Merge pull request #574 from olgn/remove-async

remove async

Author: olgn

package.json

@@ -28,7 +28,6 @@
   "homepage": "https://github.com/bids-standard/bids-validator",
   "dependencies": {
     "ajv": "^6.5.2",
-    "async": "^2.6.1",
     "bytes": "^3.0.0",
     "cliff": "^0.1.10",
     "colors": "^1.3.1",

tests/bval.spec.js

@@ -1,45 +1,45 @@
-var assert = require('assert')
-var validate = require('../index')
+const assert = require('assert')
+const bval = require('../validators/bval/bval')
 
 describe('bval', function() {
   it('should allow proper bval contents', function() {
-    var bval = '4 6 2 5 3 23 5'
-    validate.bval({}, bval, function(issues) {
+    const val = '4 6 2 5 3 23 5'
+    bval({}, val, function(issues) {
       assert.deepEqual(issues, [])
     })
   })
 
   it('should not allow more than one row', function() {
-    var bval = '0 4 3 6 1 6 2 4 1\n 4 3 5 2 4 2 4 5'
-    validate.bval({}, bval, function(issues) {
+    const val = '0 4 3 6 1 6 2 4 1\n 4 3 5 2 4 2 4 5'
+    bval({}, val, function(issues) {
       assert(issues.length == 1 && issues[0].code == 30)
     })
   })
 
   it('should catch doublespace separators', function() {
-    var bval = '4  6  2  5  3  23  5'
-    validate.bval({}, bval, function(issues) {
+    const val = '4  6  2  5  3  23  5'
+    bval({}, val, function(issues) {
       assert(issues.length == 1 && issues[0].code == 47)
     })
   })
 
   it('should not allow undefined bvals', function() {
-    const bval = undefined
-    validate.bval({}, bval, function(issues) {
+    const val = undefined
+    bval({}, val, function(issues) {
       assert(issues.length == 1 && issues[0].code == 89)
     })
   })
 
   it('should not allow bvals of types other than string', function() {
-    const bval = [0, 1, 2, 3]
-    validate.bval({}, bval, function(issues) {
+    const val = [0, 1, 2, 3]
+    bval({}, val, function(issues) {
       assert(issues.length == 1 && issues[0].code == 89)
     })
   })
 
   it('should not allow bvecs to be submitted in place of bval', function() {
-    const bvec = '4 6 7\n 2 3 4\n 4 5 6'
-    validate.bval({}, bvec, function(issues) {
+    const val = '4 6 7\n 2 3 4\n 4 5 6'
+    bval({}, val, function(issues) {
       assert(issues.length == 1 && issues[0].code == 30)
     })
   })

tests/bvec.spec.js

@@ -1,58 +1,58 @@
 var assert = require('assert')
-var validate = require('../index')
+const bvec = require('../validators/bvec/bvec')
 
 describe('bvec', function() {
   it('should allow valid bvec contents', function() {
-    var bvec = '4 6 2 5\n3 2 3 5\n6 4 3 5'
-    validate.bvec({}, bvec, function(issues) {
+    const vec = '4 6 2 5\n3 2 3 5\n6 4 3 5'
+    bvec({}, vec, function(issues) {
       assert.deepEqual(issues, [])
     })
   })
 
   it('should not allow more or less than 3 rows', function() {
-    var bvec = '0 4 3 6 1 6 2 4\n 4 3 5 2 4 2 4 5'
-    validate.bvec({}, bvec, function(issues) {
+    let vec = '0 4 3 6 1 6 2 4\n 4 3 5 2 4 2 4 5'
+    bvec({}, vec, function(issues) {
       assert(issues.length == 1 && issues[0].code == 31)
     })
 
-    bvec =
+    vec =
       '0 4 3 6 1 6 2 4\n 4 3 5 2 4 2 4 5\n 4 3 5 2 4 2 4 5\n 4 3 5 2 4 2 4 5'
-    validate.bvec({}, bvec, function(issues) {
+    bvec({}, vec, function(issues) {
       assert(issues.length == 1 && issues[0].code == 31)
     })
   })
 
   it('should not allow rows of inconsistent length', function() {
-    var bvec = '0 4 3 6 1 6 4\n 4 3 4 2 4 5\n 4 3 5 2 4 2 4 5'
-    validate.bvec({}, bvec, function(issues) {
+    const vec = '0 4 3 6 1 6 4\n 4 3 4 2 4 5\n 4 3 5 2 4 2 4 5'
+    bvec({}, vec, function(issues) {
       assert(issues.length == 1 && issues[0].code == 46)
     })
   })
 
   it('should catch doublespace separators', function() {
-    var bvec = '4  6  2  5\n3  2  3  5\n6  4  3  5'
-    validate.bvec({}, bvec, function(issues) {
+    const vec = '4  6  2  5\n3  2  3  5\n6  4  3  5'
+    bvec({}, vec, function(issues) {
       assert(issues.length == 1 && issues[0].code == 47)
     })
   })
 
   it('should not allow undefined bvecs', function() {
-    const bvec = undefined
-    validate.bvec({}, bvec, function(issues) {
+    const vec = undefined
+    bvec({}, vec, function(issues) {
       assert(issues.length == 1 && issues[0].code == 88)
     })
   })
 
   it('should not allow bvecs of types other than string', function() {
-    const bvec = [0, 1, 2, 3]
-    validate.bvec({}, bvec, function(issues) {
+    const vec = [0, 1, 2, 3]
+    bvec({}, vec, function(issues) {
       assert(issues.length == 1 && issues[0].code == 88)
     })
   })
 
   it('should not allow bvals to be submitted in place of bvec', function() {
-    const bval = '4 6 7'
-    validate.bvec({}, bval, function(issues) {
+    const vec = '4 6 7'
+    bvec({}, vec, function(issues) {
       assert(issues.length == 1 && issues[0].code == 31)
     })
   })

tests/events.spec.js

@@ -13,8 +13,6 @@ describe('Events', function() {
   ]
 
   it('all files in the /stimuli folder should be included in an _events.tsv file', function() {
-    const issues = []
-
     // stimuli.events will have all of the
     // files included in the stim_file column of every _events.tsv file.
     // stimuli.directory will have all of the
@@ -23,22 +21,20 @@ describe('Events', function() {
       events: ['/stimuli/images/red-square.jpg'],
       directory: [{ relativePath: '/stimuli/images/blue-square.jpg' }],
     }
-    validate.Events.validateEvents([], stimuli, [], {}, issues)
+    const issues = validate.Events.validateEvents([], stimuli, [], {})
     assert(issues.length === 1 && issues[0].code === 77)
   })
 
   it('should not throw issues if all files in the /stimuli folder are included in an _events.tsv file', function() {
-    const issues = []
     const stimuli = {
       events: ['/stimuli/images/red-square.jpg'],
       directory: [{ relativePath: '/stimuli/images/red-square.jpg' }],
     }
-    validate.Events.validateEvents([], stimuli, [], {}, issues)
+    const issues = validate.Events.validateEvents([], stimuli, [], {})
     assert(issues.length === 0)
   })
 
   it('should throw an issue if the onset of the last event in _events.tsv is more than TR * number of volumes in corresponding nifti header', function() {
-    const issues = []
     const events = [
       {
         file: { path: '/sub01/sub01_task-test_events.tsv' },
@@ -52,12 +48,16 @@ describe('Events', function() {
       },
     }
 
-    validate.Events.validateEvents(events, [], headers, jsonDictionary, issues)
+    const issues = validate.Events.validateEvents(
+      events,
+      [],
+      headers,
+      jsonDictionary,
+    )
     assert(issues.length === 1 && issues[0].code === 85)
   })
 
   it('should throw an issue if the onset of the last event in _events.tsv is less than .5 * TR * number of volumes in corresponding nifti header', function() {
-    const issues = []
     const events = [
       {
         file: { path: '/sub01/sub01_task-test_events.tsv' },
@@ -71,12 +71,16 @@ describe('Events', function() {
       },
     }
 
-    validate.Events.validateEvents(events, [], headers, jsonDictionary, issues)
+    const issues = validate.Events.validateEvents(
+      events,
+      [],
+      headers,
+      jsonDictionary,
+    )
     assert(issues.length === 1 && issues[0].code === 86)
   })
 
   it('should not throw any issues if the onset of the last event in _events.tsv is a reasonable value', function() {
-    const issues = []
     const events = [
       {
         file: { path: '/sub01/sub01_task-test_events.tsv' },
@@ -90,7 +94,12 @@ describe('Events', function() {
       },
     }
 
-    validate.Events.validateEvents(events, [], headers, jsonDictionary, issues)
+    const issues = validate.Events.validateEvents(
+      events,
+      [],
+      headers,
+      jsonDictionary,
+    )
     assert.deepEqual(issues, [])
   })
 })

tests/tsv.spec.js

@@ -205,7 +205,7 @@ describe('TSV', function() {
       size: 11845,
     }
     var issues = []
-    validate.TSV.checkphenotype(
+    validate.TSV.checkPhenotype(
       phenotypeParticipants,
       summary,
       issues,

utils/files/collectDirectoryStatistics.js renamed to utils/files/collectDirectorySize.js

@@ -1,16 +1,19 @@
-const async = require('async')
 const fs = require('fs')
 
-const collectDirectoryStatistics = (fileList, summary) => {
-  async.eachOfLimit(fileList, 200, function(file) {
+const collectDirectorySize = fileList => {
+  let size = 0
+  const keys = Object.keys(fileList)
+  keys.forEach(key => {
+    const file = fileList[key]
     // collect file stats
     if (typeof window !== 'undefined' && file.size) {
-      summary.size += file.size
+      size += file.size
     } else {
       file.stats = getFileStats(file)
-      summary.size += file.stats.size
+      size += file.stats.size
     }
   })
+  return size
 }
 
 const getFileStats = file => {
@@ -25,4 +28,4 @@ const getFileStats = file => {
   return stats
 }
 
-module.exports = collectDirectoryStatistics
+module.exports = collectDirectorySize

utils/files/illegalCharacterTest.js

@@ -1,4 +1,3 @@
-const async = require('async')
 const Issue = require('../../utils/issues').Issue
 
 const re = {
@@ -15,8 +14,11 @@ const illegalchar_regex_list = [
   [re.ses_re, 63, 'ses name contains illegal character:'],
 ]
 
-const illegalCharacterTest = (fileList, issues) => {
-  async.eachOfLimit(fileList, 200, function(file) {
+const illegalCharacterTest = fileList => {
+  const issues = []
+  const fileKeys = Object.keys(fileList)
+  fileKeys.forEach(key => {
+    const file = fileList[key]
     const completename = file.relativePath
     if (
       !(
@@ -42,6 +44,7 @@ const illegalCharacterTest = (fileList, issues) => {
       })
     }
   })
+  return issues
 }
 
 module.exports = illegalCharacterTest

utils/files/index.js

@@ -8,7 +8,7 @@ const readDir = require('./readDir')
 const potentialLocations = require('./potentialLocations')
 const generateMergedSidecarDict = require('./generateMergedSidecarDict')
 const getBFileContent = require('./getBFileContent')
-const collectDirectoryStatistics = require('./collectDirectoryStatistics')
+const collectDirectorySize = require('./collectDirectorySize')
 const illegalCharacterTest = require('./illegalCharacterTest')
 
 // public API ---------------------------------------------------------------------
@@ -22,7 +22,7 @@ var fileUtils = {
   generateMergedSidecarDict: generateMergedSidecarDict,
   potentialLocations: potentialLocations,
   getBFileContent: getBFileContent,
-  collectDirectoryStatistics: collectDirectoryStatistics,
+  collectDirectorySize: collectDirectorySize,
   illegalCharacterTest: illegalCharacterTest,
 }
 

utils/index.js

@@ -8,6 +8,7 @@ var json = require('./json')
 var modalities = require('./modalities')
 var options = require('./options')
 var type = require('./type')
+const collectSummary = require('./summary/collectSummary')
 
 module.exports = {
   array: array,
@@ -19,4 +20,5 @@ module.exports = {
   modalities: modalities,
   options: options,
   type: type,
+  collectSummary: collectSummary,
 }

utils/summary/collectModalities.js

@@ -0,0 +1,25 @@
+const type = require('../type')
+
+const collectModalities = fileList => {
+  const modalities = []
+  const keys = Object.keys(fileList)
+  keys.forEach(key => {
+    const file = fileList[key]
+    const path = file.relativePath
+    const pathParts = path.split('_')
+    const suffix = pathParts[pathParts.length - 1]
+
+    // check modality by data file extension ...
+    // and capture data files for later sanity checks (when available)
+    if (type.file.isModality(file.name)) {
+      // collect modality summary
+      const modality = suffix.slice(0, suffix.indexOf('.'))
+      if (modalities.indexOf(modality) === -1) {
+        modalities.push(modality)
+      }
+    }
+  })
+  return modalities
+}
+
+module.exports = collectModalities