* Additional tweaks for #4509 * More teaks * format imports
This commit is contained in:
James Agnew
GitHub
parent
26a7009277
commit
765fedfefa
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@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.ips.generator;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.RuntimeResourceDefinition;
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import ca.uhn.fhir.context.RuntimeSearchParam;
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import ca.uhn.fhir.fhirpath.IFhirPathEvaluationContext;
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import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
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@ -32,6 +33,7 @@ import ca.uhn.fhir.jpa.ips.api.SectionRegistry;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.model.api.Include;
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import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
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import ca.uhn.fhir.model.dstu2.resource.Observation;
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import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
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import ca.uhn.fhir.narrative.CustomThymeleafNarrativeGenerator;
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import ca.uhn.fhir.rest.api.server.IBundleProvider;
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@ -42,6 +44,10 @@ import ca.uhn.fhir.util.BundleBuilder;
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import ca.uhn.fhir.util.CompositionBuilder;
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import ca.uhn.fhir.util.ResourceReferenceInfo;
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import ca.uhn.fhir.util.ValidateUtil;
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import com.google.common.collect.BiMap;
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import com.google.common.collect.HashBiMap;
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import org.apache.commons.collections4.BidiMap;
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import org.apache.commons.collections4.bidimap.DualHashBidiMap;
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import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseBundle;
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import org.hl7.fhir.instance.model.api.IBaseExtension;
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@ -66,6 +72,7 @@ import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import java.util.stream.Collectors;
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import static ca.uhn.fhir.jpa.term.api.ITermLoaderSvc.LOINC_URI;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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@ -214,6 +221,8 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
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nextCandidate = previouslyExistingResource;
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sectionResourcesToInclude.addResourceIfNotAlreadyPresent(nextCandidate, originalResourceId);
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} else if (theGlobalResourcesToInclude.hasResourceWithReplacementId(originalResourceId)) {
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sectionResourcesToInclude.addResourceIfNotAlreadyPresent(nextCandidate, originalResourceId);
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} else {
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IIdType id = myGenerationStrategy.massageResourceId(theIpsContext, nextCandidate);
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nextCandidate.setId(id);
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@ -226,6 +235,19 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
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}
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}
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if (sectionResourcesToInclude.isEmpty() && theSection.getNoInfoGenerator() != null) {
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IBaseResource noInfoResource = theSection.getNoInfoGenerator().generate(theIpsContext.getSubjectId());
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String id = IdType.newRandomUuid().getValue();
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if (noInfoResource.getIdElement().isEmpty()) {
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noInfoResource.setId(id);
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}
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ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(noInfoResource, BundleEntrySearchModeEnum.MATCH);
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theGlobalResourcesToInclude.addResourceIfNotAlreadyPresent(noInfoResource, noInfoResource.getIdElement().toUnqualifiedVersionless().getValue());
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sectionResourcesToInclude.addResourceIfNotAlreadyPresent(noInfoResource, id);
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}
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/*
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* Update any references within the added candidates - This is important
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* because we might be replacing resource IDs before including them in
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@ -253,19 +275,6 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
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}
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}
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}
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if (sectionResourcesToInclude.isEmpty() && theSection.getNoInfoGenerator() != null) {
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IBaseResource noInfoResource = theSection.getNoInfoGenerator().generate(theIpsContext.getSubjectId());
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String id = IdType.newRandomUuid().getValue();
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if (noInfoResource.getIdElement().isEmpty()) {
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noInfoResource.setId(id);
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}
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ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(noInfoResource, BundleEntrySearchModeEnum.MATCH);
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theGlobalResourcesToInclude.addResourceIfNotAlreadyPresent(noInfoResource, noInfoResource.getIdElement().toUnqualifiedVersionless().getValue());
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sectionResourcesToInclude.addResourceIfNotAlreadyPresent(noInfoResource, id);
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}
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addSection(theSection, theCompositionBuilder, sectionResourcesToInclude, theGlobalResourcesToInclude);
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}
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@ -278,6 +287,9 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
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sectionBuilder.addCodeCoding(LOINC_URI, theSection.getSectionCode(), theSection.getSectionDisplay());
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for (IBaseResource next : theResourcesToInclude.getResources()) {
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if (ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.get(next) == BundleEntrySearchModeEnum.INCLUDE) {
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continue;
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}
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IBaseExtension<?, ?> narrativeLink = ((IBaseHasExtensions) next).addExtension();
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narrativeLink.setUrl("http://hl7.org/fhir/StructureDefinition/narrativeLink");
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@ -314,7 +326,18 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
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private String determinePatientCompartmentSearchParameterName(String theResourceType) {
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RuntimeResourceDefinition resourceDef = myFhirContext.getResourceDefinition(theResourceType);
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return resourceDef.getSearchParamsForCompartmentName("Patient").get(0).getName();
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Set<String> searchParams = resourceDef.getSearchParamsForCompartmentName("Patient")
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.stream()
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.map(RuntimeSearchParam::getName)
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.collect(Collectors.toSet());
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// Prefer "patient", then "subject" then anything else
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if (searchParams.contains(Observation.SP_PATIENT)) {
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return Observation.SP_PATIENT;
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}
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if (searchParams.contains(Observation.SP_SUBJECT)) {
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return Observation.SP_SUBJECT;
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}
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return searchParams.iterator().next();
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}
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private void massageResourceId(IpsContext theIpsContext, IBaseResource theResource) {
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@ -519,7 +542,7 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
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private final List<IBaseResource> myResources = new ArrayList<>();
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private final Map<String, IBaseResource> myIdToResource = new HashMap<>();
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private final Map<String, String> myOriginalIdToNewId = new HashMap<>();
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private final BiMap<String, String> myOriginalIdToNewId = HashBiMap.create();
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public List<IBaseResource> getResources() {
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return myResources;
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@ -549,6 +572,10 @@ public class IpsGeneratorSvcImpl implements IIpsGeneratorSvc {
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return getResourceById(theReference.toUnqualifiedVersionless().getValue());
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}
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public boolean hasResourceWithReplacementId(String theReplacementId) {
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return myOriginalIdToNewId.containsValue(theReplacementId);
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}
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public IBaseResource getResourceById(String theReference) {
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return myIdToResource.get(theReference);
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}
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@ -1,7 +1,7 @@
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package ca.uhn.fhir.jpa.ips.generator;
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import ca.uhn.fhir.batch2.jobs.models.BatchResourceId;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.jpa.api.config.DaoConfig;
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import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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import ca.uhn.fhir.jpa.ips.api.IIpsGenerationStrategy;
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import ca.uhn.fhir.jpa.ips.provider.IpsOperationProvider;
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@ -9,11 +9,16 @@ import ca.uhn.fhir.jpa.ips.strategy.DefaultIpsGenerationStrategy;
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import ca.uhn.fhir.jpa.model.util.JpaConstants;
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import ca.uhn.fhir.jpa.provider.BaseResourceProviderR4Test;
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import ca.uhn.fhir.util.ClasspathUtil;
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import ca.uhn.fhir.validation.FhirValidator;
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import ca.uhn.fhir.validation.ValidationResult;
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import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.r4.model.Bundle;
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import org.hl7.fhir.r4.model.Condition;
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import org.hl7.fhir.r4.model.MedicationStatement;
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import org.hl7.fhir.r4.model.Parameters;
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import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.Resource;
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import org.junit.jupiter.api.AfterEach;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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@ -22,10 +27,13 @@ import org.springframework.context.annotation.Bean;
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import org.springframework.context.annotation.Configuration;
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import org.springframework.test.context.ContextConfiguration;
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import java.util.List;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.matchesPattern;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertNull;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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@ContextConfiguration(classes = {IpsGenerationTest.IpsConfig.class})
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public class IpsGenerationTest extends BaseResourceProviderR4Test {
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@ -41,6 +49,7 @@ public class IpsGenerationTest extends BaseResourceProviderR4Test {
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@AfterEach
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public void afterEach() {
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myServer.withServer(t -> t.unregisterProvider(myIpsOperationProvider));
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myDaoConfig.setResourceClientIdStrategy(DaoConfig.ClientIdStrategyEnum.ALPHANUMERIC);
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}
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@ -65,26 +74,52 @@ public class IpsGenerationTest extends BaseResourceProviderR4Test {
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ourLog.info("Output: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(output));
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// Verify
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assertEquals(37, output.getEntry().size());
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String patientId = findFirstEntryResource(output, Patient.class).getId();
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validateDocument(outcome);
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assertEquals(117, output.getEntry().size());
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String patientId = findFirstEntryResource(output, Patient.class, 1).getId();
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assertThat(patientId, matchesPattern("urn:uuid:.*"));
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MedicationStatement medicationStatement = findFirstEntryResource(output, MedicationStatement.class);
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MedicationStatement medicationStatement = findFirstEntryResource(output, MedicationStatement.class, 2);
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assertEquals(patientId, medicationStatement.getSubject().getReference());
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assertNull(medicationStatement.getInformationSource().getReference());
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}
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@SuppressWarnings("unchecked")
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private <T extends IBaseResource> T findFirstEntryResource(Bundle theBundle, Class<T> theType) {
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return (T) theBundle
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.getEntry()
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.stream()
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.filter(t -> theType.isAssignableFrom(t.getResource().getClass()))
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.findFirst()
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.orElseThrow()
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.getResource();
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@Test
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public void testGenerateTinyPatientSummary() {
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myDaoConfig.setResourceClientIdStrategy(DaoConfig.ClientIdStrategyEnum.ANY);
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Bundle sourceData = ClasspathUtil.loadCompressedResource(myFhirContext, Bundle.class, "/tiny-patient-everything.json.gz");
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sourceData.setType(Bundle.BundleType.TRANSACTION);
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for (Bundle.BundleEntryComponent nextEntry : sourceData.getEntry()) {
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nextEntry.getRequest().setMethod(Bundle.HTTPVerb.PUT);
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nextEntry.getRequest().setUrl(nextEntry.getResource().getIdElement().toUnqualifiedVersionless().getValue());
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}
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Bundle outcome = mySystemDao.transaction(mySrd, sourceData);
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ourLog.info("Created {} resources", outcome.getEntry().size());
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Bundle output = myClient
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.operation()
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.onInstance("Patient/5342998")
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.named(JpaConstants.OPERATION_SUMMARY)
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.withNoParameters(Parameters.class)
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.returnResourceType(Bundle.class)
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.execute();
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ourLog.info("Output: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(output));
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// Verify
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validateDocument(outcome);
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assertEquals(7, output.getEntry().size());
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String patientId = findFirstEntryResource(output, Patient.class, 1).getId();
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assertThat(patientId, matchesPattern("urn:uuid:.*"));
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assertEquals(patientId, findEntryResource(output, Condition.class, 0, 2).getSubject().getReference());
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assertEquals(patientId, findEntryResource(output, Condition.class, 1, 2).getSubject().getReference());
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}
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private void validateDocument(Bundle theOutcome) {
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FhirValidator validator = myFhirContext.newValidator();
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validator.registerValidatorModule(new FhirInstanceValidator(myFhirContext));
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ValidationResult validation = validator.validateWithResult(theOutcome);
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assertTrue(validation.isSuccessful(), () -> myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(validation.toOperationOutcome()));
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}
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@Configuration
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public static class IpsConfig {
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@ -107,5 +142,21 @@ public class IpsGenerationTest extends BaseResourceProviderR4Test {
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}
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@SuppressWarnings("unchecked")
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private static <T extends IBaseResource> T findFirstEntryResource(Bundle theBundle, Class<T> theType, int theExpectedCount) {
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return findEntryResource(theBundle, theType, 0, theExpectedCount);
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}
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@SuppressWarnings("unchecked")
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static <T extends IBaseResource> T findEntryResource(Bundle theBundle, Class<T> theType, int index, int theExpectedCount) {
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List<Resource> resources = theBundle
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.getEntry()
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.stream()
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.map(Bundle.BundleEntryComponent::getResource)
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.filter(r -> theType.isAssignableFrom(r.getClass()))
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.toList();
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assertEquals(theExpectedCount, resources.size());
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return (T) resources.get(index);
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}
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}
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@ -33,6 +33,7 @@ import org.hl7.fhir.r4.model.DateTimeType;
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import org.hl7.fhir.r4.model.Device;
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import org.hl7.fhir.r4.model.DeviceUseStatement;
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import org.hl7.fhir.r4.model.DiagnosticReport;
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import org.hl7.fhir.r4.model.Encounter;
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import org.hl7.fhir.r4.model.IdType;
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import org.hl7.fhir.r4.model.Immunization;
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import org.hl7.fhir.r4.model.Medication;
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@ -60,12 +61,15 @@ import java.util.Collections;
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import java.util.List;
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import java.util.stream.Collectors;
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import static ca.uhn.fhir.jpa.ips.generator.IpsGenerationTest.findEntryResource;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.containsString;
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import static org.hamcrest.Matchers.startsWith;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.mockito.ArgumentMatchers.any;
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import static org.mockito.Mockito.mock;
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import static org.mockito.Mockito.times;
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import static org.mockito.Mockito.verify;
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import static org.mockito.Mockito.when;
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@ExtendWith(MockitoExtension.class)
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@ -74,6 +78,8 @@ public class IpsGeneratorSvcImplTest {
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public static final String MEDICATION_ID = "Medication/tyl";
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public static final String MEDICATION_STATEMENT_ID = "MedicationStatement/meds";
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public static final String MEDICATION_STATEMENT_ID2 = "MedicationStatement/meds2";
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public static final String PATIENT_ID = "Patient/123";
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public static final String ENCOUNTER_ID = "Encounter/encounter";
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private static final List<Class<? extends IBaseResource>> RESOURCE_TYPES = Lists.newArrayList(
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AllergyIntolerance.class,
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CarePlan.class,
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@ -157,7 +163,7 @@ public class IpsGeneratorSvcImplTest {
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registerRemainingResourceDaos();
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// Test
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Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType("Patient/123"));
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Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType(PATIENT_ID));
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// Verify Bundle Contents
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List<String> contentResourceTypes = toEntryResourceTypeStrings(outcome);
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@ -170,12 +176,7 @@ public class IpsGeneratorSvcImplTest {
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// Verify
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Composition compositions = (Composition) outcome.getEntry().get(0).getResource();
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Composition.SectionComponent section = compositions
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.getSection()
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.stream()
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.filter(t -> t.getTitle().equals(myStrategy.getSectionRegistry().getSection(IpsSectionEnum.MEDICATION_SUMMARY).getTitle()))
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.findFirst()
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.orElseThrow();
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Composition.SectionComponent section = findSection(compositions, IpsSectionEnum.MEDICATION_SUMMARY);
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HtmlPage narrativeHtml = HtmlUtil.parseAsHtml(section.getText().getDivAsString());
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ourLog.info("Narrative:\n{}", narrativeHtml.asXml());
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@ -191,6 +192,17 @@ public class IpsGeneratorSvcImplTest {
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assertThat(row.getCell(4).asNormalizedText(), containsString("2023"));
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}
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@Nonnull
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private Composition.SectionComponent findSection(Composition compositions, IpsSectionEnum sectionEnum) {
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Composition.SectionComponent section = compositions
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.getSection()
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.stream()
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.filter(t -> t.getTitle().equals(myStrategy.getSectionRegistry().getSection(sectionEnum).getTitle()))
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.findFirst()
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.orElseThrow();
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return section;
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}
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@Test
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public void testMedicationSummary_DuplicateSecondaryResources() {
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myStrategy.setSectionRegistry(new SectionRegistry().addGlobalCustomizer(t -> t.withNoInfoGenerator(null)));
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@ -209,7 +221,7 @@ public class IpsGeneratorSvcImplTest {
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registerRemainingResourceDaos();
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// Test
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Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType("Patient/123"));
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Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType(PATIENT_ID));
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// Verify Bundle Contents
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List<String> contentResourceTypes = toEntryResourceTypeStrings(outcome);
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@ -248,7 +260,7 @@ public class IpsGeneratorSvcImplTest {
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registerRemainingResourceDaos();
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// Test
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Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType("Patient/123"));
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Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType(PATIENT_ID));
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// Verify Bundle Contents
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List<String> contentResourceTypes = toEntryResourceTypeStrings(outcome);
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@ -263,12 +275,7 @@ public class IpsGeneratorSvcImplTest {
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// Verify narrative - should have 2 rows (one for each primary MedicationStatement)
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Composition compositions = (Composition) outcome.getEntry().get(0).getResource();
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Composition.SectionComponent section = compositions
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.getSection()
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.stream()
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.filter(t -> t.getTitle().equals(myStrategy.getSectionRegistry().getSection(IpsSectionEnum.MEDICATION_SUMMARY).getTitle()))
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.findFirst()
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.orElseThrow();
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Composition.SectionComponent section = findSection(compositions, IpsSectionEnum.MEDICATION_SUMMARY);
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HtmlPage narrativeHtml = HtmlUtil.parseAsHtml(section.getText().getDivAsString());
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ourLog.info("Narrative:\n{}", narrativeHtml.asXml());
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|
|
@ -304,16 +311,11 @@ public class IpsGeneratorSvcImplTest {
|
|||
registerRemainingResourceDaos();
|
||||
|
||||
// Test
|
||||
Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType("Patient/123"));
|
||||
Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType(PATIENT_ID));
|
||||
|
||||
// Verify
|
||||
Composition compositions = (Composition) outcome.getEntry().get(0).getResource();
|
||||
Composition.SectionComponent section = compositions
|
||||
.getSection()
|
||||
.stream()
|
||||
.filter(t -> t.getTitle().equals(myStrategy.getSectionRegistry().getSection(IpsSectionEnum.MEDICAL_DEVICES).getTitle()))
|
||||
.findFirst()
|
||||
.orElseThrow();
|
||||
Composition.SectionComponent section = findSection(compositions, IpsSectionEnum.MEDICAL_DEVICES);
|
||||
|
||||
HtmlPage narrativeHtml = HtmlUtil.parseAsHtml(section.getText().getDivAsString());
|
||||
ourLog.info("Narrative:\n{}", narrativeHtml.asXml());
|
||||
|
|
@ -356,16 +358,11 @@ public class IpsGeneratorSvcImplTest {
|
|||
registerRemainingResourceDaos();
|
||||
|
||||
// Test
|
||||
Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType("Patient/123"));
|
||||
Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType(PATIENT_ID));
|
||||
|
||||
// Verify
|
||||
Composition compositions = (Composition) outcome.getEntry().get(0).getResource();
|
||||
Composition.SectionComponent section = compositions
|
||||
.getSection()
|
||||
.stream()
|
||||
.filter(t -> t.getTitle().equals(myStrategy.getSectionRegistry().getSection(IpsSectionEnum.IMMUNIZATIONS).getTitle()))
|
||||
.findFirst()
|
||||
.orElseThrow();
|
||||
Composition.SectionComponent section = findSection(compositions, IpsSectionEnum.IMMUNIZATIONS);
|
||||
|
||||
HtmlPage narrativeHtml = HtmlUtil.parseAsHtml(section.getText().getDivAsString());
|
||||
ourLog.info("Narrative:\n{}", narrativeHtml.asXml());
|
||||
|
|
@ -383,10 +380,82 @@ public class IpsGeneratorSvcImplTest {
|
|||
assertThat(row.getCell(6).asNormalizedText(), containsString("2023"));
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testReferencesUpdatedInSecondaryInclusions() {
|
||||
// Setup Patient
|
||||
registerPatientDaoWithRead();
|
||||
|
||||
// Setup Medication + MedicationStatement
|
||||
Encounter encounter = new Encounter();
|
||||
encounter.setId(new IdType(ENCOUNTER_ID));
|
||||
encounter.setSubject(new Reference(PATIENT_ID));
|
||||
ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(encounter, BundleEntrySearchModeEnum.INCLUDE);
|
||||
|
||||
Condition conditionActive = new Condition();
|
||||
conditionActive.setId("Condition/conditionActive");
|
||||
conditionActive.getClinicalStatus().addCoding()
|
||||
.setSystem("http://terminology.hl7.org/CodeSystem/condition-clinical")
|
||||
.setCode("active");
|
||||
conditionActive.setSubject(new Reference(PATIENT_ID));
|
||||
conditionActive.setEncounter(new Reference(ENCOUNTER_ID));
|
||||
ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(conditionActive, BundleEntrySearchModeEnum.MATCH);
|
||||
|
||||
Condition conditionResolved = new Condition();
|
||||
conditionResolved.setId("Condition/conditionResolved");
|
||||
conditionResolved.getClinicalStatus().addCoding()
|
||||
.setSystem("http://terminology.hl7.org/CodeSystem/condition-clinical")
|
||||
.setCode("resolved");
|
||||
conditionResolved.setSubject(new Reference(PATIENT_ID));
|
||||
conditionResolved.setEncounter(new Reference(ENCOUNTER_ID));
|
||||
ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(conditionResolved, BundleEntrySearchModeEnum.MATCH);
|
||||
|
||||
// Conditions will be loaded from two sections (problem list and illness history) so
|
||||
// we return an active condition the first time and a resolved one the second
|
||||
IFhirResourceDao<Condition> conditionDao = registerResourceDaoWithNoData(Condition.class);
|
||||
when(conditionDao.search(any(), any())).thenReturn(
|
||||
new SimpleBundleProvider(Lists.newArrayList(conditionActive, encounter)),
|
||||
new SimpleBundleProvider(Lists.newArrayList(conditionResolved, encounter))
|
||||
);
|
||||
|
||||
registerRemainingResourceDaos();
|
||||
|
||||
// Test
|
||||
Bundle outcome = (Bundle) mySvc.generateIps(new SystemRequestDetails(), new IdType(PATIENT_ID));
|
||||
|
||||
// Verify cross-references
|
||||
Patient addedPatient = findEntryResource(outcome, Patient.class, 0, 1);
|
||||
assertThat(addedPatient.getId(), startsWith("urn:uuid:"));
|
||||
Condition addedCondition = findEntryResource(outcome, Condition.class, 0, 2);
|
||||
assertThat(addedCondition.getId(), startsWith("urn:uuid:"));
|
||||
Condition addedCondition2 = findEntryResource(outcome, Condition.class, 1, 2);
|
||||
assertThat(addedCondition2.getId(), startsWith("urn:uuid:"));
|
||||
Encounter addedEncounter = findEntryResource(outcome, Encounter.class, 0, 1);
|
||||
assertThat(addedEncounter.getId(), startsWith("urn:uuid:"));
|
||||
MedicationStatement addedMedicationStatement = findEntryResource(outcome, MedicationStatement.class, 0, 1);
|
||||
assertThat(addedMedicationStatement.getId(), startsWith("urn:uuid:"));
|
||||
assertEquals("no-medication-info", addedMedicationStatement.getMedicationCodeableConcept().getCodingFirstRep().getCode());
|
||||
assertEquals(addedPatient.getId(), addedCondition.getSubject().getReference());
|
||||
assertEquals(addedEncounter.getId(), addedCondition.getEncounter().getReference());
|
||||
assertEquals(addedPatient.getId(), addedEncounter.getSubject().getReference());
|
||||
assertEquals(addedPatient.getId(), addedMedicationStatement.getSubject().getReference());
|
||||
|
||||
// Verify sections
|
||||
ourLog.info("Resource: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
|
||||
verify(conditionDao, times(2)).search(any(), any());
|
||||
Composition composition = (Composition) outcome.getEntry().get(0).getResource();
|
||||
Composition.SectionComponent problemListSection = findSection(composition, IpsSectionEnum.PROBLEM_LIST);
|
||||
assertEquals(addedCondition.getId(), problemListSection.getEntry().get(0).getReference());
|
||||
assertEquals(1, problemListSection.getEntry().size());
|
||||
Composition.SectionComponent illnessHistorySection = findSection(composition, IpsSectionEnum.ILLNESS_HISTORY);
|
||||
assertEquals(addedCondition2.getId(), illnessHistorySection.getEntry().get(0).getReference());
|
||||
assertEquals(1, illnessHistorySection.getEntry().size());
|
||||
}
|
||||
|
||||
private void registerPatientDaoWithRead() {
|
||||
IFhirResourceDao<Patient> patientDao = registerResourceDaoWithNoData(Patient.class);
|
||||
Patient patient = new Patient();
|
||||
patient.setId("Patient/123");
|
||||
patient.setId(PATIENT_ID);
|
||||
when(patientDao.read(any(), any())).thenReturn(patient);
|
||||
}
|
||||
|
||||
|
|
@ -432,12 +501,11 @@ public class IpsGeneratorSvcImplTest {
|
|||
|
||||
@Nonnull
|
||||
private static List<String> toEntryResourceTypeStrings(Bundle outcome) {
|
||||
List<String> contentResourceTypes = outcome
|
||||
return outcome
|
||||
.getEntry()
|
||||
.stream()
|
||||
.map(t -> t.getResource().getResourceType().name())
|
||||
.collect(Collectors.toList());
|
||||
return contentResourceTypes;
|
||||
}
|
||||
|
||||
@Nonnull
|
||||
|
|
|
|||
Binary file not shown.
|
|
@ -53,6 +53,11 @@
|
|||
<artifactId>hapi-fhir-server-openapi</artifactId>
|
||||
<version>${project.version}</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-jpaserver-ips</artifactId>
|
||||
<version>${project.version}</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>com.helger</groupId>
|
||||
|
|
|
|||
|
|
@ -12,6 +12,7 @@ import ca.uhn.fhir.jpa.bulk.export.provider.BulkDataExportProvider;
|
|||
import ca.uhn.fhir.jpa.delete.ThreadSafeResourceDeleterSvc;
|
||||
import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
|
||||
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
|
||||
import ca.uhn.fhir.jpa.ips.provider.IpsOperationProvider;
|
||||
import ca.uhn.fhir.jpa.provider.DiffProvider;
|
||||
import ca.uhn.fhir.jpa.provider.JpaCapabilityStatementProvider;
|
||||
import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
|
||||
|
|
@ -152,6 +153,7 @@ public class TestRestfulServer extends RestfulServer {
|
|||
setServerConformanceProvider(confProvider);
|
||||
providers.add(myAppCtx.getBean(TerminologyUploaderProvider.class));
|
||||
providers.add(myAppCtx.getBean(GraphQLProvider.class));
|
||||
providers.add(myAppCtx.getBean(IpsOperationProvider.class));
|
||||
break;
|
||||
}
|
||||
case "R4B": {
|
||||
|
|
|
|||
|
|
@ -2,9 +2,15 @@ package ca.uhn.fhirtest.config;
|
|||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.jpa.api.config.DaoConfig;
|
||||
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
||||
import ca.uhn.fhir.jpa.config.HapiJpaConfig;
|
||||
import ca.uhn.fhir.jpa.config.r4.JpaR4Config;
|
||||
import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
|
||||
import ca.uhn.fhir.jpa.ips.api.IIpsGenerationStrategy;
|
||||
import ca.uhn.fhir.jpa.ips.generator.IIpsGeneratorSvc;
|
||||
import ca.uhn.fhir.jpa.ips.generator.IpsGeneratorSvcImpl;
|
||||
import ca.uhn.fhir.jpa.ips.provider.IpsOperationProvider;
|
||||
import ca.uhn.fhir.jpa.ips.strategy.DefaultIpsGenerationStrategy;
|
||||
import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
|
||||
import ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect;
|
||||
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
|
||||
|
|
@ -196,5 +202,19 @@ public class TestR4Config {
|
|||
return new PropertySourcesPlaceholderConfigurer();
|
||||
}
|
||||
|
||||
@Bean
|
||||
public IIpsGenerationStrategy ipsGenerationStrategy() {
|
||||
return new DefaultIpsGenerationStrategy();
|
||||
}
|
||||
|
||||
@Bean
|
||||
public IIpsGeneratorSvc ipsGeneratorSvc(FhirContext theFhirContext, IIpsGenerationStrategy theGenerationStrategy, DaoRegistry theDaoRegistry) {
|
||||
return new IpsGeneratorSvcImpl(theFhirContext, theGenerationStrategy, theDaoRegistry);
|
||||
}
|
||||
|
||||
@Bean
|
||||
public IpsOperationProvider ipsOperationProvider(IIpsGeneratorSvc theIpsGeneratorSvc) {
|
||||
return new IpsOperationProvider(theIpsGeneratorSvc);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue