Phase 2 - additional features et layout changes

.eslintrc.json

@@ -20,7 +20,11 @@
       "globalReturn": false
     }
   },
-  "extends": ["eslint:recommended", "plugin:react/recommended", "google"],
+  "extends": [
+    "eslint:recommended",
+    "plugin:react/recommended",
+    "google"
+  ],
   "rules": {
     "max-len": ["error", {
         "code": 80,
@@ -35,7 +39,9 @@
     "require-jsdoc": "error",
     "no-console": ["warn", {
       "allow": ["info", "warn", "error"]
-    }]
+    }],
+    "react/jsx-curly-brace-presence": "warn",
+    "react/jsx-key": "warn"
   },
   "globals": {
     "React": true,

package.json

@@ -30,6 +30,8 @@
     "eslint-plugin-jsx-a11y": "^6.4.1",
     "eslint-plugin-react": "^7.24.0",
     "lint-staged": "^11.0.0",
+    "react-datepicker": "^4.1.1",
+    "react-switch": "^6.0.0",
     "wait-on": "^5.3.0"
   },
   "scripts": {

public/preload.js

@@ -5,10 +5,18 @@ contextBridge.exposeInMainWorld('myAPI', {
     const {dialog} = require('@electron/remote');
     return dialog;
   },
+  visitBIDS: () => {
+    const {shell} = require('electron');
+    shell.openExternal('https://bids.neuroimaging.io');
+  },
   visitGitHub: () => {
     const {shell} = require('electron');
     shell.openExternal('https://github.com/aces/eeg2bids');
   },
+  visitIssues: () => {
+    const {shell} = require('electron');
+    shell.openExternal('https://github.com/aces/eeg2bids/issues');
+  },
   visitMNE: () => {
     const {shell} = require('electron');
     shell.openExternal('https://mne.tools/mne-bids/');

python/eeg2bids.py

@@ -3,12 +3,15 @@
 from eventlet import tpool
 import socketio
 from python.libs import iEEG
+from python.libs.Modifier import Modifier
 from python.libs import BIDS
-
+from python.libs.loris_api import LorisAPI
+import csv
 
 # Create socket listener.
 sio = socketio.Server(async_mode='eventlet', cors_allowed_origins=[])
 app = socketio.WSGIApp(sio)
+loris_api = LorisAPI()
 
 # EEG2BIDS Wizard version
 appVersion = '1.0.0'
@@ -44,6 +47,22 @@ def tarfile_bids(sid, data):
     sio.emit('response', send)
 
 
+@sio.event
+def get_loris_sites(sid):
+    sio.emit('loris_sites', loris_api.get_sites())
+
+@sio.event
+def get_loris_projects(sid):
+    sio.emit('loris_projects', loris_api.get_projects())
+
+@sio.event
+def get_loris_subprojects(sid, project):
+    sio.emit('loris_subprojects', loris_api.get_subprojects(project))
+
+@sio.event
+def get_loris_visits(sid, project):
+    sio.emit('loris_visits', loris_api.get_visits(project))
+
 @sio.event
 def ieeg_get_header(sid, data):
     # data = { file_path: 'path to iEEG file' }
@@ -59,35 +78,53 @@ def ieeg_get_header(sid, data):
         response = {
             'error': 'Failed to retrieve EDF header information',
         }
-    sio.emit('response', response)
+    sio.emit('edf_header', response)
 
+@sio.event
+def get_metadata(sid, data):
+    # data = { file_path: 'path to metadata file' }
+    print('metadata file:', data)
+
+    if not data['file_path']:
+        print('No file path found.')
+        response = {
+            'error': 'No file path found.',
+        }
+    else :    
+        try:
+            with open(data['file_path']) as fd:
+                reader = csv.DictReader(fd, delimiter="\t", quotechar='"')
+                response = {
+                    'metadata': {rows['Field']:rows['Value'] for rows in reader}
+                }
+        except IOError:
+            print("Could not read the metadata file.")
+            response = {
+                'error': 'No file path found.',
+            }
+
+    sio.emit('metadata', response)
 
 def edf_to_bids_thread(data):
     print('data is ')
     print(data)
     error_messages = []
-    if not data['file_path']:
-        error_messages.append('The file.edf to convert is missing.')
+    if not data['file_paths']:
+        error_messages.append('No .edf file(s) to convert.')
     if not data['bids_directory']:
         error_messages.append('The BIDS output directory is missing.')
-    if not data['site_id']:
-        error_messages.append('The LORIS SiteID is missing.')
-    if not data['project_id']:
-        error_messages.append('The LORIS ProjectID is missing.')
-    if not data['sub_project_id']:
-        error_messages.append('The LORIS SubProjectID is missing.')
-    if not data['visit_label']:
+    if not data['session']:
         error_messages.append('The LORIS Visit Label is missing.')
 
     if not error_messages:
         time = iEEG.Time()
         data['output_time'] = 'output-' + time.latest_output
         iEEG.Converter(data)  # EDF to BIDS format.
 
-        # store subject_id for iEEG.Modifier
+        # store subject_id for Modifier
         data['subject_id'] = iEEG.Converter.m_info['subject_id']
         data['appVersion'] = appVersion
-        iEEG.Modifier(data, sio)  # Modifies data of BIDS format
+        Modifier(data)  # Modifies data of BIDS format
         response = {
             'output_time': data['output_time']
         }
@@ -100,9 +137,9 @@ def edf_to_bids_thread(data):
 
 @sio.event
 def edf_to_bids(sid, data):
-    # data = { file_path: '', bids_directory: '', read_only: false,
+    # data = { file_paths: [], bids_directory: '', read_only: false,
     # events_tsv: '', line_freq: '', site_id: '', project_id: '',
-    # sub_project_id: '', visit_label: '', subject_id: ''}
+    # sub_project_id: '', session: '', subject_id: ''}
     print('edf_to_bids: ', data)
     response = eventlet.tpool.execute(edf_to_bids_thread, data)
     print(response)

python/libs/BIDS.py

@@ -15,6 +15,15 @@ def __init__(self, data):
         validator = BIDSValidator()
         for path, dirs, files in os.walk(start_path):
             for filename in files:
+                if filename == '.bidsignore':
+                    continue
+
+                if filename.endswith('_annotations.tsv'):
+                    continue
+
+                if filename.endswith('_annotations.json'):
+                    continue
+
                 temp = os.path.join(path, filename)
                 file_paths.append(temp[len(start_path):len(temp)])
                 result.append(validator.is_bids(temp[len(start_path):len(temp)]))