-
-
-
-
-
-
-## 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"]
-}
+```console
+$ deno run --allow-read --allow-env https://deno.land/x/bids_validator/bids-validator.ts path/to/dataset
```
-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:
+Deno by default sandboxes applications like a web browser. `--allow-read` allows the validator to read local files, and `--allow-env` enables OS-specific features.
-```JSON
-{
- "ignore": [
- {
- "and": [
- "ECHO_TIME_GREATER_THAN",
- "ECHO_TIME_NOT_DEFINED"
- ]
- }
- ]
-}
-```
+### Configuration file
-In the above example the two issues will only be ignored if both of them are
-triggered during validation.
+The schema validator accepts a JSON configuration file that reclassifies issues as
+warnings, errors or ignored.
-```JSON
+```json
{
- "ignore": [
- {
- "and": [
- "ECHO_TIME_GREATER_THAN",
- "ECHO_TIME_NOT_DEFINED"
- {
- "or": [
- "ECHO_TIME1-2_NOT_DEFINED",
- "ECHO_TIME_MUST_DEFINE"
- ]
- }
- ]
- }
- ]
+ "ignore": [
+ { "code": "JSON_KEY_RECOMMENDED", "location": "/T1w.json" }
+ ],
+ "warning": [],
+ "error": [
+ { "code": "NO_AUTHORS" }
+ ]
}
```
-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.
+The issues are partial matches of the `issues` that the validator accumulates.
+Pass the `--json` flag to see the issues in detail.
-"or" arrays are not supported at the lowest level because it wouldn't add any
-functionality. For example the following is not supported.
+### Development tools
-```JSON
-{
- "ignore": [
- {
- "or": [
- "ECHO_TIME_GREATER_THAN",
- "ECHO_TIME_NOT_DEFINED"
- ]
- }
- ]
-}
-```
-
-because it would be functionally the same as this:
+From the repository root, use `bids-validator/bids-validator-deno` to run with all permissions enabled by default:
-```JSON
-{
- "ignore": [
- "ECHO_TIME_GREATER_THAN",
- "ECHO_TIME_NOT_DEFINED"
- ]
-}
+```shell
+# Run from within the /bids-validator directory
+cd bids-validator
+# Run validator:
+./bids-validator-deno path/to/dataset
```
-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):
+## Schema validator test suite
+```shell
+# Run tests:
+deno test --allow-env --allow-read --allow-write src/
```
-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 
