Merge pull request #681 from sappelhoff/remove_optional_6_10

[MRG] remove optional arguments bep006 and bep010

Author: chrisgorgo

bids-validator/bin/bids-validator

@@ -17,10 +17,6 @@ var argv = require('yargs')
     .describe('verbose', 'Log more extensive information about issues')
     .boolean('json')
     .describe('json', 'Output results as JSON')
-    .boolean('bep006')
-    .describe('bep006', 'Enable support for BIDS Extension Proposal 006')
-    .boolean('bep010')
-    .describe('bep010', 'Enable support for BIDS extension proposal 010')
     .option('config', {
         alias: 'c',
         describe: 'Optional configuration file. See https://github.com/bids-standard/bids-validator for more info'

bids-validator/tests/utils/issues.spec.js

@@ -20,8 +20,6 @@ describe('issues', () => {
         ignoreWarnings: false,
         ignoreNiftiHeaders: false,
         verbose: false,
-        bep006: false,
-        bep010: false,
         config: {},
       }
       formattedIssues = utils.issues.exceptionHandler(

bids-validator/utils/modalities.js

@@ -40,7 +40,7 @@ module.exports = {
     return modalities
   },
 
-  isCorrectModality: (path, options) => {
+  isCorrectModality: path => {
     let isCorrectModality = false
     // MRI
     if (
@@ -57,11 +57,11 @@ module.exports = {
           break
         case 'eeg':
           // EEG
-          isCorrectModality = !!options.bep006
+          isCorrectModality = true
           break
         case 'ieeg':
           // iEEG
-          isCorrectModality = !!options.bep010
+          isCorrectModality = true
           break
         default:
           break

bids-validator/utils/options.js

@@ -11,8 +11,6 @@ module.exports = {
       ignoreWarnings: options.ignoreWarnings ? true : false,
       ignoreNiftiHeaders: options.ignoreNiftiHeaders ? true : false,
       verbose: options.verbose ? true : false,
-      bep006: options.bep006 ? true : false,
-      bep010: options.bep010 ? true : false,
       config: options.config ? options.config : {},
     }
     if (options.config && typeof options.config !== 'boolean') {

bids-validator/utils/summary/collectSessions.js

@@ -6,7 +6,7 @@ const collectSessions = (fileList, options) => {
     const file = fileList[key]
     if (
       !type.file.isStimuliData(file.relativePath) &&
-      type.isBIDS(file.relativePath, options.bep006, options.bep010)
+      type.isBIDS(file.relativePath)
     ) {
       const pathValues = type.getPathValues(file.relativePath)
       const isEmptyRoom = pathValues.sub && pathValues.sub == 'emptyroom'

bids-validator/utils/summary/collectSubjects.js

@@ -7,7 +7,7 @@ const collectSubjects = (fileList, options) => {
     const file = fileList[key]
     if (
       !type.file.isStimuliData(file.relativePath) &&
-      type.isBIDS(file.relativePath, options.bep006, options.bep010)
+      type.isBIDS(file.relativePath)
     ) {
       const pathValues = type.getPathValues(file.relativePath)
       const isEmptyRoom = pathValues.sub && pathValues.sub == 'emptyroom'

bids-validator/utils/type.js

@@ -63,7 +63,7 @@ module.exports = {
    * Check if a given path is valid within the
    * bids spec.
    */
-  isBIDS: function(path, bep006, bep010) {
+  isBIDS: function(path) {
     return (
       this.file.isTopLevel(path) ||
       this.file.isStimuliData(path) ||
@@ -73,8 +73,8 @@ module.exports = {
       this.file.isDWI(path) ||
       this.file.isFunc(path) ||
       this.file.isMeg(path) ||
-      (this.file.isIEEG(path) && bep010) ||
-      (this.file.isEEG(path) && bep006) ||
+      this.file.isIEEG(path) ||
+      this.file.isEEG(path) ||
       this.file.isBehavioral(path) ||
       this.file.isCont(path) ||
       this.file.isFieldMap(path) ||

bids-validator/validators/bids/groupFileTypes.js

@@ -26,9 +26,7 @@ const sortFiles = (fileList, options, files) => {
       // collect stimuli
       files.stimuli.push(file)
       files.misc.push(file)
-    } else if (
-      !utils.type.isBIDS(file.relativePath, options.bep006, options.bep010)
-    ) {
+    } else if (!utils.type.isBIDS(file.relativePath)) {
       // invalid file type
       files.invalid.push(file)
       files.misc.push(file)

bids-validator/validators/bids/quickTest.js

@@ -8,7 +8,7 @@ const utils = require('../../utils')
  * otherwise it will throw a callback with a
  * generic error.
  */
-const quickTest = (fileList, options) => {
+const quickTest = fileList => {
   const keys = Object.keys(fileList)
   const couldBeBIDS = keys.some(key => {
     const file = fileList[key]
@@ -17,10 +17,7 @@ const quickTest = (fileList, options) => {
       path = path.split('/')
       path = path.reverse()
 
-      const isCorrectModality = utils.modalities.isCorrectModality(
-        path,
-        options,
-      )
+      const isCorrectModality = utils.modalities.isCorrectModality(path)
       let pathIsSesOrSub =
         path[2] &&
         (path[2].indexOf('ses-') == 0 || path[2].indexOf('sub-') == 0)

bids-validator/validators/bids/start.js

@@ -24,7 +24,7 @@ const start = (dir, options, callback) => {
       BIDS.options = options
       reset(BIDS)
       utils.files.readDir(dir, function(files) {
-        const couldBeBIDS = quickTest(files, BIDS.options)
+        const couldBeBIDS = quickTest(files)
         if (couldBeBIDS) {
           // Is the dir using git-annex?
           const annexed = utils.files.remoteFiles.isGitAnnex(dir)