unittest.yaml

name: unittest
on: [push]
jobs:
  run-unittests:
    permissions:
      id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
        with:
          ref: ${{ github.head_ref }}
      - uses: actions/setup-python@v4
        name: setup python
        with:
          python-version: 3.11
      - name: Install Dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -r requirements.txt
          pip install -r requirements.dev.txt
      - name: AWS credentials configuration
        uses: aws-actions/configure-aws-credentials@v2
        with:
          role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}}
          role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-unittest
          aws-region: us-east-1
      - name: Amazon ECR login
        id: login-ecr
        uses: aws-actions/amazon-ecr-login@v1
      - name: run unit tests
        env:
          ENV_STATE: test
          HOST: 0.0.0.0
          PSQL_USERNAME: postgres
          PSQL_PASSWORD: postgres
          PSQL_HOST: localhost
          PSQL_PORT: 5432
          PSQL_DATABASE: literature-test
          PYTHONPATH: agr_literature_service/lit_processing/
          OKTA_DOMAIN: 'dev-30456587.okta.com/oauth2/default'
          OKTA_API_AUDIENCE: 'api://default'
          RESOURCE_DESCRIPTOR_URL: 'https://raw.githubusercontent.com/alliance-genome/agr_schemas/master/resourceDescriptors.yaml'
          ELASTICSEARCH_HOST: localhost
          ELASTICSEARCH_PORT: 9200
          ELASTICSEARCH_INDEX: references_index
          XML_PATH: ${GITHUB_WORKSPACE}/tests/tmp/
          OKTA_CLIENT_ID: ${{ secrets.okta_client_id }}
          OKTA_CLIENT_SECRET: ${{ secrets.okta_client_secret }}
        run: |
          docker compose --env-file .env.test down -v
          docker compose --env-file .env.test up -d postgres
          sleep 5
          docker compose --env-file .env.test up -d elasticsearch
          sleep 10
          pytest -m "not webtest"
          docker compose --env-file .env.test down -v