fhir-sheets 2.0.0__py3-none-any.whl → 2.1.0__py3-none-any.whl

fhir_sheets/core/conversion.py

@@ -69,20 +69,20 @@ def create_fhir_resource(resource_definition: ResourceDefinition, cohort_data: C
         if headerEntry.entityName == resource_definition.entity_name
     ]
     dataelements_for_resourcename = {
-        key: value
-        for key, value in cohort_data.patients[index].entries.items()
-        if value['entity_name'] == resource_definition.entity_name
+        field_name: value
+        for (entity_name, field_name), value in cohort_data.patients[index].entries.items()
+        if entity_name == resource_definition.entity_name
     }
     if len(dataelements_for_resourcename.keys()) == 0:
         print(f"WARNING: Patient index {index} - Create Fhir Resource Error - {resource_definition.entity_name} - No columns for entity '{resource_definition.entity_name}' found for resource in 'PatientData' sheet")
         return resource_dict
         all_field_entries = cohort_data.entities[resource_definition.entity_name].fields
     #For each field within the entity
-    for fieldname, dataelement in dataelements_for_resourcename.items():
+    for fieldname, value in dataelements_for_resourcename.items():
         header_element = next((header for header in header_entries_for_resourcename if header.fieldName == fieldname), None)
         if header_element is None:
             print(f"WARNING: Field Name {fieldname} - No Header Entry found.")
-        create_structure_from_jsonpath(resource_dict, header_element.jsonpath, resource_definition, header_element.value_type, dataelement['value'])
+        create_structure_from_jsonpath(resource_dict, header_element.jsonpath, resource_definition, header_element.value_type, value)
     return resource_dict
 
 #Create a resource_link for default references in the cases where only 1 resourceType of the source and destination exist

fhir_sheets/core/model/cohort_data_entity.py

@@ -1,4 +1,3 @@
-import pprint
 from typing import Dict, Any, List, Optional, Tuple
 
 class HeaderEntry:
@@ -15,14 +14,14 @@ class HeaderEntry:
     
 class PatientEntry:
 
-    def __init__(self, entries:Dict[str,str]):
+    def __init__(self, entries:Dict[Tuple[str,str],str]):
         self.entries = entries
 
     def __repr__(self) -> str:
         return (f"PatientEntry(\n\t'{self.entries}')")
     
 class CohortData:
-    def __init__(self, headers: List[Dict[str,Any]], patients: List[Dict[str,str]]):
+    def __init__(self, headers: List[Dict[str,Any]], patients: List[Dict[Tuple[str,str],str]]):
         self.headers = [HeaderEntry(header_data) for header_data in headers]
         self.patients = [PatientEntry(patient_data) for patient_data in patients]
 

fhir_sheets/core/read_input.py

@@ -140,8 +140,6 @@ def process_sheet_patient_data_revised(sheet, resource_definition_entities):
             needed_count = len(values) - len(patients)
             patients.extend([{}] * needed_count)
         for patient_dict, value in zip(patients, values):
-            patient_dict[field_name] = {}
-            patient_dict[field_name]["entity_name"] = entity_name
-            patient_dict[field_name]["value"] = value
+            patient_dict[(entity_name, field_name)] = value
     cohort_data = CohortData(headers=headers, patients=patients)
     return cohort_data

{fhir_sheets-2.0.0.dist-info → fhir_sheets-2.1.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fhir-sheets
-Version: 2.0.0
+Version: 2.1.0
 Summary: FhirSheets is a command-line tool that reads an Excel file in FHIR cohort format and generates FHIR bundle JSON files from it. Each row in the template Excel file is used to create an individual JSON file, outputting them to a specified folder.
 License-File: LICENSE
 Author: Michael Riley

{fhir_sheets-2.0.0.dist-info → fhir_sheets-2.1.0.dist-info}/RECORD

@@ -2,15 +2,15 @@ fhir_sheets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fhir_sheets/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fhir_sheets/cli/main.py,sha256=OPuiQtWgmPbN_uErdSDgnAllFlMWO43A9ZhvAY9-dN8,2675
 fhir_sheets/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-fhir_sheets/core/conversion.py,sha256=ntxBlMbC3l31QKnTHS2P55_RuHMHqzyh_HplZJStKZg,19331
+fhir_sheets/core/conversion.py,sha256=BcIPmEImW6QvKhUsp0ycPbT6QYHj_tjU0ajubsvFohg,19330
 fhir_sheets/core/fhir_formatting.py,sha256=eNM38Cp7TEdND1fIKhp2HTwzGYDqgWtr13A1qRT06cY,13011
-fhir_sheets/core/model/cohort_data_entity.py,sha256=4LJ32A9BBAsK0SIWIlbHPr7Ke3it2VEroHKgCIsk4eI,1374
+fhir_sheets/core/model/cohort_data_entity.py,sha256=tRfHxuZdXvSk-OerPpbCBEfJJAo6f1L-If-p0ltC51Q,1382
 fhir_sheets/core/model/resource_definition_entity.py,sha256=NYOBjGz2LyfjI9LVl7j34fcAp-qEmzrBTg9ZLpFfDxA,738
 fhir_sheets/core/model/resource_link_entity.py,sha256=-iCzGaKJt5ZISTSwBVmEuLIKzgRtbL_I7JRpoEc89h0,812
-fhir_sheets/core/read_input.py,sha256=WHA-OfU8mOn3Ty1ofzcnGgvAx5IaPuEDKywoBBwR_pw,8253
+fhir_sheets/core/read_input.py,sha256=ErChyIfadNKtWYOgM3hDO04btNe0T0xcFwzcUrcEYTQ,8149
 fhir_sheets/core/special_values.py,sha256=k2HcKaFlx41zMeIC-p-0DEtvqOWLT3tnMtyFX1XXXW8,15304
 fhir_sheets/core/util.py,sha256=gudEPi_xTDC9YHqUlGEkn_tA26HbhNjuqGgjtuOEINk,9
-fhir_sheets-2.0.0.dist-info/METADATA,sha256=FIfJJt7PORyICjv61E8Bombhy7sdpSEs0YHZsxHHMFY,2911
-fhir_sheets-2.0.0.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-fhir_sheets-2.0.0.dist-info/licenses/LICENSE,sha256=Qv2ilebwoUtMJnRsZwRy729xS5JZQzLauJ0tQzkAkTA,1088
-fhir_sheets-2.0.0.dist-info/RECORD,,
+fhir_sheets-2.1.0.dist-info/METADATA,sha256=Sa2ZBZJkuhtKzoukatr1ElKXR-IhdSSdoVMnKJqq0OY,2911
+fhir_sheets-2.1.0.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+fhir_sheets-2.1.0.dist-info/licenses/LICENSE,sha256=Qv2ilebwoUtMJnRsZwRy729xS5JZQzLauJ0tQzkAkTA,1088
+fhir_sheets-2.1.0.dist-info/RECORD,,