Merge pull request #634 from DaNish808/master

validate IntendedFor filetype
bids-standard · Oct 23, 2018 · a9844e7 · a9844e7
2 parents cbcb0d3 + 2c23a3d
commit a9844e7
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Showing 2 changed files with 60 additions and 4 deletions.
diff --git a/tests/nii.spec.js b/tests/nii.spec.js
@@ -125,6 +125,44 @@ describe('NIFTI', function() {
     })
   })
 
+  it('should generate warning if files listed in IntendedFor of fieldmap json are not of type .nii or .nii.gz', function() {
+    var file = {
+      name: '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/fmap/sub-09_ses-test_run-01_fieldmap.json': {
+        TaskName: 'Mixed Event Related Probe',
+        IntendedFor: [
+          'func/sub-15_task-mixedeventrelatedprobe_run-05_bold.json',
+          'func/sub-15_task-mixedeventrelatedprobe_run-02_bold.nii.gz',
+        ],
+      },
+    }
+    var fileList = []
+    fileList.push({
+      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',
+    })
+    validate.NIFTI(null, file, jsonContentsDict, {}, [], [], function(issues) {
+      assert(
+        issues.some(
+          issue =>
+            issue.reason ===
+              'Invalid filetype: IntendedFor should point to the .nii[.gz] files.' &&
+            issue.evidence ===
+              'func/sub-15_task-mixedeventrelatedprobe_run-05_bold.json',
+        ),
+      )
+    })
+  })
+
   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',
@@ -152,7 +190,7 @@ describe('NIFTI', function() {
     })
     validate.NIFTI(null, file, jsonContentsDict, {}, [], [], function(issues) {
       assert(
-        (issues.length = 2 && issues[0].code == 17 && issues[1].code == 37),
+        issues.length === 3 && issues[0].code == 17 && issues[1].code == 37,
       )
     })
   })

diff --git a/validators/nifti/nii.js b/validators/nifti/nii.js
@@ -433,6 +433,7 @@ module.exports = function NIFTI(
       for (let key = 0; key < intendedFor.length; key++) {
         const intendedForFile = intendedFor[key]
         checkIfIntendedExists(intendedForFile, fileList, issues, file)
+        checkIfValidFiletype(intendedForFile, issues, file)
       }
     }
   }
@@ -485,9 +486,11 @@ function checkIfIntendedExists(intendedForFile, fileList, issues, file) {
   let onTheList = false
 
   for (let key2 in fileList) {
-    const filePath = fileList[key2].relativePath
-    if (filePath === intendedForFileFull) {
-      onTheList = true
+    if (key2) {
+      const filePath = fileList[key2].relativePath
+      if (filePath === intendedForFileFull) {
+        onTheList = true
+      }
     }
   }
   if (!onTheList) {
@@ -509,3 +512,18 @@ function checkIfIntendedExists(intendedForFile, fileList, issues, file) {
     )
   }
 }
+
+function checkIfValidFiletype(intendedForFile, issues, file) {
+  const validFiletype = new RegExp('.nii(.gz)?$')
+  const isValidFiletype = validFiletype.test(intendedForFile)
+  if (!isValidFiletype) {
+    issues.push(
+      new Issue({
+        file: file,
+        code: 37,
+        reason: `Invalid filetype: IntendedFor should point to the .nii[.gz] files.`,
+        evidence: intendedForFile,
+      }),
+    )
+  }
+}