Validator for the Brain Imaging Data Structure
Project description
BIDS-Validator
Quickstart
- Web version:
- Open Google Chrome or Mozilla Firefox (currently the only supported browsers)
- Go to http://bids-standard.github.io/bids-validator/ and select a folder with your BIDs dataset. If the validator seems to be working longer than couple of minutes please open developer tools and report the error at https://github.com/bids-standard/bids-validator/issues.
- Command line version:
- Install Node.js (at least version 8.0)
- From a terminal run
npm install -g bids-validator - Run
bids-validatorto start validating datasets.
- Docker
- Install Docker
- From a terminal run
docker run -ti --rm -v /path/to/data:/data:ro bids/validator /data
Support
The BIDS Validator is designed to work in both the browser and in Node.js. We target support for the latest long term stable (LTS) release of Node.js and the latest version of Chrome.
Please report any issues you experience while using these support targets. If you experience issues outside of these supported environments and believe we should extend our targeted support feel free to open a new issue describing the issue, your support target and why you require extended support and we will address these issues on a case by case basis.
Use
API
The BIDS Validator has one primary method that takes a directory as either a path to the directory (node) or the object given by selecting a directory with a file input (browser), an options object, and a callback.
Available options include:
- ignoreWarnings - (boolean - defaults to false)
- ignoreNiftiHeaders - (boolean - defaults to false)
For example:
validate.BIDS(directory, {ignoreWarnings: true}, function (issues, summary) {console.log(issues.errors, issues.warnings);});
If you would like to test individual files you can use the file specific checks that we expose.
- validate.BIDS()
- validate.JSON()
- validate.TSV()
- validate.NIFTI()
Additionally you can reformat stored errors against a new config using validate.reformat()
.bidsignore
Optionally one can include a .bidsignore file in the root of the dataset. This
file lists patterns (compatible with the .gitignore syntax)
defining files that should be ignored by the validator. This option is useful
when the validated dataset includes file types not yet supported by BIDS
specification.
*_not_bids.txt
extra_data/
Configuration
You can configure the severity of errors by passing a json configuration file
with a -c or --config flag to the command line interface or by defining a
config object on the options object passed during javascript usage.
The basic configuration format is outlined below. All configuration is optional.
{
"ignore": [],
"warn": [],
"error": [],
"ignoredFiles": []
}
ignoredFiles takes a list of file paths or glob patterns you'd like to ignore.
Lets say we want to ignore all files and sub-directory under /derivatives/.
This is not the same syntax as used in the .bidsignore file
{
"ignoredFiles": ["/derivatives/**"]
}
Note that adding two stars ** in path makes validator recognize all files and
sub-dir to be ignored.
ignore, warn, and error take lists of issue codes or issue keys and change
the severity of those issues so they are either ignored or reported as warnings
or errors. You can find a list of all available issues at
utils/issues/list.
Some issues may be ignored by default, but can be elevated to warnings or errors. These provide a way to check for common things that are more specific than BIDS compatibility. An example is a check for the presence of a T1w modality. The following would raise an error if no T1W image was found in a dataset.
{
"error": ["NO_T1W"]
}
In addition to issue codes and keys these lists can also contain objects with and "and" or "or" properties set to arrays of codes or keys. These allow some level of conditional logic when configuring issues. For example:
{
"ignore": [
{
"and": [
"ECHO_TIME_GREATER_THAN",
"ECHO_TIME_NOT_DEFINED"
]
}
]
}
In the above example the two issues will only be ignored if both of them are triggered during validation.
{
"ignore": [
{
"and": [
"ECHO_TIME_GREATER_THAN",
"ECHO_TIME_NOT_DEFINED"
{
"or": [
"ECHO_TIME1-2_NOT_DEFINED",
"ECHO_TIME_MUST_DEFINE"
]
}
]
}
]
}
And in this example the listed issues will only be ignored if
ECHO_TIME_GREATER_THAN, ECHO_TIME_NOT_DEFINED and either
ECHO_TIME1-2_NOT_DEFINED or ECHO_TIME_MUST_DEFINE are triggered during
validation.
"or" arrays are not supported at the lowest level because it wouldn't add any functionality. For example the following is not supported.
{
"ignore": [
{
"or": [
"ECHO_TIME_GREATER_THAN",
"ECHO_TIME_NOT_DEFINED"
]
}
]
}
because it would be functionally the same as this:
{
"ignore": [
"ECHO_TIME_GREATER_THAN",
"ECHO_TIME_NOT_DEFINED"
]
}
For passing a configuration while using the bids-validator on the command line, note that you have to specify at least two configurations of a given type, because an array is expected. For example, the following code will ignore empty file errors (99) and files that cannot be read (44):
bids-validator --config.ignore=99 --config.ignore=44 path/to/bids/dir
This style of use puts limits on what configuration you can require, so for complex scenarios, we advise users to create a dedicated configuration file with contents as described above.
In the Browser
The BIDS Validator currently works in the browser with browserify
or webpack. You can add it to a project by cloning
the validator and requiring it with browserify syntax
var validate = require('bids-validator'); or an ES2015 webpack import
import validate from 'bids-validator'.
On the Server
The BIDS validator works like most npm packages. You can install it by running
npm install bids-validator.
Through Command Line
If you install the bids validator globally by using npm install -g bids-validator
you will be able to use it as a command line tool. Once installed you should be
able to run bids-validator /path/to/your/bids/directory and see any validation
issues logged to the terminal. Run bids-validator without a directory path to
see available options.
Development
To develop locally, clone the project and run npm install from the project
root. This will install external dependencies. If you wish to install
bids-validator globally (so that you can run it in other folders), use the
following command to install it globally: npm install -g
Running Locally in a Browser
A note about OS X, the dependencies for the browser require a npm package called node-gyp which needs xcode to be installed in order to be compiled.
- Create a separate directory with the gh-pages branch in it.
- The local version of the validator needs to be added to npm. This is done
through the command
npm link relative/path/to/bids-validator. This will install your local version of the bids-validator project instead of going to the central npm repository. - In the gh-pages directory execute
npm install --save relative/path/to/bids-validator. This will install all the dependencies of the bids-validator browser application. - The default gh-pages application minifies javascript. This make it difficult
to test things locally. To disable minification of javascript comment out the
line
.pipe(uglify())in gulpfile.js - In the gh-pages directory execute
gulp buildto build it. - Via Chrome you can now open the index.html in gh-pages generated by gulp.
- Any subsequent changes to the bids-validator will require the gh-pages
application rebuilt with
gulp build.
Testing
To start the test suite run npm test from the project root. npm test -- --watch
is useful to run tests while making changes. A coverage report is available with
npm run coverage.
To run the linter which checks code conventions run npm run lint.
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Source Distribution
Built Distribution
Hashes for bids_validator-1.1.4-py2.py3-none-any.whl
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 8c1764fa69a63a00c788131c2d50b9868d106362898250ec84b42916899bb513 |
|
| MD5 | 9c659fab349bc3b8804ded6aecb20ab7 |
|
| BLAKE2b-256 | a72e5fb028668ca7f378df898c99037c3072db22019c31b0cec7f3ebdeaa7050 |
