Add support for _lanugage SP (#5300)

* Add support for _lanugage SP

* Add changelog

* Formatting fix

* Add to JPA

* Add validator

* Validate language SP

* Assign new code

* Fixes
This commit is contained in:
James Agnew 2023-09-12 20:35:17 -04:00 committed by GitHub
parent d4717a08d6
commit 2da8aafad0
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14 changed files with 584 additions and 412 deletions

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@ -182,6 +182,11 @@ public class Constants {
public static final String PARAM_HAS = "_has";
public static final String PARAM_HISTORY = "_history";
public static final String PARAM_INCLUDE = "_include";
/**
* @since 7.0.0
*/
public static final String PARAM_LANGUAGE = "_language";
public static final String PARAM_INCLUDE_QUALIFIER_RECURSE = ":recurse";
public static final String PARAM_INCLUDE_RECURSE = "_include" + PARAM_INCLUDE_QUALIFIER_RECURSE;
public static final String PARAM_INCLUDE_QUALIFIER_ITERATE = ":iterate";

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@ -0,0 +1,6 @@
---
type: fix
issue: 5300
title: "A bug in DefaultProfileValidationSupport in R5 mode caused it to return duplicates
in the lists returned by `fetchAllStructureDefinitions()`, `fetchAllSearchParameters()`, etc.
This has been corrected."

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@ -0,0 +1,5 @@
---
type: add
issue: 5300
title: "A new configuration option has been added to `StorageSettings` which enables
support in the JPA server for the `_language` SearchParameter."

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@ -138,6 +138,13 @@ public class StorageSettings {
* Since 6.4.0
*/
private boolean myQualifySubscriptionMatchingChannelName = true;
/**
* Should the {@literal _lamguage} SearchParameter be supported
* on this server?
*
* @since 7.0.0
*/
private boolean myLanguageSearchParameterEnabled = false;
/**
* If set to true, the server will prevent the creation of Subscriptions which cannot be evaluated IN-MEMORY. This can improve
@ -1295,6 +1302,23 @@ public class StorageSettings {
return myQualifySubscriptionMatchingChannelName;
}
/**
* @return Should the {@literal _lamguage} SearchParameter be supported on this server? Defaults to {@literal false}.
* @since 7.0.0
*/
public boolean isLanguageSearchParameterEnabled() {
return myLanguageSearchParameterEnabled;
}
/**
* Should the {@literal _lamguage} SearchParameter be supported on this server? Defaults to {@literal false}.
*
* @since 7.0.0
*/
public void setLanguageSearchParameterEnabled(boolean theLanguageSearchParameterEnabled) {
myLanguageSearchParameterEnabled = theLanguageSearchParameterEnabled;
}
private static void validateTreatBaseUrlsAsLocal(String theUrl) {
Validate.notBlank(theUrl, "Base URL must not be null or empty");

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@ -165,7 +165,7 @@ public class MatchUrlService {
IQueryParameterAnd<?> param = JpaParamUtil.parseQueryParams(
myFhirContext, RestSearchParameterTypeEnum.TOKEN, nextParamName, paramList);
paramMap.add(nextParamName, param);
} else if (nextParamName.startsWith("_")) {
} else if (nextParamName.startsWith("_") && !Constants.PARAM_LANGUAGE.equals(nextParamName)) {
// ignore these since they aren't search params (e.g. _sort)
} else {
RuntimeSearchParam paramDef =

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@ -32,6 +32,8 @@ import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
import ca.uhn.fhir.jpa.cache.ResourceChangeResult;
import ca.uhn.fhir.jpa.model.entity.StorageSettings;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
@ -193,6 +195,31 @@ public class SearchParamRegistryImpl
long overriddenCount = overrideBuiltinSearchParamsWithActiveJpaSearchParams(searchParams, theJpaSearchParams);
ourLog.trace("Have overridden {} built-in search parameters", overriddenCount);
removeInactiveSearchParams(searchParams);
/*
* The _language SearchParameter is a weird exception - It is actually just a normal
* token SP, but we explcitly ban SPs from registering themselves with a prefix
* of "_" since that's system reserved so we put this one behind a settings toggle
*/
if (myStorageSettings.isLanguageSearchParameterEnabled()) {
IIdType id = myFhirContext.getVersion().newIdType();
id.setValue("SearchParameter/Resource-language");
RuntimeSearchParam sp = new RuntimeSearchParam(
id,
"http://hl7.org/fhir/SearchParameter/Resource-language",
Constants.PARAM_LANGUAGE,
"Language of the resource content",
"language",
RestSearchParameterTypeEnum.TOKEN,
Collections.emptySet(),
Collections.emptySet(),
RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE,
myFhirContext.getResourceTypes());
for (String baseResourceType : sp.getBase()) {
searchParams.add(baseResourceType, sp.getName(), sp);
}
}
myActiveSearchParams = searchParams;
myJpaSearchParamCache.populateActiveSearchParams(
@ -282,7 +309,13 @@ public class SearchParamRegistryImpl
@Override
public void forceRefresh() {
RuntimeSearchParamCache activeSearchParams = myActiveSearchParams;
myResourceChangeListenerCache.forceRefresh();
// If the refresh didn't trigger a change, proceed with one anyway
if (myActiveSearchParams == activeSearchParams) {
rebuildActiveSearchParams();
}
}
@Override

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@ -40,8 +40,10 @@ import java.util.List;
import java.util.stream.Collectors;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.junit.jupiter.api.Assertions.fail;
@ContextConfiguration(classes = TestHSearchAddInConfig.NoFT.class)
@ -51,7 +53,10 @@ public class FhirResourceDaoR5SearchNoFtTest extends BaseJpaR5Test {
@AfterEach
public void after() {
myStorageSettings.setIndexMissingFields(new JpaStorageSettings().getIndexMissingFields());
JpaStorageSettings defaults = new JpaStorageSettings();
myStorageSettings.setIndexMissingFields(defaults.getIndexMissingFields());
myStorageSettings.setLanguageSearchParameterEnabled(defaults.isLanguageSearchParameterEnabled());
mySearchParamRegistry.forceRefresh();
}
@Test
@ -79,6 +84,7 @@ public class FhirResourceDaoR5SearchNoFtTest extends BaseJpaR5Test {
IBundleProvider outcome = myPractitionerDao.search(params);
assertEquals(1, outcome.getResources(0, 1).size());
}
@Test
public void testHasWithTargetReferenceQualified() {
Organization org = new Organization();
@ -208,7 +214,7 @@ public class FhirResourceDaoR5SearchNoFtTest extends BaseJpaR5Test {
ClinicalUseDefinition def2 = new ClinicalUseDefinition();
def2.getContraindication().getDiseaseSymptomProcedure().setConcept(new CodeableConcept().addCoding(new Coding("http://foo", "bar", "baz")));
String id =myClinicalUseDefinitionDao.create(def2, mySrd).getId().toUnqualifiedVersionless().getValue();
String id = myClinicalUseDefinitionDao.create(def2, mySrd).getId().toUnqualifiedVersionless().getValue();
// Test
@ -334,5 +340,33 @@ public class FhirResourceDaoR5SearchNoFtTest extends BaseJpaR5Test {
}
}
@Test
public void testLanguageSearchParameter_DefaultDisabled() {
createObservation(withId("A"), withLanguage("en"));
createObservation(withId("B"), withLanguage("fr"));
logAllTokenIndexes();
runInTransaction(() -> assertEquals(0, myResourceIndexedSearchParamTokenDao.count()));
SearchParameterMap params = SearchParameterMap.newSynchronous();
params.add(Constants.PARAM_LANGUAGE, new TokenParam("en"));
assertThrows(InvalidRequestException.class, () -> myObservationDao.search(params, mySrd));
}
@Test
public void testLanguageSearchParameter_Enabled() {
myStorageSettings.setLanguageSearchParameterEnabled(true);
mySearchParamRegistry.forceRefresh();
createObservation(withId("A"), withLanguage("en"));
createObservation(withId("B"), withLanguage("fr"));
logAllTokenIndexes();
runInTransaction(() -> assertEquals(2, myResourceIndexedSearchParamTokenDao.count()));
SearchParameterMap params = SearchParameterMap.newSynchronous();
params.add(Constants.PARAM_LANGUAGE, new TokenParam("en"));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params, mySrd)), contains("Observation/A"));
}
}

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@ -46,19 +46,6 @@ import static org.mockito.Mockito.lenient;
@ExtendWith(MockitoExtension.class)
public class SearchParameterDaoValidatorTest {
@Spy
private FhirContext myFhirContext = FhirContext.forR5Cached();
@Mock
private ISearchParamRegistry mySearchParamRegistry;
@Spy
private JpaStorageSettings myStorageSettings = new JpaStorageSettings();
@InjectMocks
private SearchParameterDaoValidator mySvc;
private final VersionCanonicalizer myVersionCanonicalizer = new VersionCanonicalizer(myFhirContext);
private final SearchParameterCanonicalizer mySearchParameterCanonicalizer = new SearchParameterCanonicalizer(myFhirContext);
private static final String SP_COMPONENT_DEFINITION_OF_TYPE_TOKEN = "SearchParameter/observation-code";
private static final String SP_COMPONENT_DEFINITION_OF_TYPE_REFERENCE = "SearchParameter/observation-patient";
private static final String SP_COMPONENT_DEFINITION_OF_TYPE_STRING = "SearchParameter/observation-markdown";
@ -66,6 +53,16 @@ public class SearchParameterDaoValidatorTest {
private static final String SP_COMPONENT_DEFINITION_OF_TYPE_QUANTITY = "SearchParameter/observation-code";
private static final String SP_COMPONENT_DEFINITION_OF_TYPE_URI = "SearchParameter/component-value-canonical";
private static final String SP_COMPONENT_DEFINITION_OF_TYPE_NUMBER = "SearchParameter/component-value-number";
@Spy
private FhirContext myFhirContext = FhirContext.forR5Cached();
private final VersionCanonicalizer myVersionCanonicalizer = new VersionCanonicalizer(myFhirContext);
private final SearchParameterCanonicalizer mySearchParameterCanonicalizer = new SearchParameterCanonicalizer(myFhirContext);
@Mock
private ISearchParamRegistry mySearchParamRegistry;
@Spy
private JpaStorageSettings myStorageSettings = new JpaStorageSettings();
@InjectMocks
private SearchParameterDaoValidator mySvc;
@BeforeEach
public void before() {

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@ -6,5 +6,6 @@ public class CommonJpaStorageSettingsConfigurer {
public CommonJpaStorageSettingsConfigurer(JpaStorageSettings theStorageSettings) {
theStorageSettings.setIndexOnUpliftedRefchains(true);
theStorageSettings.setMarkResourcesForReindexingUponSearchParameterChange(false);
theStorageSettings.setLanguageSearchParameterEnabled(true);
}
}

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@ -98,10 +98,12 @@ public class SearchParameterDaoValidator {
return;
}
// Search parameters must have a base
if (isCompositeWithoutBase(searchParameter)) {
throw new UnprocessableEntityException(Msg.code(1113) + "SearchParameter.base is missing");
}
// Do we have a valid expression
if (isCompositeWithoutExpression(searchParameter)) {
// this is ok

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@ -80,6 +80,13 @@ public interface ITestDataBuilder {
return t -> __setPrimitiveChild(getFhirContext(), t, "active", "boolean", "false");
}
/**
* Set Resource.language
*/
default ICreationArgument withLanguage(String theLanguage) {
return t -> __setPrimitiveChild(getFhirContext(), t, "language", "string", theLanguage);
}
/**
* Set Patient.gender
*/

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@ -16,12 +16,14 @@ import org.hl7.fhir.r4.model.ValueSet;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
@ -34,10 +36,14 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class PrePopulatedValidationSupport extends BaseStaticResourceValidationSupport
implements IValidationSupport, ILockable {
private final Map<String, IBaseResource> myCodeSystems;
private final Map<String, IBaseResource> myStructureDefinitions;
private final Map<String, IBaseResource> mySearchParameters;
private final Map<String, IBaseResource> myValueSets;
private final Map<String, IBaseResource> myUrlToCodeSystems;
private final Map<String, IBaseResource> myUrlToStructureDefinitions;
private final Map<String, IBaseResource> myUrlToSearchParameters;
private final Map<String, IBaseResource> myUrlToValueSets;
private final List<IBaseResource> myCodeSystems;
private final List<IBaseResource> myStructureDefinitions;
private final List<IBaseResource> mySearchParameters;
private final List<IBaseResource> myValueSets;
private final Map<String, byte[]> myBinaries;
private boolean myLocked;
@ -51,51 +57,67 @@ public class PrePopulatedValidationSupport extends BaseStaticResourceValidationS
/**
* Constructor
*
* @param theStructureDefinitions The StructureDefinitions to be returned by this module. Keys are the logical URL for the resource, and
* @param theUrlToStructureDefinitions The StructureDefinitions to be returned by this module. Keys are the logical URL for the resource, and
* values are the resource itself.
* @param theValueSets The ValueSets to be returned by this module. Keys are the logical URL for the resource, and values are
* @param theUrlToValueSets The ValueSets to be returned by this module. Keys are the logical URL for the resource, and values are
* the resource itself.
* @param theCodeSystems The CodeSystems to be returned by this module. Keys are the logical URL for the resource, and values are
* @param theUrlToCodeSystems The CodeSystems to be returned by this module. Keys are the logical URL for the resource, and values are
* the resource itself.
**/
public PrePopulatedValidationSupport(
FhirContext theFhirContext,
Map<String, IBaseResource> theStructureDefinitions,
Map<String, IBaseResource> theValueSets,
Map<String, IBaseResource> theCodeSystems) {
this(theFhirContext, theStructureDefinitions, theValueSets, theCodeSystems, new HashMap<>(), new HashMap<>());
Map<String, IBaseResource> theUrlToStructureDefinitions,
Map<String, IBaseResource> theUrlToValueSets,
Map<String, IBaseResource> theUrlToCodeSystems) {
this(
theFhirContext,
theUrlToStructureDefinitions,
theUrlToValueSets,
theUrlToCodeSystems,
new HashMap<>(),
new HashMap<>());
}
/**
* Constructor
*
* @param theStructureDefinitions The StructureDefinitions to be returned by this module. Keys are the logical URL for the resource, and
* @param theUrlToStructureDefinitions The StructureDefinitions to be returned by this module. Keys are the logical URL for the resource, and
* values are the resource itself.
* @param theValueSets The ValueSets to be returned by this module. Keys are the logical URL for the resource, and values are
* @param theUrlToValueSets The ValueSets to be returned by this module. Keys are the logical URL for the resource, and values are
* the resource itself.
* @param theCodeSystems The CodeSystems to be returned by this module. Keys are the logical URL for the resource, and values are
* @param theUrlToCodeSystems The CodeSystems to be returned by this module. Keys are the logical URL for the resource, and values are
* the resource itself.
* @param theBinaries The binary files to be returned by this module. Keys are the unique filename for the binary, and values
* are the contents of the file as a byte array.
*/
public PrePopulatedValidationSupport(
FhirContext theFhirContext,
Map<String, IBaseResource> theStructureDefinitions,
Map<String, IBaseResource> theValueSets,
Map<String, IBaseResource> theCodeSystems,
Map<String, IBaseResource> theSearchParameters,
Map<String, IBaseResource> theUrlToStructureDefinitions,
Map<String, IBaseResource> theUrlToValueSets,
Map<String, IBaseResource> theUrlToCodeSystems,
Map<String, IBaseResource> theUrlToSearchParameters,
Map<String, byte[]> theBinaries) {
super(theFhirContext);
Validate.notNull(theFhirContext, "theFhirContext must not be null");
Validate.notNull(theStructureDefinitions, "theStructureDefinitions must not be null");
Validate.notNull(theValueSets, "theValueSets must not be null");
Validate.notNull(theCodeSystems, "theCodeSystems must not be null");
Validate.notNull(theSearchParameters, "theSearchParameters must not be null");
Validate.notNull(theUrlToStructureDefinitions, "theStructureDefinitions must not be null");
Validate.notNull(theUrlToValueSets, "theValueSets must not be null");
Validate.notNull(theUrlToCodeSystems, "theCodeSystems must not be null");
Validate.notNull(theUrlToSearchParameters, "theSearchParameters must not be null");
Validate.notNull(theBinaries, "theBinaries must not be null");
myStructureDefinitions = theStructureDefinitions;
myValueSets = theValueSets;
myCodeSystems = theCodeSystems;
mySearchParameters = theSearchParameters;
myUrlToStructureDefinitions = theUrlToStructureDefinitions;
myStructureDefinitions =
theUrlToStructureDefinitions.values().stream().distinct().collect(Collectors.toList());
myUrlToValueSets = theUrlToValueSets;
myValueSets = theUrlToValueSets.values().stream().distinct().collect(Collectors.toList());
myUrlToCodeSystems = theUrlToCodeSystems;
myCodeSystems = theUrlToCodeSystems.values().stream().distinct().collect(Collectors.toList());
myUrlToSearchParameters = theUrlToSearchParameters;
mySearchParameters =
theUrlToSearchParameters.values().stream().distinct().collect(Collectors.toList());
myBinaries = theBinaries;
}
@ -127,7 +149,7 @@ public class PrePopulatedValidationSupport extends BaseStaticResourceValidationS
public void addCodeSystem(IBaseResource theCodeSystem) {
validateNotLocked();
Set<String> urls = processResourceAndReturnUrls(theCodeSystem, "CodeSystem");
addToMap(theCodeSystem, myCodeSystems, urls);
addToMap(theCodeSystem, myCodeSystems, myUrlToCodeSystems, urls);
}
private Set<String> processResourceAndReturnUrls(IBaseResource theResource, String theResourceName) {
@ -185,16 +207,18 @@ public class PrePopulatedValidationSupport extends BaseStaticResourceValidationS
public void addStructureDefinition(IBaseResource theStructureDefinition) {
validateNotLocked();
Set<String> url = processResourceAndReturnUrls(theStructureDefinition, "StructureDefinition");
addToMap(theStructureDefinition, myStructureDefinitions, url);
addToMap(theStructureDefinition, myStructureDefinitions, myUrlToStructureDefinitions, url);
}
public void addSearchParameter(IBaseResource theSearchParameter) {
validateNotLocked();
Set<String> url = processResourceAndReturnUrls(theSearchParameter, "SearchParameter");
addToMap(theSearchParameter, mySearchParameters, url);
addToMap(theSearchParameter, mySearchParameters, myUrlToSearchParameters, url);
}
private <T extends IBaseResource> void addToMap(T theResource, Map<String, T> theMap, Collection<String> theUrls) {
private <T extends IBaseResource> void addToMap(
T theResource, List<T> theList, Map<String, T> theMap, Collection<String> theUrls) {
theList.add(theResource);
for (String urls : theUrls) {
if (isNotBlank(urls)) {
theMap.put(urls, theResource);
@ -228,7 +252,7 @@ public class PrePopulatedValidationSupport extends BaseStaticResourceValidationS
public void addValueSet(IBaseResource theValueSet) {
validateNotLocked();
Set<String> urls = processResourceAndReturnUrls(theValueSet, "ValueSet");
addToMap(theValueSet, myValueSets, urls);
addToMap(theValueSet, myValueSets, myUrlToValueSets, urls);
}
/**
@ -259,36 +283,38 @@ public class PrePopulatedValidationSupport extends BaseStaticResourceValidationS
@Override
public List<IBaseResource> fetchAllConformanceResources() {
ArrayList<IBaseResource> retVal = new ArrayList<>();
retVal.addAll(myCodeSystems.values());
retVal.addAll(myStructureDefinitions.values());
retVal.addAll(myValueSets.values());
retVal.addAll(myCodeSystems);
retVal.addAll(myStructureDefinitions);
retVal.addAll(myValueSets);
return retVal;
}
@SuppressWarnings("unchecked")
@Nullable
@Override
public <T extends IBaseResource> List<T> fetchAllSearchParameters() {
return toList(mySearchParameters);
return (List<T>) Collections.unmodifiableList(mySearchParameters);
}
@SuppressWarnings("unchecked")
@Override
public <T extends IBaseResource> List<T> fetchAllStructureDefinitions() {
return toList(myStructureDefinitions);
return (List<T>) Collections.unmodifiableList(myStructureDefinitions);
}
@Override
public IBaseResource fetchCodeSystem(String theSystem) {
return myCodeSystems.get(theSystem);
return myUrlToCodeSystems.get(theSystem);
}
@Override
public IBaseResource fetchValueSet(String theUri) {
return myValueSets.get(theUri);
return myUrlToValueSets.get(theUri);
}
@Override
public IBaseResource fetchStructureDefinition(String theUrl) {
return myStructureDefinitions.get(theUrl);
return myUrlToStructureDefinitions.get(theUrl);
}
@Override
@ -298,19 +324,23 @@ public class PrePopulatedValidationSupport extends BaseStaticResourceValidationS
@Override
public boolean isCodeSystemSupported(ValidationSupportContext theValidationSupportContext, String theSystem) {
return myCodeSystems.containsKey(theSystem);
return myUrlToCodeSystems.containsKey(theSystem);
}
@Override
public boolean isValueSetSupported(ValidationSupportContext theValidationSupportContext, String theValueSetUrl) {
return myValueSets.containsKey(theValueSetUrl);
return myUrlToValueSets.containsKey(theValueSetUrl);
}
/**
* Returns a count of all known resources
*/
public int countAll() {
return myBinaries.size() + myCodeSystems.size() + myStructureDefinitions.size() + myValueSets.size();
return myBinaries.size()
+ myCodeSystems.size()
+ myStructureDefinitions.size()
+ myValueSets.size()
+ myStructureDefinitions.size();
}
@Override

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@ -2,7 +2,6 @@ package org.hl7.fhir.dstu3.hapi.validation;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.CodeSystem;
import org.junit.jupiter.api.Test;
@ -10,7 +9,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
public class DefaultProfileValidationSupportTest {
public class DefaultProfileValidationSupportR4Test {
private static FhirContext ourCtx = FhirContext.forR4Cached();
private DefaultProfileValidationSupport mySvc = new DefaultProfileValidationSupport(ourCtx);

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@ -0,0 +1,29 @@
package org.hl7.fhir.dstu3.hapi.validation;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.junit.jupiter.api.Test;
import java.util.List;
import java.util.stream.Collectors;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class DefaultProfileValidationSupportR5Test {
private static FhirContext ourCtx = FhirContext.forR5Cached();
private DefaultProfileValidationSupport mySvc = new DefaultProfileValidationSupport(ourCtx);
@Test
public void testNoDuplicates() {
List<IBaseResource> allSds = mySvc.fetchAllStructureDefinitions()
.stream()
.map(t->(StructureDefinition)t)
.filter(t->t.getUrl().equals("http://hl7.org/fhir/StructureDefinition/language"))
.collect(Collectors.toList());
assertEquals(1, allSds.size());
}
}