YDA-5829 troubleshooting tool for published data packages #767
Workflow file for this run
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| name: Run integration and API tests | |
| on: | |
| push: | |
| branches: | |
| - development | |
| - release-1.9 | |
| - "**-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-22.04 | |
| if: | | |
| ${{ ! contains(github.event.head_commit.message, '#noapitests') && | |
| ( github.event_name == 'push' || | |
| github.event.pull_request.head.repo.full_name == github.event.pull_request.base.repo.full_name | |
| ) | |
| }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.8 | |
| - name: Extract branch name | |
| shell: bash | |
| run: echo "branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT | |
| id: extract_branch | |
| # For release branches that have a Docker setup, we use the Docker setup version of that release. | |
| # For other branches, we use the Docker setup of the development branch. | |
| - name: Determine Yoda repository branch | |
| run: | | |
| if [ "${{ steps.extract_branch.outputs.branch }}" = "release-1.9" ]; then | |
| echo "branch=release-1.9" >> $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: | | |
| until $(curl -k --output /dev/null --silent --head --fail https://portal.yoda:8443 ); 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' | |
| - name: Pull and install latest version of ruleset | |
| shell: bash | |
| run: | | |
| cd yoda/docker/compose | |
| docker exec provider.yoda sh -c 'set -x ; cd /etc/irods/yoda-ruleset && sudo chown irods:irods -R /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 python -m pip --no-cache-dir install --user -r /etc/irods/yoda-ruleset/requirements.txt && sudo -u irods make && sudo -u irods make install" | |
| docker exec provider.yoda sh -c "set -x ; sudo -u irods /var/lib/irods/irodsctl restart" | |
| - 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 ${{ steps.extract_branch.outputs.branch }} || git checkout development' | |
| docker exec portal.yoda sh -c 'set -x ; cd /var/www/yoda && git status' | |
| docker exec portal.yoda sh -c 'set -x ; touch /var/www/yoda/*.wsgi' | |
| - name: Run integration tests | |
| shell: bash | |
| run: | | |
| cd yoda/docker/compose | |
| docker exec provider.yoda sh -c 'set -x ; cd /etc/irods/yoda-ruleset && sudo -u irods /usr/bin/irule -r irods_rule_engine_plugin-python-instance -F tools/run-integration-tests.r' > test-results.txt | |
| echo "Integration test results: " | |
| echo | |
| cat test-results.txt | |
| echo | |
| echo "Statistics:" | |
| echo | |
| echo "$(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 --intake --datarequest --deposit -o cache_dir=mycache --environment environments/docker.json | |
| cat ../copytovault.log | |
| cat ../publication.log | |
| - name: Output rodsLogs | |
| if: failure() | |
| run: | | |
| docker exec provider.yoda sh -c 'set -x ; cat /var/lib/irods/log/rodsLog*' | |
| # 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 |