tests-code.yml

name: Source Code Tests

on:
  push:
    branches:
      - main
      - main-release
  pull_request:
  merge_group:
  workflow_dispatch:

env:
  AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey_FOR_TESTS }}
  BiodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey_FOR_TESTS}}
  IEEEAPIKey: ${{ secrets.IEEEAPIKey_FOR_TESTS }}
  MedlineAPiKey: ${{ secrets.MedlineApiKey_FOR_TESTS }}
  OpenAlexApiKey: ${{ secrets.OpenAlexApiKey_FOR_TESTS }}
  SpringerNatureAPIKey: ${{ secrets.SPRINGERNATUREAPIKEY_FOR_TESTS }}
  GRADLE_OPTS: -Xmx4g
  JAVA_OPTS: -Xmx4g

concurrency:
  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}"
  cancel-in-progress: true

permissions:
  # required for publish.yml
  actions: write
  contents: read
  pull-requests: write

jobs:
  upload-pr-number:
    if: github.event_name == 'pull_request'
    runs-on: ubuntu-slim
    steps:
      - name: Create pr_number.txt
        run: echo "${{ github.event.number }}" > pr_number.txt
      - uses: actions/upload-artifact@v7
        with:
          name: pr_number
          path: pr_number.txt

  checkstyle:
    name: Checkstyle
    # too slow on ubuntu-slim
    runs-on: ubuntu-latest
    steps:
      - name: Checkout source
        uses: actions/checkout@v6
        with:
          submodules: 'true'
          show-progress: 'false'
      - uses: ./.github/actions/setup-gradle
      - name: Run checkstyle using gradle
        run: gradle checkstyleMain checkstyleTest checkstyleJmh

  dependencyscopes:
    name: Dependency Scopes
    # too slow on ubuntu-slim
    runs-on: ubuntu-latest
    steps:
      - name: Checkout source
        uses: actions/checkout@v6
        with:
          submodules: 'true'
          show-progress: 'false'
      - uses: ./.github/actions/setup-gradle
      - name: Run checkAllModuleInfo using gradle
        run: gradle checkAllModuleInfo

  openrewrite:
    name: OpenRewrite
    # too slow on ubuntu-slim
    runs-on: ubuntu-latest
    steps:
      - name: Checkout source
        uses: actions/checkout@v6
        with:
          submodules: 'true'
          show-progress: 'false'
      - uses: ./.github/actions/setup-gradle
      - name: Run OpenRewrite
        run: |
          gradle --no-configuration-cache :rewriteRun
      - name: Output diff
        if: failure()
        run: |
          cat /home/runner/work/jabref/jabref/build/reports/rewrite/rewrite.patch

  format:
    # ubuntu-slim doesn't offer docker
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v6
      - uses: leventeBajczi/intellij-idea-format@master
        with:
          file-mask: "*.java"
          settings-file: ".idea/codeStyles/Project.xml"
      - name: Undo JBang changes # IntelliJ issue: https://youtrack.jetbrains.com/issue/IDEA-https://youtrack.jetbrains.com/issue/IDEA-384956/Skip-formatting-of-shebang-headers/Skip-formatting-of-shebang-headers
        run: git checkout HEAD -- jablib-examples/jbang/*.java
      # job should fail in case there are changes
      - name: Check if any files changed
        run: git diff --exit-code

  format-javadoc:
    # too slow on ubuntu-slim
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v6
        with:
          path: 'jabref'
      - uses: actions/checkout@v6
        with:
          repository: 'rmuller/Convert2MarkdownJavadoc'
          path: 'Convert2MarkdownJavadoc'
      - name: Setup JDK
        uses: actions/setup-java@v5
        with:
          java-version: '24'
          distribution: 'corretto'
          check-latest: true
      - run: |
          cd Convert2MarkdownJavadoc
          java Convert2MarkdownJavadoc.java ../jabref
      - name: Check if any files changed
        run: |
          cd jabref
          git diff --exit-code

  modernizer:
    name: Modernizer
    # too slow on ubuntu-slim
    runs-on: ubuntu-latest
    steps:
      - name: Checkout source
        uses: actions/checkout@v6
        with:
          submodules: 'true'
          show-progress: 'false'
      - uses: ./.github/actions/setup-gradle
      - name: Run modernizer
        run: |
          # enable failing of this task if modernizer complains
          # sed -i "s/failOnViolations = false/failOnViolations = true/" build.gradle.kts
          gradle modernizer

  markdown:
    name: Markdown
    runs-on: ubuntu-slim
    steps:
      - name: Checkout source
        uses: actions/checkout@v6
        with:
          submodules: 'false'
          show-progress: 'false'
      - name: markdownlint-cli2-action
        uses: DavidAnson/markdownlint-cli2-action@v23
        with:
          globs: |
            *.md
            docs/**/*.md

  changelog:
    name: CHANGELOG.md
    # JBang needs a JDK
    runs-on: ubuntu-latest
    steps:
      - name: Checkout source
        uses: actions/checkout@v6
        with:
          submodules: 'false'
          show-progress: 'false'
      - name: Generate JBang cache key
        id: cache-key
        shell: bash
        run: |
          echo "cache_key=jbang-heylogs-$(date +%F)" >> $GITHUB_OUTPUT
      - name: Use cache
        uses: actions/cache/restore@v5
        with:
          path: ~/.jbang
          key: ${{ steps.cache-key.outputs.cache_key }}
          restore-keys:
            jbang-heylogs-
      - name: Setup JBang
        uses: jbangdev/setup-jbang@main
      - name: Lint CHANGELOG.md
        run: |
          # run heylogs verification
          jbang com.github.nbbrd.heylogs:heylogs-cli:0.16.1:bin check CHANGELOG.md | tee heylogs.txt || true

          # We have two acceptable errors
          if ! grep -q "1 problem" heylogs.txt; then
            {
              echo "heylogs<<EOF"
              cat heylogs.txt
              echo "EOF"
            } >> "$GITHUB_OUTPUT"
            exit 1
          fi

  changelog-unreleased-only:
    if: github.event_name == 'pull_request'
    name: CHANGELOG.md - only unreleased touched
    runs-on: ubuntu-slim
    steps:
      - name: Checkout source
        uses: actions/checkout@v6
        with:
          submodules: 'false'
          show-progress: 'false'
          fetch-depth: 0
      - name: Cache clparse jar
        id: cache-clparse
        uses: actions/cache/restore@v5
        with:
          path: /tmp/clparse
          key: clparse-0.9.1
      - name: unzip
        if: steps.cache-clparse.outputs.cache-hit != 'true'
        run: |
          cd /tmp
          curl -LO https://github.com/marcaddeo/clparse/releases/download/0.9.1/clparse-0.9.1-x86_64-unknown-linux-musl.tar.gz
          tar xzvf clparse-0.9.1-x86_64-unknown-linux-musl.tar.gz
      - name: Install clparse
        run: sudo mv /tmp/clparse /usr/local/bin/clparse
      - uses: awalsh128/cache-apt-pkgs-action@latest
        with:
          packages: jq
          version: 1.0
      - name: Check CHANGELOG.md diff
        run: |
          diff \
            <(git show origin/main:CHANGELOG.md | clparse --format=json --separator=– - | jq '.releases[] | select(.version != null)') \
            <(git show HEAD:CHANGELOG.md | clparse --format=json --separator=– - | jq '.releases[] | select(.version != null)')

  javadoc:
    name: JavaDoc
    # Sometimes takes longer than 15 minutes, therefore not ubuntu-slim
    runs-on: ubuntu-latest
    steps:
      - name: Checkout source
        uses: actions/checkout@v6
        with:
          submodules: 'true'
          show-progress: 'false'
      - uses: ./.github/actions/setup-gradle
      - run: gradle javadoc

  tests:
    name: "Unit tests – ${{ matrix.module }}"
    runs-on: ubuntu-latest
    strategy:
      matrix:
        module: [ jablib, jabkit, jabsrv, jabgui ]
    steps:
      - name: Checkout source
        uses: actions/checkout@v6
        with:
          submodules: 'true'
          show-progress: 'false'
      - uses: ./.github/actions/setup-gradle
      - name: Run ${{ matrix.module }} tests
        run: xvfb-run --auto-servernum gradle :${{ matrix.module }}:check -x checkstyleJmh -x checkstyleMain -x checkstyleTest -x modernizer
        env:
          CI: "true"
      - name: Prepare format failed test results
        if: failure()
        uses: awalsh128/cache-apt-pkgs-action@latest
        with:
          packages: xml-twig-tools xsltproc
          version: 1.0
      - name: Format failed test results
        if: failure()
        run: scripts/after-failure.sh

  tests-windows:
    name: "Unit tests (Windows)"
    if: >
      github.repository_owner == 'JabRef' &&
      (
        github.event_name == 'push' ||
        github.event_name == 'workflow_dispatch' ||
        (github.event_name == 'pull_request' && startsWith(github.event.pull_request.title, 'Update Gradle Wrapper'))
      )
    runs-on: windows-latest
    strategy:
      matrix:
        module: [ jablib ]
    steps:
      - name: Checkout source
        uses: actions/checkout@v6
        with:
          submodules: 'true'
          show-progress: 'false'
      - uses: ./.github/actions/setup-gradle
      - name: Run ${{ matrix.module }} tests
        run: gradle :${{ matrix.module }}:check -x checkstyleJmh -x checkstyleMain -x checkstyleTest -x modernizer
        env:
          CI: "true"

  tests-windows-file-based:
    name: "Unit tests (Windows) - file-based"
    runs-on: windows-latest
    steps:
      - name: Checkout source
        uses: actions/checkout@v6
        with:
          fetch-depth: 0
          submodules: 'true'
          show-progress: 'false'
      - name: Detect changed windows-related classes
        id: changed-windows-related-files
        uses: tj-actions/changed-files@v47
        with:
          files: |
            jablib/src/main/java/org/jabref/logic/citationstyle/CSLStyleUtils.java
            jablib/src/test/java/org/jabref/logic/citationstyle/CSLStyleUtilsTest.java
            jablib/src/main/java/org/jabref/logic/exporter/AcademicPagesExporter.java
            jablib/src/test/java/org/jabref/logic/exporter/AcademicPagesExporterTest.java
      - uses: ./.github/actions/setup-gradle
        if: steps.changed-windows-related-files.outputs.any_changed == 'true'
      - name: Run jablib tests
        if: steps.changed-windows-related-files.outputs.any_changed == 'true'
        run: gradle :jablib:check -x checkstyleJmh -x checkstyleMain -x checkstyleTest -x modernizer
        env:
          CI: "true"

  tests-jabkit-smoke:
    name: "JabKit Smoke Test"
    runs-on: ubuntu-slim
    steps:
      - name: Checkout source
        uses: actions/checkout@v6
        with:
          submodules: 'true'
          show-progress: 'false'
      - uses: ./.github/actions/setup-gradle
      - run: gradle :jabkit:runJabKitPortableSmokeTest

  databasetests:
    if: (github.repository_owner == 'JabRef')
    name: Database tests
    runs-on: ubuntu-latest
    services:
      postgres:
        image: postgres:13-alpine
        env:
          POSTGRES_USER: postgres
          POSTGRES_PASSWORD: postgres
          POSTGRES_DB: postgres
        ports:
          - 5432:5432
        # needed because the postgres container does not provide a healthcheck
        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
    steps:
      - name: Shutdown Ubuntu MySQL
        run: sudo service mysql stop # Shutdown the Default MySQL to save memory, "sudo" is necessary, please do not remove it
      - name: Checkout source
        uses: actions/checkout@v6
        with:
          submodules: 'true'
          show-progress: 'false'
      - uses: ./.github/actions/setup-gradle
      - name: Run tests on PostgreSQL
        run: gradle :jablib:databaseTest --rerun-tasks
        env:
          CI: "true"
          DBMS: "postgresql"

  publish:
    if: github.ref == 'refs/heads/main'
    uses: ./.github/workflows/publish.yml
    secrets:
      KOPPOR_SIGNING_SECRETKEYRINGFILE_BASE64: ${{ secrets.KOPPOR_SIGNING_SECRETKEYRINGFILE_BASE64 }}
      KOPPOR_SIGNING_KEYID: ${{ secrets.KOPPOR_SIGNING_KEYID }}
      KOPPOR_SIGNING_PASSWORD: ${{ secrets.KOPPOR_SIGNING_PASSWORD }}
      KOPPOR_MAVENCENTRALUSERNAME: ${{ secrets.KOPPOR_MAVENCENTRALUSERNAME }}
      KOPPOR_MAVENCENTRALPASSWORD: ${{ secrets.KOPPOR_MAVENCENTRALPASSWORD }}

  jbang-main:
    name: JBang (main)
    runs-on: ubuntu-slim
    needs: publish
    if: github.ref == 'refs/heads/main'
    steps:
      - name: Checkout source
        uses: actions/checkout@v6
        with:
          fetch-depth: 0
          submodules: 'false'
          show-progress: 'false'
      - name: Detect changed jablib classes
        id: changed-jablib-files
        uses: tj-actions/changed-files@v47
        with:
          files: |
            .jbang/*.java
            jablib/src/main/java/**/*.java
            jablib-examples/jbang/**/*.java
          files_ignore: |
            jablib/src/main/java/**/*-*.java

      - uses: ./.github/actions/setup-gradle
        if: steps.changed-jablib-files.outputs.any_changed != 'true'
      - name: Setup JDK
        if: steps.changed-jablib-files.outputs.any_changed != 'true'
        uses: actions/setup-java@v5
        with:
          java-version: '25'
          distribution: 'corretto'
          check-latest: true

      # Build all JBang scripts
      - run: |
          for f in .jbang/*.java; do
            echo "Building $f..."
            jbang build --fresh "$f"
          done
        if: steps.changed-jablib-files.outputs.any_changed != 'true'
      - run: |
          for f in jablib-examples/jbang/*.java; do
            echo "Building $f..."
            jbang build --fresh "$f"
          done
        if: steps.changed-jablib-files.outputs.any_changed != 'true'

      # *Launcher.java should support "--help"
      - run: jbang run .jbang/JabKitLauncher.java --help
        if: steps.changed-jablib-files.outputs.any_changed != 'true'
      - run: jbang run .jbang/JabLsLauncher.java --help
        if: steps.changed-jablib-files.outputs.any_changed != 'true'
      - run: jbang run .jbang/JabSrvLauncher.java --help
        if: steps.changed-jablib-files.outputs.any_changed != 'true'

  jbang-pr:
    name: JBang (PR)
    runs-on: ubuntu-slim
    # does not need publish, because the JBang scripts are modified
    if: github.ref != 'refs/heads/main'
    strategy:
      fail-fast: false
      matrix:
        script: [ .jbang/JabKitLauncher.java, .jbang/JabLsLauncher.java, .jbang/JabSrvLauncher.java, jablib-examples/jbang/doi_to_bibtex.java, jablib-examples/jbang/ieee_pdf_references_to_bibtex.java ]
    steps:
      - name: Checkout source
        uses: actions/checkout@v6
        with:
          submodules: 'false'
          show-progress: 'false'
      - name: Detect changed jablib classes
        id: changed-jablib-files
        uses: tj-actions/changed-files@v47
        with:
          files: |
            .jbang/*.java
            jabkit/src/main/java/**/*.java
            jablib/src/main/java/**/*.java
            jablib-examples/jbang/**/*.java
          files_ignore: |
            jablib/src/main/java/**/*-*.java
      - uses: ./.github/actions/setup-gradle
      - name: Setup JDK
        uses: actions/setup-java@v5
        with:
          java-version: '25'
          distribution: 'corretto'
          check-latest: true
      - name: Modify ${{ matrix.script }} to include changed classes
        shell: bash
        # We always run, because changes in jabls, jabsrv also could cause JBang to fail
        run: |
          # We modify the JBang scripts directly to avoid issues with relative paths
          for f in ${{ steps.changed-jablib-files.outputs.all_changed_files }}; do
            case "$f" in
              .jbang/*)
                # skip scripts
                continue
                ;;
              jablib-examples/*)
                # skip scripts
                continue
                ;;
              jabkit/*)
                # only JabKit needs its modified sources if jabkit was modified
                if [ "${{ matrix.script }}" != ".jbang/JabKitLauncher.java" ]; then
                  continue
                fi
                ;;
            esac
            if [[ "${{ matrix.script }}" == .jbang/* ]]; then
              echo "//SOURCES ../$f" >> "${{ matrix.script }}"
            else
              echo "//SOURCES ../../$f" >> "${{ matrix.script }}"
            fi
          done
      - run: cat ${{ matrix.script }}
      - run: jbang build "${{ matrix.script }}"
        shell: bash
      - run: jbang "${{ matrix.script }}" --help
        if: ${{ contains(matrix.script, 'Launcher.java') }}
        shell: bash

  maven-examples:
    name: Maven examples
    runs-on: ubuntu-latest
    needs: publish
    if: github.ref == 'refs/heads/main'
    strategy:
      fail-fast: false
      matrix:
        project: [ jablib-examples/maven3/doi-to-bibtex ]
    steps:
      - name: Checkout source
        uses: actions/checkout@v6
        with:
          submodules: 'false'
          show-progress: 'false'
      - name: Set up JDK
        uses: actions/setup-java@v5
        with:
          java-version: 25
          distribution: 'corretto'
          cache: maven
          check-latest: true
      - run: |
          cd ${{ matrix.project }}
          mvn --batch-mode --update-snapshots verify
        shell: bash

  codecoverage:
    if: false
    name: Code coverage
    runs-on: ubuntu-slim
    services:
      postgres:
        image: postgres:10.8
        env:
          POSTGRES_USER: postgres
          POSTGRES_PASSWORD: postgres
          POSTGRES_DB: postgres
        ports:
          - 5432:5432
        # needed because the postgres container does not provide a healthcheck
        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
    steps:
      - name: Check secrets presence
        id: checksecrets
        shell: bash
        run: |
          if [ "$CODECOV_TOKEN" == "" ]; then
            echo "secretspresent=NO" >> $GITHUB_OUTPUT
            echo "❌ Secret CODECOV_TOKEN not present"
          else
            echo "secretspresent=YES" >> $GITHUB_OUTPUT
            echo "✔️ Secret CODECOV_TOKEN present"
          fi
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
      - name: Checkout source
        uses: actions/checkout@v6
        with:
          submodules: 'true'
          show-progress: 'false'
      - uses: ./.github/actions/setup-gradle
      - name: Update test coverage metrics
        if: (github.ref == 'refs/heads/main') && (steps.checksecrets.outputs.secretspresent == 'YES')
        run: xvfb-run --auto-servernum gradle jacocoTestReport
        env:
          CI: "true"
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
          DBMS: "postgresql"
      - uses: codecov/codecov-action@v6
        if: (github.ref == 'refs/heads/main') && (steps.checksecrets.outputs.secretspresent == 'YES')
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
      - name: Upload Codacy report
        if: (github.ref == 'refs/heads/main') && (steps.checksecrets.outputs.secretspresent == 'YES')
        run: bash <(curl -Ls https://coverage.codacy.com/get.sh)
        env:
          CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}

  requirements_coverage:
    name: "Validate requirement coverage"
    runs-on: ubuntu-slim
    steps:
      - uses: actions/checkout@v6
        with:
          show-progress: 'false'
      - uses: ./.github/actions/setup-gradle
      - run: gradle traceRequirements
      - if: always()
        run: cat build/reports/tracing.txt

  # This is https://github.com/marketplace/actions/gradle-wrapper-validation
  # It ensures that the jar file is from gradle and not by a strange third party.
  gradlevalidation:
    name: "Validate Gradle Wrapper"
    runs-on: ubuntu-slim
    steps:
      - uses: actions/checkout@v6
        with:
          show-progress: 'false'
      - uses: gradle/actions/wrapper-validation@v5