Merge pull request #1467 from jamesagnew/dm-add-pre-fetch-for-expansion-of-large-valuesets
Performance enhancements for large ValueSet expansion.
This commit is contained in:
commit
8c6fd9f2d9
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@ -40,8 +40,8 @@ public interface ITermValueSetConceptDao extends JpaRepository<TermValueSetConce
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@Modifying
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void deleteByTermValueSetId(@Param("pid") Long theValueSetId);
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@Query("SELECT vsc from TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid")
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Slice<TermValueSetConcept> findByTermValueSetId(Pageable thePage, @Param("pid") Long theValueSetId);
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@Query("SELECT vsc from TermValueSetConcept vsc LEFT OUTER JOIN FETCH vsc.myDesignations WHERE vsc.myValueSet.myId = :pid")
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Slice<TermValueSetConcept> findByTermValueSetIdAndPreFetchDesignations(Pageable thePage, @Param("pid") Long theValueSetId);
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@Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid AND vsc.mySystem = :system_url AND vsc.myCode = :codeval")
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Optional<TermValueSetConcept> findByTermValueSetIdSystemAndCode(@Param("pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode);
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@ -26,6 +26,7 @@ import org.apache.commons.lang3.builder.EqualsBuilder;
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import org.apache.commons.lang3.builder.HashCodeBuilder;
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import org.apache.commons.lang3.builder.ToStringBuilder;
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import org.apache.commons.lang3.builder.ToStringStyle;
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import org.hibernate.annotations.ColumnDefault;
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import javax.annotation.Nonnull;
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import javax.persistence.*;
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@ -69,6 +70,14 @@ public class TermValueSet implements Serializable {
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@OneToMany(mappedBy = "myValueSet")
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private List<TermValueSetConcept> myConcepts;
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@Column(name = "TOTAL_CONCEPTS", nullable = false)
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@ColumnDefault("0")
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private Long myTotalConcepts;
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@Column(name = "TOTAL_CONCEPT_DESIGNATIONS", nullable = false)
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@ColumnDefault("0")
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private Long myTotalConceptDesignations;
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@Enumerated(EnumType.STRING)
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@Column(name = "EXPANSION_STATUS", nullable = false, length = MAX_EXPANSION_STATUS_LENGTH)
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private TermValueSetPreExpansionStatusEnum myExpansionStatus;
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@ -76,6 +85,8 @@ public class TermValueSet implements Serializable {
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public TermValueSet() {
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super();
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myExpansionStatus = TermValueSetPreExpansionStatusEnum.NOT_EXPANDED;
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myTotalConcepts = 0L;
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myTotalConceptDesignations = 0L;
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}
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public Long getId() {
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@ -120,6 +131,48 @@ public class TermValueSet implements Serializable {
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return myConcepts;
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}
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public Long getTotalConcepts() {
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return myTotalConcepts;
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}
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public TermValueSet setTotalConcepts(Long theTotalConcepts) {
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myTotalConcepts = theTotalConcepts;
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return this;
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}
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public TermValueSet decrementTotalConcepts() {
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if (myTotalConcepts > 0) {
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myTotalConcepts--;
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}
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return this;
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}
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public TermValueSet incrementTotalConcepts() {
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myTotalConcepts++;
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return this;
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}
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public Long getTotalConceptDesignations() {
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return myTotalConceptDesignations;
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}
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public TermValueSet setTotalConceptDesignations(Long theTotalConceptDesignations) {
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myTotalConceptDesignations = theTotalConceptDesignations;
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return this;
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}
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public TermValueSet decrementTotalConceptDesignations() {
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if (myTotalConceptDesignations > 0) {
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myTotalConceptDesignations--;
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}
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return this;
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}
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public TermValueSet incrementTotalConceptDesignations() {
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myTotalConceptDesignations++;
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return this;
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}
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public TermValueSetPreExpansionStatusEnum getExpansionStatus() {
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return myExpansionStatus;
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}
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@ -157,6 +210,8 @@ public class TermValueSet implements Serializable {
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.append("myResourcePid", myResourcePid)
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.append("myName", myName)
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.append(myConcepts != null ? ("myConcepts - size=" + myConcepts.size()) : ("myConcepts=(null)"))
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.append("myTotalConcepts", myTotalConcepts)
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.append("myTotalConceptDesignations", myTotalConceptDesignations)
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.append("myExpansionStatus", myExpansionStatus)
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.toString();
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}
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@ -28,6 +28,7 @@ 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.model.entity.ResourceTable;
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import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
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import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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@ -372,13 +373,6 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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myConceptMapDao.deleteTermConceptMapById(existingTermConceptMap.getId());
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ourLog.info("Done deleting existing TermConceptMap[{}] and its children.", existingTermConceptMap.getId());
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ourLog.info("Flushing...");
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myConceptMapGroupElementTargetDao.flush();
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myConceptMapGroupElementDao.flush();
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myConceptMapGroupDao.flush();
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myConceptMapDao.flush();
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ourLog.info("Done flushing.");
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}
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}
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@ -400,12 +394,6 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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myValueSetConceptDao.deleteByTermValueSetId(existingTermValueSet.getId());
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myValueSetDao.deleteByTermValueSetId(existingTermValueSet.getId());
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ourLog.info("Done deleting existing TermValueSet[{}] and its children.", existingTermValueSet.getId());
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ourLog.info("Flushing...");
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myValueSetConceptDesignationDao.flush();
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myValueSetConceptDao.flush();
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myValueSetDao.flush();
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ourLog.info("Done flushing.");
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}
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}
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@ -524,7 +512,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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}
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private void populateExpansionComponent(ValueSet.ValueSetExpansionComponent theExpansionComponent, TermValueSet theTermValueSet, int theOffset, int theCount) {
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int total = myValueSetConceptDao.countByTermValueSetId(theTermValueSet.getId());
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int total = theTermValueSet.getTotalConcepts().intValue();
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theExpansionComponent.setTotal(total);
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theExpansionComponent.setOffset(theOffset);
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theExpansionComponent.addParameter().setName("offset").setValue(new IntegerType(theOffset));
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@ -539,72 +527,58 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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private void expandConcepts(ValueSet.ValueSetExpansionComponent theExpansionComponent, TermValueSet theTermValueSet, int theOffset, int theCount) {
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int conceptsExpanded = 0;
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for (int i = theOffset; i < (theOffset + theCount); i++) {
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final int page = i;
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Supplier<Slice<TermValueSetConcept>> loader = () -> myValueSetConceptDao.findByTermValueSetId(PageRequest.of(page, 1), theTermValueSet.getId());
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int toIndex = theOffset + theCount;
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Slice<TermValueSetConcept> slice = myValueSetConceptDao.findByTermValueSetIdAndPreFetchDesignations(SearchCoordinatorSvcImpl.toPage(theOffset, toIndex), theTermValueSet.getId());
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if (!slice.hasContent()) {
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logConceptsExpanded(theTermValueSet, conceptsExpanded);
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return;
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}
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Slice<TermValueSetConcept> slice = loader.get();
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if (!slice.hasContent()) {
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break;
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}
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for (TermValueSetConcept concept : slice.getContent()) {
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ValueSet.ValueSetExpansionContainsComponent containsComponent = theExpansionComponent.addContains();
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containsComponent.setSystem(concept.getSystem());
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containsComponent.setCode(concept.getCode());
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containsComponent.setDisplay(concept.getDisplay());
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for (TermValueSetConcept concept : slice.getContent()) {
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ValueSet.ValueSetExpansionContainsComponent containsComponent = theExpansionComponent.addContains();
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containsComponent.setSystem(concept.getSystem());
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containsComponent.setCode(concept.getCode());
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containsComponent.setDisplay(concept.getDisplay());
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// TODO: DM 2019-08-17 - Implement includeDesignations parameter for $expand operation to make this optional.
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expandDesignations(theTermValueSet, concept, containsComponent);
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// TODO: DM 2019-08-17 - Implement includeDesignations parameter for $expand operation to make this optional.
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expandDesignations(theTermValueSet, concept, containsComponent);
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if (++conceptsExpanded % 250 == 0) {
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ourLog.info("Have expanded {} concepts in ValueSet[{}]", conceptsExpanded, theTermValueSet.getUrl());
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}
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}
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if (!slice.hasNext()) {
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break;
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if (++conceptsExpanded % 250 == 0) {
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logConceptsExpanded(theTermValueSet, conceptsExpanded);
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}
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}
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if (conceptsExpanded > 0) {
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ourLog.info("Have expanded {} concepts in ValueSet[{}]", conceptsExpanded, theTermValueSet.getUrl());
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logConceptsExpanded(theTermValueSet, conceptsExpanded);
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}
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private void logConceptsExpanded(TermValueSet theTermValueSet, int theConceptsExpanded) {
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if (theConceptsExpanded > 0) {
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ourLog.info("Have expanded {} concepts in ValueSet[{}]", theConceptsExpanded, theTermValueSet.getUrl());
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}
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}
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private void expandDesignations(TermValueSet theValueSet, TermValueSetConcept theConcept, ValueSet.ValueSetExpansionContainsComponent theContainsComponent) {
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int designationsExpanded = 0;
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int index = 0;
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while (true) {
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final int page = index++;
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Supplier<Slice<TermValueSetConceptDesignation>> loader = () -> myValueSetConceptDesignationDao.findByTermValueSetConceptId(PageRequest.of(page, 1000), theConcept.getId());
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for (TermValueSetConceptDesignation designation : theConcept.getDesignations()) {
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ValueSet.ConceptReferenceDesignationComponent designationComponent = theContainsComponent.addDesignation();
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designationComponent.setLanguage(designation.getLanguage());
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designationComponent.setUse(new Coding(
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designation.getUseSystem(),
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designation.getUseCode(),
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designation.getUseDisplay()));
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designationComponent.setValue(designation.getValue());
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Slice<TermValueSetConceptDesignation> slice = loader.get();
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if (!slice.hasContent()) {
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break;
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}
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for (TermValueSetConceptDesignation designation : slice.getContent()) {
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ValueSet.ConceptReferenceDesignationComponent designationComponent = theContainsComponent.addDesignation();
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designationComponent.setLanguage(designation.getLanguage());
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designationComponent.setUse(new Coding(
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designation.getUseSystem(),
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designation.getUseCode(),
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designation.getUseDisplay()));
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designationComponent.setValue(designation.getValue());
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if (++designationsExpanded % 250 == 0) {
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ourLog.info("Have expanded {} designations for Concept[{}|{}] in ValueSet[{}]", designationsExpanded, theConcept.getSystem(), theConcept.getCode(), theValueSet.getUrl());
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}
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}
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if (!slice.hasNext()) {
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break;
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if (++designationsExpanded % 250 == 0) {
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logDesignationsExpanded(theValueSet, theConcept, designationsExpanded);
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}
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}
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if (designationsExpanded > 0) {
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ourLog.info("Have expanded {} designations for Concept[{}|{}] in ValueSet[{}]", designationsExpanded, theConcept.getSystem(), theConcept.getCode(), theValueSet.getUrl());
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logDesignationsExpanded(theValueSet, theConcept, designationsExpanded);
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}
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private void logDesignationsExpanded(TermValueSet theValueSet, TermValueSetConcept theConcept, int theDesignationsExpanded) {
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if (theDesignationsExpanded > 0) {
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ourLog.info("Have expanded {} designations for Concept[{}|{}] in ValueSet[{}]", theDesignationsExpanded, theConcept.getSystem(), theConcept.getCode(), theValueSet.getUrl());
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}
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}
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@ -1874,7 +1848,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
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TermValueSet refreshedValueSetToExpand = myValueSetDao.findById(valueSetToExpand.getId()).get();
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return getValueSetFromResourceTable(refreshedValueSetToExpand.getResource());
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});
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expandValueSet(valueSet, new ValueSetConceptAccumulator(valueSetToExpand, myValueSetConceptDao, myValueSetConceptDesignationDao));
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expandValueSet(valueSet, new ValueSetConceptAccumulator(valueSetToExpand, myValueSetDao, myValueSetConceptDao, myValueSetConceptDesignationDao));
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// We are done with this ValueSet.
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txTemplate.execute(t -> {
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@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.term;
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import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDao;
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import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDesignationDao;
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import ca.uhn.fhir.jpa.dao.data.ITermValueSetDao;
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import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
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import ca.uhn.fhir.jpa.entity.TermValueSet;
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import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
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@ -38,13 +39,15 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValueSetConceptAccumulator.class);
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private TermValueSet myTermValueSet;
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private ITermValueSetDao myValueSetDao;
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private ITermValueSetConceptDao myValueSetConceptDao;
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private ITermValueSetConceptDesignationDao myValueSetConceptDesignationDao;
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private int myConceptsSaved;
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private int myDesignationsSaved;
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public ValueSetConceptAccumulator(@Nonnull TermValueSet theTermValueSet, @Nonnull ITermValueSetConceptDao theValueSetConceptDao, @Nonnull ITermValueSetConceptDesignationDao theValueSetConceptDesignationDao) {
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public ValueSetConceptAccumulator(@Nonnull TermValueSet theTermValueSet, @Nonnull ITermValueSetDao theValueSetDao, @Nonnull ITermValueSetConceptDao theValueSetConceptDao, @Nonnull ITermValueSetConceptDesignationDao theValueSetConceptDesignationDao) {
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myTermValueSet = theTermValueSet;
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myValueSetDao = theValueSetDao;
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myValueSetConceptDao = theValueSetConceptDao;
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myValueSetConceptDesignationDao = theValueSetConceptDesignationDao;
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myConceptsSaved = 0;
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@ -79,14 +82,12 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
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ourLog.info("Excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
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for (TermValueSetConceptDesignation designation : concept.getDesignations()) {
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myValueSetConceptDesignationDao.deleteById(designation.getId());
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myTermValueSet.decrementTotalConceptDesignations();
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}
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myValueSetConceptDao.deleteById(concept.getId());
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myTermValueSet.decrementTotalConcepts();
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myValueSetDao.save(myTermValueSet);
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ourLog.info("Done excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
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ourLog.info("Flushing...");
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myValueSetConceptDesignationDao.flush();
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myValueSetConceptDao.flush();
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ourLog.info("Done flushing.");
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}
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}
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@ -102,6 +103,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
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concept.setDisplay(theDisplay);
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}
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myValueSetConceptDao.save(concept);
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myValueSetDao.save(myTermValueSet.incrementTotalConcepts());
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if (myConceptsSaved++ % 250 == 0) { // TODO: DM 2019-08-23 - This message never appears in the log. Fix it!
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ourLog.info("Have pre-expanded {} concepts in ValueSet[{}]", myConceptsSaved, myTermValueSet.getUrl());
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@ -126,6 +128,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
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}
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designation.setValue(theDesignation.getValue());
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myValueSetConceptDesignationDao.save(designation);
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myValueSetDao.save(myTermValueSet.incrementTotalConceptDesignations());
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if (myDesignationsSaved++ % 250 == 0) { // TODO: DM 2019-08-23 - This message never appears in the log. Fix it!
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ourLog.info("Have pre-expanded {} designations for Concept[{}|{}] in ValueSet[{}]", myDesignationsSaved, theConcept.getSystem(), theConcept.getCode(), myTermValueSet.getUrl());
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@ -312,6 +312,7 @@ public class SearchCoordinatorSvcImplTest {
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public void testGetPage() {
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Pageable page = SearchCoordinatorSvcImpl.toPage(50, 73);
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assertEquals(50, page.getOffset());
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assertEquals(23, page.getPageSize());
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}
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@Test
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@ -36,6 +36,7 @@ import java.util.Optional;
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import java.util.concurrent.atomic.AtomicInteger;
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import java.util.stream.Collectors;
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import static org.hamcrest.Matchers.empty;
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import static org.junit.Assert.*;
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import static org.mockito.ArgumentMatchers.*;
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import static org.mockito.Mockito.times;
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@ -643,9 +644,12 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
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ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
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ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
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Long termValueSetId = myTermValueSetDao.findByResourcePid(myExtensionalVsIdOnResourceTable).get().getId();
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TermValueSet termValueSet = myTermValueSetDao.findByResourcePid(myExtensionalVsIdOnResourceTable).get();
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Long termValueSetId = termValueSet.getId();
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assertEquals(3, myTermValueSetConceptDesignationDao.countByTermValueSetId(termValueSetId).intValue());
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assertEquals(3, termValueSet.getTotalConceptDesignations().intValue());
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assertEquals(24, myTermValueSetConceptDao.countByTermValueSetId(termValueSetId).intValue());
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assertEquals(24, termValueSet.getTotalConcepts().intValue());
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new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
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@Override
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@ -677,9 +681,12 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
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ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
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ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
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Long termValueSetId = myTermValueSetDao.findByResourcePid(myExtensionalVsIdOnResourceTable).get().getId();
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TermValueSet termValueSet = myTermValueSetDao.findByResourcePid(myExtensionalVsIdOnResourceTable).get();
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Long termValueSetId = termValueSet.getId();
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assertEquals(3, myTermValueSetConceptDesignationDao.countByTermValueSetId(termValueSetId).intValue());
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assertEquals(3, termValueSet.getTotalConceptDesignations().intValue());
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assertEquals(24, myTermValueSetConceptDao.countByTermValueSetId(termValueSetId).intValue());
|
||||
assertEquals(24, termValueSet.getTotalConcepts().intValue());
|
||||
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
|
@ -741,9 +748,17 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
|
|||
|
||||
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
|
||||
myCaptureQueriesListener.clear();
|
||||
|
||||
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
|
||||
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
|
||||
|
||||
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
|
||||
assertEquals(3, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
|
||||
assertThat(myCaptureQueriesListener.getUpdateQueriesForCurrentThread(), empty());
|
||||
assertThat(myCaptureQueriesListener.getInsertQueriesForCurrentThread(), empty());
|
||||
assertThat(myCaptureQueriesListener.getDeleteQueriesForCurrentThread(), empty());
|
||||
|
||||
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
|
||||
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), expandedValueSet.getExpansion().getOffset());
|
||||
assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
|
||||
|
|
|
@ -87,6 +87,12 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
|
|||
.addForeignKey("FK_TRM_VSCD_VS_PID")
|
||||
.toColumn("VALUESET_PID")
|
||||
.references("TRM_VALUESET", "PID");
|
||||
|
||||
// TermValueSet
|
||||
version.startSectionWithMessage("Processing table: TRM_VALUESET");
|
||||
Builder.BuilderWithTableName termValueSetTable = version.onTable("TRM_VALUESET");
|
||||
termValueSetTable.addColumn("TOTAL_CONCEPTS").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
|
||||
termValueSetTable.addColumn("TOTAL_CONCEPT_DESIGNATIONS").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
|
||||
}
|
||||
|
||||
protected void init400() {
|
||||
|
|
Loading…
Reference in New Issue