Merge branch 'master' into improve_jpa_indexes

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

@@ -1610,8 +1610,19 @@ public class SearchBuilder implements ISearchBuilder {
 		//-- preload all tags with tag definition if any
 		Map<Long, Collection<ResourceTag>> tagMap = getResourceTagMap(resultList);
 		
+		//-- pre-load all forcedId
+		Map<Long, ForcedId> forcedIdMap = getForcedIdMap(pids);
+				
+		ForcedId forcedId = null;
+		Long resourceId = null;
 		for (ResourceTable next : resultList) {
 			Class<? extends IBaseResource> resourceType = context.getResourceDefinition(next.getResourceType()).getImplementingClass();
+			
+			resourceId = next.getId();
+			forcedId = forcedIdMap.get(resourceId);
+			if (forcedId != null)
+				next.setForcedId(forcedId);
+			
 			IBaseResource resource = theDao.toResource(resourceType, next, historyMap.get(next.getId()), tagMap.get(next.getId()), theForHistoryOperation);
 			if (resource == null) {
 				ourLog.warn("Unable to find resource {}/{}/_history/{} in database", next.getResourceType(), next.getIdDt().getIdPart(), next.getVersion());
@@ -1697,6 +1708,23 @@ public class SearchBuilder implements ISearchBuilder {
 		return tagMap;		
 	}
 
+	//-- load all forcedId in to the map
+	private Map<Long, ForcedId> getForcedIdMap(Collection<Long> pids) {
+
+		Map<Long, ForcedId> forceIdMap = new HashMap<Long, ForcedId>();
+
+		if (pids.size() == 0)
+			return forceIdMap;
+
+		Collection<ForcedId> forceIdList = myForcedIdDao.findByResourcePids(pids);
+
+		for (ForcedId forcedId : forceIdList) {
+
+			forceIdMap.put(forcedId.getResourcePid(), forcedId);
+		}
+
+		return forceIdMap;
+	}
 	@Override
 	public void loadResourcesByPid(Collection<Long> theIncludePids, List<IBaseResource> theResourceListToPopulate, Set<Long> theRevIncludedPids, boolean theForHistoryOperation,
 											 EntityManager entityManager, FhirContext context, IDao theDao) {

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

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.jpa.dao.data;
 
+import java.util.Collection;
 import java.util.List;
 
 /*
@@ -38,5 +39,7 @@ public interface IForcedIdDao extends JpaRepository<ForcedId, Long> {
 
 	@Query("SELECT f FROM ForcedId f WHERE f.myResourcePid = :resource_pid")
 	public ForcedId findByResourcePid(@Param("resource_pid") Long theResourcePid);
-	
+
+	@Query("SELECT f FROM ForcedId f WHERE f.myResourcePid in (:pids)")
+	Collection<ForcedId> findByResourcePids(@Param("pids") Collection<Long> pids);
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/BaseHasResource.java

@@ -42,7 +42,7 @@ public abstract class BaseHasResource {
 	@OptimisticLock(excluded = true)
 	private FhirVersionEnum myFhirVersion;
 
-	@OneToOne(optional = true, fetch = FetchType.EAGER, cascade = {}, orphanRemoval = false)
+	@OneToOne(optional = true, fetch = FetchType.LAZY, cascade = {}, orphanRemoval = false)
 	@JoinColumn(name = "FORCED_ID_PID")
 	@OptimisticLock(excluded = true)
 	private ForcedId myForcedId;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptPropertyFieldBridge.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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 @@ package ca.uhn.fhir.jpa.term;
  * 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/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchCustomSearchParamTest.java

@@ -64,7 +64,6 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 		}
 	}
 
-
 	@Test
 	public void testCreateInvalidParamNoPath() {
 		SearchParameter fooSp = new SearchParameter();
@@ -858,6 +857,49 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
 
 	}
 
+	@Test
+	public void testSearchParameterDescendsIntoContainedResource() {
+		SearchParameter sp = new SearchParameter();
+		sp.addBase("Observation");
+		sp.setCode("specimencollectedtime");
+		sp.setType(Enumerations.SearchParamType.DATE);
+		sp.setTitle("Observation Specimen Collected Time");
+		sp.setExpression("Observation.specimen.resolve().receivedTime");
+		sp.setXpathUsage(SearchParameter.XPathUsageType.NORMAL);
+		sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(sp));
+		mySearchParameterDao.create(sp);
+
+		mySearchParamRegsitry.forceRefresh();
+
+		Specimen specimen = new Specimen();
+		specimen.setId("#FOO");
+		specimen.setReceivedTimeElement(new DateTimeType("2011-01-01"));
+		Observation o = new Observation();
+		o.setId("O1");
+		o.getContained().add(specimen);
+		o.setStatus(Observation.ObservationStatus.FINAL);
+		o.setSpecimen(new Reference("#FOO"));
+		myObservationDao.update(o);
+
+		specimen = new Specimen();
+		specimen.setId("#FOO");
+		specimen.setReceivedTimeElement(new DateTimeType("2011-01-03"));
+		o = new Observation();
+		o.setId("O2");
+		o.getContained().add(specimen);
+		o.setStatus(Observation.ObservationStatus.FINAL);
+		o.setSpecimen(new Reference("#FOO"));
+		myObservationDao.update(o);
+
+		SearchParameterMap params = new SearchParameterMap();
+		params.add("specimencollectedtime", new DateParam("2011-01-01"));
+		IBundleProvider outcome = myObservationDao.search(params);
+		List<String> ids = toUnqualifiedVersionlessIdValues(outcome);
+		ourLog.info("IDS: " + ids);
+		assertThat(ids, contains("Observation/O1"));
+	}
+
 	@Test
 	public void testSearchWithCustomParam() {
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java

@@ -128,7 +128,7 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
 	}
 
 	@Test
-	public void testCreateSearchParameterOnSearchParameterDoesntCauseEndlessReindexLoop() throws InterruptedException {
+	public void testCreateSearchParameterOnSearchParameterDoesntCauseEndlessReindexLoop() {
 		SearchParameter fooSp = new SearchParameter();
 		fooSp.setCode("foo");
 		fooSp.addBase("SearchParameter");
@@ -175,6 +175,48 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
 		assertThat(ids, contains(pid.getValue()));
 	}
 
+	@Test
+	public void testSearchParameterDescendsIntoContainedResource() {
+		SearchParameter sp = new SearchParameter();
+		sp.addBase("Observation");
+		sp.setCode("specimencollectedtime");
+		sp.setType(Enumerations.SearchParamType.DATE);
+		sp.setTitle("Observation Specimen Collected Time");
+		sp.setExpression("Observation.specimen.resolve().receivedTime");
+		sp.setXpathUsage(org.hl7.fhir.r4.model.SearchParameter.XPathUsageType.NORMAL);
+		sp.setStatus(org.hl7.fhir.r4.model.Enumerations.PublicationStatus.ACTIVE);
+		mySearchParameterDao.create(sp);
+
+		mySearchParamRegsitry.forceRefresh();
+
+		Specimen specimen = new Specimen();
+		specimen.setId("#FOO");
+		specimen.setReceivedTimeElement(new DateTimeType("2011-01-01"));
+		Observation o = new Observation();
+		o.setId("O1");
+		o.getContained().add(specimen);
+		o.setStatus(Observation.ObservationStatus.FINAL);
+		o.setSpecimen(new Reference("#FOO"));
+		myObservationDao.update(o);
+
+		specimen = new Specimen();
+		specimen.setId("#FOO");
+		specimen.setReceivedTimeElement(new DateTimeType("2011-01-03"));
+		o = new Observation();
+		o.setId("O2");
+		o.getContained().add(specimen);
+		o.setStatus(Observation.ObservationStatus.FINAL);
+		o.setSpecimen(new Reference("#FOO"));
+		myObservationDao.update(o);
+
+		SearchParameterMap params = new SearchParameterMap();
+		params.add("specimencollectedtime", new DateParam("2011-01-01"));
+		IBundleProvider outcome = myObservationDao.search(params);
+		List<String> ids = toUnqualifiedVersionlessIdValues(outcome);
+		ourLog.info("IDS: " + ids);
+		assertThat(ids, contains("Observation/O1"));
+	}
+
 	@Test
 	public void testExtensionWithNoValueIndexesWithoutFailure() {
 		SearchParameter eyeColourSp = new SearchParameter();

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.rest.server;
  * 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-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/AuthorizationFlagsEnum.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.rest.server.interceptor.auth;
 
+/*-
+ * #%L
+ * HAPI FHIR - Server Framework
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
 import java.util.Collection;
 
 /**

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/AuthorizationInterceptor.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.rest.server.interceptor.auth;
  * 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-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/RuleImplOp.java

@@ -36,9 +36,9 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  * 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-validation/src/test/java/org/hl7/fhir/dstu3/utils/FhirPathEngineTest.java

@@ -1,45 +1,59 @@
 package org.hl7.fhir.dstu3.utils;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.util.List;
-
-import org.hl7.fhir.exceptions.FHIRException;
-import org.hl7.fhir.dstu3.hapi.validation.DefaultProfileValidationSupport;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.util.TestUtil;
 import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
+import org.hl7.fhir.dstu3.hapi.validation.DefaultProfileValidationSupport;
 import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.exceptions.FHIRException;
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.util.TestUtil;
+import java.util.List;
+
+import static org.junit.Assert.*;
 
 public class FhirPathEngineTest {
 
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirPathEngineTest.class);
 	private static FhirContext ourCtx = FhirContext.forDstu3();
 	private static FHIRPathEngine ourEngine;
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirPathEngineTest.class);
 
 	@Test
 	public void testAs() throws Exception {
 		Observation obs = new Observation();
 		obs.setValue(new StringType("FOO"));
-		
+
 		List<Base> value = ourEngine.evaluate(obs, "Observation.value.as(String)");
 		assertEquals(1, value.size());
-		assertEquals("FOO", ((StringType)value.get(0)).getValue());
+		assertEquals("FOO", ((StringType) value.get(0)).getValue());
 	}
-	
+
+	@Test
+	public void testCrossResourceBoundaries() throws FHIRException {
+		Specimen specimen = new Specimen();
+		specimen.setId("#FOO");
+		specimen.setReceivedTimeElement(new DateTimeType("2011-01-01"));
+		Observation o = new Observation();
+		o.getContained().add(specimen);
+
+		o.setId("O1");
+		o.setStatus(Observation.ObservationStatus.FINAL);
+		o.setSpecimen(new Reference("#FOO"));
+
+		List<Base> value = ourEngine.evaluate(o, "Observation.specimen.resolve().receivedTime");
+		assertEquals(1, value.size());
+		assertEquals("2011-01-01", ((DateTimeType) value.get(0)).getValueAsString());
+	}
+
 	@Test
 	public void testExistsWithNoValue() throws FHIRException {
 		Patient patient = new Patient();
 		patient.setDeceased(new BooleanType());
 		List<Base> eval = ourEngine.evaluate(patient, "Patient.deceased.exists()");
 		ourLog.info(eval.toString());
-		assertFalse(((BooleanType)eval.get(0)).getValue());
+		assertFalse(((BooleanType) eval.get(0)).getValue());
 	}
 
 	@Test
@@ -48,7 +62,7 @@ public class FhirPathEngineTest {
 		patient.setDeceased(new BooleanType(false));
 		List<Base> eval = ourEngine.evaluate(patient, "Patient.deceased.exists()");
 		ourLog.info(eval.toString());
-		assertTrue(((BooleanType)eval.get(0)).getValue());
+		assertTrue(((BooleanType) eval.get(0)).getValue());
 	}
 
 	@AfterClass

hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/utils/FhirPathEngineR4Test.java

@@ -3,14 +3,12 @@ package org.hl7.fhir.r4.utils;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.util.TestUtil;
 import org.hl7.fhir.dstu3.utils.FhirPathEngineTest;
+import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport;
 import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
 import org.hl7.fhir.r4.model.*;
-import org.hl7.fhir.r4.utils.FHIRPathEngine;
-import org.hl7.fhir.exceptions.FHIRException;
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
-import org.junit.Ignore;
 import org.junit.Test;
 
 import java.util.List;
@@ -23,6 +21,23 @@ public class FhirPathEngineR4Test {
 	private static FHIRPathEngine ourEngine;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirPathEngineTest.class);
 
+	@Test
+	public void testCrossResourceBoundaries() throws FHIRException {
+		Specimen specimen = new Specimen();
+		specimen.setId("#FOO");
+		specimen.setReceivedTimeElement(new DateTimeType("2011-01-01"));
+		Observation o = new Observation();
+		o.getContained().add(specimen);
+
+		o.setId("O1");
+		o.setStatus(Observation.ObservationStatus.FINAL);
+		o.setSpecimen(new Reference("#FOO"));
+
+		List<Base> value = ourEngine.evaluate(o, "Observation.specimen.resolve().receivedTime");
+		assertEquals(1, value.size());
+		assertEquals("2011-01-01", ((DateTimeType) value.get(0)).getValueAsString());
+	}
+
 	@Test
 	public void testAs() throws Exception {
 		Observation obs = new Observation();

pom.xml

@@ -459,6 +459,11 @@
 			<id>Romanow88</id>
 			<name>Roman Doboni</name>
 		</developer>
+		<developer>
+			<id>franktao2008</id>
+			<name>Frank Tao</name>
+			<organization>Smile CDR</organization>
+		</developer>
 	</developers>
 
 	<licenses>

src/changes/changes.xml

@@ -76,6 +76,19 @@
 				scheme introduced in LOINC 2.64. Thanks to Rob Hausam for the 
 				pull request!
 			</action>
+			<action type="add">
+				In the JPA server, it is now possible for a custom search parameter
+				to use the
+				<![CDATA[<code>resolve()</code>]]> function in its path to descend into
+				contained resources and index fields within them.
+			</action>
+			<action type="fix" issue="1010">
+				Resource loading logic for the JPA server has been optimized to
+				reduce the number of database round trips required when loading
+				search results where many of the entries have a "forced ID" (an alphanumeric
+				client-assigned reosurce ID). Thanks to Frank Tao for the pull
+				request!
+			</action>
 		</release>
 		<release version="3.4.0" date="2018-05-28">
 			<action type="add">