api-and-integration-tests.yml

name: Run integration and API tests

on:
  push:
    branches:
    - development
    - 'release-[0-9]+.[0-9]+'
    - "**-atr"
    # We can force an integration/API test run without opening a PR by pushing to a branch name that ends with "-atr"
  pull_request:

jobs:
  build:
    runs-on: ubuntu-24.04
    if: |
      ${{ ! contains(github.event.head_commit.message, '#noapitests') &&
            ( github.event_name == 'push' ||
              github.event.pull_request.head.repo.full_name == github.event.pull_request.base.repo.full_name
            )
       }}
    steps:
    - uses: actions/checkout@v6

    - name: Set up Python
      uses: actions/setup-python@v6
      with:
        python-version: 3.9

    - name: Extract branch name
      shell: bash
      run: echo "branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
      id: extract_branch

    # For release branches, we use the Docker setup version of that release.
    # For other branches, we use the Docker setup of the development branch.
    - name: Determine Yoda repository branch
      shell: bash
      run: |
        if [[ "${{ steps.extract_branch.outputs.branch }}" =~ ^"release-" ]]; then
          echo "branch=${{ steps.extract_branch.outputs.branch }}" >> $GITHUB_OUTPUT
        else
          echo "branch=development" >> $GITHUB_OUTPUT
        fi
      id: yoda_repo_branch

    - name: Install API test dependencies
      run: |
        pip3 install --user -r tests/requirements.txt
        sudo apt install -y docker-compose

    - name: Clone Yoda repo for Docker Setup
      run: |
        git clone -b "${{ steps.yoda_repo_branch.outputs.branch }}" --single-branch https://github.com/UtrechtUniversity/yoda.git

    - name: Prepare hosts file for API tests
      run: |
        sudo echo "127.0.0.1 portal.yoda eus.yoda data.yoda public.yoda" | sudo tee -a /etc/hosts

    - name: Start Dockerized Yoda
      run: |
        cd yoda/docker/compose
        docker-compose pull
        ../up.sh -d

    - name: Wait until Dockerized setup is ready
      shell: bash
      run: |
        echo "Waiting for portal to be available ..."
        until $(curl -k --output /dev/null --silent --head --fail https://portal.yoda:8443 ); do printf '.' ; sleep 1; done
        echo "Waiting for EUS to be available ..."
        until $(curl -k --output /dev/null --silent --head --fail https://eus.yoda:8444 ); do printf '.' ; sleep 1; done
        docker exec provider.yoda sh -c 'while ! pgrep irodsServer > /dev/null  ; do echo Waiting for iRODS to start ...  ; sleep 1; done'

    # To diagnose failures
    - name: Docker diagnostics
      if: always()
      run: |
        cd yoda/docker/compose/
        echo "=== docker ps ==="
        docker ps -a

        echo "=== compose logs ==="
        docker compose logs --no-color || true

        echo "=== memory ==="
        free -h || true

        echo "=== disk ==="
        df -h || true

        echo "=== inspect ==="
        for c in $(docker ps -aq); do
          docker inspect $c \
            --format='{{.Name}} Exit={{.State.ExitCode}} OOM={{.State.OOMKilled}}'
        done

    - name: Pull and install latest version of ruleset
      shell: bash
      run: |
        cd yoda/docker/compose
        docker exec provider.yoda sh -c 'set -x ; find /etc/irods/yoda-ruleset -print0 2>/dev/null | sudo xargs -0 -r -I{} bash -c "chown -v irods:irods \"{}\" || true"'
        docker exec provider.yoda sh -c 'set -x ; cd /etc/irods/yoda-ruleset && sudo -u irods git config remote.origin.fetch "+refs/heads/*:refs/remotes/origin/*" && sudo -u irods git pull && sudo -u irods git status'
        docker exec provider.yoda sh -c "set -x ; cd /etc/irods/yoda-ruleset && sudo -u irods git checkout ${{ steps.extract_branch.outputs.branch }} && sudo -u irods python3 -m pip --no-cache-dir install --user --break-system-packages -r /etc/irods/yoda-ruleset/requirements.txt && sudo -u irods make && sudo -u irods make install"
        docker exec provider.yoda sh -c 'kill -HUP $(cat /var/run/irods/irods-server.pid)'

    - name: Enable code coverage measurements for ruleset
      shell: bash
      run: |
        cd yoda/docker/compose
        docker exec provider.yoda sh -c "set -x; sudo perl -pi -e \"s/^(measure_coverage\\s*=\\s*)'false'/\\1'true'/\" /etc/irods/yoda-ruleset/rules_uu.cfg"

    # We also run the unit tests in this workflow so that code covered by the unit tests is taken
    # into account for the total test coverage.
    - name: Run unit tests
      run: |
        cd yoda/docker/compose
        docker exec provider.yoda sudo -u irods bash -c 'set -x; cd /etc/irods/yoda-ruleset/unit-tests; export PYTHONPATH=$(cd ../util ; pwd):$PYTHONPATH; python3 -m coverage run --source=..,../util --omit=test_*.py,unit_tests.py --data-file /tmp/coverage.dat.unittests -m unittest unit_tests'

    - name: Pull and install latest version of portal
      shell: bash
      run: |
        cd yoda/docker/compose
        docker exec portal.yoda sh -c 'set -x ; cd /var/www/yoda && git config remote.origin.fetch  "+refs/heads/*:refs/remotes/origin/*" && git pull'
        docker exec portal.yoda sh -c 'set -x ; cd /var/www/yoda && git checkout ${{ steps.extract_branch.outputs.branch }} || git checkout development'
        docker exec portal.yoda sh -c 'set -x ; cd /var/www/yoda && . venv/bin/activate && venv/bin/pip3 install -r requirements.txt'
        docker exec portal.yoda sh -c 'set -x ; cd /var/www/yoda && git status'
        docker exec portal.yoda sh -c 'set -x ; touch /var/www/yoda/*.wsgi'

    - name: Wait until iRODS is ready for integration tests
      shell: bash
      run: |
        cd yoda/docker/compose
        echo "Waiting for iRODS to be available for integration tests ..."
        docker exec provider.yoda /bin/bash -c "until nc -vz provider.yoda 1247 >& /dev/null ; do print '.'; sleep 1; done"
        echo "iRODS is ready for integration tests."

    - name: Run integration tests
      shell: bash
      run: |
        cd yoda/docker/compose
        docker exec provider.yoda sh -c 'set -x ; cd /etc/irods/yoda-ruleset && sudo -u irods /usr/bin/irule -r irods_rule_engine_plugin-python-instance -F tools/run-integration-tests.r' > test-results.txt
        echo "Integration test results: "
        echo
        cat test-results.txt
        echo
        echo "Statistics:"
        echo
        echo "$(grep -c VERDICT_OK test-results.txt) test(s) OK"
        echo "$(grep -c VERDICT_FAILED test-results.txt) test(s) failed with unexpected return value"
        echo "$(grep -c VERDICT_EXCEPTION test-results.txt) test(s) failed with exception"
        echo "$(grep -c VERDICT_ test-results.txt) test(s) in total"
        echo
        echo "Overall result: "
        if grep -E "VERDICT_EXCEPTION|VERDICT_FAILED" test-results.txt> /dev/null ; then printf "Test failures detected"; exit 1; fi
        if grep -E "VERDICT_" test-results.txt > /dev/null ; then printf "Tests succeeded"; else printf "Failure to run tests"; exit 1; fi

    - name: Run API tests
      shell: bash
      run: |
        cd tests
        nohup bash -c 'while true ; do sleep 5 ;  ../yoda/docker/run-cronjob.sh copytovault >> ../copytovault.log 2>&1 ; ../yoda/docker/run-cronjob.sh publication >> ../publication.log 2>&1 ; done' &
        test -d mycache || mkdir -p mycache
        python3 -m pytest --skip-ui --deposit --datarequest -o cache_dir=mycache --environment environments/docker.json
        cat ../copytovault.log
        cat ../publication.log

    - name: Print test coverage report
      shell: bash
      run: |
        cd yoda/docker/compose
        docker exec provider.yoda sh -c 'cd /tmp; sudo -u irods python3 -m coverage combine -q /tmp/coverage.dat.*'
        docker exec provider.yoda sh -c 'cd /tmp; sudo -u irods python3 -m coverage report'

    # This is useful for diagnosing/confirming OOM issues
    - name: Docker diagnostics
      if: failure()
      run: |
        cd yoda/docker/compose/
        echo "=== docker ps ==="
        docker ps -a

        echo "=== compose logs ==="
        docker compose logs --no-color || true

        echo "=== memory ==="
        free -h || true

        echo "=== disk ==="
        df -h || true

        echo "=== inspect ==="
        for c in $(docker ps -aq); do
          docker inspect $c \
            --format='{{.Name}} Exit={{.State.ExitCode}} OOM={{.State.OOMKilled}}'
        done

    - name: Output rodsLogs
      if: failure()
      run: |
        docker exec provider.yoda sh -c 'cat /var/lib/irods-log/rodsLog*'

    - name: Output portal web server logs
      if: failure()
      run: |
        docker exec portal.yoda sh -c 'set -x ; for log in error.log portal_access.log ; do echo "${log}:" ; cat "/var/log/apache2/$log" ; echo; done'

    - name: Output EUS server logs
      if: failure()
      run: |
        docker exec eus.yoda sh -c 'set -x ; for log in error.log access.log ; do echo "${log}:" ; cat "/var/log/apache2/$log" ; echo; done'


# Uncomment section below when needed for debugging.
#
#    - name: Setup tmate session for debugging
#      uses: mxschmitt/action-tmate@v3
#      if: ${{ failure() }}
#      with:
#        limit-access-to-actor: true