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Remove duplicate field in JPA bundle provider (#4435) 

* Remove duplicate field in JPA bundle provider

* Add changelog

* Work on tests

* Test fixes

* Test fix

* Add logging to detect an intermittent

* Test fix

* Address review comment
This commit is contained in:
James Agnew 2023-01-18 13:42:04 -05:00 committed by GitHub
parent 2f5ffe7554
commit 6eeeb7068b
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GPG Key ID: 4AEE18F83AFDEB23
7 changed files with 124 additions and 21 deletions
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6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4435-jpa-bundle-provider-api-cleanup.yaml Normal file
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@ -0,0 +1,6 @@
---
type: fix
issue: 4435
title: "Java API callers of the JPA IFhirResourceDao#search() method could experience a NPE
if they invoked getResources() multiple times on the same response object. This is an edge case
that is very unlikely to occur, but is now corrected."

24
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java
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@ -129,6 +129,17 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
public PersistedJpaBundleProvider(RequestDetails theRequest, Search theSearch) {
myRequest = theRequest;
mySearchEntity = theSearch;
myUuid = theSearch.getUuid();
}
protected Search getSearchEntity() {
return mySearchEntity;
}
// Note: Leave as protected, HSPC depends on this
@SuppressWarnings("WeakerAccess")
protected void setSearchEntity(Search theSearchEntity) {
mySearchEntity = theSearchEntity;
}
/**
@ -292,11 +303,8 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
@Nonnull
@Override
public List<IBaseResource> getResources(final int theFromIndex, final int theToIndex) {
myTxService.withRequest(myRequest).execute(() -> {
boolean entityLoaded = ensureSearchEntityLoaded();
assert entityLoaded;
});
boolean entityLoaded = ensureSearchEntityLoaded();
assert entityLoaded;
assert mySearchEntity != null;
assert mySearchEntity.getSearchType() != null;
@ -357,12 +365,6 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
myTxService = theTxManager;
}
// Note: Leave as protected, HSPC depends on this
@SuppressWarnings("WeakerAccess")
protected void setSearchEntity(Search theSearchEntity) {
mySearchEntity = theSearchEntity;
}
@Override
public Integer size() {
ensureSearchEntityLoaded();

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaSearchFirstPageBundleProvider.java
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@ -44,7 +44,6 @@ public class PersistedJpaSearchFirstPageBundleProvider extends PersistedJpaBundl
private static final Logger ourLog = LoggerFactory.getLogger(PersistedJpaSearchFirstPageBundleProvider.class);
private final SearchTask mySearchTask;
private final ISearchBuilder mySearchBuilder;
private final Search mySearch;
/**
* Constructor
@ -54,13 +53,13 @@ public class PersistedJpaSearchFirstPageBundleProvider extends PersistedJpaBundl
setSearchEntity(theSearch);
mySearchTask = theSearchTask;
mySearchBuilder = theSearchBuilder;
mySearch = theSearch;
}
@Nonnull
@Override
public List<IBaseResource> getResources(int theFromIndex, int theToIndex) {
QueryParameterUtils.verifySearchHasntFailedOrThrowInternalErrorException(mySearch);
ensureSearchEntityLoaded();
QueryParameterUtils.verifySearchHasntFailedOrThrowInternalErrorException(getSearchEntity());
mySearchTask.awaitInitialSync();
@ -68,7 +67,9 @@ public class PersistedJpaSearchFirstPageBundleProvider extends PersistedJpaBundl
final List<JpaPid> pids = mySearchTask.getResourcePids(theFromIndex, theToIndex);
ourLog.trace("Done fetching search resource PIDs");
List<IBaseResource> retVal = myTxService.withRequest(myRequest).execute(() -> toResourceList(mySearchBuilder, pids));
List<IBaseResource> retVal = myTxService.withRequest(myRequest).execute(() -> {
return toResourceList(mySearchBuilder, pids);
});
long totalCountWanted = theToIndex - theFromIndex;
long totalCountMatch = (int) retVal
@ -77,7 +78,8 @@ public class PersistedJpaSearchFirstPageBundleProvider extends PersistedJpaBundl
.count();
if (totalCountMatch < totalCountWanted) {
if (mySearch.getStatus() == SearchStatusEnum.PASSCMPLET) {
if (getSearchEntity().getStatus() == SearchStatusEnum.PASSCMPLET
|| ((getSearchEntity().getStatus() == SearchStatusEnum.FINISHED && getSearchEntity().getNumFound() >= theToIndex))) {
/*
* This is a bit of complexity to account for the possibility that
@ -115,7 +117,8 @@ public class PersistedJpaSearchFirstPageBundleProvider extends PersistedJpaBundl
Integer size = mySearchTask.awaitInitialSync();
ourLog.trace("size() - Finished waiting for local sync");
QueryParameterUtils.verifySearchHasntFailedOrThrowInternalErrorException(mySearch);
ensureSearchEntityLoaded();
QueryParameterUtils.verifySearchHasntFailedOrThrowInternalErrorException(getSearchEntity());
if (size != null) {
return size;
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/cache/DatabaseSearchCacheSvcImpl.java vendored
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@ -122,7 +122,7 @@ public class DatabaseSearchCacheSvcImpl implements ISearchCacheSvc {
Search search = mySearchDao.findById(theSearch.getId()).orElse(theSearch);
if (search.getStatus() != SearchStatusEnum.PASSCMPLET) {
throw new IllegalStateException(Msg.code(1167) + "Can't change to LOADING because state is " + theSearch.getStatus());
throw new IllegalStateException(Msg.code(1167) + "Can't change to LOADING because state is " + search.getStatus());
}
search.setStatus(SearchStatusEnum.LOADING);
Search newSearch = mySearchDao.save(search);

3
hapi-fhir-jpaserver-test-dstu2/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java
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@ -104,7 +104,7 @@ public class SearchCoordinatorSvcImplTest extends BaseSearchSvc{
@Mock
private ISynchronousSearchSvc mySynchronousSearchSvc;
@Spy
protected FhirContext myContext = FhirContext.forR4();
protected FhirContext myContext = FhirContext.forDstu2Cached();
@Spy
private ExceptionService myExceptionSvc = new ExceptionService(myContext);
@ -307,6 +307,7 @@ public class SearchCoordinatorSvcImplTest extends BaseSearchSvc{
retVal.setDaoConfigForUnitTest(new DaoConfig());
retVal.setTxServiceForUnitTest(myTransactionService);
retVal.setSearchCoordinatorSvcForUnitTest(mySvc);
retVal.setContext(myContext);
return retVal;
});
}

87
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java
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@ -19,6 +19,7 @@ import ca.uhn.fhir.jpa.util.SqlQuery;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.HasParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.SimpleBundleProvider;
@ -57,13 +58,16 @@ import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.TestMethodOrder;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Slice;
import org.springframework.util.comparator.ComparableComparator;
import javax.annotation.Nonnull;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.function.Supplier;
import java.util.stream.Collectors;
@ -784,6 +788,89 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
}
@Test
public void testSearchAndPageThroughResults_SmallChunksOnSameBundleProvider() {
List<String> ids = create150Patients();
myCaptureQueriesListener.clear();
IBundleProvider search = myPatientDao.search(new SearchParameterMap(), mySrd);
List<String> foundIds = new ArrayList<>();
for (int i = 0; i < 170; i += 10) {
List<IBaseResource> nextChunk = search.getResources(i, i + 10);
nextChunk.forEach(t->foundIds.add(t.getIdElement().toUnqualifiedVersionless().getValue()));
}
ids.sort(new ComparableComparator<>());
foundIds.sort(new ComparableComparator<>());
assertEquals(ids, foundIds);
// This really generates a surprising number of selects and commits. We
// could stand to reduce this!
myCaptureQueriesListener.logSelectQueries();
assertEquals(56, myCaptureQueriesListener.countSelectQueries());
assertEquals(71, myCaptureQueriesListener.getCommitCount());
assertEquals(0, myCaptureQueriesListener.getRollbackCount());
}
@Test
public void testSearchAndPageThroughResults_LargeChunksOnIndependentBundleProvider() {
List<String> ids = create150Patients();
myCaptureQueriesListener.clear();
IBundleProvider search = myPatientDao.search(new SearchParameterMap(), mySrd);
List<String> foundIds = new ArrayList<>();
for (int i = 0; i < 170; i += 60) {
List<IBaseResource> nextChunk = search.getResources(i, i + 60);
nextChunk.forEach(t->foundIds.add(t.getIdElement().toUnqualifiedVersionless().getValue()));
search = myPagingProvider.retrieveResultList(mySrd, search.getUuid());
}
ids.sort(new ComparableComparator<>());
foundIds.sort(new ComparableComparator<>());
assertEquals(ids, foundIds);
assertEquals(22, myCaptureQueriesListener.countSelectQueries());
assertEquals(21, myCaptureQueriesListener.getCommitCount());
assertEquals(0, myCaptureQueriesListener.getRollbackCount());
}
@Test
public void testSearchAndPageThroughResults_LargeChunksOnSameBundleProvider_Synchronous() {
List<String> ids = create150Patients();
myCaptureQueriesListener.clear();
IBundleProvider search = myPatientDao.search(SearchParameterMap.newSynchronous(), mySrd);
List<String> foundIds = new ArrayList<>();
for (int i = 0; i < 170; i += 60) {
List<IBaseResource> nextChunk = search.getResources(i, i + 60);
nextChunk.forEach(t->foundIds.add(t.getIdElement().toUnqualifiedVersionless().getValue()));
}
ids.sort(new ComparableComparator<>());
foundIds.sort(new ComparableComparator<>());
assertEquals(ids, foundIds);
assertEquals(2, myCaptureQueriesListener.countSelectQueries());
assertEquals(1, myCaptureQueriesListener.getCommitCount());
assertEquals(0, myCaptureQueriesListener.getRollbackCount());
}
@Nonnull
private List<String> create150Patients() {
BundleBuilder b = new BundleBuilder(myFhirContext);
List<String> ids = new ArrayList<>();
for (int i = 0; i < 150; i++) {
Patient p = new Patient();
String nextId = "Patient/A" + i;
ids.add(nextId);
p.setId(nextId);
b.addTransactionUpdateEntry(p);
}
mySystemDao.transaction(mySrd, b.getBundleTyped());
return ids;
}
@Test
public void testSearchUsingOffsetMode_Explicit() {
for (int i = 0; i < 10; i++) {

8
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/interceptor/ConsentInterceptorTest.java
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@ -507,8 +507,12 @@ public class ConsentInterceptorTest {
@Test
public void testPage_SeeResourceReplacesInnerResource() throws IOException {
ourPatientProvider.store((Patient) new Patient().setActive(true).setId("PTA"));
ourPatientProvider.store((Patient) new Patient().setActive(false).setId("PTB"));
Patient pta = (Patient) new Patient().setActive(true).setId("PTA");
pta.addIdentifier().setSystem("OldSystemA");
ourPatientProvider.store(pta);
Patient ptb = (Patient) new Patient().setActive(false).setId("PTB");
ptb.addIdentifier().setSystem("OldSystemB");
ourPatientProvider.store(ptb);
when(myConsentSvc.startOperation(any(), any())).thenReturn(ConsentOutcome.PROCEED);
when(myConsentSvc.canSeeResource(any(), any(), any())).thenReturn(ConsentOutcome.PROCEED);