candig-testing.yml

name: Test-CanDIG-build
run-name: Build Validation
on:
  push:
    branches: [develop]
  pull_request:
  workflow_dispatch:
    inputs:
      module:
        type: string
jobs:
  Build-CanDIG:
    runs-on: [ubuntu-latest]
    defaults:
      run:
       shell: bash -l {0}
    steps:
      - name: Install conda
        uses: conda-incubator/setup-miniconda@v3
        with:
          miniconda-version: "latest"
          channels: conda-forge, defaults
          use-only-tar-bz2: true
          auto-update-conda: true
          auto-activate-base: true
      - name: Check out repository code
        uses: actions/checkout@v4
      - name: Setup environment file
        run: |
            cp etc/env/example.env example.env
            sed "s@CONDA_INSTALL=.*@CONDA_INSTALL=$CONDA@" example.env > .env
            sed -i "s@KEEP_TEST_DATA=false@KEEP_TEST_DATA=true@" .env
      - name: Display environment file
        run: cat ".env"
      - name: Add CanDIG local domain redirection to hosts
        run: echo "::1 candig.docker.internal" | sudo tee -a /etc/hosts
      - name: Install submodules
        run: |
             git submodule update --init --recursive
             make mkdir
      - name: Restore Conda environment cache
        id: cache-conda
        uses: actions/cache@v4
        with:
          path: ${{ env.CONDA }}
          key: ${{ runner.os }}-conda-${{ hashFiles('etc/venv/requirements.txt') }}
      - name: Install CanDIG conda environment
        if: ${{ steps.cache-conda.outputs.cache-hit != 'true' }}
        id: install-conda
        run: |
              make init-conda
      - name: Save Conda cache
        uses: actions/cache/save@v4
        if: steps.install-conda.outcome == 'success'
        with:
          path: ${{ env.CONDA }}
          key: ${{ runner.os }}-conda-${{ hashFiles('etc/venv/requirements.txt') }}
      - name: Build stack
        run: |
              conda activate candig
              (yes || true) | make build-all
      - name: Integration testing
        run: |
              conda activate candig
              export CANDIG_DEBUG_MODE=1
              make test-integration
      - name: Save docker container logs
        if: always()
        run: ./print_logs.sh > tmp/container_logs.txt 2>&1
      - name: Save any intermediate files in containers
        if: always()
        run: |
              mkdir tmp/ingest
              docker cp candigv2_candig-ingest_1:/home/candig/tmp tmp/ingest 2>&1
              mkdir tmp/index
              docker cp candigv2_htsget_1:/home/candig/tmp tmp/index 2>&1
      - name: Save vault audit logs
        if: always()
        run: docker cp candigv2_vault-runner_1:/vault/vault-audit.log tmp/vault_audit.log 2>&1
      - name: Save container and error logs as artifact
        if: always()
        uses: actions/upload-artifact@v4
        with:
          name: Post-build error log
          path: |
                tmp/progress.txt
                tmp/container_logs.txt
                tmp/vault_audit.log
                tmp/ingest
                tmp/index