qiita-ci.yml

# 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: |
          https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml
          conda env create --quiet -n qtp-biom --file qiime2-amplicon-2024.5-py39-linux-conda.yml
          rm 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 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