Merge pull request #1446 from jamesagnew/1445-an-implicit-all-loinc-valueset-needs-to-be-created-when-uploading-the-loinc-codesystem

Resolve "An implicit all-loinc ValueSet needs to be created when uploading the LOINC CodeSystem."

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

@@ -32,6 +32,7 @@ import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.ConceptMap;
+import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.springframework.beans.factory.annotation.Autowired;
 
@@ -556,6 +557,8 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 
 		IOUtils.closeQuietly(theDescriptors);
 
+		valueSets.add(getValueSetLoincAll());
+
 		for (Entry<String, TermConcept> next : code2concept.entrySet()) {
 			TermConcept nextConcept = next.getValue();
 			if (nextConcept.getParents().isEmpty()) {
@@ -573,6 +576,23 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 		return new UploadStatistics(conceptCount, target);
 	}
 
+	private ValueSet getValueSetLoincAll() {
+		ValueSet retVal = new ValueSet();
+
+		retVal.setId("loinc-all");
+		retVal.setUrl("http://loinc.org/fhir/ValueSet/loinc-all");
+		retVal.setVersion("1.0.0");
+		retVal.setName("All LOINC codes");
+		retVal.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		retVal.setDate(new Date());
+		retVal.setPublisher("Regenstrief Institute, Inc.");
+		retVal.setDescription("A value set that includes all LOINC codes");
+		retVal.setCopyright("This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/");
+		retVal.getCompose().addInclude().setSystem(IHapiTerminologyLoaderSvc.LOINC_URI);
+
+		return retVal;
+	}
+
 	private UploadStatistics processSnomedCtFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) {
 		final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
 		final Map<String, TermConcept> id2concept = new HashMap<>();

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

@@ -255,6 +255,22 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
 		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());
 
+		// All LOINC codes
+		assertTrue(valueSets.containsKey("loinc-all"));
+		vs = valueSets.get("loinc-all");
+		assertEquals("http://loinc.org/fhir/ValueSet/loinc-all", vs.getUrl());
+		assertEquals("1.0.0", vs.getVersion());
+		assertEquals("All LOINC codes", vs.getName());
+		assertEquals(Enumerations.PublicationStatus.ACTIVE, vs.getStatus());
+		assertTrue(vs.hasDate());
+		assertEquals("Regenstrief Institute, Inc.", vs.getPublisher());
+		assertEquals("A value set that includes all LOINC codes", vs.getDescription());
+		assertEquals("This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/", vs.getCopyright());
+		assertTrue(vs.hasCompose());
+		assertTrue(vs.getCompose().hasInclude());
+		assertEquals(1, vs.getCompose().getInclude().size());
+		assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, vs.getCompose().getInclude().get(0).getSystem());
+
 		// IEEE Medical Device Codes
 		conceptMap = conceptMaps.get(LoincIeeeMedicalDeviceCodeHandler.LOINC_IEEE_CM_ID);
 		ourLog.debug(FhirContext.forR4().newXmlParser().setPrettyPrint(true).encodeResourceToString(conceptMap));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java

@@ -29,6 +29,7 @@ import org.springframework.transaction.support.TransactionTemplate;
 
 import javax.annotation.Nonnull;
 import java.io.IOException;
+import java.util.Date;
 import java.util.List;
 import java.util.Optional;
 import java.util.concurrent.atomic.AtomicInteger;
@@ -606,14 +607,6 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
 		loadAndPersistCodeSystem();
 	}
 
-	@Test
-	public void testTest() {
-		ourLog.info("as is: {}", TermValueSetPreExpansionStatusEnum.EXPANSION_IN_PROGRESS);
-		ourLog.info("toString: {}", TermValueSetPreExpansionStatusEnum.EXPANSION_IN_PROGRESS.toString());
-		ourLog.info("name: {}", TermValueSetPreExpansionStatusEnum.EXPANSION_IN_PROGRESS.name());
-		ourLog.info("getCode: {}", TermValueSetPreExpansionStatusEnum.EXPANSION_IN_PROGRESS.getCode());
-	}
-
 	@Test
 	public void testDuplicateConceptMapUrls() {
 		createAndPersistConceptMap();

src/changes/changes.xml

@@ -82,6 +82,11 @@
 				LOINC concepts now include multiaxial hierarchical properties (e.g. <![CDATA[<code>parent</code>]]> and
 				<![CDATA[<code>child</code>]]>, which identify parent and child concepts.
 			</action>
+			<action type="add" issue="1445">
+				When loading LOINC terminology, a new ValueSet is automatically created with a single include element that
+				identifies the LOINC CodeSystem in <![CDATA[<code>ValueSet.compose.include.system</code>]]>. This ValueSet
+				includes all LOINC codes.
+			</action>
 		</release>
 		<release version="4.0.0" date="2019-08-14" description="Igloo">
 			<action type="add">