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Incremental work on large ValueSet expansion support; fixed broken deletion for TermValueSetConceptDesignation.

This commit is contained in:
Diederik Muylwyk 2019-08-22 14:00:08 -04:00
parent 3218bd7853
commit 72dd6b2922
6 changed files with 132 additions and 16 deletions
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2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetConceptDao.java
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@ -32,7 +32,7 @@ import java.util.Optional;
public interface ITermValueSetConceptDao extends JpaRepository<TermValueSetConcept, Long> {
@Query("SELECT COUNT(vsc) FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid")
@Query("SELECT COUNT(*) FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid")
Integer countByTermValueSetId(@Param("pid") Long theValueSetId);
@Query("DELETE FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid")

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetConceptDesignationDao.java
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@ -30,13 +30,13 @@ import org.springframework.data.repository.query.Param;
public interface ITermValueSetConceptDesignationDao extends JpaRepository<TermValueSetConceptDesignation, Long> {
@Query("SELECT COUNT(vscd) FROM TermValueSetConceptDesignation vscd WHERE vscd.myConcept.myId = :pid")
Integer countByTermValueSetConceptId(@Param("pid") Long theValueSetConceptId);
@Query("SELECT COUNT(vscd) FROM TermValueSetConceptDesignation vscd WHERE vscd.myValueSet.myId = :pid")
Integer countByTermValueSetId(@Param("pid") Long theValueSetId);
@Query("DELETE FROM TermValueSetConceptDesignation vscd WHERE vscd.myConcept.myValueSet.myId = :pid")
@Query("DELETE FROM TermValueSetConceptDesignation vscd WHERE vscd.myValueSet.myId = :pid")
@Modifying
void deleteByTermValueSetId(@Param("pid") Long theValueSetId);
@Query("SELECT vscd from TermValueSetConceptDesignation vscd WHERE vscd.myConcept.myId = :pid")
@Query("SELECT vscd FROM TermValueSetConceptDesignation vscd WHERE vscd.myConcept.myId = :pid")
Slice<TermValueSetConceptDesignation> findByTermValueSetConceptId(Pageable thePage, @Param("pid") Long theValueSetConceptId);
}

38
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetConceptDesignation.java
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@ -52,6 +52,16 @@ public class TermValueSetConceptDesignation implements Serializable {
@JoinColumn(name = "VALUESET_CONCEPT_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TRM_VALUESET_CONCEPT_PID"))
private TermValueSetConcept myConcept;
@ManyToOne()
@JoinColumn(name = "VALUESET_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TRM_VSCD_VS_PID"))
private TermValueSet myValueSet;
@Transient
private String myValueSetUrl;
@Transient
private String myValueSetName;
@Column(name = "LANG", nullable = true, length = MAX_LENGTH)
private String myLanguage;
@ -80,6 +90,31 @@ public class TermValueSetConceptDesignation implements Serializable {
return this;
}
public TermValueSet getValueSet() {
return myValueSet;
}
public TermValueSetConceptDesignation setValueSet(TermValueSet theValueSet) {
myValueSet = theValueSet;
return this;
}
public String getValueSetUrl() {
if (myValueSetUrl == null) {
myValueSetUrl = getValueSet().getUrl();
}
return myValueSetUrl;
}
public String getValueSetName() {
if (myValueSetName == null) {
myValueSetName = getValueSet().getName();
}
return myValueSetName;
}
public String getLanguage() {
return myLanguage;
}
@ -167,6 +202,9 @@ public class TermValueSetConceptDesignation implements Serializable {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("myId", myId)
.append(myConcept != null ? ("myConcept - id=" + myConcept.getId()) : ("myConcept=(null)"))
.append(myValueSet != null ? ("myValueSet - id=" + myValueSet.getId()) : ("myValueSet=(null)"))
.append("myValueSetUrl", this.getValueSetUrl())
.append("myValueSetName", this.getValueSetName())
.append("myLanguage", myLanguage)
.append("myUseSystem", myUseSystem)
.append("myUseCode", myUseCode)

43
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
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@ -612,6 +612,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
// Handle includes
ourLog.debug("Handling includes");
for (ValueSet.ConceptSetComponent include : theValueSetToExpand.getCompose().getInclude()) {
ourLog.info("Working with " + identifyValueSetForLogging(theValueSetToExpand));
boolean add = true;
expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, include, add, theCodeCounter);
}
@ -619,11 +620,48 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
// Handle excludes
ourLog.debug("Handling excludes");
for (ValueSet.ConceptSetComponent exclude : theValueSetToExpand.getCompose().getExclude()) {
ourLog.info("Working with " + identifyValueSetForLogging(theValueSetToExpand));
boolean add = false;
expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, exclude, add, theCodeCounter);
}
}
private String identifyValueSetForLogging(ValueSet theValueSet) {
StringBuilder sb = new StringBuilder();
boolean isIdentified = false;
sb
.append("ValueSet:");
if (theValueSet.hasId()) {
isIdentified = true;
sb
.append(" ValueSet.id[")
.append(theValueSet.getId())
.append("]");
}
if (theValueSet.hasUrl()) {
isIdentified = true;
sb
.append(" ValueSet.url[")
.append(theValueSet.getUrl())
.append("]");
}
if (theValueSet.hasIdentifier()) {
isIdentified = true;
sb
.append(" ValueSet.identifier[")
.append(theValueSet.getIdentifierFirstRep().getSystem())
.append("|")
.append(theValueSet.getIdentifierFirstRep().getValue())
.append("]");
}
if (!isIdentified) {
sb.append(" None of ValueSet.id, ValueSet.url, and ValueSet.identifier are provided.");
}
return sb.toString();
}
protected List<VersionIndependentConcept> expandValueSetAndReturnVersionIndependentConcepts(org.hl7.fhir.r4.model.ValueSet theValueSetToExpandR4) {
org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent expandedR4 = expandValueSet(theValueSetToExpandR4).getExpansion();
@ -768,6 +806,11 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
*/
FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, TermConcept.class);
/*
* DM 2019-08-21 - Processing slows after any ValueSets with many codes explicitly identified. This might
* be due to the dark arts that is memory management. Will monitor but not do anything about this right now.
*/
BooleanQuery.setMaxClauseCount(10000);
StopWatch sw = new StopWatch();
AtomicInteger count = new AtomicInteger(0);

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulator.java
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@ -116,6 +116,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
TermValueSetConceptDesignation designation = new TermValueSetConceptDesignation();
designation.setConcept(theConcept);
designation.setValueSet(myTermValueSet);
designation.setLanguage(theDesignation.getLanguage());
if (isNoneBlank(theDesignation.getUseSystem(), theDesignation.getUseCode())) {
designation.setUseSystem(theDesignation.getUseSystem());

56
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
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@ -562,6 +562,40 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
}
@Test
public void testDeleteValueSet() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystemAndValueSetWithDesignations();
CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
myTermSvc.preExpandValueSetToTerminologyTables();
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
Long termValueSetId = myTermValueSetDao.findByResourcePid(valueSet.getIdElement().toUnqualifiedVersionless().getIdPartAsLong()).get().getId();
assertEquals(3, myTermValueSetConceptDesignationDao.countByTermValueSetId(termValueSetId).intValue());
assertEquals(24, myTermValueSetConceptDao.countByTermValueSetId(termValueSetId).intValue());
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
myTermValueSetConceptDesignationDao.deleteByTermValueSetId(termValueSetId);
assertEquals(0, myTermValueSetConceptDesignationDao.countByTermValueSetId(termValueSetId).intValue());
myTermValueSetConceptDao.deleteByTermValueSetId(termValueSetId);
assertEquals(0, myTermValueSetConceptDao.countByTermValueSetId(termValueSetId).intValue());
myTermValueSetDao.deleteByTermValueSetId(termValueSetId);
assertFalse(myTermValueSetDao.findByResourcePid(valueSet.getIdElement().toUnqualifiedVersionless().getIdPartAsLong()).isPresent());
}
});
}
@Test
public void testDuplicateCodeSystemUrls() throws Exception {
loadAndPersistCodeSystem();
@ -895,17 +929,6 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
verify(myValueSetCodeAccumulator, times(9)).includeConceptWithDesignations(anyString(), anyString(), nullable(String.class), anyCollection());
}
@Test
public void testValidateCode() {
createCodeSystem();
IValidationSupport.CodeValidationResult validation = myTermSvc.validateCode(myFhirCtx, CS_URL, "ParentWithNoChildrenA", null);
assertEquals(true, validation.isOk());
validation = myTermSvc.validateCode(myFhirCtx, CS_URL, "ZZZZZZZ", null);
assertEquals(false, validation.isOk());
}
@Test
public void testStoreTermCodeSystemAndChildren() throws Exception {
loadAndPersistCodeSystemWithDesignations();
@ -2579,6 +2602,17 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
});
}
@Test
public void testValidateCode() {
createCodeSystem();
IValidationSupport.CodeValidationResult validation = myTermSvc.validateCode(myFhirCtx, CS_URL, "ParentWithNoChildrenA", null);
assertEquals(true, validation.isOk());
validation = myTermSvc.validateCode(myFhirCtx, CS_URL, "ZZZZZZZ", null);
assertEquals(false, validation.isOk());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();