Merge pull request #989 from Sage-Bionetworks/MasterPastures-patch-20 #113
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| on: | |
| push: | |
| branches: master | |
| name: Register schemas & update tables | |
| env: | |
| RENV_PATHS_ROOT: ~/.local/share/renv | |
| SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_PAT }} | |
| jobs: | |
| register-and-update: | |
| runs-on: macos-12 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: '4.2' | |
| - name: Cache packages | |
| uses: actions/cache@v1 | |
| with: | |
| path: ${{ env.RENV_PATHS_ROOT }} | |
| key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }} | |
| restore-keys: | | |
| ${{ runner.os }}-renv- | |
| - name: Restore packages | |
| shell: Rscript {0} | |
| run: | | |
| if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv") | |
| install.packages("sys") | |
| renv::restore() | |
| - name: Set up Synapse config file for testing | |
| run: | | |
| OUTPUT_FILE=~/.synapseConfig | |
| cat > "$OUTPUT_FILE" << EOM | |
| [authentication] | |
| authtoken = "${{ secrets.SYNAPSE_PAT }}" | |
| EOM | |
| chmod +x "$OUTPUT_FILE" | |
| - name: Get file changes | |
| id: get_file_changes | |
| uses: trilom/[email protected] | |
| with: | |
| output: ',' | |
| - name: Register schemas in Synapse | |
| run: | | |
| files="${{ steps.get_file_changes.outputs.files_added }},${{ steps.get_file_changes.outputs.files_modified }}" | |
| echo $files | tr ',' '\n' | grep -Z '^terms.*\.json$' | xargs ./register-schemas.R | |
| - name: Update Synapse key-value table | |
| run: | | |
| Rscript ./update-annotations-table.R | |
| - name: Update Synapse schema versions table | |
| run: | | |
| Rscript ./update-schema-version-table.R |