flywheel-gear-extensions

CSV Subject Splitter

Gear reads a tabular (CSV) file where each row has a NACCID and creates a JSON file for each row

The JSON file will be added to a subject/session/acquisition for the participant determined by the NACCID.

The labels for session and the file name are determined by the config input hierarchy_labels (represented as a JSON string), which is an an object with template strings for each:

{
    "session": {
        "template": "<template-text>",
        "transform": "<transform-name>",
        "delimiter": "<delimiter>"
    },
    "acquisition": {
        "template": "<template-text>",
        "transform": "<transform-name>",
        "delimiter": "<delimiter>"
    },
    "filename": {
        "template": "<template-text>",
        "transform": "<transform-name>",
        "delimiter": "<delimiter>"
    }
}

In JSON string form:

"{\"session\": {\"template\": \"<template-text>\",\"transform\": \"<transform-name>\"},\"acquisition\": {\"template\": \"<template-text>\",\"transform\": \"<transform-name>\"},\"filename\": {\"template\": \"<template-text>\",\"transform\": \"<transform-name>\"}"

templates must be given for each of session, acquisition, and filename.

A template can reference the fields in the file by preceding the field name with a dollar sign. For instance, the NACCID in the row could be included as $naccid Reference the base of the original file name with $filename (e.g., for a file base.csv the value would be base).

Supported transforms are converting the whole label to upper or lower case. So, the allowed values are upper and lower.

A delimiter is also supported; if provided, will replace all spaces in the hierarchy label with the specified string.

As an example, suppose we are splitting biomarker data from a data release designated 2024-12. Also, the data was collected with an assay designated assay-01, and we want to use the original filename except in lower case.

{
    "session": {
        "template": "biomarker-release-2024-12"
    },
    "acquisition": {
        "template": "assay-01"
    },
    "filename": {
        "template": "$filename",
        "transform": "lower"
    }
}

In JSON string form:

"{\"session\": {\"template\": \"biomarker-release-2024-12\"},\"acquisition\": {\"template\": \"assay-01\"},\"filename\": {\"template\": \"$filename\",\"transform\": \"lower\"}}"

Here the first two don’t have variables, and the last uses the filename.

Inputs

This takes a CSV file as input. The file must have a NACCID column.

Configs

Gear configs are defined in manifest.json.

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