Merge pull request #143 from hed-standard/bids-tsv-event

Make TSV validation event-based

Author: happy5214

bids/types/tsv.js

@@ -132,6 +132,9 @@ export class BidsTabularFile extends BidsTsvFile {
   }
 }
 
+/**
+ * A row in a BIDS TSV file.
+ */
 export class BidsTsvRow extends ParsedHedString {
   /**
    * The parsed string representing this row.
@@ -156,6 +159,7 @@ export class BidsTsvRow extends ParsedHedString {
 
   /**
    * Constructor.
+   *
    * @param {ParsedHedString} parsedString The parsed string representing this row.
    * @param {Map<string, string>} rowCells The column-to-value mapping for this row.
    * @param {BidsTsvFile} tsvFile The file this row belongs to.
@@ -178,4 +182,63 @@ export class BidsTsvRow extends ParsedHedString {
   toString() {
     return super.toString() + ` in TSV file "${this.tsvFile.name}" at line ${this.tsvLine}`
   }
+
+  /**
+   * The onset of this row.
+   *
+   * @return {number} The onset of this row.
+   */
+  get onset() {
+    const value = Number(this.rowCells.get('onset'))
+    if (Number.isNaN(value)) {
+      throw new Error('Attempting to access the onset of a TSV row without one.')
+    }
+    return value
+  }
+}
+
+/**
+ * An event in a BIDS TSV file.
+ */
+export class BidsTsvEvent extends ParsedHedString {
+  /**
+   * The file this row belongs to.
+   * @type {BidsTsvFile}
+   */
+  tsvFile
+  /**
+   * The TSV rows making up this event.
+   * @type {BidsTsvRow[]}
+   */
+  tsvRows
+
+  /**
+   * Constructor.
+   *
+   * @param {BidsTsvFile} tsvFile The file this row belongs to.
+   * @param {BidsTsvRow[]} tsvRows The TSV rows making up this event.
+   */
+  constructor(tsvFile, tsvRows) {
+    super(tsvRows.map((tsvRow) => tsvRow.hedString).join(', '), tsvRows.map((tsvRow) => tsvRow.parseTree).flat())
+    this.tsvFile = tsvFile
+    this.tsvRows = tsvRows
+  }
+
+  /**
+   * The lines in the TSV file corresponding to this event.
+   *
+   * @return {string} The lines in the TSV file corresponding to this event.
+   */
+  get tsvLines() {
+    return this.tsvRows.map((tsvRow) => tsvRow.tsvLine).join(', ')
+  }
+
+  /**
+   * Override of {@link Object.prototype.toString}.
+   *
+   * @returns {string}
+   */
+  toString() {
+    return super.toString() + ` in TSV file "${this.tsvFile.name}" at line(s) ${this.tsvLines}`
+  }
 }

bids/validator/bidsHedTsvValidator.js

@@ -1,11 +1,12 @@
 import { BidsHedSidecarValidator } from './bidsHedSidecarValidator'
 import { BidsHedIssue } from '../types/issues'
-import { BidsTsvRow } from '../types/tsv'
+import { BidsTsvEvent, BidsTsvRow } from '../types/tsv'
 import { parseHedString } from '../../parser/main'
 import ColumnSplicer from '../../parser/columnSplicer'
 import ParsedHedString from '../../parser/parsedHedString'
 import { generateIssue } from '../../common/issues/issues'
 import { validateHedDatasetWithContext } from '../../validator/dataset'
+import { groupBy } from '../../utils/map'
 
 /**
  * Validator for HED data in BIDS TSV files.
@@ -67,18 +68,15 @@ export class BidsHedTsvValidator {
   /**
    * Combine the BIDS sidecar HED data into a BIDS TSV file's HED data.
    *
-   * @returns {BidsTsvRow[]} The combined HED string collection for this BIDS TSV file.
+   * @returns {ParsedHedString[]} The combined HED string collection for this BIDS TSV file.
    */
   parseHed() {
     const tsvHedRows = this._generateHedRows()
-    const hedStrings = []
+    const hedStrings = this._parseHedRows(tsvHedRows)
 
-    tsvHedRows.forEach((row, index) => {
-      const hedString = this._parseHedRow(row, index + 2)
-      if (hedString !== null) {
-        hedStrings.push(hedString)
-      }
-    })
+    if (this.tsvFile.isTimelineFile) {
+      return this._mergeEventRows(hedStrings)
+    }
 
     return hedStrings
   }
@@ -91,7 +89,7 @@ export class BidsHedTsvValidator {
    */
   _generateHedRows() {
     const tsvHedColumns = Array.from(this.tsvFile.parsedTsv.entries()).filter(
-      ([header]) => this.tsvFile.sidecarHedData.has(header) || header === 'HED',
+      ([header]) => this.tsvFile.sidecarHedData.has(header) || header === 'HED' || header === 'onset',
     )
 
     const tsvHedRows = []
@@ -104,6 +102,44 @@ export class BidsHedTsvValidator {
     return tsvHedRows
   }
 
+  /**
+   * Parse the HED rows in the TSV file.
+   *
+   * @param {Map<string, string>[]} tsvHedRows A list of single-row column-to-value mappings.
+   * @return {BidsTsvRow[]} A list of row-based parsed HED strings.
+   * @private
+   */
+  _parseHedRows(tsvHedRows) {
+    const hedStrings = []
+
+    tsvHedRows.forEach((row, index) => {
+      const hedString = this._parseHedRow(row, index + 2)
+      if (hedString !== null) {
+        hedStrings.push(hedString)
+      }
+    })
+    return hedStrings
+  }
+
+  /**
+   * Merge rows with the same onset time into a single event string.
+   *
+   * @param {BidsTsvRow[]} rowStrings A list of row-based parsed HED strings.
+   * @return {BidsTsvEvent[]} A list of event-based parsed HED strings.
+   * @private
+   */
+  _mergeEventRows(rowStrings) {
+    const groupedTsvRows = groupBy(rowStrings, (rowString) => rowString.onset)
+    const sortedOnsetTimes = Array.from(groupedTsvRows.keys()).sort((a, b) => a - b)
+    const eventStrings = []
+    for (const onset of sortedOnsetTimes) {
+      const onsetRows = groupedTsvRows.get(onset)
+      const onsetEventString = new BidsTsvEvent(this.tsvFile, onsetRows)
+      eventStrings.push(onsetEventString)
+    }
+    return eventStrings
+  }
+
   /**
    * Parse a row in a TSV file.
    *
@@ -141,7 +177,7 @@ export class BidsHedTsvValidator {
     const [parsedString, parsingIssues] = parseHedString(hedString, this.hedSchemas)
     const flatParsingIssues = Object.values(parsingIssues).flat()
     if (flatParsingIssues.length > 0) {
-      this.issues.push(...BidsHedIssue.fromHedIssues(...flatParsingIssues, this.tsvFile.file, { tsvLine }))
+      this.issues.push(...BidsHedIssue.fromHedIssues(flatParsingIssues, this.tsvFile.file, { tsvLine }))
       return null
     }
 

utils/map.js

@@ -1,3 +1,4 @@
+import identity from 'lodash/identity'
 import isEqual from 'lodash/isEqual'
 
 /**
@@ -27,3 +28,24 @@ export const filterNonEqualDuplicates = function (list, equalityFunction = isEqu
   }
   return [map, duplicates]
 }
+
+/**
+ * Group a list by a given grouping function.
+ *
+ * @template T, U
+ * @param {T[]} list The list to group.
+ * @param {function (T): U} groupingFunction A function mapping a list value to the key it is to be grouped under.
+ * @return {Map<U, T[]>} The grouped map.
+ */
+export const groupBy = function (list, groupingFunction = identity) {
+  const groupingMap = new Map()
+  for (const listEntry of list) {
+    const groupingValue = groupingFunction(listEntry)
+    if (groupingMap.has(groupingValue)) {
+      groupingMap.get(groupingValue).push(listEntry)
+    } else {
+      groupingMap.set(groupingValue, [listEntry])
+    }
+  }
+  return groupingMap
+}