From a1580762260c3bfd9ea28cc9a7bf855d82943f30 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Fri, 25 Oct 2024 11:55:40 -0400 Subject: [PATCH 1/5] Build for master and main, to simplify migration --- .github/workflows/codespell.yml | 6 +++--- .github/workflows/deno_tests.yml | 4 ++-- .github/workflows/schema_web_build.yml | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml index 5a5d565e..3c554337 100644 --- a/.github/workflows/codespell.yml +++ b/.github/workflows/codespell.yml @@ -3,9 +3,9 @@ name: Codespell on: push: - branches: [master] + branches: [master, main] pull_request: - branches: [master] + branches: [master, main] concurrency: group: ${{ github.workflow }}-${{ github.ref }} @@ -21,4 +21,4 @@ jobs: - uses: codespell-project/actions-codespell@master with: ignore_words_list: ro,anser,te,tage,afterall,nwe,nin,nd,falsy - skip: package-lock.json, deps*, deno.lock + skip: deno.lock diff --git a/.github/workflows/deno_tests.yml b/.github/workflows/deno_tests.yml index f84b3aa7..1de5fe6f 100644 --- a/.github/workflows/deno_tests.yml +++ b/.github/workflows/deno_tests.yml @@ -3,10 +3,10 @@ name: Deno build on: push: - branches: [master] + branches: [master, main] tags: ['*'] pull_request: - branches: [master] + branches: [master, main] concurrency: group: ${{ github.workflow }}-${{ github.ref }} diff --git a/.github/workflows/schema_web_build.yml b/.github/workflows/schema_web_build.yml index 07cd8927..cc847151 100644 --- a/.github/workflows/schema_web_build.yml +++ b/.github/workflows/schema_web_build.yml @@ -3,10 +3,10 @@ name: Schema validator web build on: push: - branches: [master] + branches: [master, main] tags: ['*'] pull_request: - branches: [master] + branches: [master, main] concurrency: group: ${{ github.workflow }}-${{ github.ref }} From 4366602cbf47442b75994805402ea7cef438806d Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Fri, 25 Oct 2024 12:27:02 -0400 Subject: [PATCH 2/5] De-nodeify CONTRIBUTING --- CONTRIBUTING.md | 17 ++++------------- 1 file changed, 4 insertions(+), 13 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index e3270898..35a75c8b 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -60,7 +60,7 @@ To participate, be sure you know how to 1. [Make a GitHub account][link_signupinstructions] 1. Install the required software: - [git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git) - - [NodeJS](https://nodejs.org/en/download/), including `npm` of version 7 or higher (check existing version with `npm -v`, to update an existing nodejs, we can suggest [this guide](https://phoenixnap.com/kb/update-node-js-version).) + - [Deno](https://deno.com/) 1. In the GitHub interface, [make a fork][link_fork] of https://github.com/bids-standard/bids-validator to your own user (called `USER` for the sake of the example) @@ -71,18 +71,9 @@ To participate, be sure you know how to - You will now have a new directory called `bids-validator` - navigate to that directory and run `git status` to verify that it's a `git` directory - - run `npm install` to install the BIDS validator -1. Upon inspection of the `bids-validator` repository we can find the - "executable" BIDS validator, located in `<...>/bids-validator/bin`, where - `<...>` is the path to your `bids-validator` repository - - To make this executable available from the command line, we have to add it - to the path. On Unix systems with bash as their default shell, this means - editing the `.bashrc` file by adding the following line to the bottom of - it: `export PATH="$PATH:<...>/bids-validator/bin"` ... Note that `<...>` - again needs to be replaced by the path to your BIDS validator repository - - Now whenever you open a new command line, we will have the `bids-validator` - executable available. You can verify by opening a new command line and - typing `bids-validator --version`, and it should print the version number +1. Install `bids-validator` with: `deno install -Agf --reload ./bids-validator/src/bids-validator.ts` + - Deno will install the file to its `bin` directory. On Unix systems, + this should be `$HOME/.deno/bin`. You may need to add this to your `PATH`. Now your development version of BIDS validator is set up and you can use it. Whenever you _checkout_ a new branch in your git repository, the From 51bbda3117093c632340e438a7305ef856e5054f Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 31 Oct 2024 16:06:07 -0400 Subject: [PATCH 3/5] Rename bids-validator-deno entrypoint --- bids-validator/{bids-validator-deno => local-run} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename bids-validator/{bids-validator-deno => local-run} (100%) diff --git a/bids-validator/bids-validator-deno b/bids-validator/local-run similarity index 100% rename from bids-validator/bids-validator-deno rename to bids-validator/local-run From a650c0ffd5ff21001a977ac33baf03091ef581a4 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 31 Oct 2024 16:07:50 -0400 Subject: [PATCH 4/5] Add note of intended use for local-run --- bids-validator/local-run | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bids-validator/local-run b/bids-validator/local-run index 644fc756..422aa5c8 100755 --- a/bids-validator/local-run +++ b/bids-validator/local-run @@ -1,3 +1,4 @@ #!/usr/bin/env -S deno run --allow-read --allow-write --allow-env --allow-net --allow-run +// This script runs the local copy of the validator, intended as a development aid. +// You generally should run `deno run -A jsr:@bids/validator` import './src/bids-validator.ts' - From 05749772703a06714ff8baccb7efcf523de72954 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 31 Oct 2024 16:11:02 -0400 Subject: [PATCH 5/5] mv bids-validator/* into root --- .gitmodules | 2 +- README.md | 449 ++---------------- bids-validator/.gitattributes | 1 - bids-validator/.npmignore | 1 - bids-validator/README.md | 71 --- bids-validator/deno.json | 57 --- bids-validator/build.ts => build.ts | 0 deno.json | 56 ++- bids-validator/deno.lock => deno.lock | 0 bids-validator/local-run => local-run | 0 {bids-validator/src => src}/.git-meta.json | 0 {bids-validator/src => src}/bids-validator.ts | 0 .../src => 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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) -[![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) +# Deno based bids-validator -# BIDS-Validator +## Intro -- [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) - - [Development](#development) - - [Running Locally in a Browser](#running-locally-in-a-browser) - - [Testing](#testing) - - [Publishing](#publishing) - - [Acknowledgments](#acknowledgments) +This is a full rewrite of the bids-validator JavaScript implementation designed to use the [bids-specification schema](https://github.com/bids-standard/bids-specification/tree/master/src/schema) to apply the majority of validation rules. -## Quickstart +Deno is a JavaScript and TypeScript runtime that is used to run the schema based validator. Deno is simpler than Node.js and only requires one tool to use, the Deno executable itself. To install Deno, follow these [install instructions for your platform](https://deno.land/manual/getting_started/installation). -This repository houses 4 packages: -1. [./bids-validator](./bids-validator)The current deno based bids-validator cli and library -2. [./web](./web)The current web based validator -3. [./legacy/bids-validator](legacy/bids-validator)The legacy node validator -4. [./legacy/bids-validator-web](legacy/bids-validator-web)The legacy web based validator +## Usage -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 18.0.0) - 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. +To use the latest validator hosted at https://deno.land/x/bids_validator, use the following command: -## Support - - -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). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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- - - - - - -## 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. - -"or" arrays are not supported at the lowest level because it wouldn't add any -functionality. For example the following is not supported. +The issues are partial matches of the `issues` that the validator accumulates. +Pass the `--json` flag to see the issues in detail. -```JSON -{ - "ignore": [ - { - "or": [ - "ECHO_TIME_GREATER_THAN", - "ECHO_TIME_NOT_DEFINED" - ] - } - ] -} -``` +### Development tools -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 - -[![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_ - -## 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. +This test suite includes running expected output from bids-examples and may throw some expected failures for bids-examples datasets where either the schema or validator are misaligned with the example dataset while under development. -1. `npm -w bids-validator run build` -2. `npm -w bids-validator pack` -3. `npm install -g bids-validator-*.tgz` +## Refreshing latest specification -### Publishing +If you are validating with the latest specification instead of a specific version, the validator will hold onto a cached version. You can request the newest version by adding the `--reload` argument to obtain the newest specification definition. +`deno run --reload=https://bids-specification.readthedocs.io/en/latest/schema.json src/main.ts` -## Acknowledgments +## Modifying and building a new schema -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). +To modify the schema a clone of bids-standard/bids-specification will need to be made. README and schema itself live here https://github.com/bids-standard/bids-specification/tree/master/src/schema. -Development and contributions were supported through the following federally -funded projects/grants: +After changes to the schema have been made to a local copy the dereferenced single json file used by the validator will need to be built. The `bidsschematools` python package does this. It can be installed from pypi via pip or a local installation can be made. It lives in the specification repository here https://github.com/bids-standard/bids-specification/tree/master/tools/schemacode -- [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/ACI-1760950) -- [ReproNim](http://repronim.org) [(NIH-NIBIB P41 EB019936, PI: Kennedy)](https://projectreporter.nih.gov/project_info_description.cfm?aid=8999833) +The command to compile a dereferenced schema is `bst -v export --output src/schema.json` (this assumes you are in the root of the bids-specification repo). Once compiled it can be passed to the validator via the `-s` flag, `./bids-validator-deno -s ` diff --git a/bids-validator/.gitattributes b/bids-validator/.gitattributes deleted file mode 100644 index d96f1fc3..00000000 --- a/bids-validator/.gitattributes +++ /dev/null @@ -1 +0,0 @@ -bids_validator/_version.py export-subst diff --git a/bids-validator/.npmignore b/bids-validator/.npmignore deleted file mode 100644 index 4173ae8d..00000000 --- a/bids-validator/.npmignore +++ /dev/null @@ -1 +0,0 @@ -tests/data diff --git a/bids-validator/README.md b/bids-validator/README.md deleted file mode 100644 index 8a786bd6..00000000 --- a/bids-validator/README.md +++ /dev/null @@ -1,71 +0,0 @@ -# Deno based bids-validator - -## Intro - -This is a full rewrite of the bids-validator JavaScript implementation designed to use the [bids-specification schema](https://github.com/bids-standard/bids-specification/tree/master/src/schema) to apply the majority of validation rules. - -Deno is a JavaScript and TypeScript runtime that is used to run the schema based validator. Deno is simpler than Node.js and only requires one tool to use, the Deno executable itself. To install Deno, follow these [install instructions for your platform](https://deno.land/manual/getting_started/installation). - -## Usage - -To use the latest validator hosted at https://deno.land/x/bids_validator, use the following command: - -```console -$ deno run --allow-read --allow-env https://deno.land/x/bids_validator/bids-validator.ts path/to/dataset -``` - -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. - -### Configuration file - -The schema validator accepts a JSON configuration file that reclassifies issues as -warnings, errors or ignored. - -```json -{ - "ignore": [ - { "code": "JSON_KEY_RECOMMENDED", "location": "/T1w.json" } - ], - "warning": [], - "error": [ - { "code": "NO_AUTHORS" } - ] -} -``` - -The issues are partial matches of the `issues` that the validator accumulates. -Pass the `--json` flag to see the issues in detail. - -### Development tools - -From the repository root, use `bids-validator/bids-validator-deno` to run with all permissions enabled by default: - -```shell -# Run from within the /bids-validator directory -cd bids-validator -# Run validator: -./bids-validator-deno path/to/dataset -``` - -## Schema validator test suite - -```shell -# Run tests: -deno test --allow-env --allow-read --allow-write src/ -``` - -This test suite includes running expected output from bids-examples and may throw some expected failures for bids-examples datasets where either the schema or validator are misaligned with the example dataset while under development. - -## Refreshing latest specification - -If you are validating with the latest specification instead of a specific version, the validator will hold onto a cached version. You can request the newest version by adding the `--reload` argument to obtain the newest specification definition. - -`deno run --reload=https://bids-specification.readthedocs.io/en/latest/schema.json src/main.ts` - -## Modifying and building a new schema - -To modify the schema a clone of bids-standard/bids-specification will need to be made. README and schema itself live here https://github.com/bids-standard/bids-specification/tree/master/src/schema. - -After changes to the schema have been made to a local copy the dereferenced single json file used by the validator will need to be built. The `bidsschematools` python package does this. It can be installed from pypi via pip or a local installation can be made. It lives in the specification repository here https://github.com/bids-standard/bids-specification/tree/master/tools/schemacode - -The command to compile a dereferenced schema is `bst -v export --output src/schema.json` (this assumes you are in the root of the bids-specification repo). Once compiled it can be passed to the validator via the `-s` flag, `./bids-validator-deno -s ` diff --git a/bids-validator/deno.json b/bids-validator/deno.json deleted file mode 100644 index 6443e841..00000000 --- a/bids-validator/deno.json +++ /dev/null @@ -1,57 +0,0 @@ -{ - "name": "@bids/validator", - "version": "1.14.14", - "exports": { - ".": "./src/bids-validator.ts", - "./main": "./src/main.ts", - "./output": "./src/utils/output.ts", - "./files": "./src/files/deno.ts", - "./options": "./src/setup/options.ts", - "./issues": "./src/issues/datasetIssues.ts" - }, - "publish": { - "exclude": [ - "bids_validator/", - "bin/", - "tests/", - "docs/", - "utils/", - "validators/", - "bids-validator-deno", - "build.ts", - "cli.js", - "esbuild.mjs", - "index.js", - "package.json", - ".npmignore", - ".gitattributes" - ] - }, - "imports": { - "@ajv": "npm:ajv@8.17.1", - "@bids/schema": "jsr:@bids/schema@0.11.4-dev.8+6e2874ce", - "@cliffy/command": "jsr:@cliffy/command@1.0.0-rc.5", - "@cliffy/table": "jsr:@cliffy/table@1.0.0-rc.5", - "@hed/validator": "npm:hed-validator@3.15.5", - "@ignore": "npm:ignore@5.3.2", - "@libs/xml": "jsr:@libs/xml@5.4.13", - "@mango/nifti": "npm:@bids/nifti-reader-js@0.6.9", - "@std/assert": "jsr:@std/assert@1.0.2", - "@std/fmt": "jsr:@std/fmt@1.0.0", - "@std/fs": "jsr:@std/fs@1.0.1", - "@std/io": "jsr:@std/io@0.224.4", - "@std/log": "jsr:@std/log@0.224.5", - "@std/path": "jsr:@std/path@1.0.2", - "@std/yaml": "jsr:@std/yaml@^1.0.4" - }, - "tasks": { - "test": "deno test -A src/tests/" - }, - "fmt": { - "lineWidth": 99, - "semiColons": false, - "singleQuote": true, - "proseWrap": "preserve", - "include": ["src/"] - } -} diff --git a/bids-validator/build.ts b/build.ts similarity index 100% rename from bids-validator/build.ts rename to build.ts diff --git a/deno.json b/deno.json index 358b7d29..6443e841 100644 --- a/deno.json +++ b/deno.json @@ -1,3 +1,57 @@ { - "lock": false + "name": "@bids/validator", + "version": "1.14.14", + "exports": { + ".": "./src/bids-validator.ts", + "./main": "./src/main.ts", + "./output": "./src/utils/output.ts", + "./files": "./src/files/deno.ts", + "./options": "./src/setup/options.ts", + "./issues": "./src/issues/datasetIssues.ts" + }, + "publish": { + "exclude": [ + "bids_validator/", + "bin/", + "tests/", + "docs/", + "utils/", + "validators/", + "bids-validator-deno", + "build.ts", + "cli.js", + "esbuild.mjs", + "index.js", + "package.json", + ".npmignore", + ".gitattributes" + ] + }, + "imports": { + "@ajv": "npm:ajv@8.17.1", + "@bids/schema": "jsr:@bids/schema@0.11.4-dev.8+6e2874ce", + "@cliffy/command": "jsr:@cliffy/command@1.0.0-rc.5", + "@cliffy/table": "jsr:@cliffy/table@1.0.0-rc.5", + "@hed/validator": "npm:hed-validator@3.15.5", + "@ignore": "npm:ignore@5.3.2", + "@libs/xml": "jsr:@libs/xml@5.4.13", + "@mango/nifti": "npm:@bids/nifti-reader-js@0.6.9", + "@std/assert": "jsr:@std/assert@1.0.2", + "@std/fmt": "jsr:@std/fmt@1.0.0", + "@std/fs": "jsr:@std/fs@1.0.1", + "@std/io": "jsr:@std/io@0.224.4", + "@std/log": "jsr:@std/log@0.224.5", + "@std/path": "jsr:@std/path@1.0.2", + "@std/yaml": "jsr:@std/yaml@^1.0.4" + }, + "tasks": { + "test": "deno test -A src/tests/" + }, + "fmt": { + "lineWidth": 99, + "semiColons": false, + "singleQuote": true, + "proseWrap": "preserve", + "include": ["src/"] + } } diff --git a/bids-validator/deno.lock b/deno.lock similarity index 100% rename from bids-validator/deno.lock rename to deno.lock diff --git a/bids-validator/local-run b/local-run similarity index 100% rename from bids-validator/local-run rename to local-run diff --git a/bids-validator/src/.git-meta.json b/src/.git-meta.json similarity index 100% rename from bids-validator/src/.git-meta.json rename to src/.git-meta.json diff --git a/bids-validator/src/bids-validator.ts b/src/bids-validator.ts similarity index 100% rename from bids-validator/src/bids-validator.ts rename to src/bids-validator.ts diff --git a/bids-validator/src/files/browser.test.ts b/src/files/browser.test.ts similarity index 100% rename from bids-validator/src/files/browser.test.ts rename to src/files/browser.test.ts diff --git a/bids-validator/src/files/browser.ts b/src/files/browser.ts similarity index 100% rename from bids-validator/src/files/browser.ts rename to src/files/browser.ts diff --git a/bids-validator/src/files/deno.test.ts b/src/files/deno.test.ts similarity index 100% rename from bids-validator/src/files/deno.test.ts rename to src/files/deno.test.ts diff --git a/bids-validator/src/files/deno.ts b/src/files/deno.ts similarity index 100% rename from bids-validator/src/files/deno.ts rename to src/files/deno.ts diff --git a/bids-validator/src/files/dwi.ts b/src/files/dwi.ts similarity index 100% rename from bids-validator/src/files/dwi.ts rename to src/files/dwi.ts diff --git a/bids-validator/src/files/filetree.test.ts b/src/files/filetree.test.ts similarity index 100% rename from bids-validator/src/files/filetree.test.ts rename to src/files/filetree.test.ts diff --git a/bids-validator/src/files/filetree.ts b/src/files/filetree.ts similarity index 100% rename from bids-validator/src/files/filetree.ts rename to src/files/filetree.ts diff --git a/bids-validator/src/files/gzip.test.ts b/src/files/gzip.test.ts similarity index 100% rename from bids-validator/src/files/gzip.test.ts rename to src/files/gzip.test.ts diff --git a/bids-validator/src/files/gzip.ts b/src/files/gzip.ts similarity index 100% rename from bids-validator/src/files/gzip.ts rename to src/files/gzip.ts diff --git a/bids-validator/src/files/ignore.test.ts b/src/files/ignore.test.ts similarity index 100% rename from bids-validator/src/files/ignore.test.ts rename to src/files/ignore.test.ts diff --git a/bids-validator/src/files/ignore.ts b/src/files/ignore.ts similarity index 100% rename from bids-validator/src/files/ignore.ts rename to src/files/ignore.ts diff --git a/bids-validator/src/files/inheritance.test.ts b/src/files/inheritance.test.ts similarity index 100% rename from bids-validator/src/files/inheritance.test.ts rename to src/files/inheritance.test.ts diff --git a/bids-validator/src/files/inheritance.ts b/src/files/inheritance.ts similarity index 100% rename from bids-validator/src/files/inheritance.ts rename to src/files/inheritance.ts diff --git a/bids-validator/src/files/json.test.ts b/src/files/json.test.ts similarity index 100% rename from bids-validator/src/files/json.test.ts rename to src/files/json.test.ts diff --git a/bids-validator/src/files/json.ts b/src/files/json.ts similarity index 100% rename from bids-validator/src/files/json.ts rename to src/files/json.ts diff --git a/bids-validator/src/files/nifti.test.ts b/src/files/nifti.test.ts similarity index 100% rename from bids-validator/src/files/nifti.test.ts rename to src/files/nifti.test.ts diff --git a/bids-validator/src/files/nifti.ts b/src/files/nifti.ts similarity index 100% rename from bids-validator/src/files/nifti.ts rename to src/files/nifti.ts diff --git a/bids-validator/src/files/tiff.test.ts b/src/files/tiff.test.ts similarity index 100% rename from bids-validator/src/files/tiff.test.ts rename to src/files/tiff.test.ts diff --git a/bids-validator/src/files/tiff.ts b/src/files/tiff.ts similarity index 100% rename from bids-validator/src/files/tiff.ts rename to src/files/tiff.ts diff --git a/bids-validator/src/files/tsv.ts b/src/files/tsv.ts similarity index 100% rename from bids-validator/src/files/tsv.ts rename to src/files/tsv.ts diff --git a/bids-validator/src/issues/datasetIssues.test.ts b/src/issues/datasetIssues.test.ts similarity index 100% rename from bids-validator/src/issues/datasetIssues.test.ts rename to src/issues/datasetIssues.test.ts diff --git a/bids-validator/src/issues/datasetIssues.ts b/src/issues/datasetIssues.ts similarity index 100% rename from bids-validator/src/issues/datasetIssues.ts rename to src/issues/datasetIssues.ts diff --git a/bids-validator/src/issues/list.test.ts b/src/issues/list.test.ts 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a/bids-validator/src/setup/options.ts b/src/setup/options.ts similarity index 100% rename from bids-validator/src/setup/options.ts rename to src/setup/options.ts diff --git a/bids-validator/src/setup/requestPermissions.ts b/src/setup/requestPermissions.ts similarity index 100% rename from bids-validator/src/setup/requestPermissions.ts rename to src/setup/requestPermissions.ts diff --git a/bids-validator/src/summary/collectSubjectMetadata.ts b/src/summary/collectSubjectMetadata.ts similarity index 100% rename from bids-validator/src/summary/collectSubjectMetadata.ts rename to src/summary/collectSubjectMetadata.ts diff --git a/bids-validator/src/summary/summary.test.ts b/src/summary/summary.test.ts similarity index 100% rename from bids-validator/src/summary/summary.test.ts rename to src/summary/summary.test.ts diff --git a/bids-validator/src/summary/summary.ts b/src/summary/summary.ts similarity index 100% rename from bids-validator/src/summary/summary.ts rename to 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a/bids-validator/src/tests/local/valid_dataset.test.ts b/src/tests/local/valid_dataset.test.ts similarity index 100% rename from bids-validator/src/tests/local/valid_dataset.test.ts rename to src/tests/local/valid_dataset.test.ts diff --git a/bids-validator/src/tests/local/valid_filenames.test.ts b/src/tests/local/valid_filenames.test.ts similarity index 100% rename from bids-validator/src/tests/local/valid_filenames.test.ts rename to src/tests/local/valid_filenames.test.ts diff --git a/bids-validator/src/tests/local/valid_headers.test.ts b/src/tests/local/valid_headers.test.ts similarity index 100% rename from bids-validator/src/tests/local/valid_headers.test.ts rename to src/tests/local/valid_headers.test.ts diff --git a/bids-validator/src/tests/nullReadBytes.ts b/src/tests/nullReadBytes.ts similarity index 100% rename from bids-validator/src/tests/nullReadBytes.ts rename to src/tests/nullReadBytes.ts diff --git a/bids-validator/src/tests/schema-expression-language.test.ts 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