run node tests in github actions

.eslintignore

@@ -0,0 +1,2 @@
+node_modules/
+dist/

.github/workflows/node_tests.yml

@@ -0,0 +1,48 @@
+name: Node Tests
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+        node: [14]
+
+    runs-on: ${{ matrix.platform }}
+
+    steps:
+      - name: Set git to use LF
+        run: |
+          git config --global core.autocrlf false
+          git config --global core.eol lf
+      - uses: actions/checkout@v2
+      - uses: actions/setup-node@v2
+        with:
+          node-version: "14"
+          cache: "npm"
+      - name: Set git name/email
+        run: |
+          git config --global user.email "bids.maintenance@gmail.com"
+          git config --global user.name "bids-maintenance"
+      - name: Set up Node
+        run: |
+          npm install -g npm@^7
+          npm install
+      - name: Eslint
+        run: npm run lint
+      - name: Get bids-examples data
+        run: git submodule update --init
+      - name: Jest tests
+        run: npm run coverage -- --maxWorkers=2 --testTimeout=10000 --colors
+      - name: Upload to codecov
+        run: npm run codecov
+      - name: Smoke tests
+        run: |
+          bids-validator/bin/bids-validator bids-validator/tests/data/valid_headers/ --ignoreNiftiHeaders
+          bids-validator/bin/bids-validator bids-validator/tests/data/valid_headers/ --ignoreNiftiHeaders --json

bids-validator/bids_validator/rules/top_level_rules.json

@@ -51,9 +51,7 @@
   "pet_top": {
     "regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:trc-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:task-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?(@@@_pet_suffixes_@@@)\\.json$",
     "tokens": {
-      "@@@_pet_suffixes_@@@": [
-        "pet"
-      ]
+      "@@@_pet_suffixes_@@@": ["pet"]
     }
   },
 

bids-validator/cli.js

@@ -8,7 +8,7 @@ import colors from 'colors/safe'
 import fs from 'fs'
 import { filenamesOnly } from './utils/filenamesOnly.js'
 
-const errorToString = (err) => {
+const errorToString = err => {
   if (err instanceof Error) return err.stack
   else if (typeof err === 'object') return JSON.parse(err)
   else return err
@@ -39,7 +39,7 @@ export function cli(argumentOverride) {
     const argv = parseOptions(argumentOverride)
     const dir = argv._[0]
     const options = argv
-    process.on('unhandledRejection', (err) => {
+    process.on('unhandledRejection', err => {
       console.log(
         format.unexpectedError(
           // eslint-disable-next-line
@@ -61,7 +61,7 @@ export function cli(argumentOverride) {
       reject(2)
     }
 
-    validate.BIDS(dir, options, function (issues, summary) {
+    validate.BIDS(dir, options, function(issues, summary) {
       function resolveOrReject() {
         if (
           issues === 'Invalid' ||

bids-validator/utils/__tests__/filenamesOnly.spec.js

@@ -2,6 +2,7 @@ import { validateFilenames } from '../filenamesOnly.js'
 
 describe('test filenames mode', () => {
   beforeEach(() => {
+    // eslint-disable-next-line
     console.log = jest.fn()
   })
   it('throws an error when obviously non-BIDS input', async () => {

bids-validator/utils/__tests__/gitTreeMode.spec.js

@@ -87,36 +87,41 @@ describe('gitTreeMode functions', () => {
           size: 1,
         },
       ]
-      const expected = [
-        {
-          path: '/path/to/dataset/path/to/a',
-          size: 100,
-          relativePath: '/path/to/a',
-          name: 'a',
-        },
-        {
-          path: '/path/to/dataset/path/to/b',
-          size: 99,
-          relativePath: '/path/to/b',
-          name: 'b',
-        },
-        {
-          path: '/path/to/dataset/path/to/c',
-          size: 98,
-          relativePath: '/path/to/c',
-          name: 'c',
-        },
-        {
-          path: '/path/to/dataset/path/to/d',
-          size: 1,
-          relativePath: '/path/to/d',
-          name: 'd',
-        },
-      ]
+      /* Not currently in use.
+        const expected = [
+          {
+            path: '/path/to/dataset/path/to/a',
+            size: 100,
+            relativePath: '/path/to/a',
+            name: 'a',
+          },
+          {
+            path: '/path/to/dataset/path/to/b',
+            size: 99,
+            relativePath: '/path/to/b',
+            name: 'b',
+          },
+          {
+            path: '/path/to/dataset/path/to/c',
+            size: 98,
+            relativePath: '/path/to/c',
+            name: 'c',
+          },
+          {
+            path: '/path/to/dataset/path/to/d',
+            size: 1,
+            relativePath: '/path/to/d',
+            name: 'd',
+          },
+        ]
+      */
       const output = processFiles('/path/to/dataset', ig, filesA, filesB)
       const fileNames = output.map(file => file.name)
       assert(!fileNames.includes('.DS_Store'), 'filters out ignored files')
-      assert(!fileNames.includes('derivative_file'), 'filters out ignored directories',)
+      assert(
+        !fileNames.includes('derivative_file'),
+        'filters out ignored directories',
+      )
       assert.deepEqual(fileNames, ['a', 'b', 'c', 'd'], 'aggregates files')
       assert.isString(output[0].relativePath, 'adds relativePath to files')
       assert.isString(output[1].relativePath, 'adds name to files')

bids-validator/utils/__tests__/unit.spec.js

@@ -9,7 +9,11 @@ describe('unit validator', () => {
       const goodOutput = unit.validate(validRoot)
       expect(goodOutput.isValid).toBe(true)
     })
-    const invalidRoots = ['definitielynotavalidroot', `%/${validRoot}`, `n/a*${validRoot}`]
+    const invalidRoots = [
+      'definitielynotavalidroot',
+      `%/${validRoot}`,
+      `n/a*${validRoot}`,
+    ]
     invalidRoots.forEach(invalidRoot => {
       const badOutput = unit.validate(invalidRoot)
       expect(badOutput.isValid).toBe(false)
@@ -25,7 +29,14 @@ describe('unit validator', () => {
     expect(badOutput.isValid).toBe(false)
   })
 
-  const validExponents = ['^2', '^543', '¹²³', ...unit.superscriptNumbers.slice(0, 3), '^-2', '⁻³']
+  const validExponents = [
+    '^2',
+    '^543',
+    '¹²³',
+    ...unit.superscriptNumbers.slice(0, 3),
+    '^-2',
+    '⁻³',
+  ]
   it('handles simple units with exponents', () => {
     validExponents.forEach(exp => {
       const goodOutput = unit.validate(validRoot + exp)

bids-validator/utils/files/__tests__/readDir-examples.spec.js

@@ -12,7 +12,7 @@ describe('readDir.js - examples integration', () => {
           'sub-02_task-mixedeventrelatedprobe_run-01_bold.nii.gz',
         )
         expect(filenames[200]).toBe(
-          'sub-14_task-probabilisticclassification_run-02_events.tsv'
+          'sub-14_task-probabilisticclassification_run-02_events.tsv',
         )
         done()
       })

bids-validator/utils/files/generateMergedSidecarDict.js

@@ -13,7 +13,9 @@ function generateMergedSidecarDict(potentialSidecars, jsonContents) {
     const jsonObject = jsonContents[sidecarName]
     if (jsonObject) {
       for (var key in jsonObject) {
-        mergedDictionary[key] = jsonObject[key]
+        if (jsonObject.hasOwnProperty(key)) {
+          mergedDictionary[key] = jsonObject[key]
+        }
       }
     } else if (jsonObject === null) {
       mergedDictionary.invalid = true

bids-validator/utils/files/readDir.js

@@ -114,7 +114,7 @@ async function preprocessNode(dir, ig, options) {
  * @returns {string[]}
  */
 const getGitLsTree = (cwd, gitRef) =>
-  new Promise((resolve, reject) => {
+  new Promise(resolve => {
     let output = ''
     const gitProcess = child_proccess.spawn(
       'git',
@@ -181,10 +181,14 @@ const readLsTreeLines = gitTreeLines =>
 const getGitCatFile = (cwd, input) =>
   new Promise(resolve => {
     let output = ''
-    const gitProcess = spawn('git', ['cat-file', '--batch', '--buffer'], {
-      cwd,
-      encoding: 'utf-8',
-    })
+    const gitProcess = child_proccess.spawn(
+      'git',
+      ['cat-file', '--batch', '--buffer'],
+      {
+        cwd,
+        encoding: 'utf-8',
+      },
+    )
 
     // pass in symlink objects
     gitProcess.stdin.write(input)

bids-validator/utils/issues/index.js

@@ -86,6 +86,9 @@ var issues = {
 
     // organize by severity
     for (const codePropertyName in categorized) {
+      if (!categorized.hasOwnProperty(codePropertyName)) {
+        continue
+      }
       // Properties are always strings but error codes are always integers
       const code = parseInt(codePropertyName)
       issue = categorized[code]

bids-validator/utils/issues/list.js

@@ -712,7 +712,8 @@ export default {
   139: {
     key: 'BLACKLISTED_MODALITY',
     severity: 'error',
-    reason: 'Found a modality that has been blacklisted through validator configuration.',
+    reason:
+      'Found a modality that has been blacklisted through validator configuration.',
   },
   140: {
     key: '140_EMPTY',

bids-validator/utils/summary/__tests__/collectSubjectMetadata.spec.js

@@ -4,10 +4,12 @@ const CRLFParticipantsTsv = 'participant_id\tsex\tage\r\nsub-01\tM\t25\r\n'
 
 describe('collectSubjectMetadata()', () => {
   it('handles Windows newline characters in column row', () => {
-    expect(collectSubjectMetadata(CRLFParticipantsTsv)).toEqual([{
-      age: 25,
-      participantId: '01',
-      sex: 'M',
-    }])
+    expect(collectSubjectMetadata(CRLFParticipantsTsv)).toEqual([
+      {
+        age: 25,
+        participantId: '01',
+        sex: 'M',
+      },
+    ])
   })
 })

bids-validator/utils/summary/collectSessions.js

@@ -1,6 +1,6 @@
 import type from '../type'
 
-const collectSessions = (fileList, options) => {
+const collectSessions = fileList => {
   const sessions = []
   Object.keys(fileList).forEach(key => {
     const file = fileList[key]

bids-validator/utils/summary/collectSubjects.js

@@ -1,6 +1,6 @@
 import type from '../type'
 
-const collectSubjects = (fileList, options) => {
+const collectSubjects = fileList => {
   const subjects = []
   const fileKeys = Object.keys(fileList)
   fileKeys.forEach(key => {

bids-validator/validators/bids/__tests__/checkDatasetDescription.spec.js

@@ -60,9 +60,9 @@ describe('checkDatasetDescription', () => {
   })
   describe('checkGeneticDatabaseField', () => {
     it('returns code 128 when there is no Genetics.Dataset with a genetic_info.json present', () => {
-       const invalidJsonContentsDict = {
-        '/dataset_description.json': { },
-        '/genetic_info.json': { }
+      const invalidJsonContentsDict = {
+        '/dataset_description.json': {},
+        '/genetic_info.json': {},
       }
       let issues = checkDatasetDescription(invalidJsonContentsDict)
       assert(
@@ -71,19 +71,18 @@ describe('checkDatasetDescription', () => {
       )
     })
     it('does not return code 128 when GeneticDataset field and genetic_info.json present', () => {
-       const validJsonContentsDict = {
+      const validJsonContentsDict = {
         '/dataset_description.json': {
           Authors: ['Benny', 'the Jets'],
-          Genetics: {Dataset: 'GeneticGeneticDataset'},
+          Genetics: { Dataset: 'GeneticGeneticDataset' },
         },
-        '/genetic_info.json': { }
+        '/genetic_info.json': {},
       }
       let issues = checkDatasetDescription(validJsonContentsDict)
       assert(
         issues.findIndex(issue => issue.code === 128) === -1,
-        'issues does not include a code 128'
+        'issues does not include a code 128',
       )
     })
-
   })
 })

bids-validator/validators/bids/fullTest.js

@@ -56,8 +56,8 @@ const fullTest = (fileList, options, annexed, dir, schema, callback) => {
           new Issue({
             file: mod,
             evidence: `found ${mod} files`,
-            code: 139
-          })
+            code: 139,
+          }),
         )
       }
     })

bids-validator/validators/bids/start.js

@@ -26,7 +26,7 @@ const start = (dir, options, callback) => {
     console.log(`bids-specification@${options.schema}`)
   }
 
-  utils.options.parse(dir, options, async function (issues, options) {
+  utils.options.parse(dir, options, async function(issues, options) {
     if (issues && issues.length > 0) {
       // option parsing issues
       callback({ config: issues })

bids-validator/validators/json/json.js

@@ -114,7 +114,7 @@ const selectSchema = file => {
       file.name.endsWith('NLO.json') ||
       file.name.endsWith('OCT.json') ||
       file.name.endsWith('SPIM.json')
-      ) {
+    ) {
       schema = require('./schemas/microscopy.json')
     } else if (
       file.relativePath.includes('/meg/') &&