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Clean up references in IPS documents (#4509) 

* Clean up references in IPS documents

* Add changelog
This commit is contained in:
James Agnew 2023-02-04 18:40:39 -05:00 committed by GitHub
parent 64d776ac0e
commit 148cbf119b
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5 changed files with 108 additions and 19 deletions
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6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4509-fix-refs-in-ips.yaml Normal file
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@ -0,0 +1,6 @@
---
type: fix
issue: 4509
title: "References to the patient/subject in IPS documents generated using the $summary
operation were not replaced with the bundle-local UUID assigned to the patient. Also,
some dangling references were left in the generated bundle. This has been corrected."

37
hapi-fhir-jpaserver-ips/src/main/java/ca/uhn/fhir/jpa/ips/generator/IpsGeneratorSvcImpl.java
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@ -114,16 +114,18 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
}
private IBaseBundle generateIpsForPatient(RequestDetails theRequestDetails, IBaseResource thePatient) {
IIdType originalSubjectId = myFhirContext.getVersion().newIdType().setValue(thePatient.getIdElement().getValue());
IIdType originalSubjectId = myFhirContext.getVersion().newIdType().setValue(thePatient.getIdElement().getValue()).toUnqualifiedVersionless();
massageResourceId(null, thePatient);
IpsContext context = new IpsContext(thePatient, originalSubjectId);
ResourceInclusionCollection globalResourcesToInclude = new ResourceInclusionCollection();
globalResourcesToInclude.addResourceIfNotAlreadyPresent(thePatient, originalSubjectId.getValue());
IBaseResource author = myGenerationStrategy.createAuthor();
massageResourceId(context, author);
CompositionBuilder compositionBuilder = createComposition(thePatient, context, author);
ResourceInclusionCollection globalResourcesToInclude = determineInclusions(theRequestDetails, originalSubjectId, context, compositionBuilder);
determineInclusions(theRequestDetails, originalSubjectId, context, compositionBuilder, globalResourcesToInclude);
IBaseResource composition = compositionBuilder.getComposition();
@ -131,10 +133,10 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
CustomThymeleafNarrativeGenerator generator = newNarrativeGenerator(globalResourcesToInclude);
generator.populateResourceNarrative(myFhirContext, composition);
return createCompositionDocument(thePatient, author, composition, globalResourcesToInclude);
return createCompositionDocument(author, composition, globalResourcesToInclude);
}
private IBaseBundle createCompositionDocument(IBaseResource thePatient, IBaseResource author, IBaseResource composition, ResourceInclusionCollection theResourcesToInclude) {
private IBaseBundle createCompositionDocument(IBaseResource author, IBaseResource composition, ResourceInclusionCollection theResourcesToInclude) {
BundleBuilder bundleBuilder = new BundleBuilder(myFhirContext);
bundleBuilder.setType(Bundle.BundleType.DOCUMENT.toCode());
bundleBuilder.setIdentifier("urn:ietf:rfc:4122", UUID.randomUUID().toString());
@ -143,9 +145,6 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
// Add composition to document
bundleBuilder.addDocumentEntry(composition);
// Add subject to document
bundleBuilder.addDocumentEntry(thePatient);
// Add inclusion candidates
for (IBaseResource next : theResourcesToInclude.getResources()) {
bundleBuilder.addDocumentEntry(next);
@ -158,13 +157,12 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
}
@Nonnull
private ResourceInclusionCollection determineInclusions(RequestDetails theRequestDetails, IIdType originalSubjectId, IpsContext context, CompositionBuilder theCompositionBuilder) {
ResourceInclusionCollection globalResourcesToInclude = new ResourceInclusionCollection();
private ResourceInclusionCollection determineInclusions(RequestDetails theRequestDetails, IIdType originalSubjectId, IpsContext context, CompositionBuilder theCompositionBuilder, ResourceInclusionCollection theGlobalResourcesToInclude) {
SectionRegistry sectionRegistry = myGenerationStrategy.getSectionRegistry();
for (SectionRegistry.Section nextSection : sectionRegistry.getSections()) {
determineInclusionsForSection(theRequestDetails, originalSubjectId, context, theCompositionBuilder, globalResourcesToInclude, nextSection);
determineInclusionsForSection(theRequestDetails, originalSubjectId, context, theCompositionBuilder, theGlobalResourcesToInclude, nextSection);
}
return globalResourcesToInclude;
return theGlobalResourcesToInclude;
}
private void determineInclusionsForSection(RequestDetails theRequestDetails, IIdType theOriginalSubjectId, IpsContext theIpsContext, CompositionBuilder theCompositionBuilder, ResourceInclusionCollection theGlobalResourcesToInclude, SectionRegistry.Section theSection) {
@ -241,9 +239,16 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
if (isNotBlank(existingReference)) {
existingReference = new IdType(existingReference).toUnqualifiedVersionless().getValue();
String replacement = theGlobalResourcesToInclude.getIdSubstitution(existingReference);
if (isNotBlank(replacement) && !replacement.equals(existingReference)) {
if (isNotBlank(replacement)) {
if (!replacement.equals(existingReference)) {
nextReference.getResourceReference().setReference(replacement);
}
} else if (theGlobalResourcesToInclude.getResourceById(existingReference) == null) {
// If this reference doesn't point to something we have actually
// included in the bundle, clear the reference.
nextReference.getResourceReference().setReference(null);
nextReference.getResourceReference().setResource(null);
}
}
}
}
@ -541,7 +546,11 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
}
public IBaseResource getResourceById(IIdType theReference) {
return myIdToResource.get(theReference.toUnqualifiedVersionless().getValue());
return getResourceById(theReference.toUnqualifiedVersionless().getValue());
}
public IBaseResource getResourceById(String theReference) {
return myIdToResource.get(theReference);
}
@Nullable

30
hapi-fhir-jpaserver-ips/src/test/java/ca/uhn/fhir/jpa/ips/generator/IpsGenerationTest.java
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@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.ips.generator;
import ca.uhn.fhir.batch2.jobs.models.BatchResourceId;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.ips.api.IIpsGenerationStrategy;
@ -8,8 +9,11 @@ import ca.uhn.fhir.jpa.ips.strategy.DefaultIpsGenerationStrategy;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.BaseResourceProviderR4Test;
import ca.uhn.fhir.util.ClasspathUtil;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.MedicationStatement;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
@ -18,7 +22,10 @@ import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.test.context.ContextConfiguration;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.matchesPattern;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNull;
@ContextConfiguration(classes = {IpsGenerationTest.IpsConfig.class})
public class IpsGenerationTest extends BaseResourceProviderR4Test {
@ -28,12 +35,12 @@ public class IpsGenerationTest extends BaseResourceProviderR4Test {
@BeforeEach
public void beforeEach() {
myServer.withServer(t->t.registerProvider(myIpsOperationProvider));
myServer.withServer(t -> t.registerProvider(myIpsOperationProvider));
}
@AfterEach
public void afterEach() {
myServer.withServer(t->t.unregisterProvider(myIpsOperationProvider));
myServer.withServer(t -> t.unregisterProvider(myIpsOperationProvider));
}
@ -55,10 +62,27 @@ public class IpsGenerationTest extends BaseResourceProviderR4Test {
.withNoParameters(Parameters.class)
.returnResourceType(Bundle.class)
.execute();
ourLog.info("Output: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(output));
// Verify
assertEquals(37, output.getEntry().size());
String patientId = findFirstEntryResource(output, Patient.class).getId();
assertThat(patientId, matchesPattern("urn:uuid:.*"));
MedicationStatement medicationStatement = findFirstEntryResource(output, MedicationStatement.class);
assertEquals(patientId, medicationStatement.getSubject().getReference());
assertNull(medicationStatement.getInformationSource().getReference());
}
@SuppressWarnings("unchecked")
private <T extends IBaseResource> T findFirstEntryResource(Bundle theBundle, Class<T> theType) {
return (T) theBundle
.getEntry()
.stream()
.filter(t -> theType.isAssignableFrom(t.getResource().getClass()))
.findFirst()
.orElseThrow()
.getResource();
}

50
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoR5ValueSetTest.java
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@ -7,11 +7,14 @@ import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
import ca.uhn.fhir.jpa.util.ValueSetTestUtil;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@ -19,6 +22,7 @@ import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Enumerations;
import org.hl7.fhir.r5.model.IdType;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.UriType;
@ -30,6 +34,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import java.io.IOException;
import java.util.Optional;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
@ -38,6 +43,7 @@ import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
@ -56,6 +62,7 @@ public class FhirResourceDaoR5ValueSetTest extends BaseJpaR5Test {
public void after() {
myDaoConfig.setPreExpandValueSets(new DaoConfig().isPreExpandValueSets());
myDaoConfig.setMaximumExpansionSize(new DaoConfig().getMaximumExpansionSize());
myDaoConfig.setExpungeEnabled(new DaoConfig().isExpungeEnabled());
}
@ -248,6 +255,49 @@ public class FhirResourceDaoR5ValueSetTest extends BaseJpaR5Test {
}
/**
* See #4305
*/
@Test
public void testDeleteExpungePreExpandedValueSet() {
myDaoConfig.setExpungeEnabled(true);
// Create valueset
ValueSet vs = myValidationSupport.fetchResource(ValueSet.class, "http://hl7.org/fhir/ValueSet/address-use");
assertNotNull(vs);
IIdType id = myValueSetDao.create(vs).getId().toUnqualifiedVersionless();
// Update valueset
vs.setName("Hello");
assertEquals("2", myValueSetDao.update(vs, mySrd).getId().getVersionIdPart());
runInTransaction(()->{
Optional<ResourceTable> resource = myResourceTableDao.findById(id.getIdPartAsLong());
assertTrue(resource.isPresent());
});
// Precalculate
myTerminologyDeferredStorageSvc.saveAllDeferred();
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
logAllValueSets();
// Delete
myValueSetDao.delete(id, mySrd);
// Verify it's deleted
assertThrows(ResourceGoneException.class, ()-> myValueSetDao.read(id, mySrd));
// Expunge
myValueSetDao.expunge(id, new ExpungeOptions().setExpungeDeletedResources(true).setExpungeOldVersions(true), mySrd);
// Verify expunged
runInTransaction(()->{
Optional<ResourceTable> resource = myResourceTableDao.findById(id.getIdPartAsLong());
assertFalse(resource.isPresent());
});
}
@Test
public void testExpandByValueSet_ExceedsMaxSize() {
// Add a bunch of codes

2
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/ResponseHighlighterInterceptor.java
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@ -814,7 +814,7 @@ public class ResponseHighlighterInterceptor {
writeLength(theServletResponse, outputBuffer.length());
theServletResponse.getWriter().append(" total including HTML)");
theServletResponse.getWriter().append(" in estimated ");
theServletResponse.getWriter().append(" in approximately ");
theServletResponse.getWriter().append(writeSw.toString());
theServletResponse.getWriter().append("</div>");