JSON Schemas

Each of the json files that comprise a SpaceTx image fileset can be validated against one of several jsonschemas (Draft 4).

Schema location	Description
codebook/codebook.json	maps patterns of intensity in the channels and rounds of a field of view to target molecules
codebook/codeword.json	describes the individiual codes contained in a codebook
experiment.json	top-level object mapping manifests and codebook together
extras.json	extension point used in multiple schemas for storing key/value pairs
field_of_view/tiles/indices.json	describes the categorical indices (channel, round, and z-section) of a tile
field_of_view/tiles/coordinates.json	physical coordinates of a tile
field_of_view/tiles/tiles.json	specification of a 2-D image tile
field_of_view/field_of_view.json	5-D image consisting of multiple 2-D image tiles
fov_manifest.json	manifest listing one or more json files that each describe a field of view
version.json	general purpose version specification used in multiple schemas

See the API and Usage documentation for how to validate your documents against the jsonschema from your code or the command-line, respectively.

Validation

The starfish validate command provides a way to check that a fileset based on the SpaceTx Image Format Specification is valid. One of the schema requirements is that the codebook is version 0.0.0 and the experiment is 4.0.0 or 5.0.0.

Usage

starfish validate –help will provide instructions on how to use the tool:

         _              __ _     _
        | |            / _(_)   | |
     ___| |_ __ _ _ __| |_ _ ___| |__
    / __| __/ _` | '__|  _| / __| '_  `
    \__ \ || (_| | |  | | | \__ \ | | |
    |___/\__\__,_|_|  |_| |_|___/_| |_|

    
Usage: starfish validate [OPTIONS] COMMAND [ARGS]...

Options:
  --experiment-json JSON_FILE_OR_URL
  --fuzz
  --help                          Show this message and exit.

Commands:
  codebook    validate codebook against the jsonschemas
  experiment  validate experiment against the jsonschemas
  fov         validate field-of-view against the jsonschemas
  manifest    validate manifest against the jsonschemas
  xarray

Examples

$ starfish validate experiment tmp/experiment.json > /dev/null && echo ok

Validating the experiment, validates all of the included files. These files can also be individually validated:

$ starfish validate codebook tmp/codebook.json