flywheel-gear-extensions

Form Transformer

Reads a tabular (CSV) file containing form visit data, performs transformations on the data and creates a participant-visit specific JSON file for each row.

The JSON file is attached to a subject/session/acquisition for the participant determined by the NACCID. The file must have a module column.

File Metadata and Tagging

After processing, the gear updates the input CSV file with the following metadata. See the QC Conventions reference for details on the data models and conventions used.

1. QC Result: A validation QC result is added to the file’s file.info.qc metadata with:
   • name: "validation"
   • state: "PASS" or "FAIL" depending on whether transformation succeeded
   • data: List of FileError objects with error details if any errors occurred during transformation
2. File Tag: The gear name (e.g., "form-transformer") is added as a simple tag to the input file, indicating the file has been processed by this gear.

Current transformations filter columns based on the versions of forms. Data from the NACC REDCap projects will contain rows for all versions of forms, and the transformations filter out the columns specific to the versions not used.

The transformation file should contain a JSON object with module names as the key values. Each module is associated with a list of field filters, which determine the fields to be filtered for the module version.

Each field filter is used to determine the fields to be filtered based on the module version. It consists of an object indicating how to determine the version of the module to exclude.

{ 
    "fieldname": "indicator-field",
    "value_map": { "indicator-value": "version1" },
    "default": "version2"
}

This information is used to determine which fields to exclude:

- if the value of the `indicator-field` is `indicator-value`, exclude fields for `version1`
- otherwise, exclude fields for `version2`

A field filter also includes the full lists of fields for each version of the module. If nofill set to true exclude fields must be empty

This (partial) example shows field filters for the C2 forms of UDS and the version of the LBD module.

{
    "UDS": [
        {
            "version_map": { 
                "fieldname": "rmmodec2c2t",
                "value_map": { "1": "C2" },
                "default": "C2T"
            },
            "fields": {
                "C2": [],
                "C2T": []
            },
            "nofill": true
        }
    ],
    "LBD": [
        {
            "version_map": {
                "fieldname": "formver",
                "value_map": { "3.1": "v3.0" },
                "default": "v3.1"
            },
            "fields": {
                "v3.0": [],
                "v3.1": []
            },
            "nofill": true
        }
    ]
}

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