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Includes performance enhancement (#1702)

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* Includes performance enhancement

* Add changelog

* Test fix

* Fix typo

* A few coverage cleanups

* Test fix

* Fix changelog
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James Agnew 2020-02-18 14:11:48 -05:00 committed by GitHub
parent 60f16dd91d
commit 64f07e4dc0
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8 changed files with 109 additions and 46 deletions
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4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1702-includes-perf-fix.yaml Normal file
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@ -0,0 +1,4 @@
---
type: perf
issue: 1702
title: "Loading of _include and _revinclude values has been optimized to be slightly faster"

89
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java
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@ -29,17 +29,29 @@ import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.dao.data.IResourceSearchViewDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.dao.predicate.*;
import ca.uhn.fhir.jpa.dao.predicate.PredicateBuilder;
import ca.uhn.fhir.jpa.dao.predicate.PredicateBuilderFactory;
import ca.uhn.fhir.jpa.dao.predicate.QueryRoot;
import ca.uhn.fhir.jpa.dao.predicate.SearchBuilderJoinEnum;
import ca.uhn.fhir.jpa.dao.predicate.SearchBuilderJoinKey;
import ca.uhn.fhir.jpa.entity.ResourceSearchView;
import ca.uhn.fhir.jpa.interceptor.JpaPreResourceAccessDetails;
import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedCompositeStringUnique;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.entity.ResourceTag;
import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.searchparam.JpaRuntimeSearchParam;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.util.*;
import ca.uhn.fhir.jpa.util.BaseIterator;
import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
import ca.uhn.fhir.jpa.util.SqlQueryList;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.Include;
@ -80,10 +92,27 @@ import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.*;
import java.util.*;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.From;
import javax.persistence.criteria.Join;
import javax.persistence.criteria.JoinType;
import javax.persistence.criteria.Order;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import static org.apache.commons.lang3.StringUtils.*;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/**
* The SearchBuilder is responsible for actually forming the SQL query that handles
@ -103,8 +132,9 @@ public class SearchBuilder implements ISearchBuilder {
private static final List<ResourcePersistentId> EMPTY_LONG_LIST = Collections.unmodifiableList(new ArrayList<>());
private static final Logger ourLog = LoggerFactory.getLogger(SearchBuilder.class);
private static ResourcePersistentId NO_MORE = new ResourcePersistentId(-1L);
@Autowired
private DaoConfig myDaoConfig;
private final QueryRoot myQueryRoot = new QueryRoot();
private final String myResourceName;
private final Class<? extends IBaseResource> myResourceType;
@Autowired
protected IInterceptorBroadcaster myInterceptorBroadcaster;
@Autowired
@ -112,6 +142,8 @@ public class SearchBuilder implements ISearchBuilder {
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
protected EntityManager myEntityManager;
@Autowired
private DaoConfig myDaoConfig;
@Autowired
private IResourceSearchViewDao myResourceSearchViewDao;
@Autowired
private FhirContext myContext;
@ -123,7 +155,6 @@ public class SearchBuilder implements ISearchBuilder {
private ISearchParamRegistry mySearchParamRegistry;
@Autowired
private PredicateBuilderFactory myPredicateBuilderFactory;
private List<ResourcePersistentId> myAlsoIncludePids;
private CriteriaBuilder myBuilder;
private IDao myCallingDao;
@ -133,9 +164,6 @@ public class SearchBuilder implements ISearchBuilder {
private Integer myMaxResultsToFetch;
private Set<ResourcePersistentId> myPidSet;
private PredicateBuilder myPredicateBuilder;
private final QueryRoot myQueryRoot = new QueryRoot();
private final String myResourceName;
private final Class<? extends IBaseResource> myResourceType;
/**
* Constructor
@ -595,6 +623,7 @@ public class SearchBuilder implements ISearchBuilder {
return new HashSet<>();
}
String searchFieldName = theReverseMode ? "myTargetResourcePid" : "mySourceResourcePid";
String findFieldName = theReverseMode ? "mySourceResourcePid" : "myTargetResourcePid";
Collection<ResourcePersistentId> nextRoundMatches = theMatches;
HashSet<ResourcePersistentId> allAdded = new HashSet<>();
@ -619,17 +648,17 @@ public class SearchBuilder implements ISearchBuilder {
boolean matchAll = "*".equals(nextInclude.getValue());
if (matchAll) {
String sql;
sql = "SELECT r FROM ResourceLink r WHERE r." + searchFieldName + " IN (:target_pids) ";
sql = "SELECT r." + findFieldName + " FROM ResourceLink r WHERE r." + searchFieldName + " IN (:target_pids) ";
List<Collection<ResourcePersistentId>> partitions = partition(nextRoundMatches, MAXIMUM_PAGE_SIZE);
for (Collection<ResourcePersistentId> nextPartition : partitions) {
TypedQuery<ResourceLink> q = theEntityManager.createQuery(sql, ResourceLink.class);
TypedQuery<Long> q = theEntityManager.createQuery(sql, Long.class);
q.setParameter("target_pids", ResourcePersistentId.toLongList(nextPartition));
List<ResourceLink> results = q.getResultList();
for (ResourceLink resourceLink : results) {
List<Long> results = q.getResultList();
for (Long resourceLink : results) {
if (theReverseMode) {
pidsToInclude.add(new ResourcePersistentId(resourceLink.getSourceResourcePid()));
pidsToInclude.add(new ResourcePersistentId(resourceLink));
} else {
pidsToInclude.add(new ResourcePersistentId(resourceLink.getTargetResourcePid()));
pidsToInclude.add(new ResourcePersistentId(resourceLink));
}
}
}
@ -666,16 +695,16 @@ public class SearchBuilder implements ISearchBuilder {
boolean haveTargetTypesDefinedByParam = param.hasTargets();
if (targetResourceType != null) {
sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids) AND r.myTargetResourceType = :target_resource_type";
sql = "SELECT r." + findFieldName + " FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids) AND r.myTargetResourceType = :target_resource_type";
} else if (haveTargetTypesDefinedByParam) {
sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids) AND r.myTargetResourceType in (:target_resource_types)";
sql = "SELECT r." + findFieldName + " FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids) AND r.myTargetResourceType in (:target_resource_types)";
} else {
sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids)";
sql = "SELECT r." + findFieldName + " FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids)";
}
List<Collection<ResourcePersistentId>> partitions = partition(nextRoundMatches, MAXIMUM_PAGE_SIZE);
for (Collection<ResourcePersistentId> nextPartition : partitions) {
TypedQuery<ResourceLink> q = theEntityManager.createQuery(sql, ResourceLink.class);
TypedQuery<Long> q = theEntityManager.createQuery(sql, Long.class);
q.setParameter("src_path", nextPath);
q.setParameter("target_pids", ResourcePersistentId.toLongList(nextPartition));
if (targetResourceType != null) {
@ -683,18 +712,10 @@ public class SearchBuilder implements ISearchBuilder {
} else if (haveTargetTypesDefinedByParam) {
q.setParameter("target_resource_types", param.getTargets());
}
List<ResourceLink> results = q.getResultList();
for (ResourceLink resourceLink : results) {
if (theReverseMode) {
Long pid = resourceLink.getSourceResourcePid();
if (pid != null) {
pidsToInclude.add(new ResourcePersistentId(pid));
}
} else {
Long pid = resourceLink.getTargetResourcePid();
if (pid != null) {
pidsToInclude.add(new ResourcePersistentId(pid));
}
List<Long> results = q.getResultList();
for (Long resourceLink : results) {
if (resourceLink != null) {
pidsToInclude.add(new ResourcePersistentId(resourceLink));
}
}
}

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/SearchBuilderTest.java
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@ -39,11 +39,10 @@ public class SearchBuilderTest {
TypedQuery mockQuery = mock(TypedQuery.class);
when(mockEntityManager.createQuery(any(), any())).thenReturn(mockQuery);
List<ResourceLink> resultList = new ArrayList<>();
ResourceLink link = new ResourceLink();
List<Long> resultList = new ArrayList<>();
Long link = 1L;
ResourceTable target = new ResourceTable();
target.setId(1L);
link.setTargetResource(target);
resultList.add(link);
when(mockQuery.getResultList()).thenReturn(resultList);

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
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@ -162,6 +162,9 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
@Qualifier("myConditionDaoR4")
protected IFhirResourceDao<Condition> myConditionDao;
@Autowired
@Qualifier("myEpisodeOfCareDaoR4")
protected IFhirResourceDao<EpisodeOfCare> myEpisodeOfCareDao;
@Autowired
protected DaoConfig myDaoConfig;
@Autowired
protected ModelConfig myModelConfig;

39
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
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@ -4228,6 +4228,45 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
}
@Test
public void testCircularReferencesDontBreakRevIncludes() {
Patient p = new Patient();
p.setActive(true);
IIdType patientId = myPatientDao.create(p).getId().toUnqualifiedVersionless();
Encounter enc = new Encounter();
enc.setStatus(Encounter.EncounterStatus.ARRIVED);
enc.getSubject().setReference(patientId.getValue());
IIdType encId = myEncounterDao.create(enc).getId().toUnqualifiedVersionless();
Condition cond = new Condition();
cond.addIdentifier().setSystem("http://foo").setValue("123");
IIdType conditionId = myConditionDao.create(cond).getId().toUnqualifiedVersionless();
EpisodeOfCare ep = new EpisodeOfCare();
ep.setStatus(EpisodeOfCare.EpisodeOfCareStatus.ACTIVE);
IIdType epId = myEpisodeOfCareDao.create(ep).getId().toUnqualifiedVersionless();
enc.getEpisodeOfCareFirstRep().setReference(ep.getId());
myEncounterDao.update(enc);
cond.getEncounter().setReference(enc.getId());
myConditionDao.update(cond);
ep.getDiagnosisFirstRep().getCondition().setReference(cond.getId());
myEpisodeOfCareDao.update(ep);
// Search time
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.addRevInclude(new Include("*").setRecurse(true));
IBundleProvider results = myPatientDao.search(params);
List<String> values = toUnqualifiedVersionlessIdValues(results);
assertThat(values.toString(), values, containsInAnyOrder(patientId.getValue(), encId.getValue(), conditionId.getValue(), epId.getValue()));
}
private String toStringMultiline(List<?> theResults) {
StringBuilder b = new StringBuilder();
for (Object next : theResults) {

8
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceLink.java
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@ -138,10 +138,6 @@ public class ResourceLink extends BaseResourceIndex {
mySourceResourceType = theSourceResource.getResourceType();
}
public Long getSourceResourcePid() {
return mySourceResourcePid;
}
public ResourceTable getTargetResource() {
return myTargetResource;
}
@ -157,10 +153,6 @@ public class ResourceLink extends BaseResourceIndex {
return myTargetResourcePid;
}
public String getTargetResourceUrl() {
return myTargetResourceUrl;
}
public void setTargetResourceUrl(IIdType theTargetResourceUrl) {
Validate.isTrue(theTargetResourceUrl.hasBaseUrl());
Validate.isTrue(theTargetResourceUrl.hasResourceType());

2
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/ReadMethodBinding.java
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@ -160,7 +160,7 @@ public class ReadMethodBinding extends BaseResourceReturningMethodBinding {
IBundleProvider retVal = toResourceList(response);
if (retVal.size() == 1) {
if (Integer.valueOf(1).equals(retVal.size())) {
List<IBaseResource> responseResources = retVal.getResources(0, 1);
IBaseResource responseResource = responseResources.get(0);

5
hapi-fhir-server/src/test/java/ca/uhn/fhir/rest/server/method/ReadMethodBindingTest.java
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@ -59,6 +59,11 @@ public class ReadMethodBindingTest {
assertTrue(binding.incomingServerRequestMatchesMethod(myRequestDetails));
// VRead
when(myRequestDetails.getId()).thenReturn(new IdDt("Patient/123/_history/123"));
assertFalse(binding.incomingServerRequestMatchesMethod(myRequestDetails));
// Type history
when(myRequestDetails.getId()).thenReturn(new IdDt("Patient/123"));
when(myRequestDetails.getResourceName()).thenReturn("Patient");
when(myRequestDetails.getOperation()).thenReturn("_history");
assertFalse(binding.incomingServerRequestMatchesMethod(myRequestDetails));