version, empty metadata removal and \n removal in reference field

jeffersoncasimir · Sep 30, 2021 · 91be7f2 · 91be7f2
1 parent 60bc3d2
commit 91be7f2
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Showing 3 changed files with 18 additions and 19 deletions.
diff --git a/python/eeg2bids.py b/python/eeg2bids.py
@@ -14,7 +14,7 @@
 import json
 
 # EEG2BIDS Wizard version
-appVersion = '1.0.1'
+appVersion = '1.0.4'
 
 # LORIS credentials of user
 lorisCredentials = {
@@ -124,8 +124,6 @@ def create_candidate_and_visit(sid, data):
         data['site'],
     )
 
-    print(new_candidate)
-
     if new_candidate['CandID']:
         print('create_visit')
         loris_api.create_visit(new_candidate['CandID'], data['visit'], data['site'], data['project'],
@@ -215,10 +213,13 @@ def get_bids_metadata(sid, data):
             with open(data['file_path']) as fd:
                 try:
                     metadata = json.load(fd)
-                    diff = list(set(metadata.keys()) - set(metadata_fields[data['modality']]))
+                    empty_values = [k for k in metadata if metadata[k].strip() == '']
+                    diff = list(set(metadata.keys()) - set(metadata_fields[data['modality']]) - set(empty_values))
+                    ignored_keys = empty_values + diff
+
                     response = {
                         'metadata': metadata,
-                        'invalid_keys': diff,
+                        'ignored_keys': ignored_keys,
                     }
                 except ValueError as e:
                     print(e)

diff --git a/python/libs/Modifier.py b/python/libs/Modifier.py
@@ -79,6 +79,7 @@ def modify_dataset_description_json(self):
             with open(file_path, "r") as fp:
                 file_data = json.load(fp)
                 file_data['PreparedBy'] = self.data['preparedBy']
+                file_data['Eeg2bidsVersion'] = self.data['appVersion']
 
                 with open(file_path, "w") as fp:
                     json.dump(file_data, fp, indent=4)
@@ -157,9 +158,6 @@ def modify_participants_json(self):
                 },
                 'project': {
                     'Description': "Project of the participant"
-                },
-                'debug': {
-                    'Version': self.data['appVersion']
                 }
             }
             json_data.update(user_data)
@@ -300,11 +298,11 @@ def modify_eeg_json(self):
                     else:
                         referenceField = 'EGGReference'
 
-                    file_data[referenceField] = self.data['reference']
+                    file_data[referenceField] = " ".join(self.data['reference'].split())
 
-                    if 'metadata' in self.data['bidsMetadata'] and 'invalid_keys' in self.data['bidsMetadata']:
+                    if 'metadata' in self.data['bidsMetadata'] and 'ignored_keys' in self.data['bidsMetadata']:
                         for key in self.data['bidsMetadata']['metadata']:
-                            if key not in self.data['bidsMetadata']['invalid_keys']:
+                            if key not in self.data['bidsMetadata']['ignored_keys']:
                                 file_data[key] = self.data['bidsMetadata']['metadata'][key]
 
                     with open(file_path, "w") as fp:

diff --git a/src/jsx/Configuration.js b/src/jsx/Configuration.js
@@ -601,7 +601,7 @@ const Configuration = (props) => {
 
   const validateRecordingParameters = () => {
     const result = [];
-    let invalidKeyFound = false;
+    let ignoredKeyFound = false;
 
     if (!appContext.getFromTask('bidsMetadata')) {
       return formatWarning('No EEG Parameter metadata file selected');
@@ -620,18 +620,18 @@ const Configuration = (props) => {
     }
 
     const metadata = appContext.getFromTask('bidsMetadata')?.metadata;
-    const invalidKeys = appContext.getFromTask('bidsMetadata')?.invalid_keys;
+    const ignoredKeys = appContext.getFromTask('bidsMetadata')?.ignored_keys;
 
-    if (!metadata || !invalidKeys || metadata.length < 1) {
+    if (!metadata || !ignoredKeys || metadata.length < 1) {
       return formatWarning(
           'An error occured while processing ' +
           'the recording parameters file selected.',
       );
     }
 
     Object.keys(metadata).map((key) => {
-      if (invalidKeys.indexOf(key) > -1) {
-        invalidKeyFound = true;
+      if (ignoredKeys.indexOf(key) > -1) {
+        ignoredKeyFound = true;
         result.push(
             <div key={key}>
               {formatWarning(`${key}: ${metadata[key]}`)}
@@ -649,12 +649,12 @@ const Configuration = (props) => {
       }
     });
 
-    if (invalidKeyFound) {
+    if (ignoredKeyFound) {
       result.push(
           <p key="message">
             <span className='warning'>&#x26A0;</span>
-            Note: if invalid or extra parameters are found
-            in the .json file, they are ignored.
+            Note: invalid or extra parameters, as well as
+            parameters with empty values are ignored.
           </p>,
       );
     }