Bugfixes

imaging_install.sh

@@ -40,23 +40,26 @@ if [ ! -f "$MAKECHECK" ]; then
     exit
 fi
 
-echo "-- LORIS DB Configuration --\n"
+echo ""
+echo "-- LORIS DB Configuration --"
 read -p "What is the database name? " mysqldb
 read -p "What is the database host? " mysqlhost
 read -p "What is the MySQL user? " mysqluser
 stty -echo
 read -p "What is the MySQL password? " mysqlpass; echo
 stty echo
 
-echo "-- LORIS API Configuration --\n"
+echo ""
+echo "-- LORIS API Configuration --"
 read -p "What is the LORIS url (including http(s))? " lorishost
 read -p "What is the API version (min v0.0.4-dev recommended)? " apiversion
 read -p "What is the LORIS admin user? " lorisuser
 stty -echo
-read -p "What is the LORIS user admin password? " lorispass; echo
+read -p "What is the LORIS user admin password? " lorispwd; echo
 stty echo
 
-echo "-- LORIS MRI Configuration --\n"
+echo ""
+echo "-- LORIS MRI Configuration --"
 read -p "What is the Linux user which the installation will be based on? " USER
 read -p "What is the project name? " PROJ   ##this will be used to create all the corresponding directories...i.e /data/gusto/bin.....
 read -p "What is your email address? " email

imaging_install_MacOSX.sh

@@ -22,23 +22,26 @@ LOGFILE="/tmp/$(basename $0).$$.tmp"
 touch $LOGFILE
 trap "rm  $LOGFILE" EXIT
 
-echo "-- LORIS DB Configuration --\n"
+echo ""
+echo "-- LORIS DB Configuration --"
 read -p "What is the database name? " mysqldb
 read -p "What is the database host? " mysqlhost
 read -p "What is the MySQL user? " mysqluser
 stty -echo
 read -p "What is the MySQL password? " mysqlpass; echo
 stty echo
 
-echo "-- LORIS API Configuration --\n"
+echo ""
+echo "-- LORIS API Configuration --"
 read -p "What is the LORIS url (including http(s))? " lorishost
 read -p "What is the API version (min v0.0.4-dev recommended)? " apiversion
 read -p "What is the LORIS admin user? " lorisuser
 stty -echo
-read -p "What is the LORIS user admin password? " lorispass; echo
+read -p "What is the LORIS user admin password? " lorispwd; echo
 stty echo
 
-echo "-- LORIS MRI Configuration --\n"
+echo ""
+echo "-- LORIS MRI Configuration --"
 read -p "What is the Linux user which the installation will be based on? " USER
 read -p "What is the project name? " PROJ   ##this will be used to create all the corresponding directories...i.e /data/gusto/bin.....
 read -p "What prod file name would you like to use? default: prod " prodfilename

python/bids_import.py

@@ -214,7 +214,7 @@ def read_and_insert_bids(bids_dir, config_file, verbose, createcand, createvisit
                 for scan_data in bids_reader.bids_layout.get_collections('session', 'scans')
             ])
 
-            if len(scans_data.get('acq_time')) == 0:
+            if 'acq_time' not in scans_data.columns:
                 message = '\n\tERROR: Can\'t find scans acquisition time data'
                 print(message)
                 sys.exit(lib.exitcode.BIDS_SCANS_ACQ_TIME_MISSING)

python/lib/api.py

@@ -13,6 +13,8 @@ class Api:
     the LORIS-MRI python code base and the LORIS backend.
     """
 
+    token = None
+
     def __init__(self, config, verbose):
         """
         Constructor method for the Api class.
@@ -69,7 +71,7 @@ def start_next_stage(self, candid, visit, site, subproject, project, date):
             verify=False
         )
 
-        if (resp.status and resp.status.code and resp.status.code == 200):
+        if (resp.status_code and resp.status_code == 200):
             print("Next stage successfully started.")
         else:
             print("An error occured. Can't start next stage.")

python/lib/bidsreader.py

@@ -96,15 +96,24 @@ def load_bids_data(self):
         bids_pack_version = list(map(int, bids.__version__.split('.')))
         # disabled until is a workaround for https://github.com/bids-standard/pybids/issues/760 is found
         # [file] bids_import.py [function] read_and_insert_bids [line] for modality in row['modalities']: (row['modalities'] is empty)
-        #if (bids_pack_version[0] > 0
-        #    or bids_pack_version[1] > 12
-        #    or (bids_pack_version[1] == 12 and bids_pack_version[2] > 0)):
-        #    bids_layout = BIDSLayout(
-        #        root=self.bids_dir,
-        #        indexer=BIDSLayoutIndexer(config_filename=bids_config, ignore=exclude_arr, force_index=force_arr)
-        #    )
-        #else:
-        bids_layout = BIDSLayout(root=self.bids_dir, config=bids_config, ignore=exclude_arr, force_index=force_arr, derivatives=True)
+        ''' 
+        if (bids_pack_version[0] > 0
+            or bids_pack_version[1] > 12
+            or (bids_pack_version[1] == 12 and bids_pack_version[2] > 0)):
+            bids_layout = BIDSLayout(
+                root=self.bids_dir,
+                indexer=BIDSLayoutIndexer(config_filename=bids_config, ignore=exclude_arr, force_index=force_arr),
+                derivatives=True
+            )
+        else:
+        '''
+        bids_layout = BIDSLayout(
+            root=self.bids_dir,
+            config=bids_config,
+            ignore=exclude_arr,
+            force_index=force_arr,
+            derivatives=True
+        )
 
         if self.verbose:
             print('\t=> BIDS dataset loaded with BIDS layout\n')

python/lib/database.py

@@ -253,8 +253,8 @@ def grep_id_from_lookup_table(self, id_field_name, table_name, where_field_name,
             )
 
         if not id:
-            message = "\nERROR: " + where_value + " " + where_field_name + \
-                      " does not exist in " + table_name + " database table\n"
+            message = "\nERROR: " + str(where_value) + " " + str(where_field_name) + \
+                      " does not exist in " + str(table_name) + " database table\n"
             print(message)
             sys.exit(lib.exitcode.SELECT_FAILURE)
 

python/lib/session.py

@@ -128,6 +128,10 @@ def start_visit_stage(self, db, api, visit_date):
         if self.verbose:
             print("Starting visit stage for " + self.visit_label + " and CandID "  + self.cand_id)
 
+        if not self.subproject_id or not self.project_id:
+            print("Can't start the visit stage - No subproject and project associated with the participant data.")
+            return
+
         site = db.grep_id_from_lookup_table('Name', 'psc', 'CenterID', self.center_id)
         subproject = db.grep_id_from_lookup_table('title', 'subproject', 'SubprojectID', self.subproject_id)
         project = db.grep_id_from_lookup_table('Name', 'Project', 'ProjectID', self.project_id)