Update the bids_import script logic to explicitely add the --no-copy option

Author: laemtl

python/bids_import.py

@@ -37,8 +37,10 @@ def main():
     nocopy           = False
 
     long_options = [
-        "help",            "profile=",      "directory=",
-        "createcandidate", "createsession", "idsvalidation", "nobidsvalidation", "type=", "verbose"
+        "help",             "profile=",      "directory=",
+        "createcandidate",  "createsession", "idsvalidation",
+        "nobidsvalidation", "nocopy",        "type=",
+        "verbose"
     ]
     usage        = (
         '\n'
@@ -51,6 +53,7 @@ def main():
         '\t-s, --createsession    : to create BIDS sessions in LORIS (optional)\n'
         '\t-i, --idsvalidation    : to validate BIDS directory for a matching pscid/candid pair (optional)\n'
         '\t-b, --nobidsvalidation : to disable BIDS validation for BIDS compliance\n'
+        '\t-a, --nocopy           : to disable dataset copy in data assembly_bids\n'
         '\t-t, --type             : raw | derivatives. Specify the dataset type.'
                                     'If not set, the pipeline will look for both raw and derivatives files.\n'
                                     'Required if no dataset_description.json is found.\n'
@@ -81,6 +84,8 @@ def main():
             idsvalidation = True
         elif opt in ('-n', '--nobidsvalidation'):
             nobidsvalidation = True
+        elif opt in ('-a', '--nocopy'):
+            nocopy = True
         elif opt in ('-t', '--type'):
             type = arg
 
@@ -107,10 +112,6 @@ def main():
     # making sure that there is a final / in data_dir
     data_dir = data_dir if data_dir.endswith('/') else data_dir + "/"
 
-    assembly_bids_path = os.path.join(data_dir, 'assembly_bids')
-    if bids_dir.strip('/').startswith(assembly_bids_path.strip('/')):
-        nocopy = True
-
     # read and insert BIDS data
     read_and_insert_bids(
         bids_dir,

python/extract_eeg_bids_archive.py

@@ -25,7 +25,7 @@ def main():
         " EXTRACT EEG ARCHIVES\n"
         "********************************************************************\n"
         "The program gets an archive associated with an upload ID, extract it and push its content "
-        "to EEGS3DataPath, an Amazon S3 bucket or {dataDirBasepath}/assembly_bids.\n\n"
+        "to EEGS3DataPath, an Amazon S3 bucket or EEGAssemblyBIDS.\n\n"
 
         "usage  : extract_eeg_bids_archive.py -p <profile> -u <upload_id> ...\n\n"
 
@@ -214,7 +214,12 @@ def main():
                         )
                         error = True
                 else:
-                    data_eeg_modality_path = os.path.join(data_dir, 'assembly_bids', eeg_session_rel_path, modality)
+                    assembly_bids_path = config_db_obj.get_config("EEGAssemblyBIDS")
+                    if not assembly_bids_path:
+                        data_dir = config_db_obj.get_config("dataDirBasepath")
+                        assembly_bids_path = os.path.join(data_dir, 'assembly_bids')
+
+                    data_eeg_modality_path = os.path.join(assembly_bids_path, eeg_session_rel_path, modality)
 
                     """
                     If the suject/session/modality BIDS data already exists

python/ingest_eeg_bids_datasets.py

@@ -73,8 +73,10 @@ def main():
     # Get tmp dir from loris_getopt object
     # and create the log object (their basename being the name of the script run)
     # ---------------------------------------------------------------------------------------------
-    data_dir = config_db_obj.get_config("dataDirBasepath")
-    assembly_bids_path = os.path.join(data_dir, 'assembly_bids')
+    assembly_bids_path = config_db_obj.get_config("EEGAssemblyBIDS")
+    if not assembly_bids_path:
+      data_dir = config_db_obj.get_config("dataDirBasepath")
+      assembly_bids_path = os.path.join(data_dir, 'assembly_bids')
 
     # ---------------------------------------------------------------------------------------------
     # Get all EEG upload with status = Extracted
@@ -145,8 +147,9 @@ def main():
         continue
 
       script = os.environ['LORIS_MRI'] + '/python/bids_import.py'
+      # Assume eeg and raw data for now
       eeg_path = os.path.join(path, 'eeg')
-      command = 'python ' + script + ' -p ' + profile + ' -d ' + eeg_path + ' --nobidsvalidation --type raw'
+      command = 'python ' + script + ' -p ' + profile + ' -d ' + eeg_path + ' --nobidsvalidation --nocopy --type raw'
 
       try:
         result = subprocess.run(command, shell = True, capture_output=True)