Human Readable Condition Name

containers/ecr-viewer/seed-scripts/create-seed-data.py

@@ -107,6 +107,7 @@ def _process_eicrs(subfolder, folder, folder_path, payload):
         if response.status_code != 200:
             failed.append(folder_path)
             print(f"Failed to convert {folder_path}.")
+            print(response.text)
             continue
 
         responses_json = response.json()["processed_values"]["responses"]
@@ -124,7 +125,7 @@ def _process_eicrs(subfolder, folder, folder_path, payload):
         print(f"Converted {folder_path} successfully.")
 
     print(
-        f"Conversion complete: {n} records attempted with the following failues: {failed}"
+        f"Conversion complete: {n} records attempted and {len(failed)} failed : {failed}"
     )
 
 

containers/ecr-viewer/src/app/api/fhirPath.yml

@@ -59,7 +59,6 @@ compositionEncounterRef: "Bundle.entry.resource.where(resourceType = 'Compositio
 encounterIndividualRef: "Encounter.participant.where(type.coding.code = 'ATND').individual.reference"
 
 rrDetails: "Bundle.entry.resource.where(meta.profile = 'http://hl7.org/fhir/us/ecr/StructureDefinition/rr-reportability-information-observation')"
-rrDisplayNames: "Bundle.entry.resource.where(meta.profile = 'http://hl7.org/fhir/us/ecr/StructureDefinition/rr-reportability-information-observation').valueCodeableConcept.coding.display"
 rckmsTriggerSummaries: "Bundle.entry.resource.where(meta.profile = 'http://hl7.org/fhir/us/ecr/StructureDefinition/rr-reportability-information-observation').extension.where(url = 'http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-determination-of-reportability-rule-extension').valueString"
 
 # Clinical Data

containers/ecr-viewer/src/app/services/ecrMetadataService.ts

@@ -51,7 +51,10 @@ export const evaluateEcrMetadata = (
   let reportableConditionsList: ReportableConditions = {};
 
   for (const condition of rrDetails) {
-    let name = condition.valueCodeableConcept.coding[0].display;
+    console.log(condition);
+    let name =
+      condition.valueCodeableConcept?.text ||
+      condition.valueCodeableConcept.coding[0].display;
     const triggers = condition.extension
       .filter(
         (x: { url: string; valueString: string }) =>

containers/ecr-viewer/src/app/services/ecrSummaryService.tsx

@@ -158,7 +158,8 @@ export const evaluateEcrSummaryConditionSummary = (
       if (!conditionsList[snomed]) {
         conditionsList[snomed] = {
           ruleSummaries: new Set(),
-          snomedDisplay: coding.display!,
+          snomedDisplay:
+            observation?.valueCodeableConcept?.text || coding.display!,
         };
       }
 

containers/ecr-viewer/src/app/tests/assets/BundleEcrMetadata.json

@@ -734,7 +734,8 @@
               "display": "Viral hepatitis type C (disorder)",
               "system": "http://snomed.info/sct"
             }
-          ]
+          ],
+          "text": "Hepatitis C"
         },
         "extension": [
           {

containers/ecr-viewer/src/app/tests/assets/BundleEcrSummary.json

@@ -556,7 +556,8 @@
               "display": "Viral hepatitis type C (disorder)",
               "system": "http://snomed.info/sct"
             }
-          ]
+          ],
+          "text": "Hepatitis C"
         },
         "extension": [
           {

containers/ecr-viewer/src/app/tests/services/ecrMetadataService.test.ts

@@ -65,7 +65,7 @@ describe("Evaluate Ecr Metadata", () => {
     ]);
     expect(actual.ecrCustodianDetails.unavailableData).toBeEmpty();
   });
-  it("should have rrDetails", () => {
+  it("should have rrDetails, and correctly handle human-readable condition name", () => {
     const actual = evaluateEcrMetadata(
       BundleWithEcrMetadata as unknown as Bundle,
       mappings,
@@ -80,7 +80,7 @@ describe("Evaluate Ecr Metadata", () => {
           "Detection of SARS-CoV-2 nucleic acid in a clinical or post-mortem specimen by any method":
             new Set(["Tennessee Department of Health"]),
         },
-      "Viral hepatitis type C (disorder)": {
+      "Hepatitis C": {
         "Detection of Hepatitis C virus antibody in a clinical specimen by any method":
           new Set(["California Department of Public Health"]),
       },

containers/ecr-viewer/src/app/tests/services/ecrSummaryService.test.tsx

@@ -115,13 +115,13 @@ describe("Evaluate eCR Summary Relevant Lab Results", () => {
 });
 
 describe("Evaluate eCR Summary Condition Summary", () => {
-  it("should return titles based on snomed code", () => {
+  it("should return titles based on snomed code, and return human-readable name if available", () => {
     const actual = evaluateEcrSummaryConditionSummary(
       BundleEcrSummary as unknown as Bundle,
       mappings,
     );
 
-    expect(actual[0].title).toEqual("Viral hepatitis type C (disorder)");
+    expect(actual[0].title).toEqual("Hepatitis C");
     expect(actual[1].title).toEqual(
       "Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)",
     );

containers/message-parser/app/default_schemas/ecr_viewer_metadata.json

@@ -42,7 +42,7 @@
         }
       },
       "condition": {
-        "fhir_path": "Observation.valueCodeableConcept.coding.display",
+        "fhir_path": "iif(Observation.valueCodeableConcept.text.exists(), Observation.valueCodeableConcept.text, Observation.valueCodeableConcept.coding.display)",
         "data_type": "string",
         "nullable": true,
         "metadata": {

containers/message-parser/app/default_schemas/ecr_with_metadata.json

@@ -118,7 +118,7 @@
         }
       },
       "condition": {
-        "fhir_path": "Observation.valueCodeableConcept.coding.display",
+        "fhir_path": "iif(Observation.valueCodeableConcept.text.exists(), Observation.valueCodeableConcept.text, Observation.valueCodeableConcept.coding.display)",
         "data_type": "string",
         "nullable": true,
         "metadata": {

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

@@ -9,7 +9,7 @@
 from app.base_service import BaseService
 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 add_code_extension_and_human_readable_name
 from app.utils import find_conditions
 from app.utils import get_clean_snomed_code
 from app.utils import get_concepts_dict
@@ -126,7 +126,7 @@ async def stamp_condition_extensions(
                         break
 
                 if should_stamp:
-                    entry["resource"] = _stamp_resource_with_code_extension(
+                    entry["resource"] = add_code_extension_and_human_readable_name(
                         resource, cond
                     )
 

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

@@ -205,11 +205,13 @@ def _find_codes_by_resource_type(resource: dict) -> List[str]:
     return [x for x in codes if x != ""]
 
 
-def _stamp_resource_with_code_extension(resource: dict, code: str) -> dict:
+def add_code_extension_and_human_readable_name(resource: dict, code: str) -> dict:
     """
     Stamps a provided resource with an extension containing a passed-in
     SNOMED code. The stamping procedure adds an extension to the resource
-    body without altering any other existing data.
+    body without altering any other existing data. In addition, if the
+    resource is a Condition, the function will also add a human-readable
+    name to the resources valueCodeableConcept.text field.
 
     :param resource: The resource to stamp.
     :param code: The SNOMED code to insert an extension for.
@@ -223,9 +225,35 @@ def _stamp_resource_with_code_extension(resource: dict, code: str) -> dict:
             "coding": [{"code": code, "system": "http://snomed.info/sct"}],
         }
     )
+
+    # If the resource is a Condition, add a human-readable name to the
+    # valueCodeableConcept.text field. If there is no code, assume it was not a
+    # condition/observation
+    if resource.get("code"):
+        if [
+            x
+            for x in resource["code"]["coding"]
+            if x["system"] == "http://snomed.info/sct"
+            and x["code"] == "64572001"  # Condition
+        ]:
+            condition_name = _get_condition_name_from_snomed_code(code)
+            if condition_name:
+                resource["valueCodeableConcept"]["text"] = condition_name
+
     return resource
 
 
+def _get_condition_name_from_snomed_code(snomed_code: str) -> str:
+    # Connect to the SQLite database, execute sql query, then close
+    with sqlite3.connect("seed-scripts/rckms.db") as conn:
+        cursor = conn.cursor()
+        cursor.execute("SELECT name FROM conditions WHERE id = ?", (snomed_code,))
+
+        condition_name = cursor.fetchone()[0]
+
+    return condition_name
+
+
 def read_json_from_assets(filename: str) -> dict:
     """
     Reads a JSON file from the assets directory.

containers/trigger-code-reference/dev-requirements.txt

@@ -4,3 +4,4 @@ testcontainers[compose]
 mammoth==1.8.0
 beautifulsoup4==4.12.3
 lxml==5.2.2
+tqdm

containers/trigger-code-reference/seed-scripts/seed_rckms_database.py

@@ -205,7 +205,7 @@ def extract_condition_from_rckms_doc(
                 # convert the key to lowercase and strip any whitespace
                 key = parts[0].strip().lower()
                 # split the value and take the first part, then strip any whitespace
-                val = parts[1].strip().lower().split("|")[0].strip()
+                val = parts[1].strip().split("|")[0].strip()
                 # if the first part of the value is numeric, use only that
                 if val.split()[0].isnumeric():
                     val = val.split()[0]
@@ -413,41 +413,41 @@ def load_database(
     with sqlite3.connect(db) as con:
         cur = con.cursor()
         for vs in valuesets:
-            # insert the ValueSet Type into the database if it does not exist
-            cur.execute(
-                "INSERT INTO value_set_type (id, clinical_service_type) "
-                "VALUES (:category, :category) "
-                "ON CONFLICT DO NOTHING",
-                vs.__dict__,
-            )
-            # insert the ValueSet into the database if it does not exist
-            cur.execute(
-                "INSERT INTO value_sets (id, version, value_set_name, author, clinical_service_type_id) "
-                "VALUES (:oid, :version, :title, :author, :category) "
-                "ON CONFLICT DO NOTHING",
-                vs.__dict__,
-            )
-            counts["valuesets"] += cur.rowcount
+            # # insert the ValueSet Type into the database if it does not exist
+            # cur.execute(
+            #     "INSERT INTO value_set_type (id, clinical_service_type) "
+            #     "VALUES (:category, :category) "
+            #     "ON CONFLICT DO NOTHING",
+            #     vs.__dict__,
+            # )
+            # # insert the ValueSet into the database if it does not exist
+            # cur.execute(
+            #     "INSERT INTO value_sets (id, version, value_set_name, author, clinical_service_type_id) "
+            #     "VALUES (:oid, :version, :title, :author, :category) "
+            #     "ON CONFLICT DO NOTHING",
+            #     vs.__dict__,
+            # )
+            # counts["valuesets"] += cur.rowcount
             cond = {**{"oid": vs.oid}, **vs.conditions[0].__dict__}
             # insert the Condition into the database if it does not exist
             cur.execute(
-                "INSERT INTO conditions (id, value_set_id, system, name) "
-                "VALUES (:snomed, :oid, 'http://snomed.info/sct', :name) "
+                "INSERT INTO conditions (id, system, name) "
+                "VALUES (:snomed, 'http://snomed.info/sct', :name) "
                 "ON CONFLICT DO NOTHING",
                 cond,
             )
             counts["conditions"] += cur.rowcount
-        for cs in codesets:
-            oid = cs.valueset.oid
-            data = {**{"id": f"{oid}_{cs.code}", "oid": oid}, **cs.__dict__}
-            # insert the CodeSet into the database if it does not exist
-            cur.execute(
-                "INSERT INTO clinical_services (id, value_set_id, code, code_system, display, version) "
-                "VALUES (:id, :oid, :code, :system, :display, :version) "
-                "ON CONFLICT DO NOTHING",
-                data,
-            )
-            counts["codesets"] += cur.rowcount
+        # for cs in codesets:
+        #     oid = cs.valueset.oid
+        #     data = {**{"id": f"{oid}_{cs.code}", "oid": oid}, **cs.__dict__}
+        #     # insert the CodeSet into the database if it does not exist
+        #     cur.execute(
+        #         "INSERT INTO clinical_services (id, value_set_id, code, code_system, display, version) "
+        #         "VALUES (:id, :oid, :code, :system, :display, :version) "
+        #         "ON CONFLICT DO NOTHING",
+        #         data,
+        #     )
+        #     counts["codesets"] += cur.rowcount
         con.commit()
 
         # return the counts of conditions, valuesets and codesets loaded

containers/trigger-code-reference/seed-scripts/test_seed_rckms_database.py

@@ -32,7 +32,7 @@ def test_extract_condition_from_rckms_doc():
 
     result = srd.extract_condition_from_rckms_doc("test.1.docx", docx)
     assert result == srd.Condition(
-        name="test condition",
+        name="Test Condition",
         version="1",
         snomed="12345",
     )

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

@@ -104,8 +104,11 @@ def test_stamp_conditions_no_resources_to_stamp(patched_get_services_list):
     assert not found_matching_extension
 
 
+@patch("app.utils._get_condition_name_from_snomed_code")
 @patch("app.main.get_concepts_list")
-def test_stamp_condition_extensions(patched_get_services_list):
+def test_stamp_condition_extensions(
+    patched_get_services_list, patched_get_condition_name
+):
     # 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"))
@@ -138,6 +141,9 @@ def test_stamp_condition_extensions(patched_get_services_list):
         ("dxtc", "8971234987123", "code-sys-2"),
         ("lotc", "72391283|8916394-2|24", "code-sys-1"),
     ]
+
+    patched_get_condition_name.return_value = "Test Condition"
+
     input = {"bundle": message}
     response = client.post("/stamp-condition-extensions", json=input)
     assert response.status_code == 200

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

@@ -5,7 +5,7 @@
 
 import pytest
 from app.utils import _find_codes_by_resource_type
-from app.utils import _stamp_resource_with_code_extension
+from app.utils import add_code_extension_and_human_readable_name
 from app.utils import convert_inputs_to_list
 from app.utils import get_clean_snomed_code
 from app.utils import get_concepts_dict
@@ -156,7 +156,8 @@ def test_find_codes_by_resource_type():
     assert [] == _find_codes_by_resource_type(observation_resource)
 
 
-def test_stamp_resource_with_code_extension():
+@patch("app.utils._get_condition_name_from_snomed_code")
+def test_add_code_extension_and_human_readable_name(mock_get_condition_name):
     message = json.load(
         open(
             Path(__file__).parent / "assets" / "sample_ecr_with_diagnostic_report.json"
@@ -173,7 +174,10 @@ def test_stamp_resource_with_code_extension():
         if e.get("resource").get("resourceType") == "Condition"
     ][0]
 
-    stamped_obs = _stamp_resource_with_code_extension(
+    # Mock the condition name lookup
+    mock_get_condition_name.return_value = "Cyclosporiasis"
+
+    stamped_obs = add_code_extension_and_human_readable_name(
         observation_resource, "test_obs_code"
     )
     found_stamp = False
@@ -186,7 +190,9 @@ def test_stamp_resource_with_code_extension():
             break
     assert found_stamp
 
-    stamped_condition = _stamp_resource_with_code_extension(
+    assert stamped_obs["valueCodeableConcept"]["text"] == "Cyclosporiasis"
+
+    stamped_condition = add_code_extension_and_human_readable_name(
         condition_resource, "test_cond_code"
     )
     found_stamp = False