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Merge branch 'develop' of github.com:opencb/java-common-libs into dev…
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juanfeSanahuja committed Oct 2, 2024
2 parents 09241e0 + c5cb58a commit 337f805
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35 changes: 30 additions & 5 deletions .github/workflows/pull-request-approved.yml
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Expand Up @@ -6,11 +6,36 @@ on:
types: [ submitted ]

jobs:
build:
uses: ./.github/workflows/build-java-app-workflow.yml

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: |
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 ${{ github.event.pull_request.base.ref }})
echo "__Xetabase ref:__ \"${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"
uses: ./.github/workflows/test-analysis.yml
needs: build
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: ${{ github.event.pull_request.head.ref }}
secrets: inherit
46 changes: 46 additions & 0 deletions .github/workflows/scripts/get-xetabase-branch.sh
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#!/bin/bash
set -e
set -x
# Function to calculate the corresponding branch of Xetabase project
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://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git" "$input_branch" )" ] ; then
echo $input_branch;
return 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"
return 0
fi

# 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=${BASH_REMATCH[1]}
# Calculate the XETABASE_MAJOR by subtracting 3 from MAJOR
XETABASE_MAJOR=$((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
}


# Call the function with the input branch name
get_xetabase_branch "$1"
48 changes: 48 additions & 0 deletions .github/workflows/tmp-test-xetabase-branch.yml
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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
2 changes: 1 addition & 1 deletion commons-datastore/commons-datastore-core/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore</artifactId>
<version>5.3.0-SNAPSHOT</version>
<version>6.0.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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2 changes: 1 addition & 1 deletion commons-datastore/commons-datastore-mongodb/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore</artifactId>
<version>5.3.0-SNAPSHOT</version>
<version>6.0.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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2 changes: 1 addition & 1 deletion commons-datastore/commons-datastore-solr/pom.xml
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Expand Up @@ -22,7 +22,7 @@
<parent>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore</artifactId>
<version>5.3.0-SNAPSHOT</version>
<version>6.0.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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2 changes: 1 addition & 1 deletion commons-datastore/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>org.opencb.commons</groupId>
<artifactId>commons</artifactId>
<version>5.3.0-SNAPSHOT</version>
<version>6.0.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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2 changes: 1 addition & 1 deletion commons-lib/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>org.opencb.commons</groupId>
<artifactId>commons</artifactId>
<version>5.3.0-SNAPSHOT</version>
<version>6.0.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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2 changes: 1 addition & 1 deletion pom.xml
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Expand Up @@ -6,7 +6,7 @@

<groupId>org.opencb.commons</groupId>
<artifactId>commons</artifactId>
<version>5.3.0-SNAPSHOT</version>
<version>6.0.0-SNAPSHOT</version>
<packaging>pom</packaging>

<name>OpenCB commons project</name>
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