-
Notifications
You must be signed in to change notification settings - Fork 7
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
9 changed files
with
442 additions
and
16 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| import { BidsHedIssue } from '../bids' | ||
| import { generateIssue } from '../common/issues/issues' | ||
|
|
||
| export const errorBidsTests = [ | ||
| { | ||
| name: 'invalid-bids-datasets', | ||
| description: 'Who knows', | ||
| warning: false, | ||
| tests: [ | ||
| { | ||
| name: 'valid-sidecar-bad-tag-tsv', | ||
| explanation: 'Valid-sidecar, but invalid tsv', | ||
| schemaVersion: '8.3.0', | ||
| sidecar: { | ||
| event_code: { | ||
| HED: { | ||
| face: '(Red, Blue), (Green, (Yellow))', | ||
| }, | ||
| }, | ||
| }, | ||
| sidecarValid: true, | ||
| sidecarErrors: [], | ||
| eventsString: 'onset\tduration\tHED\n' + '7\t4\tBaloney', | ||
| eventsValid: false, | ||
| eventsErrors: [BidsHedIssue.fromHedIssue(generateIssue('invalidTag', {}), 'valid-sidecar-invalid-tsv.tsv')], | ||
| comboValid: false, | ||
| }, | ||
| ], | ||
| }, | ||
| ] |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,132 @@ | ||
| import chai from 'chai' | ||
| const assert = chai.assert | ||
| import { beforeAll, describe, afterAll } from '@jest/globals' | ||
| import path from 'path' | ||
| import { BidsHedIssue } from '../bids/types/issues' | ||
| import { buildSchemas } from '../validator/schema/init' | ||
| import { SchemaSpec, SchemasSpec } from '../common/schema/types' | ||
| import { BidsDataset, BidsEventFile, BidsHedTsvValidator, BidsSidecar, BidsTsvFile } from '../bids' | ||
| import { generateIssue, IssueError } from '../common/issues/issues' | ||
|
|
||
| import { HedStringTokenizerOriginal } from '../parser/tokenizerOriginal' | ||
| import { HedStringTokenizer } from '../parser/tokenizer' | ||
| import { passingBidsTests } from './bidsPassingData' | ||
| import { BidsHedTsvParser } from '../bids/validator/bidsHedTsvValidator' | ||
| import parseTSV from '../bids/tsvParser' | ||
| const fs = require('fs') | ||
|
|
||
| const displayLog = process.env.DISPLAY_LOG === 'true' | ||
|
|
||
| const skippedErrors = {} | ||
|
|
||
| describe('HED tokenizer validation', () => { | ||
| const schemaMap = new Map([ | ||
| ['8.2.0', undefined], | ||
| ['8.3.0', undefined], | ||
| ]) | ||
|
|
||
| const badLog = [] | ||
| let totalTests = 0 | ||
| let wrongErrors = 0 | ||
| let unexpectedErrors = 0 | ||
|
|
||
| beforeAll(async () => { | ||
| const spec2 = new SchemaSpec('', '8.2.0', '', path.join(__dirname, '../tests/data/HED8.2.0.xml')) | ||
| const specs2 = new SchemasSpec().addSchemaSpec(spec2) | ||
| const schemas2 = await buildSchemas(specs2) | ||
| const spec3 = new SchemaSpec('', '8.3.0', '', path.join(__dirname, '../tests/data/HED8.3.0.xml')) | ||
| const specs3 = new SchemasSpec().addSchemaSpec(spec3) | ||
| const schemas3 = await buildSchemas(specs3) | ||
| schemaMap.set('8.2.0', schemas2) | ||
| schemaMap.set('8.3.0', schemas3) | ||
| }) | ||
|
|
||
| afterAll(() => { | ||
| const outBad = path.join(__dirname, 'runLog.txt') | ||
| const summary = `Total tests:${totalTests} Unexpected errors:${unexpectedErrors}\n` | ||
| if (displayLog) { | ||
| fs.writeFileSync(outBad, summary + badLog.join('\n'), 'utf8') | ||
| } | ||
| }) | ||
|
|
||
| describe('BIDS validation - validData', () => { | ||
| const badLog = [] | ||
| let totalTests = 0 | ||
| let unexpectedErrors = 0 | ||
|
|
||
| beforeAll(async () => {}) | ||
|
|
||
| afterAll(() => { | ||
| const outBad = path.join(__dirname, 'runLog.txt') | ||
| const summary = `Total tests:${totalTests} Unexpected errors:${unexpectedErrors}\n` | ||
| if (displayLog) { | ||
| fs.writeFileSync(outBad, summary + badLog.join('\n'), 'utf8') | ||
| } | ||
| }) | ||
|
|
||
| describe.each(passingBidsTests)('$name : $description', ({ tests }) => { | ||
| let itemLog | ||
|
|
||
| const assertErrors = function (header, issues, iLog) { | ||
| iLog.push(`${header}\n`) | ||
| totalTests += 1 | ||
|
|
||
| let errors = [] | ||
| if (issues.length > 0) { | ||
| errors = issues.map((item) => item.hedIssue.hedCode) // list of hedCodes in the issues | ||
| } | ||
| const errorString = errors.join(',') | ||
| if (errors.length > 0) { | ||
| iLog.push(`---expected no errors but got errors [${errorString}]\n`) | ||
| unexpectedErrors += 1 | ||
| assert(errors.length === 0, `${header}---expected no errors but got errors [${errorString}]`) | ||
| } | ||
| } | ||
|
|
||
| const validate = function (test, iLog) { | ||
| // Make sure that the schema is available | ||
| const header = `\n[${test.name} (Expect pass)]` | ||
| const thisSchema = schemaMap.get(test.schemaVersion) | ||
| assert(thisSchema !== undefined, `${test.schemaVersion} is not available in test ${test.name}`) | ||
|
|
||
| // Validate the sidecar by itself | ||
| const sidecarName = test.name + '.json' | ||
| const bidsSidecar = new BidsSidecar('thisOne', test.sidecar, { relativePath: sidecarName, path: sidecarName }) | ||
| assert(bidsSidecar instanceof BidsSidecar, 'Test') | ||
| const sidecarIssues = bidsSidecar.validate(thisSchema) | ||
| assertErrors(header + ':Validating just the sidecar', sidecarIssues, iLog) | ||
|
|
||
| // Parse the events file | ||
| const eventName = test.name + '.tsv' | ||
| const parsedTsv = parseTSV(test.eventsString) | ||
| assert(parsedTsv instanceof Map, `${eventName} cannot be parsed`) | ||
|
|
||
| // Validate the events file by itself | ||
| const bidsTsv = new BidsTsvFile(test.name, parsedTsv, { relativePath: 'eventName' }, [], {}) | ||
| const validator = new BidsHedTsvValidator(bidsTsv, thisSchema) | ||
| validator.validate() | ||
| assertErrors(header + ':Parsing events alone', validator.issues, iLog) | ||
|
|
||
| // Validate the events file with the sidecar | ||
| const bidsTsvSide = new BidsTsvFile(test.name, parsedTsv, { relativePath: 'eventName' }, [], bidsSidecar) | ||
| const validatorSide = new BidsHedTsvValidator(bidsTsvSide, thisSchema) | ||
| validatorSide.validate() | ||
| assertErrors(header + ':Parsing events with ', validatorSide.issues, iLog) | ||
| } | ||
|
|
||
| beforeAll(async () => { | ||
| itemLog = [] | ||
| }) | ||
|
|
||
| afterAll(() => { | ||
| badLog.push(itemLog.join('\n')) | ||
| }) | ||
|
|
||
| if (tests && tests.length > 0) { | ||
| test.each(tests)('BIDS: %s ', (test) => { | ||
| validate(test, itemLog) | ||
| }) | ||
| } | ||
| }) | ||
| }) | ||
| }) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| import { BidsHedIssue } from '../bids' | ||
| import { generateIssue } from '../common/issues/issues' | ||
|
|
||
| export const bidsTestData = [ | ||
| // { | ||
| // name: 'valid-bids-datasets', | ||
| // description: 'Who knows', | ||
| // tests: [ | ||
| // { | ||
| // name: 'no-hed-at-all', | ||
| // explanation: 'Neither the sidecar or tsv has HED', | ||
| // schemaVersion: '8.3.0', | ||
| // sidecar: { | ||
| // duration: { | ||
| // description: 'Duration of the event in seconds.', | ||
| // }, | ||
| // }, | ||
| // eventsString: 'onset\tduration\n' + '7\t4', | ||
| // sidecarOnlyErrors: [], | ||
| // eventsOnlyErrors: [], | ||
| // comboErrors: [] | ||
| // }, | ||
| // { | ||
| // name: 'only-header-in-tsv', | ||
| // explanation: 'TSV only has header and some extra white space', | ||
| // schemaVersion: '8.3.0', | ||
| // sidecar: { | ||
| // duration: { | ||
| // description: 'Duration of the event in seconds.', | ||
| // }, | ||
| // }, | ||
| // eventsString: 'onset\tduration\n', | ||
| // sidecarOnlyErrors: [], | ||
| // eventsOnlyErrors: [], | ||
| // comboErrors: [] | ||
| // }, | ||
| // ] | ||
| // }, | ||
| { | ||
| name: 'invalid-bids-datasets', | ||
| description: 'Who knows this', | ||
| tests: [ | ||
| { | ||
| name: 'valid-sidecar-bad-tag-tsv', | ||
| explanation: 'Valid-sidecar, but invalid tsv', | ||
| schemaVersion: '8.3.0', | ||
| sidecar: { | ||
| event_code: { | ||
| HED: { | ||
| face: '(Red, Blue), (Green, (Yellow))', | ||
| }, | ||
| }, | ||
| }, | ||
| eventsString: 'onset\tduration\tHED\n' + '7\t4\tBaloney', | ||
| sidecarOnlyErrors: [], | ||
| eventsOnlyErrors: [ | ||
| BidsHedIssue.fromHedIssue( | ||
| generateIssue('invalidTag', { tag: 'Baloney' }), | ||
| { relativePath: 'valid-sidecar-bad-tag-tsv.tsv' }, | ||
| { tsvLine: 2 }, | ||
| ), | ||
| ], | ||
| comboErrors: [ | ||
| BidsHedIssue.fromHedIssue( | ||
| generateIssue('invalidTag', { tag: 'Baloney' }), | ||
| { relativePath: 'valid-sidecar-bad-tag-tsv.tsv' }, | ||
| { tsvLine: 2 }, | ||
| ), | ||
| ], | ||
| }, | ||
| ], | ||
| }, | ||
| ] |
Oops, something went wrong.