Merge pull request #209 from VisLab/update-tokenizer

Working on separating the data from the tests
hed-standard · Nov 1, 2024 · 90673fa · 90673fa
2 parents 9561c87 + 8182481
commit 90673fa
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Showing 28 changed files with 17,582 additions and 244 deletions.
diff --git a/bids/index.js b/bids/index.js
@@ -4,8 +4,8 @@ import { BidsJsonFile, BidsSidecar } from './types/json'
 import { BidsEventFile, BidsTabularFile, BidsTsvFile } from './types/tsv'
 import BidsDataset from './types/dataset'
 import { BidsHedIssue, BidsIssue } from './types/issues'
-import BidsHedSidecarValidator from './validator/bidsHedSidecarValidator'
-import BidsHedTsvValidator from './validator/bidsHedTsvValidator'
+import SidecarValidator from './validator/sidecarValidator'
+import TsvValidator from './validator/tsvValidator'
 
 export {
   BidsDataset,
@@ -16,8 +16,8 @@ export {
   BidsSidecar,
   BidsIssue,
   BidsHedIssue,
-  BidsHedSidecarValidator,
-  BidsHedTsvValidator,
+  SidecarValidator,
+  TsvValidator,
   buildBidsSchemas,
   validateBidsDataset,
 }
@@ -31,8 +31,8 @@ export default {
   BidsSidecar,
   BidsIssue,
   BidsHedIssue,
-  BidsHedSidecarValidator,
-  BidsHedTsvValidator,
+  BidsHedSidecarValidator: SidecarValidator,
+  BidsHedTsvValidator: TsvValidator,
   buildBidsSchemas,
   validateBidsDataset,
 }
diff --git a/bids/schema.js b/bids/schema.js
@@ -31,7 +31,7 @@ export async function buildBidsSchemas(datasetDescription, schemaDefinition) {
  * @returns {SchemasSpec|null} The schema specification to be used to build the schemas, or null if the specification is missing.
  * @throws {IssueError} If the schema specification is invalid.
  */
-function buildSchemasSpec(datasetDescription, schemaDefinition) {
+export function buildSchemasSpec(datasetDescription, schemaDefinition) {
   if (schemaDefinition) {
     return validateSchemasSpec(schemaDefinition)
   } else if (datasetDescription.jsonData?.HEDVersion) {
@@ -104,4 +104,4 @@ function splitLibraryAndVersion(schemaVersion, originalVersion) {
   return [library, version]
 }
 
-export default buildBidsSchemas
+//export default buildBidsSchemas
diff --git a/bids/types/json.js b/bids/types/json.js
@@ -4,7 +4,7 @@ import { sidecarValueHasHed } from '../utils'
 import { parseHedString } from '../../parser/parser'
 import ParsedHedString from '../../parser/parsedHedString'
 import { BidsFile } from './basic'
-import BidsHedSidecarValidator from '../validator/bidsHedSidecarValidator'
+import SidecarValidator from '../validator/sidecarValidator'
 import { IssueError } from '../../common/issues/issues'
 
 const ILLEGAL_SIDECAR_KEYS = new Set(['hed', 'n/a'])
@@ -20,7 +20,7 @@ export class BidsJsonFile extends BidsFile {
   jsonData
 
   constructor(name, jsonData, file) {
-    super(name, file, BidsHedSidecarValidator)
+    super(name, file, SidecarValidator)
     this.jsonData = jsonData
   }
 }

diff --git a/bids/types/tsv.js b/bids/types/tsv.js
@@ -4,7 +4,7 @@ import { BidsFile } from './basic'
 import { convertParsedTSVData, parseTSV } from '../tsvParser'
 import { BidsSidecar } from './json'
 import ParsedHedString from '../../parser/parsedHedString'
-import BidsHedTsvValidator from '../validator/bidsHedTsvValidator'
+import TsvValidator from '../validator/tsvValidator'
 import { IssueError } from '../../common/issues/issues'
 
 /**
@@ -49,7 +49,7 @@ export class BidsTsvFile extends BidsFile {
    * @param {object} mergedDictionary The merged sidecar data.
    */
   constructor(name, tsvData, file, potentialSidecars = [], mergedDictionary = {}) {
-    super(name, file, BidsHedTsvValidator)
+    super(name, file, TsvValidator)
 
     if (typeof tsvData === 'string') {
       this.parsedTsv = parseTSV(tsvData)

diff --git a/bids/validator/bidsHedSidecarValidator.js → bids/validator/sidecarValidator.js b/bids/validator/bidsHedSidecarValidator.js → bids/validator/sidecarValidator.js
@@ -7,7 +7,7 @@ import { generateIssue, IssueError } from '../../common/issues/issues'
 /**
  * Validator for HED data in BIDS JSON sidecars.
  */
-export class BidsHedSidecarValidator {
+export class SidecarValidator {
   /**
    * The BIDS sidecar being validated.
    * @type {BidsSidecar}
@@ -143,4 +143,4 @@ export class BidsHedSidecarValidator {
   }
 }
 
-export default BidsHedSidecarValidator
+export default SidecarValidator
diff --git a/bids/validator/bidsHedTsvValidator.js → bids/validator/tsvValidator.js b/bids/validator/bidsHedTsvValidator.js → bids/validator/tsvValidator.js
@@ -1,4 +1,4 @@
-import BidsHedSidecarValidator from './bidsHedSidecarValidator'
+import SidecarValidator from './sidecarValidator'
 import { BidsHedIssue, BidsIssue } from '../types/issues'
 import { BidsTsvEvent, BidsTsvRow } from '../types/tsv'
 import { parseHedString } from '../../parser/parser'
@@ -12,7 +12,7 @@ import { validateHedString } from '../../validator/event/init'
 /**
  * Validator for HED data in BIDS TSV files.
  */
-export class BidsHedTsvValidator {
+export class TsvValidator {
   /**
    * The BIDS TSV file being validated.
    * @type {BidsTsvFile}
@@ -55,10 +55,7 @@ export class BidsHedTsvValidator {
     if (BidsIssue.anyAreErrors(parsingIssues)) {
       return this.issues
     }
-    const curlyBraceIssues = new BidsHedSidecarValidator(
-      this.tsvFile.mergedSidecar,
-      this.hedSchemas,
-    ).validateCurlyBraces()
+    const curlyBraceIssues = new SidecarValidator(this.tsvFile.mergedSidecar, this.hedSchemas).validateCurlyBraces()
     const hedColumnIssues = this._validateHedColumn()
     this.issues.push(...curlyBraceIssues, ...hedColumnIssues)
     if (BidsIssue.anyAreErrors(this.issues)) {
@@ -386,4 +383,4 @@ export class BidsHedTsvParser {
   }
 }
 
-export default BidsHedTsvValidator
+export default TsvValidator