Bug fix and test improvements.

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java

@@ -192,7 +192,7 @@ public abstract class BaseLoincHandler implements IRecordHandler {
 		if (isNotBlank(theVersionPropertyName)) {
 			version = myUploadProperties.getProperty(theVersionPropertyName);
 		} else {
-			version = myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode());
+			version = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
 		}
 
 		ValueSet vs;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincRsnaPlaybookHandler.java

@@ -84,7 +84,10 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
 
 		// ConceptMap version from properties files
 		String loincRsnaCmVersion = myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode());
-		
+
+		// CodeSystem version from properties file
+		String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
+
 		// RSNA Codes VS
 		ValueSet vs;
 		if (!myIdToValueSet.containsKey(RSNA_CODES_VS_ID)) {
@@ -93,6 +96,7 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
 			vs.setId(RSNA_CODES_VS_ID);
 			vs.setName(RSNA_CODES_VS_NAME);
 			vs.setStatus(Enumerations.PublicationStatus.ACTIVE);
+			vs.setVersion(codeSystemVersionId);
 			myIdToValueSet.put(RSNA_CODES_VS_ID, vs);
 			myValueSets.add(vs);
 		} else {
@@ -177,7 +181,6 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
 
 		String partConceptMapId;
 		String termConceptMapId;
-		String codeSystemVersionId = myUploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
 		if (codeSystemVersionId != null) {
 			partConceptMapId = LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_ID + "-" + codeSystemVersionId;
 			termConceptMapId = LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_ID + "-" + codeSystemVersionId;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java

@@ -39,6 +39,7 @@ import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.empty;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.junit.jupiter.api.Assertions.fail;
 import static org.mockito.ArgumentMatchers.any;
@@ -183,10 +184,12 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		assertEquals(ITermLoaderSvc.LOINC_URI, vs.getCompose().getInclude().get(0).getSystem());
 		assertEquals("LA6270-8", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
 		assertEquals("Never", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
+		assertEquals("Beta.1", vs.getVersion());
 
 		// External AnswerList
 		vs = valueSets.get("LL1892-0");
 		assertEquals(0, vs.getCompose().getIncludeFirstRep().getConcept().size());
+		assertEquals("Beta.1", vs.getVersion());
 
 		// Part
 		code = concepts.get("LP101394-7");
@@ -220,6 +223,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		assertEquals(3, vs.getCompose().getInclude().get(0).getConcept().size());
 		assertEquals("11488-4", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
 		assertEquals("Consult note", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
+		assertNull(vs.getVersion());
 
 		// Document ontology parts
 		code = concepts.get("11488-4");
@@ -237,6 +241,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		assertEquals(ITermLoaderSvc.LOINC_URI, vs.getCompose().getInclude().get(0).getSystem());
 		assertEquals("17787-3", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
 		assertEquals("NM Thyroid gland Study report", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
+		assertNull(vs.getVersion());
 
 		// RSNA Playbook Code Parts - Region Imaged
 		code = concepts.get("17787-3");
@@ -305,6 +310,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		assertEquals("Creatinine [Mass/volume] in Serum or Plasma", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
 		assertEquals("718-7", vs.getCompose().getInclude().get(0).getConcept().get(1).getCode());
 		assertEquals("Hemoglobin [Mass/volume] in Blood", vs.getCompose().getInclude().get(0).getConcept().get(1).getDisplay());
+		assertNull(vs.getVersion());
 
 		// TOP 2000 - SI
 		vs = valueSets.get(LoincTop2000LabResultsSiHandler.TOP_2000_SI_VS_ID);
@@ -317,6 +323,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		assertEquals("Creatinine [Moles/volume] in Serum or Plasma", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
 		assertEquals("718-7", vs.getCompose().getInclude().get(0).getConcept().get(1).getCode());
 		assertEquals("Hemoglobin [Mass/volume] in Blood", vs.getCompose().getInclude().get(0).getConcept().get(1).getDisplay());
+		assertNull(vs.getVersion());
 
 		// Universal lab order VS
 		vs = valueSets.get(LoincUniversalOrderSetHandler.VS_ID_BASE);
@@ -325,6 +332,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		assertEquals(9, vs.getCompose().getInclude().get(0).getConcept().size());
 		assertEquals("42176-8", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
 		assertEquals("1,3 beta glucan [Mass/volume] in Serum", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
+		assertNull(vs.getVersion());
 
 		// All LOINC codes
 		assertTrue(valueSets.containsKey("loinc-all"));
@@ -341,6 +349,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		assertTrue(vs.getCompose().hasInclude());
 		assertEquals(1, vs.getCompose().getInclude().size());
 		assertEquals(ITermLoaderSvc.LOINC_URI, vs.getCompose().getInclude().get(0).getSystem());
+		assertEquals("1.0.0", vs.getVersion());
 
 		// IEEE Medical Device Codes
 		conceptMap = conceptMaps.get(LoincIeeeMedicalDeviceCodeHandler.LOINC_IEEE_CM_ID);
@@ -398,6 +407,18 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		verify(myTermCodeSystemStorageSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
 		CodeSystem loincCS = mySystemCaptor.getValue();
 		assertEquals("2.67", loincCS.getVersion());
+		List<ValueSet> loincVS_resources = myValueSetsCaptor.getValue();
+		for (ValueSet loincVS : loincVS_resources) {
+			if (loincVS.getId().startsWith("LL1000-0") || loincVS.getId().startsWith("LL1001-8") || loincVS.getId().startsWith("LL1892-0")) {
+				assertEquals("2.67.Beta.1", loincVS.getVersion());
+			} else {
+				assertEquals("2.67", loincVS.getVersion());
+			}
+		}
+		List<ConceptMap> loincCM_resources = myConceptMapCaptor.getValue();
+		for (ConceptMap loincCM : loincCM_resources) {
+			assertEquals("2.67.Beta.1", loincCM.getVersion());
+		}
 
 		// Update LOINC marked as version 2.67
 		myFiles = new ZipCollectionBuilder();
@@ -407,6 +428,18 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		verify(myTermCodeSystemStorageSvc, times(2)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
 		loincCS = mySystemCaptor.getValue();
 		assertEquals("2.67", loincCS.getVersion());
+		loincVS_resources = myValueSetsCaptor.getValue();
+		for (ValueSet loincVS : loincVS_resources) {
+			if (loincVS.getId().startsWith("LL1000-0") || loincVS.getId().startsWith("LL1001-8") || loincVS.getId().startsWith("LL1892-0")) {
+				assertEquals("2.67.Beta.1", loincVS.getVersion());
+			} else {
+				assertEquals("2.67", loincVS.getVersion());
+			}
+		}
+		loincCM_resources = myConceptMapCaptor.getValue();
+		for (ConceptMap loincCM : loincCM_resources) {
+			assertEquals("2.67.Beta.1", loincCM.getVersion());
+		}
 
 		// Load LOINC marked as version 2.68
 		myFiles = new ZipCollectionBuilder();
@@ -416,6 +449,18 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		verify(myTermCodeSystemStorageSvc, times(3)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
 		loincCS = mySystemCaptor.getValue();
 		assertEquals("2.68", loincCS.getVersion());
+		loincVS_resources = myValueSetsCaptor.getValue();
+		for (ValueSet loincVS : loincVS_resources) {
+			if (loincVS.getId().startsWith("LL1000-0") || loincVS.getId().startsWith("LL1001-8") || loincVS.getId().startsWith("LL1892-0")) {
+				assertEquals("2.68.Beta.1", loincVS.getVersion());
+			} else {
+				assertEquals("2.68", loincVS.getVersion());
+			}
+		}
+		loincCM_resources = myConceptMapCaptor.getValue();
+		for (ConceptMap loincCM : loincCM_resources) {
+			assertEquals("2.68.Beta.1", loincCM.getVersion());
+		}
 
 	}
 

hapi-fhir-jpaserver-base/src/test/resources/loinc/v267_loincupload.properties

@@ -67,11 +67,11 @@ loinc.codesystem.version=2.67
 
 # This is the version identifier for the answer list file
 ## Key may be omitted
-loinc.answerlist.version=Beta.1
+loinc.answerlist.version=2.67.Beta.1
 
 # This is the version identifier for uploaded ConceptMap resources
 ## Key may be omitted
-loinc.conceptmap.version=Beta.1
+loinc.conceptmap.version=2.67.Beta.1
 
 # Group
 ## Default value if key not provided: AccessoryFiles/GroupFile/Group.csv

hapi-fhir-jpaserver-base/src/test/resources/loinc/v268_loincupload.properties

@@ -67,11 +67,11 @@ loinc.codesystem.version=2.68
 
 # This is the version identifier for the answer list file
 ## Key may be omitted
-loinc.answerlist.version=Beta.1
+loinc.answerlist.version=2.68.Beta.1
 
 # This is the version identifier for uploaded ConceptMap resources
 ## Key may be omitted
-loinc.conceptmap.version=Beta.1
+loinc.conceptmap.version=2.68.Beta.1
 
 # Group
 ## Default value if key not provided: AccessoryFiles/GroupFile/Group.csv