tomcat-deploy.yml

name: Tomcat Deployment Test

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

jobs:
  build-and-deploy-tomcat:
    name: Build WARs and Deploy to Tomcat
    runs-on: ubuntu-latest
    
    permissions:
      contents: read
    
    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 Maven settings for better reliability
      run: |
        mkdir -p ~/.m2
        cat > ~/.m2/settings.xml << 'EOF'
        <settings xmlns="http://maven.apache.org/SETTINGS/1.0.0"
                  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                  xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0
                                      https://maven.apache.org/xsd/settings-1.0.0.xsd">
          <profiles>
            <profile>
              <id>default</id>
              <properties>
                <downloadSources>false</downloadSources>
                <downloadJavadocs>false</downloadJavadocs>
              </properties>
              <repositories>
                <repository>
                  <id>central</id>
                  <url>https://repo1.maven.org/maven2</url>
                  <releases>
                    <enabled>true</enabled>
                    <updatePolicy>never</updatePolicy>
                  </releases>
                  <snapshots>
                    <enabled>false</enabled>
                  </snapshots>
                </repository>
              </repositories>
              <pluginRepositories>
                <pluginRepository>
                  <id>central</id>
                  <url>https://repo1.maven.org/maven2</url>
                  <releases>
                    <enabled>true</enabled>
                    <updatePolicy>never</updatePolicy>
                  </releases>
                  <snapshots>
                    <enabled>false</enabled>
                  </snapshots>
                </pluginRepository>
              </pluginRepositories>
            </profile>
          </profiles>
          <activeProfiles>
            <activeProfile>default</activeProfile>
          </activeProfiles>
        </settings>
        EOF
    
    - name: Configure database properties for building
      run: |
        mkdir -p /tmp/mesquite
        
        # Create jdbc.properties for treebase-core
        cat > treebase-core/src/main/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
        
        # Create context.xml for treebase-web
        cat > treebase-web/src/main/webapp/META-INF/context.xml << EOF
        <?xml version="1.0" encoding="UTF-8"?>
        <Context reloadable="true">
          <Resource name="jdbc/TreebaseDB" auth="Container"
                    type="javax.sql.DataSource" 
                    description="The JNDI DataSource for the Treebase postgres instance."
                    driverClassName="org.postgresql.Driver" 
                    url="jdbc:postgresql://localhost:5432/treebasedb"
                    username="treebase_user" 
                    password="treebase_pass"
                    maxActive="20" maxIdle="10" maxWait="-1" />
          <Environment name="tb2/MesquiteFolder" value="/tmp/mesquite"
                 type="java.lang.String" override="false"
                 description="Absolute path to the directory where headless Mesquite is unpacked on the host system."/>
          <Environment name="tb2/SiteUrl" value="http://localhost:8080/treebase-web/"
                 type="java.lang.String" override="false"
                 description="The base URL from which this Treebase instance is served."/>
          <Environment name="tb2/PurlBase" value="http://purl.org/phylo/treebase/phylows/"
                 type="java.lang.String" override="false"
                 description="The base URL of a PURL service that redirects to this Treebase instance."/>
          <Environment name="tb2/SmtpHost" value="localhost"
                 type="java.lang.String" override="false"
                 description="Host name of an SMTP server that your instance can use without authentication."/>
        </Context>
        EOF
        
        # Create jdbc.properties for OAI-PMH data provider
        mkdir -p oai-pmh_data_provider/data_provider_web/src/main/resources
        cat > oai-pmh_data_provider/data_provider_web/src/main/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
        
        # Create context.xml for OAI-PMH data provider
        mkdir -p oai-pmh_data_provider/data_provider_web/src/main/webapp/META-INF
        cat > oai-pmh_data_provider/data_provider_web/src/main/webapp/META-INF/context.xml << EOF
        <?xml version="1.0" encoding="UTF-8"?>
        <Context reloadable="true">
          <Resource name="jdbc/TreebaseDB" auth="Container"
                    type="javax.sql.DataSource" 
                    description="The JNDI DataSource for the Treebase postgres instance."
                    driverClassName="org.postgresql.Driver" 
                    url="jdbc:postgresql://localhost:5432/treebasedb"
                    username="treebase_user" 
                    password="treebase_pass"
                    maxActive="20" maxIdle="10" maxWait="-1" />
          <Environment name="tb2/MesquiteFolder" value="/tmp/mesquite"
                 type="java.lang.String" override="false"
                 description="Absolute path to the directory where headless Mesquite is unpacked on the host system."/>
          <Environment name="tb2/SiteUrl" value="http://localhost:8080/data_provider_web/"
                 type="java.lang.String" override="false"
                 description="The base URL from which this Treebase instance is served."/>
          <Environment name="tb2/PurlBase" value="http://purl.org/phylo/treebase/phylows/"
                 type="java.lang.String" override="false"
                 description="The base URL of a PURL service that redirects to this Treebase instance."/>
          <Environment name="tb2/SmtpHost" value="localhost"
                 type="java.lang.String" override="false"
                 description="Host name of an SMTP server that your instance can use without authentication."/>
        </Context>
        EOF
    
    - name: Initialize database schema
      run: |
        sudo apt-get update
        sudo apt-get install -y postgresql-client
        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 and install to local repository
      run: |
        # Retry Maven build up to 3 times to handle transient Maven Central issues
        for i in 1 2 3; do
          echo "Build attempt $i..."
          if mvn -B clean install -DskipTests -f treebase-core/pom.xml; then
            echo "Build succeeded on attempt $i"
            break
          else
            if [ $i -lt 3 ]; then
              echo "Build failed on attempt $i, retrying in 10 seconds..."
              sleep 10
            else
              echo "Build failed after 3 attempts"
              exit 1
            fi
          fi
        done
    
    - name: Build treebase-web WAR
      run: |
        # Retry Maven build up to 3 times to handle transient Maven Central issues
        for i in 1 2 3; do
          echo "Build attempt $i..."
          if mvn -B clean package -DskipTests -f treebase-web/pom.xml; then
            echo "Build succeeded on attempt $i"
            break
          else
            if [ $i -lt 3 ]; then
              echo "Build failed on attempt $i, retrying in 10 seconds..."
              sleep 10
            else
              echo "Build failed after 3 attempts"
              exit 1
            fi
          fi
        done
        
    - name: Build OAI-PMH data provider WAR
      run: |
        # Retry Maven build up to 3 times to handle transient Maven Central issues
        for i in 1 2 3; do
          echo "Build attempt $i..."
          if mvn -B clean package -DskipTests -f oai-pmh_data_provider/pom.xml; then
            echo "Build succeeded on attempt $i"
            break
          else
            if [ $i -lt 3 ]; then
              echo "Build failed on attempt $i, retrying in 10 seconds..."
              sleep 10
            else
              echo "Build failed after 3 attempts"
              exit 1
            fi
          fi
        done
        
    - name: Verify WAR files were created
      run: |
        echo "Checking for treebase-web.war..."
        ls -lh treebase-web/target/treebase-web.war
        echo "Checking for data_provider_web.war..."
        ls -lh oai-pmh_data_provider/data_provider_web/target/data_provider_web.war
    
    - name: Install Tomcat 9
      run: |
        # Download and install Tomcat 9
        cd /tmp
        wget -q https://archive.apache.org/dist/tomcat/tomcat-9/v9.0.85/bin/apache-tomcat-9.0.85.tar.gz
        tar xzf apache-tomcat-9.0.85.tar.gz
        export CATALINA_HOME=/tmp/apache-tomcat-9.0.85
        echo "CATALINA_HOME=/tmp/apache-tomcat-9.0.85" >> $GITHUB_ENV
        
        # Download PostgreSQL JDBC driver
        wget -q -O $CATALINA_HOME/lib/postgresql-42.7.1.jar https://jdbc.postgresql.org/download/postgresql-42.7.1.jar
        
        # Make scripts executable
        chmod +x $CATALINA_HOME/bin/*.sh
    
    - name: Deploy WAR files to Tomcat
      run: |
        # Copy WAR files to Tomcat webapps directory
        cp treebase-web/target/treebase-web.war $CATALINA_HOME/webapps/
        cp oai-pmh_data_provider/data_provider_web/target/data_provider_web.war $CATALINA_HOME/webapps/
        
        echo "WAR files deployed to Tomcat webapps directory:"
        ls -lh $CATALINA_HOME/webapps/*.war
        
        # Copy DTD files to workspace root to fix validator configuration
        # The validator XML files reference ./dtd/validator_1_3_0.dtd which gets resolved
        # relative to the working directory during Spring initialization
        echo "Copying DTD files to workspace root for validator..."
        cp -r $GITHUB_WORKSPACE/treebase-web/src/main/webapp/WEB-INF/dtd $GITHUB_WORKSPACE/dtd
        ls -la $GITHUB_WORKSPACE/dtd/
    
    - name: Start Tomcat and deploy applications
      run: |
        # Set Java options for Tomcat
        export JAVA_OPTS="-Djava.awt.headless=true -Xmx512m -XX:+UseG1GC"
        export CATALINA_OPTS="--add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.base/java.lang.reflect=ALL-UNNAMED"
        
        # Start Tomcat
        JAVA_OPTS="$JAVA_OPTS" CATALINA_OPTS="$CATALINA_OPTS" $CATALINA_HOME/bin/catalina.sh start
        
        echo "Tomcat started. Waiting for applications to deploy and initialize..."
        
        # Wait for applications to fully deploy (60 seconds should be sufficient)
        sleep 60
        
        # Verify Tomcat is still running
        if ! pgrep -f "catalina" > /dev/null; then
          echo "ERROR: Tomcat process died during startup!"
          echo "Showing last 100 lines of catalina.out:"
          tail -100 $CATALINA_HOME/logs/catalina.out || true
          exit 1
        fi
        
        echo "Tomcat is running. Applications should be deployed."
    
    - name: Check Tomcat logs for severe errors
      run: |
        echo "=========================================="
        echo "Checking Tomcat logs for SEVERE errors..."
        echo "=========================================="
        
        # Display summary of all log files first
        echo ""
        echo "All Tomcat log files:"
        ls -lh $CATALINA_HOME/logs/
        echo ""
        
        # Initialize counters
        TOTAL_SEVERE=0
        TOTAL_ERROR=0
        HAS_FAILURES=0
        
        # Check all .log files and catalina.out
        echo "Scanning all log files for errors..."
        for logfile in $CATALINA_HOME/logs/*.log $CATALINA_HOME/logs/catalina.out; do
          if [ -f "$logfile" ]; then
            BASENAME=$(basename "$logfile")
            echo ""
            echo "----------------------------------------"
            echo "Checking: $BASENAME"
            echo "----------------------------------------"
            
            SEVERE_COUNT=$(grep -c "SEVERE" "$logfile" 2>/dev/null || true)
            ERROR_COUNT=$(grep -c " ERROR " "$logfile" 2>/dev/null || true)
            
            # Also check for common error patterns
            EXCEPTION_COUNT=$(grep -c "Exception" "$logfile" 2>/dev/null || true)
            
            TOTAL_SEVERE=$((TOTAL_SEVERE + SEVERE_COUNT))
            TOTAL_ERROR=$((TOTAL_ERROR + ERROR_COUNT))
            
            echo "  SEVERE: $SEVERE_COUNT"
            echo "  ERROR: $ERROR_COUNT"
            echo "  Exceptions: $EXCEPTION_COUNT"
            
            # Show SEVERE errors with context
            if [ $SEVERE_COUNT -gt 0 ]; then
              echo ""
              echo "  SEVERE errors in $BASENAME:"
              grep -B 3 -A 10 "SEVERE" "$logfile" 2>/dev/null | head -100 || true
              HAS_FAILURES=1
            fi
          fi
        done
        
        # Show last 100 lines of catalina.out for full context
        echo ""
        echo "=========================================="
        echo "Last 100 lines of catalina.out:"
        echo "=========================================="
        if [ -f "$CATALINA_HOME/logs/catalina.out" ]; then
          tail -100 "$CATALINA_HOME/logs/catalina.out"
        fi
        
        # Final summary and exit decision
        echo ""
        echo "=========================================="
        echo "LOG CHECK SUMMARY"
        echo "=========================================="
        echo "Total SEVERE errors across all logs: $TOTAL_SEVERE"
        echo "Total ERROR messages across all logs: $TOTAL_ERROR"
        echo ""
        
        if [ $HAS_FAILURES -eq 1 ]; then
          echo "❌ FAILED: SEVERE errors detected in Tomcat logs"
          echo "Please review the errors above and the uploaded log artifacts"
          echo "=========================================="
          exit 1
        else
          echo "✓ SUCCESS: No SEVERE errors found in Tomcat logs"
          echo "=========================================="
        fi
    
    - name: Test application endpoints
      run: |
        echo "=========================================="
        echo "Testing application endpoints..."
        echo "=========================================="
        
        FAILED=0
        
        # Test treebase-web
        echo "Testing treebase-web..."
        HTTP_CODE=$(curl -s -o /dev/null -w "%{http_code}" http://localhost:8080/treebase-web/ || echo "000")
        echo "treebase-web HTTP status: $HTTP_CODE"
        
        if [ "$HTTP_CODE" = "200" ] || [ "$HTTP_CODE" = "302" ]; then
          echo "✓ treebase-web is responding"
        else
          echo "✗ treebase-web returned unexpected status: $HTTP_CODE"
          # Show error response body for debugging
          echo "Response body:"
          curl -s http://localhost:8080/treebase-web/ | head -100
          FAILED=1
        fi
        
        # Test data_provider_web
        echo "Testing data_provider_web..."
        HTTP_CODE=$(curl -s -o /dev/null -w "%{http_code}" http://localhost:8080/data_provider_web/ || echo "000")
        echo "data_provider_web HTTP status: $HTTP_CODE"
        
        if [ "$HTTP_CODE" = "200" ] || [ "$HTTP_CODE" = "302" ] || [ "$HTTP_CODE" = "404" ]; then
          echo "✓ data_provider_web is deployed (status: $HTTP_CODE)"
        else
          echo "✗ data_provider_web returned unexpected status: $HTTP_CODE"
          # Show error response body for debugging
          echo "Response body:"
          curl -s http://localhost:8080/data_provider_web/ | head -100
          FAILED=1
        fi
        
        if [ "$FAILED" = "1" ]; then
          echo "=========================================="
          echo "FAILURE: One or more endpoints returned errors"
          echo "=========================================="
          exit 1
        fi
    
    - name: Upload Tomcat logs as artifact
      if: always()
      uses: actions/upload-artifact@v4
      with:
        name: tomcat-logs
        path: /tmp/apache-tomcat-9.0.85/logs/
        retention-days: 7
    
    - name: Shutdown Tomcat
      if: always()
      run: |
        if [ -f "$CATALINA_HOME/bin/catalina.sh" ]; then
          $CATALINA_HOME/bin/catalina.sh stop || true
          sleep 5
          # Force kill if still running
          pkill -9 -f catalina || true
        fi