Support inline match URL references, per Simone's requast for the next

connectathon

hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

@@ -43,6 +43,9 @@ ca.uhn.fhir.validation.ValidationResult.noIssuesDetected=No issues detected duri
 # JPA Messages
 
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.incomingNoopInTransaction=Transaction contains resource with operation NOOP. This is only valid as a response operation, not in a request.
+ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlInvalidResourceType=Invalid match URL "{0}" - Unknown resource type: "{1}"
+ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlNoMatches=Invalid match URL "{0}" - No resources match this search
+ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlMultipleMatches=Invalid match URL "{0}" - Multiple resources match this search
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationWithMultipleMatchFailure=Failed to {0} resource with match URL "{1}" because this search matched {2} resources
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationFailedNoId=Failed to {0} resource in transaction because no ID was provided 
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationFailedUnknownId=Failed to {0} resource in transaction because no resource could be found with ID {1} 

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

@@ -34,6 +34,32 @@ import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 
 public class DaoConfig {
 
+	// ***
+	// update setter javadoc if default changes
+	// ***
+	private boolean myAllowInlineMatchUrlReferences = false; 
+	
+	/**
+	 * @see #setAllowInlineMatchUrlReferences(boolean)
+	 */
+	public boolean isAllowInlineMatchUrlReferences() {
+		return myAllowInlineMatchUrlReferences;
+	}
+
+	/**
+	 * Should references containing match URLs be resolved and replaced in create and update operations. For
+	 * example, if this property is set to true and a resource is created containing a reference
+	 * to "Patient?identifier=12345", this is reference match URL will be resolved and replaced according
+	 * to the usual match URL rules.
+	 * <p>
+	 * Default is false for now, as this is an experimental feature.
+	 * </p>
+	 * @since 1.5
+	 */
+	public void setAllowInlineMatchUrlReferences(boolean theAllowInlineMatchUrlReferences) {
+		myAllowInlineMatchUrlReferences = theAllowInlineMatchUrlReferences;
+	}
+
 	private boolean myAllowMultipleDelete;
 	private int myHardSearchLimit = 1000;
 	private int myHardTagListLimit = 1000;

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

@@ -0,0 +1,34 @@
+package ca.uhn.fhir.jpa.dao.data;
+
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2016 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.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
+
+import ca.uhn.fhir.jpa.entity.ForcedId;
+
+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);
+	
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3.java

@@ -462,7 +462,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
 
 		FhirTerser terser = getContext().newTerser();
 		for (DaoMethodOutcome nextOutcome : idToPersistedOutcome.values()) {
-			IBaseResource nextResource = (IBaseResource) nextOutcome.getResource();
+			IBaseResource nextResource = nextOutcome.getResource();
 			if (nextResource == null) {
 				continue;
 			}

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

@@ -35,7 +35,8 @@ import javax.persistence.UniqueConstraint;
 //@formatter:off
 @Entity()
 @Table(name = "HFJ_FORCED_ID", uniqueConstraints = {
-		@UniqueConstraint(name = "IDX_FORCEDID", columnNames = {"FORCED_ID"})
+	@UniqueConstraint(name = "IDX_FORCEDID", columnNames = {"FORCED_ID"}),
+	@UniqueConstraint(name = "IDX_FORCEDID_RESID", columnNames = {"RESOURCE_PID"})
 })
 @NamedQueries(value = {
 		@NamedQuery(name = "Q_GET_FORCED_ID", query = "SELECT f FROM ForcedId f WHERE myForcedId = :ID")

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java

@@ -17,10 +17,8 @@ import static org.mockito.Matchers.eq;
 import static org.mockito.Mockito.times;
 import static org.mockito.Mockito.verify;
 
-import java.io.IOException;
 import java.io.InputStream;
 import java.io.UnsupportedEncodingException;
-import java.util.ArrayList;
 import java.util.List;
 
 import org.apache.commons.io.IOUtils;
@@ -44,8 +42,10 @@ import org.hl7.fhir.dstu3.model.UriType;
 import org.hl7.fhir.dstu3.model.ValueSet;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.After;
 import org.junit.Test;
 import org.mockito.ArgumentCaptor;
+import org.springframework.transaction.TransactionDefinition;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallback;
 import org.springframework.transaction.support.TransactionTemplate;
@@ -113,7 +113,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		// Try making the resource unparseable
 
 		TransactionTemplate template = new TransactionTemplate(myTxManager);
-		template.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
+		template.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
 		template.execute(new TransactionCallback<ResourceTable>() {
 			@Override
 			public ResourceTable doInTransaction(TransactionStatus theStatus) {
@@ -300,12 +300,106 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		assertThat(respEntry.getResponse().getLocation(), endsWith("/_history/1"));
 		assertEquals("1", respEntry.getResponse().getEtag());
 
-		o = (Observation) myObservationDao.read(new IdType(respEntry.getResponse().getLocationElement()));
+		o = myObservationDao.read(new IdType(respEntry.getResponse().getLocationElement()));
 		assertEquals(id.toVersionless().getValue(), o.getSubject().getReference());
 		assertEquals("1", o.getIdElement().getVersionIdPart());
 
 	}
 
+	@After
+	public void after() {
+		myDaoConfig.setAllowInlineMatchUrlReferences(false);
+	}
+	
+	@Test
+	public void testTransactionCreateInlineMatchUrlWithOneMatch() {
+		String methodName = "testTransactionCreateInlineMatchUrlWithOneMatch";
+		Bundle request = new Bundle();
+
+		myDaoConfig.setAllowInlineMatchUrlReferences(true);
+		
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.setId("Patient/" + methodName);
+		IIdType id = myPatientDao.update(p).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		Observation o = new Observation();
+		o.getCode().setText("Some Observation");
+		o.getSubject().setReference("Patient?identifier=urn%3Asystem%7C" + methodName);
+		request.addEntry().setResource(o).getRequest().setMethod(HTTPVerb.POST);
+
+		Bundle resp = mySystemDao.transaction(myRequestDetails, request);
+		assertEquals(1, resp.getEntry().size());
+
+		BundleEntryComponent respEntry = resp.getEntry().get(0);
+		assertEquals(Constants.STATUS_HTTP_201_CREATED + " Created", respEntry.getResponse().getStatus());
+		assertThat(respEntry.getResponse().getLocation(), containsString("Observation/"));
+		assertThat(respEntry.getResponse().getLocation(), endsWith("/_history/1"));
+		assertEquals("1", respEntry.getResponse().getEtag());
+
+		o = myObservationDao.read(new IdType(respEntry.getResponse().getLocationElement()));
+		assertEquals(id.toVersionless().getValue(), o.getSubject().getReference());
+		assertEquals("1", o.getIdElement().getVersionIdPart());
+
+	}
+
+	@Test
+	public void testTransactionCreateInlineMatchUrlWithNoMatches() {
+		String methodName = "testTransactionCreateInlineMatchUrlWithNoMatches";
+		Bundle request = new Bundle();
+
+		myDaoConfig.setAllowInlineMatchUrlReferences(true);
+		
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		myPatientDao.create(p).getId();
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		myPatientDao.create(p).getId();
+
+		Observation o = new Observation();
+		o.getCode().setText("Some Observation");
+		o.getSubject().setReference("Patient?identifier=urn%3Asystem%7C" + methodName);
+		request.addEntry().setResource(o).getRequest().setMethod(HTTPVerb.POST);
+
+		try {
+			mySystemDao.transaction(myRequestDetails, request);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid match URL \"Patient?identifier=urn%3Asystem%7CtestTransactionCreateInlineMatchUrlWithNoMatches\" - Multiple resources match this search", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testTransactionCreateInlineMatchUrlWithTwoMatches() {
+		String methodName = "testTransactionCreateInlineMatchUrlWithTwoMatches";
+		Bundle request = new Bundle();
+
+		myDaoConfig.setAllowInlineMatchUrlReferences(true);
+		
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		myPatientDao.create(p).getId();
+
+		p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		myPatientDao.create(p).getId();
+
+		Observation o = new Observation();
+		o.getCode().setText("Some Observation");
+		o.getSubject().setReference("Patient?identifier=urn%3Asystem%7C" + methodName);
+		request.addEntry().setResource(o).getRequest().setMethod(HTTPVerb.POST);
+
+		try {
+			mySystemDao.transaction(myRequestDetails, request);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Invalid match URL \"Patient?identifier=urn%3Asystem%7CtestTransactionCreateInlineMatchUrlWithTwoMatches\" - Multiple resources match this search", e.getMessage());
+		}
+	}
+
 	@Test
 	public void testTransactionCreateMatchUrlWithTwoMatch() {
 		String methodName = "testTransactionCreateMatchUrlWithTwoMatch";
@@ -374,7 +468,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		assertThat(respEntry.getResponse().getLocation(), endsWith("/_history/1"));
 		assertEquals("1", respEntry.getResponse().getEtag());
 
-		o = (Observation) myObservationDao.read(new IdType(respEntry.getResponse().getLocationElement()));
+		o = myObservationDao.read(new IdType(respEntry.getResponse().getLocationElement()));
 		assertEquals(new IdType(patientId).toUnqualifiedVersionless().getValue(), o.getSubject().getReference());
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu2Config.java

@@ -50,6 +50,7 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 		retVal.setSubscriptionPollDelay(5000);
 		retVal.setSubscriptionPurgeInactiveAfterMillis(DateUtils.MILLIS_PER_HOUR);
 		retVal.setAllowMultipleDelete(true);
+		retVal.setAllowInlineMatchUrlReferences(true);
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java

@@ -46,6 +46,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 		retVal.setSubscriptionPollDelay(5000);
 		retVal.setSubscriptionPurgeInactiveAfterMillis(DateUtils.MILLIS_PER_HOUR);
 		retVal.setAllowMultipleDelete(true);
+		retVal.setAllowInlineMatchUrlReferences(true);
 		return retVal;
 	}
 

src/changes/changes.xml

@@ -59,6 +59,13 @@
 			<action type="add">
 				JPA server now supports :above and :below qualifiers on URI search params
 			</action>
+			<action type="add">
+				Add optional support (disabled by default for now) to JPA server to support
+				inline references containing search URLs. These URLs will be resolved when
+				a resource is being created/updated and replaced with the single matching
+				resource. This is being used as a part of the May 2016 Connectathon for
+				a testing scenario.
+			</action>
 		</release>
 		<release version="1.4" date="2016-02-04">
 			<action type="add">