on_pr_1.yml

name: On Pull Request

on:
  workflow_dispatch: 
    inputs:
      manual-pr-number:
        description: 'PR Number'
        required: true
        default: '10'
  #pull_request:
    #paths:
    #  - '**/*.gpml'

concurrency:
  group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
  cancel-in-progress: false # to allow multiple runs to queue up rather than clobber

jobs:
  get-pr:
    # This job determines the PR number and stores it as a GITHUB_OUTPUT environment variable 
    # that can accessed by subsequent jobs.
    runs-on: ubuntu-latest
    outputs:
      pr-number:  ${{ steps.get-pr.outputs.pr-number }}
    steps:
      - name: Get PR
        id: get-pr
        # Get PR from triggering event, unless provided via manual workflow run
        run: | 
          if [ -z "${{ inputs.manual-pr-number }}" ]; then
            echo "pr-number=${{ github.event.pull_request.number }}" >> $GITHUB_OUTPUT
          else
            echo "pr-number=${{ inputs.manual-pr-number }}" >> $GITHUB_OUTPUT
          fi
  
  get-gpml:
    # This job gets the GPML file and uploads it as an artifact 
    # that can accessed by subsequent jobs. It also extracts key information from
    # the GPML file and starts a new PR description.
    #
    # A markdown text report is stored as pr-desc to be compiled and written to the PR description.
    #
    # The branch name from the submitter's fork is also extracted and stored (if needed).
    needs: [get-pr]
    #if: ${{ needs.get-pr.outputs.pr-number }}
    runs-on: ubuntu-latest
    outputs:
      gpml-filepath: ${{ steps.get-gpml.outputs.gpml-filepath }}
      gpml-file: ${{ steps.get-gpml.outputs.gpml-file }}
      pr-desc: ${{ steps.get-gpml.outputs.pr-desc }}
      branch-name: ${{ steps.get-branch.outputs.branch-name }}
    env:
      PR_NUMBER: ${{ needs.get-pr.outputs.pr-number }}
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          ref: refs/pull/${{ needs.get-pr.outputs.pr-number }}/head  
          
      - name: Install XML processing tools
        # Used to parse XML values from GPML
        run: sudo apt-get install -y libxml2-utils

      - name: Get GPML
        id: get-gpml
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 
        run: |
          GPML_FILEPATH=$(gh pr view $PR_NUMBER --json files --jq '.files.[].path' | grep '.gpml$')
          echo "Found GPML file at: $GPML_FILEPATH"
          echo "gpml-filepath=$GPML_FILEPATH" >> $GITHUB_OUTPUT #for subsequent jobs

          # Extract information from GPML
          GPML_FILE="$(basename ""$GPML_FILEPATH"")"
          echo "gpml-file=$GPML_FILE" >> $GITHUB_OUTPUT
          wpid="$($GPML_FILE | sed 's/.gpml//')"
          org="$(xmllint --xpath 'string(//*[local-name()="Pathway"]/@Organism)' "$GPML_FILEPATH")"  
          name="$(xmllint --xpath 'string(//*[local-name()="Pathway"]/@Name)' "$GPML_FILEPATH")" 
          desc="$(xmllint --xpath 'string(//*[local-name()="Comment" and @Source="WikiPathways-description"])' "$GPML_FILEPATH")"

          # Start PR description (newlines are important in NEW_DESCRIPTION string)
          NEW_DESCRIPTION="
          ## Pathway Information

          **WPID**: $wpid
          **TITLE**: $name
          **ORGANISM**: $org
          **DESCRIPTION**: $desc
        
          ---
          "
          # Store PR description for compilation in final job
          # EOF base64 needed for storing multi-line strings as output variables
          EOF=$(dd if=/dev/urandom bs=15 count=1 status=none | base64)
          echo "pr-desc<<$EOF" >> $GITHUB_OUTPUT
          echo "$NEW_DESCRIPTION" >> $GITHUB_OUTPUT
          echo "$EOF" >> $GITHUB_OUTPUT

          # Temporarily append PR description
          NEW_DESCRIPTION="$NEW_DESCRIPTION
          
          Processing...
          "
          
          # Edit PR description
          gh pr edit $PR_NUMBER --body "$NEW_DESCRIPTION"
        
      - name: Upload GPML file as artifact
        uses: actions/upload-artifact@v3
        with:
          name: gpml-file
          path: ${{ steps.get-gpml.outputs.gpml-filepath }}
          retention-days: 1
          if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
          
      - name: Get branch name
        id: get-branch
        # Determine PR branch from submitter's fork, if needed #TODO: prune if not needed
        run: |
          BRANCH_NAME=$(curl -s -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
            https://api.github.com/repos/${{ github.repository }}/pulls/${{needs.get-pr.outputs.pr-number}} \
            | jq -r .head.ref)
          echo "branch-name=$BRANCH_NAME"
          echo "branch-name=$BRANCH_NAME" >> $GITHUB_OUTPUT

          if ! git ls-remote --heads origin $BRANCH_NAME; then
            git push origin HEAD:refs/heads/$BRANCH_NAME
          fi

  metadata:
    # This job generates files dervied from the GPML, including info.json, datanodes.tsv and refs.tsv.
    # The meta-data-action Java application performs the bulk of the work: 
    # https://github.com/wikipathways/meta-data-action
    #
    # The generated files are uploaded as artifacts to be downloaded and pushed together with other files 
    # to another repo in a final sync job. This strategy allows for parallel job processing!
    #
    # A markdown text report is stored as pr-desc to be compiled and written to the PR description.
    needs: [get-pr,get-gpml]
    runs-on: ubuntu-latest
    outputs:
      pr-desc: ${{ steps.report.outputs.pr-desc }}
    env:
      GPML_FILE: ${{ needs.get-gpml.outputs.gpml-file }}
    steps:
      - name: Checkout repository for scripts
        uses: actions/checkout@v4
        
      - name: Download GPML artifact
        # Downloads gpml-file artifact to working dir
        # Note: Automatically unzips to provide GPML with original filename
        uses: actions/download-artifact@v3
        with:
          name: gpml-file
        
      - name: Setup Java
        uses: actions/setup-java@v3
        with:
          distribution: 'temurin'
          java-version: '11'

      - name: Cache meta-data-action with dependencies
        uses: actions/cache@v3
        id: cacheMetaJar
        with:
          path: ./meta-data-action-1.1.2-jar-with-dependencies.jar
          key: cached-meta-data-action-${{ hashFiles('meta-data-action-1.1.2-jar-with-dependencies.jar') }}
          restore-keys: |
            cached-meta-data-action-${{ hashFiles('meta-data-action-1.1.2-jar-with-dependencies.jar') }}
            cached-meta-data-action-
    
      - name: Install deps
        run: |
          echo "Refreshing cached-meta-data-action"
          if [ ! -e ./meta-data-action-1.1.2-jar-with-dependencies.jar ]; then
            wget -O meta-data-action-1.1.2-jar-with-dependencies.jar https://github.com/wikipathways/meta-data-action/releases/download/v1.1.2/meta-data-action-1.1.2-jar-with-dependencies.jar
          fi

      - name: Cache and install dependencies
        uses: actions/cache@v3
        id: cache
        with:
          path: ${{ github.workspace }}/Hs_Derby_Ensembl_108.bridge
          key: ${{ runner.os }}-java-Hs_Derby_Ensembl_108
          restore-keys: |
            ${{ runner.os }}-java-Hs_Derby_Ensembl_108
            ${{ runner.os }}-java-Hs_Derby_Ensembl_
                
      - if: steps.cache.outputs.cache-hit != 'true'
        name: Install deps
        run: |
          cd "${{ github.workspace }}"
          if [ ! -e ./Hs_Derby_Ensembl_108.bridge ]; then
            wget -O Hs_Derby_Ensembl_108.bridge https://zenodo.org/record/7781913/files/Hs_Derby_Ensembl_108.bridge?download=1
          fi

      - name: Generate gdb.config, fileNames.config, and fileDownloads.config
        run: scripts/meta-data-action/configGenerator.sh ./$GPML_FILE
          
      - name: Cache all bridge files
        uses: actions/cache@v3
        id: cacheAllBridge
        with:
          path: |
            ./metabolites*.bridge
            ./Ag*.bridge
            ./An*.bridge
            ./At*.bridge
            ./Bs*.bridge
            ./Bt*.bridge
            ./Ce*.bridge
            ./Cf*.bridge
            ./Ci*.bridge
            ./Dr*.bridge
            ./Da*.bridge
            ./Dp*.bridge
            ./Dm*.bridge
            ./Ec*.bridge
            ./Gg*.bridge
            ./Fg*.bridge
            ./Gm*.bridge
            ./Hs*.bridge
            ./Hv*.bridge
            ./Ml*.bridge
            ./Mm*.bridge
            ./Mx*.bridge
            ./Oa*.bridge
            ./Ova*.bridge
            ./Oi*.bridge
            ./Oj*.bridge
            ./Pi*.bridge
            ./Pt*.bridge
            ./Qc*.bridge
            ./Rn*.bridge
            ./Sc*.bridge
            ./Sl*.bridge
            ./Ss*.bridge
            ./Vv*.bridge
            ./Xt*.bridge
            ./Zm*.bridge
          key: cached-bridge-files
          restore-keys: |
            cached-bridge-files
            
      - if: steps.cacheAllBridge.outputs.cache-hit != 'true'
        name: Install all bridge files
        run: |
          echo "Cache not found: cached-bridge-files"
          declare -a OrganismNames=("Metabolites" "Anopheles gambiae" "Aspergillus niger" "Arabidopsis thaliana" "Bacillus subtilis" "Bos taurus" "Caenorhabditis elegans" "Canis familiaris" "Ciona intestinalis" "Danio rerio" "Daphnia magna" "Daphnia pulex" "Drosophila melanogaster" "Escherichia coli" "Gallus gallus" "Fusarium graminearum"  "Glycine max" "Homo sapiens" "Hordeum vulgare" "Macaca mulatta" "Mus musculus" "Mycobacterium tuberculosis" "Ornithorhynchus anatinus" "Ovis aries" "Oryza indica" "Oryza japonica" "Populus trichocarpa" "Pan troglodytes" "Equus caballus" "Rattus norvegicus" "Saccharomyces cerevisiae" "Solanum lycopersicum" "Sus scrofa" "Vitis vinifera" "Xenopus tropicalis" "Zea mays")
          for org in "${OrganismNames[@]}"; do
            echo "generating configuration files for "$org""
            scripts/meta-data-action/configGenerator.sh "$org"
            echo "installing bridgedb files for "$org""
            scripts/meta-data-action/installDependencies.sh "$org"
          done

      - name: Generate configs, install bridgeDb, generate info and tsv files
        run: |
          chmod 777 meta-data-action-1.1.2-jar-with-dependencies.jar
          f=./$GPML_FILE
          org="$(sed -n '/<Pathway /s/.*Organism=\(.*\)[^\n]*/\1/p' $f | tr -d '"' | tr -d '>' | tr -d '\r')"  
          echo "generating configuration files for "$org""
          scripts/meta-data-action/configGenerator.sh "$org"
          wpid="$(basename ""$f"" | sed 's/.gpml//')"
          cat gdb.config
          echo "generating info and datanode files for $wpid, organism "$org""
          java -jar meta-data-action-1.1.2-jar-with-dependencies.jar local "$f" $(date --utc +%F) gdb.config "$org"
          # generated files are placed in "pathways" dir
          ls -R 
          mkdir ./metadata
          mv pathways/"$wpid"-info.json metadata/.
          mv pathways/"$wpid"*.tsv metadata/.
      
      - name: Upload metadata files as artifacts
        uses: actions/upload-artifact@v3
        with:
          name: metadata
          path: metadata/
          retention-days: 1
          if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
          
      - name: Report on meta-data-action
        id: report
        run: |
          # Verify generated files 
          infojson=$(find . -path "./metadata/WP*info.json" -print -quit)
          dntsv=$(find . -path "./metadata/WP*datanodes.tsv" -print -quit)
          refstsv=$(find . -path "./metadata/WP*refs.tsv" -print -quit)

          # Update PR description
          NEW_DESCRIPTION="
          ## Generate Metadata Files
          "
          if [[ -n $infojson ]]; then
            NEW_DESCRIPTION="$NEW_DESCRIPTION
            - [x] info.json generated"
          else
            NEW_DESCRIPTION="$NEW_DESCRIPTION
            - [] info.json generated"          
          fi
          if [[ -n $dntsv ]]; then
            NEW_DESCRIPTION="$NEW_DESCRIPTION
            - [x] datanodes.tsv generated"
          else
            NEW_DESCRIPTION="$NEW_DESCRIPTION
            - [] datanodes.tsv generated"          
          fi
          if [[ -n $refstsv ]]; then
            NEW_DESCRIPTION="$NEW_DESCRIPTION
            - [x] refs.tsv generated"
          else
            NEW_DESCRIPTION="$NEW_DESCRIPTION
            - [] refs.tsv generated"          
          fi

          # Store PR description for compilation in final job
          EOF=$(dd if=/dev/urandom bs=15 count=1 status=none | base64)
          echo "pr-desc<<$EOF" >> $GITHUB_OUTPUT
          echo "$NEW_DESCRIPTION" >> $GITHUB_OUTPUT
          echo "$EOF" >> $GITHUB_OUTPUT

  pubmed:
    if: true
    needs: [get-pr,get-gpml, metadata]
    runs-on: ubuntu-latest
    outputs:
      pr-desc: ${{ steps.report.outputs.pr-desc }}
    env:
      GPML_FILE: ${{ needs.get-gpml.outputs.gpml-file }}
    steps:
    - name: Checkout repository for scripts
      uses: actions/checkout@v4
        
    - name: Download GPML artifact
      # Downloads gpml-file and metadata artifacts to working dir
      # Note: Automatically unzips to provide files with original filenames
      uses: actions/download-artifact@v3
    
    - name: Run generate-references
      run: |
        echo "TODO: Run generate-references and attach output TSV to PR"

    - name: Report on pubmed
      id: report
      run: |
        # Update PR description
        NEW_DESCRIPTION="- [x] references.tsv generated"

        # Store PR description for compilation in final job
          EOF=$(dd if=/dev/urandom bs=15 count=1 status=none | base64)
          echo "pr-desc<<$EOF" >> $GITHUB_OUTPUT
          echo "$NEW_DESCRIPTION" >> $GITHUB_OUTPUT
          echo "$EOF" >> $GITHUB_OUTPUT

  frontmatter:
    if: true
    needs: [get-pr,get-gpml,metadata]
    runs-on: ubuntu-latest
    outputs:
      pr-desc: ${{ steps.report.outputs.pr-desc }}
    env:
      GPML_FILE: ${{ needs.get-gpml.outputs.gpml-file }}
    steps:
    - name: Checkout repository for scripts
      uses: actions/checkout@v4
        
    - name: Download GPML artifact
      # Downloads gpml-file and metadata artifacts to working dir
      # Note: Automatically unzips to provide files with original filenames
      uses: actions/download-artifact@v3
    
    - name: Run create_pathway_frontmatter.py
      run: |
        echo "TODO: Run create_pathway_frontmatter.py and attach output MD to PR"

    - name: Report on pubmed
      id: report
      run: |
        # Update PR description
        NEW_DESCRIPTION="- [x] .md generated"
        
        # Store PR description for compilation in final job
          EOF=$(dd if=/dev/urandom bs=15 count=1 status=none | base64)
          echo "pr-desc<<$EOF" >> $GITHUB_OUTPUT
          echo "$NEW_DESCRIPTION" >> $GITHUB_OUTPUT
          echo "$EOF" >> $GITHUB_OUTPUT

  json-svg:
    if: true
    needs: [get-pr,get-gpml,metadata]
    runs-on: ubuntu-latest
    outputs:
      pr-desc: ${{ steps.report.outputs.pr-desc }}
    env:
      GPML_FILE: ${{ needs.get-gpml.outputs.gpml-file }}
    steps:
    - name: Checkout repository for scripts
      uses: actions/checkout@v4
        
    - name: Download GPML artifact
      # Downloads gpml-file and metadata artifacts to working dir
      # Note: Automatically unzips to provide files with original filenames
      uses: actions/download-artifact@v3
    
    - name: Run generate-svgs
      run: |
        echo "TODO: Run generate-svgs and attach output JSON, SVG and PNG to PR"

    - name: Report on pubmed
      id: report
      run: |
        # Update PR description
        NEW_DESCRIPTION="- [x] .json generated
        - [x] .svg generated
        - [x] .png generated

        *TODO: insert PNG here*
        "
        
        # Store PR description for compilation in final job
          EOF=$(dd if=/dev/urandom bs=15 count=1 status=none | base64)
          echo "pr-desc<<$EOF" >> $GITHUB_OUTPUT
          echo "$NEW_DESCRIPTION" >> $GITHUB_OUTPUT
          echo "$EOF" >> $GITHUB_OUTPUT


  testing:
    if: true
    needs: [get-pr,get-gpml,metadata]
    runs-on: ubuntu-latest
    outputs:
      pr-desc: ${{ steps.report.outputs.pr-desc }}
    env:
      GPML_FILE: ${{ needs.get-gpml.outputs.gpml-file }}
    steps:
    - name: Checkout repository for scripts
      uses: actions/checkout@v4
        
    - name: Download GPML artifact
      # Downloads gpml-file and metadata artifacts to working dir
      # Note: Automatically unzips to provide files with original filenames
      uses: actions/download-artifact@v3
    
    - name: Perform automatic test
      run: |
        # TODO: perform testing

    - name: Report on pubmed
      id: report
      run: |        
        # Update PR description
        NEW_DESCRIPTION='
        ---
        ## Automated Testing
        *As table*
        | # | Test name | Link | Notes | Result |
        |---|---|---|---|---|
        | 1 | Test one | | | \$\${\color{green}PASS}\$\$ |
        | 2 | Test two | | | \$\${\color{red}FAIL}\$\$ |
        | 3 | Test three | | | \$\${\color{green}PASS}\$\$ |

        *As checklist*
        - [ ] Interactions are connected
        - [ ] Datanodes are annotated with database references
        - [ ] Decription, consisting of 2-3 sentence overview of processes described in the pathway
        - [ ] At least one literature reference
        - [ ] At least one pathway ontology term
        - [ ] Pathway title conforms to the [guidelines](https://github.com/wikipathways/wikipathways-faq/discussions/24)
        ---
        '
        
        # Store PR description for compilation in final job
          EOF=$(dd if=/dev/urandom bs=15 count=1 status=none | base64)
          echo "pr-desc<<$EOF" >> $GITHUB_OUTPUT
          echo "$NEW_DESCRIPTION" >> $GITHUB_OUTPUT
          echo "$EOF" >> $GITHUB_OUTPUT

  update-pr-desc:
    needs: [get-pr,get-gpml,metadata,pubmed,frontmatter,json-svg,testing]
    runs-on: ubuntu-latest
    steps:
    - name: Check out code
      uses: actions/checkout@v4
      with:
        ref: refs/pull/${{ needs.get-pr.outputs.pr-number }}/head  
        
    - name: Compile and update PR description
      env:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 
        PR_NUMBER: ${{ needs.get-pr.outputs.pr-number }}
      run: |          
        NEW_DESCRIPTION="${{ needs.get-gpml.outputs.pr-desc }}
        ${{ needs.metadata.outputs.pr-desc }}
        ${{ needs.pubmed.outputs.pr-desc }}
        ${{ needs.frontmatter.outputs.pr-desc }}
        ${{ needs.json-svg.outputs.pr-desc }}
        ${{ needs.testing.outputs.pr-desc }}
        "
        
        # Edit PR description
        gh pr edit $PR_NUMBER --body "$NEW_DESCRIPTION"