Merge pull request #975 from marcocastellaro/bep005_asl

Bep005 asl

Author: rwblair

.gitignore

@@ -16,7 +16,6 @@ bids-validator-web/.next/
 # Only use global yarn.lock
 bids-validator/yarn.lock
 bids-validator-web/yarn.lock
-
 .vscode/
 
 *.swp

CODE_OF_CONDUCT.md

@@ -8,19 +8,19 @@ In the interest of fostering an open and welcoming environment, we as contributo
 
 Examples of behavior that contributes to creating a positive environment include:
 
-* Using welcoming and inclusive language
-* Being respectful of differing viewpoints and experiences
-* Gracefully accepting constructive criticism
-* Focusing on what is best for the community
-* Showing empathy towards other community members
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
 
 Examples of unacceptable behavior by participants include:
 
-* The use of sexualized language or imagery and unwelcome sexual attention or advances
-* Trolling, insulting/derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or electronic address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a professional setting
+- The use of sexualized language or imagery and unwelcome sexual attention or advances
+- Trolling, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or electronic address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a professional setting
 
 ## Our Responsibilities
 

bids-validator-code.code-workspace

@@ -0,0 +1,8 @@
+{
+	"folders": [
+		{
+			"path": "."
+		}
+	],
+	"settings": {}
+}

bids-validator/README.md

@@ -3,28 +3,27 @@
 [![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)
+- [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
 
@@ -47,7 +46,7 @@
 1. Python Library:
    1. Install [Python](https://www.python.org/) (works with python2 and python3)
    1. Install [Pip](https://pip.pypa.io/en/stable/installing/) package manager for python, if
-   not already installed.
+      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/)
    1. Open a Python terminal `python`
@@ -281,11 +280,12 @@ 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 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 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
+  to validate the dataset `/path/to/data` on your host machine
 
 See here for a brief explanation of the commands:
 
@@ -298,12 +298,12 @@ See here for a brief explanation of the commands:
 - 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*
+  - 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
 
@@ -341,17 +341,17 @@ 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.
+   `/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
-	`yarn web-dev` in the project root and navigate to `localhost:3000`.
+   `yarn 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.
+   automatically.
 4. Changes to the `/bids-validator` in the codebase will also be reflected in the
-	web application.
+   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!
+   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 `yarn web-export`
 
 ### Testing
@@ -383,6 +383,7 @@ below.
 
 Development and contributions were supported through the following federally
 funded projects/grants:
+
 - [BIDS Derivatives (NIMH: R24MH114705, PI: Poldrack)](http://grantome.com/grant/NIH/R24-MH114705-01)
 - [OpenNeuro (NIMH: R24MH117179, PI: Poldrack)](http://grantome.com/grant/NIH/R24-MH117179-01)
 - [Spokes: MEDIUM: WEST (NSF: 1760950, PI: Poldrack & Gorgolewski)](http://grantome.com/grant/NSF/IIS-1760950)

bids-validator/bids_validator/rules/file_level_rules.json

@@ -106,7 +106,8 @@
         "magnitude2",
         "magnitude",
         "fieldmap",
-        "epi"
+        "epi",
+        "m0scan"
       ],
       "@@@_field_map_ext_@@@": ["nii\\.gz", "nii", "json"]
     }
@@ -168,6 +169,22 @@
     }
   },
 
+  "asl": {
+    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?perf[\\/\\\\]\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_dir-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?_(?:@@@_asl_type_@@@)$",
+    "tokens": {
+      "@@@_asl_type_@@@": [
+        "asl\\.nii\\.gz",
+        "asl\\.nii",
+        "asl\\.json",
+        "m0scan\\.nii\\.gz",
+        "m0scan\\.nii",
+        "m0scan\\.json",
+        "aslcontext\\.tsv",
+        "asllabeling\\.jpg"
+      ]
+    }
+  },
+
   "eeg": {
     "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?eeg[\\/\\\\]\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_split-[0-9]+)?((_eeg\\.(@@@_eeg_type_@@@)|(@@@_eeg_ext_@@@))|(?:_recording-[a-zA-Z0-9]+)?(?:@@@_cont_ext_@@@))$",
     "tokens": {

bids-validator/bids_validator/rules/session_level_rules.json

@@ -20,6 +20,18 @@
     }
   },
 
+  "asl_ses": {
+    "regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(@@@_asl_ses_ext_@@@)$",
+    "tokens": {
+      "@@@_asl_ses_ext_@@@": [
+        "_asl.json",
+        "_aslcontext.tsv",
+        "_m0scan.json",
+        "_asllabeling.jpg"
+      ]
+    }
+  },
+
   "anat_ses": {
     "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+_)?(@@@_anat_ses_type_@@@).json$",
     "tokens": {

bids-validator/bids_validator/rules/subject_level_rules.json

@@ -2,10 +2,7 @@
   "subject_level": {
     "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\]\\1(@@@_subject_level_ext_@@@)$",
     "tokens": {
-      "@@@_subject_level_ext_@@@": [
-        "_sessions\\.tsv",
-        "_sessions\\.json"
-      ]
+      "@@@_subject_level_ext_@@@": ["_sessions\\.tsv", "_sessions\\.json"]
     }
   }
 }

bids-validator/bids_validator/rules/top_level_rules.json

@@ -35,6 +35,18 @@
     }
   },
 
+  "asl_top": {
+    "regexp": "^\\/(?:ses-[a-zA-Z0-9]+_)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(@@@_asl_top_ext_@@@)$",
+    "tokens": {
+      "@@@_asl_top_ext_@@@": [
+        "_asl\\.json",
+        "_m0scan\\.json",
+        "_aslcontext\\.tsv",
+        "_labeling.jpg"
+      ]
+    }
+  },
+
   "anat_top": {
     "regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?(@@@_anat_suffixes_@@@)\\.json$",
     "tokens": {

bids-validator/bids_validator/tsv/non_custom_columns.json

@@ -42,5 +42,6 @@
   "participants": ["participant_id"],
   "phenotype": ["participant_id"],
   "scans": ["acq_time", "filename"],
-  "sessions": ["acq_time", "session_id"]
+  "sessions": ["acq_time", "session_id"],
+  "aslcontext": ["volume_type"]
 }