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

This commit is contained in:
jamesagnew 2020-08-16 21:03:13 -04:00
parent cd65c298fe 7dd7f2b923
commit ad12ee4a5c
7 changed files with 195 additions and 28 deletions
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3
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/version.yaml Normal file
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@ -0,0 +1,3 @@
---
release-date: "2020-08-13"
codename: "Manticore"

8
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/changes.yaml Normal file
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@ -0,0 +1,8 @@
---
- item:
type: "add"
title: "The version of a few dependencies have been bumped to the latest versions
(dependent HAPI modules listed in brackets):
<ul>
<li>Flyway (JPA): 6.4.1-&gt; 6.5.4</li>
</ul>"

3
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IDao.java
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@ -34,8 +34,9 @@ import java.util.Collection;
* time to time, even within minor point releases.
*/
public interface IDao {
String RESOURCE_PID_KEY = "RESOURCE_PID";
MetadataKeyResourcePid RESOURCE_PID = new MetadataKeyResourcePid("RESOURCE_PID");
MetadataKeyResourcePid RESOURCE_PID = new MetadataKeyResourcePid(RESOURCE_PID_KEY);
MetadataKeyCurrentlyReindexing CURRENTLY_REINDEXING = new MetadataKeyCurrentlyReindexing("CURRENTLY_REINDEXING");

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
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@ -79,7 +79,6 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@ -114,10 +113,8 @@ import org.springframework.context.ApplicationContext;
import org.springframework.context.ApplicationContextAware;
import org.springframework.stereotype.Repository;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.support.TransactionCallback;
import org.springframework.transaction.support.TransactionSynchronizationAdapter;
import org.springframework.transaction.support.TransactionSynchronizationManager;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.PostConstruct;
import javax.persistence.EntityManager;
@ -636,7 +633,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
ResourceMetadataKeyEnum.VERSION.put(res, Long.toString(theEntity.getVersion()));
ResourceMetadataKeyEnum.PUBLISHED.put(res, theEntity.getPublished());
ResourceMetadataKeyEnum.UPDATED.put(res, theEntity.getUpdated());
IDao.RESOURCE_PID.put(res, theEntity.getId());
IDao.RESOURCE_PID.put(res, theEntity.getResourceId());
Collection<? extends BaseTag> tags = theTagList;
if (theEntity.isHasTags()) {
@ -708,7 +705,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
res.setId(res.getIdElement().withVersion(theVersion.toString()));
res.getMeta().setLastUpdated(theEntity.getUpdatedDate());
IDao.RESOURCE_PID.put(res, theEntity.getId());
IDao.RESOURCE_PID.put(res, theEntity.getResourceId());
Collection<? extends BaseTag> tags = theTagList;

108
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/HookInterceptorR4Test.java
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@ -1,13 +1,25 @@
package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IDao;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.rest.api.MethodOutcome;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.Collections;
import java.util.concurrent.atomic.AtomicLong;
import static org.junit.jupiter.api.Assertions.assertEquals;
@ -15,16 +27,24 @@ import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class HookInterceptorR4Test extends BaseResourceProviderR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(HookInterceptorR4Test.class);
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(HookInterceptorR4Test.class);
@Autowired
IdHelperService myIdHelperService;
// @Override
// @AfterEach
// public void after( ) throws Exception {
// super.after();
//
// myInterceptorRegistry.unregisterAllInterceptors();
// }
@BeforeEach
public void before() throws Exception {
super.before();
myDaoConfig.setExpungeEnabled(true);
}
@AfterEach
public void after() throws Exception {
myDaoConfig.setExpungeEnabled(new DaoConfig().isExpungeEnabled());
super.after();
}
@Test
public void testOP_PRESTORAGE_RESOURCE_CREATED_ModifyResource() {
@ -69,7 +89,7 @@ public class HookInterceptorR4Test extends BaseResourceProviderR4Test {
AtomicLong pid = new AtomicLong();
myInterceptorRegistry.registerAnonymousInterceptor(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED, (thePointcut, t) -> {
IAnyResource resource = (IAnyResource) t.get(IBaseResource.class, 0);
Long resourcePid = (Long) resource.getUserData("RESOURCE_PID");
Long resourcePid = (Long) resource.getUserData(IDao.RESOURCE_PID_KEY);
assertNotNull(resourcePid, "Expecting RESOURCE_PID to be set on resource user data.");
pid.set(resourcePid);
});
@ -77,6 +97,72 @@ public class HookInterceptorR4Test extends BaseResourceProviderR4Test {
assertTrue(pid.get() > 0);
}
@Test
public void testSTORAGE_PRECOMMIT_RESOURCE_CREATED_hasCorrectPid() {
AtomicLong pid = new AtomicLong();
myInterceptorRegistry.registerAnonymousInterceptor(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED, (thePointcut, t) -> {
IAnyResource resource = (IAnyResource) t.get(IBaseResource.class, 0);
Long resourcePid = (Long) resource.getUserData(IDao.RESOURCE_PID_KEY);
assertNotNull(resourcePid, "Expecting RESOURCE_PID to be set on resource user data.");
pid.set(resourcePid);
});
IIdType savedPatientId = myClient.create().resource(new Patient()).execute().getId();
Long savedPatientPid = myIdHelperService.resolveResourcePersistentIdsWithCache(null, Collections.singletonList(savedPatientId)).get(0).getIdAsLong();
assertEquals(savedPatientPid.longValue(), pid.get());
}
@Test
public void testSTORAGE_PRESTORAGE_EXPUNGE_RESOURCE_hasCorrectPid() {
AtomicLong pid = new AtomicLong();
myInterceptorRegistry.registerAnonymousInterceptor(Pointcut.STORAGE_PRESTORAGE_EXPUNGE_RESOURCE, (thePointcut, t) -> {
IAnyResource resource = (IAnyResource) t.get(IBaseResource.class, 0);
Long resourcePid = (Long) resource.getUserData(IDao.RESOURCE_PID_KEY);
assertNotNull(resourcePid, "Expecting RESOURCE_PID to be set on resource user data.");
pid.set(resourcePid);
});
IIdType savedPatientId = myClient.create().resource(new Patient()).execute().getId();
Long savedPatientPid = myIdHelperService.resolveResourcePersistentIdsWithCache(null, Collections.singletonList(savedPatientId)).get(0).getIdAsLong();
myClient.delete().resourceById(savedPatientId).execute();
Parameters parameters = new Parameters();
parameters.addParameter().setName(JpaConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_DELETED_RESOURCES).setValue(new BooleanType(true));
myClient
.operation()
.onInstance(savedPatientId)
.named(JpaConstants.OPERATION_EXPUNGE)
.withParameters(parameters)
.execute();
assertEquals(savedPatientPid.longValue(), pid.get());
}
@Test
public void testSTORAGE_PRECOMMIT_RESOURCE_UPDATED_hasCorrectPid() {
AtomicLong pidOld = new AtomicLong();
AtomicLong pidNew = new AtomicLong();
Patient patient = new Patient();
IIdType savedPatientId = myClient.create().resource(patient).execute().getId();
patient.setId(savedPatientId);
myInterceptorRegistry.registerAnonymousInterceptor(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED, (thePointcut, t) -> {
IAnyResource resourceOld = (IAnyResource) t.get(IBaseResource.class, 0);
IAnyResource resourceNew = (IAnyResource) t.get(IBaseResource.class, 1);
Long resourceOldPid = (Long) resourceOld.getUserData(IDao.RESOURCE_PID_KEY);
Long resourceNewPid = (Long) resourceNew.getUserData(IDao.RESOURCE_PID_KEY);
assertNotNull(resourceOldPid, "Expecting RESOURCE_PID to be set on resource user data.");
assertNotNull(resourceNewPid, "Expecting RESOURCE_PID to be set on resource user data.");
pidOld.set(resourceOldPid);
pidNew.set(resourceNewPid);
});
patient.setActive(true);
myClient.update().resource(patient).execute();
Long savedPatientPid = myIdHelperService.resolveResourcePersistentIdsWithCache(null, Collections.singletonList(savedPatientId)).get(0).getIdAsLong();
assertEquals(savedPatientPid.longValue(), pidOld.get());
assertEquals(savedPatientPid.longValue(), pidNew.get());
}
@Test
public void testSTORAGE_PRECOMMIT_RESOURCE_UPDATED_hasPid() {
AtomicLong oldPid = new AtomicLong();
@ -84,12 +170,12 @@ public class HookInterceptorR4Test extends BaseResourceProviderR4Test {
myInterceptorRegistry.registerAnonymousInterceptor(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED, (thePointcut, t) -> {
IAnyResource oldResource = (IAnyResource) t.get(IBaseResource.class, 0);
Long oldResourcePid = (Long) oldResource.getUserData("RESOURCE_PID");
Long oldResourcePid = (Long) oldResource.getUserData(IDao.RESOURCE_PID_KEY);
assertNotNull(oldResourcePid, "Expecting RESOURCE_PID to be set on resource user data.");
oldPid.set(oldResourcePid);
IAnyResource newResource = (IAnyResource) t.get(IBaseResource.class, 1);
Long newResourcePid = (Long) newResource.getUserData("RESOURCE_PID");
Long newResourcePid = (Long) newResource.getUserData(IDao.RESOURCE_PID_KEY);
assertNotNull(newResourcePid, "Expecting RESOURCE_PID to be set on resource user data.");
newPid.set(newResourcePid);
});

92
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/server/ServerExceptionDstu3Test.java
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@ -1,12 +1,14 @@
package ca.uhn.fhir.rest.server;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.test.utilities.JettyUtil;
@ -29,11 +31,13 @@ import org.hl7.fhir.dstu3.model.OperationOutcome.IssueType;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.Collections;
import java.util.List;
import java.util.concurrent.TimeUnit;
@ -44,11 +48,17 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
public class ServerExceptionDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ServerExceptionDstu3Test.class);
public static BaseServerResponseException ourException;
public static Exception ourException;
private static CloseableHttpClient ourClient;
private static FhirContext ourCtx = FhirContext.forDstu3();
private static int ourPort;
private static Server ourServer;
private static RestfulServer ourServlet;
@AfterEach
public void after() {
ourException = null;
}
@Test
public void testAddHeadersNotFound() throws Exception {
@ -56,8 +66,8 @@ public class ServerExceptionDstu3Test {
OperationOutcome operationOutcome = new OperationOutcome();
operationOutcome.addIssue().setCode(IssueType.BUSINESSRULE);
ourException = new ResourceNotFoundException("SOME MESSAGE");
ourException.addResponseHeader("X-Foo", "BAR BAR");
ourException = new ResourceNotFoundException("SOME MESSAGE")
.addResponseHeader("X-Foo", "BAR BAR");
HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient");
@ -99,6 +109,65 @@ public class ServerExceptionDstu3Test {
}
@Test
public void testMethodThrowsNonHapiUncheckedExceptionHandledCleanly() throws Exception {
ourException = new NullPointerException("Hello");
HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_format=json");
try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
assertEquals(500, status.getStatusLine().getStatusCode());
byte[] responseContentBytes = IOUtils.toByteArray(status.getEntity().getContent());
String responseContent = new String(responseContentBytes, Charsets.UTF_8);
ourLog.info(status.getStatusLine().toString());
ourLog.info(responseContent);
assertThat(responseContent, containsString("\"diagnostics\":\"Failed to call access method: java.lang.NullPointerException: Hello\""));
}
}
@Test
public void testMethodThrowsNonHapiCheckedExceptionHandledCleanly() throws Exception {
ourException = new IOException("Hello");
HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_format=json");
try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
assertEquals(500, status.getStatusLine().getStatusCode());
byte[] responseContentBytes = IOUtils.toByteArray(status.getEntity().getContent());
String responseContent = new String(responseContentBytes, Charsets.UTF_8);
ourLog.info(status.getStatusLine().toString());
ourLog.info(responseContent);
assertThat(responseContent, containsString("\"diagnostics\":\"Failed to call access method: java.io.IOException: Hello\""));
}
}
@Test
public void testInterceptorThrowsNonHapiUncheckedExceptionHandledCleanly() throws Exception {
ourServlet.getInterceptorService().registerAnonymousInterceptor(Pointcut.SERVER_INCOMING_REQUEST_PRE_HANDLED, new IAnonymousInterceptor() {
@Override
public void invoke(Pointcut thePointcut, HookParams theArgs) {
throw new NullPointerException("Hello");
}
});
HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_format=json");
try (CloseableHttpResponse status = ourClient.execute(httpGet)) {
assertEquals(500, status.getStatusLine().getStatusCode());
byte[] responseContentBytes = IOUtils.toByteArray(status.getEntity().getContent());
String responseContent = new String(responseContentBytes, Charsets.UTF_8);
ourLog.info(status.getStatusLine().toString());
ourLog.info(responseContent);
assertThat(responseContent, containsString("\"diagnostics\":\"Hello\""));
}
ourServlet.getInterceptorService().unregisterAllInterceptors();
}
@Test
public void testPostWithNoBody() throws IOException {
@ -143,7 +212,10 @@ public class ServerExceptionDstu3Test {
}
@Search()
public List<Patient> search() {
public List<Patient> search() throws Exception {
if (ourException == null) {
return Collections.emptyList();
}
throw ourException;
}
@ -168,15 +240,15 @@ public class ServerExceptionDstu3Test {
DummyPatientResourceProvider patientProvider = new DummyPatientResourceProvider();
ServletHandler proxyHandler = new ServletHandler();
RestfulServer servlet = new RestfulServer(ourCtx);
servlet.setPagingProvider(new FifoMemoryPagingProvider(10));
ourServlet = new RestfulServer(ourCtx);
ourServlet.setPagingProvider(new FifoMemoryPagingProvider(10));
servlet.setResourceProviders(patientProvider);
ServletHolder servletHolder = new ServletHolder(servlet);
ourServlet.setResourceProviders(patientProvider);
ServletHolder servletHolder = new ServletHolder(ourServlet);
proxyHandler.addServletWithMapping(servletHolder, "/*");
ourServer.setHandler(proxyHandler);
JettyUtil.startServer(ourServer);
ourPort = JettyUtil.getPortForStartedServer(ourServer);
ourPort = JettyUtil.getPortForStartedServer(ourServer);
PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
HttpClientBuilder builder = HttpClientBuilder.create();

2
pom.xml
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@ -717,7 +717,7 @@
<!-- 9.4.17 seems to have issues -->
<jetty_version>9.4.30.v20200611</jetty_version>
<jsr305_version>3.0.2</jsr305_version>
<flyway_version>6.4.1</flyway_version>
<flyway_version>6.5.4</flyway_version>
<!--<hibernate_version>5.2.10.Final</hibernate_version>-->
<hibernate_version>5.4.14.Final</hibernate_version>
<!-- Update lucene version when you update hibernate-search version -->