ci.yml

name: CI - Build and Test
# Trigger re-run to pick up deployed treebase-core JAR from gh-pages

on:
  push:
    branches: [ main, master, develop ]
  pull_request:
    branches: [ main, master, develop ]
  workflow_dispatch:

jobs:
  build-and-test:
    name: Build and Test TreeBASE
    runs-on: ubuntu-latest
    
    permissions:
      contents: write
      checks: write
      pull-requests: write
    
    services:
      postgres:
        image: postgres:12
        env:
          POSTGRES_DB: treebasedb
          POSTGRES_USER: treebase_user
          POSTGRES_PASSWORD: treebase_pass
        options: >-
          --health-cmd pg_isready
          --health-interval 10s
          --health-timeout 5s
          --health-retries 5
        ports:
          - 5432:5432
    
    steps:
    - name: Checkout code
      uses: actions/checkout@v4
      
    - name: Set up JDK 17
      uses: actions/setup-java@v4
      with:
        java-version: '17'
        distribution: 'temurin'
        cache: 'maven'
    
    - name: Configure database properties for tests
      run: |
        mkdir -p /tmp/mesquite
        cat > treebase-core/src/test/resources/jdbc.properties << EOF
        jdbc.driverClassName=org.postgresql.Driver
        jdbc.url=jdbc:postgresql://localhost:5432/treebasedb
        jdbc.username=treebase_user
        jdbc.password=treebase_pass
        mesquite.folder_dir=/tmp/mesquite
        EOF
        cat > oai-pmh_data_provider/data_provider_web/src/test/resources/jdbc.properties << EOF
        jdbc.driverClassName=org.postgresql.Driver
        jdbc.url=jdbc:postgresql://localhost:5432/treebasedb
        jdbc.username=treebase_user
        jdbc.password=treebase_pass
        mesquite.folder_dir=/tmp/mesquite
        EOF
    
    - name: Initialize database schema
      run: |
        # Install PostgreSQL client if not already available
        sudo apt-get update
        sudo apt-get install -y postgresql-client
        
        # Initialize the database with schema and data
        # The init_db_uptodate.pg script uses \i commands with relative paths,
        # so we must run it from the schema directory
        cd treebase-core/db/schema
        PGPASSWORD=treebase_pass psql -h localhost -U treebase_user -d treebasedb -f init_db_uptodate.pg
        
    - name: Build treebase-core
      run: mvn -B clean compile -f treebase-core/pom.xml
      
    - name: Run treebase-core tests
      run: mvn -B test -f treebase-core/pom.xml
      
    - name: Install treebase-core to local Maven repository
      run: mvn -B install -DskipTests -f treebase-core/pom.xml
      
    - name: Checkout gh-pages branch
      uses: actions/checkout@v4
      with:
        ref: gh-pages
        path: gh-pages
        fetch-depth: 0
        
    - name: Deploy parent POM and treebase-core JAR to Maven repository
      run: |
        # Set up Maven coordinates for parent POM
        PARENT_GROUP_ID="org.cipres.treebase"
        PARENT_ARTIFACT_ID="treebase"
        VERSION="1.0-SNAPSHOT"
        
        # Deploy parent POM
        GROUP_PATH=$(echo $PARENT_GROUP_ID | tr '.' '/')
        PARENT_REPO_PATH="gh-pages/repository/${GROUP_PATH}/${PARENT_ARTIFACT_ID}/${VERSION}"
        mkdir -p "$PARENT_REPO_PATH"
        
        # Copy parent POM file
        cp pom.xml "$PARENT_REPO_PATH/${PARENT_ARTIFACT_ID}-${VERSION}.pom"
        
        # Generate checksums for parent POM
        cd "$PARENT_REPO_PATH"
        for file in *.pom; do
          if [ -f "$file" ]; then
            sha1sum "$file" | awk '{print $1}' > "${file}.sha1"
            md5sum "$file" | awk '{print $1}' > "${file}.md5"
          fi
        done
        
        # Generate maven-metadata.xml for parent POM
        cat > maven-metadata.xml << EOF
        <?xml version="1.0" encoding="UTF-8"?>
        <metadata>
          <groupId>${PARENT_GROUP_ID}</groupId>
          <artifactId>${PARENT_ARTIFACT_ID}</artifactId>
          <versioning>
            <versions>
              <version>${VERSION}</version>
            </versions>
            <lastUpdated>$(date +%Y%m%d%H%M%S)</lastUpdated>
          </versioning>
        </metadata>
        EOF
        
        # Generate checksums for parent metadata
        sha1sum maven-metadata.xml | awk '{print $1}' > maven-metadata.xml.sha1
        md5sum maven-metadata.xml | awk '{print $1}' > maven-metadata.xml.md5
        
        # Now deploy treebase-core JAR
        cd -
        ARTIFACT_ID="treebase-core"
        REPO_PATH="gh-pages/repository/${GROUP_PATH}/${ARTIFACT_ID}/${VERSION}"
        mkdir -p "$REPO_PATH"
        
        # Verify JAR file exists
        JAR_FILE="treebase-core/target/${ARTIFACT_ID}-${VERSION}.jar"
        if [ ! -f "$JAR_FILE" ]; then
          echo "Error: JAR file not found at $JAR_FILE"
          exit 1
        fi
        
        # Copy JAR and POM files
        cp "$JAR_FILE" "$REPO_PATH/"
        cp treebase-core/pom.xml "$REPO_PATH/${ARTIFACT_ID}-${VERSION}.pom"
        
        # Generate checksums for treebase-core
        cd "$REPO_PATH"
        for file in *.jar *.pom; do
          if [ -f "$file" ]; then
            sha1sum "$file" | awk '{print $1}' > "${file}.sha1"
            md5sum "$file" | awk '{print $1}' > "${file}.md5"
          fi
        done
        
        # Generate maven-metadata.xml for treebase-core
        cat > maven-metadata.xml << EOF
        <?xml version="1.0" encoding="UTF-8"?>
        <metadata>
          <groupId>${PARENT_GROUP_ID}</groupId>
          <artifactId>${ARTIFACT_ID}</artifactId>
          <versioning>
            <versions>
              <version>${VERSION}</version>
            </versions>
            <lastUpdated>$(date +%Y%m%d%H%M%S)</lastUpdated>
          </versioning>
        </metadata>
        EOF
        
        # Generate checksums for treebase-core metadata
        sha1sum maven-metadata.xml | awk '{print $1}' > maven-metadata.xml.sha1
        md5sum maven-metadata.xml | awk '{print $1}' > maven-metadata.xml.md5
        
    - name: Commit and push to gh-pages
      run: |
        cd gh-pages
        git config user.name "github-actions[bot]"
        git config user.email "github-actions[bot]@users.noreply.github.com"
        git add repository/
        if git diff --staged --quiet; then
          echo "No changes to commit"
        else
          git commit -m "Deploy treebase-core JAR from CI build (commit: ${{ github.sha }})"
          # Pull with rebase to handle concurrent updates
          git pull --rebase origin gh-pages || {
            echo "Rebase failed, attempting force push"
            git rebase --abort
            git push --force
            exit 0
          }
          git push
        fi
      
    - name: Build treebase-web
      run: mvn -B clean compile -f treebase-web/pom.xml
      
    - name: Build oai-pmh_data_provider
      run: mvn -B clean compile -f oai-pmh_data_provider/pom.xml
      
    - name: Run oai-pmh_data_provider tests
      run: mvn -B test -f oai-pmh_data_provider/pom.xml
      
    - name: Publish Test Report
      uses: dorny/test-reporter@v1
      if: always()
      with:
        name: JUnit Test Results
        path: 'treebase-core/target/surefire-reports/*.xml,oai-pmh_data_provider/data_provider_web/target/surefire-reports/*.xml'
        reporter: java-junit
        fail-on-error: true