{
    "info": {
        "author": "PyBIDS developers",
        "author_email": "bids-discussion@googlegroups.com",
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            "Development Status :: 3 - Alpha",
            "Environment :: Console",
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        "description": "![](https://circleci.com/gh/bids-standard/bids-validator.svg?style=shield&circle-token=:circle-token)\n![](https://codecov.io/gh/bids-standard/bids-validator/branch/master/graph/badge.svg)\n\n# BIDS-Validator\n\n## Quickstart\n\n1. Web version:\n   1. Open [Google Chrome](https://www.google.com/chrome/) or\n      [Mozilla Firefox](https://mozilla.org/firefox) (currently the only\n      supported browsers)\n   1. Go to http://bids-standard.github.io/bids-validator/ and select a folder\n      with your BIDS dataset. If the validator seems to be working longer than\n      couple of minutes please open [developer tools ](https://developer.chrome.com/devtools)\n      and report the error at [https://github.com/bids-standard/bids-validator/issues](https://github.com/bids-standard/bids-validator/issues).\n1. Command line version:\n   1. Install [Node.js](https://nodejs.org) (at least version 8.0)\n   1. From a terminal run `npm install -g bids-validator`\n   1. Run `bids-validator` to start validating datasets.\n1. Docker\n   1. Install Docker\n   1. From a terminal run `docker run -ti --rm -v /path/to/data:/data:ro bids/validator /data`\n1. Python Library:\n   1. Install [Python](https://www.python.org/) (works with python2 and python3)\n   1. Install [Pip](https://pip.pypa.io/en/stable/installing/) package manager for python, if\n   not already installed.\n   1. From a terminal run `pip install bids_validator` to acquire the\n      [BIDS Validator PyPi package](https://pypi.org/project/bids-validator/)\n   1. Open a Python terminal `python`\n   1. Import the BIDS Validator package `from bids_validator import BIDSValidator`\n   1. Check if a file is BIDS compatible `BIDSValidator().is_bids('path/to/a/bids/file')`\n\n## Support\n\nThe BIDS Validator is designed to work in both the browser and in Node.js. We\ntarget support for the latest long term stable (LTS) release of Node.js and the\nlatest version of Chrome.\n\nThere is also a library of helper functions written in Python, for use with BIDS\ncompliant applications written in this language.\n\nPlease report any issues you experience while using these support targets. If\nyou experience issues outside of these supported environments and believe we\nshould extend our targeted support feel free to open a new issue describing the\nissue, your support target and why you require extended support and we will\naddress these issues on a case by case basis.\n\n## Maintainers and Contributors\n\nThis package is maintained by [@rwblair](https://github.com/rwblair/).\n\nSome of our awesome contributors include:\n\n[![](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/images/0)](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/links/0)[![](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/images/1)](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/links/1)[![](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/images/2)](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/links/2)[![](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/images/3)](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/links/3)[![](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/images/4)](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/links/4)[![](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/images/5)](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/links/5)[![](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/images/6)](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/links/6)[![](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/images/7)](https://sourcerer.io/fame/chrisfilo/bids-standard/bids-validator/links/7)\n\n## Use\n\n#### API\n\nThe BIDS Validator has one primary method that takes a directory as either a\npath to the directory (node) or the object given by selecting a directory with a\nfile input (browser), an options object, and a callback.\n\nAvailable options include:\n\n- ignoreWarnings - (boolean - defaults to false)\n- ignoreNiftiHeaders - (boolean - defaults to false)\n\nFor example:\n\n`validate.BIDS(directory, {ignoreWarnings: true}, function (issues, summary) {console.log(issues.errors, issues.warnings);});`\n\nIf you would like to test individual files you can use the file specific checks\nthat we expose.\n\n- validate.BIDS()\n- validate.JSON()\n- validate.TSV()\n- validate.NIFTI()\n\nAdditionally you can reformat stored errors against a new config using `validate.reformat()`\n\n#### .bidsignore\n\nOptionally one can include a `.bidsignore` file in the root of the dataset. This\nfile lists patterns (compatible with the [.gitignore syntax](https://git-scm.com/docs/gitignore))\ndefining files that should be ignored by the validator. This option is useful\nwhen the validated dataset includes file types not yet supported by BIDS\nspecification.\n\n```Text\n*_not_bids.txt\nextra_data/\n```\n\n#### Configuration\n\nYou can configure the severity of errors by passing a json configuration file\nwith a `-c` or `--config` flag to the command line interface or by defining a\nconfig object on the options object passed during javascript usage.\n\nThe basic configuration format is outlined below. All configuration is optional.\n\n```JSON\n{\n\t\"ignore\": [],\n\t\"warn\": [],\n\t\"error\": [],\n\t\"ignoredFiles\": []\n}\n```\n\n`ignoredFiles` takes a list of file paths or glob patterns you'd like to ignore.\nLets say we want to ignore all files and sub-directory under `/derivatives/`.\n**This is not the same syntax as used in the .bidsignore file**\n\n```JSON\n{\n\t\"ignoredFiles\": [\"/derivatives/**\"]\n}\n```\n\nNote that adding two stars `**` in path makes validator recognize all files and\nsub-dir to be ignored.\n\n`ignore`, `warn`, and `error` take lists of issue codes or issue keys and change\nthe severity of those issues so they are either ignored or reported as warnings\nor errors. You can find a list of all available issues at\n[utils/issues/list](https://github.com/bids-standard/bids-validator/tree/master/utils/issues/list.js).\n\nSome issues may be ignored by default, but can be elevated to warnings or errors.\nThese provide a way to check for common things that are more specific than BIDS\ncompatibility. An example is a check for the presence of a T1w modality. The\nfollowing would raise an error if no T1W image was found in a dataset.\n\n```JSON\n{\n\t\"error\": [\"NO_T1W\"]\n}\n```\n\nIn addition to issue codes and keys these lists can also contain objects with\nand \"and\" or \"or\" properties set to arrays of codes or keys. These allow some\nlevel of conditional logic when configuring issues. For example:\n\n```JSON\n{\n\t\"ignore\": [\n\t\t{\n\t\t\t\"and\": [\n\t\t\t\t\"ECHO_TIME_GREATER_THAN\",\n\t\t\t\t\"ECHO_TIME_NOT_DEFINED\"\n\t\t\t]\n\t\t}\n\t]\n}\n```\n\nIn the above example the two issues will only be ignored if both of them are\ntriggered during validation.\n\n```JSON\n{\n\t\"ignore\": [\n\t\t{\n\t\t\t\"and\": [\n\t\t\t\t\"ECHO_TIME_GREATER_THAN\",\n\t\t\t\t\"ECHO_TIME_NOT_DEFINED\"\n\t\t\t\t{\n\t\t\t\t\t\"or\": [\n\t\t\t\t\t\t\"ECHO_TIME1-2_NOT_DEFINED\",\n\t\t\t\t\t\t\"ECHO_TIME_MUST_DEFINE\"\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t]\n}\n```\n\nAnd in this example the listed issues will only be ignored if\n`ECHO_TIME_GREATER_THAN`, `ECHO_TIME_NOT_DEFINED` and either\n`ECHO_TIME1-2_NOT_DEFINED` or `ECHO_TIME_MUST_DEFINE` are triggered during\nvalidation.\n\n\"or\" arrays are not supported at the lowest level because it wouldn't add any\nfunctionality. For example the following is not supported.\n\n```JSON\n{\n\t\"ignore\": [\n\t\t{\n\t\t\t\"or\": [\n\t\t\t\t\"ECHO_TIME_GREATER_THAN\",\n\t\t\t\t\"ECHO_TIME_NOT_DEFINED\"\n\t\t\t]\n\t\t}\n\t]\n}\n```\n\nbecause it would be functionally the same as this:\n\n```JSON\n{\n\t\"ignore\": [\n\t\t\"ECHO_TIME_GREATER_THAN\",\n\t\t\"ECHO_TIME_NOT_DEFINED\"\n\t]\n}\n```\n\nFor passing a configuration while using the bids-validator on the command line,\nnote that you **have to specify at least two configurations of a given type**,\nbecause an array is expected. For example, the following code will ignore empty\nfile errors (99) and files that cannot be read (44):\n\n```\nbids-validator --config.ignore=99 --config.ignore=44 path/to/bids/dir\n```\n\nThis style of use puts limits on what configuration you can require, so for\ncomplex scenarios, we advise users to create a dedicated configuration file with\ncontents as described above.\n\n#### In the Browser\n\nThe BIDS Validator currently works in the browser with [browserify](http://browserify.org/)\nor [webpack](https://webpack.js.org/). You can add it to a project by cloning\nthe validator and requiring it with browserify syntax\n`var validate = require('bids-validator');` or an ES2015 webpack import\n`import validate from 'bids-validator'`.\n\n#### On the Server\n\nThe BIDS validator works like most npm packages. You can install it by running\n`npm install bids-validator`.\n\n#### Through Command Line\n\nIf you install the bids validator globally by using `npm install -g bids-validator`\nyou will be able to use it as a command line tool. Once installed you should be\nable to run `bids-validator /path/to/your/bids/directory` and see any validation\nissues logged to the terminal. Run `bids-validator` without a directory path to\nsee available options.\n\n## Python Library\n\nThere are is a limited library of helper functions written in Python. The main function\ndetermines if a file extension is compliant with the BIDS specification. You can find\nthe available functions in the library, as well as their descriptions,\n[here](https://github.com/bids-standard/bids-validator/blob/master/bids-validator/bids_validator/bids_validator.py).\nTo install, run `pip install bids_validator` (requires python and pip).\n\n#### Example\n\n```\n>>> from bids_validator import BIDSValidator\n>>> validator = BIDSValidator()\n>>> filepaths = [\"/sub-01/anat/sub-01_rec-CSD_T1w.nii.gz\", \"/sub-01/anat/sub-01_acq-23_rec-CSD_T1w.exe\"]\n>>> for filepath in filepaths:\n>>>     print( validator.is_bids(filepath) )\nTrue\nFalse\n```\n\n## Development\n\nTo develop locally, clone the project and run `yarn` from the project\nroot. This will install external dependencies. If you wish to install\n`bids-validator` globally (so that you can run it in other folders), use the\nfollowing command to install it globally: `cd bids-validator && npm install -g`\n\n#### Running Locally in a Browser\n\nA note about OS X, the dependencies for the browser require a npm package called\nnode-gyp which needs xcode to be installed in order to be compiled.\n\n1. The browser version of `bids-validator` lives in the repo subdirectory\n\t`/bids-validator-web`. It is a [React.js](https://reactjs.org/) application\n\tthat uses the [next.js](https://nextjs.org/) framework.\n2. To develop `bids-validator` and see how it will act in the browser, simply run\n\t`yarn web-dev` in the project root and navigate to `localhost:3000`.\n3. In development mode, changes to the codebase will trigger rebuilds of the application\n\tautomatically.\n4. Changes to the `/bids-validator` in the codebase will also be reflected in the\n\tweb application.\n5. Tests use the [Jest](https://jestjs.io/index.html) testing library and should be developed in `/bids-validator-web/tests`.\n\tWe can always use more tests, so please feel free to contribute a test that reduces the chance\n\tof any bugs you fix!\n6. To ensure that the web application compiles successfully in production, run `yarn web-export`\n\n#### Testing\n\nTo start the test suite run `npm test` from the project root. `npm test -- --watch`\nis useful to run tests while making changes. A coverage report is available with\n`npm run coverage`.\n\nTo run the linter which checks code conventions run `npm run lint`.\n\n\n",
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