fhir-sheets 2.0.0__tar.gz → 2.1.1__tar.gz

{fhir_sheets-2.0.0 → fhir_sheets-2.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fhir-sheets
-Version: 2.0.0
+Version: 2.1.1
 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 → fhir_sheets-2.1.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fhir-sheets"
-version = "2.0.0"
+version = "2.1.1"
 description = "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."
 authors = ["Michael Riley <Michael.Riley@gtri.gatech.edu>"]
 packages = [{include = "fhir_sheets", from = "src"}]

{fhir_sheets-2.0.0 → fhir_sheets-2.1.1}/src/fhir_sheets/cli/main.py

@@ -29,7 +29,6 @@ def main(input_file, output_folder):
     if not output_folder_path.exists():
         output_folder_path.mkdir(parents=True, exist_ok=True)  # Create the folder if it doesn't exist
     resource_definition_entities, resource_link_entities, cohort_data = read_input.read_xlsx_and_process(input_file)
-    pprint(cohort_data)
     #For each index of patients
     for i in range(0,cohort_data.get_num_patients()):
         # Construct the file path for each JSON file

{fhir_sheets-2.0.0 → fhir_sheets-2.1.1}/src/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-2.0.0 → fhir_sheets-2.1.1}/src/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-2.0.0 → fhir_sheets-2.1.1}/src/fhir_sheets/core/model/resource_definition_entity.py

@@ -17,4 +17,4 @@ class ResourceDefinition:
         self.profiles = entity_data.get('Profile(s)')
 
     def __repr__(self) -> str:
-        return f"FhirEntity(entity_name='{self.entity_name}', resource_type='{self.resource_type}', profiles={self.profiles})"
+        return f"ResourceDefinition(entity_name='{self.entity_name}', resource_type='{self.resource_type}', profiles={self.profiles})"

{fhir_sheets-2.0.0 → fhir_sheets-2.1.1}/src/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