Merge pull request #313 from suyashdb/SubSesIDMismatch

Checks if Sub and Ses ID in path and filename mismatch

Author: chrisgorgo

tests/bids.spec.js

@@ -113,7 +113,7 @@ var suite = describe('BIDS example datasets ', function() {
         var options = {ignoreNiftiHeaders: false};
         validate.BIDS("tests/data/valid_filenames", options, function (issues) {
             var errors = issues.errors;
-            assert(errors[1].code ==='62');
+            assert(errors[2].code ==='64');
             isdone();
         });
     });

tests/type.spec.js

@@ -1,6 +1,7 @@
 var assert = require('chai').assert;
 var utils   = require('../utils');
 var Test = require("mocha/lib/test");
+var BIDS = require('../validators/bids');
 
 
 var suiteAnat = describe('utils.type.isAnat', function(){
@@ -242,4 +243,42 @@ describe('utils.type.getPathValues', function () {
         assert.equal(utils.type.getPathValues('/sub-22/func/sub-22_task-rest_acq-prefrontal_physio.tsv.gz').sub, 22);
         assert.equal(utils.type.getPathValues('/sub-22/func/sub-22_task-rest_acq-prefrontal_physio.tsv.gz').ses, null);
     });
-});
+});
+
+describe('BIDS.subIDsesIDmismatchtest', function () {
+    var code64_seen = false;
+    var code65_seen = false;
+    it('should return if sub and ses doesnt match', function () {
+
+        var files = { '0':
+           { name: 'sub-22_ses-1_task-rest_acq-prefrontal_physio.tsv.gz',
+             path: 'tests/data/BIDS-examples-1.0.0-rc3u5/ds001/sub-22_ses-1_task-rest_acq-prefrontal_physio.tsv.gz',
+             relativePath: 'ds001/sub-22_ses-1_task-rest_acq-prefrontal_physio.tsv.gz' },
+          '1':
+           { name: '/sub-22/ses-1/func/sub-23_ses-1_task-rest_acq-prefrontal_physio.tsv.gz',
+             path: 'tests/data/BIDS-examples-1.0.0-rc3u5/ds001/sub-22/ses-1/func/sub-23_ses-1_task-rest_acq-prefrontal_physio.tsv.gz',
+             relativePath: 'ds001/sub-22/ses-1/func/sub-23_ses-1_task-rest_acq-prefrontal_physio.tsv.gz' },
+          '2':
+           { name: '/sub-22/ses-1/func/sub-22_ses-2_task-rest_acq-prefrontal_physio.tsv.gz',
+             path: 'tests/data/BIDS-examples-1.0.0-rc3u5/ds001/sub-22/ses-1/func/sub-22_ses-2_task-rest_acq-prefrontal_physio.tsv.gz',
+             relativePath: '/sub-22/ses-1/func/sub-22_ses-2_task-rest_acq-prefrontal_physio.tsv.gz' },
+          '3':
+           { name: '/sub-25/ses-2/func/sub-22_ses-1_task-rest_acq-prefrontal_physio.tsv.gz',
+             path: 'tests/data/BIDS-examples-1.0.0-rc3u5/ds001/sub-25/ses-2/func/sub-22_ses-1_task-rest_acq-prefrontal_physio.tsv.gz',
+             relativePath: 'ds001//sub-25/ses-2/func/sub-22_ses-1_task-rest_acq-prefrontal_physio.tsv.gz' }},
+
+        callback = function (issues) {
+            for (var i in issues) {
+                if (issues[i]['code'] === 64) {
+                    code64_seen = true;
+                }
+                else if (issues[i]['code'] === 65) {
+                    code65_seen = false;
+                }
+            }
+            assert(code64_seen);
+            assert(code65_seen);
+        };
+        assert.equal(BIDS.subIDsesIDmismatchtest(files, callback), true);
+        });
+});

utils/issues/list.js

@@ -316,5 +316,15 @@ module.exports = {
         key: 'SESSION_VALUE_CONTAINS_ILLEGAL_CHARECTER',
         severity: 'error',
         reason: 'Ses label contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spec.',
+    },
+    64: {
+        key: 'SUBJECT_LABEL_IN_FILENAME_DOESNOT_MATCH_DIRECTORY',
+        severity: 'error',
+        reason: 'Subject label in the filename doesn\'t match with the path of the file. File seems to be saved in incorrect subject directory.'
+    },
+    65: {
+        key: 'SESSION_LABEL_IN_FILENAME_DOESNOT_MATCH_DIRECTORY',
+        severity: 'error',
+        reason: 'Session label in the filename doesn\'t match with the path of the file. File seems to be saved in incorrect session directory.'
     }
 };

utils/type.js

@@ -16,28 +16,28 @@ module.exports = {
      * Check if a given path is valid within the
      * bids spec.
      */
-    isBIDS: function(path) {
+    isBIDS: function (path) {
         return (
-            this.isTopLevel(path)       ||
+            this.isTopLevel(path) ||
             this.isAssociatedData(path) ||
-            this.isSessionLevel(path)   ||
-            this.isSubjectLevel(path)   ||
-            this.isAnat(path)           ||
-            this.isDWI(path)            ||
-            this.isFunc(path)           ||
-            this.isBehavioral(path)     ||
-            this.isCont(path)           ||
-            this.isFieldMap(path)       ||
+            this.isSessionLevel(path) ||
+            this.isSubjectLevel(path) ||
+            this.isAnat(path) ||
+            this.isDWI(path) ||
+            this.isFunc(path) ||
+            this.isBehavioral(path) ||
+            this.isCont(path) ||
+            this.isFieldMap(path) ||
             this.isPhenotypic(path)
         );
     },
 
     /**
      * Check if the file has appropriate name for a top level file
      */
-    isTopLevel: function(path) {
+    isTopLevel: function (path) {
         var fixedTopLevelNames = ["/README", "/CHANGES", "/dataset_description.json", "/participants.tsv",
-            "/participants.json", "/phasediff.json", "/phase1.json", "/phase2.json" ,"/fieldmap.json"];
+            "/participants.json", "/phasediff.json", "/phase1.json", "/phase2.json", "/fieldmap.json"];
 
         var funcTopRe = new RegExp('^\\/(?:ses-[a-zA-Z0-9]+_)?(?:recording-[a-zA-Z0-9]+_)?task-[a-zA-Z0-9]+(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_echo-[0-9]+)?'
             + '(_bold.json|_sbref.json|_events.json|_events.tsv|_physio.json|_stim.json|_beh.json)$');
@@ -60,23 +60,23 @@ module.exports = {
     /**
      * Check if file is appropriate associated data.
      */
-    isAssociatedData: function(path) {
+    isAssociatedData: function (path) {
         var associatedData = new RegExp('^\\/(?:code|derivatives|sourcedata|stimuli|[.]git)\\/(?:.*)$');
         return associatedData.test(path);
     },
 
     /**
      * Check if file is phenotypic data.
      */
-    isPhenotypic: function(path) {
+    isPhenotypic: function (path) {
         var phenotypicData = new RegExp('^\\/(?:phenotype)\\/(?:.*.tsv|.*.json)$');
         return phenotypicData.test(path);
     },
 
     /**
      * Check if the file has appropriate name for a session level
      */
-    isSessionLevel: function(path) {
+    isSessionLevel: function (path) {
         var scansRe = new RegExp('^\\/(sub-[a-zA-Z0-9]+)' +
             '\\/(?:(ses-[a-zA-Z0-9]+)' +
             '\\/)?\\1(_\\2)?(_scans.tsv|_scans.json)$');
@@ -103,7 +103,7 @@ module.exports = {
     /**
      * Check if the file has appropriate name for a subject level
      */
-    isSubjectLevel: function(path) {
+    isSubjectLevel: function (path) {
         var scansRe = new RegExp('^\\/(sub-[a-zA-Z0-9]+)' +
             '\\/\\1(_sessions.tsv|_sessions.json)$');
         return scansRe.test(path);
@@ -112,7 +112,7 @@ module.exports = {
     /**
      * Check if the file has a name appropriate for an anatomical scan
      */
-    isAnat: function(path) {
+    isAnat: function (path) {
         var anatRe = new RegExp('^\\/(sub-[a-zA-Z0-9]+)' +
             '\\/(?:(ses-[a-zA-Z0-9]+)' +
             '\\/)?anat' +
@@ -125,7 +125,7 @@ module.exports = {
     /**
      * Check if the file has a name appropriate for a diffusion scan
      */
-    isDWI: function(path) {
+    isDWI: function (path) {
         var suffixes = ["dwi", "sbref"];
         var anatRe = new RegExp('^\\/(sub-[a-zA-Z0-9]+)' +
             '\\/(?:(ses-[a-zA-Z0-9]+)' +
@@ -139,7 +139,7 @@ module.exports = {
     /**
      * Check if the file has a name appropriate for a fieldmap scan
      */
-    isFieldMap: function(path) {
+    isFieldMap: function (path) {
         var suffixes = ["phasediff", "phase1", "phase2", "magnitude1", "magnitude2", "magnitude", "fieldmap", "epi"];
         var anatRe = new RegExp('^\\/(sub-[a-zA-Z0-9]+)' +
             '\\/(?:(ses-[a-zA-Z0-9]+)' +
@@ -153,7 +153,7 @@ module.exports = {
     /**
      * Check if the file has a name appropriate for a functional scan
      */
-    isFunc: function(path) {
+    isFunc: function (path) {
         var funcRe = new RegExp('^\\/(sub-[a-zA-Z0-9]+)' +
             '\\/(?:(ses-[a-zA-Z0-9]+)' +
             '\\/)?func' +
@@ -162,7 +162,7 @@ module.exports = {
         return conditionalMatch(funcRe, path);
     },
 
-    isBehavioral: function(path) {
+    isBehavioral: function (path) {
         var funcBeh = new RegExp('^\\/(sub-[a-zA-Z0-9]+)' +
             '\\/(?:(ses-[a-zA-Z0-9]+)' +
             '\\/)?beh' +
@@ -171,7 +171,7 @@ module.exports = {
         return conditionalMatch(funcBeh, path);
     },
 
-    isFuncBold: function(path) {
+    isFuncBold: function (path) {
         var funcRe = new RegExp('^\\/(sub-[a-zA-Z0-9]+)' +
             '\\/(?:(ses-[a-zA-Z0-9]+)' +
             '\\/)?func' +
@@ -180,7 +180,7 @@ module.exports = {
         return conditionalMatch(funcRe, path);
     },
 
-    isCont: function(path) {
+    isCont: function (path) {
         var contRe = new RegExp('^\\/(sub-[a-zA-Z0-9]+)' +
             '\\/(?:(ses-[a-zA-Z0-9]+)' +
             '\\/)?(?:func|beh)' +
@@ -190,7 +190,7 @@ module.exports = {
         return conditionalMatch(contRe, path);
     },
 
-    isNumber: function(n) {
+    isNumber: function (n) {
         return !isNaN(parseFloat(n)) && isFinite(n);
     },
 
@@ -229,3 +229,6 @@ function conditionalMatch (expression, path) {
         }
         return false;
 }
+
+
+

validators/bids.js

@@ -160,6 +160,9 @@ BIDS = {
             size: 0
         };
 
+        // var subses_mismatch = false;
+        self.subIDsesIDmismatchtest(fileList);
+
 
         // check for illegal character in task name and acq name
 
@@ -441,6 +444,87 @@ BIDS = {
         });
     },
 
+    /**
+     * subid and sesid mismatch test. Generates error if ses-id and sub-id are different for any file, Takes a file list and return issues
+     */
+    subIDsesIDmismatchtest: function(fileList){
+        var self = this;
+        var subses_mismatch = false;
+
+        /**
+         * getPathandFileValues
+         * Takes a file path and returns values
+         * found following keys for both path and file keys.
+         * sub-
+         * ses-
+         *
+         *
+         */
+        function getPathandFileValues(path){
+            var values = {}, match;
+            var file_name ={}, unmat;
+
+            // capture subject
+            match = (/^\/sub-([a-zA-Z0-9]+)/).exec(path);
+            values.sub = match && match[1] ? match[1] : null;
+
+            // capture session
+            match = (/^\/sub-[a-zA-Z0-9]+\/ses-([a-zA-Z0-9]+)/).exec(path);
+            values.ses = match && match[1] ? match[1] : null;
+
+            //capture session and subject id from filename to find if files are in
+            // correct sub/ses directory
+            var filename = path.replace(/^.*[\\\/]/, '');
+
+            // capture sub from file name
+            unmat = (/^sub-([a-zA-Z0-9]+)/).exec(filename);
+            file_name.sub = unmat && unmat[1] ? unmat[1] : null;
+
+
+            // capture session from file name
+            unmat = (/^sub-[a-zA-Z0-9]+_ses-([a-zA-Z0-9]+)/).exec(filename);
+            file_name.ses = unmat && unmat[1] ? unmat[1] : null;
+
+            return [values,file_name];
+        }
+
+
+        // validates if sub/ses-id in filename matches with ses/sub directory file is saved
+        async.eachOfLimit(fileList, 200, function (file) {
+            var path = utils.files.relativePath(file);
+            file.relativePath = path;
+            var values = getPathandFileValues(file.relativePath);
+
+            var pathValues = values[0];
+            var fileValues = values[1];
+            // console.log(path, '/n' ,values);
+
+            if (fileValues.sub !== null || fileValues.ses !== null) {
+                if (fileValues.sub !== pathValues.sub) {
+                    // console.log("before call  ",subses_mismatch);
+                    subses_mismatch = true;
+                    self.issues.push(new Issue({
+                        code: 64,
+                        evidence: "File: " + file.relativePath + " is saved in incorrect subject directory as per sub-id in filename.",
+                        file: file
+                    }));
+                }
+
+                if (fileValues.ses !== pathValues.ses) {
+                    subses_mismatch = true;
+                    self.issues.push(new Issue({
+                        code: 65,
+                        evidence: "File: " + file.relativePath + " is saved in incorrect session directory as per ses-id in filename.",
+                        file: file
+                    }));
+                }
+            }
+
+        });
+        return subses_mismatch;
+
+    },
+
     /**
      * Reset
      *