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Fix "is-a" ValueSet expansion, add "descendent-of" support

This commit is contained in:
Ole Hedegaard 2024-01-18 12:07:52 +01:00
parent 878e27b06d
commit b265e05823
5 changed files with 46 additions and 8 deletions
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10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcImpl.java
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@ -1596,6 +1596,16 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
TermConcept code = findCodeForFilterCriteria(theSystem, theFilter);
if (theFilter.getOp() == ValueSet.FilterOperator.ISA) {
ourLog.debug(
" * Filtering on specific code and codes with a parent of {}/{}/{}",
code.getId(),
code.getCode(),
code.getDisplay());
b.must(f.bool()
.should(f.match().field("myParentPids").matching("" + code.getId()))
.should(f.match().field("myId").matching(code.getId())));
} else if (theFilter.getOp() == ValueSet.FilterOperator.DESCENDENTOF) {
ourLog.debug(
" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());

36
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java
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@ -353,7 +353,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
.setSystem(codeSystem.getUrl())
.addFilter()
.setProperty("concept")
.setOp(FilterOperator.ISA)
.setOp(FilterOperator.DESCENDENTOF)
.setValue("dogs");
myValueSetDao.create(valueSet, mySrd);
@ -584,7 +584,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
logAndValidateValueSet(result);
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
assertThat(codes, containsInAnyOrder("childAA", "childAAA", "childAAB"));
}
@ -610,6 +610,34 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
logAndValidateValueSet(result);
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertEquals(3, codes.size());
assertThat(codes, containsInAnyOrder("childAA", "childAAA", "childAAB"));
}
@Test
public void testExpandWithDescendentOfInExternalValueSetReindex() {
TermReindexingSvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
createExternalCsAndLocalVs();
myResourceReindexingSvc.markAllResourcesForReindexing();
myResourceReindexingSvc.forceReindexingPass();
myResourceReindexingSvc.forceReindexingPass();
myTerminologyDeferredStorageSvc.saveDeferred();
myTerminologyDeferredStorageSvc.saveDeferred();
myTerminologyDeferredStorageSvc.saveDeferred();
ValueSet vs = new ValueSet();
ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(TermTestUtil.URL_MY_CODE_SYSTEM);
include.addFilter().setOp(FilterOperator.DESCENDENTOF).setValue("childAA").setProperty("concept");
ValueSet result = myValueSetDao.expand(vs, null); // breakpoint
logAndValidateValueSet(result);
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertEquals(2, codes.size());
assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
}
@ -795,7 +823,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
ValueSet vs = new ValueSet();
ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(TermTestUtil.URL_MY_CODE_SYSTEM);
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
include.addFilter().setProperty("concept").setOp(FilterOperator.DESCENDENTOF).setValue("ParentA");
ValueSet result = myValueSetDao.expand(vs, null);
logAndValidateValueSet(result);
@ -814,7 +842,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(TermTestUtil.URL_MY_CODE_SYSTEM);
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
include.addFilter().setProperty("concept").setOp(FilterOperator.DESCENDENTOF).setValue("ParentA");
result = myValueSetDao.expand(vs, null);
logAndValidateValueSet(result);

4
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetNoVerCSNoVerTest.java
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@ -202,7 +202,7 @@ public class ResourceProviderR4ValueSetNoVerCSNoVerTest extends BaseResourceProv
myLocalVs.setUrl(URL_MY_VALUE_SET);
ConceptSetComponent include = myLocalVs.getCompose().addInclude();
include.setSystem(codeSystem.getUrl());
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
include.addFilter().setProperty("concept").setOp(FilterOperator.DESCENDENTOF).setValue("ParentA");
myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
}
@ -1199,7 +1199,7 @@ public class ResourceProviderR4ValueSetNoVerCSNoVerTest extends BaseResourceProv
.setSystem(URL_MY_CODE_SYSTEM)
.addFilter()
.setProperty("concept")
.setOp(FilterOperator.ISA)
.setOp(FilterOperator.DESCENDENTOF)
.setValue("A");
myLocalVs
.getCompose()

2
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetVerCSNoVerTest.java
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@ -167,7 +167,7 @@ public class ResourceProviderR4ValueSetVerCSNoVerTest extends BaseResourceProvid
myLocalVs.setUrl(URL_MY_VALUE_SET);
ConceptSetComponent include = myLocalVs.getCompose().addInclude();
include.setSystem(codeSystem.getUrl());
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
include.addFilter().setProperty("concept").setOp(FilterOperator.DESCENDENTOF).setValue("ParentA");
myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
}

2
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetVerCSVerTest.java
View File

@ -196,7 +196,7 @@ public class ResourceProviderR4ValueSetVerCSVerTest extends BaseResourceProvider
ConceptSetComponent include = myLocalVs.getCompose().addInclude();
include.setSystem(theCodeSystemUrl);
include.setVersion(theValueSetVersion);
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
include.addFilter().setProperty("concept").setOp(FilterOperator.DESCENDENTOF).setValue("ParentA");
return myLocalVs;
}