Reorganize HED wrapper code

bids-validator/validators/bids/fullTest.js

@@ -8,6 +8,7 @@ import bval from '../bval'
 import bvec from '../bvec'
 import microscopy from '../microscopy'
 import Events from '../events'
+import hed from '../hed'
 import { session } from '../session'
 import checkAnyDataPresent from '../checkAnyDataPresent'
 import headerFields from '../headerFields'
@@ -215,17 +216,15 @@ const fullTest = (fileList, options, annexed, dir, schema, callback) => {
 
  // Events validation
  stimuli.directory = files.stimuli
- return Events.validateEvents(
- events,
- stimuli,
- headers,
- jsonContentsDict,
- jsonFiles,
- dir,
+ self.issues = self.issues.concat(
+ Events.validateEvents(events, stimuli, headers, jsonContentsDict),
  )
+
+ // check the HED strings
+ return hed(tsvs, jsonContentsDict, jsonFiles, dir)
  })
- .then((eventsIssues) => {
- self.issues = self.issues.concat(eventsIssues)
+ .then((hedIssues) => {
+ self.issues = self.issues.concat(hedIssues)
 
  // Validate custom fields in all TSVs and add any issues to the list
  self.issues = self.issues.concat(

bids-validator/validators/events/events.js

@@ -1,28 +1,16 @@
 /* eslint-disable no-unused-vars */
-import hed from './hed'
 
 import utils from '../../utils'
 const Issue = utils.issues.Issue
 
-export default function (
- events,
- stimuli,
- headers,
- jsonContents,
- jsonFiles,
- dir,
-) {
- const issues = []
+export default function (events, stimuli, headers, jsonContents) {
  // check that all stimuli files present in /stimuli are included in an _events.tsv file
  const stimuliIssues = checkStimuli(stimuli)
 
  // check the events file for suspiciously long or short durations
  const designIssues = checkDesignLength(events, headers, jsonContents)
 
- // check the HED strings
- return hed(events, jsonContents, jsonFiles, dir).then((hedIssues) => {
- return issues.concat(stimuliIssues, designIssues, hedIssues)
- })
+ return [].concat(stimuliIssues, designIssues)
 }
 
 const checkStimuli = function (stimuli) {

bids-validator/validators/events/index.js

@@ -1,9 +1,7 @@
 import events from './events'
-import hed from './hed'
 import validate from './validate'
 
 export default {
  events: events,
- hed: hed,
  validateEvents: validate,
 }

bids-validator/validators/events/hed.js → bids-validator/validators/hed.js

@@ -1,26 +1,26 @@
 import hedValidator from 'hed-validator'
+import cloneDeep from 'lodash/cloneDeep'
 import intersection from 'lodash/intersection'
-import utils from '../../utils'
-import parseTsv from '../tsv/tsvParser'
+import utils from '../utils'
 
 const Issue = utils.issues.Issue
 
-export default function checkHedStrings(events, jsonContents, jsonFiles, dir) {
- const eventData = constructEventData(events, jsonContents)
- const sidecarData = constructSidecarData(events, jsonContents, jsonFiles)
- const hedDataExists = detectHed(eventData, sidecarData)
+export default function checkHedStrings(tsvs, jsonContents, jsonFiles, dir) {
+ const tsvData = constructTsvData(tsvs, jsonContents)
+ const sidecarData = constructSidecarData(tsvData, jsonContents, jsonFiles)
+ const hedDataExists = detectHed(tsvData, sidecarData)
  if (!hedDataExists) {
  return Promise.resolve([])
  }
 
  const datasetDescription = jsonContents['/dataset_description.json']
  const datasetDescriptionData = new hedValidator.validator.BidsJsonFile(
  '/dataset_description.json',
- datasetDescription,
+ cloneDeep(datasetDescription),
  getSidecarFileObject('/dataset_description.json', jsonFiles),
  )
  const dataset = new hedValidator.validator.BidsDataset(
- eventData,
+ tsvData,
  sidecarData,
  datasetDescriptionData,
  dir,
@@ -43,61 +43,65 @@ export default function checkHedStrings(events, jsonContents, jsonFiles, dir) {
  }
 }
 
-function constructEventData(events, jsonContents) {
- return events.map((eventFile) => {
+function constructTsvData(tsvFiles, jsonContents) {
+ return tsvFiles.map((tsvFile) => {
  const potentialSidecars = utils.files.potentialLocations(
- eventFile.path.replace('.tsv', '.json'),
+ tsvFile.file.relativePath.replace('.tsv', '.json'),
  )
  const mergedDictionary = utils.files.generateMergedSidecarDict(
  potentialSidecars,
  jsonContents,
  )
- const parsedTsv = parseTsv(eventFile.contents)
- const file = eventFile.file
- return new hedValidator.validator.BidsEventFile(
- eventFile.path,
+ let TsvFileClass
+ if (tsvFile.file.relativePath.endsWith('_events.tsv')) {
+ TsvFileClass = hedValidator.bids.BidsEventFile
+ } else {
+ TsvFileClass = hedValidator.bids.BidsTabularFile
+ }
+ return new TsvFileClass(
+ tsvFile.path,
  potentialSidecars,
  mergedDictionary,
- parsedTsv,
- file,
+ tsvFile.contents,
+ tsvFile.file,
  )
  })
 }
 
-function constructSidecarData(eventData, jsonContents, jsonFiles) {
+function constructSidecarData(tsvData, jsonContents, jsonFiles) {
  const actualSidecarNames = Object.keys(jsonContents)
- let potentialEventSidecars = []
- for (const eventFileData of eventData) {
- potentialEventSidecars = potentialEventSidecars.concat(
- eventFileData.potentialSidecars,
- )
+ const potentialSidecars = []
+ for (const tsvFileData of tsvData) {
+ potentialSidecars.push(...tsvFileData.potentialSidecars)
  }
  const actualEventSidecars = intersection(
  actualSidecarNames,
- potentialEventSidecars,
+ potentialSidecars,
  )
  return actualEventSidecars.map((sidecarName) => {
  return new hedValidator.validator.BidsSidecar(
  sidecarName,
- jsonContents[sidecarName],
+ cloneDeep(jsonContents[sidecarName]),
  getSidecarFileObject(sidecarName, jsonFiles),
  )
  })
 }
 
 function getSidecarFileObject(sidecarName, jsonFiles) {
- return jsonFiles.filter((file) => {
- return file.relativePath === sidecarName
- })[0]
+ return cloneDeep(
+ jsonFiles.filter((file) => {
+ return file.relativePath === sidecarName
+ })[0],
+ )
 }
 
-function detectHed(eventData, sidecarData) {
+function detectHed(tsvData, sidecarData) {
  return (
  sidecarData.some((sidecarFileData) => {
  return Object.values(sidecarFileData.sidecarData).some(sidecarValueHasHed)
  }) ||
- eventData.some((eventFileData) => {
- return eventFileData.parsedTsv.headers.indexOf('HED') !== -1
+ tsvData.some((tsvFileData) => {
+ return tsvFileData.parsedTsv.headers.indexOf('HED') !== -1
  })
  )
 }