fixed: Remove null values from CDS Hook API responses #142

.gitignore

@@ -167,3 +167,5 @@ scrap/
 .python-version
 .cursor/
 scripts/
+.idea/
+.idea/

healthchain/gateway/events/dispatcher.py

@@ -121,7 +121,7 @@ async def publish(self, event: EHREvent, middleware_id: Optional[int] = None):
         """
         # Convert event to the format expected by fastapi-events
         event_name = event.event_type.value
-        event_data = event.model_dump()
+        event_data = event.model_dump(exclude_none=True)
 
         # Use the provided middleware_id or fall back to the class's middleware_id
         mid = middleware_id or self.middleware_id

healthchain/gateway/fhir/aio.py

@@ -414,7 +414,9 @@ async def modify(
                 updated_resource = await client.update(resource)
 
             resource.id = updated_resource.id
-            for field_name, field_value in updated_resource.model_dump().items():
+            for field_name, field_value in updated_resource.model_dump(
+                exclude_none=True
+            ).items():
                 if hasattr(resource, field_name):
                     setattr(resource, field_name, field_value)
 

healthchain/gateway/fhir/base.py

@@ -103,7 +103,7 @@ def capability_statement(
             Includes both custom transform/aggregate operations (via REST endpoints)
             and standard FHIR CRUD operations (via Python gateway methods).
             """
-            return fhir.build_capability_statement().model_dump()
+            return fhir.build_capability_statement().model_dump(exclude_none=True)
 
         # Gateway status endpoint - returns operational metadata
         @self.get("/status", response_class=JSONResponse)

healthchain/interop/generators/cda.py

@@ -133,7 +133,7 @@ def _render_entry(
             context = {
                 "timestamp": timestamp,
                 "text_reference_name": reference_name,
-                "resource": resource.model_dump(),
+                "resource": resource.model_dump(exclude_none=True),
                 "config": section_config,
             }
 

healthchain/io/containers/document.py

@@ -700,7 +700,9 @@ def update_problem_list_from_nlp(
                     system=coding_system,
                 )
                 set_problem_list_item_category(condition)
-                logger.debug(f"Adding condition from spaCy: {condition.model_dump()}")
+                logger.debug(
+                    f"Adding condition from spaCy: {condition.model_dump(exclude_none=True)}"
+                )
                 new_conditions.append(condition)
 
         # 2. Extract from generic NLP entities (framework-agnostic)
@@ -725,7 +727,7 @@ def update_problem_list_from_nlp(
                 )
                 set_problem_list_item_category(condition)
                 logger.debug(
-                    f"Adding condition from entities: {condition.model_dump()}"
+                    f"Adding condition from entities: {condition.model_dump(exclude_none=True)}"
                 )
                 new_conditions.append(condition)
 

pyproject.toml

@@ -22,7 +22,7 @@ include = [
     "healthchain/configs/**/*.liquid"
 ]
 
-[project.urls]
+[tool.poetry.urls]
 "Homepage" = "https://dotimplement.github.io/HealthChain/"
 "Repository" = "https://github.com/dotimplement/HealthChain"
 

tests/conftest.py

@@ -66,7 +66,6 @@ def empty_bundle():
     return create_bundle()
 
 
-
 @pytest.fixture
 def test_condition():
     """Provides a minimal, generic FHIR Condition resource.
@@ -261,9 +260,12 @@ def doc_ref_without_content():
         fhir.resources.documentreference.DocumentReference: An incomplete DocumentReference resource.
     """
     from fhir.resources.attachment import Attachment
+
     return DocumentReference(
         status="current",
-        content=[DocumentReferenceContent(attachment=Attachment(contentType="text/plain"))],  # Missing required data or url
+        content=[
+            DocumentReferenceContent(attachment=Attachment(contentType="text/plain"))
+        ],  # Missing required data or url
     )
 
 

tests/gateway/test_base_fhir_gateway.py

@@ -119,7 +119,10 @@ def test_empty_capability_statement_with_no_handlers(fhir_gateway):
     """Gateway with no handlers generates minimal CapabilityStatement."""
     capability = fhir_gateway.build_capability_statement()
 
-    assert capability.model_dump()["resourceType"] == "CapabilityStatement"
+    assert (
+        capability.model_dump(exclude_none=True)["resourceType"]
+        == "CapabilityStatement"
+    )
     assert capability.status == "active"
     assert capability.kind == "instance"
 

tests/gateway/test_event_dispatcher.py

@@ -143,7 +143,7 @@ async def test_event_publishing_with_default_middleware_id(
 
     mock_dispatch.assert_called_once_with(
         "fhir.read",
-        sample_ehr_event.model_dump(),
+        sample_ehr_event.model_dump(exclude_none=True),
         middleware_id=event_dispatcher.middleware_id,
     )
 
@@ -160,7 +160,9 @@ async def test_event_publishing_with_custom_middleware_id(
     await event_dispatcher.publish(sample_ehr_event, middleware_id=custom_middleware_id)
 
     mock_dispatch.assert_called_once_with(
-        "fhir.read", sample_ehr_event.model_dump(), middleware_id=custom_middleware_id
+        "fhir.read",
+        sample_ehr_event.model_dump(exclude_none=True),
+        middleware_id=custom_middleware_id,
     )
 
 
@@ -182,7 +184,7 @@ async def mock_coroutine():
     # Verify dispatch was called with correct parameters
     mock_dispatch.assert_called_once_with(
         "fhir.read",
-        sample_ehr_event.model_dump(),
+        sample_ehr_event.model_dump(exclude_none=True),
         middleware_id=event_dispatcher.middleware_id,
     )
 

tests/pipeline/test_cdsfhiradapter.py

@@ -29,7 +29,9 @@ def test_parse_with_document_reference(
     cds_fhir_adapter, test_cds_request, doc_ref_with_content
 ):
     # Add DocumentReference to prefetch data
-    test_cds_request.prefetch["document"] = doc_ref_with_content.model_dump()
+    test_cds_request.prefetch["document"] = doc_ref_with_content.model_dump(
+        exclude_none=True
+    )
 
     # Call the input method
     result = cds_fhir_adapter.parse(test_cds_request)
@@ -44,7 +46,9 @@ def test_parse_with_multiple_attachments(
     cds_fhir_adapter, test_cds_request, doc_ref_with_multiple_content
 ):
     # Add DocumentReference to prefetch data
-    test_cds_request.prefetch["document"] = doc_ref_with_multiple_content.model_dump()
+    test_cds_request.prefetch["document"] = doc_ref_with_multiple_content.model_dump(
+        exclude_none=True
+    )
 
     # Call the input method
     result = cds_fhir_adapter.parse(test_cds_request)
@@ -73,7 +77,9 @@ def test_parse_with_custom_document_key(
     cds_fhir_adapter, test_cds_request, doc_ref_with_content
 ):
     # Add DocumentReference to prefetch data with custom key
-    test_cds_request.prefetch["custom_key"] = doc_ref_with_content.model_dump()
+    test_cds_request.prefetch["custom_key"] = doc_ref_with_content.model_dump(
+        exclude_none=True
+    )
 
     # Call the input method with custom key
     result = cds_fhir_adapter.parse(
@@ -90,7 +96,9 @@ def test_parse_with_document_reference_error(
     cds_fhir_adapter, test_cds_request, doc_ref_without_content, caplog
 ):
     # Add invalid DocumentReference to prefetch data
-    test_cds_request.prefetch["document"] = doc_ref_without_content.model_dump()
+    test_cds_request.prefetch["document"] = doc_ref_without_content.model_dump(
+        exclude_none=True
+    )
 
     # Call the input method
     result = cds_fhir_adapter.parse(test_cds_request)