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Merge pull request #1933 from jamesagnew/dm-20200622-fix-valueset-expand-with-offset-and-count 

Fix ValueSet$expand with offset and count parameters.
This commit is contained in:
Diederik Muylwyk 2020-06-22 18:30:22 -04:00 committed by GitHub
parent 46c00f4efb ce0cb8916e
commit e849ff2cbc
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GPG Key ID: 4AEE18F83AFDEB23
5 changed files with 313 additions and 4 deletions
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2
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1895-fix-jpa-validation-performance-regression.yaml
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@ -1,5 +1,5 @@
---
type: fix
issue: 1895
title: "HAPI FHIR 5.0.0 introduced a regressin in JPA validator performance, where a number of unnecessary database lookups
title: "HAPI FHIR 5.0.0 introduced a regression in JPA validator performance, where a number of unnecessary database lookups
were introduced. This has been corrected."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/1933-fix-valueset-expand-with-offset-and-count-parameters.yaml Normal file
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@ -0,0 +1,6 @@
---
type: fix
issue: 1933
title: "`BaseValidationSupportWrapper.expandValueSet(...)` and `ValidationSupportChain.expandValueSet(...)` were
incorrectly replacing expansion options (i.e. offset and count) with `null`, causing these parameters to be
ignored when invoking the `ValueSet$expand` operation. This has been corrected."

305
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5ValueSetTest.java
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@ -301,6 +301,103 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
}
@Test
public void testExpandByIdWithPreExpansionWithOffset() throws Exception {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Parameters respParam = ourClient
.operation()
.onInstance(myExtensionalVsId)
.named("expand")
.withParameter(Parameters.class, "offset", new IntegerType(1))
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertEquals(24, expanded.getExpansion().getTotal());
assertEquals(1, expanded.getExpansion().getOffset());
assertEquals("offset", expanded.getExpansion().getParameter().get(0).getName());
assertEquals(1, expanded.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
assertEquals("count", expanded.getExpansion().getParameter().get(1).getName());
assertEquals(1000, expanded.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
assertEquals(23, expanded.getExpansion().getContains().size());
assertEquals("http://acme.org", expanded.getExpansion().getContains().get(0).getSystem());
assertEquals("11378-7", expanded.getExpansion().getContains().get(0).getCode());
assertEquals("Systolic blood pressure at First encounter", expanded.getExpansion().getContains().get(0).getDisplay());
assertEquals("http://acme.org", expanded.getExpansion().getContains().get(1).getSystem());
assertEquals("8493-9", expanded.getExpansion().getContains().get(1).getCode());
assertEquals("Systolic blood pressure 10 hour minimum", expanded.getExpansion().getContains().get(1).getDisplay());
}
@Test
public void testExpandByIdWithPreExpansionWithCount() throws Exception {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Parameters respParam = ourClient
.operation()
.onInstance(myExtensionalVsId)
.named("expand")
.withParameter(Parameters.class, "count", new IntegerType(1))
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertEquals(24, expanded.getExpansion().getTotal());
assertEquals(0, expanded.getExpansion().getOffset());
assertEquals("offset", expanded.getExpansion().getParameter().get(0).getName());
assertEquals(0, expanded.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
assertEquals("count", expanded.getExpansion().getParameter().get(1).getName());
assertEquals(1, expanded.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
assertEquals(1, expanded.getExpansion().getContains().size());
assertEquals("http://acme.org", expanded.getExpansion().getContainsFirstRep().getSystem());
assertEquals("8450-9", expanded.getExpansion().getContainsFirstRep().getCode());
assertEquals("Systolic blood pressure--expiration", expanded.getExpansion().getContainsFirstRep().getDisplay());
}
@Test
public void testExpandByIdWithPreExpansionWithOffsetAndCount() throws Exception {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Parameters respParam = ourClient
.operation()
.onInstance(myExtensionalVsId)
.named("expand")
.withParameter(Parameters.class, "offset", new IntegerType(1))
.andParameter("count", new IntegerType(1))
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertEquals(24, expanded.getExpansion().getTotal());
assertEquals(1, expanded.getExpansion().getOffset());
assertEquals("offset", expanded.getExpansion().getParameter().get(0).getName());
assertEquals(1, expanded.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
assertEquals("count", expanded.getExpansion().getParameter().get(1).getName());
assertEquals(1, expanded.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
assertEquals(1, expanded.getExpansion().getContains().size());
assertEquals("http://acme.org", expanded.getExpansion().getContainsFirstRep().getSystem());
assertEquals("11378-7", expanded.getExpansion().getContainsFirstRep().getCode());
assertEquals("Systolic blood pressure at First encounter", expanded.getExpansion().getContainsFirstRep().getDisplay());
}
@Test
public void testExpandByIdWithFilter() throws Exception {
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
@ -402,6 +499,106 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
}
@Test
public void testExpandByUrlWithPreExpansionWithOffset() throws Exception {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
.named("expand")
.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
.andParameter("offset", new IntegerType(1))
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertEquals(24, expanded.getExpansion().getTotal());
assertEquals(1, expanded.getExpansion().getOffset());
assertEquals("offset", expanded.getExpansion().getParameter().get(0).getName());
assertEquals(1, expanded.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
assertEquals("count", expanded.getExpansion().getParameter().get(1).getName());
assertEquals(1000, expanded.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
assertEquals(23, expanded.getExpansion().getContains().size());
assertEquals("http://acme.org", expanded.getExpansion().getContains().get(0).getSystem());
assertEquals("11378-7", expanded.getExpansion().getContains().get(0).getCode());
assertEquals("Systolic blood pressure at First encounter", expanded.getExpansion().getContains().get(0).getDisplay());
assertEquals("http://acme.org", expanded.getExpansion().getContains().get(1).getSystem());
assertEquals("8493-9", expanded.getExpansion().getContains().get(1).getCode());
assertEquals("Systolic blood pressure 10 hour minimum", expanded.getExpansion().getContains().get(1).getDisplay());
}
@Test
public void testExpandByUrlWithPreExpansionWithCount() throws Exception {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
.named("expand")
.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
.andParameter("count", new IntegerType(1))
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertEquals(24, expanded.getExpansion().getTotal());
assertEquals(0, expanded.getExpansion().getOffset());
assertEquals("offset", expanded.getExpansion().getParameter().get(0).getName());
assertEquals(0, expanded.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
assertEquals("count", expanded.getExpansion().getParameter().get(1).getName());
assertEquals(1, expanded.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
assertEquals(1, expanded.getExpansion().getContains().size());
assertEquals("http://acme.org", expanded.getExpansion().getContainsFirstRep().getSystem());
assertEquals("8450-9", expanded.getExpansion().getContainsFirstRep().getCode());
assertEquals("Systolic blood pressure--expiration", expanded.getExpansion().getContainsFirstRep().getDisplay());
}
@Test
public void testExpandByUrlWithPreExpansionWithOffsetAndCount() throws Exception {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
.named("expand")
.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
.andParameter("offset", new IntegerType(1))
.andParameter("count", new IntegerType(1))
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertEquals(24, expanded.getExpansion().getTotal());
assertEquals(1, expanded.getExpansion().getOffset());
assertEquals("offset", expanded.getExpansion().getParameter().get(0).getName());
assertEquals(1, expanded.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
assertEquals("count", expanded.getExpansion().getParameter().get(1).getName());
assertEquals(1, expanded.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
assertEquals(1, expanded.getExpansion().getContains().size());
assertEquals("http://acme.org", expanded.getExpansion().getContainsFirstRep().getSystem());
assertEquals("11378-7", expanded.getExpansion().getContainsFirstRep().getCode());
assertEquals("Systolic blood pressure at First encounter", expanded.getExpansion().getContainsFirstRep().getDisplay());
}
@Test
public void testExpandByUrlWithPreExpansionAndBogusUrl() throws Exception {
myDaoConfig.setPreExpandValueSets(true);
@ -448,7 +645,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
public void testExpandByValueSetWithPreExpansion() throws IOException {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystem(HTTPVerb.POST);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
@ -469,6 +666,112 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
}
@Test
public void testExpandByValueSetWithPreExpansionWithOffset() throws IOException {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
.named("expand")
.withParameter(Parameters.class, "valueSet", toExpand)
.andParameter("offset", new IntegerType(1))
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertEquals(24, expanded.getExpansion().getTotal());
assertEquals(1, expanded.getExpansion().getOffset());
assertEquals("offset", expanded.getExpansion().getParameter().get(0).getName());
assertEquals(1, expanded.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
assertEquals("count", expanded.getExpansion().getParameter().get(1).getName());
assertEquals(1000, expanded.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
assertEquals(23, expanded.getExpansion().getContains().size());
assertEquals("http://acme.org", expanded.getExpansion().getContains().get(0).getSystem());
assertEquals("11378-7", expanded.getExpansion().getContains().get(0).getCode());
assertEquals("Systolic blood pressure at First encounter", expanded.getExpansion().getContains().get(0).getDisplay());
assertEquals("http://acme.org", expanded.getExpansion().getContains().get(1).getSystem());
assertEquals("8493-9", expanded.getExpansion().getContains().get(1).getCode());
assertEquals("Systolic blood pressure 10 hour minimum", expanded.getExpansion().getContains().get(1).getDisplay());
}
@Test
public void testExpandByValueSetWithPreExpansionWithCount() throws IOException {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
.named("expand")
.withParameter(Parameters.class, "valueSet", toExpand)
.andParameter("count", new IntegerType(1))
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertEquals(24, expanded.getExpansion().getTotal());
assertEquals(0, expanded.getExpansion().getOffset());
assertEquals("offset", expanded.getExpansion().getParameter().get(0).getName());
assertEquals(0, expanded.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
assertEquals("count", expanded.getExpansion().getParameter().get(1).getName());
assertEquals(1, expanded.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
assertEquals(1, expanded.getExpansion().getContains().size());
assertEquals("http://acme.org", expanded.getExpansion().getContainsFirstRep().getSystem());
assertEquals("8450-9", expanded.getExpansion().getContainsFirstRep().getCode());
assertEquals("Systolic blood pressure--expiration", expanded.getExpansion().getContainsFirstRep().getDisplay());
}
@Test
public void testExpandByValueSetWithPreExpansionWithOffsetAndCount() throws IOException {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
.named("expand")
.withParameter(Parameters.class, "valueSet", toExpand)
.andParameter("offset", new IntegerType(1))
.andParameter("count", new IntegerType(1))
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertEquals(24, expanded.getExpansion().getTotal());
assertEquals(1, expanded.getExpansion().getOffset());
assertEquals("offset", expanded.getExpansion().getParameter().get(0).getName());
assertEquals(1, expanded.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
assertEquals("count", expanded.getExpansion().getParameter().get(1).getName());
assertEquals(1, expanded.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
assertEquals(1, expanded.getExpansion().getContains().size());
assertEquals("http://acme.org", expanded.getExpansion().getContainsFirstRep().getSystem());
assertEquals("11378-7", expanded.getExpansion().getContainsFirstRep().getCode());
assertEquals("Systolic blood pressure at First encounter", expanded.getExpansion().getContainsFirstRep().getDisplay());
}
@Test
public void testExpandInlineVsAgainstBuiltInCs() {
createLocalVsPointingAtBuiltInCodeSystem();

2
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/BaseValidationSupportWrapper.java
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@ -70,7 +70,7 @@ public class BaseValidationSupportWrapper extends BaseValidationSupport {
@Override
public IValidationSupport.ValueSetExpansionOutcome expandValueSet(ValidationSupportContext theValidationSupportContext, ValueSetExpansionOptions theExpansionOptions, IBaseResource theValueSetToExpand) {
return myWrap.expandValueSet(theValidationSupportContext, null, theValueSetToExpand);
return myWrap.expandValueSet(theValidationSupportContext, theExpansionOptions, theValueSetToExpand);
}
@Override

2
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationSupportChain.java
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@ -134,7 +134,7 @@ public class ValidationSupportChain implements IValidationSupport {
public ValueSetExpansionOutcome expandValueSet(ValidationSupportContext theValidationSupportContext, ValueSetExpansionOptions theExpansionOptions, IBaseResource theValueSetToExpand) {
for (IValidationSupport next : myChain) {
// TODO: test if code system is supported?
ValueSetExpansionOutcome expanded = next.expandValueSet(theValidationSupportContext, null, theValueSetToExpand);
ValueSetExpansionOutcome expanded = next.expandValueSet(theValidationSupportContext, theExpansionOptions, theValueSetToExpand);
if (expanded != null) {
return expanded;
}