Improve readDir tests and fix harmonizeRelativePath for Windows

bids-validator/tests/bids.spec.js

@@ -51,13 +51,16 @@ function assertErrorCode(errors, expected_error_code) {
   assert(matchingErrors.length > 0)
 }
 
+// Default validate.BIDS options
+const options = { ignoreNiftiHeaders: true, json: true }
+const enableNiftiHeaders = { json: true }
+
 describe('BIDS example datasets ', function() {
   describe('basic example dataset tests', () => {
     getDirectories(
       dataDirectory + 'bids-examples-' + global.test_version + '/',
     ).forEach(function testDataset(path) {
       it(path, isdone => {
-        const options = { ignoreNiftiHeaders: true }
         validate.BIDS(createExampleFileList(path), options, function(issues) {
           var warnings = issues.warnings
           var session_flag = false
@@ -80,7 +83,6 @@ describe('BIDS example datasets ', function() {
 
   // we need to have at least one non-dynamic test
   it('validates path without trailing backslash', function(isdone) {
-    var options = { ignoreNiftiHeaders: true }
     validate.BIDS(createExampleFileList('ds001'), options, function(
       issues,
       summary,
@@ -106,67 +108,69 @@ describe('BIDS example datasets ', function() {
 
   // we need to have at least one non-dynamic test
   it('validates dataset with valid nifti headers', function(isdone) {
-    var options = { ignoreNiftiHeaders: false }
-    validate.BIDS(createDatasetFileList('valid_headers'), options, function(
-      issues,
-      summary,
-    ) {
-      var errors = issues.errors
-      var warnings = issues.warnings
-      assert(summary.sessions.length === 0)
-      assert(summary.subjects.length === 1)
-      assert.deepEqual(summary.tasks, ['rhyme judgment'])
-      assert(summary.modalities.includes('T1w'))
-      assert(summary.modalities.includes('bold'))
-      assert(summary.totalFiles === 8)
-      assert(
-        errors.findIndex(error => error.code === 60) > -1,
-        'errors do not contain a code 60',
-      )
-      assert.deepEqual(warnings.length, 4)
-      assert(
-        warnings.findIndex(warning => warning.code === 13) > -1,
-        'warnings do not contain a code 13',
-      )
-      isdone()
-    })
+    validate.BIDS(
+      createDatasetFileList('valid_headers'),
+      enableNiftiHeaders,
+      function(issues, summary) {
+        var errors = issues.errors
+        var warnings = issues.warnings
+        assert(summary.sessions.length === 0)
+        assert(summary.subjects.length === 1)
+        assert.deepEqual(summary.tasks, ['rhyme judgment'])
+        assert(summary.modalities.includes('T1w'))
+        assert(summary.modalities.includes('bold'))
+        assert(summary.totalFiles === 8)
+        assert(
+          errors.findIndex(error => error.code === 60) > -1,
+          'errors do not contain a code 60',
+        )
+        assert.deepEqual(warnings.length, 4)
+        assert(
+          warnings.findIndex(warning => warning.code === 13) > -1,
+          'warnings do not contain a code 13',
+        )
+        isdone()
+      },
+    )
   })
 
   // test for duplicate files present with both .nii and .nii.gz extension
   it('validates dataset for duplicate files present with both .nii and .nii.gz extension', function(isdone) {
-    var options = { ignoreNiftiHeaders: false }
-    validate.BIDS(createDatasetFileList('valid_filenames'), options, function(
-      issues,
-    ) {
-      assertErrorCode(issues.errors, 74)
-      isdone()
-    })
+    validate.BIDS(
+      createDatasetFileList('valid_filenames'),
+      enableNiftiHeaders,
+      function(issues) {
+        assertErrorCode(issues.errors, 74)
+        isdone()
+      },
+    )
   })
 
   // test for illegal characters used in acq and task name
   it('validates dataset with illegal characters in task name', function(isdone) {
-    var options = { ignoreNiftiHeaders: false }
-    validate.BIDS(createDatasetFileList('valid_filenames'), options, function(
-      issues,
-    ) {
-      assertErrorCode(issues.errors, 58)
-      isdone()
-    })
+    validate.BIDS(
+      createDatasetFileList('valid_filenames'),
+      enableNiftiHeaders,
+      function(issues) {
+        assertErrorCode(issues.errors, 58)
+        isdone()
+      },
+    )
   })
 
   // test for illegal characters used in sub name
   it('validates dataset with illegal characters in sub name', function(isdone) {
-    var options = { ignoreNiftiHeaders: false }
-    validate.BIDS(createDatasetFileList('valid_filenames'), options, function(
-      issues,
-    ) {
-      assertErrorCode(issues.errors, 64)
-      isdone()
-    })
+    validate.BIDS(
+      createDatasetFileList('valid_filenames'),
+      enableNiftiHeaders,
+      function(issues) {
+        assertErrorCode(issues.errors, 64)
+        isdone()
+      },
+    )
   })
 
   it('checks for subjects with no valid data', function(isdone) {
-    var options = { ignoreNiftiHeaders: true }
     validate.BIDS(createDatasetFileList('no_valid_data'), options, function(
       issues,
     ) {
@@ -176,7 +180,6 @@ describe('BIDS example datasets ', function() {
   })
 
   it('validates MRI modalities', function(isdone) {
-    var options = { ignoreNiftiHeaders: true }
     validate.BIDS(createExampleFileList('ds001'), options, function(
       issues,
       summary,
@@ -201,7 +204,6 @@ describe('BIDS example datasets ', function() {
   })
 
   it('checks for data dictionaries without corresponding data files', function(isdone) {
-    var options = { ignoreNiftiHeaders: true }
     validate.BIDS(createDatasetFileList('unused_data_dict'), options, function(
       issues,
     ) {
@@ -211,7 +213,6 @@ describe('BIDS example datasets ', function() {
   })
 
   it('checks for fieldmaps with no _magnitude file', function(isdone) {
-    var options = { ignoreNiftiHeaders: true }
     validate.BIDS(
       createDatasetFileList('fieldmap_without_magnitude'),
       options,
@@ -223,7 +224,6 @@ describe('BIDS example datasets ', function() {
   })
 
   it('should not throw a warning if all _phasediff.nii are associated with _magnitude1.nii', function(isdone) {
-    var options = { ignoreNiftiHeaders: true }
     validate.BIDS(createExampleFileList('hcp_example_bids'), options, function(
       issues,
     ) {
@@ -233,7 +233,6 @@ describe('BIDS example datasets ', function() {
   })
 
   it('should throw a warning if there are _phasediff.nii without an associated _magnitude1.nii', function(isdone) {
-    var options = { ignoreNiftiHeaders: true }
     validate.BIDS(
       createDatasetFileList('phasediff_without_magnitude1'),
       options,

bids-validator/tests/data/symlinked_subject/CHANGES

@@ -0,0 +1,3 @@
+1.0.0 2011-10-06
+
+  -  initial release

bids-validator/tests/data/symlinked_subject/README

@@ -0,0 +1,16 @@
+This dataset was obtained from the OpenfMRI project (http://www.openfmri.org).
+Accession #: ds003
+Description: Rhyme judgment
+
+Release history:
+10/06/2011: initial release
+3/21/2013: Updated release with QA information
+
+This dataset is made available under the Public Domain Dedication and License 
+v1.0, whose full text can be found at 
+http://www.opendatacommons.org/licenses/pddl/1.0/. 
+We hope that all users will follow the ODC Attribution/Share-Alike 
+Community Norms (http://www.opendatacommons.org/norms/odc-by-sa/); 
+in particular, while not legally required, we hope that all users 
+of the data will acknowledge the OpenfMRI project and NSF Grant 
+OCI-1131441 (R. Poldrack, PI) in any publications.

bids-validator/tests/data/symlinked_subject/dataset_description.json

@@ -0,0 +1,5 @@
+{
+    "License": "This dataset is made available under the Public Domain Dedication and License \nv1.0, whose full text can be found at \nhttp://www.opendatacommons.org/licenses/pddl/1.0/. \nWe hope that all users will follow the ODC Attribution/Share-Alike \nCommunity Norms (http://www.opendatacommons.org/norms/odc-by-sa/); \nin particular, while not legally required, we hope that all users \nof the data will acknowledge the OpenfMRI project and NSF Grant \nOCI-1131441 (R. Poldrack, PI) in any publications.",
+    "Name": "Rhyme judgment",
+    "BIDSVersion": "1.0.1"
+}

bids-validator/tests/data/symlinked_subject/participants.tsv

@@ -0,0 +1,2 @@
+participant_id	sex	age
+sub-01	M	25

bids-validator/tests/data/symlinked_subject/sub-01

@@ -0,0 +1 @@
+../valid_filenames/sub-01/

bids-validator/tests/data/symlinked_subject/task-rhymejudgment_bold.json

@@ -0,0 +1,4 @@
+{
+    "RepetitionTime": 1.0,
+    "TaskName": "rhyme judgment"
+}

bids-validator/tests/env/load-examples.js

@@ -26,9 +26,6 @@ const loadExamples = async () => {
         test_version +
         '.zip',
     )
-    if (!fs.existsSync('bids-validator/tests/data')) {
-      fs.mkdirSync('bids-validator/tests/data')
-    }
     fs.writeFileSync('bids-validator/tests/data/examples.zip', response.body)
     const zip = new AdmZip('bids-validator/tests/data/examples.zip')
     console.log('unzipping test data')

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

@@ -0,0 +1,60 @@
+/**
+ * @jest-environment ./bids-validator/tests/env/ExamplesEnvironment.js
+ */
+const readDir = require('../readDir.js').default
+
+describe('readDir.js - examples integration', () => {
+  describe('readDir()', () => {
+    it('returns expected files', async done => {
+      readDir('bids-validator/tests/data/bids-examples-1.2.0/ds002/').then(
+        files => {
+          expect(Object.keys(files)).toHaveLength(245)
+          expect(files[0].name).toBe('CHANGES')
+          expect(files[25].name).toBe(
+            'sub-02_task-mixedeventrelatedprobe_run-01_events.tsv',
+          )
+          expect(files[200].name).toBe('sub-15_T1w.nii.gz')
+          done()
+        },
+      )
+    })
+    it('correctly follows symlinks for subjects with followSymbolicLink: true', async done => {
+      readDir('bids-validator/tests/data/symlinked_subject', {
+        followSymbolicDirectories: true,
+      }).then(files => {
+        expect(Object.keys(files)).toHaveLength(12)
+        expect(Object.values(files).map(f => f.name)).toEqual([
+          'CHANGES',
+          'README',
+          'dataset_description.json',
+          'participants.tsv',
+          'sub-01_T1w.nii',
+          'sub-01_T1w.nii.gz',
+          'sub-0-1_task-rhymejudgment_bold.nii.gz',
+          'sub-01_task-rhyme-judgment_bold.nii.gz',
+          'sub-01_task-rhyme-judgment_events.tsv',
+          'sub-01_task-rhyme_judgment_bold.nii.gz',
+          'sub-01_task-rhyme_judgment_events.tsv',
+          'task-rhymejudgment_bold.json',
+        ])
+        done()
+      })
+    })
+    it('correctly does not follow symlinks for subjects with followSymbolicLink: false', async done => {
+      readDir('bids-validator/tests/data/symlinked_subject', {
+        followSymbolicDirectories: false,
+      }).then(files => {
+        expect(Object.keys(files)).toHaveLength(6)
+        expect(Object.values(files).map(f => f.name)).toEqual([
+          'CHANGES',
+          'README',
+          'dataset_description.json',
+          'participants.tsv',
+          'sub-01',
+          'task-rhymejudgment_bold.json',
+        ])
+        done()
+      })
+    })
+  })
+})

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

@@ -1,22 +1,45 @@
-/**
- * @jest-environment ./bids-validator/tests/env/ExamplesEnvironment.js
- */
 const readDir = require('../readDir.js')
 
 describe('readDir.js', () => {
-  describe('getFiles()', () => {
-    it('returns expected files', async done => {
-      readDir('bids-validator/tests/data/bids-examples-1.2.0/ds002/').then(
-        files => {
-          expect(Object.keys(files)).toHaveLength(245)
-          expect(files[0].name).toBe('CHANGES')
-          expect(files[25].name).toBe(
-            'sub-02_task-mixedeventrelatedprobe_run-01_events.tsv',
-          )
-          expect(files[200].name).toBe('sub-15_T1w.nii.gz')
-          done()
+  describe('fileArrayToObject', () => {
+    it('transforms an array to an object', () => {
+      expect(
+        readDir.fileArrayToObject([
+          { name: 'one' },
+          { name: 'two' },
+          { name: 'three' },
+        ]),
+      ).toEqual({
+        '0': {
+          name: 'one',
         },
+        '1': {
+          name: 'two',
+        },
+        '2': {
+          name: 'three',
+        },
+      })
+    })
+  })
+  describe('harmonizeRelativePath', () => {
+    it('harmonizes a basic POSIX path', () => {
+      expect(readDir.harmonizeRelativePath('test/a/path')).toEqual('/a/path')
+    })
+    it('does not mangle absolute Windows paths', () => {
+      expect(readDir.harmonizeRelativePath('C:\\dataset\\directory')).toEqual(
+        '/dataset/directory',
+      )
+    })
+    it('does not mangle relative Windows paths', () => {
+      expect(readDir.harmonizeRelativePath('dataset\\directory')).toEqual(
+        '/directory',
       )
     })
+    it('does not mangle relative Windows paths with parent directories', () => {
+      expect(
+        readDir.harmonizeRelativePath('..\\..\\dataset\\directory'),
+      ).toEqual('/../dataset/directory')
+    })
   })
 })

bids-validator/utils/files/index.js

@@ -4,7 +4,7 @@ const FileAPI = require('./FileAPI')
 const newFile = require('./newFile')
 const readFile = require('./readFile')
 const readNiftiHeader = require('./readNiftiHeader')
-const readDir = require('./readDir')
+const readDir = require('./readDir').default
 const potentialLocations = require('./potentialLocations')
 const generateMergedSidecarDict = require('./generateMergedSidecarDict')
 const getBFileContent = require('./getBFileContent')