Walk-through -- changed order of parameters in files

spec_tests/jsonTests.spec.js

@@ -169,9 +169,8 @@ describe('HED validation using JSON tests', () => {
           assert.instanceOf(parsedTsv, Map, `${events} cannot be parsed`)
           const bidsTsv = new BidsTsvFile(
             `events`,
-            parsedTsv,
             { relativePath: 'combo test tsv' },
-            [],
+            parsedTsv,
             JSON.parse(side),
             defManager,
           )
@@ -191,7 +190,7 @@ describe('HED validation using JSON tests', () => {
           defManager.addDefinitions(defList)
           const parsedTsv = parseTSV(events)
           assert.instanceOf(parsedTsv, Map, `${events} cannot be parsed`)
-          const bidsTsv = new BidsTsvFile(`events`, parsedTsv, { relativePath: 'events test' }, [], {}, defManager)
+          const bidsTsv = new BidsTsvFile(`events`, { relativePath: 'events test' }, parsedTsv, {}, defManager)
           eventsIssues = bidsTsv.validate(hedSchema)
         } catch (e) {
           eventsIssues = [convertIssue(e)]
@@ -206,7 +205,7 @@ describe('HED validation using JSON tests', () => {
         try {
           const defManager = new DefinitionManager()
           defManager.addDefinitions(defList)
-          const bidsSide = new BidsSidecar(`sidecar`, JSON.parse(side), { relativePath: 'bidsFile test' }, defManager)
+          const bidsSide = new BidsSidecar(`sidecar`, { relativePath: 'bidsFile test' }, JSON.parse(side), defManager)
           issues = bidsSide.validate(hedSchema)
         } catch (e) {
           issues = [convertIssue(e)]
@@ -224,7 +223,7 @@ describe('HED validation using JSON tests', () => {
           defManager.addDefinitions(defList)
           const parsedTsv = parseTSV(hTsv)
           assert.instanceOf(parsedTsv, Map, `${str} cannot be parsed`)
-          const bidsTsv = new BidsTsvFile(`string`, parsedTsv, { relativePath: 'string test tsv' }, [], {}, defManager)
+          const bidsTsv = new BidsTsvFile(`string`, { relativePath: 'string test tsv' }, parsedTsv, {}, defManager)
           stringIssues = bidsTsv.validate(hedSchema)
         } catch (e) {
           stringIssues = [convertIssue(e)]

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} 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} The parsed contents of the TSV file, using the new format.
  */
 export function convertParsedTSVData(oldParsedTsv) {
   const columns = new Map()

src/bids/types/file.js

@@ -10,11 +10,13 @@ export class BidsFile {
    * @type {string}
    */
   name
+
   /**
-   * The file object representing this file data.
+   * The Object representing this file data.
    * This is used to generate {@link BidsIssue} objects.
-   * @type {object}
+   * @type {Object}
    */
+
   file
   /**
    * The validator class used to validate this file.
@@ -25,32 +27,23 @@ export class BidsFile {
   /**
    *
    * @param {string} name - The name of the file -- used for messages.
-   * @param {object} file - The representation of the file for error messages.
-   * @param validatorClass
+   * @param {Object} file - The representation of the file for error messages.
+   * @param {BidsValidator} validatorClass - The validator class corresponding to this file.
    */
   constructor(name, file, validatorClass) {
     this.name = name
     this.file = file
     this._validatorClass = validatorClass
   }
 
-  /**
-   * Determine whether this file has any HED data.
-   *
-   * @returns {boolean} - True if this file has HED data.
-   */
-  hasHedData() {
-    return false
-  }
-
   /**
    * 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.
    */
   validate(schemas) {
-    if (!this.hasHedData()) {
+    if (!this.hasHedData) {
       return []
     }
     if (!schemas) {
@@ -72,7 +65,7 @@ export class BidsFile {
 
   /**
    * The validator class used to validate this file.
-   * @returns {*}
+   * @returns {BidsValidator}
    */
   get validatorClass() {
     return this._validatorClass

src/bids/types/json.js

@@ -16,11 +16,17 @@ const ILLEGAL_SIDECAR_KEYS = new Set(['hed', 'n/a'])
 export class BidsJsonFile extends BidsFile {
   /**
    * This file's JSON data.
-   * @type {object}
+   * @type {Object}
    */
   jsonData
 
-  constructor(name, jsonData, file) {
+  /**
+   *
+   * @param {string} name - The name of the JSON file.
+   * @param {Object} file - The object representing this file.
+   * @param {Object} jsonData - The JSON data for this file.
+   */
+  constructor(name, file, jsonData) {
     super(name, file, BidsHedSidecarValidator)
     this.jsonData = jsonData
   }
@@ -32,39 +38,45 @@ export class BidsSidecar extends BidsJsonFile {
    * @type {Map}
    */
   sidecarKeys
+
   /**
    * The extracted HED data for this bidsFile (string --> string | Object: string, string
    * @type {Map}
    */
   hedData
+
   /**
-   * The parsed HED data for this bidsFile (string --> ParsedHedString | Map: string --> ParsedHedString
+   * The parsed HED data for this bidsFile (string --> ParsedHedString | Map: string --> ParsedHedString).
    * @type {Map}
    */
   parsedHedData
+
   /**
    * The extracted HED value strings.
    * @type {string[]}
    */
   hedValueStrings
+
   /**
    * The extracted HED categorical strings.
    * @type {string[]}
    */
   hedCategoricalStrings
+
   /**
-   * The mapping of column splice references (string --> Set of string)
+   * The mapping of column splice references (string --> Set of string).
    * @type {Map}
    */
   columnSpliceMapping
+
   /**
    * The set of column splice references.
    * @type {Set<string>}
    */
   columnSpliceReferences
 
   /**
-   * The object that manages definitions
+   * The object that manages definitions.
    * @type {DefinitionManager}
    */
   definitions
@@ -73,12 +85,12 @@ export class BidsSidecar extends BidsJsonFile {
    * Constructor.
    *
    * @param {string} name The name of the bidsFile file.
-   * @param {Object} sidecarData The raw JSON data.
    * @param {Object} file The file object representing this file.
+   * @param {Object} sidecarData The raw JSON data.
    * @param {DefinitionManager } defManager - The external definitions to use
    */
-  constructor(name, sidecarData = {}, file, defManager = null) {
-    super(name, sidecarData, file)
+  constructor(name, file, sidecarData = {}, defManager = undefined) {
+    super(name, file, sidecarData)
     this.columnSpliceMapping = new Map()
     this.columnSpliceReferences = new Set()
     this._setDefinitions(defManager)
@@ -168,7 +180,7 @@ export class BidsSidecar extends BidsJsonFile {
    *
    * @returns {boolean}
    */
-  hasHedData() {
+  get hasHedData() {
     return this.sidecarKeys.size > 0
   }
 

src/bids/types/tsv.js

@@ -12,19 +12,15 @@ import { IssueError } from '../../issues/issues'
 export class BidsTsvFile extends BidsFile {
   /**
    * This file's parsed TSV data.
-   * @type {Map[]}
+   * @type {Map}
    */
   parsedTsv
   /**
    * HED strings in the "HED" column of the TSV data.
    * @type {string[]}
    */
   hedColumnHedStrings
-  /**
-   * The list of potential JSON sidecars.
-   * @type {string[]}
-   */
-  potentialSidecars
+
   /**
    * The pseudo-bidsFile object representing the merged bidsFile data.
    * @type {BidsSidecar}
@@ -34,16 +30,13 @@ export class BidsTsvFile extends BidsFile {
   /**
    * Constructor.
    *
-   * @todo This interface is provisional and subject to modification in version 4.0.0.
-   *
-   * @param {string} name The name of the TSV file.
-   * @param {{headers: string[], rows: string[][]|Map[]|string} tsvData This file's TSV data.
-   * @param {object} file The file object representing this file.
-   * @param {string[]} potentialSidecars The list of potential JSON sidecars.
-   * @param {object} mergedDictionary The merged bidsFile data.
-   * @param {DefinitionManager} defManager
-   */
-  constructor(name, tsvData, file, potentialSidecars = [], mergedDictionary = {}, defManager) {
+   * @param {string} name - The name of the TSV file.
+   * @param {Object} file - The file object representing this file.
+   * @param {{headers: string[], rows: string[][]}|Map|string} tsvData - This file's TSV data.
+   * @param {Object} mergedDictionary - The merged bidsFile data.
+   * @param {DefinitionManager} defManager - The definition manager for this file.
+   */
+  constructor(name, file, tsvData, mergedDictionary = {}, defManager = undefined) {
     super(name, file, BidsHedTsvValidator)
 
     if (typeof tsvData === 'string') {
@@ -56,8 +49,7 @@ export class BidsTsvFile extends BidsFile {
       IssueError.generateAndThrow('internalError', { message: 'parsedTsv has an invalid type' })
     }
 
-    this.potentialSidecars = potentialSidecars
-    this.mergedSidecar = new BidsSidecar(name, mergedDictionary, this.file, defManager)
+    this.mergedSidecar = new BidsSidecar(name, this.file, mergedDictionary, defManager)
     this._parseHedColumn()
   }
 
@@ -73,12 +65,10 @@ export class BidsTsvFile extends BidsFile {
   /**
    * Determine whether this file has any HED data.
    *
-   * @todo To be replaced with property in version 4.0.0.
-   *
    * @returns {boolean}
    */
-  hasHedData() {
-    return this.parsedTsv.has('HED') || this.mergedSidecar.hasHedData()
+  get hasHedData() {
+    return this.parsedTsv.has('HED') || this.mergedSidecar.hasHedData
   }
 
   /**
@@ -139,7 +129,7 @@ export class BidsTsvElement {
   }
 
   /**
-   * Override of {@link Object.prototype.toString}.
+   * Override of {@link object.prototype.toString}.
    *
    * @returns {string}
    */

src/bids/utils.js

@@ -1,7 +1,7 @@
 /**
  * Determine whether a bidsFile value has HED data.
  *
- * @param {object} sidecarValue A BIDS bidsFile value.
+ * @param {Object} sidecarValue A BIDS bidsFile value.
  * @returns {boolean} Whether the bidsFile value has HED data.
  */
 export const sidecarValueHasHed = function (sidecarValue) {

src/bids/validator/tsvValidator.js

@@ -414,7 +414,7 @@ export class BidsHedTsvParser {
       columnMap.set('HED', rowCells.get('HED'))
     }
 
-    if (!this.tsvFile.mergedSidecar.hasHedData()) {
+    if (!this.tsvFile.mergedSidecar.hasHedData) {
       return columnMap
     }
 

src/parser/definitionChecker.js

@@ -1,16 +1,15 @@
 import { generateIssue } from '../issues/issues'
 import { getTagListString } from './parseUtils'
-import Set from 'lodash/_Set'
 
 const DEFINITION_TAGS = new Set(['Definition', 'Def', 'Def-expand'])
+
 const DEF_GROUP_TAGS = new Set(['Definition', 'Def-expand'])
 
 export class DefinitionChecker {
   /**
    * Check Def-expand or definition syntax for compatible tags and number of groups
    * @param {ParsedHedString} hedString - A group to check for Def-expand syntax.
    */
-
   constructor(hedString) {
     this.hedString = hedString
     this.definitionTags = this.hedString.tags.filter((tag) => tag.schemaTag.name === 'Definition')
@@ -158,33 +157,4 @@ export class DefinitionChecker {
     }
     return []
   }
-
-  // _checkDefinitionSyntax(parsedString) {
-  //
-  //   // This checks whether there are any definitions in the string if the definition is allowed.
-  //   const definitionContextIssues = this._checkDefinitionContext(parsedString)
-  //   if (definitionContextIssues.length > 0) {
-  //     return definitionContextIssues
-  //   }
-  //
-  //   // If
-  //   const definitionStructureIssues = this._checkDefinitionStructure(parsedString)
-  //   return definitionStructureIssues
-  // }
-  //
-  //
-  //
-
-  // return issues
-  // const definitionTags = parsedString.tags.filter((tag) => tag.schemaTag.name === 'Definition')
-  // if (definitionTags.length > 0) {
-  //   return [
-  //     generateIssue('illegalDefinitionContext', {
-  //       definition: getTagListString(definitionTags),
-  //       string: parsedString.hedString,
-  //     }),
-  //   ]
-  // }
-  // return []
-  // }
 }

src/parser/parsedHedTag.js

@@ -5,7 +5,7 @@ import TagConverter from './tagConverter'
 import { ReservedChecker } from './reservedChecker'
 
 const TWO_LEVEL_TAGS = new Set(['Definition', 'Def', 'Def-expand'])
-const allowedRegEx = /^[^{}\,]*$/
+const allowedRegEx = /^[^{},]*$/
 
 /**
  * A parsed HED tag.

src/parser/reservedChecker.js

@@ -40,7 +40,7 @@ export class ReservedChecker {
    * Perform syntactical checks on the provided HED string to detect violations.
    *
    * @param {ParsedHedString} hedString - The HED string to be checked.
-   * @returns {Issue[]} An array of issues if violations are found otherwise, an empty array.
+   * @returns {Issue[]} - An array of issues if violations are found otherwise, an empty array.
    */
   checkHedString(hedString) {
     const checks = [

src/schema/containers.js

@@ -38,7 +38,7 @@ export class Schema {
   /**
    * Constructor.
    *
-   * @param {object} xmlData The schema XML data.
+   * @param {Object} xmlData The schema XML data.
    * @param {SchemaEntries} entries A collection of schema entries.
    */
   constructor(xmlData, entries) {