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| # This workflow validates the current JSON documents against EGA's JSON schemas | |
| # using EGA's API endpoint (http://biovalidator.ega.ebi.ac.uk/validate) of | |
| # the tool Biovalidator (https://github.com/elixir-europe/biovalidator) and the | |
| # up-to-date EGA JSON schemas | |
| # (https://github.com/EbiEga/ega-metadata-schema/tree/main/schemas). | |
| # The logic of this workflow is: | |
| # - Details: EE-2575 | |
| # - Why: Allows us to check two things: | |
| # 1. Whether the current "main" branch of Biovalidator can be deployed as | |
| # a server instance. | |
| # 2. Whether the modified schemas-&-documents (the ones in the branch of | |
| # the PR) are compliant (i.e. would pass validation) against an up to | |
| # date Biovalidator instance. | |
| # - Would block the PR if failed? Requires interpretation depending on the | |
| # step at which it failed. | |
| # - How: (1) Clone current Biovalidator repository; (2) install dependencies | |
| # and project; (3) deploy Biovalidator local server, specifying (-r/--ref) | |
| # the schemas to be used during validation, which would be the ones within | |
| # the branch; (4) execute script .github/scripts/request_validation.py | |
| # specifying the localhost server and branch's JSON documents. | |
| # | |
| # For more information, check: | |
| # https://github.com/EbiEga/ega-metadata-schema/tree/main/docs/gh_workflows | |
| name: | | |
| [REQUIRED] JSON docs validation - Local Biovalidator | |
| (json_validation_deploying_biovalidator.yml) | |
| on: | |
| # Executes on any commit to a PR to the "main" branch | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| validate-json-docs: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| with: | |
| # Full git history | |
| fetch-depth: 0 | |
| - name: Clone Biovalidator | |
| # See https://github.com/elixir-europe/biovalidator#installation | |
| # We want to test the "main" branch of the project | |
| run: git clone https://github.com/elixir-europe/biovalidator.git | |
| - name: Install Biovalidator | |
| # We want to test with the latest Node.js version, but if not, we | |
| # could make use of action: https://github.com/actions/setup-node | |
| run: | | |
| cd biovalidator | |
| npm install | |
| # We shouldn't need to audit the issues, but for now it is what it is | |
| # npm audit fix | |
| - name: Start Biovalidator server | |
| # We want to specify the JSON schemas and documents with the new | |
| # changes. Therefore we specify the schemas at deployment level (-r) | |
| run: | | |
| schemas_dir="./schemas" | |
| node biovalidator/src/biovalidator -r "$schemas_dir/*.json" & | |
| # We stop for a few seconds to give the server time | |
| sleep 3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| # We'll use the latest version of python from major 3 release | |
| # This bit is needed for running the following python script | |
| python-version: '3.x' | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade pip | |
| requirements_f="./.github/scripts/requirements.txt" | |
| if [ -f "$requirements_f" ]; then pip install -r "$requirements_f"; fi | |
| - name: Validate JSON examples | |
| # Validate all JSON documents against their corresponding schemas | |
| # Check: | |
| # github.com/EbiEga/ega-metadata-schema/tree/main/.github/scripts | |
| run: | | |
| json_ex_dir="./examples/json_validation_tests" | |
| # The following URL points to the locally deployed server of | |
| # Biovalidator | |
| url="http://localhost:3020/validate" | |
| python3 ./.github/scripts/request_validation.py "$json_ex_dir" "$url" |