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https://github.com/bids-standard/bids-validator
Validator for the Brain Imaging Data Structure
https://github.com/bids-standard/bids-validator
bids data-standards neuroimaging-data validation
Last synced: 1 day ago
JSON representation
Validator for the Brain Imaging Data Structure
- Host: GitHub
- URL: https://github.com/bids-standard/bids-validator
- Owner: bids-standard
- License: mit
- Created: 2024-10-24T20:48:31.000Z (19 days ago)
- Default Branch: main
- Last Pushed: 2024-11-11T16:07:42.000Z (1 day ago)
- Last Synced: 2024-11-11T17:19:33.940Z (1 day ago)
- Topics: bids, data-standards, neuroimaging-data, validation
- Language: TypeScript
- Homepage: https://bids-standard.github.io/bids-validator/
- Size: 22.7 MB
- Stars: 1
- Watchers: 8
- Forks: 4
- Open Issues: 67
-
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
- awesome-bids - install the package
README
[](https://github.com/bids-standard/bids-validator/actions/workflows/deno_tests.yml)
[](https://github.com/bids-standard/bids-validator/actions/workflows/web_build.yml)
[](https://bids-validator.readthedocs.io/en/latest/?badge=latest)
[](https://doi.org/10.5281/zenodo.3688707)
# 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):
```shell
deno run -ERN jsr:@bids/validator
```
Deno by default sandboxes applications like a web browser.
`-E`, `-R` and `-N` allow the validator to read environment variables,
local files, and network locations.
### Configuration file
The schema validator accepts a JSON configuration file that reclassifies issues as
warnings, errors or ignored.
```json
{
"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:
```shell
# Run from within the /bids-validator directory
cd bids-validator
# Run validator:
./local-run path/to/dataset
```
## Schema validator test suite
```shell
# 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 --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 `
## Documentation
The BIDS validator documentation is available on [Read the Docs](https://bids-validator.readthedocs.io/en/latest/).