## 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](https://git-scm.com/docs/gitignore))
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.
```Text
*_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.
If no path is specified a default path of `.bids-validator-config.json` will be used. You can add this file to your dataset to share dataset specific validation configuration. To disable this behavior use `--no-config` and the default configuration will be used.
The basic configuration format is outlined below. All configuration is optional.
```JSON
{
"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**
```JSON
{
"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](https://github.com/bids-standard/bids-validator/blob/master/bids-validator/utils/issues/list.js).
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.
```JSON
{
"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:
```JSON
{
"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.
```JSON
{
"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.
```JSON
{
"ignore": [
{
"or": [
"ECHO_TIME_GREATER_THAN",
"ECHO_TIME_NOT_DEFINED"
]
}
]
}
```
because it would be functionally the same as this:
```JSON
{
"ignore": [
"ECHO_TIME_GREATER_THAN",
"ECHO_TIME_NOT_DEFINED"
]
}
```
For passing a configuration while using the bids-validator on the command line,
you can use the following style to for example 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](https://browserify.org/)
or [webpack](https://webpack.js.org/). You can add it to a project by cloning
the validator and requiring it with browserify syntax
`const 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.
## Docker image
[](https://hub.docker.com/r/bids/validator)
To use bids validator with [docker](https://www.docker.com/), you simply need to
[install docker](https://docs.docker.com/install/) on your system.
And then from a terminal run:
- `docker run -ti --rm bids/validator --version` to print the version of the
docker image
- `docker run -ti --rm bids/validator --help` to print the help
- `docker run -ti --rm -v /path/to/data:/data:ro bids/validator /data`
to validate the dataset `/path/to/data` on your host machine
See here for a brief explanation of the commands:
- `docker run` is the command to tell docker to run a certain docker image,
usually taking the form `docker run 
