safinea-COVIDmodel 2024_2025_1_COVID #223
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| name: Validate Submissions | |
| # Activate the validation process on pull-requests for model-output data submissions or on meta-data changes | |
| on: | |
| pull_request_target: | |
| branches: | |
| - main | |
| paths: | |
| - 'model-output/**' | |
| - 'model-metadata/*' | |
| - '!**README**' | |
| - '!**.md' | |
| - '!**.MD' | |
| jobs: | |
| validate-submission_job: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| changed_files: ${{ steps.get_changed_files.outputs.all_changed_files }} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| PR_NUMBER: ${{ github.event.pull_request.number }} | |
| steps: | |
| # Setup R env | |
| # --------------------------------- | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| install-r: false | |
| use-public-rspm: true | |
| # Install hubValidations package from HubVerse | |
| # ---------------------------------------------- | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| packages: hubverse-org/hubValidations, any::sessioninfo | |
| # Install System dependencies | |
| # --------------------------------- | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libcurl4-openssl-dev libv8-dev | |
| # Install Pyton env and lib | |
| # --------------------------- | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - run: pip install pandas pyarrow | |
| # checkout the repository with reference to the SHA of the HEAD | |
| # commit of the branch that is being merged into the Base | |
| # ------------------------------------------------------------------ | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| fetch-depth: 1 | |
| # Get changes from pull request for later use | |
| # -------------------------------------------- | |
| - name: Get changes | |
| id: get_changed_files | |
| uses: tj-actions/changed-files@v41 | |
| # Checkout the python tools repo | |
| # ------------------------------------------- | |
| - name: checkout python tools repo | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: 'european-modelling-hubs/hub-tools' | |
| ref: 'main' | |
| path: './tools/' | |
| # Trace changes | |
| # --------------------------------- | |
| - name: List all changed files | |
| run: | | |
| for file in ${{ steps.get_changed_files.outputs.all_changed_files }}; do | |
| echo "$file was changed" | |
| done | |
| # Validate data submission | |
| # --------------------------------- | |
| - name: Run validations | |
| env: | |
| files: ${{ steps.get_changed_files.outputs.all_changed_files }} | |
| PR_NUMBER: ${{ github.event.number }} | |
| run: | | |
| library("hubValidations") | |
| v <- hubValidations::validate_pr( | |
| gh_repo = Sys.getenv("GITHUB_REPOSITORY"), | |
| pr_number = Sys.getenv("PR_NUMBER"), | |
| skip_submit_window_check = FALSE, | |
| derived_task_ids = c("target_end_date", "pop_group") | |
| ) | |
| hubValidations::check_for_errors(v, verbose = TRUE) | |
| shell: Rscript {0} | |
| # Validate derived_task_ids since their validation | |
| # is currently skipped in the validate_pr | |
| - name: Validate derived task ids | |
| env: | |
| input_list: ${{ steps.get_changed_files.outputs.all_changed_files }} | |
| run: | | |
| python ./tools/code/validate_derived_task_ids.py | |
| # Eventually comment on it | |
| # --------------------------- | |
| - name: Comment PR | |
| uses: thollander/actions-comment-pull-request@v2 | |
| with: | |
| message: | | |
| All validation checks completed successfully. | |
| pr_number: ${{ github.event.pull_request.number }} | |
| # Approve the pull request | |
| # --------------------------- | |
| - name: Approve Pull Request | |
| uses: juliangruber/[email protected] | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| number: ${{ github.event.pull_request.number }} | |
| # And then finally do the merge | |
| # ------------------------------- | |
| - name: Merge the pull request | |
| id: merge_pr | |
| run: | | |
| echo ">>> Merging PR URL: ${{ github.event.pull_request.html_url }}" | |
| gh pr merge --auto --squash $PR_URL | |
| env: | |
| PR_URL: ${{ github.event.pull_request.html_url }} | |
| GH_TOKEN: ${{ github.token }} | |
| # As a last step, call a job that persists changes from the pull-request | |
| # to a json db for further upload to the web-server platform | |
| call-persisting-wf_job: | |
| needs: validate-submission_job | |
| uses: european-modelling-hubs/RespiCompass/.github/workflows/persist_changes.yml@main | |
| with: | |
| changes-list: ${{ needs.validate-submission_job.outputs.changed_files }} | |
| secrets: | |
| envPAT: ${{ secrets.GITHUB_TOKEN }} |