Merge pull request #83 from MeasureAuthoringTool/MAT-7223/updateLogic…

…ForCheckingExistingCqlMetaData

Mat 7223/update logic for checking existing cql meta data

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

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

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

@@ -128,8 +128,8 @@ public List<ValueSetForSearch> searchValueSets(String apiKey, Map<String, String
         .forEach(
             entry -> {
               Resource resource = entry.getResource();
-                ValueSet vs = (ValueSet) resource;
-                if (resource instanceof ValueSet) {
+              ValueSet vs = (ValueSet) resource;
+              if (resource instanceof ValueSet) {
                 String oid = "";
                 for (Identifier identifier : ((ValueSet) resource).getIdentifier()) {
                   if (identifier.getValue() != null && !identifier.getValue().isEmpty()) {
@@ -139,17 +139,32 @@ public List<ValueSetForSearch> searchValueSets(String apiKey, Map<String, String
                 ValueSetForSearch valueSet =
                     ValueSetForSearch.builder()
                         .title(vs.getTitle())
-                            .author(String.valueOf(vs.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/valueset-author").getValue()))
+                        .author(
+                            String.valueOf(
+                                vs.getExtensionByUrl(
+                                        "http://hl7.org/fhir/StructureDefinition/valueset-author")
+                                    .getValue()))
                         .name(vs.getName())
-                            .composedOf(vs.getCompose().getInclude().stream().map(x -> x.getSystem()).collect(Collectors.joining(",")))
-                            .effectiveDate(String.valueOf(vs.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/valueset-effectiveDate").getValue()))
-                            .lastReviewDate(String.valueOf(vs.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/resource-lastReviewDate").getValue()))
-                            .lastUpdated(vs.getMeta().getLastUpdated().toString())
+                        .composedOf(
+                            vs.getCompose().getInclude().stream()
+                                .map(x -> x.getSystem())
+                                .collect(Collectors.joining(",")))
+                        .effectiveDate(
+                            String.valueOf(
+                                vs.getExtensionByUrl(
+                                        "http://hl7.org/fhir/StructureDefinition/valueset-effectiveDate")
+                                    .getValue()))
+                        .lastReviewDate(
+                            String.valueOf(
+                                vs.getExtensionByUrl(
+                                        "http://hl7.org/fhir/StructureDefinition/resource-lastReviewDate")
+                                    .getValue()))
+                        .lastUpdated(vs.getMeta().getLastUpdated().toString())
                         .url(vs.getUrl())
                         .version(vs.getVersion())
                         .status(vs.getStatus())
-                            .publisher(vs.getPublisher())
-                            .purpose(vs.getPurpose())
+                        .publisher(vs.getPublisher())
+                        .purpose(vs.getPurpose())
                         .steward(vs.getPublisher())
                         .oid(oid)
                         .build();
@@ -219,26 +234,24 @@ public Code retrieveCode(String codeName, String codeSystemName, String version,
         || 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;
+
+    List<CodeSystemEntry> codeSystemEntries = mappingService.getCodeSystemEntries();
+    Optional<Map.Entry<String, String>> mappedVersion =
+        mapVersion(version, codeSystem.getOid(), codeSystemEntries, "fhirVersion");
+
+    if (mappedVersion.isPresent()) {
+      String vsacVersion = mappedVersion.get().getKey();
+      String fhirVersion = mappedVersion.get().getValue();
+
+      return retrieveCodes(codeName, codeSystemName, vsacVersion, fhirVersion, codeSystem, apiKey);
+    }
+    return null;
   }
 
   private void recursiveRetrieveCodeSystems(
@@ -329,22 +342,34 @@ public List<Code> retrieveCodesAndCodeSystems(List<Map<String, String>> codeList
               String oid = code.get("oid") != null ? code.get("oid").replaceAll("'|'", "") : null;
 
               Optional<Map.Entry<String, String>> mappedVersion =
-                  mapToFhirVersion(code.get("version"), oid, codeSystemEntries);
+                  mapVersion(code.get("version"), oid, codeSystemEntries, "svsVersion");
 
               if (mappedVersion.isPresent()) {
                 String vsacVersion = mappedVersion.get().getKey();
                 String fhirVersion = mappedVersion.get().getValue();
 
+                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;
+                }
+
                 return retrieveCodes(
-                    codeName, codeSystemName, vsacVersion, fhirVersion, oid, apiKey);
+                    codeName, codeSystemName, vsacVersion, fhirVersion, codeSystem, apiKey);
               }
               return null;
             })
         .collect(Collectors.toList());
   }
 
-  private Optional<Map.Entry<String, String>> mapToFhirVersion(
-      String version, String oid, List<CodeSystemEntry> codeSystemEntries) {
+  private Optional<Map.Entry<String, String>> mapVersion(
+      String version, String oid, List<CodeSystemEntry> codeSystemEntries, String versionType) {
     if (oid == null) {
       return Optional.empty();
     }
@@ -365,7 +390,14 @@ private Optional<Map.Entry<String, String>> mapToFhirVersion(
           codeSystemEntries.stream()
               .filter(codeSystemEntry -> StringUtils.equals(codeSystemEntry.getOid(), oid))
               .flatMap(codeSystemEntry -> codeSystemEntry.getVersions().stream())
-              .filter(codeSystemVersion -> StringUtils.equals(codeSystemVersion.getVsac(), version))
+              // depending on the version type suitable mapping is done
+              .filter(
+                  codeSystemVersion ->
+                      StringUtils.equals(
+                          versionType == "svsVersion"
+                              ? codeSystemVersion.getVsac()
+                              : codeSystemVersion.getFhir(),
+                          version))
               .map(
                   codeSystemVersion ->
                       Map.entry(codeSystemVersion.getVsac(), codeSystemVersion.getFhir()))
@@ -380,25 +412,16 @@ private Code retrieveCodes(
       String codeSystemName,
       String vsacVersion,
       String fhirVersion,
-      String oid,
+      CodeSystem codeSystem,
       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)
+            .fhirVersion(fhirVersion)
             .svsVersion(vsacVersion)
             .display(parameters.getParameter("display").getValue().toString())
             .codeSystemOid(parameters.getParameter("Oid").getValue().toString())

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

@@ -194,7 +194,7 @@ private String getSvsCodeSystemVersion(Code code) {
     // get corresponding SVS version for given FHIR version
     CodeSystemEntry.Version version =
         systemEntry.getVersions().stream()
-            .filter(v -> Objects.equals(v.getFhir(), code.getVersion()))
+            .filter(v -> Objects.equals(v.getFhir(), code.getFhirVersion()))
             .findFirst()
             .orElse(null);
     if (version == null || version.getVsac() == null) {

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

@@ -244,7 +244,8 @@ public void testGetCodeSuccessfully() throws Exception {
         Code.builder()
             .name(codeName)
             .codeSystem(codeSystem)
-            .version(version)
+            .fhirVersion(version)
+            .svsVersion(version)
             .display("Bicarbonate [Moles/volume] in Serum")
             .codeSystemOid("2.16.840.1.113883.6.1")
             .build();

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

@@ -193,7 +193,8 @@ void testGetCode() {
         Code.builder()
             .name(codeName)
             .codeSystem(codeSystem)
-            .version(version)
+            .svsVersion(version)
+            .fhirVersion(version)
             .display("Bicarbonate [Moles/volume] in Serum")
             .codeSystemOid("2.16.840.1.113883.6.1")
             .build();
@@ -238,7 +239,8 @@ void testGetCodesList() {
         Code.builder()
             .name("1963-8")
             .codeSystem("LOINC")
-            .version("2.72")
+            .svsVersion("2.72")
+            .fhirVersion("2.72")
             .display("Bicarbonate [Moles/volume] in Serum")
             .codeSystemOid("2.16.840.1.113883.6.1")
             .status(CodeStatus.valueOf("ACTIVE"))
@@ -258,10 +260,26 @@ void testGetCodesList() {
   @Test
   void testSearchValueSets() {
     List<ValueSetForSearch> mockValueSets = new ArrayList<>();
-    ValueSetForSearch v1 = ValueSetForSearch.builder().title("title 1").name("title1").url("url").oid("oid")
-            .steward("steward").version("version").codeSystem("cs").build();
-    ValueSetForSearch v2 = ValueSetForSearch.builder().title("title 2").name("title2").url("url").oid("oid")
-            .steward("steward").version("version").codeSystem("cs").build();
+    ValueSetForSearch v1 =
+        ValueSetForSearch.builder()
+            .title("title 1")
+            .name("title1")
+            .url("url")
+            .oid("oid")
+            .steward("steward")
+            .version("version")
+            .codeSystem("cs")
+            .build();
+    ValueSetForSearch v2 =
+        ValueSetForSearch.builder()
+            .title("title 2")
+            .name("title2")
+            .url("url")
+            .oid("oid")
+            .steward("steward")
+            .version("version")
+            .codeSystem("cs")
+            .build();
     mockValueSets.add(v1);
     mockValueSets.add(v2);
     Principal principal = mock(Principal.class);
@@ -272,7 +290,7 @@ void testSearchValueSets() {
     queryParams.put("param1", "value1");
     queryParams.put("param2", "value2");
     ResponseEntity<List<ValueSetForSearch>> response =
-            vsacFhirTerminologyController.searchValueSets(principal, queryParams);
+        vsacFhirTerminologyController.searchValueSets(principal, queryParams);
     assertEquals(response.getStatusCode(), HttpStatus.OK);
   }
 }

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

@@ -435,8 +435,29 @@ void testRetrieveCodeSuccessfully() {
             + "    \"valueString\": \"2.16.840.1.113883.6.1\"\n"
             + "  } ]\n"
             + "}";
+    codeSystemEntries = new ArrayList<>();
+    CodeSystemEntry.Version versions = new CodeSystemEntry.Version();
+    versions.setVsac("2.40");
+    versions.setFhir("2.40");
+    var codeSystemEntry =
+        CodeSystemEntry.builder()
+            .name("1963-8")
+            .oid("urn:oid:2.16.840.1.113883.6.1")
+            .url("http://loinc.org")
+            .versions(List.of(versions))
+            .build();
+    codeSystemEntries.add(codeSystemEntry);
 
-    var codeSystem = gov.cms.madie.terminology.models.CodeSystem.builder().build();
+    var codeSystem =
+        gov.cms.madie.terminology.models.CodeSystem.builder()
+            .fullUrl("http://loinc.org")
+            .title("LOINC")
+            .name("LOINC")
+            .version("2.40")
+            .versionId("2084800774")
+            .oid("urn:oid:2.16.840.1.113883.6.1")
+            .build();
+    when(mappingService.getCodeSystemEntries()).thenReturn(codeSystemEntries);
     when(codeSystemRepository.findByNameAndVersion(anyString(), anyString()))
         .thenReturn(Optional.of(codeSystem));
     when(fhirTerminologyServiceWebClient.getCodeResource(codeName, codeSystem, TEST_API_KEY))
@@ -448,7 +469,7 @@ void testRetrieveCodeSuccessfully() {
     assertThat(code.getName(), is(equalTo(codeName)));
     assertThat(code.getDisplay(), is(equalTo("Bicarbonate [Moles/volume] in Serum")));
     assertThat(code.getCodeSystem(), is(equalTo(codeSystemName)));
-    assertThat(code.getVersion(), is(equalTo(version)));
+    assertThat(code.getFhirVersion(), is(equalTo(version)));
     assertThat(code.getStatus(), is(equalTo(CodeStatus.ACTIVE)));
   }
 
@@ -514,7 +535,7 @@ void testRetrieveCodesListSuccessfully() {
     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).getFhirVersion(), is(equalTo("2.40")));
     assertThat(code.get(0).getStatus(), is(equalTo(CodeStatus.ACTIVE)));
   }
 }

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

@@ -459,7 +459,7 @@ void testGetCodeStatusIfCodeSystemMappingAbsent() {
     when(mappingService.getCodeSystemEntryByOid(anyString())).thenReturn(null);
     assertThat(
         vsacService.getCodeStatus(
-            Code.builder().codeSystemOid("oid").version("version").build(), TEST_API_KEY),
+            Code.builder().codeSystemOid("oid").fhirVersion("version").build(), TEST_API_KEY),
         is(equalTo(CodeStatus.NA)));
   }
 
@@ -469,7 +469,7 @@ void testGetCodeStatusIfCodeSystemNotInSvs() {
     when(mappingService.getCodeSystemEntryByOid(anyString())).thenReturn(cse);
     assertThat(
         vsacService.getCodeStatus(
-            Code.builder().codeSystemOid("oid").version("version").build(), TEST_API_KEY),
+            Code.builder().codeSystemOid("oid").fhirVersion("version").build(), TEST_API_KEY),
         is(equalTo(CodeStatus.NA)));
   }
 
@@ -510,7 +510,7 @@ void testGetCodeStatusActive() {
         Code.builder()
             .name("1222766008")
             .codeSystem("ABC")
-            .version("abc.info/20230901")
+            .fhirVersion("abc.info/20230901")
             .display("American Joint Committee on Cancer stage IIA")
             .codeSystemOid("1.2.3.4.96")
             .build();
@@ -543,7 +543,7 @@ void testGetCodeStatusInactive() {
         Code.builder()
             .name("1222766008")
             .codeSystem("ABC")
-            .version("abc.info/20230901")
+            .fhirVersion("abc.info/20230901")
             .display("American Joint Committee on Cancer stage IIA")
             .codeSystemOid("1.2.3.4.96")
             .build();
@@ -576,7 +576,7 @@ void testGetCodeStatusIfCodeNotFoundInSvs() {
         Code.builder()
             .name("1222766008")
             .codeSystem("ABC")
-            .version("abc.info/20230901")
+            .fhirVersion("abc.info/20230901")
             .display("American Joint Committee on Cancer stage IIA")
             .codeSystemOid("1.2.3.4.96")
             .build();