Allow terminology service to work without having Lucene enabled for

simple ValueSet expansions

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java

@@ -9,9 +9,9 @@
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- *
+ * 
  * http://www.apache.org/licenses/LICENSE-2.0
- *
+ * 
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/util/JaxRsRequest.java

@@ -9,9 +9,9 @@
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- *
+ * 
  *      http://www.apache.org/licenses/LICENSE-2.0
- *
+ * 
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java

@@ -98,9 +98,9 @@
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- *
+ * 
  * http://www.apache.org/licenses/LICENSE-2.0
- *
+ * 
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

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

@@ -9,9 +9,9 @@
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * 
+ *
  * http://www.apache.org/licenses/LICENSE-2.0
- * 
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -24,6 +24,7 @@
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
+import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
 import ca.uhn.fhir.jpa.dao.data.*;
 import ca.uhn.fhir.jpa.entity.*;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
@@ -139,35 +140,41 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 	private TransactionTemplate myTxTemplate;
 	@Autowired
 	private PlatformTransactionManager myTransactionManager;
+	@Autowired(required = false)
+	private IFulltextSearchSvc myFulltextSearchSvc;
+
 
-	/**
-	 * @param theAdd         If true, add the code. If false, remove the code.
-	 * @param theCodeCounter
-	 */
 	private void addCodeIfNotAlreadyAdded(ValueSet.ValueSetExpansionComponent theExpansionComponent, Set<String> theAddedCodes, TermConcept theConcept, boolean theAdd, AtomicInteger theCodeCounter) {
+		String codeSystem = theConcept.getCodeSystemVersion().getCodeSystem().getCodeSystemUri();
 		String code = theConcept.getCode();
-		if (theAdd && theAddedCodes.add(code)) {
-			String codeSystem = theConcept.getCodeSystemVersion().getCodeSystem().getCodeSystemUri();
+		String display = theConcept.getDisplay();
+		Collection<TermConceptDesignation> designations = theConcept.getDesignations();
+		addCodeIfNotAlreadyAdded(theExpansionComponent, theAddedCodes, designations, theAdd, theCodeCounter, codeSystem, code, display);
+	}
+
+	private void addCodeIfNotAlreadyAdded(ValueSet.ValueSetExpansionComponent theExpansionComponent, Set<String> theAddedCodes, Collection<TermConceptDesignation> theDesignations, boolean theAdd, AtomicInteger theCodeCounter, String theCodeSystem, String theCode, String theDisplay) {
+		if (isNotBlank(theCode) && theAdd && theAddedCodes.add(theCode)) {
 			ValueSet.ValueSetExpansionContainsComponent contains = theExpansionComponent.addContains();
-			contains.setCode(code);
-			contains.setSystem(codeSystem);
-			contains.setDisplay(theConcept.getDisplay());
-			for (TermConceptDesignation nextDesignation : theConcept.getDesignations()) {
-				contains
-					.addDesignation()
-					.setValue(nextDesignation.getValue())
-					.getUse()
-					.setSystem(nextDesignation.getUseSystem())
-					.setCode(nextDesignation.getUseCode())
-					.setDisplay(nextDesignation.getUseDisplay());
+			contains.setCode(theCode);
+			contains.setSystem(theCodeSystem);
+			contains.setDisplay(theDisplay);
+			if (theDesignations != null) {
+				for (TermConceptDesignation nextDesignation : theDesignations) {
+					contains
+						.addDesignation()
+						.setValue(nextDesignation.getValue())
+						.getUse()
+						.setSystem(nextDesignation.getUseSystem())
+						.setCode(nextDesignation.getUseCode())
+						.setDisplay(nextDesignation.getUseDisplay());
+				}
 			}
 
 			theCodeCounter.incrementAndGet();
 		}
 
-		if (!theAdd && theAddedCodes.remove(code)) {
-			String codeSystem = theConcept.getCodeSystemVersion().getCodeSystem().getCodeSystemUri();
-			removeCodeFromExpansion(codeSystem, code, theExpansionComponent);
+		if (!theAdd && theAddedCodes.remove(theCode)) {
+			removeCodeFromExpansion(theCodeSystem, theCode, theExpansionComponent);
 			theCodeCounter.decrementAndGet();
 		}
 	}
@@ -480,6 +487,19 @@ public void expandValueSetHandleIncludeOrExclude(ValueSet.ValueSetExpansionCompo
 			if (cs != null) {
 				TermCodeSystemVersion csv = cs.getCurrentVersion();
 				FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
+
+				/*
+				 * If FullText searching is not enabled, we can handle only basic expansions
+				 * since we're going to do it without the database.
+				 */
+				if (myFulltextSearchSvc == null) {
+					expandWithoutHibernateSearch(theExpansionComponent, theAddedCodes, theInclude, system, theAdd, theCodeCounter);
+					return;
+				}
+
+				/*
+				 * Ok, let's use hibernate search to build the expansion
+				 */
 				QueryBuilder qb = em.getSearchFactory().buildQueryBuilder().forEntity(TermConcept.class).get();
 				BooleanJunction<?> bool = qb.bool();
 
@@ -663,6 +683,20 @@ public void expandValueSetHandleIncludeOrExclude(ValueSet.ValueSetExpansionCompo
 		}
 	}
 
+	private void expandWithoutHibernateSearch(ValueSet.ValueSetExpansionComponent theExpansionComponent, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, String theSystem, boolean theAdd, AtomicInteger theCodeCounter) {
+		ourLog.trace("Hibernate search is not enabled");
+		Validate.isTrue(theExpansionComponent.getParameter().isEmpty(), "Can not exapnd ValueSet with parameters - Hibernate Search is not enabled on this server.");
+		Validate.isTrue(theInclude.getFilter().isEmpty(), "Can not expand ValueSet with filters - Hibernate Search is not enabled on this server.");
+		Validate.isTrue(isNotBlank(theSystem), "Can not expand ValueSet without explicit system - Hibernate Search is not enabled on this server.");
+
+		for (ValueSet.ConceptReferenceComponent next : theInclude.getConcept()) {
+			if (!theSystem.equals(theInclude.getSystem())) {
+				continue;
+			}
+			addCodeIfNotAlreadyAdded(theExpansionComponent, theAddedCodes, null, theAdd, theCodeCounter, theSystem, next.getCode(), next.getDisplay());
+		}
+	}
+
 	private void fetchChildren(TermConcept theConcept, Set<TermConcept> theSetToPopulate) {
 		for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
 			TermConcept nextChild = nextChildLink.getChild();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithLuceneDisabledTest.java

@@ -8,9 +8,13 @@
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.param.TokenParamModifier;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.util.TestUtil;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
 import org.hl7.fhir.r4.model.*;
@@ -27,7 +31,11 @@
 
 import javax.persistence.EntityManager;
 
+import java.util.List;
+
 import static org.junit.Assert.*;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.when;
 
 @RunWith(SpringJUnit4ClassRunner.class)
 @ContextConfiguration(classes = {TestR4WithoutLuceneConfig.class})
@@ -62,6 +70,12 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
 	@Qualifier("myCodeSystemDaoR4")
 	private IFhirResourceDao<CodeSystem> myCodeSystemDao;
 	@Autowired
+	@Qualifier("myValueSetDaoR4")
+	private IFhirResourceDao<ValueSet> myValueSetDao;
+	@Autowired
+	@Qualifier("myObservationDaoR4")
+	private IFhirResourceDao<Observation> myObservationDao;
+	@Autowired
 	@Qualifier("myCompartmentDefinitionDaoR4")
 	private IFhirResourceDao<CompartmentDefinition> myCompartmentDefinitionDao;
 	@Autowired
@@ -168,6 +182,42 @@ public void testSearchWithText() {
 		}
 	}
 
+	@Test
+	public void testSearchByCodeIn() {
+		CodeSystem cs = new CodeSystem();
+		cs.setUrl("http://fooCS");
+		cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+		cs.addConcept().setCode("CODEA");
+		cs.addConcept().setCode("CODEB");
+		myCodeSystemDao.create(cs);
+
+		ValueSet vs = new ValueSet();
+		vs.setUrl("http://fooVS");
+		vs.getCompose()
+			.addInclude()
+			.setSystem("http://fooCS")
+			.addConcept(new ValueSet.ConceptReferenceComponent().setCode("CODEA"));
+		myValueSetDao.create(vs);
+
+		Observation obs = new Observation();
+		obs.getCode().addCoding().setSystem("http://fooCS").setCode("CODEA");
+		String obs1id = myObservationDao.create(obs).getId().toUnqualifiedVersionless().getValue();
+
+		obs = new Observation();
+		obs.getCode().addCoding().setSystem("http://fooCS").setCode("CODEB");
+		myObservationDao.create(obs).getId().toUnqualifiedVersionless().getValue();
+
+		SearchParameterMap map = new SearchParameterMap();
+		map.setLoadSynchronous(true);
+		map.add("code", new TokenParam("http://fooVS").setModifier(TokenParamModifier.IN));
+		IBundleProvider results = myObservationDao.search(map);
+		List<IBaseResource> resultsList = results.getResources(0, 10);
+		assertEquals(1, resultsList.size());
+		assertEquals(obs1id, resultsList.get(0).getIdElement().toUnqualifiedVersionless().getValue());
+
+	}
+
+
 
 	@AfterClass
 	public static void afterClassClearContext() {

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java

@@ -9,9 +9,9 @@
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- *
+ * 
  * http://www.apache.org/licenses/LICENSE-2.0
- *
+ * 
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

src/changes/changes.xml

@@ -31,6 +31,11 @@
 				requesting extensions to be included caused the extensions to be included but 
 				not any values contained within. This has been corrected.
 			</action>
+			<action type="add">
+				The JPA terminology service can now detect when Hibvernate Search (Lucene)
+				is not enabled, and will perform simple ValueSet expansions without relying
+				on Hibenrate Search in such cases.
+			</action>
 		</release>
 		<release version="3.7.0" date="2019-02-06" description="Gale">
 			<action type="add">