adding NCBI datasets version 15.11.0 #689
Workflow file for this run
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| ##### --------------------------------------------------------------------------- ##### | |
| ##### This workflow looks for new dockefiles and builds them to the test target. ##### | |
| ##### This in intended to start on a pull request (PR) ##### | |
| ##### Ana06 is being used instead of jitterbit because of the filter option ##### | |
| ##### --------------------------------------------------------------------------- ##### | |
| name: Test New Dockerfiles | |
| on: pull_request | |
| jobs: | |
| find_new_dockerfiles: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| json: ${{ steps.files.outputs.added_modified }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - id: files | |
| uses: Ana06/[email protected] | |
| with: | |
| format: 'json' | |
| filter: 'Dockerfile' | |
| - run: "echo ${{ steps.files.outputs.all }}" | |
| build_to_test: | |
| needs: find_new_dockerfiles | |
| if: needs.find_new_dockerfiles.outputs.json != '[]' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| added_modified: ${{ fromJson(needs.find_new_dockerfiles.outputs.json) }} | |
| steps: | |
| - name: parse file path | |
| id: parse | |
| run: | | |
| tool=$(echo "${{ matrix.added_modified }}" | cut -f 1 -d "/" ) | |
| version=$(echo "${{ matrix.added_modified }}" | cut -f 2 -d "/" ) | |
| echo "tool=$tool" >> $GITHUB_OUTPUT | |
| echo "version=$version" >> $GITHUB_OUTPUT | |
| ##### --------------------------------------------------------------------------- ##### | |
| ##### Workflows still cannot be run in parrallel as of 2022-12-01 ##### | |
| ##### --------------------------------------------------------------------------- ##### | |
| # - name: test files | |
| # uses: ./.github/workflows/build-to-test.yml | |
| # with: | |
| # path_to_context: "./${{ steps.parse.outputs.tool }}/${{ steps.parse.outputs.version }}" | |
| # cache: ${{ steps.parse.outputs.tool }} | |
| ##### --------------------------------------------------------------------------- ##### | |
| ##### The steps of ./.github/workflows/build-to-test.yml are copied here. ##### | |
| ##### --------------------------------------------------------------------------- ##### | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Layer check | |
| run: | | |
| #checking layers | |
| warning='' | |
| app_layer=$(grep FROM ./${{ steps.parse.outputs.tool }}/${{ steps.parse.outputs.version }}/Dockerfile | grep "as app") | |
| tst_layer=$(grep FROM ./${{ steps.parse.outputs.tool }}/${{ steps.parse.outputs.version }}/Dockerfile | grep "as test") | |
| if [ -z "$app_layer" ] ; then echo "FATAL : app layer is missing" ; warning='warning' ; fi | |
| if [ -z "$tst_layer" ] ; then echo "FATAL : test layer is missing" ; warning='warning' ; fi | |
| if [ -n "$warning" ] ; then echo "Please see template for recommended format https://github.com/StaPH-B/docker-builds/blob/master/dockerfile-template/Dockerfile" ; exit 1 ; fi | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v2 | |
| - name: Set up Docker Buildx | |
| id: buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Cache Docker layers | |
| uses: actions/cache@v3 | |
| with: | |
| path: /tmp/.buildx-cache-${{ steps.parse.outputs.tool }} | |
| key: ${{ runner.os }}-buildx-${{ steps.parse.outputs.tool }}-${{ github.sha }} | |
| restore-keys: | | |
| ${{ runner.os }}-buildx-${{ steps.parse.outputs.tool }} | |
| - name: Build to test | |
| id: docker_build_to_test | |
| uses: docker/build-push-action@v3 | |
| with: | |
| context: ./${{ steps.parse.outputs.tool }}/${{ steps.parse.outputs.version }} | |
| file: ./${{ steps.parse.outputs.tool }}/${{ steps.parse.outputs.version }}/Dockerfile | |
| target: test | |
| tags: ${{ steps.parse.outputs.tool }}:${{ steps.parse.outputs.version }} | |
| load: true | |
| push: false | |
| cache-from: type=local,src=/tmp/.buildx-cache-${{ steps.parse.outputs.tool }} | |
| cache-to: type=local,mode=max,dest=/tmp/.buildx-cache-${{ steps.parse.outputs.tool }}-new | |
| - name: Check labels | |
| run: | | |
| # checking labels | |
| warning='' | |
| for label in base.image dockerfile.version software software.version description website maintainer maintainer.email | |
| do | |
| value=$(docker inspect --format '{{ index .Config.Labels "'$label'"}}' ${{ steps.parse.outputs.tool }}:${{ steps.parse.outputs.version }} ) | |
| if [ -z "$value" ] ; then warning='warning' ; echo "FATAL : $label label not found in ${{ steps.parse.outputs.tool }}:${{ steps.parse.outputs.version }}" ; fi | |
| done | |
| if [ -z "$(docker inspect --format '{{.Config.WorkingDir}}' ${{ steps.parse.outputs.tool }}:${{ steps.parse.outputs.version }} )" ] ; | |
| then | |
| warning='warning' | |
| echo "FATAL : WORKDIR not set." | |
| fi | |
| if [ -n "$warning" ] ; then echo "Please see template for recommended format https://github.com/StaPH-B/docker-builds/blob/master/dockerfile-template/Dockerfile" ; exit 1 ; fi | |
| - name: Check commonly overlooked commands | |
| run: | | |
| # checking commands | |
| docker run ${{ steps.parse.outputs.tool }}:${{ steps.parse.outputs.version }} ps --help | |
| docker run ${{ steps.parse.outputs.tool }}:${{ steps.parse.outputs.version }} update-ca-certificates -h | |
| - name: Move cache # apparently prevents the cache from growing in size forever | |
| run: | | |
| rm -rf /tmp/.buildx-cache-${{ steps.parse.outputs.tool }} | |
| mv /tmp/.buildx-cache-${{ steps.parse.outputs.tool }}-new /tmp/.buildx-cache-${{ steps.parse.outputs.tool }} | |
| - name: Image digest | |
| run: echo ${{ steps.docker_build.outputs.digest }} |