Fix metadata_reader

Author: nicolasblumenroehr

.DS_Store

@@ -2,6 +2,7 @@
 import logging
 from .attribute_mapper import Attribute_Mapper
 
+
 class Attribute_Inserter():
 
     def __init__(self, schema_skeleton: dict, key_list: list, map: object) -> None:
@@ -35,9 +36,9 @@ def fill_json_object(self, json_object: dict, key_list: list, attributes_object:
         for key in key_list:
             if (isinstance(json_object[key], str)) or (isinstance(json_object[key], tuple)):
                 if key in attributes_object.keys():
-                    new_dict[key] = self.get_json_type(json_object[key], attributes_object[key])
+                    new_dict[key] = self.get_json_type(json_object[key], attributes_object[key], key)
                 else:
-                    new_dict[key] = self.get_json_type(json_object[key], json_object[key])
+                    new_dict[key] = self.get_json_type(json_object[key], json_object[key], key)
             elif isinstance(json_object[key], dict):
                 if key in attributes_object:
                     if isinstance(attributes_object[key], Attribute_Mapper):
@@ -75,7 +76,7 @@ def fill_json_array(self, json_object: dict, json_object_property: str, json_arr
         Returns:
             list: The list that represents the filled json array.
         """
-        if isinstance(attributes, list) == False:
+        if not isinstance(attributes, list):
             if json_object_property in attributes.__dict__.keys():
                 attributes = attributes.__dict__[json_object_property]
         try:
@@ -89,7 +90,7 @@ def fill_json_array(self, json_object: dict, json_object_property: str, json_arr
         for list_item, list_index in zip(json_array, range(0, len(json_array))):
             if (isinstance(list_item, str)) or (isinstance(list_item, tuple)):
                 try:
-                    new_list.append(self.get_json_type(list_item, attributes[list_index]))
+                    new_list.append(self.get_json_type(list_item, attributes[list_index], None))
                 except TypeError as e:
                     logging.warning(e)
                     pass
@@ -106,7 +107,7 @@ def fill_json_array(self, json_object: dict, json_object_property: str, json_arr
                 pass
         return new_list
 
-    def get_json_type(self, data_type: str, attribute: str) -> Any:
+    def get_json_type(self, data_type: str, attribute: str, key) -> Any:
         """Takes an attribute and its data type. Confirms the primitive data types of the mapped attribute values and assigns these values to the schema attribute. The correct hirarchial
         position has been reached through the methods above.
 
@@ -118,19 +119,19 @@ def get_json_type(self, data_type: str, attribute: str) -> Any:
             Any: The value of the mapped attribute as the correct data type.
         """
         try:
-            if (isinstance(data_type, tuple) and (isinstance(attribute, tuple)==False)):
+            if (isinstance(data_type, tuple) and not (isinstance(attribute, tuple))):
                 if (isinstance(attribute, list)) and ("<class 'list'>" in data_type):
                     return attribute
                 else:
                     for element in data_type:
                         if element in ["<class 'int'>", "<class 'bool'>", "<class 'None'>", "<class 'float'>", "<class 'list'>"]:
-                            return (self.get_json_type(element, attribute))
+                            return (self.get_json_type(element, attribute, None))
                         else:
                             pass
-                    logging.warning(f'incorrect type provided for {attribute}, expected {data_type} but received {type(attribute)}, returning original value.')
+                    logging.warning(f'incorrect type provided for property \"{key}\", expected {data_type} but received {type(attribute)}, returning original value.')
                     return attribute
             elif isinstance(attribute, tuple):
-                logging.warning(f'No value provided for {attribute}, returning original value.')
+                logging.warning(f'No value provided for property \"{key}\", returning original value.')
                 return attribute
             elif data_type == "<class 'int'>":
                 return int(attribute)
@@ -143,11 +144,11 @@ def get_json_type(self, data_type: str, attribute: str) -> Any:
             elif data_type == "<class 'str'>":
                 return str(attribute)
             else:
-                logging.warning(f'incorrect type provided for {attribute}, expected {data_type} but received {type(attribute)}, returning original value.')
+                logging.warning(f'incorrect type provided for property \"{key}\", expected {data_type} but received {type(attribute)}, returning original value.')
                 return attribute
-        except TypeError as e:
-            logging.warning(f'incorrect type provided for {attribute}, expected {data_type} but received {type(attribute)}, returning original value.')
+        except TypeError:
+            logging.warning(f'incorrect type provided for property \"{key}\", expected {data_type} but received {type(attribute)}, returning original value.')
             return attribute
-        except ValueError as e:
-            logging.warning(f'incorrect value provided for {attribute}, expected {data_type} but received {type(attribute)}, returning original value.')
+        except ValueError:
+            logging.warning(f'incorrect value provided for property \"{key}\", expected {data_type} but received {type(attribute)}, returning original value.')
             return attribute

jammato/attribute_inserter.py

@@ -1,7 +1,6 @@
 import json
 import os
 import logging
-from typing import Any
 from .schema_reader import Schema_Reader
 from .dicom_reader import Dicom_Reader
 from .cache_schemas import Cache_Schemas
@@ -165,4 +164,4 @@ def series_extension(self, map_dict: dict, map_attribute: str, series: Dicom_Rea
             else:
                 merged_series_map=assess_type.merge_mapped_attributes(series_map, element_series_attribute, list(map_dict.keys())[3])
 
-        return merged_series_map    
+        return merged_series_map    

jammato/dicom_mapping.py

@@ -41,7 +41,8 @@ def __init__(self, metadata_document_directory: str, config_dicom_file_validatio
                         self.all_dicom_series.extend(self.post_read_processing(value, flag="single"))
 
         elif type(file_extension) == type(str()):
-            self.evaluate_file_type(None, metadata_document_directory, file_extension)
+            self.evaluate_file_type(metadata_document_directory, file_extension)
+            self.all_dicom_series.extend(self.post_read_processing(list(self.all_dicom_series_dict.values())[0], flag="single"))
         else:
             logging.error("No valid metadata file path.")
             raise FileNotFoundError("No valid metadata file path.")