bids-validator-deno 3.0.0a3

Typescript implementation of the BIDS validator

The BIDS Validator

The BIDS Validator is a web application, command-line utility, and Javascript/Typescript library for assessing compliance with the Brain Imaging Data Structure (BIDS) standard.

Getting Started

In most cases, the simplest way to use the validator is to browse to the BIDS Validator web page:

The web validator runs in-browser, and does not transfer data to any remote server.

In some contexts, such as when working on a remote server, it may be easier to use the command-line. The BIDS Validator can be run with the Deno runtime (see Deno - Installation for detailed installation instructions):

deno run -ERWN jsr:@bids/validator

Deno by default sandboxes applications like a web browser. -E, -R, -W, and -N allow the validator to read environment variables, read/write local files, and read network locations.

A pre-compiled binary is published to PyPI and may be installed with:

pip install bids-validator-deno
bids-validator-deno --help

Configuration file

The schema validator accepts a JSON configuration file that reclassifies issues as warnings, errors or ignored.

{
  "ignore": [
    { "code": "JSON_KEY_RECOMMENDED", "location": "/T1w.json" }
  ],
  "warning": [],
  "error": [
    { "code": "NO_AUTHORS" }
  ]
}

The issues are partial matches of the issues that the validator accumulates. Pass the --json flag to see the issues in detail.

Development tools

From the repository root, use ./local-run to run with all permissions enabled by default:

# Run from within the /bids-validator directory
cd bids-validator
# Run validator:
./local-run path/to/dataset

Schema validator test suite

# Run tests:
deno test --allow-env --allow-read --allow-write src/

This test suite includes running expected output from bids-examples and may throw some expected failures for bids-examples datasets where either the schema or validator are misaligned with the example dataset while under development.

Modifying and building a new schema

To modify the schema a clone of bids-standard/bids-specification will need to be made. README and schema itself live here https://github.com/bids-standard/bids-specification/tree/master/src/schema.

After changes to the schema have been made to a local copy the dereferenced single json file used by the validator will need to be built. The bidsschematools python package does this. It can be installed from pypi via pip or a local installation can be made. It lives in the specification repository here https://github.com/bids-standard/bids-specification/tree/master/tools/schemacode

The command to compile a dereferenced schema is bst -v export --schema src/schema --output src/schema.json (this assumes you are in the root of the bids-specification repo). Once compiled it can be passed to the validator via the -s flag, ./bids-validator-deno -s <path to schema> <path to dataset>

Documentation

The BIDS validator documentation is available on Read the Docs.