after-validate-submission.yaml

name: After Validate Submission Workflow

on:
  #workflow_run:
  #  workflows: ["Hub Submission Validation (R)"]  # The name of the workflow we want to trigger from
  #  types:
  #    - completed
  pull_request_target:
    types:
      - closed

jobs:
  copy-files-to-rsv-data-repo:
    runs-on: ubuntu-latest
    # if: ${{ github.event.workflow_run.conclusion == 'success' }}
    env:
        GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    if: github.event.pull_request.merged == true
    steps:
      - name: Checkout
        uses: actions/checkout@v2
        with:
          fetch-depth: 2
      - uses: r-lib/actions/setup-r@v2
        with:
          install-r: false
          use-public-rspm: true
      - name: Get list of changed files
        id: changed-files
        uses: tj-actions/changed-files@v44
        with:
           token: ${{ secrets.GITHUB_TOKEN }}
      - name: Print changed files
        run: |
          echo 'Changed files: ${{ steps.changed-files.outputs.added_files }}'
      - name: Install system dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y libcurl4-openssl-dev
      - name: Cache R packages
        uses: actions/cache@v2
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-r-${{ hashFiles('DESCRIPTION') }}
          restore-keys: ${{ runner.os }}-r-
      - name: Install gh package
        run: Rscript -e 'install.packages("gh")'
      - name: Install here package
        run: Rscript -e 'install.packages("here")'
      - name: Install readr package
        run: Rscript -e 'install.packages("readr")'
      - name: Install lubridate package
        run: Rscript -e 'install.packages("lubridate")'
      - name: Install ggridges package
        run: Rscript -e 'install.packages("ggridges")'
      - name: Install forcats package
        run: Rscript -e 'install.packages("forcats")'
      - name: Install arrow package
        run: Rscript -e 'install.packages("arrow")'
      - name: Install dplyr package
        run: Rscript -e 'install.packages("dplyr")'
      - name: Install jsonlite package
        run: Rscript -e 'install.packages("jsonlite")'
      - name: Install purrr package
        run: Rscript -e 'install.packages("purrr")'
      - name: Install hubViz
        run: |
           Rscript -e 'install.packages("remotes")'
           Rscript -e 'remotes::install_github("Infectious-Disease-Modeling-Hubs/hubVis")'
      - name: Install hubUtils
        run: |
           Rscript -e 'remotes::install_github("Infectious-Disease-Modeling-Hubs/hubUtils")'
      - name: Install hubEnsembles
        run: |
           Rscript -e 'remotes::install_github("Infectious-Disease-Modeling-Hubs/hubEnsembles")'
      - name: Install hubData
        run: |
          Rscript -e 'remotes::install_github("kjsato/hubData@feature/handle-samples", upgrade = "never")'
      - name: Check if RETRO files are present
        id: check_files
        run: |
          echo 'retro='$(echo '${{ steps.changed-files.outputs.added_files }}' | grep 'model-output' | grep -c '.*-RETRO.*\.\(csv\|parquet\)') >> $GITHUB_ENV
          echo 'conventional='$(echo '${{ steps.changed-files.outputs.added_files }}' | grep -c -v '.*-RETRO.*\.\(csv\|parquet\)') >> $GITHUB_ENV
      - name: Run R script
        run: |
          cd ./scripts
          Rscript ensemble.R
        if: ${{ env.conventional != '0' }}
      - name: Run retro_ensemble.R
        run: |
          cd ./scripts
          for file in $(echo '${{ steps.changed-files.outputs.added_files }}' | grep 'model-output' | grep '.*-RETRO.*\.\(csv\|parquet\)'); do
            Rscript retro_ensemble.R $file
          done
        if: ${{ env.retro != '0' }}

      - name: Commit and push new files to root repository
        run: |
          git config user.name "github-actions[bot]"
          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
          if [ -n "$(git status --porcelain)" ]; then
            git add model-output/hub-ensemble/*
            git commit -m "Upload new files to RSV data repo by ${GITHUB_ACTOR} in #${{ github.event.pull_request.number }}"
            git push
            echo "Data for hub-ensemble uploaded to root repo";
          else
            echo "no upload for root repo";
          fi
        shell: bash
        
      - name: Checkout and push to another repository
        uses: actions/checkout@v2
        with:
          repository: HopkinsIDD/rsv-forecast-hub_data
          #repository: kjsato/rsv-forecast-hub_data
          token: ${{ secrets.KJ3_PATC }}
          path: ./rsv-forecast-hub_data
          fetch-depth: 2
          ref: main

      - name: Copy new files
        run: |
          for FILE in model-output/**/* model-metadata/*; do
            if [ -f "$FILE" ]; then
              mkdir -p ./rsv-forecast-hub_data/$(dirname $FILE)
              cp $FILE ./rsv-forecast-hub_data/$FILE
            fi
          done
      - name: Commit and push new files
        run: |
          cd ./rsv-forecast-hub_data
          git config user.name "github-actions[bot]"
          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
          git pull origin main
          if [ -n "$(git status --porcelain)" ]; then
            git add .
            git commit -m "Upload new files to RSV data repo by ${GITHUB_ACTOR} in #${{ github.event.pull_request.number }}"
            git push
            echo "RSV data uploaded";
          else
            echo "no upload";
          fi
        shell: bash