Fix IRI of vp4cat profile in config #415
Workflow file for this run
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| # This action runs when a pull request to main is created or updated | |
| # (but not when it is merged into main). | |
| name: CI on pull request create or update | |
| on: | |
| # Using "pull_request" is not sufficient to allow commits to PR branches in | |
| # forks. Since the workflow only accesses the xlsx and turtle files, but does | |
| # not run any code, it is safe to use pull_request_target. More info: | |
| # https://securitylab.github.com/resources/github-actions-preventing-pwn-requests/ | |
| # zizmor: ignore[dangerous-triggers] OK as per comment above | |
| pull_request_target: | |
| branches: | |
| - main | |
| types: [opened, reopened, synchronize] | |
| workflow_dispatch: | |
| env: | |
| PIP_DISABLE_PIP_VERSION_CHECK: "1" | |
| PIP_PROGRESS_BAR: "off" | |
| LOGLEVEL: "DEBUG" | |
| RUN_URL: $GITHUB_SERVER_URL/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| permissions: {} | |
| jobs: | |
| build_vocab: | |
| name: Merge & build vocabulary | |
| # Run on all pull request types except merge which has its own workflow. | |
| if: ${{ !github.event.pull_request.merged }} | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 10 | |
| permissions: | |
| contents: write # Give the default GITHUB_TOKEN write permission to commit to the PR branch. | |
| steps: | |
| - name: Checkout PR branch into cwd | |
| uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd | |
| with: | |
| # Checkout the fork/head-repository to push changes to the fork. | |
| # Without this the base repository will be checked out and committed to. | |
| repository: ${{ github.event.pull_request.head.repo.full_name }} | |
| # Checkout the branch made in the fork. | |
| ref: ${{ github.head_ref }} | |
| # The full history is required for "voc4cat transform --prov-from-git" below. | |
| fetch-depth: 0 | |
| # Be specific about keeping credentials (it is the default) | |
| persist-credentials: true | |
| - name: Checkout main branch into directory _main_branch/ | |
| uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd | |
| with: | |
| ref: main | |
| path: _main_branch | |
| # This sparse-checkout includes all toplevel files and everything below vocabularies/ | |
| sparse-checkout: | | |
| vocabularies/ | |
| fetch-depth: 1 | |
| # Be specific about keeping credentials (it is the default) | |
| persist-credentials: true | |
| - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 | |
| with: | |
| python-version: '3.13' | |
| - name: Install dependencies | |
| run: | | |
| python -VV | |
| python -m pip install --upgrade pip setuptools wheel | |
| # Select to install a stable tagged version or main branch (in development) | |
| python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v1.0.4 | |
| # python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@main | |
| # install custom pylode 2.x (adds sorted collections, | |
| # uses URIs as fragment IDs and is git-installable) | |
| python -m pip install git+https://github.com/dalito/pyLODE.git@nfdi4cat-2.x | |
| - name: Set dynamic environment variables. | |
| run: | # zizmor: ignore[github-env] safe without user controllable input | |
| echo "RUN_DATE=$(date +'%Y-%m-%dT%H%M')" >> $GITHUB_ENV | |
| - name: Run voc4cat (pre-convert checks) | |
| run: | | |
| voc4cat --version | |
| # check inbox file names | |
| voc4cat check --config _main_branch/idranges.toml --logfile outbox/voc4cat.log --ci-pre inbox-excel-vocabs/ _main_branch/vocabularies | |
| # check xlsx file(s). If the check fails, write annotated file to outbox. | |
| voc4cat check --config _main_branch/idranges.toml --logfile outbox/voc4cat.log --outdir outbox inbox-excel-vocabs/ | |
| - name: Run voc4cat (convert) | |
| run: | | |
| # convert file(s) from xlsx in inbox to turtle in outbox | |
| voc4cat convert --config _main_branch/idranges.toml --logfile outbox/voc4cat.log --outdir outbox inbox-excel-vocabs/ | |
| if [ ! -f outbox/*.ttl ]; then | |
| echo "No ttl file in outbox. Building joined vocabulary ttl-file from individual ttl-files in vocabulary." | |
| voc4cat transform --join --config _main_branch/idranges.toml --logfile outbox/voc4cat.log --outdir outbox/ vocabularies/ | |
| fi | |
| - name: Run voc4cat (post-convert checks) | |
| run: | | |
| # check all ttl file(s) in outbox | |
| voc4cat check --redundant-hierarchies --config _main_branch/idranges.toml --logfile outbox/voc4cat.log outbox/ | |
| # check if vocabulary changes are allowed | |
| voc4cat check --config _main_branch/idranges.toml --logfile outbox/voc4cat.log --ci-post _main_branch/vocabularies outbox/ | |
| - name: Run voc4cat (build HTML documentation) | |
| run: | | |
| voc4cat docs --logfile outbox/voc4cat.log --force outbox/ | |
| - name: Split vocabulary, merge into vocabulary dir (in PR branch) and update provenance info | |
| run: | | |
| voc4cat transform --split --inplace --config idranges.toml --logfile outbox/voc4cat.log --outdir outbox_new_voc outbox/ | |
| voc4cat-merge --logfile outbox/voc4cat.log outbox_new_voc/ vocabularies/ | |
| # copy xlsx to outbox so that the xlsx file is part of the artifact | |
| find inbox-excel-vocabs -name '*.xlsx' -exec cp {} -t outbox/ \; | |
| git status | |
| # Add/update dct:created and dct:modified base on git history | |
| voc4cat transform --prov-from-git --diff-base origin/main --inplace --config idranges.toml --logfile outbox/voc4cat.log vocabularies/ | |
| - name: Run voc4cat (re-build updated Excel file and joined turtle vocabulary file) | |
| # Passing the config is important to make use of the prefixes therein. | |
| run: | | |
| mkdir -p outbox/updated-xlsx-ttl | |
| voc4cat transform --join --config idranges.toml --logfile outbox/voc4cat.log --outdir outbox/updated-xlsx-ttl vocabularies/ | |
| # Using a template is optional and gives just a warning if missing. | |
| voc4cat convert --config idranges.toml --logfile outbox/voc4cat.log --template templates/default_sheets.xlsx outbox/updated-xlsx-ttl | |
| - name: Store artifacts | |
| if: ${{ always() }} | |
| uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f | |
| with: | |
| name: voc4cat-outbox_${{ env.RUN_DATE }}_run${{ GITHUB.RUN_ID }} | |
| path: outbox/ | |
| - name: Add/stage vocabulary changes | |
| # Pinning of action managed by dependabot | |
| uses: stefanzweifel/git-auto-commit-action@04702edda442b2e678b25b537cec683a1493fcb9 | |
| with: | |
| # glob pattern of files which should be added to the commit | |
| file_pattern: 'vocabularies/\*.ttl' | |
| - name: Remove Excel vocabulary files from inbox | |
| run: | | |
| git rm inbox-excel-vocabs/\*.xlsx || echo "No xlsx files to remove." | |
| git status | |
| - name: Commit vocabulary changes & xlsx cleanup on behalf of PR-author | |
| # Pinning of action managed by dependabot | |
| uses: stefanzweifel/git-auto-commit-action@04702edda442b2e678b25b537cec683a1493fcb9 | |
| with: | |
| commit_user_name: voc4cat-CI-bot | |
| commit_message: 'CI: vocabulary update in ${{ GITHUB.SERVER_URL }}/${{ GITHUB.REPOSITORY }}/actions/runs/${{ GITHUB.RUN_ID }}' |