Merge pull request #375 from chrisfilo/enh/no_data_test

Added check for no compatible data.

Author: chrisgorgo

tests/bids.spec.js

@@ -138,4 +138,14 @@ var suite = describe('BIDS example datasets ', function() {
             });
         });
     });
+
+    it('checks for subjects with no valid data', function (isdone) {
+        var options = {ignoreNiftiHeaders: true};
+        validate.BIDS("tests/data/no_valid_data", options, function (issues) {
+            var errors = issues.errors;
+            assert(errors.length === 1);
+            assert(errors[0].code === '67');
+            isdone();
+        });
+    });
 });

tests/data/no_valid_data/dataset_description.json

@@ -0,0 +1,5 @@
+{
+    "License": "This dataset is made available under the Public Domain Dedication and License \nv1.0, whose full text can be found at \nhttp://www.opendatacommons.org/licenses/pddl/1.0/. \nWe hope that all users will follow the ODC Attribution/Share-Alike \nCommunity Norms (http://www.opendatacommons.org/norms/odc-by-sa/); \nin particular, while not legally required, we hope that all users \nof the data will acknowledge the OpenfMRI project and NSF Grant \nOCI-1131441 (R. Poldrack, PI) in any publications.",
+    "Name": "Rhyme judgment",
+    "BIDSVersion": "1.0.1"
+}

tests/data/no_valid_data/sub-01/anat/sub-01_T1w.nii.gz

@@ -331,5 +331,10 @@ module.exports = {
         key: 'SLICETIMING_VALUES_GREATOR_THAN_REPETITION_TIME',
         severity: 'error',
         reason: '"SliceTiming" value/s contains invalid value as it is greater than RepetitionTime.  SliceTiming values should be in seconds not milliseconds (common mistake).'
+    },
+    67: {
+        key: 'NO_VALID_DATA_FOUND_FOR_SUBJECT',
+        severity: 'error',
+        reason: 'No BIDS compatible data found for at least one subject.'
     }
 };

tests/data/no_valid_data/sub-02/anat/sub-02_anat.nii.gz

@@ -10,6 +10,7 @@ var NIFTI  = require('./nii');
 var bval   = require('./bval');
 var bvec   = require('./bvec');
 var session = require('./session');
+var checkAnyDataPresent = require('./checkAnyDataPresent');
 var headerFields = require('./headerFields');
 
 var BIDS;
@@ -436,6 +437,7 @@ BIDS = {
                 }
                 self.issues = self.issues.concat(headerFields(headers));
                 self.issues = self.issues.concat(session(fileList));
+                self.issues = self.issues.concat(checkAnyDataPresent(fileList, summary.subjects));
                 summary.modalities = utils.modalities.group(summary.modalities);
                 var issues = utils.issues.format(self.issues, summary, self.options);
                 callback(issues, summary);

utils/issues/list.js

@@ -0,0 +1,52 @@
+var utils = require('../utils');
+var Issue = utils.issues.Issue;
+
+function addIfNotPresent(folderSubjects, subject) {
+    if (folderSubjects.indexOf(subject) == -1) {
+        folderSubjects.push(subject);
+    }
+}
+
+function getFolderSubjects(fileList) {
+    var folderSubjects = [];
+    for (var key in fileList) {
+        var file = fileList[key];
+        var match = file.relativePath.match(/sub-(.*?)(?=\/)/);
+        if (match) {
+            addIfNotPresent(folderSubjects, match[1]);
+        }
+    }
+    return folderSubjects;
+}
+
+/**
+ * checkAnyDataPresent
+ *
+ * Takes a list of files and participants with valid data. Checks if they match.
+ */
+var checkAnyDataPresent = function checkAnyDataPresent(fileList, summarySubjects) {
+    var issues = [];
+    var folderSubjects = getFolderSubjects(fileList);
+
+    var subjectsWithoutAnyValidData = folderSubjects.filter(function (i) {
+        return summarySubjects.indexOf(i) < 0;
+    });
+
+    for (var i = 0; i < subjectsWithoutAnyValidData.length; i++) {
+        var missingSubject = subjectsWithoutAnyValidData[i];
+        var subFolder = "/sub-" + missingSubject;
+        issues.push(new Issue({
+            file: {
+                relativePath: subFolder,
+                webkitRelativePath: subFolder,
+                name: subFolder,
+                path: subFolder
+            },
+            reason: "No BIDS compatible data found for subject " + missingSubject,
+            code: 67
+        }));
+    }
+    return issues;
+};
+
+module.exports = checkAnyDataPresent;