Only do one pass of validation during a JPA transaction

.gitignore

@@ -15,6 +15,7 @@ nohup.out
 *.orig
 tmp.txt
 *.hprof
+tmp.txt
 
 # Vagrant stuff.
 .vagrant

hapi-fhir-cli/src/main/java/ca/uhn/fhir/cli/ExampleDataUploader.java

@@ -78,9 +78,9 @@ public class ExampleDataUploader extends BaseCommand {
 		opt.setRequired(false);
 		options.addOption(opt);
 
-		opt = new Option("c", "cache", true, "Store a copy of the downloaded example pack on the local disk using a file of the given name. Use this file instead of fetching it from the internet if the file already exists.");
+//		opt = new Option("c", "cache", true, "Store a copy of the downloaded example pack on the local disk using a file of the given name. Use this file instead of fetching it from the internet if the file already exists.");
-		opt.setRequired(false);
+//		opt.setRequired(false);
-		options.addOption(opt);
+//		options.addOption(opt);
 
 		return options;
 	}

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

@@ -1242,7 +1242,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		 * This should be the very first thing..
 		 */
 		if (theResource != null) {
+			if (thePerformIndexing) {
 				validateResourceForStorage((T) theResource, theEntity);
+			}
 			String resourceType = myContext.getResourceDefinition(theResource).getName();
 			if (isNotBlank(theEntity.getResourceType()) && !theEntity.getResourceType().equals(resourceType)) {
 				throw new UnprocessableEntityException("Existing resource ID[" + theEntity.getIdDt().toUnqualifiedVersionless() + "] is of type[" + theEntity.getResourceType() + "] - Cannot update with [" + resourceType + "]");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2SystemTest.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.dao;
+package ca.uhn.fhir.jpa.dao.dstu2;
 
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.dao;
+package ca.uhn.fhir.jpa.dao.dstu2;
 
 import static org.junit.Assert.fail;
 import static org.mockito.Mockito.mock;
@@ -27,6 +27,14 @@ import org.springframework.transaction.support.TransactionTemplate;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.config.TestDstu2Config;
+import ca.uhn.fhir.jpa.dao.BaseJpaTest;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDaoPatient;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSubscription;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
+import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.dao.ISearchDao;
 import ca.uhn.fhir.jpa.entity.ForcedId;
 import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
 import ca.uhn.fhir.jpa.entity.ResourceHistoryTag;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2InterceptorTest.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.dao;
+package ca.uhn.fhir.jpa.dao.dstu2;
 
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotEquals;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchFtTest.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.dao;
+package ca.uhn.fhir.jpa.dao.dstu2;
 
 import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsInAnyOrder;
@@ -14,6 +14,8 @@ import javax.servlet.http.HttpServletRequest;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.Test;
 
+import ca.uhn.fhir.jpa.dao.FhirSearchDao;
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.jpa.dao.FhirSearchDao.Suggestion;
 import ca.uhn.fhir.model.dstu2.resource.Device;
 import ca.uhn.fhir.model.dstu2.resource.Media;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchNoFtTest.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.dao;
+package ca.uhn.fhir.jpa.dao.dstu2;
 
 import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsInAnyOrder;
@@ -30,6 +30,8 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.Ignore;
 import org.junit.Test;
 
+import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamDate;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamNumber;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamQuantity;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SubscriptionTest.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.dao;
+package ca.uhn.fhir.jpa.dao.dstu2;
 
 import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsString;
@@ -25,6 +25,7 @@ import org.junit.Before;
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.jpa.dao.data.ISubscriptionFlaggedResourceDataDao;
 import ca.uhn.fhir.jpa.dao.data.ISubscriptionTableDao;
 import ca.uhn.fhir.jpa.entity.SubscriptionTable;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.dao;
+package ca.uhn.fhir.jpa.dao.dstu2;
 
 import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.hamcrest.Matchers.contains;
@@ -39,6 +39,10 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.Test;
 import org.mockito.ArgumentCaptor;
 
+import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
+import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.FhirResourceDaoDstu2;
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
 import ca.uhn.fhir.jpa.entity.TagTypeEnum;
 import ca.uhn.fhir.model.api.IQueryParameterType;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2UpdateTest.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.dao;
+package ca.uhn.fhir.jpa.dao.dstu2;
 
 import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsInAnyOrder;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2ValidateTest.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.dao;
+package ca.uhn.fhir.jpa.dao.dstu2;
 
 import static org.hamcrest.Matchers.containsString;
 import static org.junit.Assert.*;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoValueSetDstu2Test.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.dao;
+package ca.uhn.fhir.jpa.dao.dstu2;
 
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.not;
@@ -15,6 +15,7 @@ import org.junit.Before;
 import org.junit.Test;
 import org.springframework.transaction.annotation.Transactional;
 
+import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
 import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
 import ca.uhn.fhir.model.dstu2.composite.CodingDt;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirSearchDaoDstu2Test.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.dao;
+package ca.uhn.fhir.jpa.dao.dstu2;
 
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.empty;
@@ -9,6 +9,8 @@ import java.util.List;
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import ca.uhn.fhir.jpa.dao.ISearchDao;
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.model.dstu2.resource.Organization;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.rest.param.StringAndListParam;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirSystemDaoDstu2SearchTest.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.dao;
+package ca.uhn.fhir.jpa.dao.dstu2;
 
 import org.junit.Test;
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirSystemDaoDstu2Test.java

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.dao;
+package ca.uhn.fhir.jpa.dao.dstu2;
 
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.emptyString;
@@ -30,6 +30,7 @@ import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallback;
 import org.springframework.transaction.support.TransactionTemplate;
 
+import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.entity.ResourceEncodingEnum;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.entity.TagTypeEnum;
@@ -450,6 +451,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
 		}
 	}
 
+	@Test
 	public void testTransactionCreateWithDuplicateMatchUrl02() {
 		String methodName = "testTransactionCreateWithDuplicateMatchUrl02";
 		Bundle request = new Bundle();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu21/BaseJpaDstu21Test.java

@@ -29,13 +29,13 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.config.TestDstu21Config;
 import ca.uhn.fhir.jpa.dao.BaseJpaTest;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.dao.FhirResourceDaoDstu2SearchNoFtTest;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoPatient;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSubscription;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.dao.ISearchDao;
+import ca.uhn.fhir.jpa.dao.dstu2.FhirResourceDaoDstu2SearchNoFtTest;
 import ca.uhn.fhir.jpa.entity.ForcedId;
 import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
 import ca.uhn.fhir.jpa.entity.ResourceHistoryTag;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu21/FhirSystemDaoDstu21Test.java

@@ -17,6 +17,7 @@ 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;
@@ -451,6 +452,7 @@ public class FhirSystemDaoDstu21Test extends BaseJpaDstu21SystemTest {
 		}
 	}
 
+	@Test
 	public void testTransactionCreateWithDuplicateMatchUrl02() {
 		String methodName = "testTransactionCreateWithDuplicateMatchUrl02";
 		Bundle request = new Bundle();
@@ -472,6 +474,34 @@ public class FhirSystemDaoDstu21Test extends BaseJpaDstu21SystemTest {
 		}
 	}
 
+	@Test
+	public void testTransactionCreateWithPutUsingUrl() {
+		String methodName = "testTransactionCreateWithPutUsingUrl";
+		Bundle request = new Bundle();
+		request.setType(BundleTypeEnum.TRANSACTION);
+
+		Observation o = new Observation();
+		o.getSubject().setReference("Patient/" + methodName);
+		request.addEntry().setResource(o).getRequest().setMethod(HTTPVerbEnum.PUT).setUrl("Observation/a" + methodName);
+
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		request.addEntry().setResource(p).getRequest().setMethod(HTTPVerbEnum.PUT).setUrl("Patient/" + methodName);
+
+		mySystemDao.transaction(myRequestDetails, request);
+		
+		myObservationDao.read(new IdDt("Observation/a" + methodName));
+		myPatientDao.read(new IdDt("Patient/" + methodName));
+	}
+
+	@Test
+	public void testTransactionCreateWithPutUsingUrl2() throws Exception {
+		String req = IOUtils.toString(FhirSystemDaoDstu21Test.class.getResourceAsStream("/bundle-dstu21.xml"));
+		Bundle request = myFhirCtx.newXmlParser().parseResource(Bundle.class, req);
+		mySystemDao.transaction(myRequestDetails, request);
+	}
+
+
 	@Test
 	public void testTransactionCreateWithInvalidMatchUrl() {
 		String methodName = "testTransactionCreateWithInvalidMatchUrl";

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/BaseResourceProviderDstu2Test.java

@@ -20,7 +20,7 @@ import org.springframework.web.context.support.AnnotationConfigWebApplicationCon
 import org.springframework.web.context.support.GenericWebApplicationContext;
 import org.springframework.web.servlet.DispatcherServlet;
 
-import ca.uhn.fhir.jpa.dao.BaseJpaDstu2Test;
+import ca.uhn.fhir.jpa.dao.dstu2.BaseJpaDstu2Test;
 import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.BundleEntry;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SystemProviderDstu2Test.java

@@ -29,7 +29,7 @@ import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.jpa.dao.BaseJpaDstu2Test;
+import ca.uhn.fhir.jpa.dao.dstu2.BaseJpaDstu2Test;
 import ca.uhn.fhir.jpa.rp.dstu2.ObservationResourceProvider;
 import ca.uhn.fhir.jpa.rp.dstu2.OrganizationResourceProvider;
 import ca.uhn.fhir.jpa.rp.dstu2.PatientResourceProvider;

hapi-fhir-jpaserver-base/src/test/resources/bundle-dstu21.xml

@@ -0,0 +1,394 @@
+<Bundle xmlns="http://hl7.org/fhir">
+   <entry>
+     <resource>
+         <QuestionnaireResponse xmlns="http://hl7.org/fhir">
+            <text>
+               <status value="generated"/>
+               <div xmlns="http://www.w3.org/1999/xhtml">
+                  <p>
+                     <b>Generated Narrative with Details</b>
+                  </p>
+                  <p>
+                     <b>id</b>: gcs
+                  </p>
+                  <p>
+                     <b>questionnaire</b>: 
+                     <a>Questionnaire/gcs</a>
+                  </p>
+                  <p>
+                     <b>status</b>: completed
+                  </p>
+                  <p>
+                     <b>subject</b>: 
+                     <a>Peter James Chalmers</a>
+                  </p>
+                  <p>
+                     <b>authored</b>: Dec 11, 2014 4:44:16 AM
+                  </p>
+                  <p>
+                     <b>source</b>: 
+                     <a>Practitioner/f007</a>
+                  </p>
+                  <blockquote>
+                     <p>
+                        <b>item</b>
+                     </p>
+                     <p>
+                        <b>linkId</b>: 1.1
+                     </p>
+                     <h3>Answers</h3>
+                     <table>
+                        <tr>
+                           <td>-</td>
+                           <td>
+                              <b>Value[x]</b>
+                           </td>
+                        </tr>
+                        <tr>
+                           <td>*</td>
+                           <td>Confused (Details: LOINC code LA6560-2 = 'Confused', stated as 'Confused')</td>
+                        </tr>
+                     </table>
+                  </blockquote>
+                  <blockquote>
+                     <p>
+                        <b>item</b>
+                     </p>
+                     <p>
+                        <b>linkId</b>: 1.2
+                     </p>
+                     <h3>Answers</h3>
+                     <table>
+                        <tr>
+                           <td>-</td>
+                           <td>
+                              <b>Value[x]</b>
+                           </td>
+                        </tr>
+                        <tr>
+                           <td>*</td>
+                           <td>Localizing pain (Details: LOINC code LA6566-9 = 'Localizing pain', stated as 'Localizing pain')</td>
+                        </tr>
+                     </table>
+                  </blockquote>
+                  <blockquote>
+                     <p>
+                        <b>item</b>
+                     </p>
+                     <p>
+                        <b>linkId</b>: 1.3
+                     </p>
+                     <h3>Answers</h3>
+                     <table>
+                        <tr>
+                           <td>-</td>
+                           <td>
+                              <b>Value[x]</b>
+                           </td>
+                        </tr>
+                        <tr>
+                           <td>*</td>
+                           <td>Eyes open spontaneously (Details: LOINC code LA6556-0 = 'Eyes open spontaneously', stated as 'Eyes open spontaneously')</td>
+                        </tr>
+                     </table>
+                  </blockquote>
+               </div>
+            </text>
+            <questionnaire>
+               <reference value="Questionnaire/Questionnairegcs"/>
+            </questionnaire>
+            <status value="completed"/>
+            <authored value="2014-12-11T04:44:16Z"/>
+            <item>
+               <linkId value="1.1"/>
+               <answer>
+                  <valueCoding>
+                     <extension url="http://hl7.org/fhir/StructureDefinition/iso21090-CO-value">
+                        <valueDecimal value="4"/>
+                     </extension>
+                     <system value="http://loinc.org"/>
+                     <code value="LA6560-2"/>
+                     <display value="Confused"/>
+                  </valueCoding>
+               </answer>
+            </item>
+            <item>
+               <linkId value="1.2"/>
+               <answer>
+                  <valueCoding>
+                     <extension url="http://hl7.org/fhir/StructureDefinition/iso21090-CO-value">
+                        <valueDecimal value="5"/>
+                     </extension>
+                     <system value="http://loinc.org"/>
+                     <code value="LA6566-9"/>
+                     <display value="Localizing pain"/>
+                  </valueCoding>
+               </answer>
+            </item>
+            <item>
+               <linkId value="1.3"/>
+               <answer>
+                  <valueCoding>
+                     <extension url="http://hl7.org/fhir/StructureDefinition/iso21090-CO-value">
+                        <valueDecimal value="4"/>
+                     </extension>
+                     <system value="http://loinc.org"/>
+                     <code value="LA6556-0"/>
+                     <display value="Eyes open spontaneously"/>
+                  </valueCoding>
+               </answer>
+            </item>
+         </QuestionnaireResponse>
+      </resource>
+      <request>
+         <method value="PUT"/>
+         <url value="QuestionnaireResponse/QuestionnaireResponsegcs"/>
+      </request>
+   </entry>
+   <entry>
+      <resource>
+         <Questionnaire xmlns="http://hl7.org/fhir">
+            <text>
+               <status value="generated"/>
+               <div xmlns="http://www.w3.org/1999/xhtml">
+                  <p>
+                     <b>Generated Narrative with Details</b>
+                  </p>
+                  <p>
+                     <b>id</b>: gcs
+                  </p>
+                  <p>
+                     <b>contained</b>: , , 
+                  </p>
+                  <p>
+                     <b>status</b>: draft
+                  </p>
+                  <p>
+                     <b>date</b>: Aug 3, 2015
+                  </p>
+                  <p>
+                     <b>publisher</b>: FHIR Project team
+                  </p>
+                  <p>
+                     <b>title</b>: Glasgow Coma Score
+                  </p>
+                  <p>
+                     <b>concept</b>: Glasgow coma score total (Details: LOINC code 9269-2 = 'Glasgow coma score total', stated as 'null')
+                  </p>
+                  <p>
+                     <b>subjectType</b>: Patient
+                  </p>
+                  <blockquote>
+                     <p>
+                        <b>item</b>
+                     </p>
+                     <p>
+                        <b>linkId</b>: 1.1
+                     </p>
+                     <p>
+                        <b>concept</b>: Glasgow coma score verbal (Details: LOINC code 9270-0 = 'Glasgow coma score verbal', stated as 'null')
+                     </p>
+                     <p>
+                        <b>type</b>: choice
+                     </p>
+                     <p>
+                        <b>options</b>: id: verbal; http://loinc.org/ValueSet/LL356-7; name: GCS Verbal Value Set; status: active; description: LOINC ANSWER LIST    (LL356-7)
+                     </p>
+                  </blockquote>
+                  <blockquote>
+                     <p>
+                        <b>item</b>
+                     </p>
+                     <p>
+                        <b>linkId</b>: 1.2
+                     </p>
+                     <p>
+                        <b>concept</b>: Glasgow coma score motor (Details: LOINC code 9268-4 = 'Glasgow coma score motor', stated as 'null')
+                     </p>
+                     <p>
+                        <b>type</b>: choice
+                     </p>
+                     <p>
+                        <b>options</b>: id: motor; http://loinc.org/ValueSet/LL357-5; name: GCS Motor Value Set; status: active; description: LOINC ANSWER LIST    (LL357-5)
+                     </p>
+                  </blockquote>
+                  <blockquote>
+                     <p>
+                        <b>item</b>
+                     </p>
+                     <p>
+                        <b>linkId</b>: 1.3
+                     </p>
+                     <p>
+                        <b>concept</b>: Glasgow coma score eye opening (Details: LOINC code 9267-6 = 'Glasgow coma score eye opening', stated as 'null')
+                     </p>
+                     <p>
+                        <b>type</b>: choice
+                     </p>
+                     <p>
+                        <b>options</b>: id: eye; http://loinc.org/ValueSet/LL355-9; name: GCS Eye Value Set; status: active; description: LOINC ANSWER LIST    (LL355-9)
+                     </p>
+                  </blockquote>
+               </div>
+            </text>
+            <contained>
+               <ValueSet xmlns="http://hl7.org/fhir">
+                  <id value="verbal"/>
+                  <identifier>
+                     <system value="http://loinc.org"/>
+                     <value value="http://loinc.org/ValueSet/LL356-7"/>
+                  </identifier>
+                  <name value="GCS Verbal Value Set"/>
+                  <status value="active"/>
+                  <description value="LOINC ANSWER LIST    (LL356-7)"/>
+                  <compose>
+                     <include>
+                        <system value="http://loinc.org"/>
+                        <concept>
+                           <code value="LA6557-8"/>
+                           <display value="No verbal response (>2yrs); no vocal response (&lt;=2yrs)"/>
+                        </concept>
+                        <concept>
+                           <code value="LA6558-6"/>
+                           <display value="Incomprehensible sounds"/>
+                        </concept>
+                        <concept>
+                           <code value="LA6559-4"/>
+                           <display value="Inappropriate words"/>
+                        </concept>
+                        <concept>
+                           <code value="LA6560-2"/>
+                           <display value="Confused"/>
+                        </concept>
+                        <concept>
+                           <code value="LA6561-0"/>
+                           <display value="Oriented"/>
+                        </concept>
+                     </include>
+                  </compose>
+               </ValueSet>
+            </contained>
+            <contained>
+               <ValueSet xmlns="http://hl7.org/fhir">
+                  <id value="motor"/>
+                  <identifier>
+                     <system value="http://loinc.org"/>
+                     <value value="http://loinc.org/ValueSet/LL357-5"/>
+                  </identifier>
+                  <name value="GCS Motor Value Set"/>
+                  <status value="active"/>
+                  <description value="LOINC ANSWER LIST    (LL357-5)"/>
+                  <compose>
+                     <include>
+                        <system value="http://loinc.org"/>
+                        <concept>
+                           <code value="LA6562-8"/>
+                           <display value="No motor response"/>
+                        </concept>
+                        <concept>
+                           <code value="LA6563-6"/>
+                           <display value="Extension to pain"/>
+                        </concept>
+                        <concept>
+                           <code value="LA6564-4"/>
+                           <display value="Flexion to pain"/>
+                        </concept>
+                        <concept>
+                           <code value="LA6565-1"/>
+                           <display value="Withdrawl from pain"/>
+                        </concept>
+                        <concept>
+                           <code value="LA6566-9"/>
+                           <display value="Localizing pain"/>
+                        </concept>
+                        <concept>
+                           <code value="LA6567-7"/>
+                           <display value="Obeys commands"/>
+                        </concept>
+                     </include>
+                  </compose>
+               </ValueSet>
+            </contained>
+            <contained>
+               <ValueSet xmlns="http://hl7.org/fhir">
+                  <id value="eye"/>
+                  <identifier>
+                     <system value="http://loinc.org"/>
+                     <value value="http://loinc.org/ValueSet/LL355-9"/>
+                  </identifier>
+                  <name value="GCS Eye Value Set"/>
+                  <status value="active"/>
+                  <description value="LOINC ANSWER LIST    (LL355-9)"/>
+                  <compose>
+                     <include>
+                        <system value="http://loinc.org"/>
+                        <concept>
+                           <code value="LA6553-7"/>
+                           <display value="No eye opening"/>
+                        </concept>
+                        <concept>
+                           <code value="LA6554-5"/>
+                           <display value="Eye opening to pain"/>
+                        </concept>
+                        <concept>
+                           <code value="LA6555-2"/>
+                           <display value="Eye opening to verbal command"/>
+                        </concept>
+                        <concept>
+                           <code value="LA6556-0"/>
+                           <display value="Eyes open spontaneously"/>
+                        </concept>
+                     </include>
+                  </compose>
+               </ValueSet>
+            </contained>
+            <status value="draft"/>
+            <date value="2015-08-03"/>
+            <publisher value="FHIR Project team"/>
+            <title value="Glasgow Coma Score"/>
+            <concept>
+               <system value="http://loinc.org"/>
+               <code value="9269-2"/>
+            </concept>
+            <subjectType value="Patient"/>
+            <item>
+               <linkId value="1.1"/>
+               <concept>
+                  <system value="http://loinc.org"/>
+                  <code value="9270-0"/>
+               </concept>
+               <type value="choice"/>
+               <options>
+                  <reference value="#verbal"/>
+               </options>
+            </item>
+            <item>
+               <linkId value="1.2"/>
+               <concept>
+                  <system value="http://loinc.org"/>
+                  <code value="9268-4"/>
+               </concept>
+               <type value="choice"/>
+               <options>
+                  <reference value="#motor"/>
+               </options>
+            </item>
+            <item>
+               <linkId value="1.3"/>
+               <concept>
+                  <system value="http://loinc.org"/>
+                  <code value="9267-6"/>
+               </concept>
+               <type value="choice"/>
+               <options>
+                  <reference value="#eye"/>
+               </options>
+            </item>
+         </Questionnaire>
+      </resource>
+      <request>
+         <method value="PUT"/>
+         <url value="Questionnaire/Questionnairegcs"/>
+      </request>
+   </entry>
+</Bundle>

src/changes/changes.xml

@@ -33,6 +33,13 @@
 				disabled using a RestfulServer configuration setting). A new client interceptor has been added
 				which compresses outgoing content from the client.
 			</action>
+			<action type="fix">
+				JPA server transaction attempted to validate resources twice each,
+				with one of these times being before anything had been committed to the
+				database. This meant that if a transaction contained both a Questionnaire
+				and a QuestionnaireResponse, it would fail because the QuestionnaireResponse
+				validator wouldn't be able to find the questionnaire. This is now corrected.
+			</action>
 		</release>
 		<release version="1.3" date="2015-11-14">
 			<action type="add">