[6463] use version in canonical url of StructureDefinition to identify it (#6534)
* [6463] use version in canonical url of StructureDefinition to identify it * Add credit for #6534 --------- Co-authored-by: James Agnew <jamesagnew@gmail.com>
This commit is contained in:
Mangala Ekanayake
GitHub
parent
06580742d4
commit
f1318915fe
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@ -0,0 +1,6 @@
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---
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type: add
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issue: 6534
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title: "The JpaPersistedValidationSupport module which is used to fetch
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conformance resources from the JPA repository for validation purposes can
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now support versioned URLs. Thanks to Mangala Ekanayake for the contribution!"
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@ -235,7 +235,12 @@ public class JpaPersistedResourceValidationSupport implements IValidationSupport
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}
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SearchParameterMap params = new SearchParameterMap();
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params.setLoadSynchronousUpTo(1);
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int versionSeparator = theUri.lastIndexOf('|');
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if (versionSeparator != -1) {params.add(StructureDefinition.SP_VERSION, new TokenParam(theUri.substring(versionSeparator + 1)));
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params.add(StructureDefinition.SP_URL, new UriParam(theUri.substring(0, versionSeparator)));
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} else {
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params.add(StructureDefinition.SP_URL, new UriParam(theUri));
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}
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search = myDaoRegistry.getResourceDao("StructureDefinition").search(params);
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break;
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}
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@ -0,0 +1,119 @@
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package ca.uhn.fhir.jpa.dao;
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/*-
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* #%L
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* HAPI FHIR JPA Server
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* %%
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* Copyright (C) 2014 - 2024 Smile CDR, Inc.
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* %%
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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* #L%
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*/
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.support.IValidationSupport;
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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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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.rest.api.server.IBundleProvider;
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import ca.uhn.fhir.rest.param.TokenParam;
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import ca.uhn.fhir.rest.param.UriParam;
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import org.hl7.fhir.r4.model.StructureDefinition;
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import org.junit.jupiter.api.DisplayName;
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import org.junit.jupiter.api.Nested;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.mockito.ArgumentCaptor;
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import org.mockito.Captor;
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import org.mockito.InjectMocks;
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import org.mockito.Mock;
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import org.mockito.junit.jupiter.MockitoExtension;
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import static org.assertj.core.api.AssertionsForClassTypes.assertThat;
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import static org.mockito.ArgumentMatchers.any;
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import static org.mockito.ArgumentMatchers.anyString;
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import static org.mockito.Mockito.mock;
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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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class JpaPersistedResourceValidationSupportTest {
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private FhirContext theFhirContext = FhirContext.forR4();
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@Nested
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class FetchStructureDefinitionTests {
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@Mock
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private DaoRegistry myDaoRegistry;
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@InjectMocks
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private final JpaPersistedResourceValidationSupport testClass = new JpaPersistedResourceValidationSupport(theFhirContext);
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@Captor
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ArgumentCaptor<SearchParameterMap> searchParameterMapCaptor;
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@Test
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@DisplayName("fetch StructureDefinition by version less url")
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void fetchStructureDefinitionForUrl() {
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final String profileUrl = "http://example.com/fhir/StructureDefinition/exampleProfile";
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IFhirResourceDao mockDao = mock(IFhirResourceDao.class);
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when(mockDao.search(any())).thenReturn(mock(IBundleProvider.class));
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when(myDaoRegistry.getResourceDao(anyString())).thenReturn(mockDao);
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testClass.fetchResource(StructureDefinition.class, profileUrl);
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verify(mockDao).search(searchParameterMapCaptor.capture());
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SearchParameterMap searchParams = searchParameterMapCaptor.getValue();
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String uriParam = searchParams.get(StructureDefinition.SP_URL)
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.get(0)
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.stream()
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.map(UriParam.class::cast)
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.map(UriParam::getValue)
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.findFirst()
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.orElse(null);
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assertThat(uriParam).isEqualTo(profileUrl);
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}
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@Test
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@DisplayName("fetch StructureDefinition by versioned url")
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void fetchStructureDefinitionForVersionedUrl() {
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final String profileUrl = "http://example.com/fhir/StructureDefinition/exampleProfile|1.1.0";
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IFhirResourceDao mockDao = mock(IFhirResourceDao.class);
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when(mockDao.search(any())).thenReturn(mock(IBundleProvider.class));
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when(myDaoRegistry.getResourceDao(anyString())).thenReturn(mockDao);
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testClass.fetchResource(StructureDefinition.class, profileUrl);
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verify(mockDao).search(searchParameterMapCaptor.capture());
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SearchParameterMap searchParams = searchParameterMapCaptor.getValue();
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String uriParam = searchParams.get(StructureDefinition.SP_URL)
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.get(0)
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.stream()
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.map(UriParam.class::cast)
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.map(UriParam::getValue)
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.findFirst()
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.orElse(null);
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assertThat(uriParam).isEqualTo("http://example.com/fhir/StructureDefinition/exampleProfile");
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String versionParam = searchParams.get(StructureDefinition.SP_VERSION)
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.get(0)
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.stream()
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.map(TokenParam.class::cast)
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.map(TokenParam::getValue)
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.findFirst()
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.orElse(null);
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assertThat(versionParam).isEqualTo("1.1.0");
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}
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}
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}
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@ -123,8 +123,8 @@ public class RemoteTerminologyServiceJpaR4Test extends BaseJpaR4Test {
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// Verify 1
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Assertions.assertEquals(2, myCaptureQueriesListener.countGetConnections());
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assertThat(ourValueSetProvider.mySearchUrls).asList().containsExactlyInAnyOrder(
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"http://hl7.org/fhir/ValueSet/administrative-gender",
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"http://hl7.org/fhir/ValueSet/administrative-gender"
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"http://hl7.org/fhir/ValueSet/administrative-gender|4.0.1",
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"http://hl7.org/fhir/ValueSet/administrative-gender","http://hl7.org/fhir/ValueSet/administrative-gender"
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);
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assertThat(ourCodeSystemProvider.mySearchUrls).asList().containsExactlyInAnyOrder(
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"http://hl7.org/fhir/administrative-gender",
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@ -162,7 +162,7 @@ public class RemoteTerminologyServiceJpaR4Test extends BaseJpaR4Test {
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// Verify 1
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Assertions.assertEquals(0, myCaptureQueriesListener.countGetConnections());
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assertThat(ourValueSetProvider.mySearchUrls).asList().containsExactlyInAnyOrder(
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"http://hl7.org/fhir/ValueSet/administrative-gender",
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"http://hl7.org/fhir/ValueSet/administrative-gender|4.0.1",
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"http://hl7.org/fhir/ValueSet/administrative-gender"
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);
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assertThat(ourValueSetProvider.myValidatedCodes).asList().containsExactlyInAnyOrder(
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@ -215,14 +215,18 @@ public class RemoteTerminologyServiceJpaR4Test extends BaseJpaR4Test {
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// Verify 1
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Assertions.assertEquals(0, myCaptureQueriesListener.countGetConnections());
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assertThat(ourValueSetProvider.mySearchUrls).asList().containsExactlyInAnyOrder(
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"http://hl7.org/fhir/ValueSet/administrative-gender",
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"http://hl7.org/fhir/ValueSet/administrative-gender|4.0.1",
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"http://hl7.org/fhir/ValueSet/administrative-gender"
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);
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assertThat(ourValueSetProvider.myValidatedCodes).asList().containsExactlyInAnyOrder(
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"http://hl7.org/fhir/ValueSet/administrative-gender#null#female"
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"http://hl7.org/fhir/ValueSet/administrative-gender#http://hl7.org/fhir/administrative-gender#female"
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);
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assertThat(ourCodeSystemProvider.mySearchUrls).asList().containsExactlyInAnyOrder(
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"http://hl7.org/fhir/administrative-gender"
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);
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assertThat(ourCodeSystemProvider.myValidatedCodes).asList().containsExactlyInAnyOrder(
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"http://hl7.org/fhir/administrative-gender#female#null"
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);
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assertThat(ourCodeSystemProvider.mySearchUrls).asList().isEmpty();
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assertThat(ourCodeSystemProvider.myValidatedCodes).asList().isEmpty();
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// Test 2 (should rely on caches)
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ourCodeSystemProvider.clearCalls();
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@ -94,7 +94,7 @@ public class ValidateWithRemoteTerminologyTest extends BaseResourceProviderR4Tes
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final String classSystem = "http://terminology.hl7.org/CodeSystem/v3-ActCode";
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final String identifierTypeSystem = "http://terminology.hl7.org/CodeSystem/v2-0203";
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setupValueSetValidateCode("http://hl7.org/fhir/ValueSet/encounter-status", "http://hl7.org/fhir/encounter-status", statusCode, "validation/encounter/validateCode-ValueSet-encounter-status.json");
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setupValueSetValidateCode("http://hl7.org/fhir/ValueSet/encounter-status", "4.0.1","http://hl7.org/fhir/encounter-status", statusCode, "validation/encounter/validateCode-ValueSet-encounter-status.json");
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setupValueSetValidateCode("http://terminology.hl7.org/ValueSet/v3-ActEncounterCode", "http://terminology.hl7.org/CodeSystem/v3-ActCode", classCode, "validation/encounter/validateCode-ValueSet-v3-ActEncounterCode.json");
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setupValueSetValidateCode("http://hl7.org/fhir/ValueSet/identifier-type", "http://hl7.org/fhir/identifier-type", identifierTypeCode, "validation/encounter/validateCode-ValueSet-identifier-type.json");
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@ -138,7 +138,7 @@ public class ValidateWithRemoteTerminologyTest extends BaseResourceProviderR4Tes
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final String loincSystem = "http://loinc.org";
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final String system = "http://fhir.infoway-inforoute.ca/io/psca/CodeSystem/ICD9CM";
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setupValueSetValidateCode("http://hl7.org/fhir/ValueSet/observation-status", statusSystem, statusCode, "validation/observation/validateCode-ValueSet-observation-status.json");
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setupValueSetValidateCode("http://hl7.org/fhir/ValueSet/observation-status", "4.0.1", statusSystem, statusCode, "validation/observation/validateCode-ValueSet-observation-status.json");
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setupValueSetValidateCode("http://hl7.org/fhir/ValueSet/observation-codes", loincSystem, statusCode, "validation/observation/validateCode-ValueSet-codes.json");
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setupCodeSystemValidateCode(statusSystem, statusCode, "validation/observation/validateCode-CodeSystem-observation-status.json");
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@ -171,7 +171,7 @@ public class ValidateWithRemoteTerminologyTest extends BaseResourceProviderR4Tes
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final String statusSystem = "http://hl7.org/fhir/event-status";
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final String snomedSystem = "http://snomed.info/sct";
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setupValueSetValidateCode("http://hl7.org/fhir/ValueSet/event-status", statusSystem, statusCode, "validation/procedure/validateCode-ValueSet-event-status.json");
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setupValueSetValidateCode("http://hl7.org/fhir/ValueSet/event-status", "4.0.1", statusSystem, statusCode, "validation/procedure/validateCode-ValueSet-event-status.json");
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setupValueSetValidateCode("http://hl7.org/fhir/ValueSet/procedure-code", snomedSystem, procedureCode1, "validation/procedure/validateCode-ValueSet-procedure-code-valid.json");
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setupValueSetValidateCode("http://hl7.org/fhir/ValueSet/procedure-code", snomedSystem, procedureCode2, "validation/procedure/validateCode-ValueSet-procedure-code-invalid.json");
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@ -213,7 +213,7 @@ public class ValidateWithRemoteTerminologyTest extends BaseResourceProviderR4Tes
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final String snomedSystem = "http://snomed.info/sct";
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final String absentUnknownSystem = "http://hl7.org/fhir/uv/ips/CodeSystem/absent-unknown-uv-ips";
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setupValueSetValidateCode("http://hl7.org/fhir/ValueSet/event-status", statusSystem, statusCode, "validation/procedure/validateCode-ValueSet-event-status.json");
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setupValueSetValidateCode("http://hl7.org/fhir/ValueSet/event-status", "4.0.1", statusSystem, statusCode, "validation/procedure/validateCode-ValueSet-event-status.json");
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setupValueSetValidateCode("http://hl7.org/fhir/ValueSet/procedure-code", snomedSystem, procedureCode, "validation/procedure/validateCode-ValueSet-procedure-code-invalid-slice.json");
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setupValueSetValidateCode("http://hl7.org/fhir/uv/ips/ValueSet/absent-or-unknown-procedures-uv-ips", absentUnknownSystem, procedureCode, "validation/procedure/validateCode-ValueSet-absent-or-unknown-procedure.json");
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@ -245,6 +245,13 @@ public class ValidateWithRemoteTerminologyTest extends BaseResourceProviderR4Tes
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// which also attempts a validateCode against the CodeSystem after the validateCode against the ValueSet
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}
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private void setupValueSetValidateCode(String theUrl, String theVersion, String theSystem, String theCode, String theTerminologyResponseFile) {
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ValueSet valueSet = myValueSetProvider.addTerminologyResource(theUrl, theVersion);
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myValueSetProvider.addTerminologyResource(theSystem, theVersion);
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myValueSetProvider.addTerminologyResponse(OPERATION_VALIDATE_CODE, valueSet.getUrl(), theCode, ourCtx, theTerminologyResponseFile);
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valueSet.getCompose().addInclude().setSystem(theSystem);
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}
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private void setupCodeSystemValidateCode(String theUrl, String theCode, String theTerminologyResponseFile) {
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CodeSystem codeSystem = myCodeSystemProvider.addTerminologyResource(theUrl);
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myCodeSystemProvider.addTerminologyResponse(OPERATION_VALIDATE_CODE, codeSystem.getUrl(), theCode, ourCtx, theTerminologyResponseFile);
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@ -285,7 +285,6 @@ public class ResourceProviderR5Test extends BaseResourceProviderR5Test {
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"source": "#384dd6bccaeafa6c"
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},
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"url": "https://health.gov.on.ca/idms/fhir/SearchParameter/MedicinalProductDefinition-SearchableString",
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"version": "1.0.0",
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"name": "MedicinalProductDefinitionSearchableString",
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"status": "active",
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"publisher": "MOH-IDMS",
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@ -85,8 +85,12 @@ public interface IValidationProviders {
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myTerminologyResourceMap.put(theUrl, theResource);
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}
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protected void addVersionedTerminologyResource(String theUrl, String theVersion, T theResource) {
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myTerminologyResourceMap.put(theUrl + "|" + theVersion, theResource);
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}
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public abstract T addTerminologyResource(String theUrl);
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public abstract T addTerminologyResource(String theUrl, String theVersion);
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protected IBaseParameters getTerminologyResponse(String theOperation, String theUrl, String theCode) throws Exception {
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String inputKey = getInputKey(theOperation, theUrl, theCode);
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if (myExceptionMap.containsKey(inputKey)) {
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@ -95,6 +95,10 @@ public interface IValidationProvidersDstu3 {
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addTerminologyResource(theUrl, codeSystem);
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return codeSystem;
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}
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@Override
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public CodeSystem addTerminologyResource(String theUrl, String theVersion) {
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return addTerminologyResource(theUrl);
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}
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}
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@SuppressWarnings("unused")
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@ -133,5 +137,9 @@ public interface IValidationProvidersDstu3 {
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addTerminologyResource(theUrl, valueSet);
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return valueSet;
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}
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@Override
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public ValueSet addTerminologyResource(String theUrl, String theVersion) {
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return addTerminologyResource(theUrl);
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}
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}
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}
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@ -99,6 +99,14 @@ public interface IValidationProvidersR4 {
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addTerminologyResource(theUrl, codeSystem);
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return codeSystem;
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}
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@Override
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public CodeSystem addTerminologyResource(String theUrl, String theVersion) {
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CodeSystem codeSystem = addTerminologyResource(theUrl);
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codeSystem.setVersion(theVersion);
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addVersionedTerminologyResource(theUrl, theVersion, codeSystem);
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return codeSystem;
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}
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}
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@SuppressWarnings("unused")
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@ -138,5 +146,12 @@ public interface IValidationProvidersR4 {
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addTerminologyResource(theUrl, valueSet);
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return valueSet;
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}
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@Override
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public ValueSet addTerminologyResource(String theUrl, String theVersion) {
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ValueSet valueSet = addTerminologyResource(theUrl);
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addVersionedTerminologyResource(theUrl, theVersion, valueSet);
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return valueSet;
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}
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}
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}
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@ -12,6 +12,7 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.hapi.converters.canonical.VersionCanonicalizer;
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import jakarta.annotation.Nonnull;
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import jakarta.annotation.Nullable;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.Validate;
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import org.apache.commons.lang3.builder.EqualsBuilder;
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import org.apache.commons.lang3.builder.HashCodeBuilder;
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@ -460,20 +461,13 @@ public class VersionSpecificWorkerContextWrapper extends I18nBase implements IWo
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return null;
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}
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String uri = theUri;
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// handle profile version, if present
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if (theUri.contains("|")) {
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String[] parts = theUri.split("\\|");
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if (parts.length == 2) {
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uri = parts[0];
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} else {
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if (StringUtils.countMatches(theUri, "|") > 1) {
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ourLog.warn("Unrecognized profile uri: {}", theUri);
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}
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}
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String resourceType = getResourceType(class_);
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@SuppressWarnings("unchecked")
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T retVal = (T) fetchResource(resourceType, uri);
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T retVal = (T) fetchResource(resourceType, theUri);
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return retVal;
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}
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