2024-10-23 ECDC models - SARIMA & SOCA simplex #11
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| name: HubSubmissionValidation(R) | |
| on: | |
| workflow_dispatch: | |
| 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: | |
| - uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| # Get changes from pull request for later use | |
| # -------------------------------------------- | |
| - name: Get changes | |
| id: get_changed_files | |
| uses: tj-actions/changed-files@v41 | |
| # DEBUG ONLY | |
| - name: List all changed files | |
| run: | | |
| for file in ${{ steps.get_changed_files.outputs.all_changed_files }}; do | |
| echo "$file was changed" | |
| done | |
| # Look for file outside allowed folders | |
| # --------------------------------------- | |
| - name: Check if file are outside the allowed folders | |
| run: | | |
| # List of allowed folders | |
| ALLOWED_FOLDERS=("model-output/" "model-metadata/") | |
| # Init var for not allowed files | |
| FILES_OUTSIDE_FOLDERS="" | |
| # Iterate over changes | |
| for FILE in $(echo ${{ steps.changed-files.outputs.all_changed_files }} | jq -r '.[]'); do | |
| MATCH_FOUND=false | |
| # Check if file is under an allowed folder | |
| for FOLDER in "${ALLOWED_FOLDERS[@]}"; do | |
| if [[ "$FILE" == "$FOLDER"* ]]; then | |
| MATCH_FOUND=true | |
| break | |
| fi | |
| done | |
| # If not mathced, add to forbidden list | |
| if [ "$MATCH_FOUND" = false ]; then | |
| FILES_OUTSIDE_FOLDERS="${FILES_OUTSIDE_FOLDERS} $FILE" | |
| fi | |
| done | |
| # If one or more file outside allowed folders are present, submission fails | |
| if [ ! -z "$FILES_OUTSIDE_FOLDERS" ]; then | |
| echo "Error: PR contains files outside the allowed folders." | |
| echo "Files outside allowed folders: $FILES_OUTSIDE_FOLDERS" | |
| exit 1 | |
| fi | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| install-r: false | |
| use-public-rspm: true | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libcurl4-openssl-dev libv8-dev | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| packages: Infectious-Disease-Modeling-Hubs/hubValidations, any::sessioninfo | |
| - name: Run validations | |
| env: | |
| 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 = TRUE | |
| ) | |
| hubValidations::check_for_errors(v, verbose = TRUE) | |
| shell: Rscript {0} | |
| # 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 pull request | |
| # --------------------------- | |
| - name: Approve Pull Request | |
| uses: juliangruber/[email protected] | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| number: ${{ github.event.pull_request.number }} | |
| # And then merge it | |
| # --------------------------- | |
| - 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 }} | |
| call-persisting-wf: | |
| needs: validate-submission_job | |
| uses: european-modelling-hubs/RespiCast-Covid19/.github/workflows/persist_changes.yml@main | |
| with: | |
| changes-list: ${{ needs.validate-submission_job.outputs.changed_files }} | |
| secrets: | |
| envPAT: ${{ secrets.GITHUB_TOKEN }} |