Create Synapse Curation Task #80
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| name: Create Synapse Curation Task | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| upload_folder_id: | |
| description: 'Upload folder Synapse ID (e.g., syn12345678)' | |
| required: true | |
| type: string | |
| template: | |
| description: 'JSON Schema template name' | |
| required: true | |
| type: choice | |
| options: | |
| # Default option - most commonly used for genomics data | |
| - GenomicsAssayTemplate | |
| # Assay technical metadata templates | |
| - BehavioralAssayTemplate | |
| - BiologicalAssayDataTemplate | |
| - BulkSequencingAssayTemplate | |
| - ChIPSeqTemplate | |
| - ClinicalAssayTemplate | |
| - ElectrophysiologyAssayTemplate | |
| - EpidemiologyDataTemplate | |
| - EpigeneticsAssayTemplate | |
| - EpigenomicsAssayTemplate | |
| - FlowCytometryTemplate | |
| - GeneralMeasureDataTemplate | |
| - GeneticsAssayTemplate | |
| - GenomicsArrayTemplate | |
| - GenomicsAssayTemplateExtended | |
| - ImagingAssayTemplate | |
| - ImmunoMicroscopyTemplate | |
| - LightScatteringAssayTemplate | |
| - MassSpecAssayTemplate | |
| - MaterialScienceAssayTemplate | |
| - MethylationArrayTemplate | |
| - MicroscopyAssayTemplate | |
| - MRIAssayTemplate | |
| - NonBiologicalAssayDataTemplate | |
| - PdxGenomicsAssayTemplate | |
| - PharmacokineticsAssayTemplate | |
| - PlateBasedReporterAssayTemplate | |
| - ProteinArrayTemplate | |
| - ProteinAssayTemplate | |
| - ProteomicsAssayTemplate | |
| - RNASeqTemplate | |
| - ScRNASeqTemplate | |
| - ScSequencingAssayTemplate | |
| - WESTemplate | |
| - WGSTemplate | |
| # Processed data products (downstream analysis outputs) | |
| - ProcessedAlignedReadsTemplate | |
| - ProcessedExpressionTemplate | |
| - ProcessedMergedDataTemplate | |
| - ProcessedVariantCallsTemplate | |
| # Sample-level data templates | |
| # - AnimalIndividualTemplate | |
| # - BiospecimenTemplate | |
| # - HumanCohortTemplate | |
| # Portal/Documentation templates | |
| # - PortalDataset | |
| # - PortalPublication | |
| # - PortalStudy | |
| # - PublicationTemplate | |
| # Administrative/Workflow templates | |
| # - WorkflowReport | |
| # - UpdateMilestoneReport | |
| # Source code templates | |
| # - SourceCodeTemplate | |
| # Abstract/Generic templates (not meant for direct use) | |
| # - Template | |
| # - PartialTemplate | |
| # - Superdataset | |
| # Protocol documentation templates | |
| # - ProtocolTemplate | |
| instructions: | |
| description: 'Instructions to the data contributor' | |
| required: false | |
| type: string | |
| default: 'Please add metadata for your files' | |
| create_issue: | |
| description: 'Create mirror GitHub issue with task info' | |
| required: false | |
| type: boolean | |
| default: true | |
| jobs: | |
| create-task: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Validate inputs | |
| run: | | |
| if [[ ! "${{ inputs.upload_folder_id }}" =~ ^syn[0-9]+$ ]]; then | |
| echo "Error: upload_folder_id must be a valid Synapse ID (e.g., syn12345678)" | |
| exit 1 | |
| fi | |
| if [[ -z "${{ inputs.template }}" ]]; then | |
| echo "Error: template cannot be empty" | |
| exit 1 | |
| fi | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| - name: Install Synapse Python client | |
| run: | | |
| # Install from develop branch which has curation task support | |
| pip install git+https://github.com/Sage-Bionetworks/synapsePythonClient.git@develop | |
| - name: Create curation task and bind schema | |
| id: create_task | |
| env: | |
| SYNAPSE_AUTH_TOKEN: ${{ secrets.DATA_MODEL_SERVICE }} | |
| run: | | |
| python utils/create_curation_task.py \ | |
| --folder-id "${{ inputs.upload_folder_id }}" \ | |
| --template "${{ inputs.template }}" \ | |
| --instructions "${{ inputs.instructions }}" \ | |
| --bind-schema \ | |
| --output-format github | |
| - name: Display task summary | |
| if: success() | |
| run: | | |
| echo "## Curation Task Created Successfully" >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| echo "### Task Details" >> $GITHUB_STEP_SUMMARY | |
| echo "- **Task ID:** ${{ steps.create_task.outputs.task_id }}" >> $GITHUB_STEP_SUMMARY | |
| echo "- **Data Type:** ${{ steps.create_task.outputs.data_type }}" >> $GITHUB_STEP_SUMMARY | |
| echo "- **Template:** ${{ inputs.template }}" >> $GITHUB_STEP_SUMMARY | |
| echo "- **Schema URI:** ${{ steps.create_task.outputs.schema_uri }}" >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| echo "### Resources Created" >> $GITHUB_STEP_SUMMARY | |
| echo "- **Project:** [${{ steps.create_task.outputs.project_id }}](https://www.synapse.org/#!Synapse:${{ steps.create_task.outputs.project_id }})" >> $GITHUB_STEP_SUMMARY | |
| echo "- **Upload Folder:** [${{ inputs.upload_folder_id }}](https://www.synapse.org/#!Synapse:${{ inputs.upload_folder_id }})" >> $GITHUB_STEP_SUMMARY | |
| echo "- **File View:** [${{ steps.create_task.outputs.fileview_id }}](https://www.synapse.org/#!Synapse:${{ steps.create_task.outputs.fileview_id }})" >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| echo "### Instructions" >> $GITHUB_STEP_SUMMARY | |
| echo "${{ inputs.instructions }}" >> $GITHUB_STEP_SUMMARY | |
| - name: Create GitHub issue | |
| if: success() && inputs.create_issue == true | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| run: | | |
| gh issue create \ | |
| --title "Curation Test Task Created: ${{ inputs.template }} (${{ inputs.upload_folder_id }})" \ | |
| --assignee "${{ github.actor }}" \ | |
| --label "testing" \ | |
| --body "## Curation Task Created Successfully | |
| ### Task Details | |
| - **Task ID:** ${{ steps.create_task.outputs.task_id }} | |
| - **Data Type:** ${{ steps.create_task.outputs.data_type }} | |
| - **Template:** ${{ inputs.template }} | |
| - **Schema URI:** ${{ steps.create_task.outputs.schema_uri }} | |
| ### Resources Created | |
| - **Project:** [${{ steps.create_task.outputs.project_id }}](https://www.synapse.org/#!Synapse:${{ steps.create_task.outputs.project_id }}) | |
| - **Upload Folder:** [${{ inputs.upload_folder_id }}](https://www.synapse.org/#!Synapse:${{ inputs.upload_folder_id }}) | |
| - **File View:** [${{ steps.create_task.outputs.fileview_id }}](https://www.synapse.org/#!Synapse:${{ steps.create_task.outputs.fileview_id }}) | |
| ### Instructions | |
| ${{ inputs.instructions }} | |
| --- | |
| *Created by @${{ github.actor }} via [workflow run](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})*" |