Implementation and basic unit tests for HEDVersion with libraries (#1496

) * Added basic unit tests for HEDVersion with libraries * Removed commented out code * Updated the creation of the dataset description object * Bumped hed-validator version for hed library schema support * update package-lock.json for hed validator 3.8 Co-authored-by: Stefan Appelhoff <[email protected]> Co-authored-by: Ross Blair <[email protected]>
bids-standard · Aug 31, 2022 · 82a3a42 · 82a3a42
1 parent ee7d94c
commit 82a3a42
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Showing 11 changed files with 188 additions and 43 deletions.
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -2,12 +2,12 @@
 # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
 version: 2
 updates:
-  - package-ecosystem: "github-actions"
-    directory: "/"
+  - package-ecosystem: 'github-actions'
+    directory: '/'
     schedule:
-      interval: "monthly"
+      interval: 'monthly'
 
-  - package-ecosystem: "gitsubmodule"
-    directory: "/"
+  - package-ecosystem: 'gitsubmodule'
+    directory: '/'
     schedule:
-      interval: "monthly"
+      interval: 'monthly'
diff --git a/bids-validator/package.json b/bids-validator/package.json
@@ -44,7 +44,7 @@
     "date-fns": "^2.7.0",
     "events": "^3.3.0",
     "exifreader": "^4.1.0",
-    "hed-validator": "^3.7.1",
+    "hed-validator": "^3.8.0",
     "ignore": "^4.0.2",
     "is-utf8": "^0.2.1",
     "jshint": "^2.9.6",

diff --git a/bids-validator/src/files/deno.test.ts b/bids-validator/src/files/deno.test.ts
@@ -14,7 +14,7 @@ const testDir = dirname(testPath)
 const testFilename = basename(testPath)
 const ignore = new FileIgnoreRulesDeno([])
 
-Deno.test('Deno implementation of BIDSFile', async t => {
+Deno.test('Deno implementation of BIDSFile', async (t) => {
   await t.step('implements basic file properties', () => {
     const file = new BIDSFileDeno(testDir, testFilename, ignore)
     assertEquals(join(testDir, file.path), testPath)
@@ -45,7 +45,8 @@ Deno.test('Deno implementation of BIDSFile', async t => {
       const bomFilename = 'bom-utf16.tsv'
       const file = new BIDSFileDeno(bomDir, bomFilename, ignore)
       await assertRejects(async () => file.text(), UnicodeDecodeError)
-  })
+    },
+  )
   await t.step(
     'strips BOM characters when reading UTF-8 via .text()',
     async () => {

diff --git a/bids-validator/src/files/tsv.ts b/bids-validator/src/files/tsv.ts
@@ -13,10 +13,10 @@ export function parseTSV(contents: string) {
   const rows: string[][] = normalizeEOL(contents)
     .split('\n')
     .filter(isContentfulRow)
-    .map(str => str.split('\t'))
+    .map((str) => str.split('\t'))
   const headers = rows.length ? rows[0] : []
 
-  headers.map(x => (columns[x] = []))
+  headers.map((x) => (columns[x] = []))
   for (let i = 1; i < rows.length; i++) {
     for (let j = 0; j < headers.length; j++) {
       columns[headers[j]].push(rows[i][j])

diff --git a/bids-validator/src/tests/local/valid_dataset.test.ts b/bids-validator/src/tests/local/valid_dataset.test.ts
@@ -4,7 +4,7 @@ import { validatePath, formatAssertIssue } from './common.ts'
 
 const PATH = 'tests/data/valid_dataset'
 
-Deno.test('valid_dataset dataset', async t => {
+Deno.test('valid_dataset dataset', async (t) => {
   const { tree, result } = await validatePath(t, PATH)
 
   await t.step('correctly ignores .bidsignore files', () => {

diff --git a/bids-validator/src/tests/local/valid_filenames.test.ts b/bids-validator/src/tests/local/valid_filenames.test.ts
@@ -4,7 +4,7 @@ import { validatePath, formatAssertIssue } from './common.ts'
 
 const PATH = 'tests/data/valid_filenames'
 
-Deno.test('valid_filenames dataset', async t => {
+Deno.test('valid_filenames dataset', async (t) => {
   const { tree, result } = await validatePath(t, PATH)
 
   await t.step('correctly ignores .bidsignore files', () => {

diff --git a/bids-validator/src/tests/local/valid_headers.test.ts b/bids-validator/src/tests/local/valid_headers.test.ts
@@ -4,7 +4,7 @@ import { validatePath, formatAssertIssue } from './common.ts'
 
 const PATH = 'tests/data/valid_headers'
 
-Deno.test('valid_headers dataset', async t => {
+Deno.test('valid_headers dataset', async (t) => {
   const { tree, result } = await validatePath(t, PATH)
 
   await t.step('correctly ignores .bidsignore files', () => {

diff --git a/bids-validator/tests/events.spec.js b/bids-validator/tests/events.spec.js
@@ -184,6 +184,77 @@ describe('Events', function () {
       })
     })
 
+    it('should not throw an issue if a value column is annotated', () => {
+      const events = [
+        {
+          file: { path: '/sub01/sub01_task-test_events.tsv' },
+          path: '/sub01/sub01_task-test_events.tsv',
+          contents:
+            'onset\tduration\ttest\tHED\n' + '7\t3.0\tone\tSpeed/30 mph\n',
+        },
+      ]
+      const jsonDictionary = {
+        '/sub01/sub01_task-test_events.json': {
+          myCodes: {
+            test: {
+              HED: {
+                one: 'Label/#',
+              },
+            },
+          },
+        },
+        '/dataset_description.json': { HEDVersion: '8.0.0' },
+      }
+
+      return validate.Events.validateEvents(
+        events,
+        [],
+        headers,
+        jsonDictionary,
+        jsonFiles,
+        '',
+      ).then((issues) => {
+        assert.deepStrictEqual(issues, [])
+      })
+    })
+
+    it('should not throw an issue if a library schema is included', () => {
+      const events = [
+        {
+          file: { path: '/sub01/sub01_task-test_events.tsv' },
+          path: '/sub01/sub01_task-test_events.tsv',
+          contents:
+            'onset\tduration\ttest\tHED\n' + '7\t3.0\tone\tSpeed/30 mph\n',
+        },
+      ]
+
+      const jsonDictionary = {
+        '/sub01/sub01_task-test_events.json': {
+          myCodes: {
+            test: {
+              HED: {
+                one: 'ts:Sensory-presentation, Label/#',
+              },
+            },
+          },
+        },
+        '/dataset_description.json': {
+          HEDVersion: ['8.0.0', 'ts:testlib_1.0.2'],
+        },
+      }
+
+      return validate.Events.validateEvents(
+        events,
+        [],
+        headers,
+        jsonDictionary,
+        jsonFiles,
+        '',
+      ).then((issues) => {
+        assert.deepStrictEqual(issues, [])
+      })
+    })
+
     it('should throw an issue if the HED data is invalid', () => {
       const events = [
         {
@@ -218,6 +289,43 @@ describe('Events', function () {
       })
     })
 
+    it('should not throw an issue if multiple library schemas are included', () => {
+      const events = [
+        {
+          file: { path: '/sub01/sub01_task-test_events.tsv' },
+          path: '/sub01/sub01_task-test_events.tsv',
+          contents:
+            'onset\tduration\ttest\tHED\n' + '7\t3.0\tone\tSpeed/30 mph\n',
+        },
+      ]
+
+      const jsonDictionary = {
+        '/sub01/sub01_task-test_events.json': {
+          myCodes: {
+            test: {
+              HED: {
+                one: 'ts:Sensory-presentation, Label/#, sc:Sleep-deprivation',
+              },
+            },
+          },
+        },
+        '/dataset_description.json': {
+          HEDVersion: ['8.0.0', 'ts:testlib_1.0.2', 'sc:score_0.0.1'],
+        },
+      }
+
+      return validate.Events.validateEvents(
+        events,
+        [],
+        headers,
+        jsonDictionary,
+        jsonFiles,
+        '',
+      ).then((issues) => {
+        assert.deepStrictEqual(issues, [])
+      })
+    })
+
     it('should properly issue warnings when appropriate', () => {
       const events = [
         {

diff --git a/bids-validator/validators/events/hed.js b/bids-validator/validators/events/hed.js
@@ -1,6 +1,4 @@
 import hedValidator from 'hed-validator'
-import path from 'path'
-import semver from 'semver'
 import union from 'lodash/union'
 import utils from '../../utils'
 import parseTsv from '../tsv/tsvParser'
@@ -14,14 +12,24 @@ export default function checkHedStrings(events, jsonContents, jsonFiles, dir) {
   if (!hedDataExists) {
     return Promise.resolve([])
   }
-  const dataset = new hedValidator.validator.BidsDataset(eventData, sidecarData)
-  const [schemaDefinition, schemaDefinitionIssues] = parseHedVersion(
-    jsonContents,
+
+  const datasetDescription = jsonContents['/dataset_description.json']
+  const datasetDescriptionData = new hedValidator.validator.BidsJsonFile(
+    '/dataset_description.json',
+    datasetDescription,
+    getSidecarFileObject('/dataset_description.json', jsonFiles),
+  )
+  const dataset = new hedValidator.validator.BidsDataset(
+    eventData,
+    sidecarData,
+    datasetDescriptionData,
     dir,
   )
+  // New stuff end does parseHedVersion need to be called anymore?
+  const schemaDefinitionIssues = parseHedVersion(jsonContents)
   try {
     return hedValidator.validator
-      .validateBidsDataset(dataset, schemaDefinition)
+      .validateBidsDataset(dataset)
       .then((hedValidationIssues) => {
         return schemaDefinitionIssues.concat(
           convertHedIssuesToBidsIssues(hedValidationIssues),
@@ -99,24 +107,14 @@ function sidecarValueHasHed(sidecarValue) {
   )
 }
 
-function parseHedVersion(jsonContents, dir) {
-  const schemaDefinition = {}
+function parseHedVersion(jsonContents) {
   const datasetDescription = jsonContents['/dataset_description.json']
-  const issues = []
 
   if (!(datasetDescription && datasetDescription.HEDVersion)) {
-    issues.push(new Issue({ code: 109 }))
-  } else if (semver.valid(datasetDescription.HEDVersion)) {
-    schemaDefinition.version = datasetDescription.HEDVersion
+    return [new Issue({ code: 109 })]
   } else {
-    schemaDefinition.path = path.join(
-      path.resolve(dir),
-      'sourcedata',
-      datasetDescription.HEDVersion,
-    )
+    return []
   }
-
-  return [schemaDefinition, issues]
 }
 
 function internalHedValidatorIssue(error) {

diff --git a/bids-validator/validators/json/schemas/pet.json b/bids-validator/validators/json/schemas/pet.json
@@ -143,7 +143,7 @@
       "items": { "type": "number" }
     },
     "CogAtlasID": { "$ref": "common_definitions.json#/definitions/CogAtlasID" },
-    "CogPOID": { "$ref": "common_definitions.json#/definitions/CogPOID" }, 
+    "CogPOID": { "$ref": "common_definitions.json#/definitions/CogPOID" },
     "TaskName": {
       "type": "string"
     },
@@ -152,7 +152,7 @@
     },
     "Instructions": {
       "$ref": "common_definitions.json#/definitions/Instructions"
-    }       
+    }
   },
   "allOf": [
     {

diff --git a/package-lock.json b/package-lock.json