fix: remove all remaining ColumnType references #13
Workflow file for this run
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| name: Generate and Register JSON Schemas in Synapse | |
| on: | |
| push: | |
| tags: | |
| - 'v*' # Trigger on version tags | |
| workflow_dispatch: # Allow manual triggering | |
| inputs: | |
| version: | |
| description: 'Version to release (e.g., 1.0.0)' | |
| required: true | |
| default: '0.1.0' | |
| env: | |
| PYTHON_VERSION: '3.11' | |
| ORGANIZATION_NAME: 'HTAN2' | |
| jobs: | |
| generate-and-register-schemas: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Needed for version detection | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| - name: Install Poetry | |
| uses: snok/install-poetry@v1 | |
| with: | |
| version: latest | |
| virtualenvs-create: true | |
| virtualenvs-in-project: true | |
| - name: Load cached venv | |
| id: cached-poetry-dependencies | |
| uses: actions/cache@v4 | |
| with: | |
| path: .venv | |
| key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }} | |
| - name: Install dependencies | |
| if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' | |
| run: poetry install --no-interaction --no-root | |
| - name: Determine version | |
| id: version | |
| run: | | |
| if [ "${{ github.event_name }}" = "workflow_dispatch" ]; then | |
| echo "version=v${{ github.event.inputs.version }}" >> $GITHUB_OUTPUT | |
| else | |
| # Extract version from git tag | |
| VERSION=${GITHUB_REF#refs/tags/} | |
| echo "version=$VERSION" >> $GITHUB_OUTPUT | |
| fi | |
| echo "Version: ${{ steps.version.outputs.version }}" | |
| - name: Generate JSON Schemas | |
| run: | | |
| # Create output directory | |
| mkdir -p generated-schemas | |
| # Generate schemas for individual Clinical domains | |
| echo "Generating Clinical domain schemas..." | |
| # Demographics | |
| poetry run python scripts/linkml_to_flat_synapse_jsonschema.py \ | |
| "modules/Clinical/domains/demographics.yaml" \ | |
| --class-name "Demographics" \ | |
| --output "HTAN.Demographics-${{ steps.version.outputs.version }}-schema.json" | |
| # Diagnosis | |
| poetry run python scripts/linkml_to_flat_synapse_jsonschema.py \ | |
| "modules/Clinical/domains/diagnosis.yaml" \ | |
| --class-name "Diagnosis" \ | |
| --output "HTAN.Diagnosis-${{ steps.version.outputs.version }}-schema.json" | |
| # Therapy | |
| poetry run python scripts/linkml_to_flat_synapse_jsonschema.py \ | |
| "modules/Clinical/domains/therapy.yaml" \ | |
| --class-name "Therapy" \ | |
| --output "HTAN.Therapy-${{ steps.version.outputs.version }}-schema.json" | |
| # FollowUp | |
| poetry run python scripts/linkml_to_flat_synapse_jsonschema.py \ | |
| "modules/Clinical/domains/followup.yaml" \ | |
| --class-name "FollowUp" \ | |
| --output "HTAN.FollowUp-${{ steps.version.outputs.version }}-schema.json" | |
| # MolecularTest | |
| poetry run python scripts/linkml_to_flat_synapse_jsonschema.py \ | |
| "modules/Clinical/domains/molecular.yaml" \ | |
| --class-name "MolecularTest" \ | |
| --output "HTAN.MolecularTest-${{ steps.version.outputs.version }}-schema.json" | |
| # Exposure | |
| poetry run python scripts/linkml_to_flat_synapse_jsonschema.py \ | |
| "modules/Clinical/domains/exposure.yaml" \ | |
| --class-name "Exposure" \ | |
| --output "HTAN.Exposure-${{ steps.version.outputs.version }}-schema.json" | |
| # FamilyHistory | |
| poetry run python scripts/linkml_to_flat_synapse_jsonschema.py \ | |
| "modules/Clinical/domains/family_history.yaml" \ | |
| --class-name "FamilyHistory" \ | |
| --output "HTAN.FamilyHistory-${{ steps.version.outputs.version }}-schema.json" | |
| # VitalStatus | |
| poetry run python scripts/linkml_to_flat_synapse_jsonschema.py \ | |
| "modules/Clinical/domains/vital_status.yaml" \ | |
| --class-name "VitalStatus" \ | |
| --output "HTAN.VitalStatus-${{ steps.version.outputs.version }}-schema.json" | |
| # WES Level 1 (file-based schema) | |
| poetry run python scripts/linkml_to_flat_synapse_jsonschema.py \ | |
| "modules/WES/domains/level_1.yaml" \ | |
| --class-name "BulkWESLevel1" \ | |
| --output "HTAN.BulkWESLevel1-${{ steps.version.outputs.version }}-schema.json" | |
| - name: Register schemas in Synapse | |
| env: | |
| SYNAPSE_USERNAME: ${{ secrets.SYNAPSE_USERNAME }} | |
| SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_AUTH_TOKEN }} | |
| run: | | |
| # Register each generated schema | |
| for schema_file in JSON_Schemas/*.json; do | |
| if [ -f "$schema_file" ]; then | |
| schema_name=$(basename "$schema_file" .json) | |
| echo "Processing schema: $schema_name" | |
| poetry run python scripts/synapse_json_schema_bind.py \ | |
| -p "$schema_file" \ | |
| -n "${{ env.ORGANIZATION_NAME }}" \ | |
| --no_bind | |
| fi | |
| done | |
| - name: Bind file-based schemas to existing project subfolders | |
| env: | |
| SYNAPSE_USERNAME: ${{ secrets.SYNAPSE_USERNAME }} | |
| SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_AUTH_TOKEN }} | |
| run: | | |
| # Test with HTAN2_Ovarian and existing WES_Level_1 subfolder (syn69630475) | |
| # This will bind the schema to the existing subfolder and create a fileview | |
| # Find WES Level 1 schema | |
| WES_SCHEMA=$(find JSON_Schemas -name "*WES*Level*1*" -o -name "*level_1*" | head -1) | |
| if [ -n "$WES_SCHEMA" ]; then | |
| echo "Found WES Level 1 schema: $WES_SCHEMA" | |
| echo "Binding to existing WES_Level_1 subfolder in HTAN2_Ovarian project..." | |
| poetry run python scripts/bind_file_based_schemas.py \ | |
| --schema-file "$WES_SCHEMA" \ | |
| --project-name "HTAN2_Ovarian" \ | |
| --subfolder-name "WES_Level_1" | |
| else | |
| echo "No WES Level 1 schema found, skipping file-based binding" | |
| fi | |
| # TODO: Later expand to bind all file-based schemas to all projects with existing subfolders | |
| # for project in HTAN2_Ovarian HTAN2_Glioma HTAN2_Gastric; do | |
| # poetry run python scripts/bind_file_based_schemas.py \ | |
| # --schema-file "$WES_SCHEMA" \ | |
| # --project-name "$project" \ | |
| # --subfolder-name "WES_Level_1" | |
| # done | |
| - name: Upload generated schemas as artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: json-schemas-${{ steps.version.outputs.version }} | |
| path: JSON_Schemas/ | |
| retention-days: 30 | |
| - name: Create Release | |
| if: startsWith(github.ref, 'refs/tags/') | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| run: | | |
| gh release create ${{ github.ref_name }} \ | |
| --title "Release ${{ steps.version.outputs.version }}" \ | |
| --notes "## JSON Schema Release ${{ steps.version.outputs.version }} | |
| This release includes updated JSON schemas for the HTAN2 data model. | |
| ### Generated Schemas: | |
| - Demographics Schema | |
| - Diagnosis Schema | |
| - Therapy Schema | |
| - FollowUp Schema | |
| - MolecularTest Schema | |
| - Exposure Schema | |
| - FamilyHistory Schema | |
| - VitalStatus Schema | |
| - BulkWESLevel1 Schema (file-based) | |
| All schemas have been registered in Synapse under the ${{ env.ORGANIZATION_NAME }} organization." | |
| - name: Upload schemas as release assets | |
| if: startsWith(github.ref, 'refs/tags/') | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| run: | | |
| # Upload each schema file as a release asset | |
| for schema_file in JSON_Schemas/*.json; do | |
| if [ -f "$schema_file" ]; then | |
| echo "Uploading $schema_file as release asset..." | |
| gh release upload ${{ github.ref_name }} "$schema_file" | |
| fi | |
| done |