Revamp issue handling

src/bids/index.js

@@ -1,15 +1,14 @@
 import { buildBidsSchemas } from './schema'
 import { BidsJsonFile, BidsSidecar } from './types/json'
 import { BidsTsvFile } from './types/tsv'
-import { BidsHedIssue, BidsIssue } from './types/issues'
+import { BidsHedIssue } from './types/issues'
 import BidsHedSidecarValidator from './validator/sidecarValidator'
 import BidsHedTsvValidator from './validator/tsvValidator'
 
 export {
   BidsTsvFile,
   BidsJsonFile,
   BidsSidecar,
-  BidsIssue,
   BidsHedIssue,
   BidsHedSidecarValidator,
   BidsHedTsvValidator,
@@ -20,7 +19,6 @@ export default {
   BidsTsvFile,
   BidsJsonFile,
   BidsSidecar,
-  BidsIssue,
   BidsHedIssue,
   BidsHedSidecarValidator,
   BidsHedTsvValidator,

src/bids/tsvParser.js

@@ -13,7 +13,7 @@ const isContentfulRow = (row) => row && !/^\s*$/.test(row)
  * Parse a TSV file.
  *
  * @param {string} contents The contents of a TSV file.
- * @returns {Map} The parsed contents of the TSV file.
+ * @returns {Map<string, string[]>} The parsed contents of the TSV file.
  */
 export function parseTSV(contents) {
   const columns = new Map()
@@ -40,7 +40,7 @@ export function parseTSV(contents) {
  * Convert parsed TSV file data from the old BIDS format to the new BIDS format.
  *
  * @param {{headers: string[], rows: string[][]}} oldParsedTsv Parsed TSV data using the old format
- * @returns {Map} The parsed contents of the TSV file, using the new format.
+ * @returns {Map<string, string[]>} The parsed contents of the TSV file, using the new format.
  */
 export function convertParsedTSVData(oldParsedTsv) {
   const columns = new Map()

src/bids/types/file.js

@@ -13,7 +13,7 @@ export class BidsFile {
 
   /**
    * The Object representing this file data.
-   * This is used to generate {@link BidsIssue} objects.
+   * This is used to generate {@link BidsHedIssue} objects.
    * @type {Object}
    */
 
@@ -40,7 +40,7 @@ export class BidsFile {
    * Validate this validator's tsv file.
    *
    * @param {Schemas} schemas - The HED schemas used to validate this file.
-   * @returns {BidsIssue[]} - Any issues found during validation of this TSV file.
+   * @returns {BidsHedIssue[]} - Any issues found during validation of this TSV file.
    */
   validate(schemas) {
     if (!this.hasHedData) {
@@ -63,9 +63,19 @@ export class BidsFile {
     }
   }
 
+  /**
+   * Determine whether this file has any HED data.
+   *
+   * @returns {boolean}
+   */
+  get hasHedData() {
+    return false
+  }
+
   /**
    * The validator class used to validate this file.
-   * @returns {BidsValidator}
+   *
+   * @returns {function} (typeof BidsValidator) A subclass constructor of {@link BidsValidator}.
    */
   get validatorClass() {
     return this._validatorClass

src/bids/types/issues.js

@@ -1,13 +1,13 @@
 import { generateIssue, IssueError } from '../../issues/issues'
 
-const bidsHedErrorCodes = new Set([104, 106, 107])
+const bidsHedErrorCodes = new Set(['HED_ERROR', 'HED_INTERNAL_ERROR'])
 
-export class BidsIssue {
+export class BidsHedIssue {
   /**
    * The BIDS issue code.
-   * @type {number}
+   * @type {string}
    */
-  code
+  bidsCode
   /**
    * The file associated with this issue.
    * @type {Object}
@@ -17,72 +17,80 @@ export class BidsIssue {
    * The evidence for this issue.
    * @type {string}
    */
-  evidence
+  message
+  /**
+   * The HED Issue object corresponding to this object.
+   * @type {Issue}
+   */
+  hedIssue
 
-  constructor(issueCode, file, evidence) {
-    this.code = issueCode
+  /**
+   * Constructor.
+   *
+   * @param {Issue} hedIssue The HED issue object to be wrapped.
+   * @param {Object} file The file this error occurred in.
+   */
+  constructor(hedIssue, file) {
+    this.hedIssue = hedIssue
+    this.bidsCode = BidsHedIssue._determineBidsIssueCode(hedIssue)
+    this.message = hedIssue.message
     this.file = file
-    this.evidence = evidence
+  }
+
+  /**
+   * The HED spec code for this issue.
+   *
+   * @returns {string}
+   */
+  get hedCode() {
+    return this.hedIssue.hedCode
   }
 
   /**
    * Whether this issue is an error.
    *
    * @returns {boolean}
    */
-  isError() {
-    return bidsHedErrorCodes.has(this.code)
+  get isError() {
+    return bidsHedErrorCodes.has(this.bidsCode)
   }
 
   /**
    * Determine if any of the passed issues are errors.
    *
-   * @param {BidsIssue[]} issues A list of issues.
+   * @param {BidsHedIssue[]} issues A list of issues.
    * @returns {boolean} Whether any of the passed issues are errors (rather than warnings).
    */
   static anyAreErrors(issues) {
-    return issues.some((issue) => issue.isError())
+    return issues.some((issue) => issue.isError)
   }
 
-  static async generateInternalErrorPromise(error, errorFile) {
-    return [new BidsHedIssue(generateIssue('internalError', { message: error.message }), errorFile)]
-  }
-}
-
-export class BidsHedIssue extends BidsIssue {
   /**
-   * The HED Issue object corresponding to this object.
-   * @type {Issue}
-   */
-  hedIssue
-
-  /**
-   * Constructor.
+   * Generate a {@link Promise} with an internal error.
    *
-   * @param {Issue} hedIssue The HED issue object to be wrapped.
-   * @param {Object} file The file this error occurred in.
+   * @param {string} error The error message.
+   * @param {Object} errorFile The file this error occurred in.
+   * @return {Promise} A promise resolving to a singleton array containing an internal error {@link BidsHedIssue}.
    */
-  constructor(hedIssue, file) {
-    super(BidsHedIssue._determineBidsIssueCode(hedIssue), file, hedIssue.message)
-
-    this.hedIssue = hedIssue
+  static async generateInternalErrorPromise(error, errorFile) {
+    return [new BidsHedIssue(generateIssue('internalError', { message: error.message }), errorFile)]
   }
 
   /**
    * Determine the BIDS issue code for this issue.
    *
    * @param {Issue} hedIssue The HED issue object to be wrapped.
-   * @returns {number} The BIDS issue code for this issue.
+   * @returns {string} The BIDS issue code for this issue.
    * @private
    */
   static _determineBidsIssueCode(hedIssue) {
-    if (hedIssue.internalCode === 'internalError' || hedIssue.internalCode === 'internalConsistencyError') {
-      return 106
+    if (hedIssue.internalCode === 'internalError') {
+      return 'HED_INTERNAL_ERROR'
     }
     if (hedIssue.level === 'warning') {
-      return 105
+      return 'HED_WARNING'
     }
-    return 104
+    return 'HED_ERROR'
   }
 
   /**

src/bids/types/json.js

@@ -104,9 +104,9 @@ export class BidsSidecar extends BidsJsonFile {
     } else if (!defManager) {
       this.definitions = new DefinitionManager()
     } else {
-      IssueError.generateAndThrow('internalError', {
-        message: 'Improper format for defManager parameter -- must be null or DefinitionManager',
-      })
+      IssueError.generateAndThrowInternalError(
+        'Improper format for defManager parameter -- must be null or DefinitionManager',
+      )
     }
   }
 
@@ -222,9 +222,7 @@ export class BidsSidecar extends BidsJsonFile {
       } else if (hedData instanceof Map) {
         this._parseCategorySplice(sidecarKey, hedData)
       } else if (hedData) {
-        IssueError.generateAndThrow('internalConsistencyError', {
-          message: 'Unexpected type found in bidsFile parsedHedData map.',
-        })
+        IssueError.generateAndThrowInternalError('Unexpected type found in bidsFile parsedHedData map.')
       }
     }
   }
@@ -250,9 +248,9 @@ export class BidsSidecar extends BidsJsonFile {
 
   /**
    * Add a list of columnSplices to a key map.
-   * @param {Set} keyReferences
+   * @param {Set<string>|null} keyReferences
    * @param {ParsedHedColumnSplice[]} columnSplices
-   * @returns {*|Set<any>}
+   * @returns {Set<string>}
    * @private
    */
   _processColumnSplices(keyReferences, columnSplices) {
@@ -341,13 +339,14 @@ export class BidsSidecarKey {
   }
 
   /**
-   * Parse the value string in a bidsFile
-   * @param {Schemas} hedSchemas - The HED schemas to use.
-   * @returns {Issue[]}
-   * @private
+   * Parse the value string in a bidsFile.
    *
    * ### Note:
    *  The value strings cannot contain definitions.
+   *
+   * @param {Schemas} hedSchemas - The HED schemas to use.
+   * @returns {Issue[]}
+   * @private
    */
   _parseValueString(hedSchemas) {
     const [parsedString, parsingIssues] = parseHedString(this.valueString, hedSchemas, false, true)

src/bids/types/tsv.js

@@ -12,7 +12,7 @@ import { IssueError } from '../../issues/issues'
 export class BidsTsvFile extends BidsFile {
   /**
    * This file's parsed TSV data.
-   * @type {Map}
+   * @type {Map<string, string[]>}
    */
   parsedTsv
   /**
@@ -46,7 +46,7 @@ export class BidsTsvFile extends BidsFile {
     } else if (isPlainObject(tsvData)) {
       this.parsedTsv = convertParsedTSVData(tsvData)
     } else {
-      IssueError.generateAndThrow('internalError', { message: 'parsedTsv has an invalid type' })
+      IssueError.generateAndThrowInternalError('parsedTsv has an invalid type')
     }
 
     this.mergedSidecar = new BidsSidecar(name, this.file, mergedDictionary, defManager)
@@ -140,7 +140,7 @@ export class BidsTsvElement {
 
   /**
    * Create a string list of a list of BidsTsvElement objects.
-   * @param BidsTsvElement[] elements - A list of elements to construct line numbers from.
+   * @param {BidsTsvElement[]} elements - A list of elements to construct line numbers from.
    * @returns {string} - A string with the list of line numbers for error messages.
    */
   static getTsvLines(elements) {

src/bids/validator/sidecarValidator.js

@@ -21,7 +21,7 @@ export class BidsHedSidecarValidator extends BidsValidator {
   /**
    * Validate a BIDS JSON bidsFile file. This method returns the complete issue list for convenience.
    *
-   * @returns {BidsIssue[]} - Any issues found during validation of this bidsFile file.
+   * @returns {BidsHedIssue[]} - Any issues found during validation of this bidsFile file.
    */
   validate() {
     // Allow schema to be set a validation time -- this is checked by the superclass of BIDS file
@@ -40,7 +40,7 @@ export class BidsHedSidecarValidator extends BidsValidator {
   /**
    * Validate this bidsFile's HED strings.
    *
-   * @returns {BidsIssue[]} All issues found.
+   * @returns {BidsHedIssue[]} All issues found.
    */
   _validateStrings() {
     const issues = []
@@ -55,9 +55,7 @@ export class BidsHedSidecarValidator extends BidsValidator {
           issues.push(...this._checkDetails(sidecarKeyName, valueString))
         }
       } else {
-        IssueError.generateAndThrow('internalConsistencyError', {
-          message: 'Unexpected type found in bidsFile parsedHedData map.',
-        })
+        IssueError.generateAndThrowInternalError('Unexpected type found in bidsFile parsedHedData map.')
       }
     }
     return issues
@@ -127,7 +125,7 @@ export class BidsHedSidecarValidator extends BidsValidator {
   /**
    * Validate this bidsFile's curly braces -- checking recursion and missing columns.
    *
-   * @returns {BidsIssue[]} All issues found.
+   * @returns {BidsHedIssue[]} All issues found.
    */
   _validateCurlyBraces() {
     const issues = []