KEGG database update #7
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| name: KEGG database update | |
| # | |
| # update the KEGG sqlite database every three months | |
| # | |
| on: | |
| schedule: | |
| - cron: '0 0 1 1,3,6,9,12 *' | |
| workflow_dispatch: | |
| jobs: | |
| update-kegg-db: | |
| permissions: | |
| contents: write | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: utilities_2_0 | |
| - name: Set up JDK 17 | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: '17' | |
| distribution: 'temurin' | |
| cache: maven | |
| - name: Setup mvn cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.m2/repository | |
| key: ${{ runner.os }}-mgx-cache | |
| - name: Compile | |
| run: | | |
| mvn clean install -N | |
| mvn clean install -DskipTests=true --file JFreeSVG-OSGi/pom.xml | |
| mvn clean install -DskipTests=true --file RESTEasy-OSGi/pom.xml | |
| mvn clean install -DskipTests=true --file KEGG-Pathways/pom.xml | |
| - name: Create new KEGG database | |
| run: java -jar KEGG-Pathways/target/KEGG-Pathways-2.0.jar | |
| - name: Run KEGG CI tests | |
| run: | | |
| cp /tmp/kegg/kegg.db KEGG-Pathways/src/main/resources/de/cebitec/mgx/kegg/ | |
| mvn -B package --file KEGG-Pathways/pom.xml | |
| - name: Commit KEGG database | |
| uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: "Automated KEGG database update [ci skip]" | |
| file_pattern: 'KEGG-Pathways/src/main/resources/de/cebitec/mgx/kegg/kegg.db' | |