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This commit is contained in:
ianmarshall 2020-09-04 09:25:35 -04:00
parent 019d08a064
commit 5b707f97a9
3 changed files with 76 additions and 137 deletions
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83
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSet.java
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@ -25,13 +25,10 @@ import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.hibernate.annotations.ColumnDefault;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@ -72,29 +69,11 @@ public class TermValueSet implements Serializable {
@Column(name = "VSNAME", nullable = true, length = MAX_NAME_LENGTH)
private String myName;
@OneToMany(mappedBy = "myValueSet", fetch = FetchType.LAZY)
private List<TermValueSetConcept> myConcepts;
@Column(name = "TOTAL_CONCEPTS", nullable = false)
@ColumnDefault("0")
private Long myTotalConcepts;
@Column(name = "TOTAL_CONCEPT_DESIGNATIONS", nullable = false)
@ColumnDefault("0")
private Long myTotalConceptDesignations;
@Enumerated(EnumType.STRING)
@Column(name = "EXPANSION_STATUS", nullable = false, length = MAX_EXPANSION_STATUS_LENGTH)
private TermValueSetPreExpansionStatusEnum myExpansionStatus;
@Transient
private transient Integer myHashCode;
public TermValueSet() {
super();
myExpansionStatus = TermValueSetPreExpansionStatusEnum.NOT_EXPANDED;
myTotalConcepts = 0L;
myTotalConceptDesignations = 0L;
}
public Long getId() {
@ -140,64 +119,6 @@ public class TermValueSet implements Serializable {
return this;
}
public List<TermValueSetConcept> getConcepts() {
if (myConcepts == null) {
myConcepts = new ArrayList<>();
}
return myConcepts;
}
public Long getTotalConcepts() {
return myTotalConcepts;
}
public TermValueSet setTotalConcepts(Long theTotalConcepts) {
myTotalConcepts = theTotalConcepts;
return this;
}
public TermValueSet decrementTotalConcepts() {
if (myTotalConcepts > 0) {
myTotalConcepts--;
}
return this;
}
public TermValueSet incrementTotalConcepts() {
myTotalConcepts++;
return this;
}
public Long getTotalConceptDesignations() {
return myTotalConceptDesignations;
}
public TermValueSet setTotalConceptDesignations(Long theTotalConceptDesignations) {
myTotalConceptDesignations = theTotalConceptDesignations;
return this;
}
public TermValueSet decrementTotalConceptDesignations() {
if (myTotalConceptDesignations > 0) {
myTotalConceptDesignations--;
}
return this;
}
public TermValueSet incrementTotalConceptDesignations() {
myTotalConceptDesignations++;
return this;
}
public TermValueSetPreExpansionStatusEnum getExpansionStatus() {
return myExpansionStatus;
}
public void setExpansionStatus(TermValueSetPreExpansionStatusEnum theExpansionStatus) {
myExpansionStatus = theExpansionStatus;
}
@Override
public boolean equals(Object theO) {
if (this == theO) return true;
@ -227,10 +148,6 @@ public class TermValueSet implements Serializable {
.append(myResource != null ? ("myResource=" + myResource.toString()) : ("myResource=(null)"))
.append("myResourcePid", myResourcePid)
.append("myName", myName)
.append(myConcepts != null ? ("myConcepts - size=" + myConcepts.size()) : ("myConcepts=(null)"))
.append("myTotalConcepts", myTotalConcepts)
.append("myTotalConceptDesignations", myTotalConceptDesignations)
.append("myExpansionStatus", myExpansionStatus)
.toString();
}
}

76
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
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@ -45,6 +45,7 @@ import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDesignationDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptViewDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetVersionDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
@ -62,6 +63,7 @@ import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
import ca.uhn.fhir.jpa.entity.TermValueSetConceptView;
import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
import ca.uhn.fhir.jpa.entity.TermValueSetVersion;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.sched.HapiJob;
import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
@ -205,6 +207,8 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
@Autowired
protected ITermValueSetDao myValueSetDao;
@Autowired
protected ITermValueSetVersionDao myValueSetVersionDao;
@Autowired
protected ITermValueSetConceptDao myValueSetConceptDao;
@Autowired
protected ITermValueSetConceptDesignationDao myValueSetConceptDesignationDao;
@ -425,10 +429,17 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
}
TermValueSet termValueSet = optionalTermValueSet.get();
TermValueSetVersion termValueSetVersion;
String valueSetVersion = theValueSetToExpand.getVersion();
if (valueSetVersion != null) {
termValueSetVersion = myValueSetVersionDao.findByValueSetPidAndVersion(termValueSet.getId(),theValueSetToExpand.getVersion());
} else {
termValueSetVersion = myValueSetVersionDao.findByValueSetPidAndNullVersion(termValueSet.getId());
}
if (termValueSet.getExpansionStatus() != TermValueSetPreExpansionStatusEnum.EXPANDED) {
if (termValueSetVersion.getExpansionStatus() != TermValueSetPreExpansionStatusEnum.EXPANDED) {
ourLog.warn("{} is present in terminology tables but not ready for persistence-backed invocation of operation $expand. Will perform in-memory expansion without parameters. Current status: {} | {}",
getValueSetInfo(theValueSetToExpand), termValueSet.getExpansionStatus().name(), termValueSet.getExpansionStatus().getDescription());
getValueSetInfo(theValueSetToExpand), termValueSetVersion.getExpansionStatus().name(), termValueSetVersion.getExpansionStatus().getDescription());
return expandValueSetInMemory(theExpansionOptions, theValueSetToExpand, null); // In-memory expansion.
}
@ -439,7 +450,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
ValueSetExpansionOptions expansionOptions = provideExpansionOptions(theExpansionOptions);
int offset = expansionOptions.getOffset();
int count = expansionOptions.getCount();
populateExpansionComponent(expansionComponent, termValueSet, offset, count);
populateExpansionComponent(expansionComponent, termValueSetVersion, offset, count, termValueSet.getUrl());
ValueSet valueSet = new ValueSet();
valueSet.setStatus(Enumerations.PublicationStatus.ACTIVE);
@ -448,8 +459,8 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
return valueSet;
}
private void populateExpansionComponent(ValueSet.ValueSetExpansionComponent theExpansionComponent, TermValueSet theTermValueSet, int theOffset, int theCount) {
int total = theTermValueSet.getTotalConcepts().intValue();
private void populateExpansionComponent(ValueSet.ValueSetExpansionComponent theExpansionComponent, TermValueSetVersion theTermValueSetVersion, int theOffset, int theCount, String theValueSetUrl) {
int total = theTermValueSetVersion.getTotalConcepts().intValue();
theExpansionComponent.setTotal(total);
theExpansionComponent.setOffset(theOffset);
theExpansionComponent.addParameter().setName("offset").setValue(new IntegerType(theOffset));
@ -459,17 +470,17 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
return;
}
expandConcepts(theExpansionComponent, theTermValueSet, theOffset, theCount);
expandConcepts(theExpansionComponent, theTermValueSetVersion, theOffset, theCount, theValueSetUrl);
}
private void expandConcepts(ValueSet.ValueSetExpansionComponent theExpansionComponent, TermValueSet theTermValueSet, int theOffset, int theCount) {
private void expandConcepts(ValueSet.ValueSetExpansionComponent theExpansionComponent, TermValueSetVersion theTermValueSetVersion, int theOffset, int theCount, String theValueSetUrl) {
int conceptsExpanded = 0;
int designationsExpanded = 0;
int toIndex = theOffset + theCount;
Collection<TermValueSetConceptView> conceptViews = myTermValueSetConceptViewDao.findByTermValueSetId(theOffset, toIndex, theTermValueSet.getId());
Collection<TermValueSetConceptView> conceptViews = myTermValueSetConceptViewDao.findByTermValueSetId(theOffset, toIndex, theTermValueSetVersion.getId());
if (conceptViews.isEmpty()) {
logConceptsExpanded("No concepts to expand. ", theTermValueSet, conceptsExpanded);
logConceptsExpanded("No concepts to expand. ", theValueSetUrl, conceptsExpanded);
return;
}
@ -500,28 +511,28 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
designationComponent.setValue(conceptView.getDesignationVal());
if (++designationsExpanded % 250 == 0) {
logDesignationsExpanded("Expansion of designations in progress. ", theTermValueSet, designationsExpanded);
logDesignationsExpanded("Expansion of designations in progress. ", theValueSetUrl, designationsExpanded);
}
}
if (++conceptsExpanded % 250 == 0) {
logConceptsExpanded("Expansion of concepts in progress. ", theTermValueSet, conceptsExpanded);
logConceptsExpanded("Expansion of concepts in progress. ", theValueSetUrl, conceptsExpanded);
}
}
logDesignationsExpanded("Finished expanding designations. ", theTermValueSet, designationsExpanded);
logConceptsExpanded("Finished expanding concepts. ", theTermValueSet, conceptsExpanded);
logDesignationsExpanded("Finished expanding designations. ", theValueSetUrl, designationsExpanded);
logConceptsExpanded("Finished expanding concepts. ", theValueSetUrl, conceptsExpanded);
}
private void logConceptsExpanded(String theLogDescriptionPrefix, TermValueSet theTermValueSet, int theConceptsExpanded) {
private void logConceptsExpanded(String theLogDescriptionPrefix, String theValueSetUrl, int theConceptsExpanded) {
if (theConceptsExpanded > 0) {
ourLog.debug("{}Have expanded {} concepts in ValueSet[{}]", theLogDescriptionPrefix, theConceptsExpanded, theTermValueSet.getUrl());
ourLog.debug("{}Have expanded {} concepts in ValueSet[{}]", theLogDescriptionPrefix, theConceptsExpanded, theValueSetUrl);
}
}
private void logDesignationsExpanded(String theLogDescriptionPrefix, TermValueSet theTermValueSet, int theDesignationsExpanded) {
private void logDesignationsExpanded(String theLogDescriptionPrefix, String theValueSetUrl, int theDesignationsExpanded) {
if (theDesignationsExpanded > 0) {
ourLog.debug("{}Have expanded {} designations in ValueSet[{}]", theLogDescriptionPrefix, theDesignationsExpanded, theTermValueSet.getUrl());
ourLog.debug("{}Have expanded {} designations in ValueSet[{}]", theLogDescriptionPrefix, theDesignationsExpanded, theValueSetUrl);
}
}
@ -1262,10 +1273,17 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
}
TermValueSet termValueSet = optionalTermValueSet.get();
TermValueSetVersion termValueSetVersion;
String valueSetVersion = theValueSet.getVersion();
if (valueSetVersion != null) {
termValueSetVersion = myValueSetVersionDao.findByValueSetPidAndVersion(termValueSet.getId(), valueSetVersion);
} else {
termValueSetVersion = myValueSetVersionDao.findByValueSetPidAndNullVersion(termValueSet.getId());
}
if (termValueSet.getExpansionStatus() != TermValueSetPreExpansionStatusEnum.EXPANDED) {
if (termValueSetVersion.getExpansionStatus() != TermValueSetPreExpansionStatusEnum.EXPANDED) {
ourLog.warn("{} is present in terminology tables but not ready for persistence-backed invocation of operation $validation-code. Will perform in-memory code validation. Current status: {} | {}",
getValueSetInfo(theValueSet), termValueSet.getExpansionStatus().name(), termValueSet.getExpansionStatus().getDescription());
getValueSetInfo(theValueSet), termValueSetVersion.getExpansionStatus().name(), termValueSetVersion.getExpansionStatus().getDescription());
return false;
}
@ -1680,15 +1698,15 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
while (true) {
StopWatch sw = new StopWatch();
TermValueSet valueSetToExpand = txTemplate.execute(t -> {
Optional<TermValueSet> optionalTermValueSet = getNextTermValueSetNotExpanded();
if (!optionalTermValueSet.isPresent()) {
TermValueSetVersion valueSetToExpand = txTemplate.execute(t -> {
Optional<TermValueSetVersion> optionalTermValueSetVersion = getNextTermValueSetNotExpanded();
if (!optionalTermValueSetVersion.isPresent()) {
return null;
}
TermValueSet termValueSet = optionalTermValueSet.get();
termValueSet.setExpansionStatus(TermValueSetPreExpansionStatusEnum.EXPANSION_IN_PROGRESS);
return myValueSetDao.saveAndFlush(termValueSet);
TermValueSetVersion termValueSetVersion = optionalTermValueSetVersion.get();
termValueSetVersion.setExpansionStatus(TermValueSetPreExpansionStatusEnum.EXPANSION_IN_PROGRESS);
return myValueSetVersionDao.saveAndFlush(termValueSetVersion);
});
if (valueSetToExpand == null) {
return;
@ -1718,7 +1736,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
ourLog.error("Failed to pre-expand ValueSet: " + e.getMessage(), e);
txTemplate.execute(t -> {
valueSetToExpand.setExpansionStatus(TermValueSetPreExpansionStatusEnum.FAILED_TO_EXPAND);
myValueSetDao.saveAndFlush(valueSetToExpand);
myValueSetVersionDao.saveAndFlush(valueSetToExpand);
return null;
});
}
@ -1783,9 +1801,9 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
protected abstract ValueSet getValueSetFromResourceTable(ResourceTable theResourceTable);
private Optional<TermValueSet> getNextTermValueSetNotExpanded() {
Optional<TermValueSet> retVal = Optional.empty();
Slice<TermValueSet> page = myValueSetDao.findByExpansionStatus(PageRequest.of(0, 1), TermValueSetPreExpansionStatusEnum.NOT_EXPANDED);
private Optional<TermValueSetVersion> getNextTermValueSetNotExpanded() {
Optional<TermValueSetVersion> retVal = Optional.empty();
Slice<TermValueSetVersion> page = myValueSetVersionDao.findByExpansionStatus(PageRequest.of(0, 1), TermValueSetPreExpansionStatusEnum.NOT_EXPANDED);
if (!page.getContent().isEmpty()) {
retVal = Optional.of(page.getContent().get(0));

54
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulator.java
View File

@ -23,10 +23,12 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDesignationDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetVersionDao;
import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
import ca.uhn.fhir.jpa.entity.TermValueSetConceptDesignation;
import ca.uhn.fhir.jpa.entity.TermValueSetVersion;
import ca.uhn.fhir.util.ValidateUtil;
import javax.annotation.Nonnull;
@ -41,17 +43,18 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValueSetConceptAccumulator.class);
private TermValueSet myTermValueSet;
private ITermValueSetDao myValueSetDao;
private ITermValueSetConceptDao myValueSetConceptDao;
private ITermValueSetConceptDesignationDao myValueSetConceptDesignationDao;
private TermValueSetVersion myTermValueSetVersion;
final private ITermValueSetVersionDao myValueSetVersionDao;
final private ITermValueSetDao myValueSetDao;
final private ITermValueSetConceptDao myValueSetConceptDao;
final private ITermValueSetConceptDesignationDao myValueSetConceptDesignationDao;
private int myConceptsSaved;
private int myDesignationsSaved;
private int myConceptsExcluded;
private int myCount;
public ValueSetConceptAccumulator(@Nonnull TermValueSet theTermValueSet, @Nonnull ITermValueSetDao theValueSetDao, @Nonnull ITermValueSetConceptDao theValueSetConceptDao, @Nonnull ITermValueSetConceptDesignationDao theValueSetConceptDesignationDao) {
myTermValueSet = theTermValueSet;
public ValueSetConceptAccumulator(@Nonnull TermValueSetVersion theTermValueSetVersion, @Nonnull ITermValueSetVersionDao theValueSetVersionDao, @Nonnull ITermValueSetDao theValueSetDao, @Nonnull ITermValueSetConceptDao theValueSetConceptDao, @Nonnull ITermValueSetConceptDesignationDao theValueSetConceptDesignationDao) {
myTermValueSetVersion = theTermValueSetVersion;
myValueSetVersionDao = theValueSetVersionDao;
myValueSetDao = theValueSetDao;
myValueSetConceptDao = theValueSetConceptDao;
myValueSetConceptDesignationDao = theValueSetConceptDesignationDao;
@ -88,23 +91,23 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
}
// Get existing entity so it can be deleted.
Optional<TermValueSetConcept> optionalConcept = myValueSetConceptDao.findByTermValueSetIdSystemAndCode(myTermValueSet.getId(), theSystem, theCode);
Optional<TermValueSetConcept> optionalConcept = myValueSetConceptDao.findByTermValueSetIdSystemAndCode(myTermValueSetVersion.getId(), theSystem, theCode);
if (optionalConcept.isPresent()) {
TermValueSetConcept concept = optionalConcept.get();
ourLog.debug("Excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
ourLog.debug("Excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSetVersion.getValueSet().getUrl());
for (TermValueSetConceptDesignation designation : concept.getDesignations()) {
myValueSetConceptDesignationDao.deleteById(designation.getId());
myTermValueSet.decrementTotalConceptDesignations();
myTermValueSetVersion.decrementTotalConceptDesignations();
}
myValueSetConceptDao.deleteById(concept.getId());
myTermValueSet.decrementTotalConcepts();
myValueSetDao.save(myTermValueSet);
ourLog.debug("Done excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
myTermValueSetVersion.decrementTotalConcepts();
myValueSetVersionDao.save(myTermValueSetVersion);
ourLog.debug("Done excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSetVersion.getValueSet().getUrl());
if (++myConceptsExcluded % 250 == 0) {
ourLog.info("Have excluded {} concepts from ValueSet[{}]", myConceptsExcluded, myTermValueSet.getUrl());
ourLog.info("Have excluded {} concepts from ValueSet[{}]", myConceptsExcluded, myTermValueSetVersion.getValueSet().getUrl());
}
}
}
@ -115,7 +118,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
myTermValueSetVersion = myValueSetVersionDao.findById(myTermValueSetVersion.getId()).get();
TermValueSetConcept concept = new TermValueSetConcept();
concept.setValueSet(myTermValueSet);
concept.setValueSet(myTermValueSetVersion.getValueSet());
concept.setOrder(myConceptsSaved);
concept.setSystem(theSystem);
concept.setCode(theCode);
@ -123,21 +126,23 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
concept.setDisplay(theDisplay);
}
myValueSetConceptDao.save(concept);
myValueSetDao.save(myTermValueSet.incrementTotalConcepts());
myTermValueSetVersion.incrementTotalConcepts();
myValueSetVersionDao.save(myTermValueSetVersion);
if (++myConceptsSaved % 250 == 0) {
ourLog.info("Have pre-expanded {} concepts in ValueSet[{}]", myConceptsSaved, myTermValueSet.getUrl());
ourLog.info("Have pre-expanded {} concepts in ValueSet[{}]", myConceptsSaved, myTermValueSetVersion.getValueSet().getUrl());
}
return concept;
}
private TermValueSetConceptDesignation saveConceptDesignation(TermValueSetConcept theConcept, TermConceptDesignation theDesignation) {
private void saveConceptDesignation(TermValueSetConcept theConcept, TermConceptDesignation theDesignation) {
ValidateUtil.isNotBlankOrThrowInvalidRequest(theDesignation.getValue(), "ValueSet contains a concept designation with no value");
TermValueSetConceptDesignation designation = new TermValueSetConceptDesignation();
designation.setConcept(theConcept);
designation.setValueSet(myTermValueSet);
myTermValueSetVersion = myValueSetVersionDao.findById(myTermValueSetVersion.getId()).get();
designation.setValueSet(myTermValueSetVersion.getValueSet());
designation.setLanguage(theDesignation.getLanguage());
if (isNoneBlank(theDesignation.getUseSystem(), theDesignation.getUseCode())) {
designation.setUseSystem(theDesignation.getUseSystem());
@ -148,13 +153,12 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
}
designation.setValue(theDesignation.getValue());
myValueSetConceptDesignationDao.save(designation);
myValueSetDao.save(myTermValueSet.incrementTotalConceptDesignations());
myValueSetVersionDao.save(myTermValueSetVersion.incrementTotalConceptDesignations());
if (++myDesignationsSaved % 250 == 0) {
ourLog.debug("Have pre-expanded {} designations for Concept[{}|{}] in ValueSet[{}]", myDesignationsSaved, theConcept.getSystem(), theConcept.getCode(), myTermValueSet.getUrl());
ourLog.debug("Have pre-expanded {} designations for Concept[{}|{}] in ValueSet[{}]", myDesignationsSaved, theConcept.getSystem(), theConcept.getCode(), myTermValueSetVersion.getValueSet().getUrl());
}
return designation;
}
public Boolean removeGapsFromConceptOrder() {
@ -162,13 +166,13 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
return false;
}
ourLog.info("Removing gaps from concept order for ValueSet[{}]", myTermValueSet.getUrl());
ourLog.info("Removing gaps from concept order for ValueSet[{}]", myTermValueSetVersion.getValueSet().getUrl());
int order = 0;
List<Long> conceptIds = myValueSetConceptDao.findIdsByTermValueSetId(myTermValueSet.getId());
List<Long> conceptIds = myValueSetConceptDao.findIdsByTermValueSetId(myTermValueSetVersion.getId());
for (Long conceptId : conceptIds) {
myValueSetConceptDao.updateOrderById(conceptId, order++);
}
ourLog.info("Have removed gaps from concept order for {} concepts in ValueSet[{}]", conceptIds.size(), myTermValueSet.getUrl());
ourLog.info("Have removed gaps from concept order for {} concepts in ValueSet[{}]", conceptIds.size(), myTermValueSetVersion.getValueSet().getUrl());
return true;
}