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

This commit is contained in:
James Agnew 2019-04-04 09:26:15 -04:00
parent 75b6857902 859bc7d71b
commit 6528980662
7 changed files with 101 additions and 16 deletions
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18
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
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@ -224,6 +224,10 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
throw new MethodNotAllowedException("$expunge is not enabled on this server");
}
if (theExpungeOptions.getLimit() < 1) {
throw new InvalidRequestException("Expunge limit may not be less than 1. Received expunge limit "+theExpungeOptions.getLimit() + ".");
}
AtomicInteger remainingCount = new AtomicInteger(theExpungeOptions.getLimit());
if (theResourceName == null && theResourceId == null && theVersion == null) {
@ -275,12 +279,12 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
for (Long next : resourceIds) {
txTemplate.execute(t -> {
expungeHistoricalVersionsOfId(next, remainingCount);
return null;
});
if (remainingCount.get() <= 0) {
ourLog.debug("Expunge limit has been hit - Stopping operation");
return toExpungeOutcome(theExpungeOptions, remainingCount);
}
return null;
});
}
/*
@ -291,6 +295,10 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
expungeCurrentVersionOfResource(next, remainingCount);
return null;
});
if (remainingCount.get() <= 0) {
ourLog.debug("Expunge limit has been hit - Stopping operation");
return toExpungeOutcome(theExpungeOptions, remainingCount);
}
}
}
@ -302,8 +310,12 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
*/
Pageable page = PageRequest.of(0, remainingCount.get());
Slice<Long> historicalIds = txTemplate.execute(t -> {
if (theResourceId != null && theVersion != null) {
if (theResourceId != null) {
if (theVersion != null) {
return toSlice(myResourceHistoryTableDao.findForIdAndVersion(theResourceId, theVersion));
} else {
return myResourceHistoryTableDao.findIdsOfPreviousVersionsOfResourceId(page, theResourceId);
}
} else {
if (theResourceName != null) {
return myResourceHistoryTableDao.findIdsOfPreviousVersionsOfResources(page, theResourceName);

17
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceHistoryTableDao.java
View File

@ -1,10 +1,6 @@
package ca.uhn.fhir.jpa.dao.data;
import java.util.Collection;
import java.util.Date;
import javax.persistence.TemporalType;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.data.jpa.repository.JpaRepository;
@ -13,7 +9,9 @@ import org.springframework.data.jpa.repository.Query;
import org.springframework.data.jpa.repository.Temporal;
import org.springframework.data.repository.query.Param;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import javax.persistence.TemporalType;
import java.util.Collection;
import java.util.Date;
/*
* #%L
@ -74,6 +72,13 @@ public interface IResourceHistoryTableDao extends JpaRepository<ResourceHistoryT
@Query("SELECT t.myId FROM ResourceHistoryTable t WHERE t.myResourceId = :resId AND t.myResourceVersion != :dontWantVersion")
Slice<Long> findForResourceId(Pageable thePage, @Param("resId") Long theId, @Param("dontWantVersion") Long theDontWantVersion);
@Query("" +
"SELECT v.myId FROM ResourceHistoryTable v " +
"LEFT OUTER JOIN ResourceTable t ON (v.myResourceId = t.myId) " +
"WHERE v.myResourceVersion != t.myVersion AND " +
"t.myId = :resId")
Slice<Long> findIdsOfPreviousVersionsOfResourceId(Pageable thePage, @Param("resId") Long theResourceId);
@Query("" +
"SELECT v.myId FROM ResourceHistoryTable v " +
"LEFT OUTER JOIN ResourceTable t ON (v.myResourceId = t.myId) " +

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/ExpungeOptions.java
View File

@ -49,8 +49,9 @@ public class ExpungeOptions {
/**
* The maximum number of resource versions to expunge
*/
public void setLimit(int theLimit) {
public ExpungeOptions setLimit(int theLimit) {
myLimit = theLimit;
return this;
}
public boolean isExpungeEverything() {

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
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@ -299,6 +299,8 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
myDaoConfig.setAllowContainsSearches(new DaoConfig().isAllowContainsSearches());
myInterceptorRegistry.clearAnonymousHookForUnitTest();
myInterceptorRegistry.unregisterInterceptor(myPerformanceTracingLoggingInterceptor);
}
@After
@ -351,8 +353,6 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
myDaoConfig.setHardTagListLimit(1000);
myDaoConfig.setIncludeLimit(2000);
myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
myInterceptorRegistry.unregisterInterceptor(myPerformanceTracingLoggingInterceptor);
}
@Override

59
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderExpungeDstu3Test.java
View File

@ -4,6 +4,7 @@ import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.util.ExpungeOptions;
import ca.uhn.fhir.jpa.util.JpaConstants;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@ -17,7 +18,8 @@ import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static org.junit.Assert.*;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.fail;
public class ResourceProviderExpungeDstu3Test extends BaseResourceProviderDstu3Test {
@ -290,6 +292,61 @@ public class ResourceProviderExpungeDstu3Test extends BaseResourceProviderDstu3T
assertGone(myDeletedObservationId);
}
@Test
public void testExpungeLimitZero() {
try {
myPatientDao.expunge(new ExpungeOptions()
.setExpungeDeletedResources(true)
.setExpungeOldVersions(true)
.setLimit(0));
fail();
} catch (InvalidRequestException e) {
assertEquals("Expunge limit may not be less than 1. Received expunge limit 0.", e.getMessage());
}
}
@Test
public void testExpungeInstanceOldVersionsAndDeletedBoundaryLimit() {
myPatientDao.delete(myTwoVersionPatientId);
myPatientDao.expunge(myTwoVersionPatientId.toUnqualifiedVersionless(), new ExpungeOptions()
.setExpungeDeletedResources(true)
.setExpungeOldVersions(true)
.setLimit(2));
// Patients
assertStillThere(myOneVersionPatientId);
assertExpunged(myTwoVersionPatientId.withVersion("1"));
assertExpunged(myTwoVersionPatientId.withVersion("2"));
assertGone(myDeletedPatientId);
// No observations deleted
assertStillThere(myOneVersionObservationId);
assertStillThere(myTwoVersionObservationId.withVersion("1"));
assertStillThere(myTwoVersionObservationId.withVersion("2"));
assertGone(myDeletedObservationId);
}
@Test
public void testExpungeNothing() {
myPatientDao.expunge(myOneVersionPatientId.toUnqualifiedVersionless(), new ExpungeOptions()
.setExpungeDeletedResources(true)
.setExpungeOldVersions(true));
// Patients
assertStillThere(myOneVersionPatientId);
assertStillThere(myTwoVersionPatientId.withVersion("1"));
assertStillThere(myTwoVersionPatientId.withVersion("2"));
assertGone(myDeletedPatientId);
// No observations deleted
assertStillThere(myOneVersionObservationId);
assertStillThere(myTwoVersionObservationId.withVersion("1"));
assertStillThere(myTwoVersionObservationId.withVersion("2"));
assertGone(myDeletedObservationId);
}
@Test
public void testParameters() {
Parameters p = new Parameters();

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderInterceptorR4Test.java
View File

@ -119,6 +119,7 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
for (int i = 0; i < 30; i++) {
Patient p = new Patient();
p.addName().setFamily("FAM"+i);
ourLog.info("About to create patient");
myPatientDao.create(p);
}
@ -130,6 +131,8 @@ public class ResourceProviderInterceptorR4Test extends BaseResourceProviderR4Tes
myInterceptorRegistry.registerAnonymousInterceptor(Pointcut.PERFTRACE_SEARCH_SELECT_COMPLETE, interceptor);
myInterceptors.add(interceptor);
ourLog.info("About to perform search...");
Bundle results = ourClient.search().forResource(Patient.class).returnBundle(Bundle.class).execute();
verify(interceptor, times(1)).invoke(eq(Pointcut.PERFTRACE_SEARCH_FIRST_RESULT_LOADED), myParamsCaptor.capture());
verify(interceptor, times(1)).invoke(eq(Pointcut.PERFTRACE_SEARCH_SELECT_COMPLETE), myParamsCaptor.capture());

7
src/changes/changes.xml
View File

@ -125,6 +125,13 @@
in the built WAR, in order to prevent duplicates and conflicts in implementing
projects.
</action>
<action type="fix">
Two expunge bug fixes:
The first bug is that the expunge operation wasn't bailing once it hit its limit. This resulted in a
"Page size must not be less than one!" error.
The second bug is that one case wasn't properly handled: when a resourceId with no version is provided.
This executed the case where only resource type is provided.
</action>
</release>
<release version="3.7.0" date="2019-02-06" description="Gale">
<action type="add">