Merge pull request #393 from chrisfilo/fix/intendedfor

Fixes for IntendedFor validator
bids-standard · Feb 4, 2018 · 54fc2b9 · 54fc2b9
2 parents 24b688e + 205d0f6
commit 54fc2b9
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Showing 3 changed files with 42 additions and 30 deletions.
diff --git a/tests/nii.spec.js b/tests/nii.spec.js
@@ -91,12 +91,12 @@ describe('NIFTI', function(){
     it('should generate warning if files listed in IntendedFor of fieldmap json do not exist', function() {
       var file = {
           name: 'sub-09_ses-test_run-01_fieldmap.nii.gz',
-          path: '/ds114/sub-09/ses-test/dwi/sub-09_ses-test_run-01_fieldmap.nii.gz',
-          relativePath: '/sub-09/ses-test/dwi/sub-09_ses-test_run-01_fieldmap.nii.gz'
+          path: '/ds114/sub-09/ses-test/fmap/sub-09_ses-test_run-01_fieldmap.nii.gz',
+          relativePath: '/sub-09/ses-test/fmap/sub-09_ses-test_run-01_fieldmap.nii.gz'
       };
 
       var jsonContentsDict = {
-          '/sub-09/ses-test/dwi/sub-09_ses-test_run-01_fieldmap.json': {
+          '/sub-09/ses-test/fmap/sub-09_ses-test_run-01_fieldmap.json': {
               TaskName: 'Mixed Event Related Probe',
               IntendedFor: ['func/sub-15_task-mixedeventrelatedprobe_run-05_bold.nii.gz','func/sub-15_task-mixedeventrelatedprobe_run-02_bold.nii.gz'
             ]
@@ -129,7 +129,7 @@ describe('NIFTI', function(){
 
       var fileList = [{ name:'sub-15_task-mixedeventrelatedprobe_run-01_bold.nii.gz',
         path: 'sub-15/func/sub-15_task-mixedeventrelatedprobe_run-01_bold.nii.gz',
-        relativePath: '/func/sub-15_task-mixedeventrelatedprobe_run-01_bold.nii.gz'}];
+        relativePath: '/sub-15/func/sub-15_task-mixedeventrelatedprobe_run-01_bold.nii.gz'}];
       validate.NIFTI(null, file, jsonContentsDict, {}, fileList, [], function (issues) {
           assert.deepEqual(issues, []);
       });

diff --git a/utils/type.js b/utils/type.js
@@ -155,6 +155,17 @@ module.exports = {
         return conditionalMatch(anatRe, path);
     },
 
+    isFieldMapMainNii: function (path) {
+        var suffixes = ["phasediff", "phase1", "phase2", "fieldmap", "epi"];
+        var anatRe = new RegExp('^\\/(sub-[a-zA-Z0-9]+)' +
+            '\\/(?:(ses-[a-zA-Z0-9]+)' +
+            '\\/)?fmap' +
+            '\\/\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_dir-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?_(?:'
+            + suffixes.join("|")
+            + ').(nii.gz|nii)$');
+        return conditionalMatch(anatRe, path);
+    },
+
     /**
      * Check if the file has a name appropriate for a functional scan
      */

diff --git a/validators/nii.js b/validators/nii.js
@@ -1,7 +1,28 @@
-var async = require('async');
 var utils = require('../utils');
 var Issue = utils.issues.Issue;
 
+function checkIfIntendedExists(intendedForFile, fileList, issues, file) {
+    var intendedForFileFull = "/" + file.relativePath.split("/")[1] + "/" + intendedForFile;
+    var onTheList = false;
+
+    for (var key2 in fileList) {
+        var filePath = fileList[key2].relativePath;
+        if (filePath === intendedForFileFull) {
+            onTheList = true;
+        }
+    }
+    if (!onTheList) {
+        issues.push(new Issue({
+            file: file,
+            code: 37,
+            reason: "'IntendedFor' property of this fieldmap  ('" + file.relativePath +
+            "') does not point to an existing file('" + intendedForFile + "'). Please mind that this value should not include subject level directory " +
+            "('/" + file.relativePath.split("/")[1] + "/').",
+            evidence: intendedForFile
+        }));
+    }
+}
+
 /**
  * NIFTI
  *
@@ -218,33 +239,13 @@ module.exports = function NIFTI (header, file, jsonContentsDict, bContentsDict,
             }
         }
 
-        if (path.includes("_phasediff.nii") || path.includes("_phase1.nii") ||
-            path.includes("_phase2.nii") || path.includes("_fieldmap.nii") || path.includes("_epi.nii")){
-            if (mergedDictionary.hasOwnProperty('IntendedFor')) {
-              var intendedFor = typeof mergedDictionary['IntendedFor'] == "string" ? [mergedDictionary['IntendedFor']] : mergedDictionary['IntendedFor'];
-
-              for(var key = 0; key<intendedFor.length; key++){
-                var intendedForFile = path.split("/")[1] + "/" + intendedFor[key];
-                var onTheList = false;
-                async.eachOfLimit(fileList, 200, function (file) {
-                    var filePath = file.relativePath;
-                    if (filePath.endsWith(intendedForFile)){
-                        onTheList = true;
-                    }
+        if (utils.type.isFieldMapMainNii(path) && mergedDictionary.hasOwnProperty('IntendedFor')) {
+            var intendedFor = typeof mergedDictionary['IntendedFor'] == "string" ? [mergedDictionary['IntendedFor']] : mergedDictionary['IntendedFor'];
 
-                }, function(){
-                    if (!onTheList) {
-                        issues.push(new Issue({
-                            file: file,
-                            code: 37,
-                            reason: "'IntendedFor' property of this fieldmap  ('" + path +
-                            "') does not point to an existing file('" +  intendedForFile  + "'). Please mind that this value should not include subject level directory " +
-                            "('/" + path.split("/")[1] + "/')."
-                        }));
-                    }
-                });
+            for (var key = 0; key < intendedFor.length; key++) {
+                var intendedForFile = intendedFor[key];
+                checkIfIntendedExists(intendedForFile, fileList, issues, file);
             }
-          }
         }
     }