WIP: fix #3389 #1075
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # name: Qiita CI | |
| on: | |
| push: | |
| branches: [ dev ] | |
| pull_request: | |
| jobs: | |
| # derived from https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml | |
| main: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| include: | |
| - cover_package: "qiita_db" | |
| - cover_package: "qiita_pet qiita_core qiita_ware" | |
| services: | |
| postgres: | |
| # Docker Hub image | |
| image: postgres:13.4 | |
| env: | |
| POSTGRES_DB: postgres | |
| POSTGRES_USER: postgres | |
| POSTGRES_PASSWORD: postgres | |
| COVER_PACKAGE: ${{ matrix.cover_package }} | |
| # Set health checks to wait until postgres has started | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| ports: | |
| # based on https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml#L44-L72 | |
| - 5432/tcp | |
| steps: | |
| # Downloads a copy of the code in your repository before running CI tests | |
| - name: Check out repository code | |
| uses: actions/checkout@v2 | |
| - name: Setup for conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: '3.9' | |
| - name: Basic dependencies install | |
| env: | |
| COVER_PACKAGE: ${{ matrix.cover_package }} | |
| shell: bash -l {0} | |
| run: | | |
| echo "Testing: " $COVER_PACKAGE | |
| # pull out the port so we can modify the configuration file easily | |
| pgport=${{ job.services.postgres.ports[5432] }} | |
| sed -i "s/PORT = 5432/PORT = $pgport/" qiita_core/support_files/config_test.cfg | |
| # PGPASSWORD is read by pg_restore, which is called by the build_db process. | |
| export PGPASSWORD=postgres | |
| # Setting up main qiita conda environment | |
| conda config --add channels conda-forge | |
| conda deactivate | |
| conda create --quiet --yes -n qiita python=3.9 pip libgfortran numpy nginx cython redis | |
| conda env list | |
| conda activate qiita | |
| pip install -U pip | |
| pip install sphinx sphinx-bootstrap-theme nose-timer Click coverage | |
| # Configuring SSH | |
| cp /etc/ssh/sshd_config sshd_config | |
| echo "RSAAuthentication yes" > sshd_config | |
| echo "PubkeyAuthentication yes" > sshd_config | |
| echo "StrictModes no" > sshd_config | |
| sudo mv sshd_config /etc/ssh/sshd_config | |
| sudo systemctl restart ssh | |
| - name: Webdis install | |
| shell: bash -l {0} | |
| run: | | |
| sudo apt-get -y install libevent-dev | |
| git clone https://github.com/nicolasff/webdis | |
| cd webdis | |
| make | |
| - name: Main install | |
| shell: bash -l {0} | |
| 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 | |
| export REDBIOM_HOST="http://localhost:7379" | |
| pip install . --no-binary redbiom | |
| # 10.2022 | |
| # this is for redbiom / biom-format (so fine to delete in the future) | |
| pip install future | |
| pwd | |
| mkdir ~/.qiita_plugins | |
| - name: Install plugins | |
| shell: bash -l {0} | |
| run: | | |
| conda env create -n qtp-biom --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-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 | |
| - name: Starting services | |
| shell: bash -l {0} | |
| 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 | |
| export REDBIOM_HOST="http://localhost:7379" | |
| echo "1. Setting up redis" | |
| redis-server --daemonize yes --port 7777 | |
| redis-server --daemonize yes --port 6379 | |
| echo "2. Starting webdis" | |
| pushd webdis | |
| ./webdis & | |
| popd | |
| echo "3. Starting redbiom: " $REDBIOM_HOST | |
| curl -s http://localhost:7379/FLUSHALL > /dev/null | |
| redbiom --version | |
| redbiom admin scripts-writable | |
| redbiom admin create-context --name "qiita-test" --description "qiita-test context" | |
| redbiom admin load-sample-metadata --metadata `pwd`/qiita_db/support_files/test_data/templates/1_19700101-000000.txt | |
| redbiom admin load-sample-metadata-search --metadata `pwd`/qiita_db/support_files/test_data/templates/1_19700101-000000.txt | |
| redbiom admin load-sample-data --table `pwd`/qiita_db/support_files/test_data/processed_data/1_study_1001_closed_reference_otu_table.biom --context qiita-test --tag 4 | |
| redbiom admin load-sample-data --table `pwd`/qiita_db/support_files/test_data/processed_data/1_study_1001_closed_reference_otu_table-for_redbiom_tests.biom --context qiita-test --tag 5 | |
| echo "4. Setting up nginx" | |
| mkdir -p /usr/share/miniconda/envs/qiita/var/run/nginx/ | |
| nginx -c ${PWD}/qiita_pet/nginx_example.conf | |
| echo "5. Setting up qiita" | |
| conda activate qiita | |
| 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 -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 $QIITA_PID | |
| sleep 10 | |
| # due to qiita_db tests being more complex and taking longer than | |
| # the other tests we will only add some extra tests to the run that is | |
| # not testing qiita_db | |
| if [[ "$COVER_PACKAGE" != *"qiita_db"* ]]; then | |
| # 1. testing that we can add some "dummy" studies to the db via | |
| # CLI | |
| test_data_studies/commands.sh; | |
| # 2. making sure that all qiita cron jobs complete as expected | |
| all-qiita-cron-job; | |
| # 3. making sure than a production system has the expected rows | |
| # in all our tables; steps: a. drop test db, b. change $QIITA_CONFIG_FP | |
| # c. create new production system, c. count rows in the db. | |
| qiita-env drop; | |
| cp $QIITA_CONFIG_FP ${QIITA_CONFIG_FP}.bk | |
| sed 's/TEST_ENVIRONMENT = TRUE/TEST_ENVIRONMENT = FALSE/g' ${QIITA_CONFIG_FP}.bk > $QIITA_CONFIG_FP; | |
| qiita-env make --no-load-ontologies; | |
| export PGPASSWORD=postgres | |
| pgport=${{ job.services.postgres.ports[5432] }} | |
| row_counts=`psql -h localhost -U postgres -d qiita_test -p $pgport -c "SELECT SUM(c.reltuples) FROM pg_class c JOIN pg_namespace n on n.oid = c.relnamespace WHERE n.nspname = 'qiita' AND c.relkind = 'r' AND n.nspname NOT IN ('information_schema', 'pg_catalog');"` | |
| if [[ `echo $row_counts` != *" 0 "* ]]; then | |
| echo "***********"; | |
| echo "The number of rows in a production system is not what's expected:"; | |
| echo $row_counts; | |
| echo "***********"; | |
| exit 1 | |
| fi | |
| 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 |