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Merge branch 'master' of github.com:jamesagnew/hapi-fhir

This commit is contained in:
James Agnew 2018-03-22 07:16:36 -04:00
parent 9c5e32d7eb 1ba00f6b11
commit c6e1aac98d
8 changed files with 273 additions and 55 deletions
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22
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/impl/GenericClient.java
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@ -130,19 +130,6 @@ public class GenericClient extends BaseClient implements IGenericClient {
}
// public IResource read(UriDt url) {
// return read(inferResourceClass(url), url);
// }
//
// @SuppressWarnings("unchecked")
// public <T extends IResource> T read(final Class<T> theType, UriDt url) {
// return (T) invoke(theType, url, new ResourceResponseHandler<T>(theType));
// }
//
// public Bundle search(UriDt url) {
// return search(inferResourceClass(url), url);
// }
@Override
public IFetchConformanceUntyped fetchConformance() {
return new FetchConformanceInternal();
@ -169,11 +156,6 @@ public class GenericClient extends BaseClient implements IGenericClient {
return theResource.getIdElement().getIdPart();
}
// @Override
// public <T extends IBaseResource> T read(final Class<T> theType, IdDt theId) {
// return doReadOrVRead(theType, theId, false, null, null);
// }
@Override
public IHistory history() {
return new HistoryInternal();
@ -2105,14 +2087,14 @@ public class GenericClient extends BaseClient implements IGenericClient {
@Override
public IUpdateTyped resource(IBaseResource theResource) {
//Validate.notNull(theResource, "Resource can not be null");
Validate.notNull(theResource, "Resource can not be null");
myResource = theResource;
return this;
}
@Override
public IUpdateTyped resource(String theResourceBody) {
//Validate.notBlank(theResourceBody, "Body can not be null or blank");
Validate.notBlank(theResourceBody, "Body can not be null or blank");
myResourceBody = theResourceBody;
return this;
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -129,7 +129,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
HashSet<String> excludeElementsInEncoded = new HashSet<String>();
excludeElementsInEncoded.add("id");
excludeElementsInEncoded.add("meta");
excludeElementsInEncoded.add("*.meta");
EXCLUDE_ELEMENTS_IN_ENCODED = Collections.unmodifiableSet(excludeElementsInEncoded);
}

34
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
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@ -431,7 +431,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
// Perform actual DB update
updateEntity(theResource, entity, null, thePerformIndexing, thePerformIndexing, theUpdateTime, false, thePerformIndexing);
ResourceTable updatedEntity = updateEntity(theResource, entity, null, thePerformIndexing, thePerformIndexing, theUpdateTime, false, thePerformIndexing);
theResource.setId(entity.getIdDt());
@ -445,12 +445,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
// Notify JPA interceptors
if (theRequestDetails != null) {
theRequestDetails.getRequestOperationCallback().resourceCreated(theResource);
}
for (IServerInterceptor next : getConfig().getInterceptors()) {
if (next instanceof IServerOperationInterceptor) {
((IServerOperationInterceptor) next).resourceCreated(theRequestDetails, theResource);
if (!updatedEntity.isUnchangedInCurrentOperation()) {
if (theRequestDetails != null) {
theRequestDetails.getRequestOperationCallback().resourceCreated(theResource);
}
for (IServerInterceptor next : getConfig().getInterceptors()) {
if (next instanceof IServerOperationInterceptor) {
((IServerOperationInterceptor) next).resourceCreated(theRequestDetails, theResource);
}
}
}
@ -1262,14 +1264,16 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
// Notify interceptors
if (theRequestDetails != null) {
theRequestDetails.getRequestOperationCallback().resourceUpdated(theResource);
theRequestDetails.getRequestOperationCallback().resourceUpdated(oldResource, theResource);
}
for (IServerInterceptor next : getConfig().getInterceptors()) {
if (next instanceof IServerOperationInterceptor) {
((IServerOperationInterceptor) next).resourceUpdated(theRequestDetails, theResource);
((IServerOperationInterceptor) next).resourceUpdated(theRequestDetails, oldResource, theResource);
if (!savedEntity.isUnchangedInCurrentOperation()) {
if (theRequestDetails != null) {
theRequestDetails.getRequestOperationCallback().resourceUpdated(theResource);
theRequestDetails.getRequestOperationCallback().resourceUpdated(oldResource, theResource);
}
for (IServerInterceptor next : getConfig().getInterceptors()) {
if (next instanceof IServerOperationInterceptor) {
((IServerOperationInterceptor) next).resourceUpdated(theRequestDetails, theResource);
((IServerOperationInterceptor) next).resourceUpdated(theRequestDetails, oldResource, theResource);
}
}
}

56
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirSystemDaoDstu2Test.java
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@ -1193,6 +1193,62 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
}
@Test
public void testTransactionUpdateResourceNewVersionCreatedWhenDataChanges() {
Bundle request = new Bundle();
String patientId = "Patient/IShouldUpdate";
Patient p = new Patient();
p.addName().addFamily("Hello");
p.setId(patientId);
request.addEntry().setResource(p).getRequest().setMethod(HTTPVerbEnum.PUT).setUrl(patientId);
Bundle initialBundleResponse = mySystemDao.transaction(mySrd, request);
assertEquals(1, initialBundleResponse.getEntry().size());
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(initialBundleResponse));
Entry initialBundleResponseEntry = initialBundleResponse.getEntry().get(0);
assertEquals("201 Created", initialBundleResponseEntry.getResponse().getStatus());
assertThat(initialBundleResponseEntry.getResponse().getEtag(), is(equalTo("1")));
p.addName().addFamily("AnotherName");
Bundle secondBundleResponse = mySystemDao.transaction(mySrd, request);
assertEquals(1, secondBundleResponse.getEntry().size());
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(secondBundleResponse));
Entry secondBundleResponseEntry = secondBundleResponse.getEntry().get(0);
assertEquals("200 OK", secondBundleResponseEntry.getResponse().getStatus());
assertThat(secondBundleResponseEntry.getResponse().getEtag(), is(equalTo("2")));
}
@Test
public void testTransactionUpdateResourceNewVersionNotCreatedWhenDataNotChanged() {
Bundle request = new Bundle();
String patientId = "Patient/IShouldNotUpdate";
Patient p = new Patient();
p.addName().addFamily("Hello");
p.setId(patientId);
request.addEntry().setResource(p).getRequest().setMethod(HTTPVerbEnum.PUT).setUrl(patientId);
Bundle initialBundleResponse = mySystemDao.transaction(mySrd, request);
assertEquals(1, initialBundleResponse.getEntry().size());
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(initialBundleResponse));
Entry initialBundleResponseEntry = initialBundleResponse.getEntry().get(0);
assertEquals("201 Created", initialBundleResponseEntry.getResponse().getStatus());
assertThat(initialBundleResponseEntry.getResponse().getEtag(), is(equalTo("1")));
Bundle secondBundleResponse = mySystemDao.transaction(mySrd, request);
assertEquals(1, secondBundleResponse.getEntry().size());
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(secondBundleResponse));
Entry secondBundleResponseEntry = secondBundleResponse.getEntry().get(0);
assertEquals("200 OK", secondBundleResponseEntry.getResponse().getStatus());
assertThat(secondBundleResponseEntry.getResponse().getEtag(), is(equalTo("1")));
}
@Test
public void testTransactionUpdateMatchUrlWithTwoMatch() {
String methodName = "testTransactionUpdateMatchUrlWithTwoMatch";

147
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderInterceptorR4Test.java
View File

@ -8,6 +8,7 @@ import ca.uhn.fhir.rest.api.server.ResponseDetails;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.rest.server.interceptor.IServerOperationInterceptor;
import ca.uhn.fhir.rest.server.interceptor.InterceptorAdapter;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
@ -43,9 +44,9 @@ import static org.mockito.Mockito.*;
public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderInterceptorR4Test.class);
private IServerInterceptor myDaoInterceptor;
private IServerOperationInterceptor myDaoInterceptor;
private IServerInterceptor myServerInterceptor;
private IServerOperationInterceptor myServerInterceptor;
@Override
@After
@ -60,8 +61,8 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
public void before() throws Exception {
super.before();
myServerInterceptor = mock(IServerInterceptor.class);
myDaoInterceptor = mock(IServerInterceptor.class);
myServerInterceptor = mock(IServerOperationInterceptor.class);
myDaoInterceptor = mock(IServerOperationInterceptor.class);
resetServerInterceptor();
@ -88,6 +89,57 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
when(myServerInterceptor.outgoingResponse(any(RequestDetails.class), any(ResponseDetails.class), any(HttpServletRequest.class), any(HttpServletResponse.class))).thenReturn(true);
}
@Test
public void testCreateConditionalNoOpResourceInTransaction() throws Exception {
String methodName = "foo";
Patient pt = new Patient();
pt.addName().setFamily(methodName);
Bundle bundle = new Bundle();
bundle.setType(BundleType.TRANSACTION);
BundleEntryComponent entry = bundle.addEntry();
entry.setFullUrl("Patient");
entry.setResource(pt);
entry.getRequest().setMethod(HTTPVerb.POST);
entry.getRequest().setUrl("Patient");
// Transaction time!
transaction(bundle);
// Do it again but with a conditional create that shouldn't actually create
resetServerInterceptor();
entry.getRequest().setIfNoneExist("Patient?name=" + methodName);
transaction(bundle);
/*
* Server Interceptor
*/
ArgumentCaptor<ActionRequestDetails> ardCaptor = ArgumentCaptor.forClass(ActionRequestDetails.class);
ArgumentCaptor<RestOperationTypeEnum> opTypeCaptor = ArgumentCaptor.forClass(RestOperationTypeEnum.class);
verify(myServerInterceptor, times(1)).incomingRequestPreHandled(opTypeCaptor.capture(), ardCaptor.capture());
assertEquals(RestOperationTypeEnum.TRANSACTION, opTypeCaptor.getAllValues().get(0));
verify(myServerInterceptor, times(1)).incomingRequestPostProcessed(any(RequestDetails.class), any(HttpServletRequest.class), any(HttpServletResponse.class));
verify(myServerInterceptor, times(0)).resourceCreated(any(RequestDetails.class), any(IBaseResource.class));
verify(myServerInterceptor, times(0)).resourceUpdated(any(RequestDetails.class), any(IBaseResource.class), any(IBaseResource.class));
/*
* DAO Interceptor
*/
ardCaptor = ArgumentCaptor.forClass(ActionRequestDetails.class);
opTypeCaptor = ArgumentCaptor.forClass(RestOperationTypeEnum.class);
verify(myDaoInterceptor, times(1)).incomingRequestPreHandled(opTypeCaptor.capture(), ardCaptor.capture());
assertEquals(RestOperationTypeEnum.TRANSACTION, opTypeCaptor.getAllValues().get(0));
verify(myDaoInterceptor, times(0)).incomingRequestPostProcessed(any(RequestDetails.class), any(HttpServletRequest.class), any(HttpServletResponse.class));
verify(myDaoInterceptor, times(0)).resourceCreated(any(RequestDetails.class), any(IBaseResource.class));
verify(myDaoInterceptor, times(0)).resourceUpdated(any(RequestDetails.class), any(IBaseResource.class), any(IBaseResource.class));
}
@Test
public void testCreateResource() throws IOException {
String methodName = "testCreateResource";
@ -123,11 +175,11 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
}
/*
* This is a weird way of verifying, but because this class
* is a child of a superclass that has other test children
* it's possible that other tests are hitting the server
* at the same time
*/
* This is a weird way of verifying, but because this class
* is a child of a superclass that has other test children
* it's possible that other tests are hitting the server
* at the same time
*/
@Test
public void testCreateResourceInTransaction() throws IOException {
String methodName = "testCreateResourceInTransaction";
@ -143,16 +195,7 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
entry.getRequest().setMethod(HTTPVerb.POST);
entry.getRequest().setUrl("Patient");
String resource = myFhirCtx.newXmlParser().encodeResourceToString(bundle);
HttpPost post = new HttpPost(ourServerBase + "/");
post.setEntity(new StringEntity(resource, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
CloseableHttpResponse response = ourHttpClient.execute(post);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
} finally {
response.close();
}
transaction(bundle);
/*
* Server Interceptor
@ -246,6 +289,72 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
}
@Test
public void testUpdateNoOpResourceInTransaction() throws Exception {
String methodName = "foo";
Patient pt = new Patient();
pt.addName().setFamily(methodName);
String ptId = myPatientDao.create(pt).getId().toUnqualifiedVersionless().getValue();
Bundle bundle = new Bundle();
bundle.setType(BundleType.TRANSACTION);
BundleEntryComponent entry = bundle.addEntry();
entry.setFullUrl(ptId);
entry.setResource(pt);
entry.getRequest().setMethod(HTTPVerb.PUT);
entry.getRequest().setUrl(ptId);
// Transaction time!
transaction(bundle);
// Do it again but with an update that shouldn't actually create
resetServerInterceptor();
entry.getRequest().setIfNoneExist("Patient?name=" + methodName);
transaction(bundle);
/*
* Server Interceptor
*/
ArgumentCaptor<ActionRequestDetails> ardCaptor = ArgumentCaptor.forClass(ActionRequestDetails.class);
ArgumentCaptor<RestOperationTypeEnum> opTypeCaptor = ArgumentCaptor.forClass(RestOperationTypeEnum.class);
verify(myServerInterceptor, times(2)).incomingRequestPreHandled(opTypeCaptor.capture(), ardCaptor.capture());
assertEquals(RestOperationTypeEnum.TRANSACTION, opTypeCaptor.getAllValues().get(0));
assertEquals(RestOperationTypeEnum.UPDATE, opTypeCaptor.getAllValues().get(1));
verify(myServerInterceptor, times(1)).incomingRequestPostProcessed(any(RequestDetails.class), any(HttpServletRequest.class), any(HttpServletResponse.class));
verify(myServerInterceptor, times(0)).resourceCreated(any(RequestDetails.class), any(IBaseResource.class));
verify(myServerInterceptor, times(0)).resourceUpdated(any(RequestDetails.class), any(IBaseResource.class), any(IBaseResource.class));
/*
* DAO Interceptor
*/
ardCaptor = ArgumentCaptor.forClass(ActionRequestDetails.class);
opTypeCaptor = ArgumentCaptor.forClass(RestOperationTypeEnum.class);
verify(myDaoInterceptor, times(2)).incomingRequestPreHandled(opTypeCaptor.capture(), ardCaptor.capture());
assertEquals(RestOperationTypeEnum.TRANSACTION, opTypeCaptor.getAllValues().get(0));
assertEquals(RestOperationTypeEnum.UPDATE, opTypeCaptor.getAllValues().get(1));
verify(myDaoInterceptor, times(0)).incomingRequestPostProcessed(any(RequestDetails.class), any(HttpServletRequest.class), any(HttpServletResponse.class));
verify(myDaoInterceptor, times(0)).resourceCreated(any(RequestDetails.class), any(IBaseResource.class));
verify(myDaoInterceptor, times(0)).resourceUpdated(any(RequestDetails.class), any(IBaseResource.class), any(IBaseResource.class));
}
private void transaction(Bundle theBundle) throws IOException {
String resource = myFhirCtx.newXmlParser().encodeResourceToString(theBundle);
HttpPost post = new HttpPost(ourServerBase + "/");
post.setEntity(new StringEntity(resource, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
CloseableHttpResponse response = ourHttpClient.execute(post);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
} finally {
response.close();
}
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

35
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/r4/RestHookTestR4Test.java
View File

@ -135,6 +135,41 @@ public class RestHookTestR4Test extends BaseResourceProviderR4Test {
waitForSize(0, ourCreatedObservations);
waitForSize(1, ourUpdatedObservations);
assertEquals(Constants.CT_FHIR_JSON_NEW, ourContentTypes.get(0));
}
@Test
public void testRestHookSubscriptionNoopUpdateDoesntTriggerNewDelivery() throws Exception {
String payload = "application/fhir+json";
String code = "1000000050";
String criteria1 = "Observation?code=SNOMED-CT|" + code + "&_format=xml";
String criteria2 = "Observation?code=SNOMED-CT|" + code + "111&_format=xml";
createSubscription(criteria1, payload, ourListenerServerBase);
createSubscription(criteria2, payload, ourListenerServerBase);
Observation obs = sendObservation(code, "SNOMED-CT");
// Should see 1 subscription notification
waitForQueueToDrain();
waitForSize(0, ourCreatedObservations);
waitForSize(1, ourUpdatedObservations);
assertEquals(Constants.CT_FHIR_JSON_NEW, ourContentTypes.get(0));
// Send an update with no changes
obs.setId(obs.getIdElement().toUnqualifiedVersionless());
myClient.update().resource(obs).execute();
// Should be no further deliveries
Thread.sleep(1000);
waitForQueueToDrain();
waitForSize(0, ourCreatedObservations);
waitForSize(1, ourUpdatedObservations);
}
@Test

20
hapi-fhir-jpaserver-elasticsearch/src/main/java/ca/uhn/fhir/jpa/search/ElasticsearchMappingProvider.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.search;
/*-
* #%L
* HAPI FHIR JPA Server - ElasticSearch Integration
* %%
* 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 org.hibernate.search.elasticsearch.analyzer.definition.ElasticsearchAnalysisDefinitionRegistryBuilder;
import org.hibernate.search.elasticsearch.analyzer.definition.spi.ElasticsearchAnalysisDefinitionProvider;

12
src/changes/changes.xml
View File

@ -240,6 +240,18 @@
is supported according to the FHIR specification. Thanks
to Jeff Chung for the pull request!
</action>
<action type="fix">
JPA Server Operation Interceptor create/update methods will now no
longer be fired if the create/update operation being performed
is a no-op (e.g. a conditional create that did not need to perform
any action, or an update where the contents didn't actually change)
</action>
<action type="fix" issue="879">
JPA server sometimes updated resources even though the client
supplied an update with no actual changes in it, due to
changes in the metadata section being considered content
changes. Thanks to Kyle Meadows for the pull request!
</action>
</release>
<release version="3.2.0" date="2018-01-13">
<action type="add">