Merge v24.1.14 into main

VERSION

@@ -1 +1 @@
-24.1.13
+24.1.14

python/lib/imaging.py

@@ -169,9 +169,9 @@ def insert_parameter_file(self, file_id, parameter_name, value):
 
         # convert list values into strings that could be inserted into parameter_file
         if type(value) == list:
-            if type(value[0]) in [float, int]:
+            if value and type(value[0]) in [float, int]:
                 value = [str(f) for f in value]
-            value = f"[{', '.join(str(value))}]"
+            value = f"[{', '.join(value)}]"
 
         # Gather column name & values to insert into parameter_file
         param_type_id = self.get_parameter_type_id(parameter_name)

tools/correct_lists_incorrectly_saved_in_parameter_file.py

@@ -0,0 +1,71 @@
+#!/usr/bin/env python3
+
+import os
+
+from lib.database import Database
+from lib.lorisgetopt import LorisGetOpt
+
+
+__license__ = 'GPLv3'
+
+
+def main():
+    usage = (
+        "\n"
+
+        "********************************************************************\n"
+        " CORRECT LISTS INCORRECTLY SAVED IN PARAMETER_FILE TABLE\n"
+        "********************************************************************\n"
+        "This script will query any value in parameter_file like '[[%%]]' which is unique and typical of"
+        " incorrectly saved lists in parameter_file. It will replace the extra characters in the parameter_file"
+        " table so that the list is properly saved. This follows the correction made in PR"
+        " https://github.com/aces/Loris-MRI/pull/1025\n\n"
+
+        "usage  : correct_lists_incorrectly_saved_in_parameter_file.py -p <profile> ...\n\n"
+
+        "options: \n"
+        "\t-p, --profile  : Name of the python database config file in dicom-archive/.loris_mri\n"
+        "\t-v, --verbose  : If set, be verbose\n\n"
+
+        "required options are: \n"
+        "\t--profile\n"
+    )
+
+    options_dict = {
+        "profile": {
+            "value": None, "required": True, "expect_arg": True, "short_opt": "p", "is_path": False
+        },
+        "verbose": {
+            "value": False, "required": False, "expect_arg": False, "short_opt": "v", "is_path": False
+        },
+        "help": {
+            "value": False, "required": False, "expect_arg": False, "short_opt": "h", "is_path": False
+        },
+    }
+
+    # get the options provided by the user
+    loris_getopt_obj = LorisGetOpt(usage, options_dict, os.path.basename(__file__[:-3]))
+
+    # establish database connection
+    verbose = loris_getopt_obj.options_dict['verbose']['value']
+    db = Database(loris_getopt_obj.config_info.mysql, verbose)
+    db.connect()
+
+    # get the list of entries in parameter_file to correct and correct them
+    get_list_of_entries_in_parameter_file_to_correct(db)
+
+
+def get_list_of_entries_in_parameter_file_to_correct(db):
+
+    results = db.pselect('SELECT * FROM parameter_file WHERE Value LIKE %s', ('[[%%]]',))
+
+    for row in results:
+        param_file_id = row['ParameterFileID']
+        value_str = row['Value']
+        new_value_str = value_str.replace("[[, ', ", "[").replace(", ', ]]", "]").replace(", ", "").replace("'", "")
+        new_value_str = new_value_str.replace(" ", '').replace(",", ", ").replace("[[", "[").replace("]]", "]")
+        db.update('UPDATE parameter_file SET Value=%s WHERE ParameterFileID=%s', (new_value_str, param_file_id))
+
+
+if __name__ == "__main__":
+    main()