scheduled_bridge_cache.yml

name: Weekly caching of bridge and meta-data-action

on:
  repository_dispatch: # triggered by https://github.com/bridgedb/data/blob/main/.github/workflows/geneUpdates.yml
    types: [bridgedb-data-update-event]
  workflow_dispatch:
  schedule:
  - cron: "0 0 * * 0"

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

jobs:
  refresh-cache:
    runs-on: ubuntu-latest
    steps:
    
      - name: Checkout wikipathways-database repo
        uses: actions/checkout@v3
        with:
          fetch-depth: 0
          ref: main

      - 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-1.1.1-jar-with-dependencies.jar
          key: cached-meta-data-action-${{ hashFiles('meta-data-action-1.1.1-jar-with-dependencies.jar') }}
          restore-keys: |
            cached-meta-data-action-${{ hashFiles('meta-data-action-1.1.1-jar-with-dependencies.jar') }}
            cached-meta-data-action-
    
      - name: Install deps
        run: |
          echo "Refreshing cached-meta-data-action"
          if [ ! -e ./meta-data-action-1.1.1-jar-with-dependencies.jar ]; then
            wget -O meta-data-action-1.1.1-jar-with-dependencies.jar https://github.com/wikipathways/meta-data-action/releases/download/v1.1.1/meta-data-action-1.1.1-jar-with-dependencies.jar
          fi

                
      - name: Cache and install dependencies
        uses: actions/cache@v3
        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: Generate gdb.config, fileNames.config, and fileDownloads.config
        run: |
          for f in ${{needs.changed-gpmls.outputs.added-modified}}; do
            scripts/meta-data-action/configGenerator.sh $f
          done
          
      - 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
            
      - 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