integration test #675
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| name: integration test | |
| concurrency: | |
| group: ${{ github.workflow }} | |
| cancel-in-progress: false | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| push_containers: | |
| type: boolean | |
| required: false | |
| default: true | |
| description: Build docker images and push them to the registry | |
| schedule: | |
| - cron: '33 2 * * *' | |
| jobs: | |
| # Build and create containers | |
| build: | |
| uses: ./.github/workflows/main-build.yml | |
| with: | |
| push_containers: ${{ github.event_name == 'schedule' || inputs.push_containers }} | |
| version: 'integration_build' | |
| target_tag: 'integration_build' | |
| deploy_branch: 'integration_build' | |
| secrets: inherit | |
| # Synchronize S3 Bucket and create cache for per-component runs | |
| sync_s3: | |
| env: | |
| s3_bucket: s3://openpipelines-data/ | |
| runs-on: ubuntu-latest | |
| outputs: | |
| cache_key: ${{ steps.cache.outputs.cache_key }} | |
| dest_paths: ${{ steps.cache.outputs.dest_paths }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: viash-io/viash-actions/project/sync-and-cache@v6 | |
| id: cache | |
| # phase 3 | |
| integration_test: | |
| runs-on: ubuntu-latest | |
| needs: [ build, sync_s3 ] | |
| if: "${{ needs.build.outputs.workflow_matrix != '[]' }}" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| component: ${{ fromJson(needs.build.outputs.workflow_matrix) }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' | |
| - uses: data-intuitive/reclaim-the-bytes@v2 | |
| - name: Keep symlinks as-is | |
| run: | | |
| git config --global core.symlinks true | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: 'integration_build' | |
| - uses: viash-io/viash-actions/setup@v6 | |
| - uses: nf-core/[email protected] | |
| # use cache | |
| - name: Cache resources data | |
| if: ${{ needs.sync_s3.outputs.cache_key != '' }} | |
| uses: actions/cache/restore@v4 | |
| timeout-minutes: 10 | |
| with: | |
| path: ${{ needs.sync_s3.outputs.dest_paths }} | |
| key: ${{ needs.sync_s3.outputs.cache_key }} | |
| fail-on-cache-miss: true | |
| - name: Remove unused test resources to save space | |
| shell: bash | |
| run: | | |
| readarray -t resources < <(viash config view --format json "${{ matrix.component.config }}" -c 'del(.dependencies)' | jq -r -c '(.build_info.config | capture("^(?<dir>.*\/)").dir) as $dir | .test_resources | map(select(.type == "file")) | map($dir + .path) | unique | .[]') | |
| to_not_remove=() | |
| for resource in "${resources[@]}"; do | |
| if [[ $resource == *"resources_test"* ]]; then | |
| relative_path=${resource#*resources_test/} | |
| relative_path_trailing_slash_removed=${relative_path%/} | |
| to_not_remove+=("-path" "./resources_test/$relative_path_trailing_slash_removed" "-prune" "-o") | |
| fi | |
| done | |
| # Remove last prune and -o | |
| if (( ${#errors[@]} )); then | |
| unset 'to_not_remove[${#to_not_remove[@]}-1]' | |
| unset 'to_not_remove[${#to_not_remove[@]}-1]' | |
| to_not_remove+=( "(" "${to_not_remove[@]}" ")" "-prune" "-o") | |
| fi | |
| echo "Not removing ${to_not_remove[@]}" | |
| find ./resources_test/ "${to_not_remove[@]}" -type f -exec rm {} + | |
| tree ./resources_test/ | |
| - name: Build test dependencies | |
| run: | | |
| readarray -t test_dependencies < <(viash ns list --format json "${{ matrix.component.config }}" | jq -r -c '(.[].info.test_dependencies // []) | flatten | .[] | (.namespace + "/" + .name)') | |
| for dependency in "${test_dependencies[@]}"; do | |
| echo $dependency | |
| viash ns build -q "$dependency" -c ".version := 'integration_build'" -c ".engines[.type == 'docker'].target_tag := 'integration_build'" --setup alwayspullelsebuild | |
| done | |
| - name: Remove docker builder cache | |
| run: | | |
| docker builder prune -a -f | |
| - name: Run integration test | |
| timeout-minutes: 120 | |
| run: | | |
| # todo: replace with viash test command | |
| export NXF_VER=22.04.5 | |
| nextflow run . \ | |
| -main-script "${{ matrix.component.main_script }}" \ | |
| -entry "${{ matrix.component.entry }}" \ | |
| -profile docker,mount_temp,no_publish \ | |
| -c src/workflows/utils/labels_ci.config \ | |
| -c src/workflows/utils/integration_tests.config |