fixed some bugs in the setup of the mapping

BIH-CEI · Sep 24, 2024 · b41738b · b41738b
1 parent efde206
commit b41738b
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Showing 2 changed files with 15 additions and 7 deletions.
diff --git a/src/phenopacket_mapper/mapping/mapper.py b/src/phenopacket_mapper/mapping/mapper.py
@@ -2,7 +2,7 @@
 
 from phenopackets import Phenopacket
 
-from phenopacket_mapper.data_standards.data_model import DataModel, DataSet, DataField
+from phenopacket_mapper.data_standards.data_model import DataModel, DataSet, DataField, DataFieldValue
 from phenopacket_mapper.mapping import PhenopacketElement
 
 
@@ -61,9 +61,12 @@ def map(self, data: DataSet) -> List[Phenopacket]:
             kwargs = {}
             for key, e in self.elements.items():
                 if isinstance(e, DataField):
-                    kwargs[key] = e
+                    data_field = e
+                    value: DataFieldValue = getattr(instance, data_field.id).value
+                    kwargs[key] = value
                 elif isinstance(e, PhenopacketElement):
-                    kwargs[key] = e.map(instance)
+                    phenopacket_element = e
+                    kwargs[key] = phenopacket_element.map(instance)
 
             try:
                 phenopackets_list.append(

diff --git a/src/phenopacket_mapper/mapping/phenopacket_element.py b/src/phenopacket_mapper/mapping/phenopacket_element.py
@@ -1,6 +1,6 @@
 from typing import Union, Dict
 
-from phenopacket_mapper.data_standards import DataModelInstance, DataField
+from phenopacket_mapper.data_standards import DataModelInstance, DataField, DataFieldValue
 
 
 class PhenopacketElement:
@@ -15,7 +15,7 @@ def __init__(self, phenopacket_element, **kwargs):
         """
         self.phenopacket_element = phenopacket_element
         self.elements: Dict[str, Union[PhenopacketElement, DataField]] = {}
-        for k, v in kwargs:
+        for k, v in kwargs.items():
             setattr(self, k, v)
             self.elements[k] = v
 
@@ -34,11 +34,16 @@ def map(self, instance: DataModelInstance):
         :param instance: the ´DataModelInstance´ from which to map to a Phenopacket schema element
         :return: the resulting Phenopacket schema element
         """
+        print(self.elements)
         kwargs = {}
         for key, e in self.elements.items():
+            print(f"{key=} {e=}")
             if isinstance(e, DataField):
-                kwargs[key] = e
+                data_field = e
+                value: DataFieldValue = getattr(instance, data_field.id).value
+                kwargs[key] = value
             elif isinstance(e, PhenopacketElement):
-                kwargs[key] = e.map(instance)
+                phenopacket_element = e
+                kwargs[key] = phenopacket_element.map(instance)
 
         return self.phenopacket_element(**kwargs)