Fix FHIR Conversion for Specimen in Lab Info (#2858)

* fix FHIR conversion for specimen

* add test

* improve readability

containers/fhir-converter/Templates/eCR/Entry/Result/_entry.liquid

@@ -38,18 +38,23 @@
               {% endfor -%} 
             {% endif -%}
             {% if comp.procedure.participant.participantRole.id -%}
-                {% if comp.procedure.participant.participantRole.playingEntity.code.translation -%}
-                    {% assign translations = comp.procedure.participant.participantRole.playingEntity.code.translation | to_array -%}
+                {% assign playingEntity = comp.procedure.participant.participantRole.playingEntity -%}
+                {% if playingEntity.code.translation -%}
+                    {% assign translations = playingEntity.code.translation | to_array -%}
                     {% if translations.first.displayName -%}
                         {% assign specValue = translations.first.displayName -%}
                     {% endif -%}
                 {% elsif comp.procedure.participant.participantRole.id.displayName -%}
                     {% assign specValue = comp.procedure.participant.participantRole.id.displayName -%}
-                {% elsif entry.organizer.component.procedure.participant.participantRole.playingEntity.code.displayName -%}
-                    {% assign specValue = comp.procedure.participant.participantRole.playingEntity.code.displayName -%}
+                {% elsif playingEntity.code.originalText._ %}
+                    {% assign specValue = playingEntity.code.originalText._ -%}
+                {% elsif playingEntity.code.displayName -%}
+                     {% assign specValue = playingEntity.code.displayName -%}
                 {% else -%}
                     {% assign specValue = "None" -%}
                 {% endif -%}
+            {% else  -%}
+                {% assign specValue = "None" -%}
             {% endif -%}
         {% endif -%}
     {% endfor-%}   

containers/fhir-converter/tests/integration/test_FHIR-Converter.py

@@ -212,3 +212,26 @@ def test_encounter_diagnosis():
     assert len(diagnosis_references) == 1
 
     assert "Condition/d282a8e7-21b0-49ff-d7b0-1ce84b5d9b07" in diagnosis_references
+
+
+@pytest.mark.integration
+def test_lab_specimen():
+    input_data = open(
+        Path(__file__).parent.parent / "test_files/eICR_with_single_lab.xml"
+    ).read()
+    request = {"input_data": input_data, "input_type": "ecr", "root_template": "EICR"}
+    ecr_conversion_response = httpx.post(CONVERT_TO_FHIR, json=request)
+    assert ecr_conversion_response.status_code == 200
+
+    specimen_sources = []
+    for entry in filter(
+        lambda entry: entry["resource"]["resourceType"] == "Observation",
+        ecr_conversion_response.json()["response"]["FhirResource"]["entry"],
+    ):
+        for ext in entry["resource"].get("extension", []):
+            if ext["url"] == "http://hl7.org/fhir/R4/specimen.html":
+                for sub_ext in ext.get("extension", []):
+                    if sub_ext["url"] == "specimen source":
+                        specimen_sources.append(sub_ext["valueString"])
+
+    assert len(specimen_sources) == 4