New validation results (and 2 new pathways) #16
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| name: When GPML changed, do everything | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - main | |
| 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@v3 | |
| with: | |
| repository: wikipathways/wikipathways-database | |
| path: wikipathways-database | |
| 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 | |
| metadata: | |
| runs-on: ubuntu-latest | |
| needs: changed-gpmls | |
| # only run if gpmls were added or modified | |
| if: ${{needs.changed-gpmls.outputs.added-modified}} | |
| steps: | |
| - name: Checkout wikipathways-database repo | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: wikipathways/wikipathways-database | |
| path: wikipathways-database | |
| fetch-depth: 1 | |
| ref: main | |
| - name: Setup Java | |
| uses: actions/setup-java@v3 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '11' | |
| - name: Cache meta-data-action with dependencies | |
| uses: actions/cache@v3 | |
| id: cacheGPMLRDFJar | |
| with: | |
| path: ./GPML2RDF-3.0.0-SNAPSHOT.jar | |
| key: cached-meta-data-action-${{ hashFiles('GPML2RDF-3.0.0-SNAPSHOT.jarr') }} | |
| restore-keys: | | |
| cached-meta-data-action-${{ hashFiles('GPML2RDF-3.0.0-SNAPSHOT.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 ./GPML2RDF-3.0.0-SNAPSHOT.jar ]; then | |
| wget -O GPML2RDF-3.0.0-SNAPSHOT.jar https://github.com/wikipathways/wikipathways-curation-template/releases/download/release-7/GPML2RDF-3.0.0-SNAPSHOT.jar | |
| fi | |
| - name: Generate RDF | |
| run: | | |
| for f in ${{needs.changed-gpmls.outputs.added-modified}}; do | |
| echo "generating RDF for "$f"" | |
| done | |
| - name: Commit report | |
| run: | | |
| git config --global user.name 'GitHub Action' | |
| git config --global user.email '[email protected]' | |
| git add pathways/WP*/WP*.{json,tsv} | |
| if git diff --exit-code --staged; then | |
| echo "No changes" | |
| fi |