TCRS now finds Conditions on its own. (#2238)

* TCRS now finds condtions on its own.

* Remove old validator

* Remove unit test for removed validator

* Look for conditions in all resources

* Fix unit test

---------

Co-authored-by: Josh Nygaard <[email protected]>

Author: JNygaard-Skylight

.vscode/launch.json

@@ -10,6 +10,19 @@
       "cwd": "${workspaceFolder}/containers/orchestration",
       "justMyCode": false,
       "python": "${workspaceFolder}/containers/orchestration/.venv/bin/python"
+    },
+    {
+      "name": "Python Debugger: Trigger Code Reference",
+      "type": "debugpy",
+      "request": "launch",
+      "program": "${workspaceFolder}/containers/trigger-code-reference/app/main.py",
+      "console": "integratedTerminal",
+      "cwd": "${workspaceFolder}/containers/trigger-code-reference",
+      "justMyCode": false,
+      "python": "${workspaceFolder}/containers/trigger-code-reference/.venv/bin/python",
+      "env": {
+        "PYTHONPATH": "${workspaceFolder}/containers/trigger-code-reference"
+      }
     }
   ]
 }

containers/orchestration/app/custom_configs/seed-ecr-viewer-config.json

@@ -23,12 +23,7 @@
     {
       "name": "stamped_ecr",
       "service": "trigger_code_reference",
-      "endpoint": "/stamp-condition-extensions",
-      "params": {
-        "conditions": [
-          "840539006"
-        ]
-      }
+      "endpoint": "/stamp-condition-extensions"
     },
     {
       "name": "message_parser_values",

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

@@ -9,6 +9,7 @@
 from app.models import InsertConditionInput
 from app.utils import _find_codes_by_resource_type
 from app.utils import _stamp_resource_with_code_extension
+from app.utils import find_conditions
 from app.utils import get_clean_snomed_code
 from app.utils import get_clinical_services_dict
 from app.utils import get_clinical_services_list
@@ -61,21 +62,22 @@ async def stamp_condition_extensions(
 ) -> Response:
     """
     Extends the resources of a supplied FHIR bundle with extension tags
-    related to one or more supplied conditions. For each condition in the
-    given list of conditions, each resource in the bundle is appended with
-    an extension structure indicating which SNOMED condition code the
+    related to one or more supplied conditions. For each condition found in
+    the bundle, each resource in the bundle is appended with an extension
+    structure indicating which SNOMED condition code the
     resource is linked to.
 
     :param input: A request formatted as an InsertConditionInput, containing a
-      FHIR bundle whose resources to extend and one or more SNOMED condition
-      code strings to extend by.
+    FHIR bundle whose resources to extend.
     :return: HTTP Response containing the bundle with resources extended by
       any linked conditions.
     """
-    # Collate all clinical services for each of the supplied conditions to
-    # extend, collected by service type
+    # Collate all clinical services for each of the found conditions to extend,
+    # collected by service type
     stamp_codes_to_service_codes = {}
-    for cond in input.conditions:
+    conditions = find_conditions(input.bundle)
+
+    for cond in conditions:
         cond_list = get_clinical_services_list([cond])
         cond_dict = get_clinical_services_dict(cond_list)
         stamp_codes_to_service_codes[cond] = cond_dict
@@ -92,7 +94,7 @@ async def stamp_condition_extensions(
                 continue
 
             # Want to check each queried condition for extension codes
-            for cond in input.conditions:
+            for cond in conditions:
                 # Only need a single instance of service type lookup to contain
                 # the resource's code
                 should_stamp = False
@@ -161,3 +163,15 @@ async def get_value_sets_for_condition(
             clinical_services_list, filter_clinical_services
         )
     return values
+
+
+# This block is only executed if the script is run directly, for local development and debugging.
+if "__main__" == __name__:
+    import uvicorn
+
+    uvicorn.run(
+        app="app.main:app",
+        host="0.0.0.0",
+        port=8080,
+        reload=True,
+    )

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

@@ -1,8 +1,5 @@
-from typing import List
-
 from pydantic import BaseModel
 from pydantic import Field
-from pydantic import root_validator
 
 
 class InsertConditionInput(BaseModel):
@@ -12,31 +9,7 @@ class InsertConditionInput(BaseModel):
 
     bundle: dict = Field(
         description="The FHIR bundle to modify. Each resource in the bundle related "
-        "to one or more of the conditions in the other supplied parameter will have "
+        "to one or more of the conditions found in the bundle will have "
         "an extension added to the resource noting the SNOMED code relating to the "
         "associated condition(s)."
     )
-    conditions: List[str] = Field(
-        description="The list of SNOMED codes to insert as extensions into any "
-        "associated resources in the supplied FHIR bundle."
-    )
-
-    @root_validator
-    def require_non_empty_condition_list(cls, values):
-        """
-        Ensures that the supplied conditions list parameter is both a list
-        and has at least one element by which to extend the supplied FHIR
-        bundle.
-
-        :param cls: The InsertConditionInput class.
-        :param values: The condition list supplied by the caller.
-        :raises ValueError: Errors when supplied condition list contains no
-          elements, since this can't be used to extend a bundle.
-        :return: The endpoint's values, if the condition list is valid.
-        """
-        if len(values.get("conditions")) == 0:
-            raise ValueError(
-                "Supplied list of SNOMED conditions must contain "
-                "one or more elements; given list was empty."
-            )
-        return values

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

@@ -197,3 +197,35 @@ def read_json_from_assets(filename: str) -> dict:
     :return: A dictionary containing the contents of the file.
     """
     return json.load(open((Path(__file__).parent.parent / "assets" / filename)))
+
+
+def find_conditions(bundle: dict) -> set[str]:
+    """
+    Finds conditions in a bundle of resources.
+
+    :param bundle: The bundle of resources to search.
+    :return: A set of SNOMED codes representing the conditions found.
+    """
+    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"])
+    ]
+
+    # 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
+    }
+
+    return snomed_codes

containers/trigger-code-reference/assets/sample_stamp_condition_extensions_requests.json

@@ -3,9 +3,6 @@
     "summary": "Stamping a FHIR bundle consisting of an eICR merged with its RR",
     "description": "This is an example bundle demonstrating condition-stamping on an input eICR that's checking for COVID-related condition codes.",
     "value": {
-      "conditions": [
-        "840539006"
-      ],
       "bundle": {
         "resourceType": "Bundle",
         "type": "batch",

containers/trigger-code-reference/tests/integration/test_trigger_code_reference.py

@@ -25,7 +25,7 @@ def test_openapi():
 @pytest.mark.integration
 def test_tcr_stamping(setup, fhir_bundle):
     reportable_condition_code = "840539006"
-    request = {"bundle": fhir_bundle, "conditions": [reportable_condition_code]}
+    request = {"bundle": fhir_bundle}
     stamp_response = httpx.post(STAMP_ENDPOINT, json=request)
     assert stamp_response.status_code == 200
 

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

@@ -77,17 +77,6 @@ def test_get_value_sets_for_condition(mock_db):
     assert response.json() == expected_result
 
 
-def test_stamp_conditions_bad_input():
-    input = {"bundle": {"test_key": "test_val"}, "conditions": []}
-    response = client.post("/stamp-condition-extensions", json=input)
-    assert response.status_code == 422
-    assert (
-        response.json()["detail"][0]["msg"]
-        == "Supplied list of SNOMED conditions "
-        + "must contain one or more elements; given list was empty."
-    )
-
-
 # Note: This function is defined in utils, but we mock it in the namespace
 # coming from main because that's where the endpoint is invoking it from
 @patch("app.main.get_clinical_services_list")
@@ -143,25 +132,25 @@ def test_stamp_condition_extensions(patched_get_services_list):
         ("dxtc", "8971234987123", "code-sys-2"),
         ("lotc", "72391283|8916394-2|24", "code-sys-1"),
     ]
-    input = {"bundle": message, "conditions": ["99999-9"]}
+    input = {"bundle": message}
     response = client.post("/stamp-condition-extensions", json=input)
     assert response.status_code == 200
     stamped_message = response.json()["extended_bundle"]
 
     # Check observation: diagnostic code value came back successful
     found_matching_extension = _check_for_stamped_resource_in_bundle(
-        stamped_message, "99999-9", "Observation"
+        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, "99999-9", "Condition"
+        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, "99999-9", "Immunization"
+        stamped_message, "840539006", "Immunization"
     )
     assert found_matching_extension