flywheel-gear-extensions

Form QC Coordinator

This gear coordinates the data quality checks for a given participant. It internally triggers the Form QC Checker gear to validate each visit.

• Visits are evaluated in the order of the visit date.
• If a visit fails validation, none of the subsequent visits will be evaluated until the failed visit is fixed.
• If a visit is modified, all the subsequent visits are re-evaluated for accuracy.

Environment

This gear uses the AWS SSM parameter store, and expects that AWS credentials are available in environment variables (AWS_SECRET_ACCESS_KEY, AWS_ACCESS_KEY_ID, AWS_DEFAULT_REGION) within the Flywheel runtime.

Running

This gear can only be triggered by submission pipeline or finalization pipeline.

Inputs

• visits_file: Input file to trigger the QC process for this participant. Example
• form_configs_file: A JSON file with forms module configurations. Example
• qc_configs_file: JSON file with QC gear config information. Example

Configs

Gear configs are defined in manifest.json.

File Metadata and Tagging

This gear manages QC metadata and tags on the visit files it coordinates, not on its own input file. See the QC Conventions reference for details on the data models and conventions used.

1. File Tag (submission pipeline only): When triggered by the submission pipeline, the gear name (e.g., "form-qc-coordinator") is added as a tag to the input visits file, indicating the file has been processed.

2. Visit File QC Reset: When re-triggering QC for a visit, the coordinator resets the QC metadata on the visit file using FileQCModel and removes existing gear status tags (e.g., form-qc-checker-PASS or form-qc-checker-FAIL) using the GearTags class. This ensures the downstream Form QC Checker starts with a clean state.

   Note: The coordinator does not add QC results to its own input file. QC validation results are managed by the downstream Form QC Checker gear that it triggers for each visit.

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