Implement HED column splicing

Also add tests for "n/a" deletion.
hed-standard · Dec 14, 2023 · d6eb21e · d6eb21e
1 parent 1d6ce5e
commit d6eb21e
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Showing 3 changed files with 88 additions and 2 deletions.
diff --git a/parser/columnSplicer.js b/parser/columnSplicer.js
@@ -115,6 +115,9 @@ export class ColumnSplicer {
     if (replacementString === null) {
       return null
     }
+    if (columnName === 'HED') {
+      return this._spliceHedColumnTemplate()
+    }
     if (replacementString === undefined) {
       this.issues.push(generateIssue('undefinedCurlyBraces', { column: columnName }))
       return []
@@ -130,6 +133,18 @@ export class ColumnSplicer {
     return replacementString.parseTree
   }
 
+  /**
+   * Splice a "HED" column value string in place of a column template.
+   *
+   * @returns {ParsedHedSubstring[]} The spliced column substitution.
+   * @private
+   */
+  _spliceHedColumnTemplate() {
+    const columnName = 'HED'
+    const replacementString = this.columnValues.get(columnName)
+    return this._reparseAndSpliceString(replacementString)
+  }
+
   /**
    * Splice a value-taking replacement string in place of a column template.
    *
@@ -141,7 +156,18 @@ export class ColumnSplicer {
     const columnName = columnTemplate.originalTag
     const replacementString = this.columnReplacements.get(columnName)
     const replacedString = replacementString.hedString.replace('#', this.columnValues.get(columnName))
-    const [newParsedString, parsingIssues] = parseHedString(replacedString, this.hedSchemas)
+    return this._reparseAndSpliceString(replacedString)
+  }
+
+  /**
+   * Re-parse a string to use in splicing.
+   *
+   * @param {string} replacementString A new string to parse.
+   * @returns {ParsedHedSubstring[]} The new string's parse tree.
+   * @private
+   */
+  _reparseAndSpliceString(replacementString) {
+    const [newParsedString, parsingIssues] = parseHedString(replacementString, this.hedSchemas)
     const flatParsingIssues = Object.values(parsingIssues).flat()
     if (flatParsingIssues.length > 0) {
       this.issues.push(...flatParsingIssues)

diff --git a/tests/bids.spec.data.js b/tests/bids.spec.data.js
@@ -647,6 +647,29 @@ const tsvFiles = [
         '5.5\t0\tface\tn/a',
     ],
   ],
+  // sub11 - 'n/a' curly brace tests
+  [
+    [
+      Object.assign({}, sidecars[6][0], sidecars[6][2]),
+      'onset\tduration\tevent_code\tresponse_time\n' + '5.0\t0\tball\tn/a\n',
+    ],
+    [
+      Object.assign({}, sidecars[6][0], sidecars[6][4]),
+      'onset\tduration\tevent_code\tHED\tresponse_time\n' + '5.0\t0\tball\tGreen,Def/MyColor\tn/a\n',
+    ],
+    [
+      Object.assign({}, sidecars[6][0], sidecars[6][4]),
+      'onset\tduration\tevent_code\tHED\tresponse_time\n' + '5.0\t0\tball\tn/a\t1\n',
+    ],
+    [
+      Object.assign({}, sidecars[6][0], sidecars[6][4]),
+      'onset\tduration\tevent_code\tHED\tresponse_time\n' + '5.0\t0\tball\tn/a\tn/a\n',
+    ],
+    [
+      Object.assign({}, sidecars[6][0], sidecars[6][5]),
+      'onset\tduration\tevent_code\tresponse_time\tresponse_code\n' + '5.0\t0\tface\t1\tn/a\n',
+    ],
+  ],
 ]
 
 const datasetDescriptions = [

diff --git a/tests/bids.spec.js b/tests/bids.spec.js
@@ -3,9 +3,11 @@ const assert = chai.assert
 import converterGenerateIssue from '../converter/issues'
 import { generateIssue } from '../common/issues/issues'
 import { SchemaSpec, SchemasSpec } from '../common/schema/types'
-import { parseSchemasSpec } from '../bids/schema'
+import { buildBidsSchemas, parseSchemasSpec } from '../bids/schema'
 import { BidsDataset, BidsHedIssue, BidsIssue, validateBidsDataset } from '../bids'
 import { bidsDatasetDescriptions, bidsSidecars, bidsTsvFiles } from './bids.spec.data'
+import { parseHedString } from '../parser/main'
+import { BidsHedTsvValidator } from '../bids/validator/bidsHedTsvValidator'
 
 describe('BIDS datasets', () => {
   /**
@@ -675,5 +677,40 @@ describe('BIDS datasets', () => {
       }
       return validator(testDatasets, expectedIssues, specs)
     }, 10000)
+
+    it('should delete substrings corresponding to "n/a" TSV values', () => {
+      const tsvFiles = bidsTsvFiles[10]
+      const expectedStrings = [
+        '(Def/Acc/3.5 m-per-s^2)',
+        '(Def/Acc/3.5 m-per-s^2), (Green, Def/MyColor)',
+        'Label/1, (Def/Acc/3.5 m-per-s^2)',
+        '(Def/Acc/3.5 m-per-s^2)',
+        '(Red, Blue), (Green, (Yellow))',
+      ]
+      const dataset = new BidsDataset(tsvFiles, [])
+      return buildBidsSchemas(dataset, specs).then(([hedSchemas, schemaIssues]) => {
+        assert.isEmpty(schemaIssues, 'Schema failed to load')
+        const parsedExpectedStrings = []
+        for (const expectedString of expectedStrings) {
+          const [parsedExpectedString, parsingIssues] = parseHedString(expectedString, hedSchemas)
+          assert.isEmpty(Object.values(parsingIssues).flat(), `String "${expectedString}" failed to parse`)
+          parsedExpectedStrings.push(parsedExpectedString)
+        }
+        const tsvHedStrings = []
+        for (const tsvFile of tsvFiles) {
+          tsvFile.mergedSidecar.parseHedStrings(hedSchemas)
+          const tsvValidator = new BidsHedTsvValidator(tsvFile, hedSchemas)
+          const tsvHed = tsvValidator.parseHed()
+          assert.isEmpty(tsvValidator.issues, 'TSV file failed to parse')
+          tsvHedStrings.push(...tsvHed)
+        }
+        const formatMap = (hedString) => hedString.format()
+        assert.deepStrictEqual(
+          tsvHedStrings.map(formatMap),
+          parsedExpectedStrings.map(formatMap),
+          'Mismatch in parsed strings',
+        )
+      })
+    }, 10000)
   })
 })