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Add common getExpansion() function (#763)
* Add common getExpansion() function * Mock out server calls * Specify charset * Add TerminologyServerClient Bean to config * Refactor - make client non VSAC specific & add statuc variables * getExpansion changes * Refactor - take credentials from properties, cleanup, add IT * Fix issue with authoritative source url and system-version parameter Update test file to reflect actual value set * Remove addition of ValueSet level system-version param & update test to reflect. Privatise getters/setters. --------- Co-authored-by: Adam Stevenson <stevenson_adam@yahoo.com>
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79 changes: 79 additions & 0 deletions
79
plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/TerminologyServerClient.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,79 @@ | ||
| package org.opencds.cqf.ruler.cr; | ||
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| import ca.uhn.fhir.context.FhirContext; | ||
| import ca.uhn.fhir.rest.client.api.IGenericClient; | ||
| import ca.uhn.fhir.rest.client.interceptor.AdditionalRequestHeadersInterceptor; | ||
| import org.apache.commons.lang3.StringUtils; | ||
| import org.hl7.fhir.r4.model.Parameters; | ||
| import org.hl7.fhir.r4.model.ValueSet; | ||
| import org.jetbrains.annotations.NotNull; | ||
| import org.opencds.cqf.cql.evaluator.fhir.util.Canonicals; | ||
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| import java.nio.charset.StandardCharsets; | ||
| import java.util.Base64; | ||
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| public class TerminologyServerClient { | ||
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| private final FhirContext ctx; | ||
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| private String username; | ||
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| private String getUsername() { | ||
| return username; | ||
| } | ||
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| private void setUsername(String username) { | ||
| this.username = username; | ||
| } | ||
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| private String apiKey; | ||
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| private String getApiKey() { | ||
| return apiKey; | ||
| } | ||
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| private void setApiKey(String apiKey) { | ||
| this.apiKey = apiKey; | ||
| } | ||
| public TerminologyServerClient() { | ||
| ctx = FhirContext.forR4(); | ||
| } | ||
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| public TerminologyServerClient(String username, String apiKey) { | ||
| this(); | ||
| setUsername(username); | ||
| setApiKey(apiKey); | ||
| } | ||
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| public ValueSet expand(ValueSet valueSet, String authoritativeSource, Parameters expansionParameters) { | ||
| IGenericClient fhirClient = ctx.newRestfulGenericClient(getAuthoritativeSourceBase(authoritativeSource)); | ||
| fhirClient.registerInterceptor(getAuthInterceptor(getUsername(), getApiKey())); | ||
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| // Invoke by Value Set ID | ||
| return fhirClient | ||
| .operation() | ||
| .onInstance(valueSet.getId()) | ||
| .named("$expand") | ||
| .withParameters(expansionParameters) | ||
| .returnResourceType(ValueSet.class) | ||
| .execute(); | ||
| } | ||
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| private AdditionalRequestHeadersInterceptor getAuthInterceptor(String username, String apiKey) { | ||
| String authString = StringUtils.join("Basic ", Base64.getEncoder() | ||
| .encodeToString(StringUtils.join(username, ":", apiKey).getBytes(StandardCharsets.UTF_8))); | ||
| AdditionalRequestHeadersInterceptor authInterceptor = new AdditionalRequestHeadersInterceptor(); | ||
| authInterceptor.addHeaderValue("Authorization", authString); | ||
| return authInterceptor; | ||
| } | ||
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| // Strips resource and id from the authoritative source URL, these are not needed as the client constructs the URL. | ||
| // Converts http URLs to https | ||
| private String getAuthoritativeSourceBase(String authoritativeSource) { | ||
| authoritativeSource = authoritativeSource.substring(0, authoritativeSource.indexOf(Canonicals.getResourceType(authoritativeSource))); | ||
| if (authoritativeSource.startsWith("http://")) { | ||
| authoritativeSource = authoritativeSource.replaceFirst("http://", "https://"); | ||
| } | ||
| return authoritativeSource; | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -2,3 +2,5 @@ hapi: | |
| fhir: | ||
| rulercr: | ||
| enabled: true | ||
| vsac-username: | ||
| vsac-api-key: | ||
51 changes: 51 additions & 0 deletions
51
plugin/cr/src/test/java/org/opencds/cqf/ruler/cr/KnowledgeArtifactProcessorIT.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| package org.opencds.cqf.ruler.cr; | ||
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| import ca.uhn.fhir.context.FhirContext; | ||
| import ca.uhn.fhir.parser.IParser; | ||
| import org.hl7.fhir.r4.model.Parameters; | ||
| import org.hl7.fhir.r4.model.ValueSet; | ||
| import org.junit.jupiter.api.Disabled; | ||
| import org.junit.jupiter.api.Test; | ||
| import org.opencds.cqf.ruler.test.RestIntegrationTest; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.boot.test.context.SpringBootTest; | ||
| import org.springframework.context.annotation.Lazy; | ||
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| import java.io.IOException; | ||
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| import static org.junit.jupiter.api.Assertions.*; | ||
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| @Lazy | ||
| @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, | ||
| classes = {KnowledgeArtifactProcessorIT.class, CrConfig.class}, | ||
| properties = {"hapi.fhir.fhir_version=r4", "hapi.fhir.security.basic_auth.enabled=false"}) | ||
| public class KnowledgeArtifactProcessorIT extends RestIntegrationTest { | ||
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| @Autowired | ||
| KnowledgeArtifactProcessor processor; | ||
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| @Autowired | ||
| TerminologyServerClient client; | ||
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| @Disabled | ||
| @Test | ||
| void testGetExpansionVSAC() throws IOException { | ||
| // given | ||
| FhirContext ctx = FhirContext.forR4(); | ||
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| String input = new String(this.getClass().getResourceAsStream("r4/valueset/valueset-2.16.840.1.113762.1.4.1116.89.json").readAllBytes()); | ||
| IParser parser = ctx.newJsonParser(); | ||
| ValueSet valueSet = parser.parseResource(ValueSet.class, input); | ||
| String codeSystemVersion = valueSet.getCompose().getInclude().get(0).getVersion(); | ||
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| Parameters expansionParameters = new Parameters(); | ||
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| // when | ||
| processor.expandValueSet(valueSet, expansionParameters); | ||
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| // then | ||
| assertNotNull(valueSet.getExpansion()); | ||
| assertEquals(16, valueSet.getExpansion().getTotal()); | ||
| } | ||
|
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| } |
75 changes: 75 additions & 0 deletions
75
plugin/cr/src/test/java/org/opencds/cqf/ruler/cr/KnowledgeArtifactProcessorTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,75 @@ | ||
| package org.opencds.cqf.ruler.cr; | ||
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| import ca.uhn.fhir.context.FhirContext; | ||
| import ca.uhn.fhir.parser.IParser; | ||
| import org.hl7.fhir.r4.model.Parameters; | ||
| import org.hl7.fhir.r4.model.ValueSet; | ||
| import org.junit.jupiter.api.Test; | ||
| import org.junit.jupiter.api.extension.ExtendWith; | ||
| import org.mockito.InjectMocks; | ||
| import org.mockito.Mock; | ||
| import org.mockito.Mockito; | ||
| import org.mockito.junit.jupiter.MockitoExtension; | ||
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| import java.io.IOException; | ||
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| import static org.junit.jupiter.api.Assertions.assertEquals; | ||
| import static org.junit.jupiter.api.Assertions.assertNotNull; | ||
| import static org.junit.jupiter.api.Assertions.assertTrue; | ||
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| @ExtendWith(MockitoExtension.class) | ||
| public class KnowledgeArtifactProcessorTest { | ||
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| @InjectMocks | ||
| KnowledgeArtifactProcessor processor; | ||
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| @Mock | ||
| TerminologyServerClient client; | ||
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| @Test | ||
| void testGetExpansionVSAC() throws IOException { | ||
| // given | ||
| FhirContext ctx = FhirContext.forR4(); | ||
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| String input = new String(this.getClass().getResourceAsStream("r4/valueset/valueset-2.16.840.1.113762.1.4.1116.89.json").readAllBytes()); | ||
| IParser parser = ctx.newJsonParser(); | ||
| ValueSet valueSet = parser.parseResource(ValueSet.class, input); | ||
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| Parameters expansionParameters = new Parameters(); | ||
| expansionParameters.addParameter("system-version", "http://snomed.info/sct|http://snomed.info/sct/731000124108/version/20230901"); | ||
|
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| // when | ||
| String expandedValueSetString = new String(this.getClass().getResourceAsStream("r4/test/valueset-expanded.json").readAllBytes()); | ||
| ValueSet expandedValueSet = parser.parseResource(ValueSet.class, expandedValueSetString); | ||
| Mockito.when(client.expand(Mockito.eq(valueSet), Mockito.eq(valueSet.getUrl()), Mockito.eq(expansionParameters))).thenReturn(expandedValueSet); | ||
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| processor.expandValueSet(valueSet, expansionParameters); | ||
|
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| // then | ||
| assertNotNull(valueSet.getExpansion()); | ||
| assertEquals(16, valueSet.getExpansion().getTotal()); | ||
| } | ||
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| @Test | ||
| void testGetExpansionNaive() throws IOException { | ||
| FhirContext ctx = FhirContext.forR4(); | ||
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| String input = new String(this.getClass().getResourceAsStream("r4/valueset/valueset-vsm-authored.json").readAllBytes()); | ||
| IParser parser = ctx.newJsonParser(); | ||
| ValueSet valueSet = parser.parseResource(ValueSet.class, input); | ||
| Parameters expansionParameters = new Parameters(); | ||
| expansionParameters.addParameter("system-version", "http://snomed.info/sct|http://snomed.info/sct/731000124108/version/20230901"); | ||
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| // when | ||
| processor.expandValueSet(valueSet, expansionParameters); | ||
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| // then | ||
| assertNotNull(valueSet.getExpansion()); | ||
| assertNotNull(valueSet.getExpansion().getParameter().get(0)); | ||
| assertEquals("naive", valueSet.getExpansion().getParameter().get(0).getName()); | ||
| assertTrue(valueSet.getExpansion().getParameter().get(0).getValueBooleanType().booleanValue()); | ||
| assertEquals(1, valueSet.getExpansion().getContains().size()); | ||
| assertEquals("ANC.A.DE13", valueSet.getExpansion().getContains().get(0).getCode()); | ||
| assertEquals("Co-habitants", valueSet.getExpansion().getContains().get(0).getDisplay()); | ||
| } | ||
| } |
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