Merge pull request #631 from olgn/fix-missing-trims

Fix missing trims

Author: chrisgorgo

tests/bids.spec.js

@@ -147,19 +147,6 @@ describe('BIDS example datasets ', function() {
     })
   })
 
-  it('checks for tabular files with custom columns not described in a data dictionary', function(isdone) {
-    var options = { ignoreNiftiHeaders: true }
-    validate.BIDS(
-      'tests/data/bids-examples-' + global.test_version + '/ds001',
-      //'tests/data/ds001344-1.0.0',
-      options,
-      function(issues) {
-        assert(issues.warnings.length === 2 && issues.warnings[1].code === '82')
-        isdone()
-      },
-    )
-  })
-
   it('validates MRI modalities', function(isdone) {
     var options = { ignoreNiftiHeaders: true }
     validate.BIDS(

validators/events.js

@@ -85,7 +85,7 @@ const checkDesignLength = function(events, headers, jsonContents) {
         .filter(row => !(!row || /^\s*$/.test(row)))
 
       // get the 'onset' field of the last event (lastEventOnset)
-      const lastEventOnset = rows[rows.length - 1].split('\t')[0]
+      const lastEventOnset = rows[rows.length - 1].trim().split('\t')[0]
 
       // check if lastEventOnset > longDurationThreshold - append issue if so
       if (lastEventOnset > longDurationThreshold) {

validators/tsv/__tests__/validateTsvColumns.spec.js

@@ -0,0 +1,58 @@
+const assert = require('chai').assert
+const validateTsvColumns = require('../validateTsvColumns')
+
+describe('validateTsvColumns', () => {
+  const file = {
+    name: 'participants.tsv',
+    relativePath: '/participants.tsv',
+  }
+  const jsonContentsDict = {
+    '/participants.json': { NewColumn: 'description' },
+  }
+
+  it('allows for tabular files with columns that are described in the bids spec', () => {
+    const tsvs = [
+      {
+        contents: 'participant_id\n',
+        file: file,
+      },
+    ]
+    const issues = validateTsvColumns(tsvs, {})
+    assert.lengthOf(issues, 0)
+  })
+  it('checks for tabular files with custom columns not described in a data dictionary', () => {
+    const tsvs = [
+      {
+        contents: 'header1\n',
+        file: file,
+      },
+    ]
+    const issues = validateTsvColumns(tsvs, {})
+    assert.lengthOf(issues, 1)
+    assert.equal(issues[0].code, 82)
+  })
+  it('allows custom columns if they are described in a data dictionary', () => {
+    const tsvs = [
+      {
+        contents: 'NewColumn\n',
+        file: file,
+      },
+    ]
+    const issues = validateTsvColumns(tsvs, jsonContentsDict)
+    assert.lengthOf(issues, 0)
+  })
+  it('should trim the new line carriages created by windows tabular files,', () => {
+    const tsvs = [
+      {
+        contents: 'participant_id\t\r\n',
+        file: file,
+      },
+      {
+        contents: 'participant_id\r\n',
+        file: file,
+      },
+    ]
+    const issues = validateTsvColumns(tsvs, {})
+    assert.lengthOf(issues, 0)
+  })
+})

validators/tsv/tsv.js

@@ -27,7 +27,7 @@ const TSV = (file, contents, fileList, callback) => {
   }
 
   const rows = contents.split('\n')
-  const headers = rows[0].split('\t')
+  const headers = rows[0].trim().split('\t')
 
   // generic checks -----------------------------------------------------------
 
@@ -46,7 +46,7 @@ const TSV = (file, contents, fileList, callback) => {
       continue
     }
 
-    const values = row.split('\t')
+    const values = row.trim().split('\t')
 
     // check for different length rows
     if (values.length !== headers.length && !columnMismatch) {
@@ -150,7 +150,9 @@ const TSV = (file, contents, fileList, callback) => {
     const stimFiles = []
     if (headers.indexOf('stim_file') > -1) {
       for (let k = 0; k < rows.length; k++) {
-        const stimFile = rows[k].split('\t')[headers.indexOf('stim_file')]
+        const stimFile = rows[k].trim().split('\t')[
+          headers.indexOf('stim_file')
+        ]
         const stimPath = '/stimuli/' + stimFile
         if (
           stimFile &&
@@ -199,7 +201,7 @@ const TSV = (file, contents, fileList, callback) => {
     } else {
       participants = []
       for (let l = 1; l < rows.length; l++) {
-        const row = rows[l].split('\t')
+        const row = rows[l].trim().split('\t')
         // skip empty rows
         if (!row || /^\s*$/.test(row)) {
           continue

validators/tsv/validateTsvColumns.js

@@ -52,7 +52,10 @@ const validateTsvColumns = function(tsvs, jsonContentsDict) {
   const tsvIssues = []
   tsvs.map(tsv => {
     const customColumns = getCustomColumns(
-      tsv.contents.split('\n')[0].split('\t'),
+      tsv.contents
+        .split('\n')[0]
+        .trim()
+        .split('\t'),
       getTsvType(tsv.file),
     )
     if (customColumns.length > 0) {