Merge branch 'develop' into MAT-6923-update-pom.xml

MeasureAuthoringTool · Apr 16, 2024 · 24e1e1a · 24e1e1a
2 parents 0d1279a + d2d6b98
commit 24e1e1a
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Showing 14 changed files with 564 additions and 90 deletions.
diff --git a/src/main/java/gov/cms/madie/terminology/controller/VsacFhirTerminologyController.java b/src/main/java/gov/cms/madie/terminology/controller/VsacFhirTerminologyController.java
@@ -1,17 +1,16 @@
 package gov.cms.madie.terminology.controller;
 
 import gov.cms.madie.models.measure.ManifestExpansion;
+import gov.cms.madie.terminology.dto.Code;
 import gov.cms.madie.terminology.dto.QdmValueSet;
 import gov.cms.madie.terminology.dto.ValueSetsSearchCriteria;
-import gov.cms.madie.terminology.exceptions.VsacUnauthorizedException;
 import gov.cms.madie.terminology.models.CodeSystem;
 import gov.cms.madie.terminology.models.UmlsUser;
 import gov.cms.madie.terminology.service.FhirTerminologyService;
 import gov.cms.madie.terminology.service.VsacService;
 import jakarta.servlet.http.HttpServletRequest;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
-import org.apache.commons.lang3.StringUtils;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
@@ -20,7 +19,6 @@
 
 import java.security.Principal;
 import java.util.List;
-import java.util.Optional;
 
 @RestController
 @RequestMapping(path = "/terminology")
@@ -34,15 +32,8 @@ public class VsacFhirTerminologyController {
   public ResponseEntity<List<ManifestExpansion>> getManifests(Principal principal) {
     final String username = principal.getName();
     log.info("Retrieving List of available manifests, requested by HARP ID : [{}}]", username);
-    Optional<UmlsUser> umlsUser = vsacService.findByHarpId(username);
-    if (umlsUser.isPresent() && !StringUtils.isBlank(umlsUser.get().getApiKey())) {
-      return ResponseEntity.ok().body(fhirTerminologyService.getManifests(umlsUser.get()));
-    }
-    log.error(
-        "Unable to Retrieve List of available manifests, "
-            + "UMLS Authentication Key Not found for user : [{}}]",
-        username);
-    throw new VsacUnauthorizedException("Please login to UMLS before proceeding");
+    UmlsUser umlsUser = vsacService.verifyUmlsAccess(username);
+    return ResponseEntity.ok().body(fhirTerminologyService.getManifests(umlsUser));
   }
 
   @PutMapping("/value-sets/expansion/qdm")
@@ -52,17 +43,10 @@ public ResponseEntity<List<QdmValueSet>> getValueSetsExpansions(
     log.info(
         "User [{}] is attempting to fetch value sets expansions from VSAC FHIR Terminology Server.",
         username);
-    Optional<UmlsUser> umlsUser = vsacService.findByHarpId(username);
-    if (umlsUser.isPresent() && !StringUtils.isBlank(umlsUser.get().getApiKey())) {
-      List<QdmValueSet> qdmValueSets =
-          fhirTerminologyService.getValueSetsExpansionsForQdm(searchCriteria, umlsUser.get());
-      return ResponseEntity.ok().body(qdmValueSets);
-    }
-    log.error(
-        "Unable to Retrieve Value Sets Expansions, "
-            + "UMLS Authentication Key Not found for user : [{}}]",
-        username);
-    throw new VsacUnauthorizedException("Please login to UMLS before proceeding");
+    UmlsUser umlsUser = vsacService.verifyUmlsAccess(username);
+    List<QdmValueSet> qdmValueSets =
+        fhirTerminologyService.getValueSetsExpansionsForQdm(searchCriteria, umlsUser);
+    return ResponseEntity.ok().body(qdmValueSets);
   }
 
   @GetMapping(path = "/update-code-systems", produces = MediaType.APPLICATION_JSON_VALUE)
@@ -73,18 +57,8 @@ public ResponseEntity<List<CodeSystem>> retrieveAndUpdateCodeSystems(
       @Value("${admin-api-key}") String apiKey,
       @RequestHeader("Authorization") String accessToken) {
     final String username = principal.getName();
-    Optional<UmlsUser> umlsUser = vsacService.findByHarpId(username);
-
-    if (umlsUser.isPresent() && !StringUtils.isBlank(umlsUser.get().getApiKey())) {
-      return ResponseEntity.ok()
-          .body(fhirTerminologyService.retrieveAllCodeSystems(umlsUser.get()));
-    } else {
-      log.error(
-          "Unable to Retrieve List of code systems, "
-              + "UMLS Authentication Key Not found for user : [{}}]",
-          username);
-      throw new VsacUnauthorizedException("Please login to UMLS before proceeding");
-    }
+    UmlsUser umlsUser = vsacService.verifyUmlsAccess(username);
+    return ResponseEntity.ok().body(fhirTerminologyService.retrieveAllCodeSystems(umlsUser));
   }
 
   @GetMapping(path = "/get-code-systems", produces = MediaType.APPLICATION_JSON_VALUE)
@@ -93,4 +67,22 @@ public ResponseEntity<List<CodeSystem>> getAllCodeSystems(Principal principal) {
     log.info("Retrieving list of codeSystems for user: {}", username);
     return ResponseEntity.ok().body(fhirTerminologyService.getAllCodeSystems());
   }
+
+  @GetMapping(path = "/code", produces = MediaType.APPLICATION_JSON_VALUE)
+  public ResponseEntity<Code> getCode(
+      @RequestParam() String code,
+      @RequestParam() String codeSystem,
+      @RequestParam() String version,
+      Principal principal) {
+    final String username = principal.getName();
+    log.info(
+        "User {} is performing code retrieve for code: {}, system: {} and version: {}",
+        username,
+        code,
+        codeSystem,
+        version);
+    UmlsUser user = vsacService.verifyUmlsAccess(username);
+    return ResponseEntity.ok()
+        .body(fhirTerminologyService.retrieveCode(code, codeSystem, version, user.getApiKey()));
+  }
 }
diff --git a/src/main/java/gov/cms/madie/terminology/dto/Code.java b/src/main/java/gov/cms/madie/terminology/dto/Code.java
@@ -0,0 +1,15 @@
+package gov.cms.madie.terminology.dto;
+
+import lombok.Builder;
+import lombok.Data;
+
+@Data
+@Builder(toBuilder = true)
+public class Code {
+  private String name;
+  private String display;
+  private String version;
+  private String codeSystem;
+  private String codeSystemOid;
+  private CodeStatus status;
+}
diff --git a/src/main/java/gov/cms/madie/terminology/dto/CodeStatus.java b/src/main/java/gov/cms/madie/terminology/dto/CodeStatus.java
@@ -0,0 +1,13 @@
+package gov.cms.madie.terminology.dto;
+
+public enum CodeStatus {
+  ACTIVE("active"),
+  INACTIVE("inactive"),
+  NA("Not available");
+
+  private final String value;
+
+  CodeStatus(String value) {
+    this.value = value;
+  }
+}
diff --git a/src/main/java/gov/cms/madie/terminology/repositories/CodeSystemRepository.java b/src/main/java/gov/cms/madie/terminology/repositories/CodeSystemRepository.java
@@ -6,4 +6,6 @@
 
 public interface CodeSystemRepository extends MongoRepository<CodeSystem, String> {
   Optional<CodeSystem> findById(String id);
+
+  Optional<CodeSystem> findByNameAndVersion(String name, String version);
 }
diff --git a/src/main/java/gov/cms/madie/terminology/service/FhirTerminologyService.java b/src/main/java/gov/cms/madie/terminology/service/FhirTerminologyService.java
@@ -4,6 +4,8 @@
 import ca.uhn.fhir.parser.IParser;
 import gov.cms.madie.models.mapping.CodeSystemEntry;
 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.models.CodeSystem;
@@ -13,7 +15,9 @@
 import gov.cms.madie.terminology.webclient.FhirTerminologyServiceWebClient;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
+import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Parameters;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.springframework.cache.annotation.Cacheable;
 import org.springframework.stereotype.Service;
@@ -32,6 +36,7 @@ public class FhirTerminologyService {
   private final FhirTerminologyServiceWebClient fhirTerminologyServiceWebClient;
   private final MappingService mappingService;
   private final CodeSystemRepository codeSystemRepository;
+  private final VsacService vsacService;
 
   @Cacheable("manifest-list")
   public List<ManifestExpansion> getManifests(UmlsUser umlsUser) {
@@ -129,6 +134,34 @@ public List<CodeSystem> retrieveAllCodeSystems(UmlsUser umlsUser) {
     return allCodeSystems;
   }
 
+  public Code retrieveCode(String codeName, String codeSystemName, String version, String apiKey) {
+    if (StringUtils.isEmpty(codeName)
+        || StringUtils.isEmpty(codeSystemName)
+        || StringUtils.isEmpty(version)) {
+      return null;
+    }
+    CodeSystem codeSystem =
+        codeSystemRepository.findByNameAndVersion(codeSystemName, version).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(version)
+            .display(parameters.getParameter("display").getValue().toString())
+            .codeSystemOid(parameters.getParameter("Oid").getValue().toString())
+            .build();
+    // FHIR terminology API doesn't support code status yet. workaround is to get it from SVS.
+    // TODO: remove once it is supported by fhir terminology service
+    CodeStatus status = vsacService.getCodeStatus(code, apiKey);
+    code.setStatus(status);
+    return code;
+  }
+
   private void recursiveRetrieveCodeSystems(
       UmlsUser umlsUser, Integer offset, Integer count, List<CodeSystem> allCodeSystems) {
     log.info("requesting page offset: {} count: {}", offset, count);

diff --git a/src/main/java/gov/cms/madie/terminology/service/MappingService.java b/src/main/java/gov/cms/madie/terminology/service/MappingService.java
@@ -6,12 +6,14 @@
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
+import org.springframework.util.CollectionUtils;
 
 import java.io.IOException;
 import java.net.URL;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
+import java.util.Objects;
 
 @Service
 @Slf4j
@@ -35,4 +37,15 @@ public List<CodeSystemEntry> getCodeSystemEntries() {
     }
     return Collections.emptyList();
   }
+
+  public CodeSystemEntry getCodeSystemEntry(String codeSystemName) {
+    List<CodeSystemEntry> codeSystemEntries = getCodeSystemEntries();
+    if (CollectionUtils.isEmpty(codeSystemEntries)) {
+      return null;
+    }
+    return codeSystemEntries.stream()
+        .filter(entry -> Objects.equals(entry.getName(), codeSystemName))
+        .findFirst()
+        .orElse(null);
+  }
 }
diff --git a/src/main/java/gov/cms/madie/terminology/service/VsacService.java b/src/main/java/gov/cms/madie/terminology/service/VsacService.java
@@ -4,8 +4,11 @@
 import gov.cms.madie.models.cql.terminology.CqlCode;
 import gov.cms.madie.models.cql.terminology.VsacCode;
 import gov.cms.madie.models.mapping.CodeSystemEntry;
+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;
 import gov.cms.madie.terminology.mapper.VsacToFhirValueSetMapper;
 import gov.cms.madie.terminology.models.UmlsUser;
 import gov.cms.madie.terminology.repositories.UmlsUserRepository;
@@ -20,6 +23,7 @@
 
 import java.time.Instant;
 import java.util.List;
+import java.util.Objects;
 import java.util.Optional;
 import java.util.stream.Collectors;
 
@@ -156,6 +160,54 @@ public List<CqlCode> validateCodes(List<CqlCode> cqlCodes, UmlsUser umlsUser, St
     return cqlCodes;
   }
 
+  public CodeStatus getCodeStatus(Code code, String apiKey) {
+    CodeSystemEntry systemEntry = mappingService.getCodeSystemEntry(code.getCodeSystem());
+    // 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;
+    }
+
+    // get corresponding SVS version for given FHIR version
+    CodeSystemEntry.Version version =
+        systemEntry.getVersions().stream()
+            .filter(v -> Objects.equals(v.getFhir(), code.getVersion()))
+            .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 CodeStatus.NA;
+  }
+
+  /**
+   * Verify if the user with given harp id has valid UMLS user
+   *
+   * @param harpId
+   * @return Instance of UmlsUser
+   */
+  public UmlsUser verifyUmlsAccess(String harpId) {
+    UmlsUser user = findByHarpId(harpId).orElse(null);
+    if (user == null || StringUtils.isBlank(user.getApiKey())) {
+      log.error("UMLS API Key Not found for user : [{}}]", harpId);
+      throw new VsacUnauthorizedException("Please login to UMLS before proceeding");
+    }
+    return user;
+  }
+
   private VsacCode validateCodeAgainstVsac(String codePath, UmlsUser umlsUser) {
     return terminologyWebClient.getCode(codePath, umlsUser.getApiKey());
   }