fhir-sheets 2.1.1__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
@@ -11,22 +13,37 @@ 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):
+    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)
+        created_resources[entity_name] = fhir_resource
+        if entity_name == singleton_entity_name:
+            singleton_fhir_resource = fhir_resource
+    add_default_resource_links(created_resources, resource_link_entities)
+    create_resource_links(created_resources, resource_link_entities, preview_mode=True)
+    return singleton_fhir_resource
+
 #Initialize root bundle definition
 def initialize_bundle():
     root_bundle = {}
@@ -60,7 +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 = [
@@ -150,12 +167,21 @@ def add_default_resource_links(created_resources: dict, resource_link_entities:
     return
         
             
-#Create resource references/links with created entities
-def create_resource_links(created_resources, resource_link_entites):
+#List function to create resource references/links with created entities
+def create_resource_links(created_resources, resource_link_entites, preview_mode = False):
+    #TODO: Build resource links
+    print("Building resource links")
+    for resource_link_entity in resource_link_entites:
+        create_resource_link(created_resources, resource_link_entity, preview_mode)
+    return
+    
+#Singular function to create a resource link.
+def create_resource_link(created_resources, resource_link_entity, preview_mode = False):
+    # template scaffolding
     reference_json_block = {
         "reference" : "$value"
     }
-
+    #Special reference handling blocks, in the form of (origin_resource, destination_resource, reference_path)
     arrayType_references = [
         ('diagnosticreport', 'specimen', 'specimen'),
         ('diagnosticreport', 'practitioner', 'performer'),
@@ -165,35 +191,36 @@ def create_resource_links(created_resources, resource_link_entites):
         ('diagnosticreport', 'observation', 'result'),
         ('diagnosticreport', 'imagingStudy', 'imagingStudy'),
     ]
-    #TODO: Build resource links
-    print("Building resource links")
-    for resource_link_entity in resource_link_entites:
-        try:
-            origin_resource = created_resources[resource_link_entity.origin_resource]
-        except KeyError:
-            print(f"WARNING: In ResourceLinks tab, found a Origin Resource of : {resource_link_entity.origin_resource}  but no such entity found in PatientData")
-            continue
-        try:
-            destination_resource = created_resources[resource_link_entity.destination_resource]
-        except KeyError:
-            print(f"WARNING: In ResourceLinks tab, found a Desitnation Resource  of : {resource_link_entity.destination_resource}  but no such entity found in PatientData")
-            continue
-        destination_resource_type = created_resources[resource_link_entity.destination_resource]['resourceType']
-        destination_resource_id = created_resources[resource_link_entity.destination_resource]['id']
-        link_tuple = (created_resources[resource_link_entity.origin_resource]['resourceType'].strip().lower(),
-                      created_resources[resource_link_entity.destination_resource]['resourceType'].strip().lower(),
-                      resource_link_entity.reference_path.strip().lower())
-        if link_tuple in arrayType_references:
-            if resource_link_entity.reference_path.strip().lower() not in origin_resource:
-                origin_resource[resource_link_entity.reference_path.strip().lower()] = []
-            new_reference = reference_json_block.copy()
-            new_reference['reference'] = destination_resource_type + "/" + destination_resource_id
-            origin_resource[resource_link_entity.reference_path.strip().lower()].append(new_reference)
-        else:
-            origin_resource[resource_link_entity.reference_path.strip().lower()] = reference_json_block.copy()
-            origin_resource[resource_link_entity.reference_path.strip().lower()]["reference"] = destination_resource_type + "/" + destination_resource_id
+    #Find the origin and destination resource from the link
+    try:
+        origin_resource = created_resources[resource_link_entity.origin_resource]
+    except KeyError:
+        print(f"WARNING: In ResourceLinks tab, found a Origin Resource of : {resource_link_entity.origin_resource}  but no such entity found in PatientData")
+        return
+    try:
+        destination_resource = created_resources[resource_link_entity.destination_resource]
+    except KeyError:
+        print(f"WARNING: In ResourceLinks tab, found a Desitnation Resource  of : {resource_link_entity.destination_resource}  but no such entity found in PatientData")
+        return
+    #Estable the value of the refence
+    if preview_mode:
+        reference_value = destination_resource['resourceType'] + "/" + resource_link_entity.destination_resource
+    else:
+        reference_value = destination_resource['resourceType'] + "/" + destination_resource['id']
+    link_tuple = (origin_resource['resourceType'].strip().lower(),
+                    destination_resource['resourceType'].strip().lower(),
+                    resource_link_entity.reference_path.strip().lower())
+    if link_tuple in arrayType_references:
+        if resource_link_entity.reference_path.strip().lower() not in origin_resource:
+            origin_resource[resource_link_entity.reference_path.strip().lower()] = []
+        new_reference = reference_json_block.copy()
+        new_reference['reference'] = reference_value
+        origin_resource[resource_link_entity.reference_path.strip().lower()].append(new_reference)
+    else:
+        origin_resource[resource_link_entity.reference_path.strip().lower()] = reference_json_block.copy()
+        origin_resource[resource_link_entity.reference_path.strip().lower()]["reference"] = reference_value
     return
-    
+
 def add_resource_to_transaction_bundle(root_bundle, fhir_resource):
     entry = {}
     entry['fullUrl'] = "urn:uuid:"+fhir_resource['id']
@@ -235,7 +262,7 @@ def build_structure(current_struct: Dict, json_path: str, resource_definition: R
     #SPECIAL HANDLING CLAUSE
     matching_handler = next((handler for handler in special_values.custom_handlers if (json_path.startswith(handler) or json_path == handler)), None)
     if matching_handler is not None:
-        return special_values.custom_handlers[matching_handler].assign_value(json_path, resource_definition,  current_struct, parts[-1], value)
+        return special_values.custom_handlers[matching_handler].assign_value(json_path, resource_definition, dataType,  current_struct, parts[-1], value)
     #Ignore dollar sign ($) and drill farther down
     if part == '$' or part == resource_definition.resource_type.strip():
         #Ignore the dollar sign and the resourcetype
@@ -331,4 +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.py

@@ -33,7 +33,7 @@ def process_sheet_resource_definitions(sheet):
     headers = [cell.value for cell in next(sheet.iter_rows(min_row=1, max_row=1))]  # Get headers
 
     for row in sheet.iter_rows(min_row=3, values_only=True):
-        row_data = dict(zip(headers, row))  # Create a dictionary for each row
+        row_data = dict((h, r) for h, r in zip(headers, row) if h is not None)  # Create a dictionary for each row
         if all(cell is None or cell == "" for cell in row_data.values()):
             continue
         # Split 'Profile(s)' column into a list of URLs
@@ -41,7 +41,7 @@ def process_sheet_resource_definitions(sheet):
             row_data["Profile(s)"] = [url.strip() for url in row_data["Profile(s)"].split(",")]
         resource_definition_entities.append(ResourceDefinition(row_data))
         resource_definitions.append(row_data)
-
+    print(f"Resource Definitions\n----------{resource_definitions}")
     return resource_definition_entities
 
 # Function to process the specific sheet with 'OriginResource', 'ReferencePath', and 'DestinationResource'
@@ -55,57 +55,9 @@ def process_sheet_resource_links(sheet):
             continue
         resource_links.append(row_data)
         resource_link_entities.append(ResourceLink(row_data))
-
+    print(f"Resource Links\n----------{resource_links}")
     return resource_link_entities
 
-# Function to process the "PatientData" sheet
-def process_sheet_patient_data(sheet, resource_definition_entities):
-    # Initialize the dictionary to store the processed data
-    patient_data = {}
-    cohort_data = CohortData()
-    # Extract the data from the first 6 rows (Entity To Query, JsonPath, etc.)
-    for col in sheet.iter_cols(min_row=1, max_row=6, min_col=3, values_only=True):  # Start from 3rd column
-        if all(entry is None for entry in col):
-            continue
-        entity_name = col[0]  # The entity name comes from the first row (Entity To Query)
-        field_name = col[5]  #The "Data Element" comes from the fifth row
-        if (entity_name is None or entity_name == "") and (field_name is not None and field_name != ""):
-            print(f"WARNING: - Reading Patient Data Issue - {field_name} - 'Entity To Query' cell missing for column labelled '{field_name}', please provide entity name from the ResourceDefinitions tab.")
-
-        if entity_name not in [entry.entity_name for entry in resource_definition_entities]:
-            print(f"WARNING: - Reading Patient Data Issue - {field_name} - 'Entity To Query' cell has entity named '{entity_name}', however, the ResourceDefinition tab has no matching resource. Please provide a corresponding entry in the ResourceDefinition tab.")
-        # Create structure for this entity if not already present
-        if entity_name not in patient_data:
-            patient_data[entity_name] = {}
-            cohort_data.insert_entity(entity_name, EntityData({}))
-
-        # Add jsonpath, valuesets, and initialize an empty list for 'values'
-        if field_name not in patient_data[entity_name]:
-            field_data = {
-                "jsonpath": col[1],  # JsonPath from the second row
-                "valueType": col[2], # Value Type from the third row
-                "valuesets": col[3], # Value Set from the fourth row
-                "values": []         # Initialize empty list for actual values
-            }
-            patient_data[entity_name][field_name] = field_data
-            cohort_data.entities[entity_name].insert(field_name, FieldEntry(field_data))
-    
-    # Now process the rows starting from the 6th row (the actual data entries)
-    num_entries = 0
-    for row in sheet.iter_rows(min_row=7, values_only=True):  # Start from row 6 for actual data
-        if all(cell is None for cell in row):
-            continue
-        num_entries = num_entries + 1
-        entity_name = row[0]  # The entity name comes from the first column of each row
-        for i, value in enumerate(row[2:], start=1):  # Iterate through the values in the columns
-            entity_name = sheet.cell(row=1, column=i + 2).value
-            field_name = sheet.cell(row=6, column=i + 2).value  # Get the Data Element for this column
-            if entity_name in patient_data and field_name in patient_data[entity_name]:
-                # Append the actual data values to the 'values' array
-                cohort_data.entities[entity_name].fields[field_name].values.append(value)
-    cohort_data.num_entries = num_entries
-    return cohort_data
-
 # Function to process the "PatientData" sheet for the Revised CohortData
 def process_sheet_patient_data_revised(sheet, resource_definition_entities):
     headers = []
@@ -141,5 +93,7 @@ def process_sheet_patient_data_revised(sheet, resource_definition_entities):
             patients.extend([{}] * needed_count)
         for patient_dict, value in zip(patients, values):
             patient_dict[(entity_name, field_name)] = value
+    print(f"Headers\n----------{headers}")
+    print(f"Patients\n----------{patients}")
     cohort_data = CohortData(headers=headers, patients=patients)
     return cohort_data

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.py

@@ -7,7 +7,7 @@ from abc import ABC, abstractmethod
 class AbstractCustomValueHandler(ABC):
     
     @abstractmethod
-    def assign_value(self, json_path, resource_definition, final_struct, key, value):
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value):
         pass
     
 class PatientRaceExtensionValueHandler(AbstractCustomValueHandler):
@@ -67,7 +67,7 @@ class PatientRaceExtensionValueHandler(AbstractCustomValueHandler):
       "url" : "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race"
     }
     #Create an ombcategory and detailed section of race extension
-    def assign_value(self, json_path, resource_definition, final_struct, key, value):
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value):
         #Retrieve the race extension if it exists; make it if it does not.
         if 'extension' not in final_struct:
             final_struct['extension'] = []
@@ -128,7 +128,7 @@ class PatientEthnicityExtensionValueHandler(AbstractCustomValueHandler):
       "url" : "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity"
     }
     #Create an ombcategory and detailed section of ethnicitiy extension
-    def assign_value(self, json_path, resource_definition, final_struct, key, value):
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value):
         #Retrieve the ethncitiy extension if it exists; make it if it does not.
         if 'extension' not in final_struct:
             final_struct['extension'] = []
@@ -154,7 +154,7 @@ class PatientBirthSexExtensionValueHandler(AbstractCustomValueHandler):
       "valueCode" : "$value"
     }
     #Assigna birthsex extension
-    def assign_value(self, json_path, resource_definition, final_struct, key, value):
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value):
         #Retrieve the birthsex extension if it exists; make it if it does not.
         if 'extension' not in final_struct:
             final_struct['extension'] = []
@@ -182,7 +182,7 @@ class PatientMRNIdentifierValueHandler(AbstractCustomValueHandler):
       "value" : "$value"
     }
     #Assign a MRN identifier
-    def assign_value(self, json_path, resource_definition, final_struct, key, value):
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value):
         #Retrieve the MRN identifier if it exists; make it if it does not.
         target_identifier = self.patient_mrn_block
         new_identifier = True
@@ -215,7 +215,7 @@ class PatientSSNIdentifierValueHandler(AbstractCustomValueHandler):
       "value" : "$value"
     }
     #Assign a MRN identifier
-    def assign_value(self, json_path, resource_definition, final_struct, key, value):
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value):
         #Retrieve the MRN identifier if it exists; make it if it does not.
         target_identifier = self.patient_mrn_block
         new_identifier = True
@@ -238,7 +238,7 @@ class OrganizationIdentiferNPIValueHandler(AbstractCustomValueHandler):
       "value" : "$value"
     }
     #Assigna birthsex extension
-    def assign_value(self, json_path, resource_definition, final_struct, key, value):
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value):
         #Retrieve the birthsex extension if it exists; make it if it does not.
         if 'identifier' not in final_struct:
             final_struct['identifier'] = []
@@ -255,7 +255,7 @@ class OrganizationIdentiferCLIAValueHandler(AbstractCustomValueHandler):
       "value" : "$value"
     }
     #Assign a birthsex extension
-    def assign_value(self, json_path, resource_definition, final_struct, key, value):
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value):
         #Retrieve the birthsex extension if it exists; make it if it does not.
         if 'identifier' not in final_struct:
             final_struct['identifier'] = []
@@ -272,7 +272,7 @@ class PractitionerIdentiferNPIValueHandler(AbstractCustomValueHandler):
       "value" : "$value"
     }
     #Assigna birthsex extension
-    def assign_value(self, json_path, resource_definition, final_struct, key, value):
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value):
         #Retrieve the birthsex extension if it exists; make it if it does not.
         if 'identifier' not in final_struct:
             final_struct['identifier'] = []
@@ -309,7 +309,7 @@ class ObservationComponentHandler(AbstractCustomValueHandler):
       }
     }
     #Find the appropriate component for the observaiton; then call build_structure again to continue the drill down
-    def assign_value(self, json_path, resource_definition, final_struct, key, value):
+    def assign_value(self, json_path, resource_definition, dataType, final_struct, key, value):
         #Check to make sure the component part exists
         if 'component' not in final_struct:
           final_struct['component'] = []
@@ -330,7 +330,8 @@ class ObservationComponentHandler(AbstractCustomValueHandler):
           if target_component is self.pulse_oximetry_oxygen_concentration:
             components.append(target_component)
         #Recurse back down into 
-        return conversion.build_structure(target_component, '.'.join(parts[2:]), resource_definition, parts[2:], value, parts[:2])
+        # current_struct: Dict, json_path: str, resource_definition: ResourceDefinition, dataType: str, parts: List[str], value: Any, previous_parts: List[str]
+        return conversion.build_structure(target_component, '.'.join(parts[2:]), resource_definition, dataType, parts[2:], value, parts[:2])
         pass
 
 def utilFindExtensionWithURL(extension_block, url):

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-2.1.1.dist-info → fhir_sheets-2.1.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fhir-sheets
-Version: 2.1.1
+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
@@ -14,6 +14,7 @@ Requires-Dist: jsonpath-ng (==1.6.1)
 Requires-Dist: openpyxl (==3.1.5)
 Requires-Dist: orjson (==3.10.7)
 Requires-Dist: ply (==3.11)
+Requires-Dist: pytest_cov (==7.0.0)
 Description-Content-Type: text/markdown
 
 # FHIRSheets

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
+fhir_sheets/core/fhir_formatting.py,sha256=16IJtSm8ZZ4WNwnLHZXdePIbCA7wPz57ynUSuRpI1pA,13021
+fhir_sheets/core/fhir_formatting.pyi,sha256=JVju6WwzG7H9iI-5MO5Q0V-8-dNoWVxCzWLCFUW3cl4,512
+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/read_input.pyi,sha256=AU7XNMyqslTv183-fKQDZtUURvNEdvLdfpj9DPWZFbg,439
+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-2.1.1.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=BcIPmEImW6QvKhUsp0ycPbT6QYHj_tjU0ajubsvFohg,19330
-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=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-2.1.1.dist-info/METADATA,sha256=AlU4z_1F5CXwmSEaMT6rvGnR9RAp1JvyYpb3INJjThw,2911
-fhir_sheets-2.1.1.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-fhir_sheets-2.1.1.dist-info/licenses/LICENSE,sha256=Qv2ilebwoUtMJnRsZwRy729xS5JZQzLauJ0tQzkAkTA,1088
-fhir_sheets-2.1.1.dist-info/RECORD,,