From b40fa793587ba72da152d82f65975635873e0c22 Mon Sep 17 00:00:00 2001 From: CoprDistGit Date: Wed, 8 Mar 2023 06:22:05 +0000 Subject: automatic import of python-bids-validator --- .gitignore | 1 + python-bids-validator.spec | 1518 ++++++++++++++++++++++++++++++++++++++++++++ sources | 1 + 3 files changed, 1520 insertions(+) create mode 100644 python-bids-validator.spec create mode 100644 sources diff --git a/.gitignore b/.gitignore index e69de29..6a18140 100644 --- a/.gitignore +++ b/.gitignore @@ -0,0 +1 @@ +/bids-validator-1.10.0.tar.gz diff --git a/python-bids-validator.spec b/python-bids-validator.spec new file mode 100644 index 0000000..c01a2be --- /dev/null +++ b/python-bids-validator.spec @@ -0,0 +1,1518 @@ +%global _empty_manifest_terminate_build 0 +Name: python-bids-validator +Version: 1.10.0 +Release: 1 +Summary: Validator for the Brain Imaging Data Structure +License: MIT +URL: https://github.com/bids-standard/bids-validator +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/83/1a/49b54987bf00d2f4e1fcdb21e29de6c1f9bac6e6d796a4e1291476a92528/bids-validator-1.10.0.tar.gz +BuildArch: noarch + + +%description +[![Node Tests](https://github.com/bids-standard/bids-validator/actions/workflows/node_tests.yml/badge.svg)](https://github.com/bids-standard/bids-validator/actions/workflows/node_tests.yml) +[![Python tests](https://github.com/bids-standard/bids-validator/actions/workflows/python_tests.yml/badge.svg)](https://github.com/bids-standard/bids-validator/actions/workflows/python_tests.yml) +[![bids-examples tests](https://github.com/bids-standard/bids-validator/actions/workflows/test-bids-examples.yml/badge.svg)](https://github.com/bids-standard/bids-validator/actions/workflows/test-bids-examples.yml) +[![CircleCI](https://circleci.com/gh/bids-standard/bids-validator.svg?style=shield&circle-token=:circle-token)](https://circleci.com/gh/bids-standard/bids-validator) +[![Codecov](https://codecov.io/gh/bids-standard/bids-validator/branch/master/graph/badge.svg)](https://codecov.io/gh/bids-standard/bids-validator) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3688707.svg)](https://doi.org/10.5281/zenodo.3688707) + +# BIDS-Validator + +- [BIDS-Validator](#bids-validator) + - [Quickstart](#quickstart) + - [Support](#support) + - [Maintainers and Contributors](#maintainers-and-contributors) + - [Use](#use) + - [API](#api) + - [.bidsignore](#bidsignore) + - [Configuration](#configuration) + - [In the Browser](#in-the-browser) + - [On the Server](#on-the-server) + - [Through Command Line](#through-command-line) + - [Docker image](#docker-image) + - [Python Library](#python-library) + - [Example](#example) + - [Development](#development) + - [Running Locally in a Browser](#running-locally-in-a-browser) + - [Testing](#testing) + - [Publishing](#publishing) + - [Acknowledgments](#acknowledgments) + +## Quickstart + +1. Web version: + 1. Open [Google Chrome](https://www.google.com/chrome/) or + [Mozilla Firefox](https://mozilla.org/firefox) (currently the only + supported browsers) + 1. Go to https://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 ](https://developer.chrome.com/devtools) + and report the error at [https://github.com/bids-standard/bids-validator/issues](https://github.com/bids-standard/bids-validator/issues). +1. Command line version: + 1. Install [Node.js](https://nodejs.org) (at least version 12.12.0) + 1. Update `npm` to be at least version 7 (`npm install --global npm@^7`) + 1. From a terminal run `npm install -g bids-validator` + 1. Run `bids-validator` to start validating datasets. +1. Docker + 1. Install Docker + 1. From a terminal run `docker run -ti --rm -v /path/to/data:/data:ro bids/validator /data` + but replace the `/path/to/data` part of the command with your own path on your machine. +1. Python Library: + 1. Install [Python](https://www.python.org/) + 1. Install [Pip](https://pip.pypa.io/en/stable/installing/) package manager for Python, if + not already installed. + 1. From a terminal run `pip install bids_validator` to acquire the + [BIDS Validator PyPI package](https://pypi.org/project/bids-validator/) + or `conda install bids-validator` for the + [Conda package](https://anaconda.org/conda-forge/bids-validator). + 1. Open a Python terminal and type: `python` + 1. Import the BIDS Validator package `from bids_validator import BIDSValidator` + 1. Check if a file is BIDS compatible `BIDSValidator().is_bids('path/to/a/bids/file')` + +## 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. + +There is also a library of helper functions written in Python, for use with BIDS +compliant applications written in this language. + +Please report any issues you experience while using these support targets via +the [GitHub issue tracker](https://github.com/bids-standard/bids-validator/issues). +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. + +## Maintainers and Contributors + + + +[![All Contributors](https://img.shields.io/badge/all_contributors-43-orange.svg?style=flat-square)](#contributors-) + + + +This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. +Contributions of any kind are welcome! + +The project is maintained by [@rwblair](https://github.com/rwblair/) with the help of many contributors listed below. +(The [emoji key](https://allcontributors.org/docs/en/emoji-key) is indicating the kind of contribution) + +Please also see [Acknowledgments](#acknowledgments). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Adam Li
πŸ’» ⚠️ πŸ““ πŸ›
Adam Thomas
πŸ“–
Alexander Jones
πŸ’» ⚠️ πŸ€”
Ben Beasley
πŸ“¦
Chris Gorgolewski
πŸ› πŸ’» πŸ”£ πŸ“– πŸ’‘ πŸ€” πŸš‡ 🚧 πŸ§‘β€πŸ« πŸ’¬ πŸ‘€ ⚠️ βœ… πŸ“’ πŸ““
Chris Holdgraf
πŸ’»
Chris Markiewicz
πŸ’» ⚠️ πŸ€” πŸ› πŸ’¬ πŸ”§ 🚧

David Nishikawa
πŸ’» ⚠️
Dimitri Papadopoulos Orfanos
πŸ’»
Duncan Macleod
πŸš‡
Franklin Feingold
πŸ“–
Gregory noack
πŸ’» ⚠️
Horea Christian
πŸ’»
Jakub Kaczmarzyk
πŸš‡

Joke Durnez
πŸ’»
Mainak Jas
πŸ’» ⚠️ πŸ€” πŸ‘€ πŸ““
Marco Castellaro
πŸ’» ⚠️
Max
πŸ’» πŸ›
Michael Hanke
πŸ“–
Mikael Naveau
πŸ’»
Nell Hardcastle
πŸ’» πŸ€” πŸš‡ πŸ’¬ πŸ‘€

Nicolas Traut
πŸ’»
Parul Sethi
πŸ’» ⚠️
Patricia Clement
πŸ’»
Remi Gau
πŸ’» πŸ“– πŸ““
Richard HΓΆchenberger
πŸ’» πŸ““ ⚠️ πŸ›
Robert Oostenveld
πŸ’» πŸ€” πŸ› ⚠️
Rohan Goyal
πŸ’»

Ross Blair
🚧 πŸ€” πŸ’» πŸ› πŸš‡ πŸ“† πŸ’¬ πŸ‘€ πŸ”§ ⚠️
Russ Poldrack
πŸ’» πŸ’΅ πŸ”
Soichi Hayashi
πŸ›
Stefan Appelhoff
πŸ› πŸ’» πŸ”£ πŸ“– πŸ’‘ πŸ€” πŸš‡ 🚧 πŸ§‘β€πŸ« πŸ’¬ πŸ‘€ ⚠️ βœ… πŸ“’ πŸ““
Suyash
πŸ’»
Taylor Salo
πŸ’»
Teal Hobson-Lowther
πŸ’» ⚠️

Travis Riddle
πŸ›
VisLab
πŸ€” πŸ’»
Wazeer Zulfikar
πŸ“–
Yaroslav Halchenko
πŸ€” πŸ’» πŸ“– πŸ““
constellates
πŸ’» ⚠️
dewarrn1
πŸ’»
dkp
πŸ’»

goldmund
πŸ’» ⚠️
+ + + + + + +## 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 + +[![Docker Image Version (latest by date)](https://img.shields.io/docker/v/bids/validator?label=docker)](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 ` +- the `-ti` flag means the inputs are accepted and outputs are printed to the + terminal +- the `--rm` flag means that the state of the docker container is not saved + after it has run +- the `-v` flag is adding your local data to the docker container + ([bind-mounts](https://docs.docker.com/storage/bind-mounts/)). Importantly, + the input after the `-v` flag consists of three fields separated colons: `:` + - the first field is the path to the directory on the host machine: + `/path/to/data` + - the second field is the path where the directory is mounted in the + container + - the third field is optional. In our case, we use `ro` to specify that the + mounted data is _read only_ + +## Python Library + +[![PyPI version](https://badge.fury.io/py/bids-validator.svg)](https://badge.fury.io/py/bids-validator) +[![Conda version](https://img.shields.io/conda/vn/conda-forge/bids-validator)](https://anaconda.org/conda-forge/bids-validator) + +There are is a limited library of helper functions written in Python. The main function +determines if a file extension is compliant with the BIDS specification. You can find +the available functions in the library, as well as their descriptions, +[here](https://github.com/bids-standard/bids-validator/blob/master/bids-validator/bids_validator/bids_validator.py). +To install, run `pip install -U bids_validator` (requires python and pip) or +`conda install bids-validator` (requires a Conda environment). + +### Example + +```Python +from bids_validator import BIDSValidator +validator = BIDSValidator() +filepaths = ["/sub-01/anat/sub-01_rec-CSD_T1w.nii.gz", "/sub-01/anat/sub-01_acq-23_rec-CSD_T1w.exe"] +for filepath in filepaths: + print(validator.is_bids(filepath)) # will print True, and then False +``` + +## 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: `cd bids-validator && npm install -g` (for windows users, if in a different drive add /d, e.g. `cd /d F:\bids-validator && npm install -g`) + +Please see the [CONTRIBUTING.md](../CONTRIBUTING.md) +for additional details. + +### Bundling + +bids-validator is bundled with esbuild. While developing, the script `bids-validator/bin/bids-validator` will automatically bundle the project each time it is run. To test a build without publishing it `npm -w bids-validator run build`. This will generate a bids-validator/dist directory containing the local build and `bids-validator/bin/bids-validator` will use this build. To return to automatic bundling on each run, remove the dist directory. + +### 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. + +1. The browser version of `bids-validator` lives in the repo subdirectory + `/bids-validator-web`. It is a [React.js](https://reactjs.org/) application + that uses the [next.js](https://nextjs.org/) framework. +2. To develop `bids-validator` and see how it will act in the browser, simply run + `npm run web-dev` in the project root and navigate to `localhost:3000`. +3. In development mode, changes to the codebase will trigger rebuilds of the application + automatically. +4. Changes to the `/bids-validator` in the codebase will also be reflected in the + web application. +5. Tests use the [Jest](https://jestjs.io/index.html) testing library and should be developed in `/bids-validator-web/tests`. + We can always use more tests, so please feel free to contribute a test that reduces the chance + of any bugs you fix! +6. To ensure that the web application compiles successfully in production, run `npm run web-export` + +### Testing + +If it's your first time running tests, first use the command `git submodule update --init --depth 1` to pull the test example data. This repo contains the [bids-examples github repository](https://github.com/bids-standard/bids-examples) as a [submodule](https://git-scm.com/book/en/v2/Git-Tools-Submodules). + +To start the test suite run `npm run test` from the project root. `npm run 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`. + +### Install globally from a development branch + +Global installs are not recommended for development because of the possibility of package conflicts with other Node.js projects. If you do need to test with a global install from a development tree, follow these steps to generate the NPM package without publishing it and install the package locally. + +1. `npm -w bids-validator run build` +2. `npm -w bids-validator pack` +3. `npm install -g bids-validator-*.tgz` + +### Publishing + +Publishing is done with [Lerna](https://github.com/lerna/lerna). Use the command `npx lerna publish` and follow instructions to set a new version. + +Using lerna publish will create a git commit with updated version information and create a version number tag for it, push the tag to GitHub, then publish to NPM and PyPI. The GitHub release is manual following that. + +## Acknowledgments + +Many contributions to the `bids-validator` were done by members of the +BIDS community. See the +[list of contributors](https://bids-specification.readthedocs.io/en/stable/99-appendices/01-contributors.html). + +A large part of the development of `bids-validator` is currently done by +[Squishymedia](https://squishymedia.com/), who are in turn financed through +different grants offered for the general development of BIDS. See the list +below. + +Development and contributions were supported through the following federally +funded projects/grants: + +- [BIDS Derivatives (NIMH: R24MH114705, PI: Poldrack)](https://grantome.com/grant/NIH/R24-MH114705-01) +- [OpenNeuro (NIMH: R24MH117179, PI: Poldrack)](https://grantome.com/grant/NIH/R24-MH117179-01) +- [Spokes: MEDIUM: WEST (NSF: 1760950, PI: Poldrack & Gorgolewski)](https://grantome.com/grant/NSF/IIS-1760950) +- [ReproNim](http://repronim.org) [(NIH-NIBIB P41 EB019936, PI: Kennedy)](https://projectreporter.nih.gov/project_info_description.cfm?aid=8999833) + + +%package -n python3-bids-validator +Summary: Validator for the Brain Imaging Data Structure +Provides: python-bids-validator +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-bids-validator +[![Node Tests](https://github.com/bids-standard/bids-validator/actions/workflows/node_tests.yml/badge.svg)](https://github.com/bids-standard/bids-validator/actions/workflows/node_tests.yml) +[![Python tests](https://github.com/bids-standard/bids-validator/actions/workflows/python_tests.yml/badge.svg)](https://github.com/bids-standard/bids-validator/actions/workflows/python_tests.yml) +[![bids-examples tests](https://github.com/bids-standard/bids-validator/actions/workflows/test-bids-examples.yml/badge.svg)](https://github.com/bids-standard/bids-validator/actions/workflows/test-bids-examples.yml) +[![CircleCI](https://circleci.com/gh/bids-standard/bids-validator.svg?style=shield&circle-token=:circle-token)](https://circleci.com/gh/bids-standard/bids-validator) +[![Codecov](https://codecov.io/gh/bids-standard/bids-validator/branch/master/graph/badge.svg)](https://codecov.io/gh/bids-standard/bids-validator) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3688707.svg)](https://doi.org/10.5281/zenodo.3688707) + +# BIDS-Validator + +- [BIDS-Validator](#bids-validator) + - [Quickstart](#quickstart) + - [Support](#support) + - [Maintainers and Contributors](#maintainers-and-contributors) + - [Use](#use) + - [API](#api) + - [.bidsignore](#bidsignore) + - [Configuration](#configuration) + - [In the Browser](#in-the-browser) + - [On the Server](#on-the-server) + - [Through Command Line](#through-command-line) + - [Docker image](#docker-image) + - [Python Library](#python-library) + - [Example](#example) + - [Development](#development) + - [Running Locally in a Browser](#running-locally-in-a-browser) + - [Testing](#testing) + - [Publishing](#publishing) + - [Acknowledgments](#acknowledgments) + +## Quickstart + +1. Web version: + 1. Open [Google Chrome](https://www.google.com/chrome/) or + [Mozilla Firefox](https://mozilla.org/firefox) (currently the only + supported browsers) + 1. Go to https://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 ](https://developer.chrome.com/devtools) + and report the error at [https://github.com/bids-standard/bids-validator/issues](https://github.com/bids-standard/bids-validator/issues). +1. Command line version: + 1. Install [Node.js](https://nodejs.org) (at least version 12.12.0) + 1. Update `npm` to be at least version 7 (`npm install --global npm@^7`) + 1. From a terminal run `npm install -g bids-validator` + 1. Run `bids-validator` to start validating datasets. +1. Docker + 1. Install Docker + 1. From a terminal run `docker run -ti --rm -v /path/to/data:/data:ro bids/validator /data` + but replace the `/path/to/data` part of the command with your own path on your machine. +1. Python Library: + 1. Install [Python](https://www.python.org/) + 1. Install [Pip](https://pip.pypa.io/en/stable/installing/) package manager for Python, if + not already installed. + 1. From a terminal run `pip install bids_validator` to acquire the + [BIDS Validator PyPI package](https://pypi.org/project/bids-validator/) + or `conda install bids-validator` for the + [Conda package](https://anaconda.org/conda-forge/bids-validator). + 1. Open a Python terminal and type: `python` + 1. Import the BIDS Validator package `from bids_validator import BIDSValidator` + 1. Check if a file is BIDS compatible `BIDSValidator().is_bids('path/to/a/bids/file')` + +## 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. + +There is also a library of helper functions written in Python, for use with BIDS +compliant applications written in this language. + +Please report any issues you experience while using these support targets via +the [GitHub issue tracker](https://github.com/bids-standard/bids-validator/issues). +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. + +## Maintainers and Contributors + + + +[![All Contributors](https://img.shields.io/badge/all_contributors-43-orange.svg?style=flat-square)](#contributors-) + + + +This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. +Contributions of any kind are welcome! + +The project is maintained by [@rwblair](https://github.com/rwblair/) with the help of many contributors listed below. +(The [emoji key](https://allcontributors.org/docs/en/emoji-key) is indicating the kind of contribution) + +Please also see [Acknowledgments](#acknowledgments). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Adam Li
πŸ’» ⚠️ πŸ““ πŸ›
Adam Thomas
πŸ“–
Alexander Jones
πŸ’» ⚠️ πŸ€”
Ben Beasley
πŸ“¦
Chris Gorgolewski
πŸ› πŸ’» πŸ”£ πŸ“– πŸ’‘ πŸ€” πŸš‡ 🚧 πŸ§‘β€πŸ« πŸ’¬ πŸ‘€ ⚠️ βœ… πŸ“’ πŸ““
Chris Holdgraf
πŸ’»
Chris Markiewicz
πŸ’» ⚠️ πŸ€” πŸ› πŸ’¬ πŸ”§ 🚧

David Nishikawa
πŸ’» ⚠️
Dimitri Papadopoulos Orfanos
πŸ’»
Duncan Macleod
πŸš‡
Franklin Feingold
πŸ“–
Gregory noack
πŸ’» ⚠️
Horea Christian
πŸ’»
Jakub Kaczmarzyk
πŸš‡

Joke Durnez
πŸ’»
Mainak Jas
πŸ’» ⚠️ πŸ€” πŸ‘€ πŸ““
Marco Castellaro
πŸ’» ⚠️
Max
πŸ’» πŸ›
Michael Hanke
πŸ“–
Mikael Naveau
πŸ’»
Nell Hardcastle
πŸ’» πŸ€” πŸš‡ πŸ’¬ πŸ‘€

Nicolas Traut
πŸ’»
Parul Sethi
πŸ’» ⚠️
Patricia Clement
πŸ’»
Remi Gau
πŸ’» πŸ“– πŸ““
Richard HΓΆchenberger
πŸ’» πŸ““ ⚠️ πŸ›
Robert Oostenveld
πŸ’» πŸ€” πŸ› ⚠️
Rohan Goyal
πŸ’»

Ross Blair
🚧 πŸ€” πŸ’» πŸ› πŸš‡ πŸ“† πŸ’¬ πŸ‘€ πŸ”§ ⚠️
Russ Poldrack
πŸ’» πŸ’΅ πŸ”
Soichi Hayashi
πŸ›
Stefan Appelhoff
πŸ› πŸ’» πŸ”£ πŸ“– πŸ’‘ πŸ€” πŸš‡ 🚧 πŸ§‘β€πŸ« πŸ’¬ πŸ‘€ ⚠️ βœ… πŸ“’ πŸ““
Suyash
πŸ’»
Taylor Salo
πŸ’»
Teal Hobson-Lowther
πŸ’» ⚠️

Travis Riddle
πŸ›
VisLab
πŸ€” πŸ’»
Wazeer Zulfikar
πŸ“–
Yaroslav Halchenko
πŸ€” πŸ’» πŸ“– πŸ““
constellates
πŸ’» ⚠️
dewarrn1
πŸ’»
dkp
πŸ’»

goldmund
πŸ’» ⚠️
+ + + + + + +## 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 + +[![Docker Image Version (latest by date)](https://img.shields.io/docker/v/bids/validator?label=docker)](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 ` +- the `-ti` flag means the inputs are accepted and outputs are printed to the + terminal +- the `--rm` flag means that the state of the docker container is not saved + after it has run +- the `-v` flag is adding your local data to the docker container + ([bind-mounts](https://docs.docker.com/storage/bind-mounts/)). Importantly, + the input after the `-v` flag consists of three fields separated colons: `:` + - the first field is the path to the directory on the host machine: + `/path/to/data` + - the second field is the path where the directory is mounted in the + container + - the third field is optional. In our case, we use `ro` to specify that the + mounted data is _read only_ + +## Python Library + +[![PyPI version](https://badge.fury.io/py/bids-validator.svg)](https://badge.fury.io/py/bids-validator) +[![Conda version](https://img.shields.io/conda/vn/conda-forge/bids-validator)](https://anaconda.org/conda-forge/bids-validator) + +There are is a limited library of helper functions written in Python. The main function +determines if a file extension is compliant with the BIDS specification. You can find +the available functions in the library, as well as their descriptions, +[here](https://github.com/bids-standard/bids-validator/blob/master/bids-validator/bids_validator/bids_validator.py). +To install, run `pip install -U bids_validator` (requires python and pip) or +`conda install bids-validator` (requires a Conda environment). + +### Example + +```Python +from bids_validator import BIDSValidator +validator = BIDSValidator() +filepaths = ["/sub-01/anat/sub-01_rec-CSD_T1w.nii.gz", "/sub-01/anat/sub-01_acq-23_rec-CSD_T1w.exe"] +for filepath in filepaths: + print(validator.is_bids(filepath)) # will print True, and then False +``` + +## 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: `cd bids-validator && npm install -g` (for windows users, if in a different drive add /d, e.g. `cd /d F:\bids-validator && npm install -g`) + +Please see the [CONTRIBUTING.md](../CONTRIBUTING.md) +for additional details. + +### Bundling + +bids-validator is bundled with esbuild. While developing, the script `bids-validator/bin/bids-validator` will automatically bundle the project each time it is run. To test a build without publishing it `npm -w bids-validator run build`. This will generate a bids-validator/dist directory containing the local build and `bids-validator/bin/bids-validator` will use this build. To return to automatic bundling on each run, remove the dist directory. + +### 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. + +1. The browser version of `bids-validator` lives in the repo subdirectory + `/bids-validator-web`. It is a [React.js](https://reactjs.org/) application + that uses the [next.js](https://nextjs.org/) framework. +2. To develop `bids-validator` and see how it will act in the browser, simply run + `npm run web-dev` in the project root and navigate to `localhost:3000`. +3. In development mode, changes to the codebase will trigger rebuilds of the application + automatically. +4. Changes to the `/bids-validator` in the codebase will also be reflected in the + web application. +5. Tests use the [Jest](https://jestjs.io/index.html) testing library and should be developed in `/bids-validator-web/tests`. + We can always use more tests, so please feel free to contribute a test that reduces the chance + of any bugs you fix! +6. To ensure that the web application compiles successfully in production, run `npm run web-export` + +### Testing + +If it's your first time running tests, first use the command `git submodule update --init --depth 1` to pull the test example data. This repo contains the [bids-examples github repository](https://github.com/bids-standard/bids-examples) as a [submodule](https://git-scm.com/book/en/v2/Git-Tools-Submodules). + +To start the test suite run `npm run test` from the project root. `npm run 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`. + +### Install globally from a development branch + +Global installs are not recommended for development because of the possibility of package conflicts with other Node.js projects. If you do need to test with a global install from a development tree, follow these steps to generate the NPM package without publishing it and install the package locally. + +1. `npm -w bids-validator run build` +2. `npm -w bids-validator pack` +3. `npm install -g bids-validator-*.tgz` + +### Publishing + +Publishing is done with [Lerna](https://github.com/lerna/lerna). Use the command `npx lerna publish` and follow instructions to set a new version. + +Using lerna publish will create a git commit with updated version information and create a version number tag for it, push the tag to GitHub, then publish to NPM and PyPI. The GitHub release is manual following that. + +## Acknowledgments + +Many contributions to the `bids-validator` were done by members of the +BIDS community. See the +[list of contributors](https://bids-specification.readthedocs.io/en/stable/99-appendices/01-contributors.html). + +A large part of the development of `bids-validator` is currently done by +[Squishymedia](https://squishymedia.com/), who are in turn financed through +different grants offered for the general development of BIDS. See the list +below. + +Development and contributions were supported through the following federally +funded projects/grants: + +- [BIDS Derivatives (NIMH: R24MH114705, PI: Poldrack)](https://grantome.com/grant/NIH/R24-MH114705-01) +- [OpenNeuro (NIMH: R24MH117179, PI: Poldrack)](https://grantome.com/grant/NIH/R24-MH117179-01) +- [Spokes: MEDIUM: WEST (NSF: 1760950, PI: Poldrack & Gorgolewski)](https://grantome.com/grant/NSF/IIS-1760950) +- [ReproNim](http://repronim.org) [(NIH-NIBIB P41 EB019936, PI: Kennedy)](https://projectreporter.nih.gov/project_info_description.cfm?aid=8999833) + + +%package help +Summary: Development documents and examples for bids-validator +Provides: python3-bids-validator-doc +%description help +[![Node Tests](https://github.com/bids-standard/bids-validator/actions/workflows/node_tests.yml/badge.svg)](https://github.com/bids-standard/bids-validator/actions/workflows/node_tests.yml) +[![Python tests](https://github.com/bids-standard/bids-validator/actions/workflows/python_tests.yml/badge.svg)](https://github.com/bids-standard/bids-validator/actions/workflows/python_tests.yml) +[![bids-examples tests](https://github.com/bids-standard/bids-validator/actions/workflows/test-bids-examples.yml/badge.svg)](https://github.com/bids-standard/bids-validator/actions/workflows/test-bids-examples.yml) +[![CircleCI](https://circleci.com/gh/bids-standard/bids-validator.svg?style=shield&circle-token=:circle-token)](https://circleci.com/gh/bids-standard/bids-validator) +[![Codecov](https://codecov.io/gh/bids-standard/bids-validator/branch/master/graph/badge.svg)](https://codecov.io/gh/bids-standard/bids-validator) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3688707.svg)](https://doi.org/10.5281/zenodo.3688707) + +# BIDS-Validator + +- [BIDS-Validator](#bids-validator) + - [Quickstart](#quickstart) + - [Support](#support) + - [Maintainers and Contributors](#maintainers-and-contributors) + - [Use](#use) + - [API](#api) + - [.bidsignore](#bidsignore) + - [Configuration](#configuration) + - [In the Browser](#in-the-browser) + - [On the Server](#on-the-server) + - [Through Command Line](#through-command-line) + - [Docker image](#docker-image) + - [Python Library](#python-library) + - [Example](#example) + - [Development](#development) + - [Running Locally in a Browser](#running-locally-in-a-browser) + - [Testing](#testing) + - [Publishing](#publishing) + - [Acknowledgments](#acknowledgments) + +## Quickstart + +1. Web version: + 1. Open [Google Chrome](https://www.google.com/chrome/) or + [Mozilla Firefox](https://mozilla.org/firefox) (currently the only + supported browsers) + 1. Go to https://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 ](https://developer.chrome.com/devtools) + and report the error at [https://github.com/bids-standard/bids-validator/issues](https://github.com/bids-standard/bids-validator/issues). +1. Command line version: + 1. Install [Node.js](https://nodejs.org) (at least version 12.12.0) + 1. Update `npm` to be at least version 7 (`npm install --global npm@^7`) + 1. From a terminal run `npm install -g bids-validator` + 1. Run `bids-validator` to start validating datasets. +1. Docker + 1. Install Docker + 1. From a terminal run `docker run -ti --rm -v /path/to/data:/data:ro bids/validator /data` + but replace the `/path/to/data` part of the command with your own path on your machine. +1. Python Library: + 1. Install [Python](https://www.python.org/) + 1. Install [Pip](https://pip.pypa.io/en/stable/installing/) package manager for Python, if + not already installed. + 1. From a terminal run `pip install bids_validator` to acquire the + [BIDS Validator PyPI package](https://pypi.org/project/bids-validator/) + or `conda install bids-validator` for the + [Conda package](https://anaconda.org/conda-forge/bids-validator). + 1. Open a Python terminal and type: `python` + 1. Import the BIDS Validator package `from bids_validator import BIDSValidator` + 1. Check if a file is BIDS compatible `BIDSValidator().is_bids('path/to/a/bids/file')` + +## 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. + +There is also a library of helper functions written in Python, for use with BIDS +compliant applications written in this language. + +Please report any issues you experience while using these support targets via +the [GitHub issue tracker](https://github.com/bids-standard/bids-validator/issues). +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. + +## Maintainers and Contributors + + + +[![All Contributors](https://img.shields.io/badge/all_contributors-43-orange.svg?style=flat-square)](#contributors-) + + + +This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. +Contributions of any kind are welcome! + +The project is maintained by [@rwblair](https://github.com/rwblair/) with the help of many contributors listed below. +(The [emoji key](https://allcontributors.org/docs/en/emoji-key) is indicating the kind of contribution) + +Please also see [Acknowledgments](#acknowledgments). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Adam Li
πŸ’» ⚠️ πŸ““ πŸ›
Adam Thomas
πŸ“–
Alexander Jones
πŸ’» ⚠️ πŸ€”
Ben Beasley
πŸ“¦
Chris Gorgolewski
πŸ› πŸ’» πŸ”£ πŸ“– πŸ’‘ πŸ€” πŸš‡ 🚧 πŸ§‘β€πŸ« πŸ’¬ πŸ‘€ ⚠️ βœ… πŸ“’ πŸ““
Chris Holdgraf
πŸ’»
Chris Markiewicz
πŸ’» ⚠️ πŸ€” πŸ› πŸ’¬ πŸ”§ 🚧

David Nishikawa
πŸ’» ⚠️
Dimitri Papadopoulos Orfanos
πŸ’»
Duncan Macleod
πŸš‡
Franklin Feingold
πŸ“–
Gregory noack
πŸ’» ⚠️
Horea Christian
πŸ’»
Jakub Kaczmarzyk
πŸš‡

Joke Durnez
πŸ’»
Mainak Jas
πŸ’» ⚠️ πŸ€” πŸ‘€ πŸ““
Marco Castellaro
πŸ’» ⚠️
Max
πŸ’» πŸ›
Michael Hanke
πŸ“–
Mikael Naveau
πŸ’»
Nell Hardcastle
πŸ’» πŸ€” πŸš‡ πŸ’¬ πŸ‘€

Nicolas Traut
πŸ’»
Parul Sethi
πŸ’» ⚠️
Patricia Clement
πŸ’»
Remi Gau
πŸ’» πŸ“– πŸ““
Richard HΓΆchenberger
πŸ’» πŸ““ ⚠️ πŸ›
Robert Oostenveld
πŸ’» πŸ€” πŸ› ⚠️
Rohan Goyal
πŸ’»

Ross Blair
🚧 πŸ€” πŸ’» πŸ› πŸš‡ πŸ“† πŸ’¬ πŸ‘€ πŸ”§ ⚠️
Russ Poldrack
πŸ’» πŸ’΅ πŸ”
Soichi Hayashi
πŸ›
Stefan Appelhoff
πŸ› πŸ’» πŸ”£ πŸ“– πŸ’‘ πŸ€” πŸš‡ 🚧 πŸ§‘β€πŸ« πŸ’¬ πŸ‘€ ⚠️ βœ… πŸ“’ πŸ““
Suyash
πŸ’»
Taylor Salo
πŸ’»
Teal Hobson-Lowther
πŸ’» ⚠️

Travis Riddle
πŸ›
VisLab
πŸ€” πŸ’»
Wazeer Zulfikar
πŸ“–
Yaroslav Halchenko
πŸ€” πŸ’» πŸ“– πŸ““
constellates
πŸ’» ⚠️
dewarrn1
πŸ’»
dkp
πŸ’»

goldmund
πŸ’» ⚠️
+ + + + + + +## 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 + +[![Docker Image Version (latest by date)](https://img.shields.io/docker/v/bids/validator?label=docker)](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 ` +- the `-ti` flag means the inputs are accepted and outputs are printed to the + terminal +- the `--rm` flag means that the state of the docker container is not saved + after it has run +- the `-v` flag is adding your local data to the docker container + ([bind-mounts](https://docs.docker.com/storage/bind-mounts/)). Importantly, + the input after the `-v` flag consists of three fields separated colons: `:` + - the first field is the path to the directory on the host machine: + `/path/to/data` + - the second field is the path where the directory is mounted in the + container + - the third field is optional. In our case, we use `ro` to specify that the + mounted data is _read only_ + +## Python Library + +[![PyPI version](https://badge.fury.io/py/bids-validator.svg)](https://badge.fury.io/py/bids-validator) +[![Conda version](https://img.shields.io/conda/vn/conda-forge/bids-validator)](https://anaconda.org/conda-forge/bids-validator) + +There are is a limited library of helper functions written in Python. The main function +determines if a file extension is compliant with the BIDS specification. You can find +the available functions in the library, as well as their descriptions, +[here](https://github.com/bids-standard/bids-validator/blob/master/bids-validator/bids_validator/bids_validator.py). +To install, run `pip install -U bids_validator` (requires python and pip) or +`conda install bids-validator` (requires a Conda environment). + +### Example + +```Python +from bids_validator import BIDSValidator +validator = BIDSValidator() +filepaths = ["/sub-01/anat/sub-01_rec-CSD_T1w.nii.gz", "/sub-01/anat/sub-01_acq-23_rec-CSD_T1w.exe"] +for filepath in filepaths: + print(validator.is_bids(filepath)) # will print True, and then False +``` + +## 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: `cd bids-validator && npm install -g` (for windows users, if in a different drive add /d, e.g. `cd /d F:\bids-validator && npm install -g`) + +Please see the [CONTRIBUTING.md](../CONTRIBUTING.md) +for additional details. + +### Bundling + +bids-validator is bundled with esbuild. While developing, the script `bids-validator/bin/bids-validator` will automatically bundle the project each time it is run. To test a build without publishing it `npm -w bids-validator run build`. This will generate a bids-validator/dist directory containing the local build and `bids-validator/bin/bids-validator` will use this build. To return to automatic bundling on each run, remove the dist directory. + +### 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. + +1. The browser version of `bids-validator` lives in the repo subdirectory + `/bids-validator-web`. It is a [React.js](https://reactjs.org/) application + that uses the [next.js](https://nextjs.org/) framework. +2. To develop `bids-validator` and see how it will act in the browser, simply run + `npm run web-dev` in the project root and navigate to `localhost:3000`. +3. In development mode, changes to the codebase will trigger rebuilds of the application + automatically. +4. Changes to the `/bids-validator` in the codebase will also be reflected in the + web application. +5. Tests use the [Jest](https://jestjs.io/index.html) testing library and should be developed in `/bids-validator-web/tests`. + We can always use more tests, so please feel free to contribute a test that reduces the chance + of any bugs you fix! +6. To ensure that the web application compiles successfully in production, run `npm run web-export` + +### Testing + +If it's your first time running tests, first use the command `git submodule update --init --depth 1` to pull the test example data. This repo contains the [bids-examples github repository](https://github.com/bids-standard/bids-examples) as a [submodule](https://git-scm.com/book/en/v2/Git-Tools-Submodules). + +To start the test suite run `npm run test` from the project root. `npm run 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`. + +### Install globally from a development branch + +Global installs are not recommended for development because of the possibility of package conflicts with other Node.js projects. If you do need to test with a global install from a development tree, follow these steps to generate the NPM package without publishing it and install the package locally. + +1. `npm -w bids-validator run build` +2. `npm -w bids-validator pack` +3. `npm install -g bids-validator-*.tgz` + +### Publishing + +Publishing is done with [Lerna](https://github.com/lerna/lerna). Use the command `npx lerna publish` and follow instructions to set a new version. + +Using lerna publish will create a git commit with updated version information and create a version number tag for it, push the tag to GitHub, then publish to NPM and PyPI. The GitHub release is manual following that. + +## Acknowledgments + +Many contributions to the `bids-validator` were done by members of the +BIDS community. See the +[list of contributors](https://bids-specification.readthedocs.io/en/stable/99-appendices/01-contributors.html). + +A large part of the development of `bids-validator` is currently done by +[Squishymedia](https://squishymedia.com/), who are in turn financed through +different grants offered for the general development of BIDS. See the list +below. + +Development and contributions were supported through the following federally +funded projects/grants: + +- [BIDS Derivatives (NIMH: R24MH114705, PI: Poldrack)](https://grantome.com/grant/NIH/R24-MH114705-01) +- [OpenNeuro (NIMH: R24MH117179, PI: Poldrack)](https://grantome.com/grant/NIH/R24-MH117179-01) +- [Spokes: MEDIUM: WEST (NSF: 1760950, PI: Poldrack & Gorgolewski)](https://grantome.com/grant/NSF/IIS-1760950) +- [ReproNim](http://repronim.org) [(NIH-NIBIB P41 EB019936, PI: Kennedy)](https://projectreporter.nih.gov/project_info_description.cfm?aid=8999833) + + +%prep +%autosetup -n bids-validator-1.10.0 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-bids-validator -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed Mar 08 2023 Python_Bot - 1.10.0-1 +- Package Spec generated diff --git a/sources b/sources new file mode 100644 index 0000000..27a111a --- /dev/null +++ b/sources @@ -0,0 +1 @@ +739b05c78655c10d12c0aa702fc0308d bids-validator-1.10.0.tar.gz -- cgit v1.2.3