Merge pull request #106 from MeasureAuthoringTool/MAT-7855

MAT-7855 Integrate HAPI FHIR Server into Test Case Builder for internal value set expansion

pom.xml

@@ -14,6 +14,7 @@
   <name>Terminology Service</name>
   <description>Terminology Service for MADiE</description>
   <properties>
+    <hapifhir.version>7.6.0</hapifhir.version>
     <java.version>16</java.version>
     <jxbmavenplugin.version>2.5.0</jxbmavenplugin.version>
     <maven.compiler.source>17</maven.compiler.source>
@@ -81,7 +82,13 @@
     <dependency>
       <groupId>ca.uhn.hapi.fhir</groupId>
       <artifactId>hapi-fhir-structures-r4</artifactId>
-      <version>7.6.0</version>
+      <version>${hapifhir.version}</version>
+    </dependency>
+    <!-- https://mvnrepository.com/artifact/ca.uhn.hapi.fhir/hapi-fhir-client -->
+    <dependency>
+      <groupId>ca.uhn.hapi.fhir</groupId>
+      <artifactId>hapi-fhir-client</artifactId>
+      <version>${hapifhir.version}</version>
     </dependency>
 
     <dependency>

src/main/java/gov/cms/madie/terminology/config/HapiFhirConfig.java

@@ -0,0 +1,21 @@
+package gov.cms.madie.terminology.config;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public class HapiFhirConfig {
+  @Value("${hapi-fhir-url}")
+  private String hapiFhirUrl;
+
+  @Bean
+  @Qualifier("hapiClient")
+  public IGenericClient createHapiClient(@Autowired FhirContext fhirContext) {
+    return fhirContext.newRestfulGenericClient(hapiFhirUrl);
+  }
+}

src/main/java/gov/cms/madie/terminology/controller/InternalTerminologyController.java

@@ -0,0 +1,27 @@
+package gov.cms.madie.terminology.controller;
+
+import ca.uhn.fhir.context.FhirContext;
+import gov.cms.madie.terminology.service.InternalTerminologyService;
+import lombok.RequiredArgsConstructor;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
+
+@RestController
+@RequestMapping(path = "/internal-terminology")
+@RequiredArgsConstructor
+public class InternalTerminologyController {
+
+  private final FhirContext fhirContext;
+  private final InternalTerminologyService internalTerminologyService;
+
+  @GetMapping(path = "ValueSet/{id}/expand", produces = MediaType.APPLICATION_JSON_VALUE)
+  public ResponseEntity<String> valueSetExpansion(@PathVariable String id) {
+    ValueSet valueSet = internalTerminologyService.getValueSetExpansionById(id);
+    return ResponseEntity.ok().body(fhirContext.newJsonParser().encodeResourceToString(valueSet));
+  }
+}

src/main/java/gov/cms/madie/terminology/controller/VsacControllerAdvice.java

@@ -19,7 +19,7 @@
 import org.springframework.web.context.request.WebRequest;
 import org.springframework.web.reactive.function.client.WebClientResponseException;
 
-import gov.cms.madie.terminology.exceptions.VsacGenericException;
+import gov.cms.madie.terminology.exceptions.HapiOperationException;
 import gov.cms.madie.terminology.exceptions.VsacResourceNotFoundException;
 import gov.cms.madie.terminology.exceptions.VsacUnauthorizedException;
 
@@ -107,14 +107,14 @@ Map<String, Object> onVsacResourceNotFoundException(
     return errorAttributes1;
   }
 
-  @ExceptionHandler(VsacGenericException.class)
+  @ExceptionHandler(HapiOperationException.class)
   @ResponseStatus(HttpStatus.BAD_REQUEST)
   @ResponseBody
-  Map<String, Object> onVsacGenericException(VsacGenericException ex, WebRequest request) {
-    Map<String, String> validationErrors = new HashMap<>();
-    validationErrors.put(request.getContextPath(), ex.getMessage());
+  Map<String, Object> onHapiOperationException(HapiOperationException ex, WebRequest request) {
+    Map<String, String> errors = new HashMap<>();
+    errors.put(request.getContextPath(), ex.getMessage());
     Map<String, Object> errorAttributes = getErrorAttributes(request, HttpStatus.BAD_REQUEST);
-    errorAttributes.put("validationErrors", validationErrors);
+    errorAttributes.put("errors", errors);
     return errorAttributes;
   }
 

src/main/java/gov/cms/madie/terminology/exceptions/HapiOperationException.java

@@ -0,0 +1,7 @@
+package gov.cms.madie.terminology.exceptions;
+
+public class HapiOperationException extends RuntimeException {
+  public HapiOperationException(String message) {
+    super(message);
+  }
+}

src/main/java/gov/cms/madie/terminology/service/InternalTerminologyService.java

@@ -0,0 +1,53 @@
+package gov.cms.madie.terminology.service;
+
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.server.exceptions.*;
+import gov.cms.madie.terminology.exceptions.HapiOperationException;
+import lombok.RequiredArgsConstructor;
+import lombok.extern.slf4j.Slf4j;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.OperationOutcome;
+import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.springframework.stereotype.Service;
+
+import java.util.stream.Collectors;
+
+@Slf4j
+@Service
+@RequiredArgsConstructor
+public class InternalTerminologyService {
+  private final IGenericClient hapiClient;
+
+  /**
+   * This method fetches the ValueSet expansion by id from HAPI server
+   *
+   * @param id -> Value Set id
+   * @return ValueSet -> Value Set with expansion details
+   */
+  public ValueSet getValueSetExpansionById(String id) {
+    try {
+      log.info("Fetching ValueSet expansion for {}", id);
+      Parameters parameters =
+          hapiClient
+              .operation()
+              .onInstance(new IdType("ValueSet", id))
+              .named("$expand")
+              .withNoParameters(Parameters.class)
+              .execute();
+      return (ValueSet) parameters.getParameter().get(0).getResource();
+    } catch (BaseServerResponseException ex) {
+      log.error("An error occurred while fetching expansion for the ValueSet[{}]", id, ex);
+      OperationOutcome outcome = (OperationOutcome) ex.getOperationOutcome();
+      if (outcome != null) {
+        String errors =
+            outcome.getIssue().stream()
+                .map(OperationOutcome.OperationOutcomeIssueComponent::getDiagnostics)
+                .collect(Collectors.joining("\n"));
+        throw new HapiOperationException(errors);
+      } else {
+        throw new HapiOperationException(ex.getMessage());
+      }
+    }
+  }
+}

src/main/resources/application.yml

@@ -34,6 +34,8 @@ client:
     code-system-urn: /CodeSystem
     code-lookups: /CodeSystem/$lookup?system={fullUrl}&code={code}&version={version}
 
+hapi-fhir-url: ${HAPI_FHIR_URL:http://localhost:8888/fhir}
+
 spring:
   session:
     store-type: none

src/test/java/gov/cms/madie/terminology/controller/InternalTerminologyControllerMvcTest.java

@@ -0,0 +1,95 @@
+package gov.cms.madie.terminology.controller;
+
+import ca.uhn.fhir.context.FhirContext;
+import gov.cms.madie.terminology.exceptions.HapiOperationException;
+import gov.cms.madie.terminology.service.InternalTerminologyService;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest;
+import org.springframework.boot.test.mock.mockito.MockBean;
+import org.springframework.http.MediaType;
+import org.springframework.test.web.servlet.MockMvc;
+import org.springframework.test.web.servlet.MvcResult;
+import org.springframework.test.web.servlet.request.MockMvcRequestBuilders;
+
+import java.security.Principal;
+
+import static org.hamcrest.CoreMatchers.containsString;
+import static org.hamcrest.CoreMatchers.is;
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.equalTo;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.Mockito.*;
+import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf;
+import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user;
+import static org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
+import static org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
+
+@WebMvcTest(InternalTerminologyController.class)
+class InternalTerminologyControllerMvcTest {
+
+  @MockBean private InternalTerminologyService internalTerminologyService;
+  @MockBean private FhirContext fhirContext;
+
+  @Autowired private MockMvc mockMvc;
+  private static final String TEST_USER = "test.user";
+
+  @Test
+  void testGetValueSetExpansion() throws Exception {
+    Principal principal = mock(Principal.class);
+    when(principal.getName()).thenReturn(TEST_USER);
+
+    var contains = new ValueSetExpansionContainsComponent();
+    contains.setCode("02").setDisplay("trivalent poliovirus vaccine, live, oral").setSystem("CVX");
+    var expansion = new ValueSetExpansionComponent();
+    expansion.addContains(contains);
+    ValueSet valueSet = new ValueSet();
+    valueSet.setId("us-core-vaccines-cvx-1");
+    valueSet.setExpansion(expansion);
+
+    when(internalTerminologyService.getValueSetExpansionById(anyString())).thenReturn(valueSet);
+    when(fhirContext.newJsonParser()).thenReturn(FhirContext.forR4().newJsonParser());
+    MvcResult result =
+        mockMvc
+            .perform(
+                MockMvcRequestBuilders.get(
+                        "/internal-terminology/ValueSet/us-core-vaccines-cvx-1/expand")
+                    .with(user(TEST_USER))
+                    .with(csrf())
+                    .contentType(MediaType.APPLICATION_JSON_VALUE))
+            .andExpect(status().isOk())
+            .andReturn();
+    assertThat(result.getResponse().getStatus(), is(equalTo(200)));
+    String content = result.getResponse().getContentAsString();
+    verify(internalTerminologyService, times(1)).getValueSetExpansionById(anyString());
+    assertThat(
+        content,
+        containsString(
+            "{\"resourceType\":\"ValueSet\",\"id\":\"us-core-vaccines-cvx-1\",\"expansion\":{\"contains\":[{\"system\":\"CVX\",\"code\":\"02\",\"display\":\"trivalent poliovirus vaccine, live, oral\"}]}}"));
+  }
+
+  @Test
+  void testGetValueSetExpansionIfNotFound() throws Exception {
+    Principal principal = mock(Principal.class);
+    when(principal.getName()).thenReturn(TEST_USER);
+
+    doThrow(new HapiOperationException("Value set not found"))
+        .when(internalTerminologyService)
+        .getValueSetExpansionById(anyString());
+    MvcResult result =
+        mockMvc
+            .perform(
+                MockMvcRequestBuilders.get(
+                        "/internal-terminology/ValueSet/us-core-vaccines-cvx-1/expand")
+                    .with(user(TEST_USER))
+                    .with(csrf())
+                    .contentType(MediaType.APPLICATION_JSON_VALUE))
+            .andExpect(status().isBadRequest())
+            .andReturn();
+    String content = result.getResponse().getContentAsString();
+    verify(internalTerminologyService, times(1)).getValueSetExpansionById(anyString());
+    assertThat(content, containsString("Value set not found"));
+  }
+}

src/test/java/gov/cms/madie/terminology/service/InternalTerminologyServiceTest.java

@@ -0,0 +1,92 @@
+package gov.cms.madie.terminology.service;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.gclient.*;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.util.OperationOutcomeUtil;
+import gov.cms.madie.terminology.exceptions.HapiOperationException;
+import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.InjectMocks;
+
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+
+import static org.hamcrest.CoreMatchers.*;
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.mockito.Mockito.*;
+
+@ExtendWith(MockitoExtension.class)
+public class InternalTerminologyServiceTest {
+
+  @Mock private IGenericClient hapiClient;
+
+  @InjectMocks private InternalTerminologyService service;
+
+  private IOperation operation;
+  private IOperationUnnamed operationUnnamed;
+  private IOperationUntyped operationUntyped;
+  private IOperationUntypedWithInput operationUntypedWithInput;
+
+  @BeforeEach
+  public void setUp() {
+    operation = mock(IOperation.class);
+    operationUnnamed = mock(IOperationUnnamed.class);
+    operationUntyped = mock(IOperationUntyped.class);
+    operationUntypedWithInput =
+        (IOperationUntypedWithInput<Parameters>) mock(IOperationUntypedWithInput.class);
+  }
+
+  @Test
+  void testGetValueSetExpansionById() {
+    String valueSetId = "us-core-vaccines-cvx-1";
+    var idType = new IdType("ValueSet", valueSetId);
+
+    // mock hapi client operation
+    when(hapiClient.operation()).thenReturn(operation);
+    when(operation.onInstance(idType)).thenReturn(operationUnnamed);
+    when(operationUnnamed.named("$expand")).thenReturn(operationUntyped);
+    when(operationUntyped.withNoParameters(Parameters.class)).thenReturn(operationUntypedWithInput);
+
+    // mock response
+    ValueSet valueSet = new ValueSet();
+    Parameters parameters = new Parameters();
+    parameters.addParameter().setResource(valueSet);
+    when(operationUntypedWithInput.execute()).thenReturn(parameters);
+
+    ValueSet expansion = service.getValueSetExpansionById(valueSetId);
+    assertThat(expansion, is(not(nullValue())));
+  }
+
+  @Test
+  void testGetValueSetExpansionByIdIfValueSetNotFound() {
+    String valueSetId = "us-core-vaccines-cvx-1";
+    var idType = new IdType("ValueSet", valueSetId);
+    FhirContext fhirContext = FhirContext.forR4();
+    // mock hapi client operation
+    when(hapiClient.operation()).thenReturn(operation);
+    when(operation.onInstance(idType)).thenReturn(operationUnnamed);
+    when(operationUnnamed.named("$expand")).thenReturn(operationUntyped);
+    when(operationUntyped.withNoParameters(Parameters.class)).thenReturn(operationUntypedWithInput);
+
+    // mock response
+    IBaseOperationOutcome operationOutcome = OperationOutcomeUtil.newInstance(fhirContext);
+    OperationOutcomeUtil.addIssue(
+        fhirContext, operationOutcome, "warning", "Resource not found", null, null);
+    ResourceNotFoundException resourceNotFoundException = new ResourceNotFoundException(idType);
+    resourceNotFoundException.setOperationOutcome(operationOutcome);
+    doThrow(resourceNotFoundException).when(operationUntypedWithInput).execute();
+
+    Exception ex =
+        Assertions.assertThrows(
+            HapiOperationException.class, () -> service.getValueSetExpansionById(valueSetId));
+    assertThat(ex.getMessage(), is(equalTo("Resource not found")));
+  }
+}