validate_submission.yml

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/approve-pull-request-action@v2.0.0
            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 }}