fhir-sheets 2.1.3__py3-none-any.whl → 2.1.4__py3-none-any.whl

fhir_sheets/cli/main.py

@@ -1,3 +1,4 @@
+from ..core.config.FhirSheetsConfiguration import FhirSheetsConfiguration
 from ..core import read_input
 from ..core import conversion
 
@@ -18,7 +19,7 @@ def find_sets(d, path=""):
     elif isinstance(d, set):
         print(f"Set found at path: {path}")
         
-def main(input_file, output_folder):
+def main(input_file, output_folder, config=FhirSheetsConfiguration({})):
     # Step 1: Read the input file using read_input module
     
     # Check if the output folder exists, and create it if not
@@ -34,7 +35,7 @@ def main(input_file, output_folder):
         # Construct the file path for each JSON file
         file_path = output_folder_path / f"{i}.json"
         #Create a bundle
-        fhir_bundle = conversion.create_transaction_bundle(resource_definition_entities, resource_link_entities, cohort_data, i)
+        fhir_bundle = conversion.create_transaction_bundle(resource_definition_entities, resource_link_entities, cohort_data, i, config)
         # Step 3: Write the processed data to the output file
         find_sets(fhir_bundle)
         json_string = orjson.dumps(fhir_bundle)
@@ -55,8 +56,14 @@ if __name__ == "__main__":
     # Define the output file argument
     parser.add_argument('--output_folder', type=str, help="Path to save the output files", default="output/")
     
+    # Config object arguments
+    parser.add_argument('--preview_mode', type=str, help="Configuration option to generate resources as 'preview mode' references will reference the entity name. Will primarily be used to render a singular resource for preview.", default=False)
+    
+    # Define the output file argument
+    parser.add_argument('--medications_as_reference', type=str, help="Configuration option to create medication references. You may still provide medicationCodeableConcept, but a post process will convert the codeableconcepts to medication resources", default=False)
     # Parse the arguments
     args = parser.parse_args()
 
     # Call the main function with the provided arguments
-    main(args.input_file, args.output_folder)
+    config = FhirSheetsConfiguration(vars(args))
+    main(args.input_file, args.output_folder, config)

fhir_sheets/cli/main.pyi

@@ -0,0 +1,6 @@
+from ..core import conversion as conversion, read_input as read_input
+from ..core.config.FhirSheetsConfiguration import FhirSheetsConfiguration as FhirSheetsConfiguration
+from pprint import pprint as pprint
+
+def find_sets(d, path: str = '') -> None: ...
+def main(input_file, output_folder, config) -> None: ...

fhir_sheets/core/config/FhirSheetsConfiguration.py

@@ -0,0 +1,12 @@
+from typing import Any, Dict
+
+
+class FhirSheetsConfiguration():
+    def __init__(self, data: Dict[str, Any]):
+        self.preview_mode = data.get('preview_mode', False)
+        self.medications_as_reference = data.get('medications_as_reference', False)
+    
+    def __repr__(self) -> str:
+        return (f"FhirSheetsConfiguration("
+                f"preview_mode={self.preview_mode}, "
+                f"medications_as_reference={self.medications_as_reference})")

fhir_sheets/core/conversion.py

@@ -3,6 +3,8 @@ import uuid
 from jsonpath_ng.jsonpath import Fields, Slice, Where
 from jsonpath_ng.ext import parse as parse_ext
 
+from .config.FhirSheetsConfiguration import FhirSheetsConfiguration
+
 from .model.cohort_data_entity import CohortData, CohortData
 from .model.resource_definition_entity import ResourceDefinition
 from .model.resource_link_entity import ResourceLink
@@ -11,20 +13,22 @@ from . import special_values
 
 #Main top level function
 #Creates a full transaction bundle for a patient at index
-def create_transaction_bundle(resource_definition_entities: List[ResourceDefinition], resource_link_entities: List[ResourceLink], cohort_data: CohortData, index = 0):
+def create_transaction_bundle(resource_definition_entities: List[ResourceDefinition], resource_link_entities: List[ResourceLink], cohort_data: CohortData, index = 0, config: FhirSheetsConfiguration = FhirSheetsConfiguration({})):
     root_bundle = initialize_bundle()
     created_resources = {}
     for resource_definition in resource_definition_entities:
         entity_name = resource_definition.entity_name
         #Create and collect fhir resources
-        fhir_resource = create_fhir_resource(resource_definition, cohort_data, index)
+        fhir_resource = create_fhir_resource(resource_definition, cohort_data, index, config)
         created_resources[entity_name] = fhir_resource
     #Link resources after creation
     add_default_resource_links(created_resources, resource_link_entities)
-    create_resource_links(created_resources, resource_link_entities)
+    create_resource_links(created_resources, resource_link_entities, config.preview_mode)
     #Construct into fhir bundle
     for fhir_resource in created_resources.values():
         add_resource_to_transaction_bundle(root_bundle, fhir_resource)
+    if config.medications_as_reference:
+        post_process_create_medication_references(root_bundle)
     return root_bundle
 
 def create_singular_resource(singleton_entity_name: str, resource_definition_entities: List[ResourceDefinition], resource_link_entities: List[ResourceLink], cohort_data: CohortData, index = 0):
@@ -73,7 +77,7 @@ def initialize_resource(resource_definition):
     return initial_resource
 
 # Creates a fhir-json structure from a resource definition entity and the patient_data_sheet
-def create_fhir_resource(resource_definition: ResourceDefinition, cohort_data: CohortData, index = 0):
+def create_fhir_resource(resource_definition: ResourceDefinition, cohort_data: CohortData, index: int = 0, config: FhirSheetsConfiguration = None):
     resource_dict = initialize_resource(resource_definition)
     #Get field entries for this entity
     header_entries_for_resourcename = [
@@ -354,4 +358,27 @@ def build_structure(current_struct: Dict, json_path: str, resource_definition: R
 def build_structure_recurse(current_struct, json_path, resource_definition, dataType, parts, value, previous_parts, part):
     previous_parts.append(part)
     return_struct = build_structure(current_struct, json_path, resource_definition, dataType, parts[1:], value, previous_parts)
-    return return_struct
+    return return_struct
+
+#Post-process function to add medication reference in specific references
+def post_process_create_medication_references( root_bundle: dict):
+    medication_resources = [resource['resource'] for resource in root_bundle['entry'] if resource['resource']['resourceType'] == "Medication"]
+    medication_request_resources = [resource['resource'] for resource in root_bundle['entry'] if resource['resource']['resourceType'] == "MedicationRequest"]
+    for medication_request_resource in medication_request_resources:
+        #Get candidates
+        medication_candidates = [resource for resource in medication_resources if resource['code'] == medication_request_resource['medicationCodeableConcept']]
+        if not medication_candidates: #If no candidates, create, else get the first candidate
+            medication_target = target_medication = createMedicationResource(root_bundle, medication_request_resource['medicationCodeableConcept'])
+            medication_resources.append(target_medication)
+        else:
+            target_medication = medication_candidates[0]
+            
+        del(medication_request_resource['medicationCodeableConcept'])
+        medication_request_resource['medicationReference'] = target_medication['resourceType'] + "/" + target_medication['id']
+    return
+
+def createMedicationResource(root_bundle, medicationCodeableConcept):
+    target_medication = initialize_resource(ResourceDefinition({'ResourceType': 'Medication'}))
+    target_medication['code'] = medicationCodeableConcept
+    add_resource_to_transaction_bundle(root_bundle, target_medication)
+    return target_medication

fhir_sheets/core/conversion.pyi

@@ -0,0 +1,22 @@
+from . import fhir_formatting as fhir_formatting, special_values as special_values
+from .config.FhirSheetsConfiguration import FhirSheetsConfiguration as FhirSheetsConfiguration
+from .model.cohort_data_entity import CohortData as CohortData
+from .model.resource_definition_entity import ResourceDefinition as ResourceDefinition
+from .model.resource_link_entity import ResourceLink as ResourceLink
+from jsonpath_ng.jsonpath import Fields as Fields, Slice as Slice, Where as Where
+from typing import Any
+
+def create_transaction_bundle(resource_definition_entities: list[ResourceDefinition], resource_link_entities: list[ResourceLink], cohort_data: CohortData, index: int = 0, config: FhirSheetsConfiguration = ...): ...
+def create_singular_resource(singleton_entity_name: str, resource_definition_entities: list[ResourceDefinition], resource_link_entities: list[ResourceLink], cohort_data: CohortData, index: int = 0): ...
+def initialize_bundle(): ...
+def initialize_resource(resource_definition): ...
+def create_fhir_resource(resource_definition: ResourceDefinition, cohort_data: CohortData, index: int = 0, config: FhirSheetsConfiguration = None): ...
+def add_default_resource_links(created_resources: dict, resource_link_entities: list[ResourceLink]): ...
+def create_resource_links(created_resources, resource_link_entites, preview_mode: bool = False) -> None: ...
+def create_resource_link(created_resources, resource_link_entity, preview_mode: bool = False) -> None: ...
+def add_resource_to_transaction_bundle(root_bundle, fhir_resource): ...
+def create_structure_from_jsonpath(root_struct: dict, json_path: str, resource_definition: ResourceDefinition, dataType: str, value: Any): ...
+def build_structure(current_struct: dict, json_path: str, resource_definition: ResourceDefinition, dataType: str, parts: list[str], value: Any, previous_parts: list[str]): ...
+def build_structure_recurse(current_struct, json_path, resource_definition, dataType, parts, value, previous_parts, part): ...
+def post_process_create_medication_references(root_bundle: dict): ...
+def createMedicationResource(root_bundle, medicationCodeableConcept): ...

fhir_sheets/core/fhir_formatting.py

@@ -3,14 +3,14 @@ from datetime import datetime, time, timezone
 
 #Dictionary of regexes
 type_regexes = {
-    'code': '[^\s]+( [^\s]+)*',
-    'decimal': '-?(0|[1-9][0-9]{0,17})(\.[0-9]{1,17})?([eE][+-]?[0-9]{1,9}})?',
-    'id': '[A-Za-z0-9\-\.]{1,64}',
-    'integer': '[0]|[-+]?[1-9][0-9]*',
-    'oid': 'urn:oid:[0-2](\.(0|[1-9][0-9]*))+',
-    'positiveInt': '[1-9][0-9]*',
-    'unsignedInt':'[0]|([1-9][0-9]*)',
-    'uuid':'urn:uuid:[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}'
+    'code': r'[^\s]+( [^\s]+)*',
+    'decimal': r'-?(0|[1-9][0-9]{0,17})(\.[0-9]{1,17})?([eE][+-]?[0-9]{1,9}})?',
+    'id': r'[A-Za-z0-9\-\.]{1,64}',
+    'integer': r'[0]|[-+]?[1-9][0-9]*',
+    'oid': r'urn:oid:[0-2](\.(0|[1-9][0-9]*))+',
+    'positiveInt': r'[1-9][0-9]*',
+    'unsignedInt': r'[0]|([1-9][0-9]*)',
+    'uuid': r'urn:uuid:[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}'
 }
 # Assign final_struct[key] to value; with formatting given the valueType
 def assign_value(final_struct, key, value, valueType):

fhir_sheets/core/fhir_formatting.pyi

@@ -0,0 +1,13 @@
+from _typeshed import Incomplete
+
+type_regexes: Incomplete
+
+def assign_value(final_struct, key, value, valueType): ...
+def parse_iso8601_date(input_string): ...
+def parse_iso8601_datetime(input_string): ...
+def parse_iso8601_instant(input_string): ...
+def parse_iso8601_time(input_string): ...
+def parse_flexible_address(address): ...
+def caret_delimited_string_to_codeableconcept(caret_delimited_str): ...
+def caret_delimited_string_to_coding(caret_delimited_str): ...
+def string_to_quantity(quantity_str): ...

fhir_sheets/core/read_input.pyi

@@ -0,0 +1,8 @@
+from .model.cohort_data_entity import CohortData as CohortData
+from .model.resource_definition_entity import ResourceDefinition as ResourceDefinition
+from .model.resource_link_entity import ResourceLink as ResourceLink
+
+def read_xlsx_and_process(file_path): ...
+def process_sheet_resource_definitions(sheet): ...
+def process_sheet_resource_links(sheet): ...
+def process_sheet_patient_data_revised(sheet, resource_definition_entities): ...

fhir_sheets/core/special_values.pyi

@@ -0,0 +1,52 @@
+import abc
+from . import conversion as conversion
+from _typeshed import Incomplete
+from abc import ABC, abstractmethod
+
+class AbstractCustomValueHandler(ABC, metaclass=abc.ABCMeta):
+    @abstractmethod
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value): ...
+
+class PatientRaceExtensionValueHandler(AbstractCustomValueHandler):
+    omb_categories: Incomplete
+    initial_race_json: Incomplete
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value): ...
+
+class PatientEthnicityExtensionValueHandler(AbstractCustomValueHandler):
+    omb_categories: Incomplete
+    initial_ethnicity_json: Incomplete
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value): ...
+
+class PatientBirthSexExtensionValueHandler(AbstractCustomValueHandler):
+    birth_sex_block: Incomplete
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value) -> None: ...
+
+class PatientMRNIdentifierValueHandler(AbstractCustomValueHandler):
+    patient_mrn_block: Incomplete
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value) -> None: ...
+
+class PatientSSNIdentifierValueHandler(AbstractCustomValueHandler):
+    patient_mrn_block: Incomplete
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value) -> None: ...
+
+class OrganizationIdentiferNPIValueHandler(AbstractCustomValueHandler):
+    npi_identifier_block: Incomplete
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value) -> None: ...
+
+class OrganizationIdentiferCLIAValueHandler(AbstractCustomValueHandler):
+    clia_identifier_block: Incomplete
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value) -> None: ...
+
+class PractitionerIdentiferNPIValueHandler(AbstractCustomValueHandler):
+    npi_identifier_block: Incomplete
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value) -> None: ...
+
+class ObservationComponentHandler(AbstractCustomValueHandler):
+    pulse_oximetry_oxygen_flow_rate: Incomplete
+    pulse_oximetry_oxygen_concentration: Incomplete
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value): ...
+
+def utilFindExtensionWithURL(extension_block, url): ...
+def findComponentWithCoding(components, code): ...
+
+custom_handlers: Incomplete

{fhir_sheets-2.1.3.dist-info → fhir_sheets-2.1.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fhir-sheets
-Version: 2.1.3
+Version: 2.1.4
 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-2.1.4.dist-info/RECORD

@@ -0,0 +1,26 @@
+fhir_sheets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+fhir_sheets/__init__.pyi,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+fhir_sheets/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+fhir_sheets/cli/__init__.pyi,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+fhir_sheets/cli/main.py,sha256=zpCieUZUyC1JVVGo8eV4slaTxjHPhsJDUYpX3Pq-BaY,3417
+fhir_sheets/cli/main.pyi,sha256=9bGkkzW5u2Clbt6DQJ7HAYH1YfYguT4DlnomgX-vFkg,311
+fhir_sheets/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+fhir_sheets/core/__init__.pyi,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+fhir_sheets/core/config/FhirSheetsConfiguration.py,sha256=YFXfNaA5hpFPwp9wBeNogo7u2VR11-KO5uBY-Ckh8QY,465
+fhir_sheets/core/conversion.py,sha256=JmI62neonuPH0EbKed3i7tiUnT67l0ykSRLbKasfe-Q,22413
+fhir_sheets/core/conversion.pyi,sha256=YfPZjxsqcLf4pgS_2-R1mTlucBnV2kmGqwIlOOIvt0A,2135
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+fhir_sheets/core/special_values.py,sha256=WpwHpf1BHs5SerXi4x9WjjkiR1tIQL8CuGlZ0iEB_2A,15575
+fhir_sheets/core/special_values.pyi,sha256=fs3bm8QdzohNLQ_9roX79pYhuUDEJv_2NNzta3jFAJk,2472
+fhir_sheets/core/util.py,sha256=gudEPi_xTDC9YHqUlGEkn_tA26HbhNjuqGgjtuOEINk,9
+fhir_sheets/core/util.pyi,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+fhir_sheets-2.1.4.dist-info/METADATA,sha256=ZzOYeqcWaKKigoYgaMRc_PbnCik8I1_DLvfXceNEnFQ,2947
+fhir_sheets-2.1.4.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+fhir_sheets-2.1.4.dist-info/licenses/LICENSE,sha256=Qv2ilebwoUtMJnRsZwRy729xS5JZQzLauJ0tQzkAkTA,1088
+fhir_sheets-2.1.4.dist-info/RECORD,,

fhir_sheets-2.1.3.dist-info/RECORD

@@ -1,16 +0,0 @@
-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=0ctZTB30KwIHpjYyJgrEdJorDbn5WQIQuclIwHvp4Js,2650
-fhir_sheets/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-fhir_sheets/core/conversion.py,sha256=dCoB3tktiSibl8tp5_IyCV_ACO04GdrUcU9yztPgqAk,20463
-fhir_sheets/core/fhir_formatting.py,sha256=eNM38Cp7TEdND1fIKhp2HTwzGYDqgWtr13A1qRT06cY,13011
-fhir_sheets/core/model/cohort_data_entity.py,sha256=tRfHxuZdXvSk-OerPpbCBEfJJAo6f1L-If-p0ltC51Q,1382
-fhir_sheets/core/model/resource_definition_entity.py,sha256=1yRzNWwewCSle_6u8CBW_l7nGg1aQDVIJCprKKdv_MU,746
-fhir_sheets/core/model/resource_link_entity.py,sha256=-iCzGaKJt5ZISTSwBVmEuLIKzgRtbL_I7JRpoEc89h0,812
-fhir_sheets/core/read_input.py,sha256=QSk-TzXRX9tmJZ3Qa3qQJxGQa3PwBrN93KlHKN8DpJA,5229
-fhir_sheets/core/special_values.py,sha256=WpwHpf1BHs5SerXi4x9WjjkiR1tIQL8CuGlZ0iEB_2A,15575
-fhir_sheets/core/util.py,sha256=gudEPi_xTDC9YHqUlGEkn_tA26HbhNjuqGgjtuOEINk,9
-fhir_sheets-2.1.3.dist-info/METADATA,sha256=Rt7DoOg5Xewtfxe86IhW3z1qK-dPL3tECjp_9kRSjgI,2947
-fhir_sheets-2.1.3.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-fhir_sheets-2.1.3.dist-info/licenses/LICENSE,sha256=Qv2ilebwoUtMJnRsZwRy729xS5JZQzLauJ0tQzkAkTA,1088
-fhir_sheets-2.1.3.dist-info/RECORD,,