Weekly caching of bridge and meta-data-action #83
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| 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 |