One more deadlock
This commit is contained in:
James Agnew
parent
9d08e1e211
commit
82171da0cc
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@ -10,7 +10,7 @@ package ca.uhn.fhir.jpa.term;
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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@ -19,21 +19,10 @@ package ca.uhn.fhir.jpa.term;
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* limitations under the License.
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* #L%
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*/
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.IdentityHashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.*;
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import java.util.concurrent.TimeUnit;
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import javax.persistence.EntityManager;
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import javax.persistence.PersistenceContext;
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import javax.persistence.PersistenceContextType;
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import javax.persistence.*;
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import org.apache.commons.lang3.Validate;
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import org.apache.commons.lang3.time.DateUtils;
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@ -51,19 +40,12 @@ import org.springframework.transaction.support.TransactionTemplate;
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import com.google.common.annotations.VisibleForTesting;
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import com.google.common.base.Stopwatch;
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import com.google.common.collect.ArrayListMultimap;
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import com.google.common.collect.Multimaps;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
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import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
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import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
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import ca.uhn.fhir.jpa.entity.TermCodeSystem;
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import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
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import ca.uhn.fhir.jpa.entity.TermConcept;
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import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
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import ca.uhn.fhir.jpa.dao.data.*;
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import ca.uhn.fhir.jpa.entity.*;
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import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
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import ca.uhn.fhir.jpa.util.StopWatch;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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@ -76,6 +58,8 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiTerminologySvc.class);
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private static final Object PLACEHOLDER_OBJECT = new Object();
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private ArrayListMultimap<Long, Long> myChildToParentPidCache;
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@Autowired
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protected ITermCodeSystemDao myCodeSystemDao;
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@ -100,8 +84,8 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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@PersistenceContext(type = PersistenceContextType.TRANSACTION)
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protected EntityManager myEntityManager;
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private long myNextReindexPass;
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private boolean myProcessDeferred = true;
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@Autowired
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@ -121,7 +105,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
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ourLog.trace("Checking {} parents", theParents.size());
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int retVal = 0;
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for (TermConceptParentChildLink nextLink : theParents) {
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if (nextLink.getRelationshipType() == RelationshipTypeEnum.ISA) {
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TermConcept nextParent = nextLink.getParent();
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@ -133,7 +117,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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}
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}
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}
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return retVal;
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}
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@ -206,8 +190,11 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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/**
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* Subclasses may override
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* @param theSystem The code system
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* @param theCode The code
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*
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* @param theSystem
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* The code system
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* @param theCode
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* The code
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*/
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protected List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
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return Collections.emptyList();
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@ -244,15 +231,19 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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ArrayList<VersionIndependentConcept> retVal = toVersionIndependentConcepts(theSystem, codes);
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return retVal;
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}
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/**
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* Subclasses may override
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* @param theSystem The code system
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* @param theCode The code
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*
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* @param theSystem
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* The code system
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* @param theCode
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* The code
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*/
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protected List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode) {
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return Collections.emptyList();
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}
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private TermCodeSystemVersion findCurrentCodeSystemVersionForSystem(String theCodeSystem) {
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TermCodeSystem cs = getCodeSystem(theCodeSystem);
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if (cs == null || cs.getCurrentVersion() == null) {
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@ -274,7 +265,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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if (theConceptsStack.size() == 1 || theConceptsStack.size() % 10000 == 0) {
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float pct = (float) theConceptsStack.size() / (float) theTotalConcepts;
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ourLog.info("Have processed {}/{} concepts ({}%)", theConceptsStack.size(), theTotalConcepts, (int)( pct*100.0f));
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ourLog.info("Have processed {}/{} concepts ({}%)", theConceptsStack.size(), theTotalConcepts, (int) (pct * 100.0f));
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}
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theConcept.setCodeSystem(theCodeSystem);
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@ -285,7 +276,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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} else {
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myConceptsToSaveLater.add(theConcept);
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}
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for (TermConceptParentChildLink next : theConcept.getChildren()) {
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persistChildren(next.getChild(), theCodeSystem, theConceptsStack, theTotalConcepts);
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}
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@ -297,7 +288,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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myConceptLinksToSaveLater.add(next);
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}
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}
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}
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private void populateVersion(TermConcept theNext, TermCodeSystemVersion theCodeSystemVersion) {
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@ -310,48 +301,56 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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}
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}
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private ArrayListMultimap<Long, Long> myChildToParentPidCache;
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private void processDeferredConcepts() {
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int codeCount = 0, relCount = 0;
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StopWatch stopwatch = new StopWatch();
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int count = Math.min(myDaoConfig.getDeferIndexingForCodesystemsOfSize(), myConceptsToSaveLater.size());
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ourLog.info("Saving {} deferred concepts...", count);
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while (codeCount < count && myConceptsToSaveLater.size() > 0) {
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TermConcept next = myConceptsToSaveLater.remove(0);
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codeCount += saveConcept(next);
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}
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if (codeCount > 0) {
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ourLog.info("Saved {} deferred concepts ({} codes remain and {} relationships remain) in {}ms ({}ms / code)",
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new Object[] { codeCount, myConceptsToSaveLater.size(), myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(codeCount) });
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}
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if (codeCount == 0) {
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count = Math.min(myDaoConfig.getDeferIndexingForCodesystemsOfSize(), myConceptLinksToSaveLater.size());
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ourLog.info("Saving {} deferred concept relationships...", count);
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while (relCount < count && myConceptLinksToSaveLater.size() > 0) {
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TermConceptParentChildLink next = myConceptLinksToSaveLater.remove(0);
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if (myConceptDao.findOne(next.getChild().getId()) == null || myConceptDao.findOne(next.getParent().getId()) == null) {
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ourLog.warn("Not inserting link from child {} to parent {} because it appears to have been deleted", next.getParent().getCode(), next.getChild().getCode());
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continue;
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}
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saveConceptLink(next);
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relCount++;
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}
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}
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if (relCount > 0) {
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ourLog.info("Saved {} deferred relationships ({} remain) in {}ms ({}ms / code)",
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new Object[] { relCount, myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(codeCount) });
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}
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if ((myConceptsToSaveLater.size() + myConceptLinksToSaveLater.size()) == 0) {
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ourLog.info("All deferred concepts and relationships have now been synchronized to the database");
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}
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}
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private void processReindexing() {
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if (System.currentTimeMillis() < myNextReindexPass && !ourForceSaveDeferredAlwaysForUnitTest) {
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return;
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}
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TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
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tt.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
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tt.execute(new TransactionCallbackWithoutResult() {
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@Override
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protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
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int maxResult = 1000;
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Page<TermConcept> concepts = myConceptDao.findResourcesRequiringReindexing(new PageRequest(0, maxResult));
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if (concepts.hasContent() == false) {
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myNextReindexPass = System.currentTimeMillis() + DateUtils.MILLIS_PER_MINUTE;
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myChildToParentPidCache = null;
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return;
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}
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if (myChildToParentPidCache == null) {
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myChildToParentPidCache = ArrayListMultimap.create();
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}
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ourLog.info("Indexing {} / {} concepts", concepts.getContent().size(), concepts.getTotalElements());
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int count = 0;
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StopWatch stopwatch = new StopWatch();
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for (TermConcept nextConcept : concepts) {
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StringBuilder parentsBuilder = new StringBuilder();
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createParentsString(parentsBuilder, nextConcept.getId());
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nextConcept.setParentPids(parentsBuilder.toString());
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saveConcept(nextConcept);
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count++;
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}
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ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", new Object[] { count, concepts.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count) });
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}
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private void createParentsString(StringBuilder theParentsBuilder, Long theConceptPid) {
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Validate.notNull(theConceptPid, "theConceptPid must not be null");
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List<Long> parents = myChildToParentPidCache.get(theConceptPid);
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@ -368,8 +367,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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}
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}
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}
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for (Long nextParent : parents) {
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if (theParentsBuilder.length() > 0) {
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theParentsBuilder.append(' ');
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@ -378,13 +376,45 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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createParentsString(theParentsBuilder, nextParent);
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}
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}
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@Override
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protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
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int maxResult = 1000;
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Page<TermConcept> concepts = myConceptDao.findResourcesRequiringReindexing(new PageRequest(0, maxResult));
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if (concepts.hasContent() == false) {
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myNextReindexPass = System.currentTimeMillis() + DateUtils.MILLIS_PER_MINUTE;
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myChildToParentPidCache = null;
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return;
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}
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if (myChildToParentPidCache == null) {
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myChildToParentPidCache = ArrayListMultimap.create();
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}
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ourLog.info("Indexing {} / {} concepts", concepts.getContent().size(), concepts.getTotalElements());
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int count = 0;
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StopWatch stopwatch = new StopWatch();
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for (TermConcept nextConcept : concepts) {
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StringBuilder parentsBuilder = new StringBuilder();
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createParentsString(parentsBuilder, nextConcept.getId());
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nextConcept.setParentPids(parentsBuilder.toString());
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saveConcept(nextConcept);
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count++;
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}
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ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", new Object[] { count, concepts.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count) });
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}
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});
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}
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private int saveConcept(TermConcept theConcept) {
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int retVal = 0;
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/*
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* If the concept has an ID, we're reindexing, so there's no need to
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* save parent concepts first (it's way too slow to do that)
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@ -392,25 +422,25 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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if (theConcept.getId() == null) {
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retVal += ensureParentsSaved(theConcept.getParents());
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}
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if (theConcept.getId() == null || theConcept.getIndexStatus() == null) {
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retVal++;
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theConcept.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
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myConceptDao.save(theConcept);
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}
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ourLog.trace("Saved {} and got PID {}", theConcept.getCode(), theConcept.getId());
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return retVal;
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}
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private void saveConceptLink(TermConceptParentChildLink next) {
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if (next.getId() == null) {
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myConceptParentChildLinkDao.save(next);
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}
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}
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@Scheduled(fixedRate=5000)
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@Transactional(propagation=Propagation.REQUIRED)
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@Scheduled(fixedRate = 5000)
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@Transactional(propagation = Propagation.NOT_SUPPORTED)
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@Override
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public synchronized void saveDeferred() {
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if (!myProcessDeferred) {
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@ -419,46 +449,18 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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processReindexing();
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return;
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}
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int codeCount = 0, relCount = 0;
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StopWatch stopwatch = new StopWatch();
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int count = Math.min(myDaoConfig.getDeferIndexingForCodesystemsOfSize(), myConceptsToSaveLater.size());
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ourLog.info("Saving {} deferred concepts...", count);
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while (codeCount < count && myConceptsToSaveLater.size() > 0) {
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TermConcept next = myConceptsToSaveLater.remove(0);
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codeCount += saveConcept(next);
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}
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if (codeCount > 0) {
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ourLog.info("Saved {} deferred concepts ({} codes remain and {} relationships remain) in {}ms ({}ms / code)", new Object[] {codeCount, myConceptsToSaveLater.size(), myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(codeCount)});
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}
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if (codeCount == 0) {
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count = Math.min(myDaoConfig.getDeferIndexingForCodesystemsOfSize(), myConceptLinksToSaveLater.size());
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ourLog.info("Saving {} deferred concept relationships...", count);
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while (relCount < count && myConceptLinksToSaveLater.size() > 0) {
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TermConceptParentChildLink next = myConceptLinksToSaveLater.remove(0);
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if (myConceptDao.findOne(next.getChild().getId()) == null || myConceptDao.findOne(next.getParent().getId()) == null) {
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ourLog.warn("Not inserting link from child {} to parent {} because it appears to have been deleted", next.getParent().getCode(), next.getChild().getCode());
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continue;
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}
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saveConceptLink(next);
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relCount++;
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TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
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tt.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
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tt.execute(new TransactionCallbackWithoutResult() {
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@Override
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protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
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processDeferredConcepts();
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}
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}
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if (relCount > 0) {
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ourLog.info("Saved {} deferred relationships ({} remain) in {}ms ({}ms / code)", new Object[] {relCount, myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(codeCount)});
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}
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if ((myConceptsToSaveLater.size() + myConceptLinksToSaveLater.size()) == 0) {
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ourLog.info("All deferred concepts and relationships have now been synchronized to the database");
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}
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});
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}
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@Override
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public void setProcessDeferred(boolean theProcessDeferred) {
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myProcessDeferred = theProcessDeferred;
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@ -487,7 +489,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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}
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ourLog.info("Flushing...");
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myConceptParentChildLinkDao.flush();
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myConceptDao.flush();
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@ -540,7 +542,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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}
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ourLog.info("Saving {} concepts...", totalCodeCount);
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IdentityHashMap<TermConcept, Object> conceptsStack2 = new IdentityHashMap<TermConcept, Object>();
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for (TermConcept next : theCodeSystemVersion.getConcepts()) {
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persistChildren(next, codeSystemVersion, conceptsStack2, totalCodeCount);
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@ -552,7 +554,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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myConceptParentChildLinkDao.flush();
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ourLog.info("Done deleting old code system versions");
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if (myConceptsToSaveLater.size() > 0 || myConceptLinksToSaveLater.size() > 0) {
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ourLog.info("Note that some concept saving was deferred - still have {} concepts and {} relationships", myConceptsToSaveLater.size(), myConceptLinksToSaveLater.size());
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}
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@ -563,7 +565,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
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TermCodeSystem cs = getCodeSystem(theSystem);
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return cs != null;
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}
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|
||||
|
||||
private ArrayList<VersionIndependentConcept> toVersionIndependentConcepts(String theSystem, Set<TermConcept> codes) {
|
||||
ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>(codes.size());
|
||||
for (TermConcept next : codes) {
|
||||
|
|
@ -582,7 +584,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
|
|||
throw new InvalidRequestException("CodeSystem contains circular reference around code " + theConcept.getCode());
|
||||
}
|
||||
theConceptsStack.add(theConcept.getCode());
|
||||
|
||||
|
||||
int retVal = 0;
|
||||
if (theAllConcepts.put(theConcept, theAllConcepts) == null) {
|
||||
if (theAllConcepts.size() % 1000 == 0) {
|
||||
|
|
|
|||
Loading…
Reference in New Issue