on_gpml_change.yml

name: When GPML changed, do everything

on:
  workflow_dispatch:
  push:
    branches:
      - main
    paths:
      - pathways/**/*.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:
  # inspired by https://dev.to/scienta/get-changed-files-in-github-actions-1p36
  changed-gpmls:
    runs-on: ubuntu-latest
    # Map a step output to a job output
    outputs:
      added-modified: ${{ steps.changes.outputs.added-modified }}
      copied: ${{ steps.changes.outputs.copied }}
      deleted: ${{ steps.changes.outputs.deleted }}
      renamed: ${{ steps.changes.outputs.renamed }}
    steps:
        # Make sure we have some code to diff.
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
          ref: main
      - name: Get changed files
        id: changes
        # Set outputs using the command.
        run: |
          echo "GPML files were changed in pull request ${{ github.event.before }} -> ${{ github.event.after }}"
          
          #echo "::set-output name=added-modified::$(git diff --name-only --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$ | xargs)"
          echo "added-modified=$(git diff --name-only --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$ | xargs)" >> $GITHUB_OUTPUT
          if git diff --name-only --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$; then
            echo 'added or modified:'
            git diff --name-only --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$
          fi
          
          #echo "::set-output name=copied::$(git diff --name-only --diff-filter=C ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$ | xargs)"
          echo "copied=$(git diff --name-only --diff-filter=C ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$ | xargs)" >> $GITHUB_OUTPUT
          if git diff --name-only --diff-filter=C ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$; then
            echo 'copied:'
            git diff --name-only --diff-filter=C ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$
          fi

          #echo "::set-output name=deleted::$(git diff --name-only --diff-filter=D ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$ | xargs)"
          echo "deleted=$(git diff --name-only --diff-filter=D ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$ | xargs)" >> $GITHUB_OUTPUT
          if git diff --name-only --diff-filter=D ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$; then
            echo 'deleted:'
            git diff --name-only --diff-filter=D ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$
          fi
            
          #echo "::set-output name=renamed::$(git diff --name-only --diff-filter=R ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$ | xargs)"
          echo "renamed=$(git diff --name-only --diff-filter=R ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$ | xargs)" >> $GITHUB_OUTPUT
          if git diff --name-only --diff-filter=R ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$; then
            echo 'renamed:'
            git diff --name-only --diff-filter=R ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$
          fi
          
  author-list:
    runs-on: ubuntu-latest
    needs: changed-gpmls
    # only run if gpmls were added or modified
    if: ${{needs.changed-gpmls.outputs.added-modified}}
    steps:
      - name: Checkout wikipathways-database repo
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
          ref: main
                
      - name: Checkout jekyll repo
        uses: actions/checkout@v4
        with:
          repository: wikipathways/wikipathways.github.io
          path: wikipathways.github.io
          submodules: true
          fetch-depth: 1
          ref: main
          ssh-key: ${{ secrets.ACTIONS_DEPLOY_KEY }}
          
      - name: Update author list and create md profiles
        run: |
          authorList=() 
          {
            read #skip header line
            while IFS=, read -r username realname orcid wikidata github; do
              authorList+=("$username") 
            done 
          }< scripts/author_list.csv
          echo ${#authorList[@]}
          uniqueAuthors=()
          for f in ${{needs.changed-gpmls.outputs.added-modified}}; do
            auth="$(sed -n '/<Pathway /s/.*Author=\"\[\(.*\)\]\".*/\1/p' $f )"
            IFS=',' read -r -a curAuthors <<< "$auth"
            echo $curAuthors
            echo ${#curAuthors[@]}
            for i in "${curAuthors[@]}"; do
              skip=
              for j in "${uniqueAuthors[@]}"; do
                [[ $i == $j ]] && { skip=1; break; }
              done
              [[ -n $skip ]] || uniqueAuthors+=("$i")
            done
          done
          echo ${uniqueAuthors[@]}
          echo ${#uniqueAuthors[@]}
          for a in "${uniqueAuthors[@]}"; do
            a=$(echo "$a" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//')
            a1=${a//AAR&Co/AARandCo}
            a1=${a//Önder/Onder}
            a2=$(echo "$a" | tr ' ' '_')
            if [[ ! " ${authorList[*]} " =~ " ${a} " ]]; then
              echo "Adding $a"
              echo $a","$a",,," >> scripts/author_list.csv
              echo "---" > "wikipathways.github.io/_authors/$a1.md"
              echo "username: $a1" >> "wikipathways.github.io/_authors/$a1.md"
              echo "realname: $a" >> "wikipathways.github.io/_authors/$a1.md"
              echo "website: " >> "wikipathways.github.io/_authors/$a1.md"
              echo "affiliation: " >> "wikipathways.github.io/_authors/$a1.md"
              echo "bio: " >> "wikipathways.github.io/_authors/$a1.md"
              echo "github: " >> "wikipathways.github.io/_authors/$a1.md"
              echo "orcid: " >> "wikipathways.github.io/_authors/$a1.md"
              echo "linkedin: " >> "wikipathways.github.io/_authors/$a1.md"
              echo "googlescholar: " >> "wikipathways.github.io/_authors/$a1.md"
              echo "wikidata: " >> "wikipathways.github.io/_authors/$a1.md"
              echo "twitter: " >> "wikipathways.github.io/_authors/$a1.md"
              echo "mastodon-url: " >> "wikipathways.github.io/_authors/$a1.md"
              echo "meta:" >> "wikipathways.github.io/_authors/$a1.md"
              echo "instagram:" >> "wikipathways.github.io/_authors/$a1.md"
              echo "email:" >> "wikipathways.github.io/_authors/$a1.md"
              echo "redirect_from:" >> "wikipathways.github.io/_authors/$a1.md"
              echo "- /index.php/User:$a2" >> "wikipathways.github.io/_authors/$a1.md"
              echo "- /index.php/Special:Contributions/$a2" >> "wikipathways.github.io/_authors/$a1.md"
              echo "---" >> "wikipathways.github.io/_authors/$a1.md"
            fi
          done

      - name: Commit report
        run: |
          git config --global user.name 'GitHub Action'
          git config --global user.email 'action@github.com'
          git add scripts/author_list.csv
          if git diff --exit-code --staged; then
              echo "No changes"
          else
              git commit -m 'Update author_list file'
              git pull --rebase
              git push
          fi
          cd "${{ github.workspace }}/wikipathways.github.io/_authors"
          git add .
          if git diff --exit-code --staged > /dev/null; then
              echo "No changes"
          else
              git commit -m 'Created new author profiles'
              git pull --rebase
              git push
          fi

  metadata:
    runs-on: ubuntu-latest
    needs: changed-gpmls
    # only run if gpmls were added or modified
    if: ${{needs.changed-gpmls.outputs.added-modified}}
    steps:
        
      - name: Checkout wikipathways-database repo
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
          ref: main
          
      - name: Setup Java
        uses: actions/setup-java@v4
        with:
          distribution: 'temurin'
          java-version: '11'
            
      - name: Cache meta-data-action with dependencies
        uses: actions/cache@v4
        id: cacheMetaJar
        with:
          path: ./meta-data-action-1.1.4-jar-with-dependencies.jar
          key: cached-meta-data-action-${{ hashFiles('meta-data-action-1.1.4-jar-with-dependencies.jar') }}
          restore-keys: |
            cached-meta-data-action-${{ hashFiles('meta-data-action-1.1.4-jar-with-dependencies.jar') }}
            cached-meta-data-action-
    
      - if: steps.cacheMetaJar.outputs.cache-hit != 'true'
        name: Install deps
        run: |
          echo "Cache not found: cached-meta-data-action"
          if [ ! -e ./meta-data-action-1.1.4-jar-with-dependencies.jar ]; then
            wget -O meta-data-action-1.1.4-jar-with-dependencies.jar https://github.com/wikipathways/meta-data-action/releases/download/v1.1.4/meta-data-action-1.1.4-jar-with-dependencies.jar
          fi

      - name: Cache all bridge files
        uses: actions/cache@v4
        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 datanode files
        run: |
          chmod 777 meta-data-action-1.1.4-jar-with-dependencies.jar
          for f in ${{needs.changed-gpmls.outputs.added-modified}}; do
            org="$(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-1.1.4-jar-with-dependencies.jar wikipathways/wikipathways-database "$f" $(date --utc +%F) gdb.config "$org"
          done
      
      - name: Commit report
        run: |
          git config --global user.name 'GitHub Action'
          git config --global user.email 'action@github.com'
          git add pathways/WP*/WP*.{json,tsv}
          if git diff --exit-code --staged; then
              echo "No changes"
          else
              git commit -m 'Update metadata files'
              git pull --rebase
              git push
          fi
          
  pubmed:
    runs-on: ubuntu-latest
    needs: [changed-gpmls, metadata]
    # only run if gpmls were added or modified
    if: ${{needs.changed-gpmls.outputs.added-modified}}
    steps:

      - name: Setup Node
        uses: actions/setup-node@v4
        with:
          node-version: 20

      - name: Cache dependencies
        uses: actions/cache@v4
        with:
          path: ~/.npm
          key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
          restore-keys: |
            ${{ runner.os }}-node-

      - uses: actions/checkout@v4
        with:
          submodules: true
          fetch-depth: 1
          ref: main

      - name: Install dependencies
        working-directory: scripts/generate-references
        run: npm install

      - name: Generate references
        working-directory: scripts/generate-references
        run: node index.js

      - name: Commit report
        run: |
          git config --global user.name 'GitHub Action'
          git config --global user.email 'action@github.com'
          git add pathways/*/*-bibliography.tsv
          if git diff --exit-code --staged; then
              echo "No changes"
          else
              git commit -m 'Update formatted references'
              git pull --rebase
              git push
          fi
          
  frontmatter:
    runs-on: ubuntu-latest
    needs: [changed-gpmls, metadata, pubmed]
    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          submodules: true
          fetch-depth: 1
          ref: main

      - name: Setup Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.x'
          
      - name: Install deps
        run: |
          pip install python-frontmatter
          
      - name: Create pathway frontmatter
        run: |        
          for f in ${{needs.changed-gpmls.outputs.added-modified}}; do
            wpid="$(basename ""$f"" | sed 's/.gpml//')"
            echo "generating frontmatter file for $wpid"
            json_info_f=./pathways/"$wpid"/"$wpid"-info.json
            if [ -e "$json_info_f" ]; then
              python scripts/create_pathway_frontmatter.py "$json_info_f"
              sed -i 's/AAR&amp;Co/AARandCo/g' ./pathways/"$wpid"/"$wpid".md
              sed -i 's/&Ouml;nder/Onder/g' ./pathways/"$wpid"/"$wpid".md
            else
              echo "info.json file missing for $wpid" >2
            fi
          done

      - name: Commit report
        run: |
          git config --global user.name 'GitHub Action'
          git config --global user.email 'action@github.com'
          git add pathways/*/*.md
          if git diff --exit-code --staged; then
              echo "No changes"
          else
              git commit -m 'Update frontmatter .md files'
              git pull --rebase
              git push
          fi

  homology-conversion:
    runs-on: ubuntu-latest
    needs: changed-gpmls
    # only run if gpmls were added or modified
    if: ${{needs.changed-gpmls.outputs.added-modified}}
    steps:
      - name: Checkout wikipathways-database repo
        uses: actions/checkout@v4
        with:
          path: wikipathways-database
          fetch-depth: 1
          ref: main

      - name: Checkout homology repo
        uses: actions/checkout@v4
        with:
          repository: wikipathways/wikipathways-homology
          path: wikipathways-homology
          fetch-depth: 1
          ref: main
          ssh-key: ${{ secrets.ACTIONS_HOMOLOGY_KEY }}

      - name: Set up ssh-agent
        uses: webfactory/ssh-agent@v0.9.0
        with:
          ssh-private-key: ${{ secrets.ACTIONS_HOMOLOGY_KEY }} ## for push into wp-homology repo      
          
      - name: Setup Java
        uses: actions/setup-java@v4
        with:
          distribution: 'temurin'
          java-version: '11'
          
      - name: Cache and install dependencies
        uses: actions/cache@v4
        id: cache
        with:
          path: ${{ github.workspace }}/wikipathways-database/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 }}/wikipathways-database"
          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: Perform homology conversion
        run: |
          cd "${{ github.workspace }}/wikipathways-database"
          for value in Bt Cf Dr Qc Gg Mm Pt Rn Ss
            do   
            mkdir -p scripts/homology-converter/outputs/"$value"
          done
          for f in ${{needs.changed-gpmls.outputs.added-modified}}; do
            wpid="$(basename ""$f"" | sed 's/.gpml//')"
            echo "perfoming homology conversion for $wpid ($f)"
            java -jar HomologyMapperAuto-WithDependencies.jar scripts/homology-converter/properties/autorun.properties $wpid
          done
            
      - name: Move gpml and log files from database repo to homology repo
        run: |
          cd "${{ github.workspace }}/wikipathways-database"
          HM_PATH="${{ github.workspace }}/wikipathways-homology"
          echo "move logs to wikipathways-homology"
          mkdir -p $HM_PATH/logs
          mv scripts/homology-converter/logs/*.txt $HM_PATH/logs/.
          for f in ${{needs.changed-gpmls.outputs.added-modified}}; do
            wpid="$(basename ""$f"" | sed 's/.gpml//')"
            echo "copying gpml files for $wpid for all species"
            for value in Bt Cf Dr Qc Gg Mm Pt Rn Ss
            do             
              for hom_f in scripts/homology-converter/outputs/$value/$wpid/"$wpid"_"$value".gpml; do 
                echo "For $hom_f"
                if [ -e "$hom_f" ]; then
                  echo "move to wikipathways-homology" 
                  mkdir -p $HM_PATH/pathways/$value/$wpid
                  mv "$hom_f" $HM_PATH/pathways/$value/$wpid/"$wpid"_"$value".gpml
                fi
              done
            done  
          done

      - name: Commit gpml to homology repo
        run: |
          cd "${{ github.workspace }}/wikipathways-homology"
          git config --global user.name 'GitHub Action'
          git config --global user.email 'action@github.com'
          git add logs/*
          for value in Bt Cf Dr Qc Gg Mm Pt Rn Ss
          do
            git add pathways/$value/WP*/WP*_$value.gpml
          done
          if git diff --exit-code --staged; then
              echo "No changes"
          else
              git commit -m 'Update GPML files'
              git pull --rebase
              git push
          fi
          
  json-svg:
    needs: [changed-gpmls, pubmed, frontmatter]
    runs-on: ubuntu-latest
    steps:
      - name: Checkout wikipathways-database repo
        uses: actions/checkout@v4
        with:
          path: wikipathways-database
          submodules: true
          fetch-depth: 1
          ref: main

      - name: Checkout assets repo
        uses: actions/checkout@v4
        with:
          repository: wikipathways/wikipathways-assets
          path: wikipathways-assets
          submodules: true
          fetch-depth: 1
          ref: main
          ssh-key: ${{ secrets.ACTIONS_ASSETS_KEY }}

      - name: Set up ssh-agent
        uses: webfactory/ssh-agent@v0.9.0
        with:
          ssh-private-key: ${{ secrets.ACTIONS_ASSETS_KEY }} ## for push into wp-assets repo

      - name: Setup Node
        uses: actions/setup-node@v4
        with:
          node-version: 18

      - name: Cache NPM dependencies
        uses: actions/cache@v4
        with:
          path: ~/.npm
          key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
          restore-keys: |
            ${{ runner.os }}-node-

      - name: Install deps
        working-directory: wikipathways-database/scripts/generate-svgs
        run: |
          npm install
          sudo apt-get update
          sudo apt-get install -y xmlstarlet
            
      - name: Convert GPML to JSON and SVG
        run: |
          DB_PATH="${{ github.workspace }}/wikipathways-database"
          AS_PATH="${{ github.workspace }}/wikipathways-assets"
          for f in ${{needs.changed-gpmls.outputs.added-modified}}; do
            wpid="$(basename ""$f"" | sed 's/.gpml//')"
            echo "generating JSON and SVG files for $wpid"
            cd "$AS_PATH"
            mkdir -p pathways/"$wpid"
            
            for old_f in pathways/"$wpid"/"$wpid".{json,svg}; do 
              if [ -e "$old_f" ]; then
                rm "$old_f"
              fi
            done

            # cp gpml and tsv to assets
            cp $DB_PATH/pathways/"$wpid"/"$wpid".gpml $AS_PATH/pathways/"$wpid"/
            cp $DB_PATH/pathways/"$wpid"/"$wpid"-bibliography.tsv $AS_PATH/pathways/"$wpid"/
            cp $DB_PATH/pathways/"$wpid"/"$wpid"-datanodes.tsv $AS_PATH/pathways/"$wpid"/
            
            cd "$DB_PATH/scripts/generate-svgs"
            ./gpmlconverter --id "$wpid" -i $DB_PATH/pathways/"$wpid"/"$wpid".gpml -o $AS_PATH/pathways/"$wpid"/"$wpid".svg
            
            # delete intermediate JSON files
            rm $AS_PATH/pathways/"$wpid"/"$wpid".json.b4bridgedb.json || true
            rm $AS_PATH/pathways/"$wpid"/"$wpid".b4wd.json || true
            rm $AS_PATH/pathways/"$wpid"/"$wpid".b4hgnc.json || true
            
            # mv thumbnail png
            mv $AS_PATH/pathways/"$wpid"/"$wpid"-thumb.png $DB_PATH/pathways/"$wpid"/

            # pretty print the JSON
            for json_f in $AS_PATH/pathways/"$wpid"/"$wpid".json; do
              mv "$json_f" "$json_f".tmp.json 
              jq -S . "$json_f".tmp.json >"$json_f"
              rm "$json_f".tmp.json
            done
          done

      - name: Commit report for assets
        run: |
          git config --global user.name 'GitHub Action'
          git config --global user.email 'action@github.com'
          cd wikipathways-assets
          git add pathways/WP*/WP*.{json,svg,png,gpml,tsv}
          if git diff --exit-code --staged; then
              echo "No changes"
          else
              git commit -m 'Update JSON, SVG, PNG, TSV and GPML files'
              git pull --rebase
              git push
          fi
          
      - name: Commit report for database
        run: |
          git config --global user.name 'GitHub Action'
          git config --global user.email 'action@github.com'
          cd wikipathways-database
          git add pathways/WP*/WP*-thumb.png
          if git diff --exit-code --staged; then
              echo "No changes"
          else
              git commit -m 'Update PNG files'
              git pull --rebase --autostash
              git push
          fi

  sync-site-repo-added-modified:
    runs-on: ubuntu-latest
    needs: [changed-gpmls, metadata, pubmed, frontmatter, json-svg]
    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          path: wikipathways-database
          submodules: true
          fetch-depth: 1
          ref: main
          
      - name: Checkout jekyll repo
        uses: actions/checkout@v4
        with:
          repository: wikipathways/wikipathways.github.io
          path: wikipathways.github.io
          submodules: true
          fetch-depth: 1
          ref: main
          ssh-key: ${{ secrets.ACTIONS_DEPLOY_KEY }}

      - name: Set up ssh-agent
        uses: webfactory/ssh-agent@v0.9.0
        with:
          ssh-private-key: ${{ secrets.ACTIONS_DEPLOY_KEY }}   ## for push into wp.gh.io repo

      - name: Commit report
        run: |
          git config --global user.name 'GitHub Action'
          git config --global user.email 'action@github.com'
          for f in ${{needs.changed-gpmls.outputs.added-modified}}; do
            wpid="$(basename ""$f"" | sed 's/.gpml//')"
            cp wikipathways-database/pathways/"$wpid"/"$wpid".md wikipathways.github.io/_pathways/
            cp wikipathways-database/pathways/"$wpid"/"$wpid"-bibliography.tsv wikipathways.github.io/_data/
            cp wikipathways-database/pathways/"$wpid"/"$wpid"-datanodes.tsv wikipathways.github.io/_data/
            mkdir -p wikipathways.github.io/assets/img/"$wpid"
            cp wikipathways-database/pathways/"$wpid"/"$wpid"-thumb.png wikipathways.github.io/assets/img/"$wpid"/
          done
          cd wikipathways.github.io
          git add .
          if git diff --exit-code --staged > /dev/null; then
              echo "No changes"
          else
              git commit -m 'Update tsv, md and png files'
              git pull --rebase
              git push
          fi

  sync-assets-repo-deleted:
    runs-on: ubuntu-latest
    needs: changed-gpmls
    # only run if gpmls were deleted
    if: ${{needs.changed-gpmls.outputs.deleted}}
    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          path: wikipathways-database
          submodules: true
          fetch-depth: 1
          ref: main
          
      - name: Checkout assets repo
        uses: actions/checkout@v4
        with:
          repository: wikipathways/wikipathways-assets
          path: wikipathways-assets
          submodules: true
          fetch-depth: 1
          ref: main
          ssh-key: ${{ secrets.ACTIONS_ASSETS_KEY }}

      - name: Set up ssh-agent
        uses: webfactory/ssh-agent@v0.9.0
        with:
          ssh-private-key: ${{ secrets.ACTIONS_ASSETS_KEY }}   ## for push into wp-assets rep 

      - name: Commit report
        run: |
          git config --global user.name 'GitHub Action'
          git config --global user.email 'action@github.com'
          cd wikipathways-assets
          for f in ${{needs.changed-gpmls.outputs.deleted}}; do
            wpid="$(basename ""$f"" | sed 's/.gpml//')"
            echo "deleting $wpid from wikipathways-assets"
            git rm pathways/"$wpid"/*
          done          
          if git diff --exit-code --staged > /dev/null; then
              echo "No changes"
          else
              git commit -m 'Remove deleted asset files'
              git pull --rebase
              git push
          fi

  sync-site-repo-deleted:
    runs-on: ubuntu-latest
    needs: changed-gpmls
    # only run if gpmls were deleted
    if: ${{needs.changed-gpmls.outputs.deleted}}
    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          path: wikipathways-database
          submodules: true
          fetch-depth: 1
          ref: main

      - name: Checkout jekyll repo
        uses: actions/checkout@v4
        with:
          repository: wikipathways/wikipathways.github.io
          path: wikipathways.github.io
          submodules: true
          fetch-depth: 1
          ref: main
          ssh-key: ${{ secrets.ACTIONS_DEPLOY_KEY }}

      - name: Set up ssh-agent
        uses: webfactory/ssh-agent@v0.9.0
        with:
          ssh-private-key: ${{ secrets.ACTIONS_DEPLOY_KEY }}   ## for push into wp.gh.io rep

      - name: Commit report
        run: |
          git config --global user.name 'GitHub Action'
          git config --global user.email 'action@github.com'
          cd wikipathways.github.io
          for f in ${{needs.changed-gpmls.outputs.deleted}}; do
            wpid="$(basename ""$f"" | sed 's/.gpml//')"
            echo "deleting $wpid from wikipathways.github.io"
            if [ -e _pathways/"$wpid".md ]; then
              git rm _pathways/"$wpid".md
            fi
            if [ -e _data/"$wpid"-bibliography.tsv ]; then
              git rm _data/"$wpid"-bibliography.tsv
            fi
            if [ -e _data/"$wpid"-datanodes.tsv ]; then
              git rm _data/"$wpid"-datanodes.tsv
            fi
            if [ -e assets/img/"$wpid"/"$wpid"-thumb.png ]; then
              git rm assets/img/"$wpid"/"$wpid"-thumb.png
            fi
          done
          if git diff --exit-code --staged > /dev/null; then
              echo "No changes"
          else
              git commit -m 'Remove deleted tsv, md and png file(s)'
              git pull --rebase
              git push
          fi