Improvement/fhir resources transition

healthchain/data_generators/basegenerators.py

@@ -4,29 +4,10 @@
 import string
 
 from faker import Faker
-from healthchain.fhir_resources.primitives import (
-    booleanModel,
-    canonicalModel,
-    codeModel,
-    dateModel,
-    dateTimeModel,
-    decimalModel,
-    idModel,
-    instantModel,
-    integerModel,
-    markdownModel,
-    positiveIntModel,
-    stringModel,
-    timeModel,
-    unsignedIntModel,
-    uriModel,
-    urlModel,
-    uuidModel,
-)
-from healthchain.fhir_resources.generalpurpose import (
-    CodeableConcept,
-    Coding,
-)
+
+
+from fhir.resources.codeableconcept import CodeableConcept
+from fhir.resources.coding import Coding
 
 
 faker = Faker()
@@ -65,122 +46,120 @@ def generate():
 class BooleanGenerator(BaseGenerator):
     @staticmethod
     def generate():
-        return booleanModel(random.choice(["true", "false"]))
+        return random.choice([True, False])
 
 
 @register_generator
 class CanonicalGenerator(BaseGenerator):
     @staticmethod
     def generate():
-        return canonicalModel(f"https://example/{faker.uri_path()}")
+        return f"https://example/{faker.uri_path()}"
 
 
 @register_generator
 class CodeGenerator(BaseGenerator):
     # TODO: Codes can technically have whitespace but here I've left it out for simplicity
     @staticmethod
     def generate():
-        return codeModel(
-            "".join(random.choices(string.ascii_uppercase + string.digits, k=6))
-        )
+        return "".join(random.choices(string.ascii_uppercase + string.digits, k=6))
 
 
 @register_generator
 class DateGenerator(BaseGenerator):
     @staticmethod
     def generate():
-        return dateModel(faker.date())
+        return faker.date()
 
 
 @register_generator
 class DateTimeGenerator(BaseGenerator):
     @staticmethod
     def generate():
-        return dateTimeModel(faker.date_time().isoformat())
+        return faker.date_time().isoformat()
 
 
 @register_generator
 class DecimalGenerator(BaseGenerator):
     @staticmethod
     def generate():
-        return decimalModel(faker.random_number())
+        return faker.random_number()
 
 
 @register_generator
 class IdGenerator(BaseGenerator):
     @staticmethod
     def generate():
-        return idModel(faker.uuid4())
+        return faker.uuid4()
 
 
 @register_generator
 class InstantGenerator(BaseGenerator):
     @staticmethod
     def generate():
-        return instantModel(faker.date_time().isoformat())
+        return faker.date_time().isoformat()
 
 
 @register_generator
 class IntegerGenerator(BaseGenerator):
     @staticmethod
     def generate():
-        return integerModel(faker.random_int())
+        return faker.random_int()
 
 
 @register_generator
 class MarkdownGenerator(BaseGenerator):
     @staticmethod
     def generate():
-        return markdownModel(faker.text())
+        return faker.text()
 
 
 @register_generator
 class PositiveIntGenerator(BaseGenerator):
     @staticmethod
     def generate():
-        return positiveIntModel(faker.random_int(min=1))
+        return faker.random_int(min=1)
 
 
 @register_generator
 class StringGenerator(BaseGenerator):
     @staticmethod
     def generate():
-        return stringModel(faker.word())
+        return faker.word()
 
 
 @register_generator
 class TimeGenerator(BaseGenerator):
     @staticmethod
     def generate():
-        return timeModel(faker.time())
+        return faker.time()
 
 
 @register_generator
 class UnsignedIntGenerator(BaseGenerator):
     @staticmethod
     def generate():
-        return unsignedIntModel(faker.random_int(min=0))
+        return faker.random_int(min=0)
 
 
 @register_generator
 class UriGenerator(BaseGenerator):
     @staticmethod
     def generate():
-        return uriModel(f"https://example/{faker.uri_path()}")
+        return f"https://example/{faker.uri_path()}"
 
 
 @register_generator
 class UrlGenerator(BaseGenerator):
     @staticmethod
     def generate():
-        return urlModel(f"https://example/{faker.uri_path()}")
+        return f"https://example/{faker.uri_path()}"
 
 
 @register_generator
 class UuidGenerator(BaseGenerator):
     @staticmethod
     def generate():
-        return uuidModel(faker.uuid4())
+        return faker.uuid4()
 
 
 class CodeableConceptGenerator(BaseGenerator):
@@ -201,7 +180,7 @@ def generate_from_valueset(ValueSet):
                     system=value_set_instance.system,
                     code=code,
                     display=display,
-                    # extension=[ExtensionModel(value_set_instance.extension)],
+                    # extension=[Extension(value_set_instance.extension)],
                 )
             ]
         )

healthchain/data_generators/cdsdatagenerator.py

@@ -7,10 +7,10 @@
 from pathlib import Path
 
 from healthchain.base import Workflow
-from healthchain.fhir_resources.bundleresources import Bundle, BundleEntry
+from fhir.resources.bundle import Bundle, BundleEntry
 from healthchain.data_generators.basegenerators import generator_registry
-from healthchain.fhir_resources.documentreference import DocumentReference
-from healthchain.fhir_resources.generalpurpose import Narrative
+from fhir.resources.documentreference import DocumentReference
+from fhir.resources.narrative import Narrative
 from healthchain.models.data.cdsfhirdata import CdsFhirData
 
 logger = logging.getLogger(__name__)

healthchain/data_generators/conditiongenerators.py

@@ -7,16 +7,13 @@
     register_generator,
     CodeableConceptGenerator,
 )
-from healthchain.fhir_resources.generalpurpose import (
-    CodeableConcept,
-    Coding,
-    Reference,
-)
-from healthchain.fhir_resources.condition import (
-    Condition,
-    ConditionStage,
-    ConditionParticipant,
-)
+
+from fhir.resources.codeableconcept import CodeableConcept
+from fhir.resources.coding import Coding
+from fhir.resources.reference import Reference
+
+from fhir.resources.condition import Condition, ConditionStage, ConditionParticipant
+
 from healthchain.data_generators.value_sets.conditioncodes import (
     ConditionCodeSimple,
     ConditionCodeComplex,
@@ -156,7 +153,6 @@ def generate(
             constraints=constraints
         )
         return Condition(
-            resourceType="Condition",
             id=generator_registry.get("IdGenerator").generate(),
             clinicalStatus=generator_registry.get("ClinicalStatusGenerator").generate(),
             verificationStatus=generator_registry.get(

healthchain/data_generators/encountergenerators.py

@@ -1,45 +1,37 @@
 from typing import Optional
 from faker import Faker
 
-from healthchain.fhir_resources.encounter import (
-    Encounter,
-    EncounterLocation,
-)
-from healthchain.fhir_resources.primitives import dateTimeModel
-from healthchain.fhir_resources.generalpurpose import (
-    Coding,
-    CodeableConcept,
-    Period,
-    Reference,
-)
+from fhir.resources.encounter import Encounter, EncounterLocation
+
+from fhir.resources.coding import Coding
+from fhir.resources.codeableconcept import CodeableConcept
+from fhir.resources.period import Period
+from fhir.resources.reference import Reference
 from healthchain.data_generators.basegenerators import (
     BaseGenerator,
     generator_registry,
     register_generator,
 )
 
+from datetime import datetime
+
 
 faker = Faker()
 
 
 @register_generator
 class PeriodGenerator(BaseGenerator):
-    """
-    A generator class for creating FHIR Period resources.
-
-    Methods:
-        generate() -> Period:
-            Generates a FHIR Period resource with random start and end times.
-    """
-
     @staticmethod
     def generate():
-        start = faker.date_time()
-        end = faker.date_time_between(start_date=start).isoformat()
-        start = start.isoformat()
+        # Use date_between instead of date() for more control
+        start = faker.date_between(
+            start_date="-30y",  # You can adjust this range
+            end_date="today",
+        )
+        end = faker.date_between_dates(date_start=start, date_end=datetime.now())
         return Period(
-            start=dateTimeModel(start),
-            end=dateTimeModel(end),
+            start=start,
+            end=end,
         )
 
 
@@ -155,7 +147,6 @@ def generate(
         Faker.seed(random_seed)
         patient_reference = "Patient/123"
         return Encounter(
-            resourceType="Encounter",
             id=generator_registry.get("IdGenerator").generate(),
             status=faker.random_element(
                 elements=(
@@ -166,9 +157,9 @@ def generate(
                     "cancelled",
                 )
             ),
-            class_field=[generator_registry.get("ClassGenerator").generate()],
+            class_fhir=[generator_registry.get("ClassGenerator").generate()],
             priority=generator_registry.get("EncounterPriorityGenerator").generate(),
-            type_field=[generator_registry.get("EncounterTypeGenerator").generate()],
+            type=[generator_registry.get("EncounterTypeGenerator").generate()],
             subject={"reference": patient_reference, "display": patient_reference},
             actualPeriod=generator_registry.get("PeriodGenerator").generate(),
             location=[generator_registry.get("EncounterLocationGenerator").generate()],

healthchain/data_generators/medicationadministrationgenerators.py

@@ -1,15 +1,10 @@
 from typing import Optional
 from faker import Faker
 
-from healthchain.fhir_resources.medicationadministration import (
-    MedicationAdministration,
-    MedicationAdministrationDosage,
-)
-from healthchain.fhir_resources.generalpurpose import (
-    Reference,
-    CodeableReference,
-)
-from healthchain.fhir_resources.medicationrequest import Medication
+from fhir.resources.medicationadministration import MedicationAdministration
+from fhir.resources.medicationadministration import MedicationAdministrationDosage
+from fhir.resources.reference import Reference
+from fhir.resources.codeablereference import CodeableReference
 from healthchain.data_generators.basegenerators import (
     BaseGenerator,
     generator_registry,
@@ -42,16 +37,9 @@ def generate(
         encounter_reference: str,
         constraints: Optional[list] = None,
     ):
-        contained_medication = Medication(
-            code=generator_registry.get(
-                "MedicationRequestContainedGenerator"
-            ).generate()
-        )
         return MedicationAdministration(
-            resourceType="MedicationAdministration",
             id=generator_registry.get("IdGenerator").generate(),
             status=generator_registry.get("EventStatusGenerator").generate(),
-            contained=[contained_medication],
             medication=CodeableReference(
                 reference=Reference(reference="Medication/123")
             ),

healthchain/data_generators/medicationrequestgenerators.py

@@ -1,15 +1,6 @@
 from typing import Optional
 from faker import Faker
 
-from healthchain.fhir_resources.medicationrequest import (
-    MedicationRequest,
-    Medication,
-    Dosage,
-)
-from healthchain.fhir_resources.generalpurpose import (
-    Reference,
-    CodeableReference,
-)
 from healthchain.data_generators.basegenerators import (
     BaseGenerator,
     generator_registry,
@@ -19,6 +10,10 @@
 from healthchain.data_generators.value_sets.medicationcodes import (
     MedicationRequestMedication,
 )
+from fhir.resources.medicationrequest import MedicationRequest
+from fhir.resources.dosage import Dosage
+from fhir.resources.reference import Reference
+from fhir.resources.codeablereference import CodeableReference
 
 
 faker = Faker()
@@ -51,16 +46,10 @@ def generate(
         Faker.seed(random_seed)
         subject_reference = "Patient/123"
         encounter_reference = "Encounter/123"
-        contained_medication = Medication(
-            code=generator_registry.get(
-                "MedicationRequestContainedGenerator"
-            ).generate()
-        )
         return MedicationRequest(
             resourceType="MedicationRequest",
             id=generator_registry.get("IdGenerator").generate(),
             status=generator_registry.get("EventStatusGenerator").generate(),
-            contained=[contained_medication],
             medication=CodeableReference(
                 reference=Reference(reference="Medication/123")
             ),