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Merge pull request #205 from imi-ms/v3.3.0
v3.3.0 Release
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‎.env‎

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@@ -13,8 +13,9 @@ MYSQL_MOPAT_AUDIT_URL=jdbc:mysql://db-container:3306/moPat_audit?autoReconnect=t
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# Local volume paths
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HL7_VOLUME=./data/export/HL7
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FHIR_VOLUME=./data/export/HL7
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ODM_VOLUME=./data/export/HL7
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FHIR_VOLUME=./data/export/FHIR
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ODM_VOLUME=./data/export/ODM
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REDCAP_VOLUME=./data/export/REDCap
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UPLOAD_VOLUME=./data/upload
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IMAGES_VOLUME=./data/images
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CONFIG_DIR=/etc/mopat

‎.github/docker_testenv/.env‎

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# .env file
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# DB settings
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# !!! ADJUST THESE SETTINGS !!!
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MYSQL_ROOT_PASSWORD=root
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MYSQL_USER=mopat
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MYSQL_PASSWORD=mopat
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PEPPER=AdP5ktlaIVaon53yJg8zEZSnFr33Dinil69ZtZMTWXubKMUEpfyNvOgWLdwNLhedY3WT5TVcqgg
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# DB Connection settings - The hostname is corresponding to the container name of the db
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MYSQL_MOPAT_URL=jdbc:mysql://db-container:3306/moPat?autoReconnect=true&useUnicode=true&useEncoding=true&characterEncoding=UTF-8
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MYSQL_MOPAT_USER_URL=jdbc:mysql://db-container:3306/moPat_user?autoReconnect=true&useUnicode=true&useEncoding=true&characterEncoding=UTF-8
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MYSQL_MOPAT_AUDIT_URL=jdbc:mysql://db-container:3306/moPat_audit?autoReconnect=true&useUnicode=true&useEncoding=true&characterEncoding=UTF-8
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# Local volume paths
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HL7_VOLUME=./data/export/HL7
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FHIR_VOLUME=./data/export/FHIR
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ODM_VOLUME=./data/export/ODM
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UPLOAD_VOLUME=./data/upload
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IMAGES_VOLUME=./data/images
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CONFIG_DIR=/etc/mopat
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# Path for the database data
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DB_DATA_PATH=./data/db
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# Port configuration
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WEBAPP_PORT=8080

‎.github/docker_testenv/Dockerfile‎

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FROM maven:3.9.11-eclipse-temurin-17-noble as builder
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WORKDIR /app
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COPY pom.xml .
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COPY src ./src
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COPY .git ./.git
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RUN mvn -B -f pom.xml dependency:go-offline
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RUN mvn -B install -DskipTests
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FROM tomcat:10-jdk17-temurin-noble
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RUN rm -rf /usr/local/tomcat/webapps/*
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COPY src/main/resources/docker-server.xml /usr/local/tomcat/conf/server.xml
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COPY --from=builder /app/target/*.war /usr/local/tomcat/webapps/ROOT.war
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EXPOSE 8080
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CMD ["catalina.sh", "run"]

‎.github/docker_testenv/docker-compose.yml‎

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services:
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db-container:
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image: mariadb
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restart: always
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environment:
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MYSQL_ROOT_PASSWORD: ${MYSQL_ROOT_PASSWORD}
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MYSQL_USER: ${MYSQL_USER}
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MYSQL_PASSWORD: ${MYSQL_PASSWORD}
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MYSQL_DATABASE: initDb
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ports:
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- "127.0.0.1:3306:3306"
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volumes:
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- ${DB_DATA_PATH}:/var/lib/mysql
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- ./db:/docker-entrypoint-initdb.d
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webapp-container:
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build:
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context: ../..
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dockerfile: .github/docker_testenv/Dockerfile
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depends_on:
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- db-container
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ports:
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- "127.0.0.1:${WEBAPP_PORT}:8080"
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volumes:
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- ${HL7_VOLUME}:/var/lib/tomcat10/export/HL7
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- ${FHIR_VOLUME}:/var/lib/tomcat10/export/FHIR
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- ${ODM_VOLUME}:/var/lib/tomcat10/export/ODM
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- ${UPLOAD_VOLUME}:/var/lib/tomcat10/upload
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- ${IMAGES_VOLUME}:/var/lib/tomcat10/images
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- ${CONFIG_DIR}:/etc/mopat
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- ./src/main/resources/docker-server.xml:/usr/local/tomcat/conf/server.xml:ro
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environment:
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- MYSQL_USER=${MYSQL_USER}
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- MYSQL_PASSWORD=${MYSQL_PASSWORD}
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- MYSQL_MOPAT_URL=${MYSQL_MOPAT_URL}
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- MYSQL_MOPAT_USER_URL=${MYSQL_MOPAT_USER_URL}
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- MYSQL_MOPAT_AUDIT_URL=${MYSQL_MOPAT_AUDIT_URL}
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- PEPPER=${PEPPER}

‎.github/workflows/pr-checks.yml‎

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name: test
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on: pull_request
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jobs:
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unit-tests:
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permissions:
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checks: write
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pull-requests: write
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runs-on: ubuntu-latest
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outputs:
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unittest-results: ${{ steps.decode-results.outputs.content }}
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services:
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mariadb:
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image: mariadb:latest
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env:
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MARIADB_ROOT_PASSWORD: root
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ports:
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- 3306:3306
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options: >-
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--health-cmd="healthcheck.sh
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--connect
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--innodb_initialized"
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--health-interval=10s
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--health-timeout=5s
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--health-retries=3
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steps:
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- uses: actions/checkout@v4
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- name: Set up JDK
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uses: actions/setup-java@v4
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with:
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java-version: '17'
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distribution: 'temurin'
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cache: 'maven'
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- name: Install MySQL client and Load Database Schema
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run: |
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sudo apt-get update
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sudo apt-get install -y default-mysql-client
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mysql -h 127.0.0.1 -u root --password=root -e "CREATE USER IF NOT EXISTS 'mopat'@'%' IDENTIFIED BY 'mopat';"
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mysql -h 127.0.0.1 -u root --password=root -e "GRANT ALL PRIVILEGES ON *.* TO 'mopat'@'%'; FLUSH PRIVILEGES;"
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mysql -h 127.0.0.1 -u root --password=root < db/installationInitTest.sql
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- name: Test with Maven
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run: mvn -B test --file pom.xml
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- name: Publish Test Report
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id: testReport
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uses: mikepenz/action-junit-report@v5
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if: success() || failure() # always run even if the previous step fails
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with:
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report_paths: '**/target/surefire-reports/*.xml'
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- name: Decode results
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id: decode-results
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if: always() && github.event_name == 'pull_request'
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run: |
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echo "<details><summary>🧪 Unit Test Results</summary>" >> unit-results.md
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echo "${{ steps.testReport.outputs.summary }}" >> unit-results.md
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echo "</details>" >> unit-results.md
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# Save content as output
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echo "content<<EOF" >> $GITHUB_OUTPUT
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cat unit-results.md >> $GITHUB_OUTPUT
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echo "EOF" >> $GITHUB_OUTPUT
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selenium-tests:
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permissions:
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checks: write
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pull-requests: write
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runs-on: ubuntu-latest
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outputs:
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selenium-results: ${{ steps.decode-results.outputs.content }}
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steps:
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# Checkout the repository
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- name: Check out the repository
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uses: actions/checkout@v4
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# Set up Docker
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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# Pull the Chrome image
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- name: Pull Selenoid Chrome Image
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run: docker pull selenoid/chrome:latest
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# Setup Docker-Compose
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- name: Docker Compose Action
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uses: hoverkraft-tech/compose-action@v2.0.2
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with:
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compose-file: "selenium/docker-compose.yml"
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# Wait for the server to be ready before running tests
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- name: Wait for the application to be ready
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run: |
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until curl --output /dev/null --silent --head --fail http://localhost:8080; do
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echo 'Waiting for the application to be ready...'
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sleep 5
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done
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until curl --output /dev/null --silent --head --fail http://localhost:4444/status; do
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echo 'Waiting for Selenoid to be ready...'
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sleep 5
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done
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# Set up Python and run Selenium tests
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.13' # Specify the version of Python you are using
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- name: Install dependencies
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run: pip install -r selenium/requirements.txt # Ensure your Selenium and other dependencies are listed here
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- name: Run Selenium tests
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run: |
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python3 selenium/selenium_tests.py > test-results.log
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- name: Save results to env
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if: always() && github.event_name == 'pull_request'
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id: test_report
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run: echo "SELENIUM_TEST_SUMMARY=$(base64 -w 0 test-results.log)" >> $GITHUB_ENV
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# Install GitHub CLI
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- name: Install GitHub CLI
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run: sudo apt-get update && sudo apt-get install -y gh
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- name: Decode results
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id: decode-results
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if: always() && github.event_name == 'pull_request'
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run: |
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decoded_results=$(echo "${{ env.SELENIUM_TEST_SUMMARY }}" | base64 --decode)
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echo "<details><summary>🌐 Selenium Test Results</summary>" > selenium_block.md
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echo "$decoded_results" >> selenium_block.md
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echo "</details>" >> selenium_block.md
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# Save content as output
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echo "content<<EOF" >> $GITHUB_OUTPUT
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cat selenium_block.md >> $GITHUB_OUTPUT
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echo "EOF" >> $GITHUB_OUTPUT
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trivy-scan:
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runs-on: ubuntu-latest
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outputs:
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trivy-results: ${{ steps.trivy-table.outputs.content }}
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permissions:
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contents: read
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pull-requests: write
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steps:
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- name: Checkout code
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uses: actions/checkout@v5
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Build Docker images with docker compose
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working-directory: ./.github/docker_testenv
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run: |
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docker compose build
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- name: Run Trivy vulnerability scanner on image
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id: trivy
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uses: aquasecurity/trivy-action@0.34.2
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env:
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TRIVY_DISABLE_VEX_NOTICE: "true"
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with:
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image-ref: docker_testenv-webapp-container:latest
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format: json
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exit-code: 0
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output: trivy-report.json
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- name: Convert Trivy JSON to Markdown table (split OS vs app)
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id: trivy-table
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run: |
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# Check if any vulnerabilities exist
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if ! jq -e '.Results[].Vulnerabilities | select(length > 0)' trivy-report.json > /dev/null; then
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echo "✅ No vulnerabilities found!" >> trivy-comment.md
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exit 0
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fi
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#####################################
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# 🐳 1️⃣ Base Image Vulnerabilities (os-pkgs)
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#####################################
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os_total=$(jq '[.Results[] | select(.Class=="os-pkgs") | .Vulnerabilities[]?] | length' trivy-report.json)
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os_with_fixes=$(jq '[.Results[] | select(.Class=="os-pkgs") | .Vulnerabilities[]? | select(.FixedVersion != null and .FixedVersion != "")] | length' trivy-report.json)
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echo "<details><summary>🐳 Base Image Vulnerabilities: $os_total vulnerabilities found, $os_with_fixes with fixes</summary>" >> trivy-comment.md
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echo "" >> trivy-comment.md
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jq -r '
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[ .Results[]
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| select(.Class == "os-pkgs")
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| .Vulnerabilities[]?
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]
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| select(length > 0)
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| group_by(.PkgName)
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| sort_by(.[0].PkgName)
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| .[]
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| "#### 📦 Package: \([.[0].PkgName])\n"
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+ "| Severity | Vulnerability ID | Installed Version | Fixed Version |\n"
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+ "|-----------|------------------|------------------|----------------|\n"
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+ (map("| \(.Severity) | \(.VulnerabilityID) | \(.InstalledVersion) | \(.FixedVersion // "-") |") | join("\n"))
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+ "\n"
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' trivy-report.json >> trivy-comment.md
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echo "</details>" >> trivy-comment.md
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echo "" >> trivy-comment.md
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#####################################
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# ☕️ 2️⃣ Tomcat / Java / Library Vulnerabilities
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#####################################
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app_total=$(jq '[.Results[] | select(.Class!="os-pkgs") | .Vulnerabilities[]?] | length' trivy-report.json)
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app_with_fixes=$(jq '[.Results[] | select(.Class!="os-pkgs") | .Vulnerabilities[]? | select(.FixedVersion != null and .FixedVersion != "")] | length' trivy-report.json)
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echo "<details><summary>☕️ Application / Library Vulnerabilities: $app_total vulnerabilities found, $app_with_fixes with fixes</summary>" >> trivy-comment.md
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echo "" >> trivy-comment.md
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jq -r '
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[ .Results[]
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| select(.Class != "os-pkgs")
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| .Vulnerabilities[]?
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]
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| select(length > 0)
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| group_by(.PkgName)
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| sort_by(.[0].PkgName)
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| .[]
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| "#### 📦 Package: \([.[0].PkgName])\n"
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+ "| Severity | Vulnerability ID | Installed Version | Fixed Version |\n"
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+ "|-----------|------------------|------------------|----------------|\n"
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+ (map("| \(.Severity) | \(.VulnerabilityID) | \(.InstalledVersion) | \(.FixedVersion // "-") |") | join("\n"))
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+ "\n"
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' trivy-report.json >> trivy-comment.md
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echo "</details>" >> trivy-comment.md
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# Save content as output
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echo "content<<EOF" >> $GITHUB_OUTPUT
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cat trivy-comment.md >> $GITHUB_OUTPUT
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echo "EOF" >> $GITHUB_OUTPUT
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comment:
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runs-on: ubuntu-latest
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needs: [unit-tests, selenium-tests, trivy-scan]
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if: always()
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permissions:
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contents: read
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pull-requests: write
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steps:
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- name: Post PR comment
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uses: peter-evans/create-or-update-comment@v4
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with:
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issue-number: ${{ github.event.pull_request.number }}
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body: |
256+
### Test Results
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${{ needs.unit-tests.outputs.unittest-results }}
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${{ needs.selenium-tests.outputs.selenium-results }}
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### Vulnerability Scan Results
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${{ needs.trivy-scan.outputs.trivy-results }}
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

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