honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Fix offset error when returning multiple pages in JPA search

This commit is contained in:
James Agnew 2016-10-07 17:42:02 -04:00
parent 0093403860
commit b37a1edaae
7 changed files with 122 additions and 38 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java
View File

@ -669,7 +669,9 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
next.processingCompletedNormally(requestDetails);
}
outputStreamOrWriter.close();
if (outputStreamOrWriter != null) {
outputStreamOrWriter.close();
}
} catch (NotModifiedException e) {

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java
View File

@ -256,7 +256,7 @@ public final class PersistedJpaBundleProvider implements IBundleProvider {
return mySearchEntity.getTotalCount();
}
private Pageable toPage(int theFromIndex, int theToIndex) {
public static Pageable toPage(final int theFromIndex, int theToIndex) {
int pageSize = theToIndex - theFromIndex;
if (pageSize < 1) {
return null;
@ -264,7 +264,14 @@ public final class PersistedJpaBundleProvider implements IBundleProvider {
int pageIndex = theFromIndex / pageSize;
Pageable page = new PageRequest(pageIndex, pageSize);
Pageable page = new PageRequest(pageIndex, pageSize) {
private static final long serialVersionUID = 1L;
@Override
public int getOffset() {
return theFromIndex;
}};
return page;
}
}

115
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java
View File

@ -42,10 +42,7 @@ import org.apache.http.entity.ContentType;
import org.apache.http.entity.StringEntity;
import org.apache.http.message.BasicNameValuePair;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.Bundle.BundleType;
import org.hl7.fhir.dstu3.model.Bundle.HTTPVerb;
import org.hl7.fhir.dstu3.model.Bundle.SearchEntryMode;
import org.hl7.fhir.dstu3.model.Bundle.*;
import org.hl7.fhir.dstu3.model.Encounter.EncounterLocationComponent;
import org.hl7.fhir.dstu3.model.Encounter.EncounterStatus;
import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
@ -74,6 +71,7 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.SummaryEnum;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.gclient.StringClientParam;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.IBundleProvider;
@ -101,13 +99,13 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
obs1.setValue(new Quantity(123));
obs1.setComment("obs1");
IIdType id1 = myObservationDao.create(obs1, mySrd).getId().toUnqualifiedVersionless();
Observation obs2 = new Observation();
obs2.getCode().setText("Diastolic Blood Pressure");
obs2.setStatus(ObservationStatus.FINAL);
obs2.setValue(new Quantity(81));
IIdType id2 = myObservationDao.create(obs2, mySrd).getId().toUnqualifiedVersionless();
HttpGet get = new HttpGet(ourServerBase + "/Observation?_content=systolic&_pretty=true");
CloseableHttpResponse response = ourHttpClient.execute(get);
try {
@ -119,7 +117,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
response.close();
}
}
/**
* See #441
*/
@ -128,7 +126,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
Medication medication = new Medication();
medication.getCode().addCoding().setSystem("SYSTEM").setCode("04823543");
IIdType medId = myMedicationDao.create(medication).getId().toUnqualifiedVersionless();
MedicationAdministration ma = new MedicationAdministration();
ma.setMedication(new Reference(medId));
IIdType moId = myMedicationAdministrationDao.create(ma).getId().toUnqualifiedVersionless();
@ -146,8 +144,6 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
}
/**
* Per message from David Hay on Skype
*/
@ -156,32 +152,26 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
String inputString = IOUtils.toString(getClass().getResourceAsStream("/david_big_bundle.json"), StandardCharsets.UTF_8);
Bundle inputBundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, inputString);
inputBundle.setType(BundleType.TRANSACTION);
Set<String> allIds = new TreeSet<String>();
for (BundleEntryComponent nextEntry : inputBundle.getEntry()) {
nextEntry.getRequest().setMethod(HTTPVerb.PUT);
nextEntry.getRequest().setUrl(nextEntry.getResource().getId());
allIds.add(nextEntry.getResource().getIdElement().toUnqualifiedVersionless().getValue());
}
mySystemDao.transaction(mySrd, inputBundle);
Bundle responseBundle = ourClient
.operation()
.onInstance(new IdType("Patient/A161443"))
.named("everything")
.withParameter(Parameters.class, "_count", new IntegerType(50))
.useHttpGet()
.returnResourceType(Bundle.class)
.execute();
Bundle responseBundle = ourClient.operation().onInstance(new IdType("Patient/A161443")).named("everything").withParameter(Parameters.class, "_count", new IntegerType(50)).useHttpGet()
.returnResourceType(Bundle.class).execute();
TreeSet<String> ids = new TreeSet<String>();
for (int i = 0; i < responseBundle.getEntry().size(); i++) {
for (BundleEntryComponent nextEntry : responseBundle.getEntry()) {
ids.add(nextEntry.getResource().getIdElement().toUnqualifiedVersionless().getValue());
}
}
String nextUrl = responseBundle.getLink("next").getUrl();
responseBundle = ourClient.fetchResourceFromUrl(Bundle.class, nextUrl);
for (int i = 0; i < responseBundle.getEntry().size(); i++) {
@ -189,20 +179,84 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
ids.add(nextEntry.getResource().getIdElement().toUnqualifiedVersionless().getValue());
}
}
assertThat(ids, hasItem("List/A161444"));
assertThat(ids, hasItem("List/A161468"));
assertThat(ids, hasItem("List/A161500"));
assertEquals(null, responseBundle.getLink("next"));
ourLog.info("Expected {} - {}", allIds.size(), allIds);
ourLog.info("Actual {} - {}", ids.size(), ids);
assertEquals(allIds, ids);
}
/**
* Per message from David Hay on Skype
*/
@Test
public void testEverythingWithLargeSet2() throws Exception {
Patient p = new Patient();
p.setActive(true);
IIdType id = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
for (int i = 1; i < 77; i++) {
Observation obs = new Observation();
obs.setId("A" + StringUtils.leftPad(Integer.toString(i), 2, '0'));
obs.setSubject(new Reference(id));
ourClient.update().resource(obs).execute();
}
Bundle responseBundle = ourClient.operation().onInstance(id).named("everything").withParameter(Parameters.class, "_count", new IntegerType(50)).useHttpGet().returnResourceType(Bundle.class)
.execute();
TreeSet<String> ids = new TreeSet<String>();
for (int i = 0; i < responseBundle.getEntry().size(); i++) {
for (BundleEntryComponent nextEntry : responseBundle.getEntry()) {
ids.add(nextEntry.getResource().getIdElement().getIdPart());
}
}
ourLog.info("Have {} IDs: {}", ids.size(), ids);
BundleLinkComponent nextLink = responseBundle.getLink("next");
while (nextLink != null) {
String nextUrl = nextLink.getUrl();
responseBundle = ourClient.fetchResourceFromUrl(Bundle.class, nextUrl);
for (int i = 0; i < responseBundle.getEntry().size(); i++) {
for (BundleEntryComponent nextEntry : responseBundle.getEntry()) {
ids.add(nextEntry.getResource().getIdElement().getIdPart());
}
}
ourLog.info("Have {} IDs: {}", ids.size(), ids);
nextLink = responseBundle.getLink("next");
}
assertThat(ids, hasItem(id.getIdPart()));
for (int i = 1; i < 77; i++) {
assertThat(ids, hasItem("A" + StringUtils.leftPad(Integer.toString(i), 2, '0')));
}
assertEquals(77, ids.size());
}
@Test
public void testEmptySearch() throws Exception {
Bundle responseBundle;
responseBundle = ourClient.search().forResource(Patient.class).returnBundle(Bundle.class).execute();
assertEquals(0, responseBundle.getTotal());
responseBundle = ourClient.search().forResource(Patient.class).where(Patient.NAME.matches().value("AAA")).returnBundle(Bundle.class).execute();
assertEquals(0, responseBundle.getTotal());
responseBundle = ourClient.search().forResource(Patient.class).where(new StringClientParam("_content").matches().value("AAA")).returnBundle(Bundle.class).execute();
assertEquals(0, responseBundle.getTotal());
}
/**
* See #411
*
@ -214,15 +268,15 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
patient.addIdentifier().setSystem("urn:system").setValue("0");
patient.addName().addFamily("testSearchWithMixedParams").addGiven("Joe");
myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
HttpPost httpPost = new HttpPost(ourServerBase + "/Patient/_search?_format=application/xml");
httpPost.addHeader("Cache-Control","no-cache");
HttpPost httpPost = new HttpPost(ourServerBase + "/Patient/_search?_format=application/xml");
httpPost.addHeader("Cache-Control", "no-cache");
List<NameValuePair> parameters = Lists.newArrayList();
parameters.add(new BasicNameValuePair("name", "Smith"));
httpPost.setEntity(new UrlEncodedFormEntity(parameters));
ourLog.info("Outgoing post: {}", httpPost);
CloseableHttpResponse status = ourHttpClient.execute(httpPost);
try {
String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
@ -234,7 +288,6 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
}
@Test
public void testSearchPagingKeepsOldSearches() throws Exception {
String methodName = "testSearchPagingKeepsOldSearches";
@ -1875,7 +1928,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
assertEquals(id.withVersion("1").getValue(), history.getEntry().get(2).getResource().getId());
assertEquals(1, ((Patient) history.getEntry().get(2).getResource()).getName().size());
try {
myBundleDao.validate(history, null, null, null, null, null, mySrd);
} catch (PreconditionFailedException e) {

17
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProviderTest.java Normal file
View File

@ -0,0 +1,17 @@
package ca.uhn.fhir.jpa.search;
import static org.junit.Assert.*;
import org.junit.Test;
import org.springframework.data.domain.Pageable;
public class PersistedJpaBundleProviderTest {
@Test
public void testGetPage() {
Pageable page = PersistedJpaBundleProvider.toPage(50, 73);
assertEquals(50, page.getOffset());
// assertEquals(50, page.get);
}
}

6
hapi-fhir-jpaserver-base/src/test/resources/logback-test.xml
View File

@ -10,11 +10,11 @@
</encoder>
</appender>
<logger name="org.springframework.web.socket.handler.ExceptionWebSocketHandlerDecorator" additivity="false" level="debug">
<logger name="org.springframework.web.socket.handler.ExceptionWebSocketHandlerDecorator" additivity="false" level="info">
<appender-ref ref="STDOUT" />
</logger>
<logger name="ca.uhn.fhir.jpa.dao.FhirResourceDaoSubscriptionDstu2" additivity="false" level="debug">
<logger name="ca.uhn.fhir.jpa.dao.FhirResourceDaoSubscriptionDstu2" additivity="false" level="info">
<appender-ref ref="STDOUT" />
</logger>
@ -34,7 +34,7 @@
</logger>
<!-- Set to 'trace' to enable SQL logging -->
<logger name="org.hibernate.SQL" additivity="false" level="trace">
<logger name="org.hibernate.SQL" additivity="false" level="info">
<appender-ref ref="STDOUT" />
</logger>
<!-- Set to 'trace' to enable SQL Value logging -->

2
hapi-fhir-jpaserver-uhnfhirtest/src/test/java/ca/uhn/fhirtest/UhnFhirTestApp.java
View File

@ -28,7 +28,7 @@ public class UhnFhirTestApp {
System.setProperty("fhir.db.location", "./target/testdb");
System.setProperty("fhir.db.location.dstu2", "./target/testdb_dstu2");
System.setProperty("fhir.lucene.location.dstu2", "./target/testlucene_dstu2");
System.setProperty("fhir.db.location.dstu3", "./target/testdb_dstu3");
System.setProperty("fhir.db.location.dstu3", "./target/fhirtest_dstu3");
System.setProperty("fhir.lucene.location.dstu3", "./target/testlucene_dstu3");
System.setProperty("fhir.db.location.tdl2", "./target/testdb_tdl2");
System.setProperty("fhir.lucene.location.tdl2", "./target/testlucene_tdl2");

5
src/changes/changes.xml
View File

@ -16,6 +16,11 @@
</ul>
]]>
</action>
<action type="fix">
Fix a fairly significant issue in JPA Server when using the <![CDATA[<code>DatabaseBackedPagingProvider</code>]]>: When paging over the results
of a search / $everything operation, under certain circumstances resources may be missing from the last page of results
that is returned. Thanks to David Hay for reporting!
</action>
<action type="add">
Client, Server, and JPA server now support experimental support
for