,10 +19,7 @@ jobs: - id: get_xetabase_branch name: "Get current branch for Xetabase from target branch" run: | - chmod +x ./.github/workflows/scripts/xetabase-branch.sh - ls ./.github/workflows/scripts/ - ls ./.github/workflows/ - bash --version + chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.base.ref }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 411c0ee8..1dbfed69 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -133,5 +133,10 @@ jobs: username: ${{ env.SSH_TESTING_SERVER_USER }} password: ${{ env.SSH_TESTING_SERVER_PASSWORD }} concurrency: 2 + - name: Log summary + run: | + cat ./opencga-enterprise/build.log | tee -a $GITHUB_STEP_SUMMARY + + From 1f896dcdcc3535a58951e414a421a717ccad45d9 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 1 Jul 2024 17:47:53 +0200 Subject: [PATCH 034/107] cicd: Removed test step in develop.yml #TASK-6399 --- .github/workflows/develop.yml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml index 196fc122..f4d59ed6 100644 --- a/.github/workflows/develop.yml +++ b/.github/workflows/develop.yml @@ -10,11 +10,6 @@ jobs: build: uses: ./.github/workflows/build-java-app-workflow.yml - test: - uses: ./.github/workflows/test-analysis.yml - needs: build - secrets: inherit - deploy-maven: uses: ./.github/workflows/deploy-maven-repository-workflow.yml needs: test From af9e16d2ee192734fdc48769439c789e7e3ebab6 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 1 Jul 2024 21:12:50 +0200 Subject: [PATCH 035/107] cicd: Add debug outputs #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 1dbfed69..3d01cf42 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -61,6 +61,8 @@ jobs: name: Get OpenCGA branch from 'pom.xml' property run: | pwd + ls -lrtha + ls -lrtha ./opencga-enterprise chmod +x ./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh false) echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT From a0861c29c8afefd1665ca364f496efdef562f9cf Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 1 Jul 2024 21:15:24 +0200 Subject: [PATCH 036/107] cicd: delete param to opencga_branch #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 3d01cf42..0cc01303 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -64,7 +64,7 @@ jobs: ls -lrtha ls -lrtha ./opencga-enterprise chmod +x ./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh - opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh false) + opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh) echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT - name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}' uses: actions/checkout@v4 From 9de5d3c998b7cf23d5e5a3777fc0d08d6ec885bf Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 1 Jul 2024 21:19:05 +0200 Subject: [PATCH 037/107] cicd: delete param to opencga_branch #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 0cc01303..c4e3e099 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -65,6 +65,7 @@ jobs: ls -lrtha ./opencga-enterprise chmod +x ./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh) + echo "opencga_branch=${opencga_branch}" echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT - name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}' uses: actions/checkout@v4 From 98d385234221b50c4d732c16ed13cc78bf3dcbc7 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 1 Jul 2024 21:24:32 +0200 Subject: [PATCH 038/107] cicd:call to xetabase-branch.sh #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index c4e3e099..950c0b2f 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -63,8 +63,8 @@ jobs: pwd ls -lrtha ls -lrtha ./opencga-enterprise - chmod +x ./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh - opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh) + chmod +x ./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh + opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh) echo "opencga_branch=${opencga_branch}" echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT - name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}' From 75536daaf8c52917cd82cd521221211441742c5c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 2 Jul 2024 10:39:31 +0200 Subject: [PATCH 039/107] cicd: Change AZURE_KUBE_CONFIG to secrets #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 950c0b2f..eab8d1c0 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -91,7 +91,7 @@ jobs: run: | wget https://dl.k8s.io/release/v1.28.2/bin/linux/amd64/kubectl chmod +x ./kubectl - echo "${{ env.AZURE_KUBE_CONFIG }}" > admin.conf + echo "${{ secrets.AZURE_KUBE_CONFIG }}" > admin.conf ./kubectl -n cellbase-db port-forward services/cellbase-rs0-svc 27018:27017 --kubeconfig ./admin.conf & - name: Install Azure AZCOPY uses: kheiakiyama/install-azcopy-action@v1 From 3bfbf9a51afa6d13bd71f492b23aafb082e513f3 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 9 Jul 2024 15:32:54 +0200 Subject: [PATCH 040/107] Rename get-opencga-xetabase-branch.sh reference --- .github/workflows/test-xetabase-workflow.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index eab8d1c0..1dfcdc78 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -63,8 +63,8 @@ jobs: pwd ls -lrtha ls -lrtha ./opencga-enterprise - chmod +x ./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh - opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh) + chmod +x ./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh + opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh) echo "opencga_branch=${opencga_branch}" echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT - name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}' From 8431eb89a25088057483dc8690c07e59e0b5a08a Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 9 Jul 2024 15:32:54 +0200 Subject: [PATCH 041/107] cicd: Rename get-opencga-xetabase-branch.sh reference #TASK-6399 --- .github/workflows/test-xetabase-workflow.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index eab8d1c0..1dfcdc78 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -63,8 +63,8 @@ jobs: pwd ls -lrtha ls -lrtha ./opencga-enterprise - chmod +x ./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh - opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh) + chmod +x ./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh + opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh) echo "opencga_branch=${opencga_branch}" echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT - name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}' From 17eb2d6a61c856d10331e7d0f3e8daa7f1825501 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 17 Jul 2024 10:19:29 +0200 Subject: [PATCH 042/107] Prepare new development branch release-5.2.x --- commons-datastore/commons-datastore-core/pom.xml | 2 +- commons-datastore/commons-datastore-mongodb/pom.xml | 2 +- commons-datastore/commons-datastore-solr/pom.xml | 2 +- commons-datastore/pom.xml | 2 +- commons-lib/pom.xml | 2 +- pom.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/commons-datastore/commons-datastore-core/pom.xml b/commons-datastore/commons-datastore-core/pom.xml index ed5c139e..08935cc5 100644 --- a/commons-datastore/commons-datastore-core/pom.xml +++ b/commons-datastore/commons-datastore-core/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.3.0-SNAPSHOT + 5.2.1-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-mongodb/pom.xml b/commons-datastore/commons-datastore-mongodb/pom.xml index 294dd6ec..695c20e7 100644 --- a/commons-datastore/commons-datastore-mongodb/pom.xml +++ b/commons-datastore/commons-datastore-mongodb/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.3.0-SNAPSHOT + 5.2.1-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-solr/pom.xml b/commons-datastore/commons-datastore-solr/pom.xml index a6d4bc14..43df674d 100644 --- a/commons-datastore/commons-datastore-solr/pom.xml +++ b/commons-datastore/commons-datastore-solr/pom.xml @@ -22,7 +22,7 @@ org.opencb.commons commons-datastore - 5.3.0-SNAPSHOT + 5.2.1-SNAPSHOT ../pom.xml diff --git a/commons-datastore/pom.xml b/commons-datastore/pom.xml index db85378f..54e31ca6 100644 --- a/commons-datastore/pom.xml +++ b/commons-datastore/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.3.0-SNAPSHOT + 5.2.1-SNAPSHOT ../pom.xml diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index b00de26c..7addadf1 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.3.0-SNAPSHOT + 5.2.1-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 8a184d38..2028f0e0 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.3.0-SNAPSHOT + 5.2.1-SNAPSHOT pom OpenCB commons project From d18cc5a1bf6ed157a4f3c7a3baae41b508026da0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Wed, 21 Aug 2024 09:07:27 +0100 Subject: [PATCH 043/107] cicd: Fix "needs" dependency at develop.yml #TASK-6753 --- .github/workflows/develop.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml index f4d59ed6..3029b0fd 100644 --- a/.github/workflows/develop.yml +++ b/.github/workflows/develop.yml @@ -12,5 +12,5 @@ jobs: deploy-maven: uses: ./.github/workflows/deploy-maven-repository-workflow.yml - needs: test + needs: build secrets: inherit From e28046696f378bc1371b5347c0eae4bcf202d43c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 4 Sep 2024 18:08:03 +0200 Subject: [PATCH 044/107] cicd: Upload reference to develop branch in pull-request-approve to test-xetabase-workflow #TASK-6807 --- .github/workflows/pull-request-approved.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index d96c9562..8f41edff 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -27,7 +27,7 @@ jobs: test: name: "Run all tests before merging" needs: calculate-xetabase-branch - uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@TASK-6399 + uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@develop with: branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }} task: ${{ github.event.pull_request.head.ref }} From e8552edc847bf0393e007825b5a79e9f99b95bd9 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 10:35:53 +0200 Subject: [PATCH 045/107] cicd: Refactor and fix SSH env values #TASK-6807 --- .github/workflows/test-xetabase-workflow.yml | 20 +++++--------------- 1 file changed, 5 insertions(+), 15 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 1dfcdc78..4e14074c 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -41,10 +41,10 @@ jobs: AZURE_KUBE_CONFIG/field/Secret Value > env:AZURE_KUBE_CONFIG DOCKER_HUB_USER/field/Secret Value > env:DOCKER_HUB_USER DOCKER_HUB_PASSWORD/field/Secret Value > env:DOCKER_HUB_PASSWORD - SSH_TESTING_SERVER_HOST/field/Secret Value > env:SSH_TESTING_SERVER_HOST - SSH_TESTING_SERVER_PORT/field/Secret Value > env:SSH_TESTING_SERVER_PORT - SSH_TESTING_SERVER_USER/field/Secret Value > env:SSH_TESTING_SERVER_USER - SSH_TESTING_SERVER_PASSWORD/field/Secret Value > env:SSH_TESTING_SERVER_PASSWORD + SSH_TESTING_SERVER_HOST/field/Secret Value > env:SSH_HOST + SSH_TESTING_SERVER_PORT/field/Secret Value > env:SSH_PORT + SSH_TESTING_SERVER_USER/field/Secret Value > env:SSH_USER + SSH_TESTING_SERVER_PASSWORD/field/Secret Value > env:SSH_PASS - name: Log inputs run: | echo "__OpenCGA-enterprise branch:__ \"${{ inputs.branch }}\"" | tee -a $GITHUB_STEP_SUMMARY @@ -114,8 +114,8 @@ jobs: ln -s ../opencga opencga-home echo "------------------------------------" ls -lrtha - #./build.sh -t -l runShortTests,runMediumTests,runLongTests -b -s -f -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 ./build.sh -t -l runShortTests -b -s -f -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 + - name: Upload reports results to Github uses: actions/upload-artifact@v4 with: @@ -126,16 +126,6 @@ jobs: with: name: build-log path: ./opencga-enterprise/build.log - - name: Upload junit reports to a remote scp server - uses: garygrossgarten/github-action-scp@release - with: - local: opencga-enterprise/reports/test - remote: /var/www/html/reports/xetabase/${{ inputs.task }}/ - host: ${{ env.SSH_TESTING_SERVER_HOST}} - port: ${{ env.SSH_TESTING_SERVER_PORT}} - username: ${{ env.SSH_TESTING_SERVER_USER }} - password: ${{ env.SSH_TESTING_SERVER_PASSWORD }} - concurrency: 2 - name: Log summary run: | cat ./opencga-enterprise/build.log | tee -a $GITHUB_STEP_SUMMARY From 59ad86b10ed4f8757207378a64d4d3579a27141e Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 11:21:10 +0200 Subject: [PATCH 046/107] Env variables to FIX error #TASK-6807 --- .github/workflows/test-xetabase-workflow.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 4e14074c..c37de784 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -115,7 +115,11 @@ jobs: echo "------------------------------------" ls -lrtha ./build.sh -t -l runShortTests -b -s -f -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 - + env: + SSH_HOST: ${{ env.SSH_HOST }} + SSH_PORT: ${{ env.SSH_PORT }} + SSH_USER: ${{ env.SSH_USER }} + SSH_PASS: ${{ env.SSH_PASS }} - name: Upload reports results to Github uses: actions/upload-artifact@v4 with: From 85e297a925ae39cdadfb78b52c343b33b54013da Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 11:22:45 +0200 Subject: [PATCH 047/107] Env variables to FIX error #TASK-6807 --- .github/workflows/test-xetabase-workflow.yml | 11 +---------- 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index c37de784..eb441cfe 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -104,16 +104,7 @@ jobs: password: ${{ env.DOCKER_HUB_PASSWORD }} - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise run: | - pwd - ls -lrtha - echo "------------------------------------" - cd opencga-enterprise - pwd - ls -lrtha - echo "------------------------------------" - ln -s ../opencga opencga-home - echo "------------------------------------" - ls -lrtha + printenv ./build.sh -t -l runShortTests -b -s -f -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 env: SSH_HOST: ${{ env.SSH_HOST }} From abb3b6b368747ca7949d1d55f37e1cbc65a8596d Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 11:42:43 +0200 Subject: [PATCH 048/107] Fix get-xetabase-branch #TASK-6807 --- .github/workflows/pull-request-approved.yml | 1 + .github/workflows/scripts/get-xetabase-branch.sh | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 8f41edff..0cd0fdaa 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -20,6 +20,7 @@ jobs: name: "Get current branch for Xetabase from target branch" run: | chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh + echo "github.event.pull_request.base.ref: ${{ github.event.pull_request.base.ref }}" xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.base.ref }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT diff --git a/.github/workflows/scripts/get-xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh index 0be5cb32..bb1b18d6 100644 --- a/.github/workflows/scripts/get-xetabase-branch.sh +++ b/.github/workflows/scripts/get-xetabase-branch.sh @@ -8,8 +8,8 @@ get_xetabase_branch() { # If the branch begins with 'TASK' and exists in the opencga-enterprise repository, I return it if [[ $input_branch == TASK* ]]; then if [ "$(git ls-remote https://github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then - echo "$GIT_BRANCH"; - exit 0; + echo "$input_branch"; + return 0; fi fi From 12a515909947bc0f997460d1b38c64e5cb6cfb46 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 11:52:10 +0200 Subject: [PATCH 049/107] Fix get-xetabase-branch #TASK-6807 --- .github/workflows/pull-request-approved.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 0cd0fdaa..e6b13f3c 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -21,7 +21,8 @@ jobs: run: | chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh echo "github.event.pull_request.base.ref: ${{ github.event.pull_request.base.ref }}" - xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.base.ref }}) + echo "github.event.pull_request.head.ref: ${{ github.event.pull_request.head.ref }}" + xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.head.ref }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT From 9182e1ea9349605fd2f9018a2c6cd27a7dd9f6f4 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 12:06:36 +0200 Subject: [PATCH 050/107] Fix get-xetabase-branch #TASK-6807 --- .github/workflows/pull-request-approved.yml | 3 +++ .github/workflows/scripts/get-xetabase-branch.sh | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index e6b13f3c..d33577a4 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -5,6 +5,9 @@ on: pull_request_review: types: [ submitted ] +env: + ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }} + jobs: calculate-xetabase-branch: name: Calculate Xetabase branch diff --git a/.github/workflows/scripts/get-xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh index bb1b18d6..9e25d9aa 100644 --- a/.github/workflows/scripts/get-xetabase-branch.sh +++ b/.github/workflows/scripts/get-xetabase-branch.sh @@ -7,7 +7,7 @@ get_xetabase_branch() { # If the branch begins with 'TASK' and exists in the opencga-enterprise repository, I return it if [[ $input_branch == TASK* ]]; then - if [ "$(git ls-remote https://github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then + if [ "$(git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then echo "$input_branch"; return 0; fi From 2d940e334d34e940e2494cb29cbc3508f456cd76 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 12:11:37 +0200 Subject: [PATCH 051/107] Fix get-xetabase-branch #TASK-6807 --- .github/workflows/pull-request-approved.yml | 3 ++- .github/workflows/scripts/get-xetabase-branch.sh | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index d33577a4..64792e5e 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -25,7 +25,8 @@ jobs: chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh echo "github.event.pull_request.base.ref: ${{ github.event.pull_request.base.ref }}" echo "github.event.pull_request.head.ref: ${{ github.event.pull_request.head.ref }}" - xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.head.ref }}) + echo "ZETTA_REPO_ACCESS_TOKEN: ${{ env.ZETTA_REPO_ACCESS_TOKEN }}" + xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.head.ref }} ${{ env.ZETTA_REPO_ACCESS_TOKEN }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT diff --git a/.github/workflows/scripts/get-xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh index 9e25d9aa..ab86f9b3 100644 --- a/.github/workflows/scripts/get-xetabase-branch.sh +++ b/.github/workflows/scripts/get-xetabase-branch.sh @@ -7,7 +7,7 @@ get_xetabase_branch() { # If the branch begins with 'TASK' and exists in the opencga-enterprise repository, I return it if [[ $input_branch == TASK* ]]; then - if [ "$(git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then + if [ "$(git ls-remote https://$2@github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then echo "$input_branch"; return 0; fi From 230010e4dbb585b544f5cb9c36cc0dd0fa2cb2ca Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 12:19:46 +0200 Subject: [PATCH 052/107] Fix get-xetabase-branch #TASK-6807 --- .github/workflows/pull-request-approved.yml | 6 +----- .github/workflows/scripts/get-xetabase-branch.sh | 2 +- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 64792e5e..1d768695 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -5,9 +5,6 @@ on: pull_request_review: types: [ submitted ] -env: - ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }} - jobs: calculate-xetabase-branch: name: Calculate Xetabase branch @@ -25,8 +22,7 @@ jobs: chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh echo "github.event.pull_request.base.ref: ${{ github.event.pull_request.base.ref }}" echo "github.event.pull_request.head.ref: ${{ github.event.pull_request.head.ref }}" - echo "ZETTA_REPO_ACCESS_TOKEN: ${{ env.ZETTA_REPO_ACCESS_TOKEN }}" - xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.head.ref }} ${{ env.ZETTA_REPO_ACCESS_TOKEN }}) + xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.head.ref }} ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT diff --git a/.github/workflows/scripts/get-xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh index ab86f9b3..2c6aaad9 100644 --- a/.github/workflows/scripts/get-xetabase-branch.sh +++ b/.github/workflows/scripts/get-xetabase-branch.sh @@ -7,7 +7,7 @@ get_xetabase_branch() { # If the branch begins with 'TASK' and exists in the opencga-enterprise repository, I return it if [[ $input_branch == TASK* ]]; then - if [ "$(git ls-remote https://$2@github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then + if [ "$(git ls-remote "https://$2@github.com/zetta-genomics/opencga-enterprise.git" "$input_branch" )" ] ; then echo "$input_branch"; return 0; fi From a4d2fbb30c92e27c6c814a49ff212d35dc7d248f Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 12:33:44 +0200 Subject: [PATCH 053/107] Fix get-xetabase-branch #TASK-6807 --- .github/workflows/scripts/get-xetabase-branch.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/scripts/get-xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh index 2c6aaad9..4cdfe5fc 100644 --- a/.github/workflows/scripts/get-xetabase-branch.sh +++ b/.github/workflows/scripts/get-xetabase-branch.sh @@ -4,10 +4,10 @@ get_xetabase_branch() { # Input parameter (branch name) input_branch="$1" - + ZETTA_REPO_ACCESS_TOKEN="$2" # If the branch begins with 'TASK' and exists in the opencga-enterprise repository, I return it if [[ $input_branch == TASK* ]]; then - if [ "$(git ls-remote "https://$2@github.com/zetta-genomics/opencga-enterprise.git" "$input_branch" )" ] ; then + if [ "$(git ls-remote "https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git" "$input_branch" )" ] ; then echo "$input_branch"; return 0; fi @@ -47,4 +47,4 @@ if [ "$#" -ne 1 ]; then fi # Call the function with the input branch name -get_xetabase_branch "$1" +get_xetabase_branch "$1" "$2" From 8e3cc8832c12f74aa06d4416d5c773f4f1458614 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 12:52:59 +0200 Subject: [PATCH 054/107] Fix get-xetabase-branch #TASK-6807 --- .github/workflows/pull-request-approved.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 1d768695..517f159d 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -22,7 +22,7 @@ jobs: chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh echo "github.event.pull_request.base.ref: ${{ github.event.pull_request.base.ref }}" echo "github.event.pull_request.head.ref: ${{ github.event.pull_request.head.ref }}" - xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.head.ref }} ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}) + xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.head.ref }} ${{ secrets.ZETTA_TOKEN }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT From f84ebf318d8c72ffd8d8259a5641b6a88cae79f8 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 13:02:21 +0200 Subject: [PATCH 055/107] Fix get-xetabase-branch #TASK-6807 --- .github/workflows/pull-request-approved.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 517f159d..5341b5f7 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -22,9 +22,10 @@ jobs: chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh echo "github.event.pull_request.base.ref: ${{ github.event.pull_request.base.ref }}" echo "github.event.pull_request.head.ref: ${{ github.event.pull_request.head.ref }}" - xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.head.ref }} ${{ secrets.ZETTA_TOKEN }}) + xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.head.ref }} ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT + test: name: "Run all tests before merging" From 6ca7c8c4c7985e050af072c335c2755e6059caff Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 13:09:41 +0200 Subject: [PATCH 056/107] Fix get-xetabase-branch #TASK-6807 --- .github/workflows/pull-request-approved.yml | 3 ++- .github/workflows/scripts/get-xetabase-branch.sh | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 5341b5f7..cfc9110c 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -22,10 +22,11 @@ jobs: chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh echo "github.event.pull_request.base.ref: ${{ github.event.pull_request.base.ref }}" echo "github.event.pull_request.head.ref: ${{ github.event.pull_request.head.ref }}" + echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.head.ref }} ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT - + test: name: "Run all tests before merging" diff --git a/.github/workflows/scripts/get-xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh index 4cdfe5fc..559e686a 100644 --- a/.github/workflows/scripts/get-xetabase-branch.sh +++ b/.github/workflows/scripts/get-xetabase-branch.sh @@ -1,5 +1,6 @@ #!/bin/bash - +set -e +set -x # Function to calculate the corresponding branch of Xetabase project get_xetabase_branch() { # Input parameter (branch name) From 9272829d16ce36f6a443a2e8a8fd46ec903df2b0 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 13:18:37 +0200 Subject: [PATCH 057/107] TEST workflow for pull-request #TASK-6807 --- .../workflows/test-pull-request-approved.yml | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 .github/workflows/test-pull-request-approved.yml diff --git a/.github/workflows/test-pull-request-approved.yml b/.github/workflows/test-pull-request-approved.yml new file mode 100644 index 00000000..13123074 --- /dev/null +++ b/.github/workflows/test-pull-request-approved.yml @@ -0,0 +1,38 @@ +name: Pull request approve workflow +run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref }} -> ${{ github.event.pull_request.base.ref }} by @${{ github.actor }}' + +on: + + push: + branches: + - TASK-* + +jobs: + calculate-xetabase-branch: + name: Calculate Xetabase branch + runs-on: ubuntu-22.04 + outputs: + xetabase_branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }} + steps: + - name: Clone java-common-libs + uses: actions/checkout@v4 + with: + fetch-depth: '10' + - id: get_xetabase_branch + name: "Get current branch for Xetabase from target branch" + run: | + chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh + echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" + xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "TASK-6807" ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}) + echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} + echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT + + + test: + name: "Run all tests before merging" + needs: calculate-xetabase-branch + uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@develop + with: + branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }} + task: TASK-6807 + secrets: inherit \ No newline at end of file From 5d473dd6b8d81863ef47930f7631748f7941ec9a Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 13:20:22 +0200 Subject: [PATCH 058/107] TEST workflow for pull-request #TASK-6807 --- .github/workflows/scripts/get-xetabase-branch.sh | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.github/workflows/scripts/get-xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh index 559e686a..b2b6f998 100644 --- a/.github/workflows/scripts/get-xetabase-branch.sh +++ b/.github/workflows/scripts/get-xetabase-branch.sh @@ -41,11 +41,6 @@ get_xetabase_branch() { return 1 } -# Check if the script receives exactly one argument -if [ "$#" -ne 1 ]; then - echo "Usage: $0 " - exit 1 -fi # Call the function with the input branch name get_xetabase_branch "$1" "$2" From 7b2a8b095ef20a894291bc1bab956293947cb443 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 13:23:27 +0200 Subject: [PATCH 059/107] TEST workflow for pull-request #TASK-6807 --- .github/workflows/test-pull-request-approved.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-pull-request-approved.yml b/.github/workflows/test-pull-request-approved.yml index 13123074..04bd9de9 100644 --- a/.github/workflows/test-pull-request-approved.yml +++ b/.github/workflows/test-pull-request-approved.yml @@ -23,7 +23,7 @@ jobs: run: | chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" - xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "TASK-6807" ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}) + xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "TASK-6807" "${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" ) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT From c3fbf526ea87a690f3f09cf89801b465bdecf40d Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 14:25:26 +0200 Subject: [PATCH 060/107] TEST workflow for pull-request #TASK-6807 --- .github/workflows/test-pull-request-approved.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-pull-request-approved.yml b/.github/workflows/test-pull-request-approved.yml index 04bd9de9..473185bd 100644 --- a/.github/workflows/test-pull-request-approved.yml +++ b/.github/workflows/test-pull-request-approved.yml @@ -22,7 +22,7 @@ jobs: name: "Get current branch for Xetabase from target branch" run: | chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh - echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" + echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" | tee -a ${GITHUB_STEP_SUMMARY} xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "TASK-6807" "${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" ) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT From 546ea977fa23d18aa1bd1e275175dd52c879d687 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 14:35:55 +0200 Subject: [PATCH 061/107] TEST workflow for pull-request #TASK-6807 --- .github/workflows/scripts/get-xetabase-branch.sh | 4 ++-- .github/workflows/test-pull-request-approved.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/scripts/get-xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh index b2b6f998..68b19832 100644 --- a/.github/workflows/scripts/get-xetabase-branch.sh +++ b/.github/workflows/scripts/get-xetabase-branch.sh @@ -5,7 +5,7 @@ set -x get_xetabase_branch() { # Input parameter (branch name) input_branch="$1" - ZETTA_REPO_ACCESS_TOKEN="$2" + # If the branch begins with 'TASK' and exists in the opencga-enterprise repository, I return it if [[ $input_branch == TASK* ]]; then if [ "$(git ls-remote "https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git" "$input_branch" )" ] ; then @@ -43,4 +43,4 @@ get_xetabase_branch() { # Call the function with the input branch name -get_xetabase_branch "$1" "$2" +get_xetabase_branch "$1" diff --git a/.github/workflows/test-pull-request-approved.yml b/.github/workflows/test-pull-request-approved.yml index 473185bd..d1f62898 100644 --- a/.github/workflows/test-pull-request-approved.yml +++ b/.github/workflows/test-pull-request-approved.yml @@ -23,7 +23,7 @@ jobs: run: | chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" | tee -a ${GITHUB_STEP_SUMMARY} - xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "TASK-6807" "${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" ) + xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "TASK-6807" ) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT From b870aa047e5c3b0416a505a70e1c70c686eeae67 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 14:40:11 +0200 Subject: [PATCH 062/107] TEST workflow for pull-request #TASK-6807 --- .github/workflows/test-pull-request-approved.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-pull-request-approved.yml b/.github/workflows/test-pull-request-approved.yml index d1f62898..5e4e3943 100644 --- a/.github/workflows/test-pull-request-approved.yml +++ b/.github/workflows/test-pull-request-approved.yml @@ -2,11 +2,12 @@ name: Pull request approve workflow run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref }} -> ${{ github.event.pull_request.base.ref }} by @${{ github.actor }}' on: - push: branches: - TASK-* - +env: + ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }} + jobs: calculate-xetabase-branch: name: Calculate Xetabase branch From ba5a19e2c75f3003764a38402969a68a09ddd508 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 14:42:53 +0200 Subject: [PATCH 063/107] TEST workflow for pull-request #TASK-6807 --- .github/workflows/test-pull-request-approved.yml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test-pull-request-approved.yml b/.github/workflows/test-pull-request-approved.yml index 5e4e3943..ee9609b3 100644 --- a/.github/workflows/test-pull-request-approved.yml +++ b/.github/workflows/test-pull-request-approved.yml @@ -7,7 +7,7 @@ on: - TASK-* env: ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }} - + jobs: calculate-xetabase-branch: name: Calculate Xetabase branch @@ -22,13 +22,15 @@ jobs: - id: get_xetabase_branch name: "Get current branch for Xetabase from target branch" run: | + if [ "$(git ls-remote "https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git" "$input_branch" )" ] ; then + echo "Here it is TASK-6807 branch"; + fi chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" | tee -a ${GITHUB_STEP_SUMMARY} xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "TASK-6807" ) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT - - + test: name: "Run all tests before merging" needs: calculate-xetabase-branch From ca2ede13502012c5715478b64940361cf42aaae4 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 14:44:14 +0200 Subject: [PATCH 064/107] TEST workflow for pull-request #TASK-6807 --- .github/workflows/test-pull-request-approved.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test-pull-request-approved.yml b/.github/workflows/test-pull-request-approved.yml index ee9609b3..f23215fe 100644 --- a/.github/workflows/test-pull-request-approved.yml +++ b/.github/workflows/test-pull-request-approved.yml @@ -5,8 +5,7 @@ on: push: branches: - TASK-* -env: - ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }} + jobs: calculate-xetabase-branch: @@ -30,7 +29,8 @@ jobs: xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "TASK-6807" ) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT - + env: + ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }} test: name: "Run all tests before merging" needs: calculate-xetabase-branch From 9241eb2f82f028b421687901cd7fdc867f65d511 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 15:11:01 +0200 Subject: [PATCH 065/107] TEST workflow for pull-request #TASK-6807 --- .github/workflows/test-pull-request-approved.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/test-pull-request-approved.yml b/.github/workflows/test-pull-request-approved.yml index f23215fe..2377cba9 100644 --- a/.github/workflows/test-pull-request-approved.yml +++ b/.github/workflows/test-pull-request-approved.yml @@ -21,6 +21,10 @@ jobs: - id: get_xetabase_branch name: "Get current branch for Xetabase from target branch" run: | + if [ "$( git ls-remote https://github.com/opencb/opencga.git "TASK-6807" )" ] ; then + echo "OPENCGA TASK-6807 branch"; + fi + if [ "$(git ls-remote "https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git" "$input_branch" )" ] ; then echo "Here it is TASK-6807 branch"; fi From ca6debc69032831a527d5258ffdbaac290d6eef0 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 15:12:44 +0200 Subject: [PATCH 066/107] TEST workflow for pull-request #TASK-6807 --- .github/workflows/test-pull-request-approved.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-pull-request-approved.yml b/.github/workflows/test-pull-request-approved.yml index 2377cba9..e4b3c33d 100644 --- a/.github/workflows/test-pull-request-approved.yml +++ b/.github/workflows/test-pull-request-approved.yml @@ -21,7 +21,7 @@ jobs: - id: get_xetabase_branch name: "Get current branch for Xetabase from target branch" run: | - if [ "$( git ls-remote https://github.com/opencb/opencga.git "TASK-6807" )" ] ; then + if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/opencb/opencga.git "TASK-6807" )" ] ; then echo "OPENCGA TASK-6807 branch"; fi From 47688af142d78e73e694a17e5c53b8e8923c6d8f Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 15:14:46 +0200 Subject: [PATCH 067/107] TEST workflow for pull-request #TASK-6807 --- .github/workflows/test-pull-request-approved.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-pull-request-approved.yml b/.github/workflows/test-pull-request-approved.yml index e4b3c33d..9b378be1 100644 --- a/.github/workflows/test-pull-request-approved.yml +++ b/.github/workflows/test-pull-request-approved.yml @@ -25,7 +25,7 @@ jobs: echo "OPENCGA TASK-6807 branch"; fi - if [ "$(git ls-remote "https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git" "$input_branch" )" ] ; then + if [ "$(git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then echo "Here it is TASK-6807 branch"; fi chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh From 3efd0b513c3ad382bb0184864c03f42ca7583ebf Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 15:16:38 +0200 Subject: [PATCH 068/107] TEST workflow for pull-request #TASK-6807 --- .github/workflows/test-pull-request-approved.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-pull-request-approved.yml b/.github/workflows/test-pull-request-approved.yml index 9b378be1..91254286 100644 --- a/.github/workflows/test-pull-request-approved.yml +++ b/.github/workflows/test-pull-request-approved.yml @@ -25,7 +25,7 @@ jobs: echo "OPENCGA TASK-6807 branch"; fi - if [ "$(git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then + if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then echo "Here it is TASK-6807 branch"; fi chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh From 45e3902e7265f2ead52c6d0a89ccad95245b26bd Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 15:22:16 +0200 Subject: [PATCH 069/107] TEST workflow for pull-request #TASK-6807 --- .github/workflows/test-pull-request-approved.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/test-pull-request-approved.yml b/.github/workflows/test-pull-request-approved.yml index 91254286..afc6e146 100644 --- a/.github/workflows/test-pull-request-approved.yml +++ b/.github/workflows/test-pull-request-approved.yml @@ -35,6 +35,8 @@ jobs: echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT env: ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }} + with: + persist-credentials: false test: name: "Run all tests before merging" needs: calculate-xetabase-branch From f4a286fde616d14813bcf6589a58dfff9d3cbf53 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 15:24:50 +0200 Subject: [PATCH 070/107] TEST workflow for pull-request #TASK-6807 --- .github/workflows/test-pull-request-approved.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-pull-request-approved.yml b/.github/workflows/test-pull-request-approved.yml index afc6e146..c1c9e56e 100644 --- a/.github/workflows/test-pull-request-approved.yml +++ b/.github/workflows/test-pull-request-approved.yml @@ -18,6 +18,7 @@ jobs: uses: actions/checkout@v4 with: fetch-depth: '10' + persist-credentials: false - id: get_xetabase_branch name: "Get current branch for Xetabase from target branch" run: | @@ -35,8 +36,7 @@ jobs: echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT env: ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }} - with: - persist-credentials: false + test: name: "Run all tests before merging" needs: calculate-xetabase-branch From 534106c700301117719f6ee03a5aaba3ffc879da Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 5 Sep 2024 15:31:53 +0200 Subject: [PATCH 071/107] TEST workflow for pull-request #TASK-6807 --- .github/workflows/pull-request-approved.yml | 7 +++++-- .github/workflows/scripts/get-xetabase-branch.sh | 2 +- .github/workflows/test-pull-request-approved.yml | 1 + 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index cfc9110c..de0bbc57 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -16,6 +16,8 @@ jobs: uses: actions/checkout@v4 with: fetch-depth: '10' + ## This is important to avoid the error in the next step: "fatal: repository 'https://github.com/zetta-genomics/opencga-enterprise.git/' not found" + persist-credentials: false - id: get_xetabase_branch name: "Get current branch for Xetabase from target branch" run: | @@ -23,10 +25,11 @@ jobs: echo "github.event.pull_request.base.ref: ${{ github.event.pull_request.base.ref }}" echo "github.event.pull_request.head.ref: ${{ github.event.pull_request.head.ref }}" echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" - xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.head.ref }} ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}) + xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.head.ref }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT - + env: + ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }} test: name: "Run all tests before merging" diff --git a/.github/workflows/scripts/get-xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh index 68b19832..139e6a0a 100644 --- a/.github/workflows/scripts/get-xetabase-branch.sh +++ b/.github/workflows/scripts/get-xetabase-branch.sh @@ -9,7 +9,7 @@ get_xetabase_branch() { # If the branch begins with 'TASK' and exists in the opencga-enterprise repository, I return it if [[ $input_branch == TASK* ]]; then if [ "$(git ls-remote "https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git" "$input_branch" )" ] ; then - echo "$input_branch"; + echo $input_branch; return 0; fi fi diff --git a/.github/workflows/test-pull-request-approved.yml b/.github/workflows/test-pull-request-approved.yml index c1c9e56e..41f878cf 100644 --- a/.github/workflows/test-pull-request-approved.yml +++ b/.github/workflows/test-pull-request-approved.yml @@ -18,6 +18,7 @@ jobs: uses: actions/checkout@v4 with: fetch-depth: '10' + ## This is important to avoid the error in the next step: "fatal: repository 'https://github.com/zetta-genomics/opencga-enterprise.git/' not found" persist-credentials: false - id: get_xetabase_branch name: "Get current branch for Xetabase from target branch" From 039c4fd69277b38d20aba926e0497aae7f3a2bdb Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 9 Sep 2024 12:04:41 +0200 Subject: [PATCH 072/107] Fix ssh to report server #TASK-6807 --- .github/workflows/test-xetabase-workflow.yml | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index eb441cfe..a2dde507 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -93,15 +93,20 @@ jobs: chmod +x ./kubectl echo "${{ secrets.AZURE_KUBE_CONFIG }}" > admin.conf ./kubectl -n cellbase-db port-forward services/cellbase-rs0-svc 27018:27017 --kubeconfig ./admin.conf & - - name: Install Azure AZCOPY - uses: kheiakiyama/install-azcopy-action@v1 - with: - version: 'v10' - name: DockerHub login uses: docker/login-action@v3 with: username: ${{ env.DOCKER_HUB_USER }} password: ${{ env.DOCKER_HUB_PASSWORD }} + - name: Install sshpass + run: sudo apt-get install sshpass + - name: Add SSH Host to known_hosts + run: | + mkdir -p ~/.ssh + ssh-keyscan -p ${{ env.SSH_PORT }} ${{ env.SSH_HOST }} >> ~/.ssh/known_hosts + env: + SSH_HOST: ${{ env.SSH_HOST }} + SSH_PORT: ${{ env.SSH_PORT }} - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise run: | printenv From c07c90248b7143b29b6483e507ccbfd3719442f0 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 12 Sep 2024 09:53:08 +0200 Subject: [PATCH 073/107] pull-request-approve Remove fail-never #TASK-6807 --- .github/workflows/test-xetabase-workflow.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index a2dde507..4793f828 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -110,7 +110,7 @@ jobs: - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise run: | printenv - ./build.sh -t -l runShortTests -b -s -f -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 + ./build.sh -t -l runShortTests -b -s -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 env: SSH_HOST: ${{ env.SSH_HOST }} SSH_PORT: ${{ env.SSH_PORT }} From 502537f26a379001e56f68799bed0e9c168294ff Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 12 Sep 2024 09:54:54 +0200 Subject: [PATCH 074/107] pull-request-approve Remove fail-never #TASK-6807 --- .github/workflows/test-xetabase-workflow.yml | 15 ++------------- 1 file changed, 2 insertions(+), 13 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 4793f828..ed802879 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -20,10 +20,6 @@ on: description: 'Branch of opencga-enterprise to be tested and built.' required: true -env: - AZCOPY_AUTO_LOGIN_TYPE: "SPN" - - jobs: test: name: Execute JUnit and Jacoco tests @@ -35,9 +31,6 @@ jobs: with: keeper-secret-config: ${{ secrets.KEEPER_SM_GH_OPENCB }} secrets: | - AZCOPY_SPA_CLIENT_SECRET/field/Secret Value > env:AZCOPY_SPA_CLIENT_SECRET - AZCOPY_SPA_APPLICATION_ID/field/Secret Value > env:AZCOPY_SPA_APPLICATION_ID - AZCOPY_TENANT_ID/field/Secret Value > env:AZCOPY_TENANT_ID AZURE_KUBE_CONFIG/field/Secret Value > env:AZURE_KUBE_CONFIG DOCKER_HUB_USER/field/Secret Value > env:DOCKER_HUB_USER DOCKER_HUB_PASSWORD/field/Secret Value > env:DOCKER_HUB_PASSWORD @@ -109,13 +102,9 @@ jobs: SSH_PORT: ${{ env.SSH_PORT }} - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise run: | - printenv + cd opencga-enterprise + ln -s ../opencga opencga-home ./build.sh -t -l runShortTests -b -s -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 - env: - SSH_HOST: ${{ env.SSH_HOST }} - SSH_PORT: ${{ env.SSH_PORT }} - SSH_USER: ${{ env.SSH_USER }} - SSH_PASS: ${{ env.SSH_PASS }} - name: Upload reports results to Github uses: actions/upload-artifact@v4 with: From e44daec9aecce7dcc82772019ee8961821c65097 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 13 Sep 2024 11:48:25 +0200 Subject: [PATCH 075/107] release:Updated release plugint to v2 #TASK-6564 --- .github/workflows/release-github-workflow.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release-github-workflow.yml b/.github/workflows/release-github-workflow.yml index 74324373..568b0de4 100644 --- a/.github/workflows/release-github-workflow.yml +++ b/.github/workflows/release-github-workflow.yml @@ -20,7 +20,7 @@ jobs: with: name: ${{ inputs.artifact }} - name: GitHub Release - uses: softprops/action-gh-release@v1 + uses: softprops/action-gh-release@v2 if: startsWith(github.ref, 'refs/tags/') with: name: ${{ github.ref_name }} From 113c1f23877afafdf7485addcc1ece1213afd625 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 13 Sep 2024 11:50:03 +0200 Subject: [PATCH 076/107] Prepare release 5.2.1 --- commons-datastore/commons-datastore-core/pom.xml | 2 +- commons-datastore/commons-datastore-mongodb/pom.xml | 2 +- commons-datastore/commons-datastore-solr/pom.xml | 2 +- commons-datastore/pom.xml | 2 +- commons-lib/pom.xml | 2 +- pom.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/commons-datastore/commons-datastore-core/pom.xml b/commons-datastore/commons-datastore-core/pom.xml index 08935cc5..b07eb280 100644 --- a/commons-datastore/commons-datastore-core/pom.xml +++ b/commons-datastore/commons-datastore-core/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.2.1-SNAPSHOT + 5.2.1 ../pom.xml diff --git a/commons-datastore/commons-datastore-mongodb/pom.xml b/commons-datastore/commons-datastore-mongodb/pom.xml index 695c20e7..b668b844 100644 --- a/commons-datastore/commons-datastore-mongodb/pom.xml +++ b/commons-datastore/commons-datastore-mongodb/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.2.1-SNAPSHOT + 5.2.1 ../pom.xml diff --git a/commons-datastore/commons-datastore-solr/pom.xml b/commons-datastore/commons-datastore-solr/pom.xml index 43df674d..3f519840 100644 --- a/commons-datastore/commons-datastore-solr/pom.xml +++ b/commons-datastore/commons-datastore-solr/pom.xml @@ -22,7 +22,7 @@ org.opencb.commons commons-datastore - 5.2.1-SNAPSHOT + 5.2.1 ../pom.xml diff --git a/commons-datastore/pom.xml b/commons-datastore/pom.xml index 54e31ca6..7e1766ef 100644 --- a/commons-datastore/pom.xml +++ b/commons-datastore/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.1-SNAPSHOT + 5.2.1 ../pom.xml diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index 30da55ed..f6845f0f 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.1-SNAPSHOT + 5.2.1 ../pom.xml diff --git a/pom.xml b/pom.xml index 2028f0e0..16820bf8 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.1-SNAPSHOT + 5.2.1 pom OpenCB commons project From 864b1d4719306310e99b9a6e35d2dd3961e53c60 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 13 Sep 2024 11:50:30 +0200 Subject: [PATCH 077/107] Prepare next release 5.2.2-SNAPSHOT --- commons-datastore/commons-datastore-core/pom.xml | 2 +- commons-datastore/commons-datastore-mongodb/pom.xml | 2 +- commons-datastore/commons-datastore-solr/pom.xml | 2 +- commons-datastore/pom.xml | 2 +- commons-lib/pom.xml | 2 +- pom.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/commons-datastore/commons-datastore-core/pom.xml b/commons-datastore/commons-datastore-core/pom.xml index b07eb280..fb5aa9c4 100644 --- a/commons-datastore/commons-datastore-core/pom.xml +++ b/commons-datastore/commons-datastore-core/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.2.1 + 5.2.2-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-mongodb/pom.xml b/commons-datastore/commons-datastore-mongodb/pom.xml index b668b844..ea27c46b 100644 --- a/commons-datastore/commons-datastore-mongodb/pom.xml +++ b/commons-datastore/commons-datastore-mongodb/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.2.1 + 5.2.2-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-solr/pom.xml b/commons-datastore/commons-datastore-solr/pom.xml index 3f519840..8ac28bb8 100644 --- a/commons-datastore/commons-datastore-solr/pom.xml +++ b/commons-datastore/commons-datastore-solr/pom.xml @@ -22,7 +22,7 @@ org.opencb.commons commons-datastore - 5.2.1 + 5.2.2-SNAPSHOT ../pom.xml diff --git a/commons-datastore/pom.xml b/commons-datastore/pom.xml index 7e1766ef..ce2e7cdc 100644 --- a/commons-datastore/pom.xml +++ b/commons-datastore/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.1 + 5.2.2-SNAPSHOT ../pom.xml diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index f6845f0f..c9549985 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.1 + 5.2.2-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 16820bf8..2ca4a9f5 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.1 + 5.2.2-SNAPSHOT pom OpenCB commons project From afde81c48bc868be22fe7b84f1bcf1e1ecf162bd Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 16 Sep 2024 12:52:16 +0200 Subject: [PATCH 078/107] Clean ls in test-xetabase workflow #TASK-6879 --- .github/workflows/test-xetabase-workflow.yml | 11 +---------- 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 1dfcdc78..3341554d 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -104,18 +104,9 @@ jobs: password: ${{ env.DOCKER_HUB_PASSWORD }} - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise run: | - pwd - ls -lrtha - echo "------------------------------------" cd opencga-enterprise - pwd - ls -lrtha - echo "------------------------------------" ln -s ../opencga opencga-home - echo "------------------------------------" - ls -lrtha - #./build.sh -t -l runShortTests,runMediumTests,runLongTests -b -s -f -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 - ./build.sh -t -l runShortTests -b -s -f -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 + ./build.sh -t -l runShortTests -b -s -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 - name: Upload reports results to Github uses: actions/upload-artifact@v4 with: From c62cd6055a435194634ddccb1971668b11966234 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 16 Sep 2024 13:09:17 +0200 Subject: [PATCH 079/107] Delete test pll request approve cicd #TASK-6879 --- .../workflows/test-pull-request-approved.yml | 48 ------------------- 1 file changed, 48 deletions(-) delete mode 100644 .github/workflows/test-pull-request-approved.yml diff --git a/.github/workflows/test-pull-request-approved.yml b/.github/workflows/test-pull-request-approved.yml deleted file mode 100644 index 41f878cf..00000000 --- a/.github/workflows/test-pull-request-approved.yml +++ /dev/null @@ -1,48 +0,0 @@ -name: Pull request approve workflow -run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref }} -> ${{ github.event.pull_request.base.ref }} by @${{ github.actor }}' - -on: - push: - branches: - - TASK-* - - -jobs: - calculate-xetabase-branch: - name: Calculate Xetabase branch - runs-on: ubuntu-22.04 - outputs: - xetabase_branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }} - steps: - - name: Clone java-common-libs - uses: actions/checkout@v4 - with: - fetch-depth: '10' - ## This is important to avoid the error in the next step: "fatal: repository 'https://github.com/zetta-genomics/opencga-enterprise.git/' not found" - persist-credentials: false - - id: get_xetabase_branch - name: "Get current branch for Xetabase from target branch" - run: | - if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/opencb/opencga.git "TASK-6807" )" ] ; then - echo "OPENCGA TASK-6807 branch"; - fi - - if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then - echo "Here it is TASK-6807 branch"; - fi - chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh - echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" | tee -a ${GITHUB_STEP_SUMMARY} - xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "TASK-6807" ) - echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} - echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT - env: - ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }} - - test: - name: "Run all tests before merging" - needs: calculate-xetabase-branch - uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@develop - with: - branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }} - task: TASK-6807 - secrets: inherit \ No newline at end of file From 8cafa9f983028692d28589ba8163d4ef39c26bfb Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 16 Sep 2024 15:00:08 +0200 Subject: [PATCH 080/107] SDLC: Prepare release 2.3.0 de Xetabase #TASK-6879 --- commons-datastore/commons-datastore-core/pom.xml | 2 +- commons-datastore/commons-datastore-mongodb/pom.xml | 2 +- commons-datastore/commons-datastore-solr/pom.xml | 2 +- commons-datastore/pom.xml | 2 +- commons-lib/pom.xml | 2 +- pom.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/commons-datastore/commons-datastore-core/pom.xml b/commons-datastore/commons-datastore-core/pom.xml index fb5aa9c4..73214d6e 100644 --- a/commons-datastore/commons-datastore-core/pom.xml +++ b/commons-datastore/commons-datastore-core/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.2.2-SNAPSHOT + 3.3.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-mongodb/pom.xml b/commons-datastore/commons-datastore-mongodb/pom.xml index ea27c46b..0ffa5c61 100644 --- a/commons-datastore/commons-datastore-mongodb/pom.xml +++ b/commons-datastore/commons-datastore-mongodb/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.2.2-SNAPSHOT + 3.3.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-solr/pom.xml b/commons-datastore/commons-datastore-solr/pom.xml index 8ac28bb8..69ad2cb8 100644 --- a/commons-datastore/commons-datastore-solr/pom.xml +++ b/commons-datastore/commons-datastore-solr/pom.xml @@ -22,7 +22,7 @@ org.opencb.commons commons-datastore - 5.2.2-SNAPSHOT + 3.3.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/pom.xml b/commons-datastore/pom.xml index ce2e7cdc..464343a2 100644 --- a/commons-datastore/pom.xml +++ b/commons-datastore/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.2-SNAPSHOT + 3.3.0-SNAPSHOT ../pom.xml diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index c9549985..1e5bb366 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.2-SNAPSHOT + 3.3.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 2ca4a9f5..c853b234 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.2-SNAPSHOT + 3.3.0-SNAPSHOT pom OpenCB commons project From 18819ff743b31f74e1a8a4e6aad86e410b472326 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 16 Sep 2024 15:01:28 +0200 Subject: [PATCH 081/107] SDLC: Prepare release 2.3.0 de Xetabase #TASK-6879 --- commons-datastore/commons-datastore-core/pom.xml | 2 +- commons-datastore/commons-datastore-mongodb/pom.xml | 2 +- commons-datastore/commons-datastore-solr/pom.xml | 2 +- commons-datastore/pom.xml | 2 +- commons-lib/pom.xml | 2 +- pom.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/commons-datastore/commons-datastore-core/pom.xml b/commons-datastore/commons-datastore-core/pom.xml index 73214d6e..ed5c139e 100644 --- a/commons-datastore/commons-datastore-core/pom.xml +++ b/commons-datastore/commons-datastore-core/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 3.3.0-SNAPSHOT + 5.3.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-mongodb/pom.xml b/commons-datastore/commons-datastore-mongodb/pom.xml index 0ffa5c61..294dd6ec 100644 --- a/commons-datastore/commons-datastore-mongodb/pom.xml +++ b/commons-datastore/commons-datastore-mongodb/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 3.3.0-SNAPSHOT + 5.3.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-solr/pom.xml b/commons-datastore/commons-datastore-solr/pom.xml index 69ad2cb8..a6d4bc14 100644 --- a/commons-datastore/commons-datastore-solr/pom.xml +++ b/commons-datastore/commons-datastore-solr/pom.xml @@ -22,7 +22,7 @@ org.opencb.commons commons-datastore - 3.3.0-SNAPSHOT + 5.3.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/pom.xml b/commons-datastore/pom.xml index 464343a2..db85378f 100644 --- a/commons-datastore/pom.xml +++ b/commons-datastore/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 3.3.0-SNAPSHOT + 5.3.0-SNAPSHOT ../pom.xml diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index 1e5bb366..d2077fc7 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 3.3.0-SNAPSHOT + 5.3.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index c853b234..8a184d38 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 3.3.0-SNAPSHOT + 5.3.0-SNAPSHOT pom OpenCB commons project From aa8dc1269b95e94b51a94c3f5ec355423474ee70 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 16 Sep 2024 15:01:28 +0200 Subject: [PATCH 082/107] SDLC: Prepare release 2.3.0 of Xetabase #TASK-6879 --- commons-datastore/commons-datastore-core/pom.xml | 2 +- commons-datastore/commons-datastore-mongodb/pom.xml | 2 +- commons-datastore/commons-datastore-solr/pom.xml | 2 +- commons-datastore/pom.xml | 2 +- commons-lib/pom.xml | 2 +- pom.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/commons-datastore/commons-datastore-core/pom.xml b/commons-datastore/commons-datastore-core/pom.xml index 73214d6e..ed5c139e 100644 --- a/commons-datastore/commons-datastore-core/pom.xml +++ b/commons-datastore/commons-datastore-core/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 3.3.0-SNAPSHOT + 5.3.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-mongodb/pom.xml b/commons-datastore/commons-datastore-mongodb/pom.xml index 0ffa5c61..294dd6ec 100644 --- a/commons-datastore/commons-datastore-mongodb/pom.xml +++ b/commons-datastore/commons-datastore-mongodb/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 3.3.0-SNAPSHOT + 5.3.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-solr/pom.xml b/commons-datastore/commons-datastore-solr/pom.xml index 69ad2cb8..a6d4bc14 100644 --- a/commons-datastore/commons-datastore-solr/pom.xml +++ b/commons-datastore/commons-datastore-solr/pom.xml @@ -22,7 +22,7 @@ org.opencb.commons commons-datastore - 3.3.0-SNAPSHOT + 5.3.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/pom.xml b/commons-datastore/pom.xml index 464343a2..db85378f 100644 --- a/commons-datastore/pom.xml +++ b/commons-datastore/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 3.3.0-SNAPSHOT + 5.3.0-SNAPSHOT ../pom.xml diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index 1e5bb366..d2077fc7 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 3.3.0-SNAPSHOT + 5.3.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index c853b234..8a184d38 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 3.3.0-SNAPSHOT + 5.3.0-SNAPSHOT pom OpenCB commons project From bdc9fa4e7fde04ead51e8637233c8b7884b6be3c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 17 Sep 2024 11:06:32 +0200 Subject: [PATCH 083/107] cicd: Review cicd after brnch renames #TASK-6879 --- .../workflows/scripts/get-xetabase-branch.sh | 4 +- .github/workflows/test-xetabase-branch.yml | 48 +++++++++++++++++++ 2 files changed, 50 insertions(+), 2 deletions(-) create mode 100644 .github/workflows/test-xetabase-branch.yml diff --git a/.github/workflows/scripts/get-xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh index 139e6a0a..be89ffbf 100644 --- a/.github/workflows/scripts/get-xetabase-branch.sh +++ b/.github/workflows/scripts/get-xetabase-branch.sh @@ -20,8 +20,8 @@ get_xetabase_branch() { return 0 fi - # Check if the branch name starts with "release-" and follows the patterns "release-a.b.x" or "release-a.b.c.x" - if [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.x$ ]] || [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.([0-9]+)\.x$ ]]; then + # Check if the branch name starts with "release-" and follows the patterns "release-a.x.x" or "release-a.b.x" + if [[ "$input_branch" =~ ^release-([0-9]+)\.x\.x$ ]] || [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.x$ ]]; then # Extract the MAJOR part of the branch name MAJOR=${BASH_REMATCH[1]} # Calculate the XETABASE_MAJOR by subtracting 3 from MAJOR diff --git a/.github/workflows/test-xetabase-branch.yml b/.github/workflows/test-xetabase-branch.yml new file mode 100644 index 00000000..e90aeebd --- /dev/null +++ b/.github/workflows/test-xetabase-branch.yml @@ -0,0 +1,48 @@ +name: TMP test-xetabase-branch +run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref }} -> ${{ github.event.pull_request.base.ref }} by @${{ github.actor }}' + +on: + push: + branches: + - TASK-* + + +jobs: + calculate-xetabase-branch: + name: Calculate Xetabase branch + runs-on: ubuntu-22.04 + outputs: + xetabase_branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }} + steps: + - name: Clone java-common-libs + uses: actions/checkout@v4 + with: + fetch-depth: '10' + ## This is important to avoid the error in the next step: "fatal: repository 'https://github.com/zetta-genomics/opencga-enterprise.git/' not found" + persist-credentials: false + - id: get_xetabase_branch + name: "Get current branch for Xetabase from target branch" + run: | + if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/opencb/opencga.git "TASK-6807" )" ] ; then + echo "OPENCGA TASK-6807 branch"; + fi + + if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then + echo "Here it is TASK-6807 branch"; + fi + chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh + echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" | tee -a ${GITHUB_STEP_SUMMARY} + xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "TASK-6807" ) + echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} + echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT + env: + ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }} + + test: + name: "Run all tests before merging" + needs: calculate-xetabase-branch + uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@develop + with: + branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }} + task: TASK-6807 + secrets: inherit \ No newline at end of file From c9a79d9e1e5a46c771b84366ec310a3505fff94c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 17 Sep 2024 11:12:52 +0200 Subject: [PATCH 084/107] cicd: Review cicd after brnch renames #TASK-6879 --- .github/workflows/pull-request-approved.yml | 2 +- .github/workflows/test-xetabase-branch.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index de0bbc57..c68cc16b 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -25,7 +25,7 @@ jobs: echo "github.event.pull_request.base.ref: ${{ github.event.pull_request.base.ref }}" echo "github.event.pull_request.head.ref: ${{ github.event.pull_request.head.ref }}" echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" - xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.head.ref }}) + xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.base.ref }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT env: diff --git a/.github/workflows/test-xetabase-branch.yml b/.github/workflows/test-xetabase-branch.yml index e90aeebd..e10a41c9 100644 --- a/.github/workflows/test-xetabase-branch.yml +++ b/.github/workflows/test-xetabase-branch.yml @@ -32,7 +32,7 @@ jobs: fi chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" | tee -a ${GITHUB_STEP_SUMMARY} - xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "TASK-6807" ) + xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "release-5.x.x" ) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT env: @@ -44,5 +44,5 @@ jobs: uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@develop with: branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }} - task: TASK-6807 + task: TASK-6879 secrets: inherit \ No newline at end of file From a6a843441c8fabf875f07c90ff269c09575e9d4e Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 17 Sep 2024 13:26:43 +0200 Subject: [PATCH 085/107] cicd: Refactor tmp test to cicd after brnch renames #TASK-6879 --- .../{test-xetabase-branch.yml => tmp-test-xetabase-branch.yml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .github/workflows/{test-xetabase-branch.yml => tmp-test-xetabase-branch.yml} (100%) diff --git a/.github/workflows/test-xetabase-branch.yml b/.github/workflows/tmp-test-xetabase-branch.yml similarity index 100% rename from .github/workflows/test-xetabase-branch.yml rename to .github/workflows/tmp-test-xetabase-branch.yml From a1efd8f8ebec16ae4bce77972293efd331af0714 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 17 Sep 2024 13:30:20 +0200 Subject: [PATCH 086/107] cicd: Refactor tmp test to cicd after brnch renames #TASK-6879 --- .github/workflows/tmp-test-xetabase-branch.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/tmp-test-xetabase-branch.yml b/.github/workflows/tmp-test-xetabase-branch.yml index e10a41c9..c10d99ec 100644 --- a/.github/workflows/tmp-test-xetabase-branch.yml +++ b/.github/workflows/tmp-test-xetabase-branch.yml @@ -23,8 +23,8 @@ jobs: - id: get_xetabase_branch name: "Get current branch for Xetabase from target branch" run: | - if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/opencb/opencga.git "TASK-6807" )" ] ; then - echo "OPENCGA TASK-6807 branch"; + if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/opencb/opencga.git "TASK-6879" )" ] ; then + echo "OPENCGA TASK-6879 branch"; fi if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then @@ -32,7 +32,7 @@ jobs: fi chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" | tee -a ${GITHUB_STEP_SUMMARY} - xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "release-5.x.x" ) + xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "TASK-6879" ) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT env: From 38d096734705298760fa48ea7a5afb1abe32a0e9 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 26 Sep 2024 21:20:45 +0200 Subject: [PATCH 087/107] Prepare release in hotfix branch release-5.2.x --- commons-datastore/commons-datastore-core/pom.xml | 2 +- commons-datastore/commons-datastore-mongodb/pom.xml | 2 +- commons-datastore/commons-datastore-solr/pom.xml | 2 +- commons-datastore/pom.xml | 2 +- commons-lib/pom.xml | 2 +- pom.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/commons-datastore/commons-datastore-core/pom.xml b/commons-datastore/commons-datastore-core/pom.xml index b07eb280..fb5aa9c4 100644 --- a/commons-datastore/commons-datastore-core/pom.xml +++ b/commons-datastore/commons-datastore-core/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.2.1 + 5.2.2-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-mongodb/pom.xml b/commons-datastore/commons-datastore-mongodb/pom.xml index e22c8381..fd2645a4 100644 --- a/commons-datastore/commons-datastore-mongodb/pom.xml +++ b/commons-datastore/commons-datastore-mongodb/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.2.1 + 5.2.2-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-solr/pom.xml b/commons-datastore/commons-datastore-solr/pom.xml index 3485cfd5..13da9261 100644 --- a/commons-datastore/commons-datastore-solr/pom.xml +++ b/commons-datastore/commons-datastore-solr/pom.xml @@ -22,7 +22,7 @@ org.opencb.commons commons-datastore - 5.2.1 + 5.2.2-SNAPSHOT ../pom.xml diff --git a/commons-datastore/pom.xml b/commons-datastore/pom.xml index 7e1766ef..ce2e7cdc 100644 --- a/commons-datastore/pom.xml +++ b/commons-datastore/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.1 + 5.2.2-SNAPSHOT ../pom.xml diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index b4a7323c..02b040c3 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.1 + 5.2.2-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 1cd2bb2b..6ca622fd 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.1 + 5.2.2-SNAPSHOT pom OpenCB commons project From 09241e0fd8d1cdf7b2246892a8e1f0609574308c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 2 Oct 2024 14:42:39 +0200 Subject: [PATCH 088/107] cicd: Fix calculating opencga branch in pull request approve workflow #TASK-6981 --- .github/workflows/test-xetabase-workflow.yml | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index ed802879..57445f9a 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -51,13 +51,18 @@ jobs: path: opencga-enterprise fetch-depth: "10" - id: get_opencga_branch - name: Get OpenCGA branch from 'pom.xml' property + name: Get OpenCGA branch run: | - pwd - ls -lrtha - ls -lrtha ./opencga-enterprise - chmod +x ./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh - opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh) + # If the task exists in the opencga repository, this is the branch to be tested + if [[ "${{ inputs.task }}" == TASK* ]]; then + if [ "$(git ls-remote "https://github.com/opencb/opencga.git" "${{ inputs.task }}" ] ; then + opencga_branch="${{ inputs.task }}"; + return 0; + fi + else + chmod +x ./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh + opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh) + fi echo "opencga_branch=${opencga_branch}" echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT - name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}' From 8375d99fc90d25a984a82793ea787e9965fc5ee7 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 2 Oct 2024 15:23:43 +0200 Subject: [PATCH 089/107] cicd: Fix calculating opencga branch in pull request approve workflow #TASK-6981 --- .github/workflows/test-xetabase-workflow.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 57445f9a..93fe9798 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -55,7 +55,7 @@ jobs: run: | # If the task exists in the opencga repository, this is the branch to be tested if [[ "${{ inputs.task }}" == TASK* ]]; then - if [ "$(git ls-remote "https://github.com/opencb/opencga.git" "${{ inputs.task }}" ] ; then + if [ "$(git ls-remote "https://github.com/opencb/opencga.git" "${{ inputs.task }}") ] ; then opencga_branch="${{ inputs.task }}"; return 0; fi From 5a697548384bf98b9ced2594654ddcf45cc964c5 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 2 Oct 2024 15:29:07 +0200 Subject: [PATCH 090/107] cicd: Fix calculating opencga branch in pull request approve workflow #TASK-6981 --- .github/workflows/test-xetabase-workflow.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 93fe9798..673a6dc7 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -55,7 +55,7 @@ jobs: run: | # If the task exists in the opencga repository, this is the branch to be tested if [[ "${{ inputs.task }}" == TASK* ]]; then - if [ "$(git ls-remote "https://github.com/opencb/opencga.git" "${{ inputs.task }}") ] ; then + if [ "$(git ls-remote "https://github.com/opencb/opencga.git" "${{ inputs.task }}")" ]; then opencga_branch="${{ inputs.task }}"; return 0; fi From 0840f50395eba8282fb980ad26bd6e8fe6970b70 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 2 Oct 2024 15:30:28 +0200 Subject: [PATCH 091/107] cicd: Fix calculating opencga branch in pull request approve workflow #TASK-6981 --- .github/workflows/test-xetabase-workflow.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 673a6dc7..21ea9731 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -57,7 +57,6 @@ jobs: if [[ "${{ inputs.task }}" == TASK* ]]; then if [ "$(git ls-remote "https://github.com/opencb/opencga.git" "${{ inputs.task }}")" ]; then opencga_branch="${{ inputs.task }}"; - return 0; fi else chmod +x ./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh From b41110c5467f015c76a7f5213ec909004c9102b6 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 3 Oct 2024 11:10:59 +0200 Subject: [PATCH 092/107] Prepare Port Patch 5.2.1 -> 6.0.0 XB 2.2.1 -> 3.0.0 #TASK-6780 --- commons-datastore/commons-datastore-core/pom.xml | 2 +- commons-datastore/commons-datastore-mongodb/pom.xml | 2 +- commons-datastore/commons-datastore-solr/pom.xml | 2 +- commons-datastore/pom.xml | 2 +- commons-lib/pom.xml | 2 +- pom.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/commons-datastore/commons-datastore-core/pom.xml b/commons-datastore/commons-datastore-core/pom.xml index b07eb280..f75e11a9 100644 --- a/commons-datastore/commons-datastore-core/pom.xml +++ b/commons-datastore/commons-datastore-core/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.2.1 + 6.0.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-mongodb/pom.xml b/commons-datastore/commons-datastore-mongodb/pom.xml index e22c8381..202d066c 100644 --- a/commons-datastore/commons-datastore-mongodb/pom.xml +++ b/commons-datastore/commons-datastore-mongodb/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.2.1 + 6.0.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-solr/pom.xml b/commons-datastore/commons-datastore-solr/pom.xml index 3485cfd5..789a9a91 100644 --- a/commons-datastore/commons-datastore-solr/pom.xml +++ b/commons-datastore/commons-datastore-solr/pom.xml @@ -22,7 +22,7 @@ org.opencb.commons commons-datastore - 5.2.1 + 6.0.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/pom.xml b/commons-datastore/pom.xml index 7e1766ef..1e503e66 100644 --- a/commons-datastore/pom.xml +++ b/commons-datastore/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.1 + 6.0.0-SNAPSHOT ../pom.xml diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index b4a7323c..84a6c880 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.1 + 6.0.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 1cd2bb2b..3542c53b 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.1 + 6.0.0-SNAPSHOT pom OpenCB commons project From b1a19c63bc3923fb18c549b28a301604f1e7d43e Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 3 Oct 2024 16:11:57 +0200 Subject: [PATCH 093/107] CICD: deleted tmp yml file #TASK-6780 --- .../workflows/tmp-test-xetabase-branch.yml | 48 ------------------- 1 file changed, 48 deletions(-) delete mode 100644 .github/workflows/tmp-test-xetabase-branch.yml diff --git a/.github/workflows/tmp-test-xetabase-branch.yml b/.github/workflows/tmp-test-xetabase-branch.yml deleted file mode 100644 index c10d99ec..00000000 --- a/.github/workflows/tmp-test-xetabase-branch.yml +++ /dev/null @@ -1,48 +0,0 @@ -name: TMP test-xetabase-branch -run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref }} -> ${{ github.event.pull_request.base.ref }} by @${{ github.actor }}' - -on: - push: - branches: - - TASK-* - - -jobs: - calculate-xetabase-branch: - name: Calculate Xetabase branch - runs-on: ubuntu-22.04 - outputs: - xetabase_branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }} - steps: - - name: Clone java-common-libs - uses: actions/checkout@v4 - with: - fetch-depth: '10' - ## This is important to avoid the error in the next step: "fatal: repository 'https://github.com/zetta-genomics/opencga-enterprise.git/' not found" - persist-credentials: false - - id: get_xetabase_branch - name: "Get current branch for Xetabase from target branch" - run: | - if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/opencb/opencga.git "TASK-6879" )" ] ; then - echo "OPENCGA TASK-6879 branch"; - fi - - if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then - echo "Here it is TASK-6807 branch"; - fi - chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh - echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" | tee -a ${GITHUB_STEP_SUMMARY} - xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "TASK-6879" ) - echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} - echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT - env: - ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }} - - test: - name: "Run all tests before merging" - needs: calculate-xetabase-branch - uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@develop - with: - branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }} - task: TASK-6879 - secrets: inherit \ No newline at end of file From 1918805ec569687cfb7ad7936176dba4bd8d00e1 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 3 Oct 2024 16:13:49 +0200 Subject: [PATCH 094/107] CICD: deleted tmp yml file #TASK-6780 --- .../workflows/test-pull-request-approved.yml | 48 ------------------- 1 file changed, 48 deletions(-) delete mode 100644 .github/workflows/test-pull-request-approved.yml diff --git a/.github/workflows/test-pull-request-approved.yml b/.github/workflows/test-pull-request-approved.yml deleted file mode 100644 index 41f878cf..00000000 --- a/.github/workflows/test-pull-request-approved.yml +++ /dev/null @@ -1,48 +0,0 @@ -name: Pull request approve workflow -run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref }} -> ${{ github.event.pull_request.base.ref }} by @${{ github.actor }}' - -on: - push: - branches: - - TASK-* - - -jobs: - calculate-xetabase-branch: - name: Calculate Xetabase branch - runs-on: ubuntu-22.04 - outputs: - xetabase_branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }} - steps: - - name: Clone java-common-libs - uses: actions/checkout@v4 - with: - fetch-depth: '10' - ## This is important to avoid the error in the next step: "fatal: repository 'https://github.com/zetta-genomics/opencga-enterprise.git/' not found" - persist-credentials: false - - id: get_xetabase_branch - name: "Get current branch for Xetabase from target branch" - run: | - if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/opencb/opencga.git "TASK-6807" )" ] ; then - echo "OPENCGA TASK-6807 branch"; - fi - - if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then - echo "Here it is TASK-6807 branch"; - fi - chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh - echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" | tee -a ${GITHUB_STEP_SUMMARY} - xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "TASK-6807" ) - echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} - echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT - env: - ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }} - - test: - name: "Run all tests before merging" - needs: calculate-xetabase-branch - uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@develop - with: - branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }} - task: TASK-6807 - secrets: inherit \ No newline at end of file From 2332d0026f222518035aa0912f814059af8a5a9e Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 7 Oct 2024 18:10:53 +0200 Subject: [PATCH 095/107] Prepare release 5.2.2 --- commons-datastore/commons-datastore-core/pom.xml | 2 +- commons-datastore/commons-datastore-mongodb/pom.xml | 2 +- commons-datastore/commons-datastore-solr/pom.xml | 2 +- commons-datastore/pom.xml | 2 +- commons-lib/pom.xml | 2 +- pom.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/commons-datastore/commons-datastore-core/pom.xml b/commons-datastore/commons-datastore-core/pom.xml index fb5aa9c4..b5ceadb1 100644 --- a/commons-datastore/commons-datastore-core/pom.xml +++ b/commons-datastore/commons-datastore-core/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.2.2-SNAPSHOT + 5.2.2 ../pom.xml diff --git a/commons-datastore/commons-datastore-mongodb/pom.xml b/commons-datastore/commons-datastore-mongodb/pom.xml index fd2645a4..4932a89b 100644 --- a/commons-datastore/commons-datastore-mongodb/pom.xml +++ b/commons-datastore/commons-datastore-mongodb/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.2.2-SNAPSHOT + 5.2.2 ../pom.xml diff --git a/commons-datastore/commons-datastore-solr/pom.xml b/commons-datastore/commons-datastore-solr/pom.xml index 13da9261..059a125d 100644 --- a/commons-datastore/commons-datastore-solr/pom.xml +++ b/commons-datastore/commons-datastore-solr/pom.xml @@ -22,7 +22,7 @@ org.opencb.commons commons-datastore - 5.2.2-SNAPSHOT + 5.2.2 ../pom.xml diff --git a/commons-datastore/pom.xml b/commons-datastore/pom.xml index ce2e7cdc..a3bc8380 100644 --- a/commons-datastore/pom.xml +++ b/commons-datastore/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.2-SNAPSHOT + 5.2.2 ../pom.xml diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index 02b040c3..7e22936d 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.2-SNAPSHOT + 5.2.2 ../pom.xml diff --git a/pom.xml b/pom.xml index 6ca622fd..03036e9d 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.2-SNAPSHOT + 5.2.2 pom OpenCB commons project From f55f1531137f69702c90c6d8eab97121b381abc1 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 8 Oct 2024 16:33:23 +0200 Subject: [PATCH 096/107] Prepare Port Patch 2.2.2 -> 2.3.0 #TASK-7038 --- commons-datastore/commons-datastore-core/pom.xml | 2 +- commons-datastore/commons-datastore-mongodb/pom.xml | 2 +- commons-datastore/commons-datastore-solr/pom.xml | 2 +- commons-datastore/pom.xml | 2 +- commons-lib/pom.xml | 2 +- pom.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/commons-datastore/commons-datastore-core/pom.xml b/commons-datastore/commons-datastore-core/pom.xml index b5ceadb1..ed5c139e 100644 --- a/commons-datastore/commons-datastore-core/pom.xml +++ b/commons-datastore/commons-datastore-core/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.2.2 + 5.3.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-mongodb/pom.xml b/commons-datastore/commons-datastore-mongodb/pom.xml index 4932a89b..af0f669b 100644 --- a/commons-datastore/commons-datastore-mongodb/pom.xml +++ b/commons-datastore/commons-datastore-mongodb/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.2.2 + 5.3.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-solr/pom.xml b/commons-datastore/commons-datastore-solr/pom.xml index 059a125d..698f327e 100644 --- a/commons-datastore/commons-datastore-solr/pom.xml +++ b/commons-datastore/commons-datastore-solr/pom.xml @@ -22,7 +22,7 @@ org.opencb.commons commons-datastore - 5.2.2 + 5.3.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/pom.xml b/commons-datastore/pom.xml index a3bc8380..db85378f 100644 --- a/commons-datastore/pom.xml +++ b/commons-datastore/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.2 + 5.3.0-SNAPSHOT ../pom.xml diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index 7e22936d..7c6e2bd5 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.2 + 5.3.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 03036e9d..dca9d5d9 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.2.2 + 5.3.0-SNAPSHOT pom OpenCB commons project From 92a5865c7b263ca82716b3a6981c4df9d56cf852 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 8 Oct 2024 18:01:57 +0200 Subject: [PATCH 097/107] CICD: deleted tmp yml file #TASK-6780 --- .../workflows/tmp-test-xetabase-branch.yml | 48 ------------------- 1 file changed, 48 deletions(-) delete mode 100644 .github/workflows/tmp-test-xetabase-branch.yml diff --git a/.github/workflows/tmp-test-xetabase-branch.yml b/.github/workflows/tmp-test-xetabase-branch.yml deleted file mode 100644 index c10d99ec..00000000 --- a/.github/workflows/tmp-test-xetabase-branch.yml +++ /dev/null @@ -1,48 +0,0 @@ -name: TMP test-xetabase-branch -run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref }} -> ${{ github.event.pull_request.base.ref }} by @${{ github.actor }}' - -on: - push: - branches: - - TASK-* - - -jobs: - calculate-xetabase-branch: - name: Calculate Xetabase branch - runs-on: ubuntu-22.04 - outputs: - xetabase_branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }} - steps: - - name: Clone java-common-libs - uses: actions/checkout@v4 - with: - fetch-depth: '10' - ## This is important to avoid the error in the next step: "fatal: repository 'https://github.com/zetta-genomics/opencga-enterprise.git/' not found" - persist-credentials: false - - id: get_xetabase_branch - name: "Get current branch for Xetabase from target branch" - run: | - if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/opencb/opencga.git "TASK-6879" )" ] ; then - echo "OPENCGA TASK-6879 branch"; - fi - - if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then - echo "Here it is TASK-6807 branch"; - fi - chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh - echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" | tee -a ${GITHUB_STEP_SUMMARY} - xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "TASK-6879" ) - echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} - echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT - env: - ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }} - - test: - name: "Run all tests before merging" - needs: calculate-xetabase-branch - uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@develop - with: - branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }} - task: TASK-6879 - secrets: inherit \ No newline at end of file From d0f8720328da4e076d324de467c7f88a69c7d73e Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 10 Oct 2024 09:21:28 +0200 Subject: [PATCH 098/107] pom update versions to fix unmerged changes --- commons-datastore/commons-datastore-mongodb/pom.xml | 1 - commons-lib/pom.xml | 1 - pom.xml | 9 ++++++--- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/commons-datastore/commons-datastore-mongodb/pom.xml b/commons-datastore/commons-datastore-mongodb/pom.xml index af0f669b..294dd6ec 100644 --- a/commons-datastore/commons-datastore-mongodb/pom.xml +++ b/commons-datastore/commons-datastore-mongodb/pom.xml @@ -50,7 +50,6 @@ org.hamcrest hamcrest-core - test junit diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index 7c6e2bd5..e614697c 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -31,7 +31,6 @@ com.fasterxml.jackson.core jackson-databind - test org.apache.commons diff --git a/pom.xml b/pom.xml index dca9d5d9..0105ec92 100644 --- a/pom.xml +++ b/pom.xml @@ -19,9 +19,9 @@ - 2.11.4 - 3.12.0 - 1.7.32 + 2.14.3 + 3.14.0 + 1.7.36 1.7.7 4.8.2 8.8.2 @@ -296,6 +296,9 @@ * + + * + From da136960a06cc28804f3adee41c39e515cf1ec5a Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 10 Oct 2024 09:22:46 +0200 Subject: [PATCH 099/107] pom update versions to fix unmerged changes --- commons-lib/pom.xml | 1 - 1 file changed, 1 deletion(-) diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index e614697c..e3871111 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -66,7 +66,6 @@ com.fasterxml.jackson.core jackson-databind - test commons-io From 32b5f40a14346efa15eb907125d3dacb1d99ff6d Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 10 Oct 2024 09:23:33 +0200 Subject: [PATCH 100/107] pom update versions to fix unmerged changes --- commons-lib/pom.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index e3871111..e614697c 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -66,6 +66,7 @@ com.fasterxml.jackson.core jackson-databind + test commons-io From 923964e8eace7d9c256a7a1056398abbd1f5dd0f Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 10 Oct 2024 09:25:39 +0200 Subject: [PATCH 101/107] Delete duplicated jackson-databind library --- commons-lib/pom.xml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index e614697c..cf0e9bd5 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -63,11 +63,6 @@ slf4j-simple test - - com.fasterxml.jackson.core - jackson-databind - test - commons-io commons-io From 55ac86e2a1dfce71807c260c507794148cb8a3db Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Thu, 10 Oct 2024 11:41:16 +0200 Subject: [PATCH 102/107] test: fix JUnit test, #TASK-4974 --- .../datastore/mongodb/MongoDBCollectionTest.java | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/commons-datastore/commons-datastore-mongodb/src/test/java/org/opencb/commons/datastore/mongodb/MongoDBCollectionTest.java b/commons-datastore/commons-datastore-mongodb/src/test/java/org/opencb/commons/datastore/mongodb/MongoDBCollectionTest.java index f33b7033..377d610c 100644 --- a/commons-datastore/commons-datastore-mongodb/src/test/java/org/opencb/commons/datastore/mongodb/MongoDBCollectionTest.java +++ b/commons-datastore/commons-datastore-mongodb/src/test/java/org/opencb/commons/datastore/mongodb/MongoDBCollectionTest.java @@ -441,15 +441,13 @@ public void testAggregate() { queryResult = mongoDBCollection.aggregate(dbObjectList, new QueryOptions(QueryOptions.LIMIT, 1).append(QueryOptions.SKIP, 0)); assertEquals("There must be 1 results", 1, queryResult.getResults().size()); - assertTrue(queryResult.getResults().contains(result.get(0))); + // As the order of result list change between executions, we must ensure the assertTrue doesn't depend on the order + assertTrue(result.contains(queryResult.getResults().get(0))); queryResult = mongoDBCollection.aggregate(dbObjectList, new QueryOptions(QueryOptions.LIMIT, 1).append(QueryOptions.SKIP, 1)); assertEquals("There must be 1 results", 1, queryResult.getResults().size()); - - System.out.println("result = " + result); - System.out.println("queryResult.getResults() = " + queryResult.getResults()); - - assertTrue(queryResult.getResults().contains(result.get(1))); + // As the order of result list change between executions, we must ensure the assertTrue doesn't depend on the order + assertTrue(result.contains(queryResult.getResults().get(0))); } @Test From 0c17d64d7ef8469441a544bbc9bbcb3bf1b51103 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 11 Oct 2024 11:33:16 +0200 Subject: [PATCH 103/107] Fix get-opencga-xetabase-branch.sh --- .github/workflows/test-xetabase-workflow.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 21ea9731..4c8449f3 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -60,7 +60,7 @@ jobs: fi else chmod +x ./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh - opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh) + opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh "${{ inputs.task }}") fi echo "opencga_branch=${opencga_branch}" echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT From 853f3b87cb4a0321c160f4d46fecc215281f4d08 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 11 Oct 2024 11:37:52 +0200 Subject: [PATCH 104/107] Fix get-opencga-xetabase-branch.sh --- .github/workflows/test-xetabase-workflow.yml | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 4c8449f3..85061118 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -53,15 +53,8 @@ jobs: - id: get_opencga_branch name: Get OpenCGA branch run: | - # If the task exists in the opencga repository, this is the branch to be tested - if [[ "${{ inputs.task }}" == TASK* ]]; then - if [ "$(git ls-remote "https://github.com/opencb/opencga.git" "${{ inputs.task }}")" ]; then - opencga_branch="${{ inputs.task }}"; - fi - else - chmod +x ./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh - opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh "${{ inputs.task }}") - fi + chmod +x ./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh + opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh "${{ inputs.task }}") echo "opencga_branch=${opencga_branch}" echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT - name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}' From 2b1d96c8f0db69e7b9437fb07eac0035d34abf9c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 14 Oct 2024 11:54:24 +0200 Subject: [PATCH 105/107] Fix downgrade versions in merge #TASK-6780 --- commons-datastore/commons-datastore-mongodb/pom.xml | 1 - commons-datastore/commons-datastore-solr/pom.xml | 2 -- pom.xml | 10 ++++++---- 3 files changed, 6 insertions(+), 7 deletions(-) diff --git a/commons-datastore/commons-datastore-mongodb/pom.xml b/commons-datastore/commons-datastore-mongodb/pom.xml index 202d066c..842daef6 100644 --- a/commons-datastore/commons-datastore-mongodb/pom.xml +++ b/commons-datastore/commons-datastore-mongodb/pom.xml @@ -50,7 +50,6 @@ org.hamcrest hamcrest-core - test junit diff --git a/commons-datastore/commons-datastore-solr/pom.xml b/commons-datastore/commons-datastore-solr/pom.xml index 789a9a91..e178396a 100644 --- a/commons-datastore/commons-datastore-solr/pom.xml +++ b/commons-datastore/commons-datastore-solr/pom.xml @@ -34,7 +34,6 @@ org.opencb.commons commons-datastore-core - org.apache.solr solr-solrj @@ -52,5 +51,4 @@ slf4j-api - diff --git a/pom.xml b/pom.xml index 3542c53b..34df5f27 100644 --- a/pom.xml +++ b/pom.xml @@ -19,9 +19,9 @@ - 2.11.4 - 3.12.0 - 1.7.32 + 2.14.3 + 3.14.0 + 1.7.36 1.7.7 4.8.2 8.8.2 @@ -31,7 +31,6 @@ 1.3 4.13.2 - opencb https://sonarcloud.io 1.8 @@ -296,6 +295,9 @@ * + + * + From 507c5dce8f82201cb3339545ac98fdbf64681ee7 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 15 Oct 2024 15:19:23 +0200 Subject: [PATCH 106/107] Prepare release 5.3.0 --- commons-datastore/commons-datastore-core/pom.xml | 2 +- commons-datastore/commons-datastore-mongodb/pom.xml | 2 +- commons-datastore/commons-datastore-solr/pom.xml | 2 +- commons-datastore/pom.xml | 2 +- commons-lib/pom.xml | 2 +- pom.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/commons-datastore/commons-datastore-core/pom.xml b/commons-datastore/commons-datastore-core/pom.xml index ed5c139e..dfa4bf70 100644 --- a/commons-datastore/commons-datastore-core/pom.xml +++ b/commons-datastore/commons-datastore-core/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.3.0-SNAPSHOT + 5.3.0 ../pom.xml diff --git a/commons-datastore/commons-datastore-mongodb/pom.xml b/commons-datastore/commons-datastore-mongodb/pom.xml index 294dd6ec..c44b9cc0 100644 --- a/commons-datastore/commons-datastore-mongodb/pom.xml +++ b/commons-datastore/commons-datastore-mongodb/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.3.0-SNAPSHOT + 5.3.0 ../pom.xml diff --git a/commons-datastore/commons-datastore-solr/pom.xml b/commons-datastore/commons-datastore-solr/pom.xml index 698f327e..45eb7f44 100644 --- a/commons-datastore/commons-datastore-solr/pom.xml +++ b/commons-datastore/commons-datastore-solr/pom.xml @@ -22,7 +22,7 @@ org.opencb.commons commons-datastore - 5.3.0-SNAPSHOT + 5.3.0 ../pom.xml diff --git a/commons-datastore/pom.xml b/commons-datastore/pom.xml index db85378f..ee91c649 100644 --- a/commons-datastore/pom.xml +++ b/commons-datastore/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.3.0-SNAPSHOT + 5.3.0 ../pom.xml diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index cf0e9bd5..1d463eca 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.3.0-SNAPSHOT + 5.3.0 ../pom.xml diff --git a/pom.xml b/pom.xml index 0105ec92..eee09ada 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.3.0-SNAPSHOT + 5.3.0 pom OpenCB commons project From 3acfb33e1f3d36958ebad9a852de1d8de8382013 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 17 Oct 2024 10:17:30 +0200 Subject: [PATCH 107/107] Prepare Port Patch 5.3.0 -> 6.0.0 Xetabase 2.3.0 -> 3.0.0 #TASK-7097 --- commons-datastore/commons-datastore-core/pom.xml | 2 +- commons-datastore/commons-datastore-mongodb/pom.xml | 2 +- commons-datastore/commons-datastore-solr/pom.xml | 2 +- commons-datastore/pom.xml | 2 +- commons-lib/pom.xml | 2 +- pom.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/commons-datastore/commons-datastore-core/pom.xml b/commons-datastore/commons-datastore-core/pom.xml index dfa4bf70..f75e11a9 100644 --- a/commons-datastore/commons-datastore-core/pom.xml +++ b/commons-datastore/commons-datastore-core/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.3.0 + 6.0.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-mongodb/pom.xml b/commons-datastore/commons-datastore-mongodb/pom.xml index c44b9cc0..842daef6 100644 --- a/commons-datastore/commons-datastore-mongodb/pom.xml +++ b/commons-datastore/commons-datastore-mongodb/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons-datastore - 5.3.0 + 6.0.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/commons-datastore-solr/pom.xml b/commons-datastore/commons-datastore-solr/pom.xml index 45eb7f44..789a9a91 100644 --- a/commons-datastore/commons-datastore-solr/pom.xml +++ b/commons-datastore/commons-datastore-solr/pom.xml @@ -22,7 +22,7 @@ org.opencb.commons commons-datastore - 5.3.0 + 6.0.0-SNAPSHOT ../pom.xml diff --git a/commons-datastore/pom.xml b/commons-datastore/pom.xml index ee91c649..1e503e66 100644 --- a/commons-datastore/pom.xml +++ b/commons-datastore/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.3.0 + 6.0.0-SNAPSHOT ../pom.xml diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml index 1d463eca..a660edcf 100644 --- a/commons-lib/pom.xml +++ b/commons-lib/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.3.0 + 6.0.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index eee09ada..ec022c4f 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.opencb.commons commons - 5.3.0 + 6.0.0-SNAPSHOT pom OpenCB commons project