Additional reagents associated with doi: 10.1101/2024.02.28.582563 #287
Workflow file for this run
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| name: IBEX Knowledge-Base Data Validation and Update | |
| on: | |
| push: | |
| branches: | |
| - main | |
| paths-ignore: # ignore auto-generated files, only run when source files change | |
| - docs/contrib.md | |
| - docs/fluorescent_probes.md | |
| - docs/index.md | |
| - docs/protocols.md | |
| - docs/publications.md | |
| - docs/reagent_resources.md | |
| - docs/the_who.md | |
| - docs/videos.md | |
| - docs/data_and_software.md | |
| pull_request: | |
| branches: | |
| - main | |
| # Enable manual running of workflow, so that if the validation or | |
| # markdown generation code changes we can force execution | |
| workflow_dispatch: | |
| jobs: | |
| preliminary_test: | |
| # run all pre-commit tests (see .pre-commit-config.yaml) | |
| runs-on: macos-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Run pre-commit tests | |
| run: | | |
| pip install pre-commit | |
| pre-commit run --all-files | |
| pr_preliminary_test: | |
| # check that no auto-generated file was modified in a PR on main so just check we're dealing with a PR | |
| # (workflow "on" event settings are all on main branch) | |
| needs: preliminary_test | |
| if: github.event_name == 'pull_request' | |
| runs-on: macos-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: dorny/paths-filter@v3 | |
| id: filter | |
| with: | |
| filters: | | |
| autogenerated_docs: | |
| - docs/contrib.md | |
| - docs/fluorescent_probes.md | |
| - docs/index.md | |
| - docs/protocols.md | |
| - docs/publications.md | |
| - docs/reagent_resources.md | |
| - docs/the_who.md | |
| - docs/videos.md | |
| - docs/data_and_software.md | |
| - name: modified autogenerated docs # succeed if no auto-generated files modified, otherwise fail | |
| if: steps.filter.outputs.autogenerated_docs != 'false' | |
| run: | | |
| echo "The pull request includes changes to auto-generated files, this is not allowed. Please modify the relevant files in the docs_in and data directories." | |
| exit 1 | |
| validate_data: | |
| needs: preliminary_test | |
| runs-on: macos-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Install dependencies and validate data | |
| run: | # validate the various data files, update the wheel version here whenever the validation scripts are updated | |
| pip install --upgrade pip | |
| pip install https://github.com/IBEXImagingCommunity/ibex_imaging_knowledge_base_utilities/releases/download/v0.8.2/ibex_imaging_knowledge_base_utilities-0.8.2-py3-none-any.whl | |
| validate_zenodo_json .zenodo.json | |
| validate_bibfile data/publications.bib | |
| validate_basic data/protocols.csv .github/data_validation_configs/protocols.json | |
| validate_basic data/vendor_urls.csv .github/data_validation_configs/vendors.json | |
| validate_basic data/datasets.csv .github/data_validation_configs/datasets.json | |
| validate_basic data/software.csv .github/data_validation_configs/software.json | |
| validate_basic data/fluorescent_probes.csv .github/data_validation_configs/fluorescent_probes.json | |
| validate_videos data/videos.csv .github/data_validation_configs/videos.json .zenodo.json | |
| validate_image_resources data/image_resources.csv .github/data_validation_configs/image_resources.json docs/supporting_material | |
| validate_reagent_resources data/reagent_resources.csv .github/data_validation_configs/reagent_resources.json .zenodo.json data/vendor_urls.csv docs/supporting_material | |
| data_2_md: | |
| # run the data to markdown updates only when pushing to the main branch or forced execution via workflow_dispatch | |
| needs: validate_data | |
| if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' || github.event_name == 'workflow_dispatch'}} | |
| runs-on: macos-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Install dependencies | |
| run: | | |
| brew update | |
| brew install pandoc | |
| pip install --upgrade pip | |
| pip install https://github.com/IBEXImagingCommunity/ibex_imaging_knowledge_base_utilities/releases/download/v0.7.0/ibex_imaging_knowledge_base_utilities-0.7.0-py3-none-any.whl | |
| - name: Fine tune data to markdown conversion | |
| id: ft | |
| shell: bash | |
| run: | | |
| convert_bib=0 | |
| convert_reagents=0 | |
| update_index=0 | |
| convert_fluorescent=0 | |
| convert_the_who=0 | |
| update_how_to_contrib=0 | |
| convert_protocols=0 | |
| convert_videos=0 | |
| convert_data_software=0 | |
| if [ "${{ github.event_name }}" = "workflow_dispatch" ]; then | |
| convert_bib=1 | |
| convert_reagents=1 | |
| update_index=1 | |
| convert_fluorescent=1 | |
| convert_the_who=1 | |
| update_how_to_contrib=1 | |
| convert_protocols=1 | |
| convert_videos=1 | |
| convert_data_software=1 | |
| else | |
| if ! git diff --quiet HEAD\^ HEAD -- data/publications.bib data/ibex.csl; then | |
| convert_bib=1 | |
| fi | |
| if ! git diff --quiet HEAD\^ HEAD -- docs_in/reagent_resources.md.in data/reagent_resources.csv data/vendor_urls.csv; then | |
| convert_reagents=1 | |
| fi | |
| if ! git diff --quiet HEAD\^ HEAD -- docs_in/index.md.in data/reagent_resources.csv; then | |
| update_index=1 | |
| fi | |
| if ! git diff --quiet HEAD\^ HEAD -- docs_in/fluorescent_probes.md.in data/fluorescent_probes.csv; then | |
| convert_fluorescent=1 | |
| fi | |
| if ! git diff --quiet HEAD\^ HEAD -- docs_in/the_who.md.in .zenodo.json; then | |
| convert_the_who=1 | |
| fi | |
| if ! git diff --quiet HEAD\^ HEAD -- docs_in/contrib.md.in data/reagent_data_dict.csv data/reagent_glossary.csv; then | |
| update_how_to_contrib=1 | |
| fi | |
| if ! git diff --quiet HEAD\^ HEAD -- docs_in/protocols.md.in data/protocols.csv; then | |
| convert_protocols=1 | |
| fi | |
| if ! git diff --quiet HEAD\^ HEAD -- docs_in/videos.md.in data/videos.csv; then | |
| convert_videos=1 | |
| fi | |
| if ! git diff --quiet HEAD\^ HEAD -- docs_in/data_and_software.md.in data/datasets.csv data/software.csv; then | |
| convert_data_software=1 | |
| fi | |
| fi | |
| echo "convert_bib=$convert_bib" >> $GITHUB_OUTPUT | |
| echo "convert_reagents=$convert_reagents" >> $GITHUB_OUTPUT | |
| echo "update_index=$update_index" >> $GITHUB_OUTPUT | |
| echo "convert_fluorescent=$convert_fluorescent" >> $GITHUB_OUTPUT | |
| echo "convert_the_who=$convert_the_who" >> $GITHUB_OUTPUT | |
| echo "update_how_to_contrib=$update_how_to_contrib" >> $GITHUB_OUTPUT | |
| echo "convert_protocols=$convert_protocols" >> $GITHUB_OUTPUT | |
| echo "convert_videos=$convert_videos" >> $GITHUB_OUTPUT | |
| echo "convert_data_software=$convert_data_software" >> $GITHUB_OUTPUT | |
| - name: Convert bibliography to markdown | |
| if: ${{ steps.ft.outputs.convert_bib == '1' }} | |
| run: | | |
| pandoc --version | |
| bib2md data/publications.bib data/ibex.csl docs/publications.md | |
| - name: Convert reagent resources csv to markdown | |
| if: ${{ steps.ft.outputs.convert_reagents == '1' }} | |
| run: | | |
| reagent_resources_csv_2_md_url docs_in/reagent_resources.md.in data/reagent_resources.csv data/vendor_urls.csv docs/supporting_material | |
| - name: Update the index.md file statistics | |
| if: ${{ steps.ft.outputs.update_index == '1' }} | |
| run: | | |
| update_index_md_stats docs_in/index.md.in data/reagent_resources.csv docs/ | |
| - name: Convert fluorescent probes csv to markdown | |
| if: ${{ steps.ft.outputs.convert_fluorescent == '1' }} | |
| run: | | |
| fluorescent_probes_csv_2_md docs_in/fluorescent_probes.md.in data/fluorescent_probes.csv docs/ | |
| - name: Convert Zenodo data to contributors list markdown | |
| if: ${{ steps.ft.outputs.convert_the_who == '1' }} | |
| run: | | |
| zenodo_json_2_thewho_md docs_in/the_who.md.in .zenodo.json docs/ | |
| - name: Update how to contribute markdown | |
| if: ${{ steps.ft.outputs.update_how_to_contrib == '1' }} | |
| run: | | |
| data_dict_glossary_2_contrib_md docs_in/contrib.md.in data/reagent_data_dict.csv data/reagent_glossary.csv docs/ | |
| - name: Convert protocols csv to markdown | |
| if: ${{ steps.ft.outputs.convert_protocols == '1' }} | |
| run: | | |
| protocols_csv_2_md docs_in/protocols.md.in data/protocols.csv docs/ | |
| - name: Convert videos csv to markdown | |
| if: ${{ steps.ft.outputs.convert_videos == '1' }} | |
| run: | | |
| videos_csv_2_md docs_in/videos.md.in data/videos.csv docs/ | |
| - name: Convert datasets and software csv files to markdown | |
| if: ${{ steps.ft.outputs.convert_data_software == '1' }} | |
| run: | | |
| data_software_csv_2_md docs_in/data_and_software.md.in data/datasets.csv data/software.csv docs/ | |
| - name: Commit and push | |
| shell: bash | |
| run: | | |
| if ! git diff --quiet; then | |
| git config --local user.email "$(git log --format='%ae' HEAD^!)" | |
| git config --local user.name "$(git log --format='%an' HEAD^!)" | |
| git add docs/*.md | |
| git commit -m "Adding converted markdowns." | |
| git push | |
| fi |