Remove Biospecimen preparation from BulkMCseq L1 #40
Workflow file for this run
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name: Lint, validate and convert CSV to JSON-LD | |
on: | |
pull_request: | |
branches: 'main' | |
paths: 'HTAN.model.csv' | |
workflow_dispatch: | |
jobs: | |
lint: | |
name: Lint CSV | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
- name: csvlinter | |
uses: kcheriyath/[email protected] | |
with: | |
find_pattern: "*.csv" | |
validate: | |
name: Validate CSV | |
runs-on: ubuntu-latest | |
env: | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: '3.10' | |
- name: Install Schematic | |
shell: bash | |
run: | | |
pip3 install poetry | |
git clone --single-branch --branch main https://github.com/Sage-Bionetworks/schematic.git | |
cd schematic | |
poetry build | |
pip3 install dist/schematicpy-*-py3-none-any.whl | |
pip install --force-reinstall typing-extensions==4.5.0 | |
- name: Convert CSV schema | |
shell: bash | |
run: | | |
schematic schema convert .github/CSV.model.csv | |
- name: Validate data model CSV | |
shell: bash | |
run: | | |
schematic model -c .github/CSV_schematic_config.yml validate -mp HTAN.model.csv -dt "DataModel" | | |
grep "Your manifest has been validated successfully. There are no errors in your manifest, and it can be submitted without any modifications." | |
component_check: | |
name: Check Component DependsOn entries | |
runs-on: ubuntu-latest | |
env: | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: '3.10' | |
- name: Install Python dependencies | |
run: python -m pip install --upgrade pip pandas | |
- name: Run script | |
shell: bash | |
run: | | |
python .github/workflows/check_components.py | |
convert: | |
name: Convert CSV to JSON-LD | |
needs: | |
- lint | |
- validate | |
- component_check | |
runs-on: ubuntu-latest | |
env: | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: '3.9' | |
- name: Install Schematic | |
shell: bash | |
run: | | |
pip3 install poetry | |
git clone --single-branch --branch main https://github.com/Sage-Bionetworks/schematic.git | |
cd schematic | |
poetry build | |
pip3 install dist/schematicpy-*-py3-none-any.whl | |
- name: Convert .csv to .jsonld | |
shell: bash | |
run: | | |
schematic schema convert HTAN.model.csv | |
- uses: r-lib/actions/pr-fetch@v2 | |
with: | |
repo-token: ${{ secrets.GITHUB_TOKEN }} | |
- name: Commit the changes | |
run: | | |
git config --local user.name "$GITHUB_ACTOR" | |
git config --local user.email "[email protected]" | |
git add HTAN.model.jsonld | |
git commit -m "GitHub Action: convert *.model.csv to *.model.jsonld" || echo "No changes to commit" | |
- uses: r-lib/actions/pr-push@v2 | |
with: | |
repo-token: ${{ secrets.GITHUB_TOKEN }} |