FM2-623: MedicationQuantityCodingTranslator should only use SAME-AS C… (

#525)

api-2.6/src/test/java/org/openmrs/module/fhir2/api/translators/impl/MedicationDispenseTranslatorImpl_2_6Test.java

@@ -13,6 +13,7 @@
 import static org.hamcrest.CoreMatchers.notNullValue;
 import static org.hamcrest.CoreMatchers.nullValue;
 import static org.hamcrest.MatcherAssert.assertThat;
+import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.Mockito.when;
 
@@ -320,17 +321,17 @@ public void toFhirResource_shouldTranslateMedicationDrug() {
 
 	@Test
 	public void toFhirResource_shouldTranslateDoseQuantityAndUnits() {
-		Concept openmrsObject = new Concept();
-		CodeableConcept fhirObject = newCodeableConcept();
-		when(conceptTranslator.toFhirResource(any())).thenReturn(fhirObject);
+		String uuid = "b485f97d-3836-4aed-8c90-81b536cc6e3a";
+		Concept concept = new Concept();
+		concept.setUuid(uuid);
 		openmrsDispense.setDose(100d);
-		openmrsDispense.setDoseUnits(openmrsObject);
+		openmrsDispense.setDoseUnits(concept);
 		org.hl7.fhir.r4.model.MedicationDispense dispense = translator.toFhirResource(openmrsDispense);
 		Quantity quantity = dispense.getDosageInstructionFirstRep().getDoseAndRateFirstRep().getDoseQuantity();
 		assertThat(quantity, notNullValue());
 		assertThat(quantity.getValue().doubleValue(), equalTo(openmrsDispense.getDose()));
-		assertThat(quantity.getSystem(), equalTo("system"));
-		assertThat(quantity.getCode(), equalTo("code"));
+		assertNull(quantity.getSystem());
+		assertThat(quantity.getCode(), equalTo(uuid));
 	}
 
 	@Test
@@ -375,17 +376,17 @@ public void toFhirResource_shouldTranslateDosingInstructions() {
 
 	@Test
 	public void toFhirResource_shouldTranslateDispenseQuantityAndUnits() {
-		Concept openmrsObject = new Concept();
-		CodeableConcept fhirObject = newCodeableConcept();
-		when(conceptTranslator.toFhirResource(openmrsObject)).thenReturn(fhirObject);
+		String uuid = "b485f97d-3836-4aed-8c90-81b536cc6e3a";
+		Concept concept = new Concept();
+		concept.setUuid(uuid);
 		openmrsDispense.setQuantity(100d);
-		openmrsDispense.setQuantityUnits(openmrsObject);
+		openmrsDispense.setQuantityUnits(concept);
 		org.hl7.fhir.r4.model.MedicationDispense dispense = translator.toFhirResource(openmrsDispense);
 		Quantity quantity = dispense.getQuantity();
 		assertThat(quantity, notNullValue());
 		assertThat(quantity.getValue().doubleValue(), equalTo(openmrsDispense.getQuantity()));
-		assertThat(quantity.getSystem(), equalTo("system"));
-		assertThat(quantity.getCode(), equalTo("code"));
+		assertNull(quantity.getSystem());
+		assertThat(quantity.getCode(), equalTo(uuid));
 	}
 
 	@Test

api/src/main/java/org/openmrs/module/fhir2/api/translators/impl/MedicationQuantityCodingTranslatorImpl.java

@@ -11,43 +11,68 @@
 
 import javax.annotation.Nonnull;
 
-import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
 import org.openmrs.Concept;
+import org.openmrs.ConceptMap;
+import org.openmrs.ConceptMapType;
 import org.openmrs.module.fhir2.FhirConstants;
+import org.openmrs.module.fhir2.api.FhirConceptSourceService;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
 /**
  * This is an implementation of Coding Translator that maps a Medication Quantity Concept to/from a
  * Coding in FHIR with a preferred set of systems and codes to prioritize. This will first favor
- * using RxNorm as the coding system. If this is not present on the OpenMRS concept, it will next
- * favor SNOMED-CT. Finally, if neither are present, it will favor the Concept UUID with a null
- * system.
+ * using RxNorm coding with SAME-AS mapping. If this is not present on the OpenMRS concept, it will
+ * next favor SNOMED-CT, also with SAME-AS mapping. Finally, if neither are present, it will favor
+ * the Concept UUID with a null system.
  */
 @Component
 public class MedicationQuantityCodingTranslatorImpl extends BaseCodingTranslator {
 
+	@Autowired
+	private FhirConceptSourceService conceptSourceService;
+
 	@Override
 	public Coding toFhirResource(@Nonnull Concept concept) {
-		CodeableConcept codeableConcept = conceptTranslator.toFhirResource(concept);
-		if (codeableConcept == null) {
-			return null;
-		}
 
-		Coding coding = getCodingForSystem(codeableConcept, FhirConstants.RX_NORM_SYSTEM_URI);
-		if (coding == null) {
-			coding = getCodingForSystem(codeableConcept, FhirConstants.SNOMED_SYSTEM_URI);
-		}
-		if (coding == null) {
-			coding = getCodingForSystem(codeableConcept, null);
+		Coding coding = null;
+
+		if (concept.getConceptMappings() != null && !concept.getConceptMappings().isEmpty()) {
+			coding = getSameAsCodingForSystem(concept, FhirConstants.RX_NORM_SYSTEM_URI);
+			if (coding == null) {
+				coding = getSameAsCodingForSystem(concept, FhirConstants.SNOMED_SYSTEM_URI);
+			}
 		}
+
 		if (coding == null) {
-			coding = codeableConcept.getCodingFirstRep();
+			coding = createCoding(null, concept.getUuid(), concept);
 		}
 
-		coding.setDisplay(codeableConcept.getCoding().stream().filter(c -> c.getSystem() == null || c.getSystem().isEmpty())
-		        .findFirst().map(Coding::getDisplay).orElse(null));
-
 		return coding;
 	}
+
+	private Coding getSameAsCodingForSystem(Concept concept, String system) {
+		for (ConceptMap conceptMap : concept.getConceptMappings()) {
+			String conceptSourceUrl = conceptSourceService
+			        .getUrlForConceptSource(conceptMap.getConceptReferenceTerm().getConceptSource());
+			if (conceptSourceUrl != null && conceptSourceUrl.equals(system)
+			        && conceptMap.getConceptMapType().getUuid().equals(ConceptMapType.SAME_AS_MAP_TYPE_UUID)) {
+				return createCoding(system, conceptMap.getConceptReferenceTerm().getCode(), concept);
+			}
+		}
+		return null;
+	}
+
+	private Coding createCoding(String system, String code, Concept concept) {
+		Coding coding = new Coding();
+		coding.setSystem(system);
+		coding.setCode(code);
+		coding.setDisplay(concept.getDisplayString());
+		return coding;
+	}
+
+	public void setConceptSourceService(FhirConceptSourceService conceptSourceService) {
+		this.conceptSourceService = conceptSourceService;
+	}
 }

api/src/test/java/org/openmrs/module/fhir2/api/translators/impl/DosageTranslatorImplTest.java

@@ -82,6 +82,7 @@ public void setup() {
 
 		quantityCodingTranslator = new MedicationQuantityCodingTranslatorImpl();
 		quantityCodingTranslator.setConceptTranslator(conceptTranslator);
+		quantityCodingTranslator.setConceptSourceService(conceptSourceService);
 
 		timingTranslator = new MedicationRequestTimingTranslatorImpl();
 		timingTranslator.setConceptTranslator(conceptTranslator);

api/src/test/java/org/openmrs/module/fhir2/api/translators/impl/MedicationQuantityCodingTranslatorImplTest.java

@@ -61,7 +61,7 @@ public void setup() {
 
 		quantityCodingTranslator = new MedicationQuantityCodingTranslatorImpl();
 		quantityCodingTranslator.setConceptTranslator(conceptTranslator);
-
+		quantityCodingTranslator.setConceptSourceService(conceptSourceService);
 		LocaleUtility.setLocalesAllowedListCache(Arrays.asList(Locale.ENGLISH));
 	}
 
@@ -112,9 +112,19 @@ public void toFhirResource_shouldTranslateMedicationQuantityPreferringSnomedCtIf
 
 	@Test
 	public void toFhirResource_shouldTranslateMedicationQuantityDefaultingToUuid() {
+
+		ConceptMapType notSameAs = new ConceptMapType();
+		notSameAs.setUuid("5d4b9c92-ed26-45ca-8f6e-08c48b00648d"); // this is just a random uuid, so should *not* be a match for SAME_AS_MAP_TYPE_UUID
+
+		ConceptSource snomed = new ConceptSource();
+		snomed.setHl7Code(Duration.SNOMED_CT_CONCEPT_SOURCE_HL7_CODE);
+		when(conceptSourceService.getUrlForConceptSource(snomed)).thenReturn(FhirConstants.SNOMED_SYSTEM_URI);
+
 		Concept mg = new Concept();
 		mg.setUuid(CONCEPT_UUID);
 		mg.addName(new ConceptName("mg", Locale.ENGLISH));
+		mg.addConceptMapping(
+		    new ConceptMap(new ConceptReferenceTerm(snomed, "snomed-ct-mg-code-not-same-as", "snomed"), notSameAs));
 
 		Coding result = quantityCodingTranslator.toFhirResource(mg);
 		assertThat(result, notNullValue());