(preliminary to SQLAlchemy) Rename database.py

python/bids_import.py

@@ -10,12 +10,12 @@
 import lib.exitcode
 import lib.utilities
 import lib.physiological
-from lib.database   import Database
-from lib.candidate  import Candidate
+from lib.database_lib import Database
+from lib.candidate import Candidate
 from lib.bidsreader import BidsReader
-from lib.session    import Session
-from lib.eeg        import Eeg
-from lib.mri        import Mri
+from lib.session import Session
+from lib.eeg import Eeg
+from lib.mri import Mri
 from lib.database_lib.config import Config
 
 __license__ = "GPLv3"

python/extract_eeg_bids_archive.py

@@ -7,7 +7,7 @@
 import re
 from lib.lorisgetopt import LorisGetOpt
 from lib.imaging_io import ImagingIO
-from lib.database import Database
+from lib.database_lib import Database
 from lib.database_lib.config import Config
 from lib.exitcode import SUCCESS, BAD_CONFIG_SETTING
 from lib.log import Log

python/ingest_eeg_bids_datasets.py

@@ -5,7 +5,7 @@
 import os
 import sys
 from lib.lorisgetopt import LorisGetOpt
-from lib.database import Database
+from lib.database_lib import Database
 from lib.database_lib.config import Config
 from lib.exitcode import SUCCESS, INVALID_ARG
 import subprocess
@@ -112,7 +112,7 @@ def main():
       if not session_data:
         print('Session ID ' + eeg_dataset['SessionID'] + ' associated with UploadID ' + uploadid + ' does not exist.')
         sys.exit(INVALID_ARG)
-         
+
       candid = session_data[0]['CandID']
       pscid = session_data[0]['PSCID']
       visit = session_data[0]['Visit_label']
@@ -150,13 +150,13 @@ def main():
       # Assume eeg and raw data for now
       eeg_path = os.path.join(path, 'eeg')
       command = 'python ' + script + ' -p ' + profile + ' -d ' + eeg_path + ' --nobidsvalidation --nocopy --type raw'
-      
+
       try:
         result = subprocess.run(command, shell = True, capture_output=True)
 
         if result.stdout:
           print(result.stdout.decode('utf-8'))
-        
+
         if result.stderr:
           print(
             f'ERROR: EEG Dataset with uploadID {uploadid} ingestion log:\n ' + result.stderr.decode('utf-8')
@@ -177,7 +177,7 @@ def main():
         "UPDATE electrophysiology_uploader SET Status = 'Failed Ingestion' WHERE UploadID = %s",
         (uploadid,)
       )
-      
+
     # TODO: reupload of archive after ingestion
     # Delete if already exist
 

python/lib/candidate.py

@@ -16,7 +16,7 @@ class Candidate:
     :Example:
 
         from lib.candidate import Candidate
-        from lib.database  import Database
+        from lib.database_lib import Database
 
         # database connection
         db = Database(config.mysql, verbose)