From d3def54a12c38f8bdccebd9143694aa4cd4040af Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 23 Feb 2024 11:38:38 +0100 Subject: [PATCH] abusing github action to show that productive DB is not void of test entries --- .github/workflows/qiita-ci.yml | 112 +++------------------------------ 1 file changed, 10 insertions(+), 102 deletions(-) diff --git a/.github/workflows/qiita-ci.yml b/.github/workflows/qiita-ci.yml index 6c3b06be1..bbffc69f7 100644 --- a/.github/workflows/qiita-ci.yml +++ b/.github/workflows/qiita-ci.yml @@ -7,14 +7,14 @@ on: jobs: # derived from https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml - main: + nonclearDB: runs-on: ubuntu-latest strategy: matrix: include: - cover_package: "qiita_db" - - cover_package: "qiita_pet qiita_core qiita_ware" + # - cover_package: "qiita_pet qiita_core qiita_ware" services: postgres: @@ -57,6 +57,8 @@ jobs: # pull out the port so we can modify the configuration file easily pgport=${{ job.services.postgres.ports[5432] }} sed -i "s/PORT = 5432/PORT = $pgport/" qiita_core/support_files/config_test.cfg + # SMJ: set to productive mode! + sed -i "s/TEST_ENVIRONMENT = TRUE/TEST_ENVIRONMENT = FALSE/" qiita_core/support_files/config_test.cfg # PGPASSWORD is read by pg_restore, which is called by the build_db process. export PGPASSWORD=postgres @@ -101,25 +103,7 @@ jobs: pwd mkdir ~/.qiita_plugins - - name: Install plugins - shell: bash -l {0} - run: | - wget https://data.qiime2.org/distro/core/qiime2-2022.11-py38-linux-conda.yml - conda env create --quiet -n qtp-biom --file qiime2-2022.11-py38-linux-conda.yml - rm qiime2-2022.11-py38-linux-conda.yml - export QIITA_ROOTCA_CERT=`pwd`/qiita_core/support_files/ci_rootca.crt - export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg - export REDBIOM_HOST="http://localhost:7379" - conda activate qtp-biom - pip install -U pip - pip install https://github.com/qiita-spots/qiita_client/archive/master.zip - pip install https://github.com/qiita-spots/qtp-biom/archive/master.zip - - # if QIITA_ROOTCA_CERT is appended to certifi's cacert.pem file, - # then --server-cert does not need to be specified to any plugin, - # including configure_biom. - # echo `python -c "import certifi;print(certifi.where())"` - configure_biom --env-script "source /home/runner/.profile; conda activate qtp-biom" --server-cert $QIITA_ROOTCA_CERT + # SMJ: don't install any plugins! ~/.qiita_plugins directory should remain empty - name: Starting services shell: bash -l {0} @@ -156,84 +140,8 @@ jobs: conda activate qiita # adapt environment_script for private qiita plugins from travis to github actions. sed 's#export PATH="/home/travis/miniconda3/bin:$PATH"; source #source /home/runner/.profile; conda #' -i qiita_db/support_files/patches/54.sql - qiita-env make --no-load-ontologies - qiita-test-install - qiita plugins update - - echo "6. Starting supervisord => multiple qiita instances" - supervisord -c ${PWD}/qiita_pet/supervisor_example.conf - sleep 10 - cat /tmp/supervisord.log - - echo "7. Starting plugins" - conda deactivate - conda activate qtp-biom - export QIITA_CLIENT_DEBUG_LEVEL=DEBUG - start_biom https://localhost:8383 register ignored - conda deactivate - - echo "8. Setting up SSH" - ssh-keygen -t rsa -b 4096 -N '' -f $PWD/qiita_ware/test/test_data/test_key - mkdir ~/.ssh/ - cp $PWD/qiita_ware/test/test_data/test_key* ~/.ssh/ - cat ~/.ssh/test_key.pub > ~/.ssh/authorized_keys - chmod 600 $PWD/qiita_ware/test/test_data/test_key* - chmod 600 ~/.ssh/* - chmod 700 ~/.ssh/ - echo "Connecting as $USER@localhost" - # this line (and the -o StrictHostKeyChecking=no) is so the server - # is added to the list of known servers - scp -o StrictHostKeyChecking=no -i $PWD/qiita_ware/test/test_data/test_key $USER@localhost:/home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key /home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key_copy_1 - - - name: Main tests - shell: bash -l {0} - env: - COVER_PACKAGE: ${{ matrix.cover_package }} - run: | - conda activate qiita - export QIITA_ROOTCA_CERT=`pwd`/qiita_core/support_files/ci_rootca.crt - export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg - # for testing we only need to have this set, not actually exist - export QIITA_JOB_SCHEDULER_EPILOGUE=`/path/to/epilogue/file` - export REDBIOM_HOST="http://localhost:7379" - - nosetests $COVER_PACKAGE --with-doctest --with-coverage --with-timer -v --cover-package=${COVER_PACKAGE// / --cover-package=} -e 'test_submit_EBI_parse_EBI_reply_failure' -e 'test_full_submission' - - # killing the qiita server to run the next commands - QIITA_PID=`cat /tmp/supervisord.pid` - kill $QIITA_PID - sleep 10 - if [[ "$COVER_PACKAGE" != *"qiita_db"* ]]; then test_data_studies/commands.sh; all-qiita-cron-job; fi - - - name: Submit coveralls - uses: AndreMiras/coveralls-python-action@develop - with: - github-token: ${{ secrets.github_token }} - flag-name: "${{ matrix.cover_package }}" - parallel: true - - coveralls_finish: - needs: main - runs-on: ubuntu-latest - steps: - - name: Coveralls Finished - uses: AndreMiras/coveralls-python-action@develop - with: - github-token: ${{ secrets.github_token }} - parallel-finished: true - - lint: - runs-on: ubuntu-latest - steps: - - name: flake8 - uses: actions/setup-python@v2 - with: - python-version: '3.9' - - name: install dependencies - run: python -m pip install --upgrade pip - - name: Check out repository code - uses: actions/checkout@v2 - - name: lint - run: | - pip install -q flake8 - flake8 qiita_* setup.py scripts/qiita* notebooks/*/*.py + qiita-env make #--no-load-ontologies + + PGPASSWORD=postgres psql -U postgres --host=localhost --port=32768 -d qiita_test -c "SELECT * FROM qiita.software;" + PGPASSWORD=postgres psql -U postgres --host=localhost --port=32768 -d qiita_test -c "SELECT * FROM qiita.default_workflow;" + \ No newline at end of file