Merge pull request #78 from MeasureAuthoringTool/MAT-6856/populateSav…

…edCodesSubTab

validate codes list for saved codes tab

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

@@ -19,6 +19,7 @@
 
 import java.security.Principal;
 import java.util.List;
+import java.util.Map;
 
 @RestController
 @RequestMapping(path = "/terminology")
@@ -85,4 +86,13 @@ public ResponseEntity<Code> getCode(
     return ResponseEntity.ok()
         .body(fhirTerminologyService.retrieveCode(code, codeSystem, version, user.getApiKey()));
   }
+
+  @PostMapping(path = "/codes", produces = MediaType.APPLICATION_JSON_VALUE)
+  public ResponseEntity<List<Code>> getCodesAndCodeSystems(
+      @RequestBody() List<Map<String, String>> codeList, Principal principal) {
+    final String username = principal.getName();
+    UmlsUser user = vsacService.verifyUmlsAccess(username);
+    return ResponseEntity.ok()
+        .body(fhirTerminologyService.retrieveCodesAndCodeSystems(codeList, user.getApiKey()));
+  }
 }

src/main/java/gov/cms/madie/terminology/dto/Code.java

@@ -8,7 +8,8 @@
 public class Code {
   private String name;
   private String display;
-  private String version;
+  private String version; // 'fhir' in the code-system-entry.json
+  private String svsVersion; // 'vsac' in the code-system-entry.json
   private String codeSystem;
   private String codeSystemOid;
   private CodeStatus status;

src/main/java/gov/cms/madie/terminology/repositories/CodeSystemRepository.java

@@ -8,4 +8,6 @@ public interface CodeSystemRepository extends MongoRepository<CodeSystem, String
   Optional<CodeSystem> findById(String id);
 
   Optional<CodeSystem> findByNameAndVersion(String name, String version);
+
+  Optional<CodeSystem> findByOidAndVersion(String oid, String version);
 }

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

@@ -24,9 +24,8 @@
 import org.springframework.web.util.UriComponentsBuilder;
 
 import java.time.Instant;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Optional;
+import java.util.*;
+import java.util.stream.Collectors;
 
 @Service
 @Slf4j
@@ -278,4 +277,94 @@ private void updateOrInsertAllCodeSystems(List<CodeSystem> codeSystemList) {
       }
     }
   }
+
+  public List<Code> retrieveCodesAndCodeSystems(List<Map<String, String>> codeList, String apiKey) {
+    return codeList.stream()
+        .map(
+            code -> {
+              List<CodeSystemEntry> codeSystemEntries = mappingService.getCodeSystemEntries();
+              String codeName = code.get("code");
+              String codeSystemName = code.get("codeSystem");
+              String oid = code.get("oid") != null ? code.get("oid").replaceAll("'|'", "") : null;
+
+              Optional<Map.Entry<String, String>> mappedVersion =
+                  mapToFhirVersion(code.get("version"), oid, codeSystemEntries);
+
+              if (mappedVersion.isPresent()) {
+                String vsacVersion = mappedVersion.get().getKey();
+                String fhirVersion = mappedVersion.get().getValue();
+
+                return retrieveCodes(
+                    codeName, codeSystemName, vsacVersion, fhirVersion, oid, apiKey);
+              }
+              return null;
+            })
+        .collect(Collectors.toList());
+  }
+
+  private Optional<Map.Entry<String, String>> mapToFhirVersion(
+      String version, String oid, List<CodeSystemEntry> codeSystemEntries) {
+    if (oid == null) {
+      return Optional.empty();
+    }
+
+    Optional<Map.Entry<String, String>> result;
+    if (version == null) {
+      result =
+          codeSystemEntries.stream()
+              .filter(codeSystemEntry -> StringUtils.equals(codeSystemEntry.getOid(), oid))
+              .findFirst()
+              .map(
+                  codeSystemVersion ->
+                      Map.entry(
+                          codeSystemVersion.getVersions().get(0).getVsac(),
+                          codeSystemVersion.getVersions().get(0).getFhir()));
+    } else {
+      result =
+          codeSystemEntries.stream()
+              .filter(codeSystemEntry -> StringUtils.equals(codeSystemEntry.getOid(), oid))
+              .flatMap(codeSystemEntry -> codeSystemEntry.getVersions().stream())
+              .filter(codeSystemVersion -> StringUtils.equals(codeSystemVersion.getVsac(), version))
+              .map(
+                  codeSystemVersion ->
+                      Map.entry(codeSystemVersion.getVsac(), codeSystemVersion.getFhir()))
+              .findFirst();
+    }
+
+    return result;
+  }
+
+  private Code retrieveCodes(
+      String codeName,
+      String codeSystemName,
+      String vsacVersion,
+      String fhirVersion,
+      String oid,
+      String apiKey) {
+    if (StringUtils.isEmpty(codeName)
+        || StringUtils.isEmpty(codeSystemName)
+        || StringUtils.isEmpty(fhirVersion)) {
+      return null;
+    }
+    CodeSystem codeSystem = codeSystemRepository.findByOidAndVersion(oid, fhirVersion).orElse(null);
+    if (codeSystem == null) {
+      return null;
+    }
+    String codeJson = fhirTerminologyServiceWebClient.getCodeResource(codeName, codeSystem, apiKey);
+
+    Parameters parameters = fhirContext.newJsonParser().parseResource(Parameters.class, codeJson);
+    Code code =
+        Code.builder()
+            .name(codeName)
+            .codeSystem(codeSystemName)
+            .version(fhirVersion)
+            .svsVersion(vsacVersion)
+            .display(parameters.getParameter("display").getValue().toString())
+            .codeSystemOid(parameters.getParameter("Oid").getValue().toString())
+            .build();
+
+    CodeStatus status = vsacService.getCodeStatus(code, apiKey);
+    code.setStatus(status);
+    return code;
+  }
 }

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

@@ -38,13 +38,15 @@ public List<CodeSystemEntry> getCodeSystemEntries() {
     return Collections.emptyList();
   }
 
-  public CodeSystemEntry getCodeSystemEntry(String codeSystemName) {
+  public CodeSystemEntry getCodeSystemEntryByOid(String oid) {
     List<CodeSystemEntry> codeSystemEntries = getCodeSystemEntries();
     if (CollectionUtils.isEmpty(codeSystemEntries)) {
       return null;
     }
     return codeSystemEntries.stream()
-        .filter(entry -> Objects.equals(entry.getName(), codeSystemName))
+        .filter(
+            entry ->
+                Objects.equals(entry.getOid(), oid.startsWith("urn:oid:") ? oid : "urn:oid:" + oid))
         .findFirst()
         .orElse(null);
   }

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

@@ -161,12 +161,34 @@ public List<CqlCode> validateCodes(List<CqlCode> cqlCodes, UmlsUser umlsUser, St
   }
 
   public CodeStatus getCodeStatus(Code code, String apiKey) {
-    CodeSystemEntry systemEntry = mappingService.getCodeSystemEntry(code.getCodeSystem());
+    String svsVersion = getSvsCodeSystemVersion(code);
+    if (svsVersion == null) {
+      return CodeStatus.NA;
+    }
+    // prepare code path e.g. CODE:/CodeSystem/ActCode/Version/9.0.0/Code/AMB/Info
+    String codePath =
+        TerminologyServiceUtil.buildCodePath(code.getCodeSystem(), svsVersion, code.getName());
+    VsacCode svsCode = terminologyWebClient.getCode(codePath, apiKey);
+    if (svsCode.getStatus().equalsIgnoreCase("ok")) {
+      if ("Yes".equals(svsCode.getData().getResultSet().get(0).getActive())) {
+        return CodeStatus.ACTIVE;
+      } else {
+        return CodeStatus.INACTIVE;
+      }
+    }
+    return CodeStatus.NA;
+  }
+
+  private String getSvsCodeSystemVersion(Code code) {
+    if (StringUtils.isNotBlank(code.getSvsVersion())) {
+      return code.getSvsVersion();
+    }
+    CodeSystemEntry systemEntry = mappingService.getCodeSystemEntryByOid(code.getCodeSystemOid());
     // do not call SVS API to get code status if the system is not in SVS API
     if (systemEntry == null
         || systemEntry.getOid().contains("NOT.IN.VSAC")
         || CollectionUtils.isEmpty(systemEntry.getVersions())) {
-      return CodeStatus.NA;
+      return null;
     }
 
     // get corresponding SVS version for given FHIR version
@@ -176,21 +198,9 @@ public CodeStatus getCodeStatus(Code code, String apiKey) {
             .findFirst()
             .orElse(null);
     if (version == null || version.getVsac() == null) {
-      return CodeStatus.NA;
-    }
-    // prepare code path e.g. CODE:/CodeSystem/ActCode/Version/9.0.0/Code/AMB/Info
-    String codePath =
-        TerminologyServiceUtil.buildCodePath(
-            code.getCodeSystem(), version.getVsac(), code.getName());
-    VsacCode svsCode = terminologyWebClient.getCode(codePath, apiKey);
-    if (svsCode.getStatus().equalsIgnoreCase("ok")) {
-      if ("Yes".equals(svsCode.getData().getResultSet().get(0).getActive())) {
-        return CodeStatus.ACTIVE;
-      } else {
-        return CodeStatus.INACTIVE;
-      }
+      return null;
     }
-    return CodeStatus.NA;
+    return version.getVsac();
   }
 
   /**

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

@@ -2,6 +2,7 @@
 
 import gov.cms.madie.models.measure.ManifestExpansion;
 import gov.cms.madie.terminology.dto.Code;
+import gov.cms.madie.terminology.dto.CodeStatus;
 import gov.cms.madie.terminology.dto.QdmValueSet;
 import gov.cms.madie.terminology.dto.ValueSetsSearchCriteria;
 import gov.cms.madie.terminology.exceptions.VsacUnauthorizedException;
@@ -22,10 +23,7 @@
 
 import java.security.Principal;
 import java.time.Instant;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-import java.util.Optional;
+import java.util.*;
 
 import static org.junit.jupiter.api.Assertions.*;
 import static org.mockito.ArgumentMatchers.any;
@@ -230,4 +228,33 @@ void testGetCodeIfNoUmlsUserFound() {
             () -> vsacFhirTerminologyController.getCode(codeName, codeSystem, version, principal));
     assertEquals(ex.getMessage(), "Please login to UMLS before proceeding");
   }
+
+  @Test
+  void testGetCodesList() {
+    List<Map<String, String>> codeList =
+        List.of(
+            Map.of(
+                "code", "1963-8", "codeSystem", "LOINC", "oid", "'urn:oid:2.16.840.1.113883.6.1'"),
+            Map.of(
+                "code", "8462-4", "codeSystem", "LOINC", "oid", "'urn:oid:2.16.840.1.113883.6.1'"));
+    Code code =
+        Code.builder()
+            .name("1963-8")
+            .codeSystem("LOINC")
+            .version("2.72")
+            .display("Bicarbonate [Moles/volume] in Serum")
+            .codeSystemOid("2.16.840.1.113883.6.1")
+            .status(CodeStatus.valueOf("ACTIVE"))
+            .build();
+
+    Principal principal = mock(Principal.class);
+    when(principal.getName()).thenReturn(TEST_USER);
+    when(vsacService.verifyUmlsAccess(anyString())).thenReturn(umlsUser);
+    when(fhirTerminologyService.retrieveCodesAndCodeSystems(any(), anyString()))
+        .thenReturn(List.of(code));
+    ResponseEntity<List<Code>> response =
+        vsacFhirTerminologyController.getCodesAndCodeSystems(codeList, principal);
+    assertEquals(response.getStatusCode(), HttpStatus.OK);
+    assertEquals(response.getBody().get(0), code);
+  }
 }

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

@@ -451,4 +451,70 @@ void testRetrieveCodeSuccessfully() {
     assertThat(code.getVersion(), is(equalTo(version)));
     assertThat(code.getStatus(), is(equalTo(CodeStatus.ACTIVE)));
   }
+
+  @Test
+  void testRetrieveCodesListSuccessfully() {
+    List<Map<String, String>> codeList =
+        List.of(
+            Map.of(
+                "code", "1963-8", "codeSystem", "LOINC", "oid", "'urn:oid:2.16.840.1.113883.6.1'"));
+
+    String codeJson =
+        "{\n"
+            + "  \"resourceType\": \"Parameters\",\n"
+            + "  \"parameter\": [ {\n"
+            + "    \"name\": \"name\",\n"
+            + "    \"valueString\": \"LOINC\"\n"
+            + "  }, {\n"
+            + "    \"name\": \"version\",\n"
+            + "    \"valueString\": \"2.40\"\n"
+            + "  }, {\n"
+            + "    \"name\": \"display\",\n"
+            + "    \"valueString\": \"Bicarbonate [Moles/volume] in Serum\"\n"
+            + "  }, {\n"
+            + "    \"name\": \"Oid\",\n"
+            + "    \"valueString\": \"2.16.840.1.113883.6.1\"\n"
+            + "  } ]\n"
+            + "}";
+
+    codeSystemEntries = new ArrayList<>();
+    CodeSystemEntry.Version version = new CodeSystemEntry.Version();
+    version.setVsac("2.40");
+    version.setFhir("2.40");
+    var codeSystemEntry =
+        CodeSystemEntry.builder()
+            .name("8462-4")
+            .oid("urn:oid:2.16.840.1.113883.6.1")
+            .url("http://loinc.org")
+            .versions(List.of(version))
+            .build();
+    codeSystemEntries.add(codeSystemEntry);
+
+    gov.cms.madie.terminology.models.CodeSystem codeSystem =
+        gov.cms.madie.terminology.models.CodeSystem.builder()
+            .id("LOINC2.40")
+            .fullUrl("http://loinc.org")
+            .title("LOINC")
+            .name("LOINC")
+            .version("2.40")
+            .versionId("404676818")
+            .oid("urn:oid:2.16.840.1.113883.6.1")
+            .lastUpdated(Instant.parse("2024-04-30T20:18:48.706Z"))
+            .lastUpdatedUpstream(new Date("Fri Apr 01 00:00:00 EDT 2022"))
+            .build();
+
+    when(mappingService.getCodeSystemEntries()).thenReturn(codeSystemEntries);
+    when(codeSystemRepository.findByOidAndVersion(anyString(), anyString()))
+        .thenReturn(Optional.ofNullable(codeSystem));
+    when(fhirTerminologyServiceWebClient.getCodeResource(anyString(), any(), any()))
+        .thenReturn(codeJson);
+    when(fhirContext.newJsonParser()).thenReturn(FhirContext.forR4().newJsonParser());
+    when(vsacService.getCodeStatus(any(), anyString())).thenReturn(CodeStatus.ACTIVE);
+    List<Code> code = fhirTerminologyService.retrieveCodesAndCodeSystems(codeList, TEST_API_KEY);
+    assertThat(code.get(0).getName(), is(equalTo("1963-8")));
+    assertThat(code.get(0).getDisplay(), is(equalTo("Bicarbonate [Moles/volume] in Serum")));
+    assertThat(code.get(0).getCodeSystem(), is(equalTo("LOINC")));
+    assertThat(code.get(0).getVersion(), is(equalTo("2.40")));
+    assertThat(code.get(0).getStatus(), is(equalTo(CodeStatus.ACTIVE)));
+  }
 }