[7401] Smileutil upload-terminology command does not load all concept properties from CSV file

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_8_0/7401-fix-smileutil-upload-terminology-not-load-all-concept-properties.yaml

@@ -0,0 +1,8 @@
+---
+type: fix
+issue: 7401
+jira: SMILE-11256
+title: "Previously, `smileutil upload-terminology` failed to load and save multiple concept properties that 
+used the same property code for a single `CodeSystem.concept`. This is now fixed."
+
+

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/custom/PropertyHandler.java

@@ -22,8 +22,6 @@
 import ca.uhn.fhir.jpa.entity.TermConceptProperty;
 import ca.uhn.fhir.jpa.entity.TermConceptPropertyTypeEnum;
 import ca.uhn.fhir.jpa.term.IZipContentsHandlerCsv;
-import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
-import ca.uhn.fhir.util.ValidateUtil;
 import org.apache.commons.csv.CSVRecord;
 
 import java.util.ArrayList;
@@ -50,18 +48,14 @@ public void accept(CSVRecord theRecord) {
 		String code = trim(theRecord.get(CODE));
 		String key = trim(theRecord.get(KEY));
 
-		if (isNotBlank(code) && isNotBlank(KEY)) {
+		if (isNotBlank(code) && isNotBlank(key)) {
 			String value = trim(theRecord.get(VALUE));
 			String type = trim(theRecord.get(TYPE));
 
 			List<TermConceptProperty> conceptProperties = myCode2Properties.get(code);
 			if (conceptProperties == null) conceptProperties = new ArrayList<>();
 
-			TermConceptProperty conceptProperty =
-					TermLoaderSvcImpl.getOrCreateConceptProperty(myCode2Properties, code, key);
-			ValidateUtil.isNotNullOrThrowUnprocessableEntity(
-					conceptProperty, "Concept property %s not found in file", conceptProperty);
-
+			TermConceptProperty conceptProperty = new TermConceptProperty();
 			conceptProperty.setKey(key);
 			conceptProperty.setValue(value);
 			// TODO: check this for different types, other types should be added once TermConceptPropertyTypeEnum

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java

@@ -30,6 +30,7 @@
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.List;
 import java.util.Optional;
 import java.util.zip.ZipEntry;
@@ -318,6 +319,52 @@ public void testApplyDeltaAdd_UsingCsv_withPropertiesCsv() throws IOException {
 		});
 	}
 
+	@Test
+	public void testApplyDeltaAdd_duplicateConceptPropertyKeys_allPropertiesSaved() throws IOException {
+		String inputParamJson = loadResource("/custom_term/codeSystem-duplicatePropertyKeys.json");
+		Parameters inputParameters = myFhirContext.newJsonParser().parseResource(Parameters.class, inputParamJson);
+
+		LoggingInterceptor interceptor = new LoggingInterceptor(true);
+		myClient.registerInterceptor(interceptor);
+		Parameters outcome = myClient
+			.operation()
+			.onType(CodeSystem.class)
+			.named(JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD)
+			.withParameters(inputParameters)
+			.prettyPrint()
+			.execute();
+		myClient.unregisterInterceptor(interceptor);
+
+		String encoded = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
+		ourLog.info(encoded);
+		assertThat(encoded).containsSubsequence(
+			"\"name\": \"conceptCount\"",
+			"\"valueInteger\": 1",
+			"\"name\": \"target\"",
+			"\"reference\": \"CodeSystem/"
+		);
+		runInTransaction(() -> {
+			TermCodeSystem cs = myTermCodeSystemDao.findByCodeSystemUri("http://www.nlm.nih.gov/research/umls/rxnorm_resource");
+			TermCodeSystemVersion version = cs.getCurrentVersion();
+			Optional<TermConcept> optional = myTermConceptDao.findByCodeSystemAndCode(version.getPid(), "748856");
+			assertThat(optional).isPresent();
+
+			TermConcept concept = optional.get();
+			Collection<TermConceptProperty> properties = concept.getProperties();
+
+			properties.forEach(prop -> ourLog.info("Property: {} = {}", prop.getKey(), prop.getValue()));
+			assertThat(properties).hasSize(3);
+
+			// Check that a property with key "STY" appears twice
+			List<String> valuesForSTY = properties.stream()
+				.filter(p -> "STY".equalsIgnoreCase(p.getKey()))
+				.map(TermConceptProperty::getValue)
+				.toList();
+			assertThat(valuesForSTY).hasSize(2);
+			assertThat(valuesForSTY).containsExactlyInAnyOrder("STN:A1.3.1.1", "STY:Drug Delivery Device");
+		});
+	}
+
 	@Test
 	public void testApplyDeltaAdd_UsingCodeSystem() {
 		CodeSystem codeSystem = new CodeSystem();

hapi-fhir-jpaserver-test-utilities/src/main/resources/custom_term/codeSystem-duplicatePropertyKeys.json

@@ -0,0 +1,35 @@
+{
+	"resourceType": "Parameters",
+	"parameter": [
+		{
+			"name": "system",
+			"valueUri": "http://www.nlm.nih.gov/research/umls/rxnorm_resource"
+		},
+		{
+			"name": "codeSystem",
+			"resource": {
+				"resourceType": "CodeSystem",
+				"concept": [
+					{
+						"code": "748856",
+						"display": "{24 (drospirenone 3 MG / ethinyl estradiol 0.02 MG Oral Tablet) / 4 (inert ingredients 1 MG Oral Tablet) } Pack [Yaz 28 Day]",
+						"property": [
+							{
+								"code": "STY",
+								"valueString": "STN:A1.3.1.1"
+							},
+							{
+								"code": "STY",
+								"valueString": "STY:Drug Delivery Device"
+							},
+							{
+								"code": "TTY",
+								"valueString": "BPCK"
+							}
+						]
+					}
+				]
+			}
+		}
+	]
+}