hed-standard · VisLab · Mar 3, 2025 · Mar 2, 2025
diff --git a/src/bids/types/tsv.js b/src/bids/types/tsv.js
@@ -15,6 +15,7 @@ export class BidsTsvFile extends BidsFile {
    * @type {Map<string, string[]>}
    */
   parsedTsv
+
   /**
    * HED strings in the "HED" column of the TSV data.
    * @type {string[]}

diff --git a/src/bids/validator/sidecarValidator.js b/src/bids/validator/sidecarValidator.js
@@ -8,14 +8,21 @@ import { BidsValidator } from './validator'
  * Validator for HED data in BIDS JSON sidecars.
  */
 export class BidsHedSidecarValidator extends BidsValidator {
+  /**
+   * The BIDS sidecar being validated.
+   * @type {BidsSidecar}
+   */
+  sidecar
+
   /**
    * Constructor for the BidsHedSidecarValidator.
    *
    * @param {BidsSidecar} sidecar - The BIDS bidsFile being validated.
    * @param {Schemas} hedSchemas - The schemas used for the sidecar validation.
    */
   constructor(sidecar, hedSchemas) {
-    super(sidecar, hedSchemas)
+    super(hedSchemas)
+    this.sidecar = sidecar
   }
 
   /**
@@ -24,9 +31,9 @@ export class BidsHedSidecarValidator extends BidsValidator {
    */
   validate() {
     // Allow schema to be set a validation time -- this is checked by the superclass of BIDS file
-    const [errorIssues, warningIssues] = this.bidsFile.parseHed(this.hedSchemas)
-    this.errors.push(...BidsHedIssue.fromHedIssues(errorIssues, this.bidsFile.file))
-    this.warnings.push(...BidsHedIssue.fromHedIssues(warningIssues, this.bidsFile.file))
+    const [errorIssues, warningIssues] = this.sidecar.parseHed(this.hedSchemas)
+    this.errors.push(...BidsHedIssue.fromHedIssues(errorIssues, this.sidecar.file))
+    this.warnings.push(...BidsHedIssue.fromHedIssues(warningIssues, this.sidecar.file))
     if (errorIssues.length > 0) {
       return
     }
@@ -42,7 +49,7 @@ export class BidsHedSidecarValidator extends BidsValidator {
   _validateStrings() {
     const issues = []
 
-    for (const [sidecarKeyName, hedData] of this.bidsFile.parsedHedData) {
+    for (const [sidecarKeyName, hedData] of this.sidecar.parsedHedData) {
       if (hedData instanceof ParsedHedString) {
         // Value options have HED as string.
         issues.push(...this._checkDetails(sidecarKeyName, hedData))
@@ -82,37 +89,37 @@ export class BidsHedSidecarValidator extends BidsValidator {
    * @private
    */
   _checkDefs(sidecarKeyName, hedString, placeholdersAllowed) {
-    let issues = this.bidsFile.definitions.validateDefs(hedString, this.hedSchemas, placeholdersAllowed)
+    let issues = this.sidecar.definitions.validateDefs(hedString, this.hedSchemas, placeholdersAllowed)
     if (issues.length > 0) {
-      return BidsHedIssue.fromHedIssues(issues, this.bidsFile.file, { sidecarKeyName: sidecarKeyName })
+      return BidsHedIssue.fromHedIssues(issues, this.sidecar.file, { sidecarKeyName: sidecarKeyName })
     }
-    issues = this.bidsFile.definitions.validateDefExpands(hedString, this.hedSchemas, placeholdersAllowed)
-    return BidsHedIssue.fromHedIssues(issues, this.bidsFile.file, { sidecarKeyName: sidecarKeyName })
+    issues = this.sidecar.definitions.validateDefExpands(hedString, this.hedSchemas, placeholdersAllowed)
+    return BidsHedIssue.fromHedIssues(issues, this.sidecar.file, { sidecarKeyName: sidecarKeyName })
   }
 
   _checkPlaceholders(sidecarKeyName, hedString) {
     const numberPlaceholders = getCharacterCount(hedString.hedString, '#')
-    const sidecarKey = this.bidsFile.sidecarKeys.get(sidecarKeyName)
+    const sidecarKey = this.sidecar.sidecarKeys.get(sidecarKeyName)
     if (!sidecarKey.valueString && !sidecarKey.hasDefinitions && numberPlaceholders > 0) {
       return [
         BidsHedIssue.fromHedIssue(
           generateIssue('invalidSidecarPlaceholder', { column: sidecarKeyName, string: hedString.hedString }),
-          this.bidsFile.file,
+          this.sidecar.file,
         ),
       ]
     } else if (sidecarKey.valueString && numberPlaceholders === 0) {
       return [
         BidsHedIssue.fromHedIssue(
           generateIssue('missingPlaceholder', { column: sidecarKeyName, string: hedString.hedString }),
-          this.bidsFile.file,
+          this.sidecar.file,
         ),
       ]
     }
     if (sidecarKey.valueString && numberPlaceholders > 1) {
       return [
         BidsHedIssue.fromHedIssue(
           generateIssue('invalidSidecarPlaceholder', { column: sidecarKeyName, string: hedString.hedString }),
-          this.bidsFile.file,
+          this.sidecar.file,
         ),
       ]
     }
@@ -126,23 +133,23 @@ export class BidsHedSidecarValidator extends BidsValidator {
    */
   _validateCurlyBraces() {
     const issues = []
-    const references = this.bidsFile.columnSpliceMapping
+    const references = this.sidecar.columnSpliceMapping
 
     for (const [key, referredKeys] of references) {
       for (const referredKey of referredKeys) {
         if (references.has(referredKey)) {
           issues.push(
             BidsHedIssue.fromHedIssue(
               generateIssue('recursiveCurlyBracesWithKey', { column: referredKey, referrer: key }),
-              this.bidsFile.file,
+              this.sidecar.file,
             ),
           )
         }
-        if (!this.bidsFile.parsedHedData.has(referredKey) && referredKey !== 'HED') {
+        if (!this.sidecar.parsedHedData.has(referredKey) && referredKey !== 'HED') {
           issues.push(
             BidsHedIssue.fromHedIssue(
               generateIssue('undefinedCurlyBraces', { column: referredKey }),
-              this.bidsFile.file,
+              this.sidecar.file,
             ),
           )
         }

diff --git a/src/bids/validator/tsvValidator.js b/src/bids/validator/tsvValidator.js
@@ -12,6 +12,12 @@ import { EventManager } from '../../parser/eventManager'
  * Validator for HED data in BIDS TSV files.
  */
 export class BidsHedTsvValidator extends BidsValidator {
+  /**
+   * The BIDS TSV file being validated.
+   * @type {BidsTsvFile}
+   */
+  tsvFile
+
   /**
    * The singleton instance of the checker for reserved requirements.
    * @type {ReservedChecker}
@@ -25,7 +31,8 @@ export class BidsHedTsvValidator extends BidsValidator {
    * @param {Schemas} hedSchemas - The HED schemas used to validate the tsv file.
    */
   constructor(tsvFile, hedSchemas) {
-    super(tsvFile, hedSchemas)
+    super(hedSchemas)
+    this.tsvFile = tsvFile
     this.reserved = ReservedChecker.getInstance()
   }
 
@@ -35,8 +42,8 @@ export class BidsHedTsvValidator extends BidsValidator {
    */
   validate() {
     // Validate the BIDS bidsFile if it exists and return if there are errors
-    if (this.bidsFile.mergedSidecar) {
-      const issues = this.bidsFile.mergedSidecar.validate(this.hedSchemas)
+    if (this.tsvFile.mergedSidecar) {
+      const issues = this.tsvFile.mergedSidecar.validate(this.hedSchemas)
       const splitErrors = BidsHedIssue.splitErrors(issues)
       this.errors.push(...(splitErrors.error ?? []))
       this.warnings.push(...(splitErrors.warning ?? []))
@@ -51,24 +58,24 @@ export class BidsHedTsvValidator extends BidsValidator {
       return
     }
     // Now do a full validation
-    const bidsHedTsvParser = new BidsHedTsvParser(this.bidsFile, this.hedSchemas)
+    const bidsHedTsvParser = new BidsHedTsvParser(this.tsvFile, this.hedSchemas)
     const [bidsEvents, errorIssues, warningIssues] = bidsHedTsvParser.parse()
     this.errors.push(...errorIssues)
     this.warnings.push(...warningIssues)
     if (this.errors.length > 0) {
       return
     }
     this.validateDataset(bidsEvents)
-    if (this.errors.length === 0 && this.bidsFile.mergedSidecar?.hasHedData) {
+    if (this.errors.length === 0 && this.tsvFile.mergedSidecar?.hasHedData) {
       this._checkMissingHedWarning()
       this._checkMissingValueWarnings()
     }
   }
 
   _checkMissingHedWarning() {
     // Check for HED column used as splice but no HED column
-    if (this.bidsFile.mergedSidecar.columnSpliceReferences.has('HED') && !this.bidsFile.parsedTsv.has('HED')) {
-      this.warnings.push(BidsHedIssue.fromHedIssue(generateIssue('hedUsedAsSpliceButNoTsvHed'), this.bidsFile.file))
+    if (this.tsvFile.mergedSidecar.columnSpliceReferences.has('HED') && !this.tsvFile.parsedTsv.has('HED')) {
+      this.warnings.push(BidsHedIssue.fromHedIssue(generateIssue('hedUsedAsSpliceButNoTsvHed'), this.tsvFile.file))
     }
   }
 
@@ -77,21 +84,21 @@ export class BidsHedTsvValidator extends BidsValidator {
    * @private
    */
   _checkMissingValueWarnings() {
-    for (const columnName of this.bidsFile.parsedTsv.keys()) {
-      const sidecarColumn = this.bidsFile.mergedSidecar?.sidecarKeys.get(columnName)
+    for (const columnName of this.tsvFile.parsedTsv.keys()) {
+      const sidecarColumn = this.tsvFile.mergedSidecar?.sidecarKeys.get(columnName)
       if (!sidecarColumn || sidecarColumn.isValueKey) {
         continue
       }
       const toRemove = new Set(['', 'n/a', null, undefined])
-      const tsvColumnValues = new Set(this.bidsFile.parsedTsv.get(columnName))
+      const tsvColumnValues = new Set(this.tsvFile.parsedTsv.get(columnName))
       const cleanedValues = new Set([...tsvColumnValues].filter((value) => !toRemove.has(value)))
       const missingValues = [...cleanedValues].filter((value) => !sidecarColumn.categoryMap.has(value))
       if (missingValues.length > 0) {
         const values = '[' + missingValues.join(', ') + ']'
         this.warnings.push(
           BidsHedIssue.fromHedIssue(
             generateIssue('sidecarKeyMissing', { column: columnName, values: values }),
-            this.bidsFile.file,
+            this.tsvFile.file,
           ),
         )
       }
@@ -104,8 +111,8 @@ export class BidsHedTsvValidator extends BidsValidator {
    * @private
    */
   _validateHedColumn() {
-    if (this.bidsFile.hedColumnHedStrings.length > 0) {
-      this.bidsFile.hedColumnHedStrings.flatMap((hedString, rowIndexMinusTwo) =>
+    if (this.tsvFile.hedColumnHedStrings.length > 0) {
+      this.tsvFile.hedColumnHedStrings.flatMap((hedString, rowIndexMinusTwo) =>
         this._validateHedColumnString(hedString, rowIndexMinusTwo + 2),
       )
     }
@@ -125,8 +132,8 @@ export class BidsHedTsvValidator extends BidsValidator {
 
     // Find basic parsing issues and return if unable to parse the string. (Warnings are okay.)
     const [parsedString, errorIssues, warningIssues] = parseHedString(hedString, this.hedSchemas, false, false)
-    this.errors.push(...BidsHedIssue.fromHedIssues(errorIssues, this.bidsFile.file, { tsvLine: rowIndex }))
-    this.warnings.push(...BidsHedIssue.fromHedIssues(warningIssues, this.bidsFile.file, { tsvLine: rowIndex }))
+    this.errors.push(...BidsHedIssue.fromHedIssues(errorIssues, this.tsvFile.file, { tsvLine: rowIndex }))
+    this.warnings.push(...BidsHedIssue.fromHedIssues(warningIssues, this.tsvFile.file, { tsvLine: rowIndex }))
     if (parsedString === null) {
       return
     }
@@ -139,18 +146,18 @@ export class BidsHedTsvValidator extends BidsValidator {
             string: parsedString.hedString,
             tsvLine: rowIndex.toString(),
           }),
-          this.bidsFile.file,
+          this.tsvFile.file,
         ),
       )
       return
     }
 
     // Check whether definitions used exist and are used correctly.
     const defIssues = [
-      ...this.bidsFile.mergedSidecar.definitions.validateDefs(parsedString, this.hedSchemas, false),
-      ...this.bidsFile.mergedSidecar.definitions.validateDefExpands(parsedString, this.hedSchemas, false),
+      ...this.tsvFile.mergedSidecar.definitions.validateDefs(parsedString, this.hedSchemas, false),
+      ...this.tsvFile.mergedSidecar.definitions.validateDefExpands(parsedString, this.hedSchemas, false),
     ]
-    this.errors.push(...BidsHedIssue.fromHedIssues(defIssues, this.bidsFile.file, { tsvLine: rowIndex }))
+    this.errors.push(...BidsHedIssue.fromHedIssues(defIssues, this.tsvFile.file, { tsvLine: rowIndex }))
   }
 
   /**
@@ -163,7 +170,7 @@ export class BidsHedTsvValidator extends BidsValidator {
       return
     }
     // Temporal files have to check Onset, Inset, Offset consistency.
-    if (this.bidsFile.isTimelineFile) {
+    if (this.tsvFile.isTimelineFile) {
       this._validateTemporal(elements)
     } else {
       // Non-temporal files cannot have temporal tags.
@@ -213,8 +220,8 @@ export class BidsHedTsvValidator extends BidsValidator {
       const rowString = elementList.map((element) => element.hedString).join(',')
       const [parsedString, errorIssues, warningIssues] = parseHedString(rowString, this.hedSchemas, false, false)
       const tsvLines = BidsTsvElement.getTsvLines(elementList)
-      this.errors.push(...BidsHedIssue.fromHedIssues(errorIssues, this.bidsFile.file, { tsvLine: tsvLines }))
-      this.warnings.push(...BidsHedIssue.fromHedIssues(warningIssues, this.bidsFile.file, { tsvLine: tsvLines }))
+      this.errors.push(...BidsHedIssue.fromHedIssues(errorIssues, this.tsvFile.file, { tsvLine: tsvLines }))
+      this.warnings.push(...BidsHedIssue.fromHedIssues(warningIssues, this.tsvFile.file, { tsvLine: tsvLines }))
     }
   }
 
@@ -273,7 +280,7 @@ export class BidsHedTsvValidator extends BidsValidator {
         this.errors.push(
           BidsHedIssue.fromHedIssue(
             generateIssue('temporalTagInNonTemporalContext', { string: element.hedString, tsvLine: element.tsvLine }),
-            this.bidsFile.file,
+            this.tsvFile.file,
           ),
         )
       }

diff --git a/src/bids/validator/validator.js b/src/bids/validator/validator.js
@@ -1,17 +1,14 @@
 /**
  * Validator base class for HED data in BIDS TSV files.
+ * @abstract
  */
 export class BidsValidator {
-  /**
-   * The BIDS file being validated.
-   * @type {BidsFile}
-   */
-  bidsFile
   /**
    * The HED schema collection being validated against.
    * @type {Schemas}
    */
   hedSchemas
+
   /**
    * The issues found during validation.
    * @type {BidsHedIssue[]}
@@ -27,21 +24,17 @@ export class BidsValidator {
   /**
    * Bids validator base class.
    *
-   * @param {BidsFile} bidsFile - The BIDS TSV file being validated.
    * @param {Schemas} hedSchemas - The HED schemas used for validation.
    */
-  constructor(bidsFile, hedSchemas) {
-    this.bidsFile = bidsFile
+  constructor(hedSchemas) {
     this.hedSchemas = hedSchemas // Will be set when the file is validated
     this.errors = []
     this.warnings = []
   }
 
   /**
    * Validate a BIDS file. Overridden by particular types of BIDS files.
-   *
+   * @abstract
    */
-  validate() {
-    return
-  }
+  validate() {}
 }
diff --git a/src/issues/data.js b/src/issues/data.js
@@ -478,9 +478,15 @@ export default {
     level: 'error',
     message: stringTemplate`The key 'HED' was illegally used within a non-HED sidecar column.`,
   },
+  // Internal errors
   internalError: {
     hedCode: 'INTERNAL_ERROR',
     level: 'error',
     message: stringTemplate`Internal error - message: "${'message'}".`,
   },
+  genericError: {
+    hedCode: 'INTERNAL_ERROR',
+    level: 'error',
+    message: stringTemplate`Unknown HED error "${'internalCode'}" - parameters: "${'parameters'}".`,
+  },
 }