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hapi-fhir
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Improve the loinc uploader

This commit is contained in:
James Agnew 2018-04-06 17:34:52 -04:00
parent 26710f7608
commit 260aa9e9fa
1 changed files with 35 additions and 23 deletions
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58
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
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@ -63,6 +63,7 @@ import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType; import javax.persistence.PersistenceContextType;
import java.util.*; import java.util.*;
import java.util.concurrent.TimeUnit; import java.util.concurrent.TimeUnit;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.isBlank; import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank; import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -535,6 +536,16 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
} }
} }
private void processDeferredConceptMaps() {
int count = Math.min(myDeferredConceptMaps.size(), 5);
for (ConceptMap nextConceptMap : new ArrayList<>(myDeferredConceptMaps.subList(0, count))) {
ourLog.info("Creating ConceptMap: {}", nextConceptMap.getId());
createOrUpdateConceptMap(nextConceptMap);
myDeferredConceptMaps.remove(nextConceptMap);
}
ourLog.info("Saved {} deferred ConceptMap resources, have {} remaining", count, myDeferredConceptMaps.size());
}
private void processDeferredConcepts() { private void processDeferredConcepts() {
int codeCount = 0, relCount = 0; int codeCount = 0, relCount = 0;
StopWatch stopwatch = new StopWatch(); StopWatch stopwatch = new StopWatch();
@ -577,6 +588,16 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
} }
} }
private void processDeferredValueSets() {
int count = Math.min(myDeferredValueSets.size(), 5);
for (ValueSet nextValueSet : new ArrayList<>(myDeferredValueSets.subList(0, count))) {
ourLog.info("Creating ValueSet: {}", nextValueSet.getId());
createOrUpdateValueSet(nextValueSet);
myDeferredValueSets.remove(nextValueSet);
}
ourLog.info("Saved {} deferred ValueSet resources, have {} remaining", count, myDeferredConceptMaps.size());
}
private void processReindexing() { private void processReindexing() {
if (System.currentTimeMillis() < myNextReindexPass && !ourForceSaveDeferredAlwaysForUnitTest) { if (System.currentTimeMillis() < myNextReindexPass && !ourForceSaveDeferredAlwaysForUnitTest) {
return; return;
@ -701,9 +722,9 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
TransactionTemplate tt = new TransactionTemplate(myTransactionMgr); TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
tt.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW); tt.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
tt.execute(t->{ tt.execute(t -> {
processDeferredConcepts(); processDeferredConcepts();
return null; return null;
}); });
if (myDeferredValueSets.size() > 0) { if (myDeferredValueSets.size() > 0) {
@ -721,26 +742,6 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
} }
private void processDeferredValueSets() {
int count = Math.min(myDeferredValueSets.size(), 5);
for (ValueSet nextValueSet : myDeferredValueSets.subList(0, count)) {
ourLog.info("Creating ValueSet: {}", nextValueSet.getId());
createOrUpdateValueSet(nextValueSet);
myDeferredValueSets.remove(nextValueSet);
}
ourLog.info("Saved {} deferred ValueSet resources, have {} remaining", count, myDeferredConceptMaps.size());
}
private void processDeferredConceptMaps() {
int count = Math.min(myDeferredConceptMaps.size(), 5);
for (ConceptMap nextConceptMap : myDeferredConceptMaps.subList(0, count)) {
ourLog.info("Creating ConceptMap: {}", nextConceptMap.getId());
createOrUpdateConceptMap(nextConceptMap);
myDeferredConceptMaps.remove(nextConceptMap);
}
ourLog.info("Saved {} deferred ConceptMap resources, have {} remaining", count, myDeferredConceptMaps.size());
}
@Override @Override
public void setProcessDeferred(boolean theProcessDeferred) { public void setProcessDeferred(boolean theProcessDeferred) {
myProcessDeferred = theProcessDeferred; myProcessDeferred = theProcessDeferred;
@ -757,6 +758,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
// Grab the existing versions so we can delete them later // Grab the existing versions so we can delete them later
List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResource(theCodeSystemResourcePid); List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResource(theCodeSystemResourcePid);
verifyNoDuplicates(theCodeSystemVersion.getConcepts(), new HashSet<String>());
/* /*
* For now we always delete old versions.. At some point it would be nice to allow configuration to keep old versions * For now we always delete old versions.. At some point it would be nice to allow configuration to keep old versions
*/ */
@ -908,6 +911,15 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
return retVal; return retVal;
} }
private void verifyNoDuplicates(Collection<TermConcept> theConcepts, Set<String> theCodes) {
for (TermConcept next : theConcepts) {
if (!theCodes.add(next.getCode())) {
throw new InvalidRequestException("Duplicate code " + next.getCode() + " found in codesystem after checking " + theCodes.size() + " codes");
}
verifyNoDuplicates(next.getChildren().stream().map(TermConceptParentChildLink::getChild).collect(Collectors.toList()), theCodes);
}
}
/** /**
* This method is present only for unit tests, do not call from client code * This method is present only for unit tests, do not call from client code
*/ */