chore: Remove schema experiment from legacy validator

bids-validator/utils/options.js

@@ -23,7 +23,6 @@ export default {
       remoteFiles: Boolean(options.remoteFiles),
       gitRef: options.gitRef || 'HEAD',
       config: options.config || {},
-      schema: options.schema !== 'disable' ? options.schema : false,
     }
     if (options.config && typeof options.config !== 'boolean') {
       this.parseConfig(dir, options.config, function (issues, config) {

bids-validator/utils/type.js

@@ -17,13 +17,6 @@ import session_level_rules from '../bids_validator/rules/session_level_rules.jso
 import subject_level_rules from '../bids_validator/rules/subject_level_rules.json'
 import top_level_rules from '../bids_validator/rules/top_level_rules.json'
 
-let bids_schema
-
-// Alternative method of loading from bids-specification schema
-export function schemaSetup(schema) {
-  bids_schema = schema
-}
-
 // Associated data
 const associatedData = buildRegExp(associated_data_rules.associated_data)
 // File level
@@ -146,57 +139,30 @@ export default {
      * Check if the file has appropriate name for a top level file
      */
     isTopLevel: function (path) {
-      if (bids_schema) {
-        return (
-          bids_schema.top_level_files.some((regex) => regex.exec(path)) ||
-          funcTop.test(path) ||
-          aslTop.test(path) ||
-          dwiTop.test(path) ||
-          anatTop.test(path) ||
-          vfaTop.test(path) ||
-          megreTop.test(path) ||
-          irt1Top.test(path) ||
-          mpmTop.test(path) ||
-          mtsTop.test(path) ||
-          mtrTop.test(path) ||
-          mp2rageTop.test(path) ||
-          fmapEpiTop.test(path) ||
-          fmapGreTop.test(path) ||
-          otherTopFiles.test(path) ||
-          megTop.test(path) ||
-          eegTop.test(path) ||
-          ieegTop.test(path) ||
-          petTop.test(path) ||
-          motionTop.test(path) ||
-          nirsTop.test(path) ||
-          microscopyTop.test(path)
-        )
-      } else {
-        return (
-          rootTop.test(path) ||
-          funcTop.test(path) ||
-          aslTop.test(path) ||
-          dwiTop.test(path) ||
-          anatTop.test(path) ||
-          vfaTop.test(path) ||
-          megreTop.test(path) ||
-          irt1Top.test(path) ||
-          mpmTop.test(path) ||
-          mtsTop.test(path) ||
-          mtrTop.test(path) ||
-          mp2rageTop.test(path) ||
-          fmapEpiTop.test(path) ||
-          fmapGreTop.test(path) ||
-          otherTopFiles.test(path) ||
-          megTop.test(path) ||
-          eegTop.test(path) ||
-          ieegTop.test(path) ||
-          petTop.test(path) ||
-          motionTop.test(path) ||
-          nirsTop.test(path) ||
-          microscopyTop.test(path)
-        )
-      }
+      return (
+        rootTop.test(path) ||
+        funcTop.test(path) ||
+        aslTop.test(path) ||
+        dwiTop.test(path) ||
+        anatTop.test(path) ||
+        vfaTop.test(path) ||
+        megreTop.test(path) ||
+        irt1Top.test(path) ||
+        mpmTop.test(path) ||
+        mtsTop.test(path) ||
+        mtrTop.test(path) ||
+        mp2rageTop.test(path) ||
+        fmapEpiTop.test(path) ||
+        fmapGreTop.test(path) ||
+        otherTopFiles.test(path) ||
+        megTop.test(path) ||
+        eegTop.test(path) ||
+        ieegTop.test(path) ||
+        petTop.test(path) ||
+        motionTop.test(path) ||
+        nirsTop.test(path) ||
+        microscopyTop.test(path)
+      )
     },
 
     /**
@@ -267,51 +233,39 @@ export default {
      * Check if the file has a name appropriate for an anatomical scan
      */
     isAnat: function (path) {
-      if (bids_schema) {
-        return bids_schema.datatypes['anat'].some((regex) => regex.exec(path))
-      } else {
-        return (
-          conditionalMatch(anatNonparametric, path) ||
-          conditionalMatch(anatParametric, path) ||
-          conditionalMatch(anatDefacemask, path) ||
-          conditionalMatch(anatMultiEcho, path) ||
-          conditionalMatch(anatMultiFlip, path) ||
-          conditionalMatch(anatMultiInv, path) ||
-          conditionalMatch(anatMP2RAGE, path) ||
-          conditionalMatch(anatVFAMT, path) ||
-          conditionalMatch(anatMTR, path)
-        )
-      }
+      return (
+        conditionalMatch(anatNonparametric, path) ||
+        conditionalMatch(anatParametric, path) ||
+        conditionalMatch(anatDefacemask, path) ||
+        conditionalMatch(anatMultiEcho, path) ||
+        conditionalMatch(anatMultiFlip, path) ||
+        conditionalMatch(anatMultiInv, path) ||
+        conditionalMatch(anatMP2RAGE, path) ||
+        conditionalMatch(anatVFAMT, path) ||
+        conditionalMatch(anatMTR, path)
+      )
     },
 
     /**
      * Check if the file has a name appropriate for a diffusion scan
      */
     isDWI: function (path) {
-      if (bids_schema) {
-        return bids_schema.datatypes['dwi'].some((regex) => regex.exec(path))
-      } else {
-        return conditionalMatch(dwiData, path)
-      }
+      return conditionalMatch(dwiData, path)
     },
 
     /**
      * Check if the file has a name appropriate for a fieldmap scan
      */
     isFieldMap: function (path) {
-      if (bids_schema) {
-        return bids_schema.datatypes['fmap'].some((regex) => regex.exec(path))
-      } else {
-        return (
-          conditionalMatch(fmapGre, path) ||
-          conditionalMatch(fmapPepolarAsl, path) ||
-          conditionalMatch(fmapTB1DAM, path) ||
-          conditionalMatch(fmapTB1EPI, path) ||
-          conditionalMatch(fmapTB1SRGE, path) ||
-          conditionalMatch(fmapRF, path) ||
-          conditionalMatch(fmapParametric, path)
-        )
-      }
+      return (
+        conditionalMatch(fmapGre, path) ||
+        conditionalMatch(fmapPepolarAsl, path) ||
+        conditionalMatch(fmapTB1DAM, path) ||
+        conditionalMatch(fmapTB1EPI, path) ||
+        conditionalMatch(fmapTB1SRGE, path) ||
+        conditionalMatch(fmapRF, path) ||
+        conditionalMatch(fmapParametric, path)
+      )
     },
 
     isFieldMapMainNii: function (path) {
@@ -332,73 +286,47 @@ export default {
      * Check if the file has a name appropriate for a functional scan
      */
     isFunc: function (path) {
-      if (bids_schema) {
-        return bids_schema.datatypes['func'].some((regex) => regex.exec(path))
-      } else {
-        return (
-          conditionalMatch(func, path) ||
-          conditionalMatch(funcPhaseDeprecated, path) ||
-          conditionalMatch(funcEvents, path) ||
-          conditionalMatch(funcTimeseries, path)
-        )
-      }
+      return (
+        conditionalMatch(func, path) ||
+        conditionalMatch(funcPhaseDeprecated, path) ||
+        conditionalMatch(funcEvents, path) ||
+        conditionalMatch(funcTimeseries, path)
+      )
     },
 
     isAsl: function (path) {
       return conditionalMatch(aslData, path)
     },
 
     isPET: function (path) {
-      if (bids_schema) {
-        return bids_schema.datatypes['pet'].some((regex) => regex.exec(path))
-      } else {
-        return conditionalMatch(petData, path)
-      }
+      return conditionalMatch(petData, path)
     },
 
     isPETBlood: function (path) {
       return conditionalMatch(petBlood, path)
     },
 
     isMeg: function (path) {
-      if (bids_schema) {
-        return bids_schema.datatypes['meg'].some((regex) => regex.exec(path))
-      } else {
-        return (
-          conditionalMatch(megData, path) ||
-          conditionalMatch(megCalibrationData, path) ||
-          conditionalMatch(megCrosstalkData, path)
-        )
-      }
+      return (
+        conditionalMatch(megData, path) ||
+        conditionalMatch(megCalibrationData, path) ||
+        conditionalMatch(megCrosstalkData, path)
+      )
     },
     isNIRS: function (path) {
       return conditionalMatch(nirsData, path)
     },
 
     isEEG: function (path) {
-      if (bids_schema) {
-        return bids_schema.datatypes['eeg'].some((regex) => regex.exec(path))
-      } else {
-        return conditionalMatch(eegData, path)
-      }
+      return conditionalMatch(eegData, path)
     },
 
     isIEEG: function (path) {
-      if (bids_schema) {
-        return bids_schema.datatypes['ieeg'].some((regex) => regex.exec(path))
-      } else {
-        return conditionalMatch(ieegData, path)
-      }
+      return conditionalMatch(ieegData, path)
     },
 
     isMOTION: function (path) {
-      if (bids_schema) {
-        // Motion not currently in schema
-        // return bids_schema.datatypes['motion'].some(regex => regex.exec(path))
-        return conditionalMatch(motion, path)
-      } else {
-        return conditionalMatch(motion, path)
-      }
+      return conditionalMatch(motion, path)
     },
 
     isMicroscopy: function (path) {
@@ -414,11 +342,7 @@ export default {
     },
 
     isBehavioral: function (path) {
-      if (bids_schema) {
-        return bids_schema.datatypes['beh'].some((regex) => regex.exec(path))
-      } else {
-        return conditionalMatch(behavioralData, path)
-      }
+      return conditionalMatch(behavioralData, path)
     },
 
     isFuncBold: function (path) {
@@ -479,9 +403,6 @@ export default {
 
     return values
   },
-
-  // CommonJS default export
-  schemaSetup,
 }
 
 function conditionalMatch(expression, path) {

bids-validator/validators/bids/fullTest.js

@@ -28,7 +28,7 @@ import collectModalities from '../../utils/summary/collectModalities'
  * Takes on an array of files, callback, and boolean indicating if git-annex is used.
  * Starts the validation process for a BIDS package.
  */
-const fullTest = (fileList, options, annexed, dir, schema, callback) => {
+const fullTest = (fileList, options, annexed, dir, callback) => {
   const self = BIDS
   self.options = options
 
@@ -64,7 +64,7 @@ const fullTest = (fileList, options, annexed, dir, schema, callback) => {
     })
   }
 
-  const summary = utils.collectSummary(fileList, self.options, schema)
+  const summary = utils.collectSummary(fileList, self.options)
 
   // remove size redundancies
   for (const key in fileList) {

bids-validator/validators/bids/start.js

@@ -5,8 +5,6 @@ import quickTest from './quickTest'
 import quickTestError from './quickTestError'
 import fullTest from './fullTest'
 import utils from '../../utils'
-import { schemaRegex } from '../../validators/schemaTypes'
-import { schemaSetup } from '../../utils/type'
 
 /**
  * Start
@@ -31,17 +29,11 @@ const start = (dir, options, callback) => {
     } else {
       BIDS.options = options
       reset(BIDS)
-      // Load the bids-spec schema ahead of any validation
-      let schema
-      if (options.schema) {
-        schema = await schemaRegex(options.schema)
-        schemaSetup(schema)
-      }
       const files = await utils.files.readDir(dir, options)
       if (quickTest(files)) {
         // Is the dir using git-annex?
         const annexed = utils.files.remoteFiles.isGitAnnex(dir)
-        fullTest(files, BIDS.options, annexed, dir, schema, callback)
+        fullTest(files, BIDS.options, annexed, dir, callback)
       } else {
         // Return an error immediately if quickTest fails
         const issue = quickTestError(dir)

bids-validator/validators/options.js

@@ -66,13 +66,6 @@ export function parseOptions(argumentOverride) {
       'A less accurate check that reads filenames one per line from stdin.',
     )
     .hide('filenames')
-    .option('schema', {
-      alias: 's',
-      describe:
-        'BIDS specification schema version to use for validation, e.g. "v1.6.0" (beta)',
-      default: 'disable',
-      choices: ['disable', 'v1.6.0', 'v1.7.0', 'master'],
-    })
     .epilogue(
       'This tool checks if a dataset in a given directory is \
 compatible with the Brain Imaging Data Structure specification. To learn \