Add test for #226 and refactor $everything into DAO

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoPatientDstu2.java

@@ -0,0 +1,31 @@
+package ca.uhn.fhir.jpa.dao;
+
+import java.util.Collections;
+
+import javax.servlet.http.HttpServletRequest;
+
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.UnsignedIntDt;
+import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.rest.server.IBundleProvider;
+
+public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>implements IFhirResourceDaoPatient<Patient> {
+
+	@Override
+	public IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount) {
+		SearchParameterMap paramMap = new SearchParameterMap();
+		if (theCount != null) {
+			paramMap.setCount(theCount.getValue());
+		}
+
+		paramMap.setRevIncludes(Collections.singleton(IResource.INCLUDE_ALL.asRecursive()));
+		paramMap.setIncludes(Collections.singleton(IResource.INCLUDE_ALL.asRecursive()));
+		paramMap.setEverythingMode(true);
+		paramMap.add("_id", new StringParam(theId.getIdPart()));
+		ca.uhn.fhir.rest.server.IBundleProvider retVal = search(paramMap);
+		return retVal;
+	}
+
+}

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

@@ -0,0 +1,35 @@
+package ca.uhn.fhir.jpa.dao;
+
+import javax.servlet.http.HttpServletRequest;
+
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2015 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 org.hl7.fhir.instance.model.api.IBaseResource;
+
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.UnsignedIntDt;
+import ca.uhn.fhir.rest.server.IBundleProvider;
+
+public interface IFhirResourceDaoPatient<T extends IBaseResource> extends IFhirResourceDao<T> {
+
+	IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount);
+
+}

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

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.dao.data;
 
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2015 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 org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.jpa.repository.JpaRepository;

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

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.dao.data;
 
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2015 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;
 import java.util.Date;
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaResourceProviderPatientDstu2.java

@@ -1,35 +1,11 @@
 package ca.uhn.fhir.jpa.provider;
 
-/*
+import ca.uhn.fhir.jpa.dao.IFhirResourceDaoPatient;
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2015 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.Collections;
-
-import ca.uhn.fhir.jpa.dao.SearchParameterMap;
-import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.annotation.Description;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.Operation;
 import ca.uhn.fhir.rest.annotation.OperationParam;
-import ca.uhn.fhir.rest.param.StringParam;
 
 public class BaseJpaResourceProviderPatientDstu2 extends JpaResourceProviderDstu2<Patient> {
 
@@ -47,17 +23,7 @@ public class BaseJpaResourceProviderPatientDstu2 extends JpaResourceProviderDstu
 
 		startRequest(theServletRequest);
 		try {
-			SearchParameterMap paramMap = new SearchParameterMap();
+			return ((IFhirResourceDaoPatient<Patient>)getDao()).everything(theServletRequest, theId, theCount);
-			if (theCount != null) {
-				paramMap.setCount(theCount.getValue());
-			}
-
-			paramMap.setRevIncludes(Collections.singleton(IResource.INCLUDE_ALL.asRecursive()));
-			paramMap.setIncludes(Collections.singleton(IResource.INCLUDE_ALL.asRecursive()));
-			paramMap.setEverythingMode(true);
-			paramMap.add("_id", new StringParam(theId.getIdPart()));
-			ca.uhn.fhir.rest.server.IBundleProvider retVal = getDao().search(paramMap);
-			return retVal;
 		} finally {
 			endRequest(theServletRequest);
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/ISubscriptionWebsocketHandler.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.subscription;
 
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2015 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 org.springframework.web.socket.WebSocketHandler;
 
 public interface ISubscriptionWebsocketHandler extends WebSocketHandler {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/SubscriptionWebsocketHandler.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.subscription;
 
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2015 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.io.IOException;
 import java.util.List;
 import java.util.concurrent.ScheduledFuture;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/SubscriptionWebsocketHandlerFactory.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.subscription;
 
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2015 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 org.springframework.beans.factory.FactoryBean;
 
 public class SubscriptionWebsocketHandlerFactory implements FactoryBean<ISubscriptionWebsocketHandler> {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaDstu2Test.java

@@ -50,6 +50,8 @@ import ca.uhn.fhir.model.dstu2.resource.DiagnosticReport;
 import ca.uhn.fhir.model.dstu2.resource.Encounter;
 import ca.uhn.fhir.model.dstu2.resource.Immunization;
 import ca.uhn.fhir.model.dstu2.resource.Location;
+import ca.uhn.fhir.model.dstu2.resource.Medication;
+import ca.uhn.fhir.model.dstu2.resource.MedicationOrder;
 import ca.uhn.fhir.model.dstu2.resource.Observation;
 import ca.uhn.fhir.model.dstu2.resource.Organization;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
@@ -79,6 +81,12 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 	@Qualifier("myConceptMapDaoDstu2")
 	protected IFhirResourceDao<ConceptMap> myConceptMapDao;
 	@Autowired
+	@Qualifier("myMedicationDaoDstu2")
+	protected IFhirResourceDao<Medication> myMedicationDao;
+	@Autowired
+	@Qualifier("myMedicationOrderDaoDstu2")
+	protected IFhirResourceDao<MedicationOrder> myMedicationOrderDao;
+	@Autowired
 	protected DaoConfig myDaoConfig;
 	@Autowired
 	@Qualifier("myDeviceDaoDstu2")

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java

@@ -61,6 +61,8 @@ import ca.uhn.fhir.model.dstu2.resource.DocumentReference;
 import ca.uhn.fhir.model.dstu2.resource.Encounter;
 import ca.uhn.fhir.model.dstu2.resource.ImagingStudy;
 import ca.uhn.fhir.model.dstu2.resource.Location;
+import ca.uhn.fhir.model.dstu2.resource.Medication;
+import ca.uhn.fhir.model.dstu2.resource.MedicationOrder;
 import ca.uhn.fhir.model.dstu2.resource.Observation;
 import ca.uhn.fhir.model.dstu2.resource.Organization;
 import ca.uhn.fhir.model.dstu2.resource.Parameters;
@@ -635,12 +637,45 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 
 	}
 
+	/**
+	 * Test for #226
+	 */
+	@Test
+	public void testEverythingIncludesBackReferences() throws Exception {
+		String methodName = "testEverythingIncludesBackReferences";
+		
+		Medication med = new Medication();
+		med.getCode().setText(methodName);
+		IIdType medId = myMedicationDao.create(med).getId().toUnqualifiedVersionless();
+		
+		Patient pat = new Patient();
+		pat.addAddress().addLine(methodName);
+		IIdType patId = myPatientDao.create(pat).getId().toUnqualifiedVersionless();
+
+		MedicationOrder mo = new MedicationOrder();
+		mo.getPatient().setReference(patId);
+		mo.setMedication(new ResourceReferenceDt(medId));
+		IIdType moId = myMedicationOrderDao.create(mo).getId().toUnqualifiedVersionless();
+		
+		Parameters output = ourClient.operation().onInstance(patId).named("everything").withNoParameters(Parameters.class).execute();
+		ca.uhn.fhir.model.dstu2.resource.Bundle b = (ca.uhn.fhir.model.dstu2.resource.Bundle) output.getParameterFirstRep().getResource();
+		Set<IdDt> ids = toIdList(b);
+		ourLog.info(ids.toString());
+		assertThat(ids, containsInAnyOrder(patId, medId, moId));
+	}
+	
 	@Test
 	public void testEverythingOperation() throws Exception {
 		String methodName = "testEverythingOperation";
 
+		Organization org1parent = new Organization();
+		org1parent.setId("org1parent");
+		org1parent.setName(methodName + "1parent");
+		IIdType orgId1parent = ourClient.update().resource(org1parent).execute().getId().toUnqualifiedVersionless();
+
 		Organization org1 = new Organization();
 		org1.setName(methodName + "1");
+		org1.getPartOf().setReference(orgId1parent);
 		IIdType orgId1 = ourClient.create().resource(org1).execute().getId().toUnqualifiedVersionless();
 
 		Patient p = new Patient();
@@ -669,17 +704,18 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
 		Parameters output = ourClient.operation().onInstance(patientId).named("everything").withNoParameters(Parameters.class).execute();
 		ca.uhn.fhir.model.dstu2.resource.Bundle b = (ca.uhn.fhir.model.dstu2.resource.Bundle) output.getParameterFirstRep().getResource();
 
+		Set<IdDt> ids = toIdList(b);
+		assertThat(ids, containsInAnyOrder(patientId, devId, obsId, encId, orgId1, orgId2, orgId1parent));
+
+		ourLog.info(ids.toString());
+	}
+
+	private Set<IdDt> toIdList(ca.uhn.fhir.model.dstu2.resource.Bundle b) {
 		Set<IdDt> ids = new HashSet<IdDt>();
 		for (Entry next : b.getEntry()) {
 			ids.add(next.getResource().getId().toUnqualifiedVersionless());
 		}
-
+		return ids;
-		assertThat(ids, containsInAnyOrder(patientId, devId, obsId, encId, orgId1, orgId2));
-
-		// Should include everything
-		assertEquals(6, b.getTotal().intValue());
-
-		ourLog.info(ids.toString());
 	}
 
 	@Test

hapi-tinder-plugin/src/main/resources/vm/jpa_spring_beans.vm

@@ -41,7 +41,7 @@
 #foreach ( $res in $resources )
 	<bean id="my${res.name}Dao${versionCapitalized}" 
 ## Some resource types have customized DAOs for resource specific functionality
-#if ( ${versionCapitalized} == 'Dstu2' && ( ${res.name} == 'Bundle' || ${res.name} == 'Subscription' || ${res.name} == 'QuestionnaireResponse' || ${res.name} == 'ValueSet'))
+#if ( ${versionCapitalized} == 'Dstu2' && ( ${res.name} == 'Bundle' || ${res.name} == 'Patient' || ${res.name} == 'Subscription' || ${res.name} == 'QuestionnaireResponse' || ${res.name} == 'ValueSet'))
 		class="ca.uhn.fhir.jpa.dao.FhirResourceDao${res.name}${versionCapitalized}">
 #else
 		class="ca.uhn.fhir.jpa.dao.FhirResourceDao${versionCapitalized}">