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gear config

Running a Flywheel gear requires a config.json file that tells the gear where the inputs are located, and what the config values are.

When running a gear on Flywheel, this file is generated automatically. In order to run it locally, you will need to generate it. gear config is provided to make that process simpler.

Usage

Config option types

The manifest in the current directory is used to apply types to passed in config options, meaning you can set config options that have various types, such as:

  • boolean gear config -c my_bool=true
  • Valid options: True, true, T, t, False, false, F, f
  • string gear config -c my_str='my long string'
  • numbers gear config -c my_int=2 OR gear config -c my_float=2.45
  • arrays gear config -c my_array=1,2,3

NOTE arrays are parsed by splitting on commas

File Inputs

When you add a file input with gear config -i <file_input>=<path/to/file>, the gear config command populates a file in your current directory called .input_map.json that stores a dictionary mapping the location of the file on your computer to where it should be mounted to the gear. When you use gear run --prepare, this .input_map.json file is used to populate the gear run directory.

Local filepaths and Flywheel filepaths are both valid. A Flywheel filepath is of the form fw://<group>/<project>/<subject>/<session>/<acquisition>/<file>. When a Flywheel filepath is supplied, the file will be downloaded and its metadata will be populated in the config.json.