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Try to reuse index rows in JPA server (#1133) 

* Try to reuse index rows in JPA server

* Address review comments

* One more test fix

* One more test
This commit is contained in:
James Agnew 2018-12-05 19:25:59 -05:00 committed by GitHub
parent 31f6a0b22b
commit cbaa39fd63
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20 changed files with 462 additions and 208 deletions
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2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
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@ -1414,7 +1414,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
if (thePerformIndexing) {
myDatabaseSearchParamSynchronizer.synchronizeSearchParamsToDatabase(newParams, theEntity, existingParams);
mySearchParamWithInlineReferencesExtractor.storeCompositeStringUniques(newParams, theEntity, existingParams);
} // if thePerformIndexing
}
if (theResource != null) {
populateResourceIdFromEntity(theEntity, theResource);

35
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FulltextSearchSvcImpl.java
View File

@ -21,8 +21,8 @@ package ca.uhn.fhir.jpa.dao;
*/
import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.api.Constants;
@ -42,7 +42,7 @@ import org.hibernate.search.jpa.FullTextEntityManager;
import org.hibernate.search.jpa.FullTextQuery;
import org.hibernate.search.query.dsl.BooleanJunction;
import org.hibernate.search.query.dsl.QueryBuilder;
import org.hl7.fhir.dstu3.model.BaseResource;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.annotation.Transactional;
@ -181,7 +181,7 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
addTextSearch(qb, bool, textAndTerms, "myNarrativeText", "myNarrativeTextEdgeNGram", "myNarrativeTextNGram");
if (theReferencingPid != null) {
bool.must(qb.keyword().onField("myResourceLinks.myTargetResourcePid").matching(theReferencingPid).createQuery());
bool.must(qb.keyword().onField("myResourceLinksField").matching(theReferencingPid.toString()).createQuery());
}
if (bool.isEmpty()) {
@ -201,13 +201,11 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
// execute search
List<?> result = jpaQuery.getResultList();
HashSet<Long> pidsSet = pids != null ? new HashSet<Long>(pids) : null;
ArrayList<Long> retVal = new ArrayList<Long>();
ArrayList<Long> retVal = new ArrayList<>();
for (Object object : result) {
Object[] nextArray = (Object[]) object;
Long next = (Long) nextArray[0];
if (next != null && (pidsSet == null || pidsSet.contains(next))) {
if (next != null) {
retVal.add(next);
}
}
@ -219,9 +217,9 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
public List<Long> everything(String theResourceName, SearchParameterMap theParams) {
Long pid = null;
if (theParams.get(BaseResource.SP_RES_ID) != null) {
if (theParams.get(IAnyResource.SP_RES_ID) != null) {
String idParamValue;
IQueryParameterType idParam = theParams.get(BaseResource.SP_RES_ID).get(0).get(0);
IQueryParameterType idParam = theParams.get(IAnyResource.SP_RES_ID).get(0).get(0);
if (idParam instanceof TokenParam) {
TokenParam idParm = (TokenParam) idParam;
idParamValue = idParm.getValue();
@ -298,7 +296,8 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
.sentence(theText.toLowerCase()).createQuery();
Query query = qb.bool()
.must(qb.keyword().onField("myResourceLinks.myTargetResourcePid").matching(pid).createQuery())
// .must(qb.keyword().onField("myResourceLinks.myTargetResourcePid").matching(pid).createQuery())
.must(qb.keyword().onField("myResourceLinksField").matching(pid.toString()).createQuery())
.must(textQuery)
.createQuery();
@ -345,7 +344,7 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
}
long delay = System.currentTimeMillis() - start;
ourLog.info("Provided {} suggestions for term {} in {} ms", new Object[]{terms.size(), theText, delay});
ourLog.info("Provided {} suggestions for term {} in {} ms", terms.size(), theText, delay);
return suggestions;
}
@ -358,14 +357,14 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
private ArrayList<Float> myPartialMatchScores;
private String myOriginalSearch;
public MySuggestionFormatter(String theOriginalSearch, List<Suggestion> theSuggestions) {
MySuggestionFormatter(String theOriginalSearch, List<Suggestion> theSuggestions) {
myOriginalSearch = theOriginalSearch;
mySuggestions = theSuggestions;
}
@Override
public String highlightTerm(String theOriginalText, TokenGroup theTokenGroup) {
ourLog.debug("{} Found {} with score {}", new Object[]{myAnalyzer, theOriginalText, theTokenGroup.getTotalScore()});
ourLog.debug("{} Found {} with score {}", myAnalyzer, theOriginalText, theTokenGroup.getTotalScore());
if (theTokenGroup.getTotalScore() > 0) {
float score = theTokenGroup.getTotalScore();
if (theOriginalText.equalsIgnoreCase(myOriginalSearch)) {
@ -385,13 +384,13 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
return null;
}
public void setAnalyzer(String theString) {
void setAnalyzer(String theString) {
myAnalyzer = theString;
}
public void setFindPhrasesWith() {
myPartialMatchPhrases = new ArrayList<String>();
myPartialMatchScores = new ArrayList<Float>();
void setFindPhrasesWith() {
myPartialMatchPhrases = new ArrayList<>();
myPartialMatchScores = new ArrayList<>();
for (Suggestion next : mySuggestions) {
myPartialMatchPhrases.add(' ' + next.myTerm);
@ -408,7 +407,7 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
private String myTerm;
private float myScore;
public Suggestion(String theTerm, float theScore) {
Suggestion(String theTerm, float theScore) {
myTerm = theTerm;
myScore = theScore;
}

142
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DatabaseSearchParamSynchronizer.java
View File

@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.dao.index;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
import org.apache.commons.lang3.Validate;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
@ -31,6 +32,7 @@ import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
@Service
public class DatabaseSearchParamSynchronizer {
@ -41,95 +43,75 @@ public class DatabaseSearchParamSynchronizer {
protected EntityManager myEntityManager;
public void synchronizeSearchParamsToDatabase(ResourceIndexedSearchParams theParams, ResourceTable theEntity, ResourceIndexedSearchParams existingParams) {
theParams.calculateHashes(theParams.stringParams);
for (ResourceIndexedSearchParamString next : synchronizeSearchParamsToDatabase(existingParams.stringParams, theParams.stringParams)) {
next.setModelConfig(myDaoConfig.getModelConfig());
myEntityManager.remove(next);
theEntity.getParamsString().remove(next);
}
for (ResourceIndexedSearchParamString next : synchronizeSearchParamsToDatabase(theParams.stringParams, existingParams.stringParams)) {
myEntityManager.persist(next);
}
theParams.calculateHashes(theParams.tokenParams);
for (ResourceIndexedSearchParamToken next : synchronizeSearchParamsToDatabase(existingParams.tokenParams, theParams.tokenParams)) {
myEntityManager.remove(next);
theEntity.getParamsToken().remove(next);
}
for (ResourceIndexedSearchParamToken next : synchronizeSearchParamsToDatabase(theParams.tokenParams, existingParams.tokenParams)) {
myEntityManager.persist(next);
}
theParams.calculateHashes(theParams.numberParams);
for (ResourceIndexedSearchParamNumber next : synchronizeSearchParamsToDatabase(existingParams.numberParams, theParams.numberParams)) {
myEntityManager.remove(next);
theEntity.getParamsNumber().remove(next);
}
for (ResourceIndexedSearchParamNumber next : synchronizeSearchParamsToDatabase(theParams.numberParams, existingParams.numberParams)) {
myEntityManager.persist(next);
}
theParams.calculateHashes(theParams.quantityParams);
for (ResourceIndexedSearchParamQuantity next : synchronizeSearchParamsToDatabase(existingParams.quantityParams, theParams.quantityParams)) {
myEntityManager.remove(next);
theEntity.getParamsQuantity().remove(next);
}
for (ResourceIndexedSearchParamQuantity next : synchronizeSearchParamsToDatabase(theParams.quantityParams, existingParams.quantityParams)) {
myEntityManager.persist(next);
}
// Store date SP's
theParams.calculateHashes(theParams.dateParams);
for (ResourceIndexedSearchParamDate next : synchronizeSearchParamsToDatabase(existingParams.dateParams, theParams.dateParams)) {
myEntityManager.remove(next);
theEntity.getParamsDate().remove(next);
}
for (ResourceIndexedSearchParamDate next : synchronizeSearchParamsToDatabase(theParams.dateParams, existingParams.dateParams)) {
myEntityManager.persist(next);
}
// Store URI SP's
theParams.calculateHashes(theParams.uriParams);
for (ResourceIndexedSearchParamUri next : synchronizeSearchParamsToDatabase(existingParams.uriParams, theParams.uriParams)) {
myEntityManager.remove(next);
theEntity.getParamsUri().remove(next);
}
for (ResourceIndexedSearchParamUri next : synchronizeSearchParamsToDatabase(theParams.uriParams, existingParams.uriParams)) {
myEntityManager.persist(next);
}
// Store Coords SP's
theParams.calculateHashes(theParams.coordsParams);
for (ResourceIndexedSearchParamCoords next : synchronizeSearchParamsToDatabase(existingParams.coordsParams, theParams.coordsParams)) {
myEntityManager.remove(next);
theEntity.getParamsCoords().remove(next);
}
for (ResourceIndexedSearchParamCoords next : synchronizeSearchParamsToDatabase(theParams.coordsParams, existingParams.coordsParams)) {
myEntityManager.persist(next);
}
// Store resource links
for (ResourceLink next : synchronizeSearchParamsToDatabase(existingParams.links, theParams.links)) {
myEntityManager.remove(next);
theEntity.getResourceLinks().remove(next);
}
for (ResourceLink next : synchronizeSearchParamsToDatabase(theParams.links, existingParams.links)) {
myEntityManager.persist(next);
}
synchronize(theParams, theEntity, theParams.stringParams, existingParams.stringParams);
synchronize(theParams, theEntity, theParams.tokenParams, existingParams.tokenParams);
synchronize(theParams, theEntity, theParams.numberParams, existingParams.numberParams);
synchronize(theParams, theEntity, theParams.quantityParams, existingParams.quantityParams);
synchronize(theParams, theEntity, theParams.dateParams, existingParams.dateParams);
synchronize(theParams, theEntity, theParams.uriParams, existingParams.uriParams);
synchronize(theParams, theEntity, theParams.coordsParams, existingParams.coordsParams);
synchronize(theParams, theEntity, theParams.links, existingParams.links);
// make sure links are indexed
theEntity.setResourceLinks(theParams.links);
}
public <T> Collection<T> synchronizeSearchParamsToDatabase(Collection<T> theInput, Collection<T> theToRemove) {
assert theInput != theToRemove;
private <T extends BaseResourceIndex> void synchronize(ResourceIndexedSearchParams theParams, ResourceTable theEntity, Collection<T> theNewParms, Collection<T> theExistingParms) {
theParams.calculateHashes(theNewParms);
List<T> quantitiesToRemove = subtract(theExistingParms, theNewParms);
List<T> quantitiesToAdd = subtract(theNewParms, theExistingParms);
tryToReuseIndexEntities(quantitiesToRemove, quantitiesToAdd);
for (T next : quantitiesToRemove) {
myEntityManager.remove(next);
theEntity.getParamsQuantity().remove(next);
}
for (T next : quantitiesToAdd) {
myEntityManager.merge(next);
}
}
if (theInput.isEmpty()) {
return theInput;
/**
* The logic here is that often times when we update a resource we are dropping
* one index row and adding another. This method tries to reuse rows that would otherwise
* have been deleted by updating them with the contents of rows that would have
* otherwise been added. In other words, we're trying to replace
* "one delete + one insert" with "one update"
*
* @param theIndexesToRemove The rows that would be removed
* @param theIndexesToAdd The rows that would be added
*/
private <T extends BaseResourceIndex> void tryToReuseIndexEntities(List<T> theIndexesToRemove, List<T> theIndexesToAdd) {
for (int addIndex = 0; addIndex < theIndexesToAdd.size(); addIndex++) {
// If there are no more rows to remove, there's nothing we can reuse
if (theIndexesToRemove.isEmpty()) {
break;
}
T targetEntity = theIndexesToAdd.get(addIndex);
if (targetEntity.getId() != null) {
continue;
}
// Take a row we were going to remove, and repurpose its ID
T entityToReuse = theIndexesToRemove.remove(theIndexesToRemove.size() - 1);
targetEntity.setId(entityToReuse.getId());
}
}
<T> List<T> subtract(Collection<T> theSubtractFrom, Collection<T> theToSubtract) {
assert theSubtractFrom != theToSubtract;
if (theSubtractFrom.isEmpty()) {
return new ArrayList<>();
}
ArrayList<T> retVal = new ArrayList<>(theInput);
retVal.removeAll(theToRemove);
ArrayList<T> retVal = new ArrayList<>(theSubtractFrom);
retVal.removeAll(theToSubtract);
return retVal;
}
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java
View File

@ -258,12 +258,12 @@ public class SearchParamWithInlineReferencesExtractor {
// Store composite string uniques
if (myDaoConfig.isUniqueIndexesEnabled()) {
for (ResourceIndexedCompositeStringUnique next : myDatabaseSearchParamSynchronizer.synchronizeSearchParamsToDatabase(existingParams.compositeStringUniques, theParams.compositeStringUniques)) {
for (ResourceIndexedCompositeStringUnique next : myDatabaseSearchParamSynchronizer.subtract(existingParams.compositeStringUniques, theParams.compositeStringUniques)) {
ourLog.debug("Removing unique index: {}", next);
myEntityManager.remove(next);
theEntity.getParamsCompositeStringUnique().remove(next);
}
for (ResourceIndexedCompositeStringUnique next : myDatabaseSearchParamSynchronizer.synchronizeSearchParamsToDatabase(theParams.compositeStringUniques, existingParams.compositeStringUniques)) {
for (ResourceIndexedCompositeStringUnique next : myDatabaseSearchParamSynchronizer.subtract(theParams.compositeStringUniques, existingParams.compositeStringUniques)) {
if (myDaoConfig.isUniqueIndexesCheckedBeforeSave()) {
ResourceIndexedCompositeStringUnique existing = myResourceIndexedCompositeStringUniqueDao.findByQueryString(next.getIndexString());
if (existing != null) {

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java
View File

@ -102,7 +102,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
DataSource dataSource = ProxyDataSourceBuilder
.create(retVal)
// .logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL")
.logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL")
.logSlowQueryBySlf4j(10, TimeUnit.SECONDS)
// .countQuery(new ThreadQueryCountHolder())
.countQuery(singleQueryCountHolder())

156
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java
View File

@ -3,11 +3,16 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.util.TestUtil;
import net.ttddyy.dsproxy.QueryCount;
import net.ttddyy.dsproxy.listener.SingleQueryCountHolder;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.junit.After;
import org.junit.AfterClass;
@ -63,9 +68,9 @@ public class FhirResourceDaoR4QueryCountTest extends BaseJpaR4Test {
ourLog.info("** Done performing write 2");
assertEquals(2, getQueryCount().getInsert());
assertEquals(1, getQueryCount().getUpdate());
assertEquals(1, getQueryCount().getDelete());
assertEquals(1, getQueryCount().getInsert());
assertEquals(2, getQueryCount().getUpdate());
assertEquals(0, getQueryCount().getDelete());
}
@Test
@ -128,7 +133,7 @@ public class FhirResourceDaoR4QueryCountTest extends BaseJpaR4Test {
p.getPhotoFirstRep().setCreationElement(new DateTimeType("2012")); // non-indexed field
myPatientDao.update(p).getId().toUnqualifiedVersionless();
assertEquals(5, getQueryCount().getSelect());
assertEquals(4, getQueryCount().getSelect());
assertEquals(1, getQueryCount().getInsert());
assertEquals(0, getQueryCount().getDelete());
assertEquals(1, getQueryCount().getUpdate());
@ -157,6 +162,8 @@ public class FhirResourceDaoR4QueryCountTest extends BaseJpaR4Test {
assertEquals(1, myResourceHistoryTableDao.count());
});
myCountHolder.clear();
p = new Patient();
p.setId(id);
@ -183,8 +190,6 @@ public class FhirResourceDaoR4QueryCountTest extends BaseJpaR4Test {
pt.addName().setFamily("FAMILY1").addGiven("GIVEN1A").addGiven("GIVEN1B");
IIdType id = myPatientDao.create(pt).getId().toUnqualifiedVersionless();
ourLog.info("Now have {} deleted", getQueryCount().getDelete());
ourLog.info("Now have {} inserts", getQueryCount().getInsert());
myCountHolder.clear();
ourLog.info("** About to update");
@ -193,13 +198,148 @@ public class FhirResourceDaoR4QueryCountTest extends BaseJpaR4Test {
pt.getNameFirstRep().addGiven("GIVEN1C");
myPatientDao.update(pt);
ourLog.info("Now have {} deleted", getQueryCount().getDelete());
ourLog.info("Now have {} inserts", getQueryCount().getInsert());
assertEquals(0, getQueryCount().getDelete());
assertEquals(2, getQueryCount().getInsert());
}
@Test
public void testUpdateReusesIndexesString() {
myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.DISABLED);
SearchParameterMap m1 = new SearchParameterMap().add("family", new StringParam("family1")).setLoadSynchronous(true);
SearchParameterMap m2 = new SearchParameterMap().add("family", new StringParam("family2")).setLoadSynchronous(true);
myCountHolder.clear();
Patient pt = new Patient();
pt.addName().setFamily("FAMILY1");
IIdType id = myPatientDao.create(pt).getId().toUnqualifiedVersionless();
myCountHolder.clear();
assertEquals(1, myPatientDao.search(m1).size().intValue());
assertEquals(0, myPatientDao.search(m2).size().intValue());
ourLog.info("** About to update");
pt = new Patient();
pt.setId(id);
pt.addName().setFamily("FAMILY2");
myPatientDao.update(pt);
assertEquals(0, getQueryCount().getDelete());
assertEquals(1, getQueryCount().getInsert()); // Add an entry to HFJ_RES_VER
assertEquals(2, getQueryCount().getUpdate()); // Update SPIDX_STRING and HFJ_RESOURCE
assertEquals(0, myPatientDao.search(m1).size().intValue());
assertEquals(1, myPatientDao.search(m2).size().intValue());
}
@Test
public void testUpdateReusesIndexesToken() {
myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.DISABLED);
SearchParameterMap m1 = new SearchParameterMap().add("gender", new TokenParam("male")).setLoadSynchronous(true);
SearchParameterMap m2 = new SearchParameterMap().add("gender", new TokenParam("female")).setLoadSynchronous(true);
myCountHolder.clear();
Patient pt = new Patient();
pt.setGender(Enumerations.AdministrativeGender.MALE);
IIdType id = myPatientDao.create(pt).getId().toUnqualifiedVersionless();
assertEquals(0, getQueryCount().getSelect());
assertEquals(0, getQueryCount().getDelete());
assertEquals(3, getQueryCount().getInsert());
assertEquals(0, getQueryCount().getUpdate());
assertEquals(1, myPatientDao.search(m1).size().intValue());
assertEquals(0, myPatientDao.search(m2).size().intValue());
/*
* Change a value
*/
ourLog.info("** About to update");
myCountHolder.clear();
pt = new Patient();
pt.setId(id);
pt.setGender(Enumerations.AdministrativeGender.FEMALE);
myPatientDao.update(pt);
/*
* Current SELECTs:
* Select the resource from HFJ_RESOURCE
* Select the version from HFJ_RES_VER
* Select the current token indexes
*/
assertEquals(3, getQueryCount().getSelect());
assertEquals(0, getQueryCount().getDelete());
assertEquals(1, getQueryCount().getInsert()); // Add an entry to HFJ_RES_VER
assertEquals(2, getQueryCount().getUpdate()); // Update SPIDX_STRING and HFJ_RESOURCE
assertEquals(0, myPatientDao.search(m1).size().intValue());
assertEquals(1, myPatientDao.search(m2).size().intValue());
myCountHolder.clear();
/*
* Drop a value
*/
ourLog.info("** About to update again");
pt = new Patient();
pt.setId(id);
myPatientDao.update(pt);
assertEquals(1, getQueryCount().getDelete());
assertEquals(1, getQueryCount().getInsert());
assertEquals(1, getQueryCount().getUpdate());
assertEquals(0, myPatientDao.search(m1).size().intValue());
assertEquals(0, myPatientDao.search(m2).size().intValue());
}
@Test
public void testUpdateReusesIndexesResourceLink() {
Organization org1 = new Organization();
org1.setName("org1");
IIdType orgId1 = myOrganizationDao.create(org1).getId().toUnqualifiedVersionless();
Organization org2 = new Organization();
org2.setName("org2");
IIdType orgId2 = myOrganizationDao.create(org2).getId().toUnqualifiedVersionless();
myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.DISABLED);
SearchParameterMap m1 = new SearchParameterMap().add("organization", new ReferenceParam(orgId1.getValue())).setLoadSynchronous(true);
SearchParameterMap m2 = new SearchParameterMap().add("organization", new ReferenceParam(orgId2.getValue())).setLoadSynchronous(true);
myCountHolder.clear();
Patient pt = new Patient();
pt.getManagingOrganization().setReference(orgId1.getValue());
IIdType id = myPatientDao.create(pt).getId().toUnqualifiedVersionless();
myCountHolder.clear();
assertEquals(1, myPatientDao.search(m1).size().intValue());
assertEquals(0, myPatientDao.search(m2).size().intValue());
ourLog.info("** About to update");
pt = new Patient();
pt.setId(id);
pt.getManagingOrganization().setReference(orgId2.getValue());
myPatientDao.update(pt);
assertEquals(0, getQueryCount().getDelete());
assertEquals(1, getQueryCount().getInsert()); // Add an entry to HFJ_RES_VER
assertEquals(2, getQueryCount().getUpdate()); // Update SPIDX_STRING and HFJ_RESOURCE
assertEquals(0, myPatientDao.search(m1).size().intValue());
assertEquals(1, myPatientDao.search(m2).size().intValue());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

13
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/SystemProviderR4Test.java
View File

@ -4,11 +4,14 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
import ca.uhn.fhir.jpa.rp.r4.*;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.interceptor.SimpleRequestHeaderInterceptor;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -411,6 +414,13 @@ public class SystemProviderR4Test extends BaseJpaR4Test {
myPatientDao.read(new IdType("Patient/Patient1063259"));
SearchParameterMap params = new SearchParameterMap();
params.add("subject", new ReferenceParam("Patient1063259"));
params.setLoadSynchronous(true);
IBundleProvider result = myDiagnosticReportDao.search(params);
assertEquals(1, result.size().intValue());
deleteAllOfType("Binary");
deleteAllOfType("Location");
deleteAllOfType("DiagnosticReport");
@ -427,6 +437,9 @@ public class SystemProviderR4Test extends BaseJpaR4Test {
// good
}
result = myDiagnosticReportDao.search(params);
assertEquals(0, result.size().intValue());
}
}

25
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/BaseResourceIndex.java Normal file
View File

@ -0,0 +1,25 @@
package ca.uhn.fhir.jpa.model.entity;
import java.io.Serializable;
public abstract class BaseResourceIndex implements Serializable {
public abstract Long getId();
public abstract void setId(Long theId);
public abstract void calculateHashes();
/**
* Subclasses must implement
*/
@Override
public abstract int hashCode();
/**
* Subclasses must implement
*/
@Override
public abstract boolean equals(Object obj);
}

8
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/BaseResourceIndexedSearchParam.java
View File

@ -31,11 +31,10 @@ import org.hibernate.search.annotations.ContainedIn;
import org.hibernate.search.annotations.Field;
import javax.persistence.*;
import java.io.Serializable;
import java.util.Date;
@MappedSuperclass
public abstract class BaseResourceIndexedSearchParam implements Serializable {
public abstract class BaseResourceIndexedSearchParam extends BaseResourceIndex {
static final int MAX_SP_NAME = 100;
/**
* Don't change this without careful consideration. You will break existing hashes!
@ -80,7 +79,8 @@ public abstract class BaseResourceIndexedSearchParam implements Serializable {
// nothing
}
protected abstract Long getId();
@Override
public abstract Long getId();
public String getParamName() {
return myParamName;
@ -129,8 +129,6 @@ public abstract class BaseResourceIndexedSearchParam implements Serializable {
public abstract IQueryParameterType toQueryParameterType();
public abstract void calculateHashes();
public static long calculateHashIdentity(String theResourceType, String theParamName) {
return hash(theResourceType, theParamName);
}

9
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamCoords.java
View File

@ -112,10 +112,16 @@ public class ResourceIndexedSearchParamCoords extends BaseResourceIndexedSearchP
}
@Override
protected Long getId() {
public Long getId() {
return myId;
}
@Override
public void setId(Long theId) {
myId =theId;
}
public double getLatitude() {
return myLatitude;
}
@ -156,4 +162,5 @@ public class ResourceIndexedSearchParamCoords extends BaseResourceIndexedSearchP
b.append("lon", getLongitude());
return b.build();
}
}

12
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamDate.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.model.entity;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -130,10 +130,15 @@ public class ResourceIndexedSearchParamDate extends BaseResourceIndexedSearchPar
}
@Override
protected Long getId() {
public Long getId() {
return myId;
}
@Override
public void setId(Long theId) {
myId =theId;
}
protected Long getTimeFromDate(Date date) {
if (date != null) {
return date.getTime();
@ -212,4 +217,5 @@ public class ResourceIndexedSearchParamDate extends BaseResourceIndexedSearchPar
}
return result;
}
}

14
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamNumber.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.model.entity;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -114,10 +114,15 @@ public class ResourceIndexedSearchParamNumber extends BaseResourceIndexedSearchP
}
@Override
protected Long getId() {
public Long getId() {
return myId;
}
@Override
public void setId(Long theId) {
myId =theId;
}
public BigDecimal getValue() {
return myValue;
}
@ -155,7 +160,8 @@ public class ResourceIndexedSearchParamNumber extends BaseResourceIndexedSearchP
if (!(theParam instanceof NumberParam)) {
return false;
}
NumberParam number = (NumberParam)theParam;
NumberParam number = (NumberParam) theParam;
return getValue().equals(number.getValue());
}
}

30
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantity.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.model.entity;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -166,10 +166,15 @@ public class ResourceIndexedSearchParamQuantity extends BaseResourceIndexedSearc
}
@Override
protected Long getId() {
public Long getId() {
return myId;
}
@Override
public void setId(Long theId) {
myId =theId;
}
public String getSystem() {
return mySystem;
}
@ -227,20 +232,12 @@ public class ResourceIndexedSearchParamQuantity extends BaseResourceIndexedSearc
return b.build();
}
public static long calculateHashSystemAndUnits(String theResourceType, String theParamName, String theSystem, String theUnits) {
return hash(theResourceType, theParamName, theSystem, theUnits);
}
public static long calculateHashUnits(String theResourceType, String theParamName, String theUnits) {
return hash(theResourceType, theParamName, theUnits);
}
@Override
public boolean matches(IQueryParameterType theParam) {
if (!(theParam instanceof QuantityParam)) {
return false;
}
QuantityParam quantity = (QuantityParam)theParam;
QuantityParam quantity = (QuantityParam) theParam;
boolean retval = false;
// Only match on system if it wasn't specified
@ -268,4 +265,13 @@ public class ResourceIndexedSearchParamQuantity extends BaseResourceIndexedSearc
return retval;
}
public static long calculateHashSystemAndUnits(String theResourceType, String theParamName, String theSystem, String theUnits) {
return hash(theResourceType, theParamName, theSystem, theUnits);
}
public static long calculateHashUnits(String theResourceType, String theParamName, String theUnits) {
return hash(theResourceType, theParamName, theUnits);
}
}

8
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamString.java
View File

@ -221,10 +221,16 @@ public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchP
}
@Override
protected Long getId() {
public Long getId() {
return myId;
}
@Override
public void setId(Long theId) {
myId =theId;
}
public String getValueExact() {
return myValueExact;
}

46
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamToken.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.model.entity;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -159,6 +159,10 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
return myHashSystem;
}
private void setHashSystem(Long theHashSystem) {
myHashSystem = theHashSystem;
}
private Long getHashIdentity() {
calculateHashes();
return myHashIdentity;
@ -168,10 +172,6 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
myHashIdentity = theHashIdentity;
}
private void setHashSystem(Long theHashSystem) {
myHashSystem = theHashSystem;
}
Long getHashSystemAndValue() {
calculateHashes();
return myHashSystemAndValue;
@ -192,10 +192,15 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
}
@Override
protected Long getId() {
public Long getId() {
return myId;
}
@Override
public void setId(Long theId) {
myId =theId;
}
public String getSystem() {
return mySystem;
}
@ -240,24 +245,12 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
return b.build();
}
public static long calculateHashSystem(String theResourceType, String theParamName, String theSystem) {
return hash(theResourceType, theParamName, trim(theSystem));
}
public static long calculateHashSystemAndValue(String theResourceType, String theParamName, String theSystem, String theValue) {
return hash(theResourceType, theParamName, defaultString(trim(theSystem)), trim(theValue));
}
public static long calculateHashValue(String theResourceType, String theParamName, String theValue) {
return hash(theResourceType, theParamName, trim(theValue));
}
@Override
public boolean matches(IQueryParameterType theParam) {
if (!(theParam instanceof TokenParam)) {
return false;
}
TokenParam token = (TokenParam)theParam;
TokenParam token = (TokenParam) theParam;
boolean retval = false;
// Only match on system if it wasn't specified
if (token.getSystem() == null || token.getSystem().isEmpty()) {
@ -276,4 +269,17 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
}
return retval;
}
public static long calculateHashSystem(String theResourceType, String theParamName, String theSystem) {
return hash(theResourceType, theParamName, trim(theSystem));
}
public static long calculateHashSystemAndValue(String theResourceType, String theParamName, String theSystem, String theValue) {
return hash(theResourceType, theParamName, defaultString(trim(theSystem)), trim(theValue));
}
public static long calculateHashValue(String theResourceType, String theParamName, String theValue) {
return hash(theResourceType, theParamName, trim(theValue));
}
}

23
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamUri.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.model.entity;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -138,10 +138,16 @@ public class ResourceIndexedSearchParamUri extends BaseResourceIndexedSearchPara
}
@Override
protected Long getId() {
public Long getId() {
return myId;
}
@Override
public void setId(Long theId) {
myId =theId;
}
public String getUri() {
return myUri;
}
@ -175,17 +181,18 @@ public class ResourceIndexedSearchParamUri extends BaseResourceIndexedSearchPara
return b.toString();
}
public static long calculateHashUri(String theResourceType, String theParamName, String theUri) {
return hash(theResourceType, theParamName, theUri);
}
@Override
public boolean matches(IQueryParameterType theParam) {
if (!(theParam instanceof UriParam)) {
return false;
}
UriParam uri = (UriParam)theParam;
UriParam uri = (UriParam) theParam;
return getUri().equalsIgnoreCase(uri.getValueNotNull());
}
public static long calculateHashUri(String theResourceType, String theParamName, String theUri) {
return hash(theResourceType, theParamName, theUri);
}
}

87
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceLink.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.model.entity;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -27,7 +27,6 @@ import org.hibernate.search.annotations.Field;
import org.hl7.fhir.instance.model.api.IIdType;
import javax.persistence.*;
import java.io.Serializable;
import java.util.Date;
@Entity
@ -36,11 +35,10 @@ import java.util.Date;
@Index(name = "IDX_RL_SRC", columnList = "SRC_RESOURCE_ID"),
@Index(name = "IDX_RL_DEST", columnList = "TARGET_RESOURCE_ID")
})
public class ResourceLink implements Serializable {
public class ResourceLink extends BaseResourceIndex {
private static final long serialVersionUID = 1L;
public static final int SRC_PATH_LENGTH = 200;
private static final long serialVersionUID = 1L;
@SequenceGenerator(name = "SEQ_RESLINK_ID", sequenceName = "SEQ_RESLINK_ID")
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_RESLINK_ID")
@Id
@ -126,10 +124,20 @@ public class ResourceLink implements Serializable {
return mySourcePath;
}
public void setSourcePath(String theSourcePath) {
mySourcePath = theSourcePath;
}
public ResourceTable getSourceResource() {
return mySourceResource;
}
public void setSourceResource(ResourceTable theSourceResource) {
mySourceResource = theSourceResource;
mySourceResourcePid = theSourceResource.getId();
mySourceResourceType = theSourceResource.getResourceType();
}
public Long getSourceResourcePid() {
return mySourceResourcePid;
}
@ -138,6 +146,13 @@ public class ResourceLink implements Serializable {
return myTargetResource;
}
public void setTargetResource(ResourceTable theTargetResource) {
Validate.notNull(theTargetResource);
myTargetResource = theTargetResource;
myTargetResourcePid = theTargetResource.getId();
myTargetResourceType = theTargetResource.getResourceType();
}
public Long getTargetResourcePid() {
return myTargetResourcePid;
}
@ -146,37 +161,6 @@ public class ResourceLink implements Serializable {
return myTargetResourceUrl;
}
public Date getUpdated() {
return myUpdated;
}
@Override
public int hashCode() {
HashCodeBuilder b = new HashCodeBuilder();
b.append(mySourcePath);
b.append(mySourceResource);
b.append(myTargetResourcePid);
b.append(myTargetResourceUrl);
return b.toHashCode();
}
public void setSourcePath(String theSourcePath) {
mySourcePath = theSourcePath;
}
public void setSourceResource(ResourceTable theSourceResource) {
mySourceResource = theSourceResource;
mySourceResourcePid = theSourceResource.getId();
mySourceResourceType = theSourceResource.getResourceType();
}
public void setTargetResource(ResourceTable theTargetResource) {
Validate.notNull(theTargetResource);
myTargetResource = theTargetResource;
myTargetResourcePid = theTargetResource.getId();
myTargetResourceType = theTargetResource.getResourceType();
}
public void setTargetResourceUrl(IIdType theTargetResourceUrl) {
Validate.isTrue(theTargetResourceUrl.hasBaseUrl());
Validate.isTrue(theTargetResourceUrl.hasResourceType());
@ -194,10 +178,39 @@ public class ResourceLink implements Serializable {
myTargetResourceUrl = theTargetResourceUrl.getValue();
}
public Date getUpdated() {
return myUpdated;
}
public void setUpdated(Date theUpdated) {
myUpdated = theUpdated;
}
@Override
public Long getId() {
return myId;
}
@Override
public void setId(Long theId) {
myId = theId;
}
@Override
public void calculateHashes() {
// nothing right now
}
@Override
public int hashCode() {
HashCodeBuilder b = new HashCodeBuilder();
b.append(mySourcePath);
b.append(mySourceResource);
b.append(myTargetResourcePid);
b.append(myTargetResourceUrl);
return b.toHashCode();
}
@Override
public String toString() {
StringBuilder b = new StringBuilder();

43
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceTable.java
View File

@ -32,10 +32,8 @@ import org.hibernate.search.annotations.*;
import javax.persistence.Index;
import javax.persistence.*;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.Set;
import java.util.*;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.defaultString;
@ -177,10 +175,27 @@ public class ResourceTable extends BaseHasResource implements Serializable {
@OptimisticLock(excluded = true)
private Collection<ResourceIndexedCompositeStringUnique> myParamsCompositeStringUnique;
@IndexedEmbedded
@OneToMany(mappedBy = "mySourceResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
@OptimisticLock(excluded = true)
private Collection<ResourceLink> myResourceLinks;
/**
* This is a clone of {@link #myResourceLinks} but without the hibernate annotations.
* Before we persist we copy the contents of {@link #myResourceLinks} into this field. We
* have this separate because that way we can only populate this field if
* {@link #myHasLinks} is true, meaning that there are actually resource links present
* right now. This avoids Hibernate Search triggering a select on the resource link
* table.
*
* This field is used by FulltextSearchSvcImpl
*
* You can test that any changes don't cause extra queries by running
* FhirResourceDaoR4QueryCountTest
*/
@Field
@Transient
private String myResourceLinksField;
@OneToMany(mappedBy = "myTargetResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
@OptimisticLock(excluded = true)
private Collection<ResourceLink> myResourceLinksAsTarget;
@ -589,4 +604,22 @@ public class ResourceTable extends BaseHasResource implements Serializable {
return b.build();
}
@PrePersist
@PreUpdate
public void preSave() {
if (myHasLinks && myResourceLinks != null) {
myResourceLinksField = getResourceLinks()
.stream()
.map(t->{
Long retVal = t.getTargetResourcePid();
return retVal;
})
.filter(Objects::nonNull)
.map(t->t.toString())
.collect(Collectors.joining(" "));
} else {
myResourceLinksField = null;
}
}
}

5
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceIndexedSearchParams.java
View File

@ -208,8 +208,8 @@ public final class ResourceIndexedSearchParams {
public void calculateHashes(Collection<? extends BaseResourceIndexedSearchParam> theStringParams) {
for (BaseResourceIndexedSearchParam next : theStringParams) {
public void calculateHashes(Collection<? extends BaseResourceIndex> theStringParams) {
for (BaseResourceIndex next : theStringParams) {
next.calculateHashes();
}
}
@ -353,6 +353,7 @@ public final class ResourceIndexedSearchParams {
case COMPOSITE:
case HAS:
case REFERENCE:
case SPECIAL:
default:
continue;
}

6
src/changes/changes.xml
View File

@ -122,6 +122,12 @@
adjust the most recent version to
account for this.
</action>
<action type="add">
When updating existing resources, the JPA server will now attempt to reuse/update
rows in the index tables if one row is being removed and one row is being added (e.g.
because a Patient's name is changing from "A" to "B"). This has the net effect
of reducing the number
</action>
</release>
<release version="3.6.0" date="2018-11-12" description="Food">
<action type="add">