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Removing gaps from concept order when pre-expanding ValueSets.

This commit is contained in:
Diederik Muylwyk 2019-09-09 15:24:37 -04:00
parent 4fc0ad6f0a
commit c82c3a093f
4 changed files with 48 additions and 16 deletions
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7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetConceptDao.java
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@ -46,4 +46,11 @@ public interface ITermValueSetConceptDao extends JpaRepository<TermValueSetConce
@Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myResourcePid = :resource_pid AND vsc.mySystem = :system_url AND vsc.myCode = :codeval")
Optional<TermValueSetConcept> findByValueSetResourcePidSystemAndCode(@Param("resource_pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode);
@Query("SELECT vsc.myId FROM TermValueSetConcept vsc WHERE vsc.myValueSetPid = :pid ORDER BY vsc.myId")
List<Long> findIdsByTermValueSetId(@Param("pid") Long theValueSetId);
@Query("UPDATE TermValueSetConcept vsc SET vsc.myOrder = :order WHERE vsc.myId = :pid")
@Modifying
void updateOrderById(@Param("pid") Long theId, @Param("order") int theOrder);
}

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
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@ -607,10 +607,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
ourLog.debug("Handling includes");
for (ValueSet.ConceptSetComponent include : theValueSetToExpand.getCompose().getInclude()) {
for (int i = 0; ; i++) {
int finalI = i;
int queryIndex = i;
Boolean shouldContinue = myTxTemplate.execute(t -> {
boolean add = true;
return expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, include, add, theCodeCounter, finalI);
return expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, include, add, theCodeCounter, queryIndex);
});
if (!shouldContinue) {
break;
@ -622,10 +622,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
ourLog.debug("Handling excludes");
for (ValueSet.ConceptSetComponent exclude : theValueSetToExpand.getCompose().getExclude()) {
for (int i = 0; ; i++) {
int finalI = i;
int queryIndex = i;
Boolean shouldContinue = myTxTemplate.execute(t -> {
boolean add = false;
return expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, exclude, add, theCodeCounter, finalI);
return expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, exclude, add, theCodeCounter, queryIndex);
});
if (!shouldContinue) {
break;
@ -633,7 +633,9 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
}
// FIXME: DM 2019-09-06 - After handling excludes, we need to adjust TermValueSetConcept.myOrder to account for any gaps.
if (theValueSetCodeAccumulator instanceof ValueSetConceptAccumulator) {
myTxTemplate.execute(t -> ((ValueSetConceptAccumulator) theValueSetCodeAccumulator).removeGapsFromConceptOrder());
}
ourLog.info("Done working with {} in {}ms", valueSetInfo, sw.getMillis());
}

29
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulator.java
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@ -31,6 +31,7 @@ import ca.uhn.fhir.util.ValidateUtil;
import javax.annotation.Nonnull;
import java.util.Collection;
import java.util.List;
import java.util.Optional;
import static org.apache.commons.lang3.StringUtils.*;
@ -44,6 +45,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
private ITermValueSetConceptDesignationDao myValueSetConceptDesignationDao;
private int myConceptsSaved;
private int myDesignationsSaved;
private int myConceptsExcluded;
public ValueSetConceptAccumulator(@Nonnull TermValueSet theTermValueSet, @Nonnull ITermValueSetDao theValueSetDao, @Nonnull ITermValueSetConceptDao theValueSetConceptDao, @Nonnull ITermValueSetConceptDesignationDao theValueSetConceptDesignationDao) {
myTermValueSet = theTermValueSet;
@ -52,6 +54,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
myValueSetConceptDesignationDao = theValueSetConceptDesignationDao;
myConceptsSaved = 0;
myDesignationsSaved = 0;
myConceptsExcluded = 0;
}
@Override
@ -88,6 +91,10 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
myTermValueSet.decrementTotalConcepts();
myValueSetDao.save(myTermValueSet);
ourLog.info("Done excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
if (++myConceptsExcluded % 250 == 0) {
ourLog.info("Have excluded {} concepts from ValueSet[{}]", myConceptsExcluded, myTermValueSet.getUrl());
}
}
}
@ -138,7 +145,23 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
return designation;
}
// TODO: DM 2019-07-16 - We need TermValueSetConceptProperty, similar to TermConceptProperty.
// TODO: DM 2019-07-16 - We should also populate TermValueSetConceptProperty entities here.
// TODO: DM 2019-07-30 - Expansions don't include the properties themselves; they are needed to facilitate filters and parameterized expansions.
public Boolean removeGapsFromConceptOrder() {
if (myConceptsExcluded <= 0) {
return false;
}
ourLog.info("Removing gaps from concept order for ValueSet[{}]", myTermValueSet.getUrl());
int order = 0;
List<Long> conceptIds = myValueSetConceptDao.findIdsByTermValueSetId(myTermValueSet.getId());
for (Long conceptId : conceptIds) {
myValueSetConceptDao.updateOrderById(conceptId, order++);
}
ourLog.info("Have remove gaps from concept order for {} concepts in ValueSet[{}]", conceptIds.size(), myTermValueSet.getUrl());
return true;
}
// TODO: DM 2019-07-16 - We may need TermValueSetConceptProperty, similar to TermConceptProperty.
// TODO: DM 2019-07-16 - If so, we should also populate TermValueSetConceptProperty entities here.
// TODO: DM 2019-07-30 - Expansions don't include the properties themselves; they may be needed to facilitate filters and parameterized expansions.
}

16
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
View File

@ -2332,13 +2332,13 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
// ...
concept = termValueSet.getConcepts().get(22 - 2);
concept = termValueSet.getConcepts().get(20);
ourLog.info("Concept:\n" + concept.toString());
assertEquals("http://acme.org", concept.getSystem());
assertEquals("8491-3", concept.getCode());
assertEquals("Systolic blood pressure 1 hour minimum", concept.getDisplay());
assertEquals(1, concept.getDesignations().size());
assertEquals(22, concept.getOrder());
assertEquals(20, concept.getOrder());
designation = concept.getDesignations().get(0);
assertEquals("nl", designation.getLanguage());
@ -2347,13 +2347,13 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
assertEquals("Synonym", designation.getUseDisplay());
assertEquals("Systolische bloeddruk minimaal 1 uur", designation.getValue());
concept = termValueSet.getConcepts().get(23 - 2);
concept = termValueSet.getConcepts().get(21);
ourLog.info("Concept:\n" + concept.toString());
assertEquals("http://acme.org", concept.getSystem());
assertEquals("8492-1", concept.getCode());
assertEquals("Systolic blood pressure 8 hour minimum", concept.getDisplay());
assertEquals(0, concept.getDesignations().size());
assertEquals(23, concept.getOrder());
assertEquals(21, concept.getOrder());
});
}
@ -2434,13 +2434,13 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
// ...
concept = termValueSet.getConcepts().get(22 - 2);
concept = termValueSet.getConcepts().get(20);
ourLog.info("Concept:\n" + concept.toString());
assertEquals("http://acme.org", concept.getSystem());
assertEquals("8491-3", concept.getCode());
assertEquals("Systolic blood pressure 1 hour minimum", concept.getDisplay());
assertEquals(1, concept.getDesignations().size());
assertEquals(22, concept.getOrder());
assertEquals(20, concept.getOrder());
designation = concept.getDesignations().get(0);
assertEquals("nl", designation.getLanguage());
@ -2449,13 +2449,13 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
assertEquals("Synonym", designation.getUseDisplay());
assertEquals("Systolische bloeddruk minimaal 1 uur", designation.getValue());
concept = termValueSet.getConcepts().get(23 - 2);
concept = termValueSet.getConcepts().get(21);
ourLog.info("Concept:\n" + concept.toString());
assertEquals("http://acme.org", concept.getSystem());
assertEquals("8492-1", concept.getCode());
assertEquals("Systolic blood pressure 8 hour minimum", concept.getDisplay());
assertEquals(0, concept.getDesignations().size());
assertEquals(23, concept.getOrder());
assertEquals(21, concept.getOrder());
});
}