HED Validator integration into bids schema based validator.

.github/workflows/codespell.yml

@@ -21,4 +21,4 @@ jobs:
       - uses: codespell-project/actions-codespell@master
         with:
           ignore_words_list: ro,anser,te,tage,afterall,nwe,nin,nd,falsy
-          skip: package-lock.json
+          skip: package-lock.json, deps*

bids-validator/src/deps/hed-validator.ts

@@ -0,0 +1 @@
+export { default } from "https://esm.sh/[email protected]?deps=node@16"

bids-validator/src/issues/list.ts

@@ -91,4 +91,42 @@ export const filenameIssues: IssueDefinitionRecord = {
   },
 }
 
-export const nonSchemaIssues = { ...filenameIssues }
+const hedIssues: IssueDefinitionRecord = {
+  HED_ERROR: {
+    severity: 'error',
+    reason: 'The validation on this HED string returned an error.',
+  },
+  HED_WARNING: {
+    severity: 'warning',
+    reason: 'The validation on this HED string returned a warning.',
+  },
+  HED_INTERNAL_ERROR: {
+    severity: 'error',
+    reason: 'An internal error occurred during HED validation.',
+  },
+  HED_INTERNAL_WARNING: {
+    severity: 'warning',
+    reason: 'An internal warning occurred during HED validation.',
+  },
+  HED_MISSING_VALUE_IN_SIDECAR: {
+    severity: 'warning',
+    reason:
+      'The json sidecar does not contain this column value as a possible key to a HED string.',
+  },
+  HED_VERSION_NOT_DEFINED: {
+    severity: 'warning',
+    reason:
+      "You should define 'HEDVersion' for this file. If you don't provide this information, the HED validation will use the latest version available.",
+  },
+}
+
+export const hedOldToNewLookup: Record<number, Partial<keyof IssueDefinitionRecord>> = {
+  104: 'HED_ERROR',
+  105: 'HED_WARNING',
+  106: 'HED_INTERNAL_ERROR',
+  107: 'HED_INTERNAL_WARNING',
+  108: 'HED_MISSING_VALUE_IN_SIDECAR',
+  109: 'HED_VERSION_NOT_DEFINED'
+}
+
+export const nonSchemaIssues = { ...filenameIssues, ...hedIssues }

bids-validator/src/schema/context.ts

@@ -16,6 +16,7 @@ import { loadHeader } from '../files/nifti.ts'
 import { buildAssociations } from './associations.ts'
 import { ValidatorOptions } from '../setup/options.ts'
 import { logger } from '../utils/logger.ts'
+import { HEDArgs } from '../types/hed.ts'
 
 export class BIDSContextDataset implements ContextDataset {
   dataset_description: Record<string, unknown>
@@ -25,6 +26,7 @@ export class BIDSContextDataset implements ContextDataset {
   ignored: any[]
   modalities: any[]
   subjects: ContextDatasetSubjects[]
+  hedArgs: HEDArgs
 
   constructor(options?: ValidatorOptions, description = {}) {
     this.dataset_description = description
@@ -33,6 +35,7 @@ export class BIDSContextDataset implements ContextDataset {
     this.ignored = []
     this.modalities = []
     this.subjects = [] as ContextDatasetSubjects[]
+    this.hedArgs = new HEDArgs()
     if (options) {
       this.options = options
     }

bids-validator/src/tests/local/hed-integration.test.ts

@@ -0,0 +1,36 @@
+import { assert, assertEquals } from '../../deps/asserts.ts'
+import { validatePath, formatAssertIssue } from './common.ts'
+import { validate } from '../../validators/bids.ts'
+import { parseOptions } from '../../setup/options.ts'
+import { testDetectHed } from '../../validators/hed.ts'
+import { BIDSContextDataset } from '../../schema/context.ts'
+
+Deno.test('hed-validator not triggered', async (t) => {
+  const PATH = 'tests/data/bids-examples/ds003'
+  const { tree, result } = await validatePath(t, PATH)
+
+  await t.step('detect hed returns false', async () => {
+    const new_result = await validate(tree, {
+      ...(await parseOptions([PATH]))
+    })
+
+    // Dummy dscontext until I can figure out how to extract a good one from validate
+    const dsContext = new BIDSContextDataset()
+    assert(!testDetectHed(dsContext))
+  })
+})
+
+Deno.test('hed-validator integration test', async (t) => {
+  const PATH = 'tests/data/bids-examples/eeg_ds003645s_hed_inheritance'
+  const { tree, result } = await validatePath(t, PATH)
+
+  tree.files = tree.files.filter(f => f.name !== 'task-FacePerception_events.json')
+  await t.step('generates hed error on missing events json', async () => {
+    const new_result = await validate(tree, {
+      ...(await parseOptions([PATH]))
+    })
+    assert(new_result.issues.has("HED_ERROR"))
+  })
+})
+
+

bids-validator/src/tests/local/valid_headers.test.ts

@@ -30,7 +30,7 @@ Deno.test('valid_headers dataset', async (t) => {
   })
 
   await t.step('summary has correct totalFiles', () => {
-    assertEquals(result.summary.totalFiles, 8)
+    assertEquals(result.summary.totalFiles, 7)
   })
 
   await t.step('summary has correct subjectMetadata', () => {

bids-validator/src/types/check.ts

@@ -1,8 +1,9 @@
 import { GenericSchema } from './schema.ts'
-import { BIDSContext } from '../schema/context.ts'
+import { BIDSContext, BIDSContextDataset } from '../schema/context.ts'
+import { DatasetIssues } from '../issues/datasetIssues.ts'
 
 /** Function interface for writing a check */
-export type CheckFunction = (
+export type ContextCheckFunction = (
   schema: GenericSchema,
   context: BIDSContext,
 ) => Promise<void>
@@ -13,3 +14,9 @@ export type RuleCheckFunction = (
   schema: GenericSchema,
   context: BIDSContext,
 ) => void
+
+export type DSCheckFunction = (
+  schema: GenericSchema,
+  dsContext: BIDSContextDataset,
+  issues: DatasetIssues,
+) => Promise<void>

bids-validator/src/types/context.ts

@@ -1,10 +1,12 @@
 import { ValidatorOptions } from '../setup/options.ts'
+import { HEDArgs } from './hed.ts'
 
 export interface ContextDatasetSubjects {
   sub_dirs: string[]
   participant_id: string[]
   phenotype: string[]
 }
+
 export interface ContextDataset {
   dataset_description: Record<string, unknown>
   files: any[]
@@ -13,6 +15,7 @@ export interface ContextDataset {
   modalities: any[]
   subjects: ContextDatasetSubjects[]
   options?: ValidatorOptions
+  hedArgs: HEDArgs
 }
 export interface ContextSubjectSessions {
   ses_dirs: string[]

bids-validator/src/types/hed.ts

@@ -0,0 +1,19 @@
+import hedValidator from '../deps/hed-validator.ts'
+export class BidsSidecar extends hedValidator.validator.BidsSidecar {}
+export class BidsEventFile extends hedValidator.bids.BidsEventFile {} 
+export class BidsJsonFile extends hedValidator.bids.BidsJsonFile {} 
+
+export class HEDArgs {
+  eventData: BidsEventFile[]
+  sidecarData: BidsSidecar[]
+  datasetDescription: BidsJsonFile
+  dir: string
+
+  constructor() {
+    this.eventData = [] as BidsEventFile[]
+    this.sidecarData = [] as BidsSidecar[]
+    this.datasetDescription = {} as BidsJsonFile
+    this.dir = ''
+  }
+}
+

bids-validator/src/validators/bids.ts

@@ -1,4 +1,4 @@
-import { CheckFunction } from '../types/check.ts'
+import { DSCheckFunction, ContextCheckFunction } from '../types/check.ts'
 import { FileTree } from '../types/filetree.ts'
 import { GenericSchema } from '../types/schema.ts'
 import { ValidationResult } from '../types/validation-result.ts'
@@ -14,17 +14,21 @@ import { emptyFile } from './internal/emptyFile.ts'
 import { BIDSContext, BIDSContextDataset } from '../schema/context.ts'
 import { BIDSFile } from '../types/file.ts'
 import { parseOptions } from '../setup/options.ts'
+import { hedAccumulator, hedValidate } from './hed.ts'
 
 /**
  * Ordering of checks to apply
  */
-const CHECKS: CheckFunction[] = [
+const perContextChecks: ContextCheckFunction[] = [
   emptyFile,
   filenameIdentify,
   filenameValidate,
   applyRules,
+  hedAccumulator,
 ]
 
+const perDSChecks: DSCheckFunction[] = [hedValidate]
+
 /**
  * Full BIDS schema validation entrypoint
  */
@@ -77,12 +81,15 @@ export async function validate(
     }
     await context.asyncLoads()
     // Run majority of checks
-    for (const check of CHECKS) {
+    for (const check of perContextChecks) {
       // TODO - Resolve this double casting?
       await check(schema as unknown as GenericSchema, context)
     }
     await summary.update(context)
   }
+  for (const check of perDSChecks) {
+    await check(schema as unknown as GenericSchema, dsContext, issues)
+  }
 
   let derivativesSummary: Record<string, ValidationResult> = {}
   await Promise.allSettled(

bids-validator/src/validators/filenameValidate.ts

@@ -1,4 +1,4 @@
-import { CheckFunction, RuleCheckFunction } from '../types/check.ts'
+import { ContextCheckFunction, RuleCheckFunction } from '../types/check.ts'
 import { DatasetIssues } from '../issues/datasetIssues.ts'
 import { BIDSContext } from '../schema/context.ts'
 import { GenericSchema, Schema, Entity, Format } from '../types/schema.ts'
@@ -7,7 +7,7 @@ import { hasProp } from '../utils/objectPathHandler.ts'
 
 const sidecarExtensions = ['.json', '.tsv', '.bvec', '.bval']
 
-const CHECKS: CheckFunction[] = [
+const CHECKS: ContextCheckFunction[] = [
   missingLabel,
   atRoot,
   entityLabelCheck,

bids-validator/src/validators/hed.ts

@@ -0,0 +1,109 @@
+import hedValidator from '../deps/hed-validator.ts'
+import { hedOldToNewLookup } from '../issues/list.ts'
+import { GenericSchema } from '../types/schema.ts'
+import { IssueFile } from '../types/issues.ts'
+import { BIDSContext, BIDSContextDataset } from '../schema/context.ts'
+import { DatasetIssues } from '../issues/datasetIssues.ts'
+import { ColumnsMap } from '../types/columns.ts'
+
+export class BidsSidecar extends hedValidator.validator.BidsSidecar {}
+export class BidsEventFile extends hedValidator.bids.BidsEventFile {} 
+
+// https://stackoverflow.com/questions/17428587/transposing-a-2d-array-in-javascript
+function transpose(matrix: string[][]) {
+  return matrix[0].map((col, i) => matrix.map((row) => row[i]))
+}
+
+function columnsToContent(columns: ColumnsMap) {
+  const cols = [] as [][]
+  for (let header in columns) {
+    // @ts-expect-error
+    cols.push(columns[header])
+  }
+  const rows = transpose(cols)
+  return {
+    headers: Object.keys(columns),
+    rows,
+  }
+}
+
+function detectHed(tsvData: BidsEventFile[], sidecarData: BidsSidecar[]) {
+  return (
+    sidecarData.some((sidecarFileData) => {
+      return Object.values(sidecarFileData.sidecarData).some(sidecarValueHasHed)
+    }) ||
+    tsvData.some((tsvFileData) => {
+      return 'HED' in tsvFileData.parsedTsv
+    })
+  )
+} 
+
+export function testDetectHed(dsContext: BIDSContextDataset) {
+  return detectHed(dsContext.hedArgs.eventData, dsContext.hedArgs.sidecarData)
+}
+
+function sidecarValueHasHed(sidecarValue: unknown) {
+  return ( 
+    sidecarValue !== null &&
+    typeof sidecarValue === 'object' &&
+    'HED' in sidecarValue &&
+    sidecarValue.HED !== undefined
+  )
+}
+
+export async function hedAccumulator(schema: GenericSchema, context: BIDSContext) {
+  if (context.file.name == 'dataset_description.json') {
+    context.dataset.hedArgs.datasetDescription = new hedValidator.validator.BidsJsonFile(
+      '/dataset_description.json',
+      await context.json,
+      context.file,
+    )
+    context.dataset.hedArgs.dir = context.datasetPath
+  }
+  if (context.suffix == 'events' && context.extension == '.tsv') {
+    const tsvContent = columnsToContent(context.columns)
+
+    const eventFile = new BidsEventFile(
+      context.path,
+      [],
+      context.sidecar,
+      tsvContent,
+      context.file,
+    )
+    context.dataset.hedArgs.eventData.push(eventFile)
+  }
+
+  if (context.extension == '.json') {
+    const sidecarFile = new BidsSidecar(context.path, await context.json, context.file)
+    context.dataset.hedArgs.sidecarData.push(
+      sidecarFile
+    )
+  }
+}
+
+export interface HedIssue {
+  code: number
+  file: IssueFile
+  evidence: string
+}
+
+export async function hedValidate(schema: GenericSchema, dsContext: BIDSContextDataset, issues: DatasetIssues): Promise<void>{
+  if (!detectHed(dsContext.hedArgs.eventData, dsContext.hedArgs.sidecarData)) {
+    return Promise.resolve()
+  }
+  let hedDs = new hedValidator.validator.BidsDataset(...Object.values(dsContext.hedArgs))
+  await hedValidator.validator
+    .validateBidsDataset(hedDs)
+    .then((hedValidationIssues: HedIssue[]) => {
+      const newStyle = hedValidationIssues.map((hedIssue) => {
+        const code = hedIssue.code
+        if (code in hedOldToNewLookup) {
+          issues.addNonSchemaIssue(
+            hedOldToNewLookup[code], [{...hedIssue.file, evidence: hedIssue.evidence}]
+          )
+        }
+      })
+    })
+  return Promise.resolve()
+}
+

bids-validator/src/validators/internal/emptyFile.ts

@@ -1,7 +1,7 @@
-import { CheckFunction } from '../../types/check.ts'
+import { ContextCheckFunction } from '../../types/check.ts'
 
 // Non-schema EMPTY_FILE implementation
-export const emptyFile: CheckFunction = (schema, context) => {
+export const emptyFile: ContextCheckFunction = (schema, context) => {
   if (context.file.size === 0) {
     context.issues.addNonSchemaIssue('EMPTY_FILE', [context.file])
   }

bids-validator/src/validators/isBidsy.ts

@@ -5,11 +5,11 @@
 // @ts-nocheck
 import { SEPARATOR } from '../deps/path.ts'
 import { BIDSContext } from '../schema/context.ts'
-import { CheckFunction } from '../../types/check.ts'
+import { ContextCheckFunction } from '../../types/check.ts'
 import { BIDSFile } from '../types/file.ts'
 import { Schema } from '../types/schema.ts'
 
-export const isBidsyFilename: CheckFunction = (schema, context) => {
+export const isBidsyFilename: ContextCheckFunction = (schema, context) => {
   // every '.', '-', '_' followed by an alnum
   // only contains '.', '-', '_' and alnum
 }