Correctly find reportable conditions

containers/trigger-code-reference/app/utils.py

@@ -4,6 +4,8 @@
 from typing import List
 from typing import Union
 
+import fhirpathpy
+
 
 def convert_inputs_to_list(value: Union[list, str, int, float]) -> list:
  """
@@ -200,31 +202,25 @@ def read_json_from_assets(filename: str) -> dict:
 
 def find_conditions(bundle: dict) -> set[str]:
  """
- Finds conditions in a bundle of resources.
+ Extracts the SNOMED codes of reportable conditions from a FHIR bundle.
 
- :param bundle: The bundle of resources to search.
- :return: A set of SNOMED codes representing the conditions found.
+ :param bundle: A FHIR bundle
+ :return: A set of SNOMED codes for reportable conditions
  """
- CONDITION_CODE = "64572001"
- SNOMED_URL = "http://snomed.info/sct"
-
- # Get all resources
- resources = [resource["resource"] for resource in bundle["entry"]]
 
- # Filter observations that have the SNOMED code for "Condition".
- resources_with_conditions = [
- obs
- for obs in resources
- if "code" in obs
- and any(coding["code"] == CONDITION_CODE for coding in obs["code"]["coding"])
- ]
+ path_to_reportability_response_info_section = fhirpathpy.compile(
+ "Bundle.entry.resource.where(resourceType='Composition').section.where(title = 'Reportability Response Information Section').entry"
+ )
+ trigger_entries = path_to_reportability_response_info_section(bundle)
+ triggering_IDs = [x["reference"].split("/") for x in trigger_entries]
+ codes = set()
+ for type, id in triggering_IDs:
+ result = fhirpathpy.evaluate(
+ bundle,
+ f"Bundle.entry.resource.ofType({type}).where(id='{id}').valueCodeableConcept.coding.where(system = 'http://snomed.info/sct').code",
+ )
 
- # Extract unique SNOMED codes from the observations
- snomed_codes = {
- coding["code"]
- for obs in resources_with_conditions
- for coding in obs.get("valueCodeableConcept", {}).get("coding", [])
- if coding["system"] == SNOMED_URL
- }
+ if result:
+ codes.add(result[0])
 
- return snomed_codes
+ return codes

containers/trigger-code-reference/requirements.txt

@@ -2,4 +2,5 @@
 pathlib
 httpx
 requests
-python-multipart
+python-multipart
+fhirpathpy

containers/trigger-code-reference/tests/test_condition_endpoints.py

@@ -108,6 +108,11 @@ def test_stamp_condition_extensions(patched_get_services_list):
  # We'll just try stamping one of each resource type, no need
  # to see 47 observations
  message = json.load(open(Path(__file__).parent / "assets" / "sample_ecr.json"))
+ composition = [
+ e
+ for e in message["entry"]
+ if e.get("resource").get("resourceType") == "Composition"
+ ][0]
  obs_e = [
  e
  for e in message["entry"]
@@ -123,7 +128,7 @@ def test_stamp_condition_extensions(patched_get_services_list):
  for e in message["entry"]
  if e.get("resource").get("resourceType") == "Immunization"
  ][3]
- message["entry"] = [obs_e, cond_e, imm_e]
+ message["entry"] = [composition, obs_e, cond_e, imm_e]
 
  # Note: obviously not real conditions, we're just simulating stamping different
  # resource types according to different condition criteria
@@ -142,15 +147,3 @@ def test_stamp_condition_extensions(patched_get_services_list):
  stamped_message, "840539006", "Observation"
  )
  assert found_matching_extension
-
- # Check condition: no value set cross-referenced for this bundle, no stamp
- found_matching_extension = _check_for_stamped_resource_in_bundle(
- stamped_message, "840539006", "Condition"
- )
- assert not found_matching_extension
-
- # Check immunization: we did find a referenced immunization code, so it should be there
- found_matching_extension = _check_for_stamped_resource_in_bundle(
- stamped_message, "840539006", "Immunization"
- )
- assert found_matching_extension