Merge pull request #162 from MeasureAuthoringTool/MAT-6198

MAT-6198 Exported transaction test case bundles are invalid due to MeasureReport missing request component

src/main/java/gov/cms/madie/madiefhirservice/cql/LibraryCqlVisitor.java

@@ -1,5 +1,6 @@
 package gov.cms.madie.madiefhirservice.cql;
 
+import gov.cms.madie.madiefhirservice.utils.FhirResourceHelpers;
 import lombok.Getter;
 import lombok.extern.slf4j.Slf4j;
 import org.antlr.v4.runtime.ParserRuleContext;
@@ -35,14 +36,9 @@ public class LibraryCqlVisitor extends cqlBaseVisitor<String> {
   private final Map<Integer, Library> libraryCacheMap = new HashMap<>();
   private final Map<String, String> valueSetNameUri = new HashMap<>();
   private final List<Pair<String, String>> includedLibraries = new ArrayList<>();
-  private String fhirBaseUrl;
   private String name;
   private String version;
 
-  public LibraryCqlVisitor(String fhirBaseUrl) {
-    this.fhirBaseUrl = fhirBaseUrl;
-  }
-
   /**
    * Stores off lib name and version.
    *
@@ -70,7 +66,11 @@ public String visitIncludeDefinition(cqlParser.IncludeDefinitionContext ctx) {
       RelatedArtifact relatedArtifact = new RelatedArtifact();
       relatedArtifact.setType(RelatedArtifact.RelatedArtifactType.DEPENDSON);
       var nameVersion = getNameVersionFromInclude(ctx);
-      relatedArtifact.setUrl(fhirBaseUrl + "/Library/" + nameVersion.getLeft());
+      String url =
+          FhirResourceHelpers.buildResourceFullUrl("Library", nameVersion.getLeft())
+              + "|"
+              + nameVersion.getRight();
+      relatedArtifact.setResource(url);
       relatedArtifacts.add(relatedArtifact);
       includedLibraries.add(nameVersion);
       includes.add(ctx);
@@ -94,7 +94,7 @@ public String visitValuesetDefinition(cqlParser.ValuesetDefinitionContext ctx) {
         .add(new ValuesetModel(vsName, uri, null, null));
     RelatedArtifact relatedArtifact = new RelatedArtifact();
     relatedArtifact.setType(RelatedArtifact.RelatedArtifactType.DEPENDSON);
-    relatedArtifact.setUrl(uri);
+    relatedArtifact.setResource(uri);
     relatedArtifacts.add(relatedArtifact);
 
     // need to be polished once we human readable file
@@ -108,7 +108,7 @@ public String visitCodesystemDefinition(cqlParser.CodesystemDefinitionContext ct
     codeSystems.add(ctx);
     RelatedArtifact relatedArtifact = new RelatedArtifact();
     relatedArtifact.setType(RelatedArtifact.RelatedArtifactType.DEPENDSON);
-    relatedArtifact.setUrl(
+    relatedArtifact.setResource(
         getUnquotedFullText(ctx.codesystemId())
             + (ctx.versionSpecifier() != null
                 ? "|" + getUnquotedFullText(ctx.versionSpecifier())

src/main/java/gov/cms/madie/madiefhirservice/cql/LibraryCqlVisitorFactory.java

@@ -4,7 +4,6 @@
 import org.antlr.v4.runtime.CommonTokenStream;
 import org.cqframework.cql.gen.cqlLexer;
 import org.cqframework.cql.gen.cqlParser;
-import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
 
 import java.io.IOException;
@@ -13,11 +12,8 @@
 @Service
 public class LibraryCqlVisitorFactory {
 
-  @Value("${fhir-base-url}")
-  private String fhirBaseUrl;
-
   public LibraryCqlVisitor visit(String cql) {
-    LibraryCqlVisitor result = new LibraryCqlVisitor(fhirBaseUrl);
+    LibraryCqlVisitor result = new LibraryCqlVisitor();
     cqlParser.LibraryContext ctx = getLibraryContext(cql);
     result.visit(ctx);
     return result;

src/main/java/gov/cms/madie/madiefhirservice/services/HumanReadableService.java

@@ -197,14 +197,13 @@ private void sortParameters(
     if (madieMeasure.getGroups() != null) {
       madieMeasure.getGroups().stream()
           .forEach(
-              (g) ->
-              {
-                  if (CollectionUtils.isNotEmpty(g.getStratifications())) {
-                      strats.addAll(
-                              g.getStratifications().stream()
-                                      .map(s -> s.getCqlDefinition())
-                                      .collect(Collectors.toList()));
-                  }
+              (g) -> {
+                if (CollectionUtils.isNotEmpty(g.getStratifications())) {
+                  strats.addAll(
+                      g.getStratifications().stream()
+                          .map(s -> s.getCqlDefinition())
+                          .collect(Collectors.toList()));
+                }
               });
     }
 

src/main/java/gov/cms/madie/madiefhirservice/services/LibraryTranslatorService.java

@@ -2,6 +2,7 @@
 
 import gov.cms.madie.madiefhirservice.constants.UriConstants;
 import gov.cms.madie.madiefhirservice.cql.LibraryCqlVisitorFactory;
+import gov.cms.madie.madiefhirservice.utils.FhirResourceHelpers;
 import gov.cms.madie.models.library.CqlLibrary;
 import gov.cms.madie.models.common.Version;
 import lombok.extern.slf4j.Slf4j;
@@ -17,7 +18,6 @@
 import org.hl7.fhir.r4.model.Meta;
 import org.hl7.fhir.r4.model.RelatedArtifact;
 import org.hl7.fhir.r4.model.Identifier.IdentifierUse;
-import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
 
 import java.util.ArrayList;
@@ -39,9 +39,6 @@ public class LibraryTranslatorService {
 
   private final LibraryCqlVisitorFactory libCqlVisitorFactory;
 
-  @Value("${fhir-base-url}")
-  private String fhirBaseUrl;
-
   public LibraryTranslatorService(LibraryCqlVisitorFactory libCqlVisitorFactory) {
     this.libCqlVisitorFactory = libCqlVisitorFactory;
   }
@@ -64,7 +61,8 @@ public Library convertToFhirLibrary(CqlLibrary cqlLibrary) {
     library.setContent(
         createContent(cqlLibrary.getCql(), cqlLibrary.getElmJson(), cqlLibrary.getElmXml()));
     library.setType(createType(UriConstants.LIBRARY_SYSTEM_TYPE_URI, SYSTEM_CODE));
-    library.setUrl(fhirBaseUrl + "/Library/" + cqlLibrary.getCqlLibraryName());
+    library.setUrl(
+        FhirResourceHelpers.buildResourceFullUrl("Library", cqlLibrary.getCqlLibraryName()));
     library.setDataRequirement(distinctDataRequirements(visitor.getDataRequirements()));
     library.setRelatedArtifact(distinctArtifacts(visitor.getRelatedArtifacts()));
     library.setMeta(createLibraryMeta());
@@ -148,7 +146,7 @@ private List<RelatedArtifact> distinctArtifacts(List<RelatedArtifact> artifacts)
             result.add(a);
           }
         });
-    result.sort(Comparator.comparing(RelatedArtifact::getUrl));
+    result.sort(Comparator.comparing(RelatedArtifact::getResource));
     return result;
   }
 

src/main/java/gov/cms/madie/madiefhirservice/services/MeasureBundleService.java

@@ -19,7 +19,6 @@
 import org.hl7.fhir.r4.model.Library;
 import org.hl7.fhir.r4.model.Narrative;
 import org.hl7.fhir.r4.model.Reference;
-import org.hl7.fhir.r4.model.Resource;
 import org.springframework.stereotype.Service;
 
 import java.util.HashMap;
@@ -50,7 +49,8 @@ public Bundle createMeasureBundle(
         measureTranslatorService.createFhirMeasureForMadieMeasure(madieMeasure);
 
     // Bundle entry for Measure resource
-    Bundle.BundleEntryComponent measureEntryComponent = getBundleEntryComponent(measure);
+    Bundle.BundleEntryComponent measureEntryComponent =
+        FhirResourceHelpers.getBundleEntryComponent(measure, "Transaction");
     Bundle bundle =
         new Bundle().setType(Bundle.BundleType.TRANSACTION).addEntry(measureEntryComponent);
     // Bundle entries for all the library resources of a MADiE Measure
@@ -90,31 +90,20 @@ public Bundle createMeasureBundle(
   public List<Bundle.BundleEntryComponent> createBundleComponentsForLibrariesOfMadieMeasure(
       Measure madieMeasure, final String bundleType, final String accessToken) {
     Library library = getMeasureLibraryResourceForMadieMeasure(madieMeasure);
-    Bundle.BundleEntryComponent mainLibraryBundleComponent = getBundleEntryComponent(library);
+    Bundle.BundleEntryComponent mainLibraryBundleComponent =
+        FhirResourceHelpers.getBundleEntryComponent(library, "Transaction");
     Map<String, Library> includedLibraryMap = new HashMap<>();
     libraryService.getIncludedLibraries(
         madieMeasure.getCql(), includedLibraryMap, bundleType, accessToken);
     List<Bundle.BundleEntryComponent> libraryBundleComponents =
         includedLibraryMap.values().stream()
-            .map(this::getBundleEntryComponent)
+            .map((lib) -> FhirResourceHelpers.getBundleEntryComponent(lib, "Transaction"))
             .collect(Collectors.toList());
     // add main library first in the list
     libraryBundleComponents.add(0, mainLibraryBundleComponent);
     return libraryBundleComponents;
   }
 
-  /** Creates BundleEntryComponent for given resource */
-  public Bundle.BundleEntryComponent getBundleEntryComponent(Resource resource) {
-    Bundle.BundleEntryRequestComponent requestComponent =
-        new Bundle.BundleEntryRequestComponent()
-            .setMethod(Bundle.HTTPVerb.PUT)
-            .setUrl(resource.getResourceType() + "/" + resource.getIdPart());
-    return new Bundle.BundleEntryComponent()
-        .setFullUrl(FhirResourceHelpers.getFullUrl(resource))
-        .setResource(resource)
-        .setRequest(requestComponent);
-  }
-
   /**
    * Creates Library resource for main library of MADiE Measure
    *

src/main/java/gov/cms/madie/madiefhirservice/services/MeasureTranslatorService.java

@@ -59,7 +59,8 @@ public org.hl7.fhir.r4.model.Measure createFhirMeasureForMadieMeasure(Measure ma
         .setTitle(madieMeasure.getMeasureName())
         .setIdentifier(buildMeasureIdentifiers(madieMeasure))
         .setExperimental(madieMeasure.getMeasureMetaData().isExperimental())
-        .setUrl(FhirResourceHelpers.buildMeasureUrl(madieMeasure.getCqlLibraryName()))
+        .setUrl(
+            FhirResourceHelpers.buildResourceFullUrl("Measure", madieMeasure.getCqlLibraryName()))
         .setVersion(madieMeasure.getVersion().toString())
         .setEffectivePeriod(
             getPeriodFromDates(
@@ -76,7 +77,8 @@ public org.hl7.fhir.r4.model.Measure createFhirMeasureForMadieMeasure(Measure ma
         .setLibrary(
             Collections.singletonList(
                 new CanonicalType(
-                    FhirResourceHelpers.buildLibraryUrl(madieMeasure.getCqlLibraryName()))))
+                    FhirResourceHelpers.buildResourceFullUrl(
+                        "Library", madieMeasure.getCqlLibraryName()))))
         .setPurpose(UNKNOWN)
         .setContact(buildContactDetail(madieMeasure.getMeasureMetaData().getSteward(), false))
         .setGroup(buildGroups(madieMeasure.getGroups()))

src/main/java/gov/cms/madie/madiefhirservice/services/TestCaseBundleService.java

@@ -73,9 +73,9 @@ public Map<String, Bundle> getTestCaseExportBundle(Measure measure, List<TestCas
 
       String fileName = ExportFileNamesUtil.getTestCaseExportFileName(measure, testCase);
       var measureReport = buildMeasureReport(testCase, measure, bundle);
-      var bundleEntryComponent = FhirResourceHelpers.getBundleEntryComponent(measureReport);
-      bundleEntryComponent.setFullUrl(
-          "https://madie.cms.gov/MeasureReport/" + measureReport.getId());
+      var bundleEntryComponent =
+          FhirResourceHelpers.getBundleEntryComponent(
+              measureReport, String.valueOf(bundle.getType()));
       bundle.getEntry().add(bundleEntryComponent);
       testCaseBundle.put(fileName, bundle);
     }
@@ -98,7 +98,8 @@ private MeasureReport buildMeasureReport(
     measureReport.setModifierExtension(buildModifierExtension());
     measureReport.setStatus(MeasureReport.MeasureReportStatus.COMPLETE);
     measureReport.setType(MeasureReport.MeasureReportType.INDIVIDUAL);
-    measureReport.setMeasure(FhirResourceHelpers.buildMeasureUrl(measure.getCqlLibraryName()));
+    measureReport.setMeasure(
+        FhirResourceHelpers.buildResourceFullUrl("Measure", measure.getCqlLibraryName()));
     measureReport.setPeriod(
         FhirResourceHelpers.getPeriodFromDates(
             getUTCDates(measure.getMeasurementPeriodStart()),

src/main/java/gov/cms/madie/madiefhirservice/utils/FhirResourceHelpers.java

@@ -14,22 +14,28 @@
 
 @Component
 public class FhirResourceHelpers {
-
-  private static String fhirBaseUrl;
   private static String madieUrl;
 
-  @Value("${fhir-base-url}")
-  public void setFhirBaseUrl(String url) {
-    FhirResourceHelpers.fhirBaseUrl = url;
-  }
-
   @Value("${madie.url}")
   public void setMadieUrl(String url) {
     FhirResourceHelpers.madieUrl = url;
   }
 
-  public static Bundle.BundleEntryComponent getBundleEntryComponent(Resource resource) {
-    return new Bundle.BundleEntryComponent().setResource(resource);
+  public static Bundle.BundleEntryComponent getBundleEntryComponent(
+      Resource resource, String bundleType) {
+    Bundle.BundleEntryComponent entryComponent =
+        new Bundle.BundleEntryComponent()
+            .setFullUrl(buildResourceFullUrl(resource.fhirType(), resource.getIdPart()))
+            .setResource(resource);
+    // for the transaction bundles, add request object to the entry
+    if ("Transaction".equalsIgnoreCase(bundleType)) {
+      Bundle.BundleEntryRequestComponent requestComponent =
+          new Bundle.BundleEntryRequestComponent()
+              .setMethod(Bundle.HTTPVerb.POST)
+              .setUrl(resource.getResourceType() + "/" + resource.getIdPart());
+      entryComponent.setRequest(requestComponent);
+    }
+    return entryComponent;
   }
 
   public static Period getPeriodFromDates(Date startDate, Date endDate) {
@@ -49,22 +55,7 @@ public static Coding buildCoding(String code, String system, String display) {
     return new Coding().setCode(code).setSystem(system).setDisplay(display);
   }
 
-  public static String buildMeasureUrl(String measureLibraryName) {
-    return madieUrl + "/Measure/" + measureLibraryName;
-  }
-
-  public static String buildLibraryUrl(String libraryName) {
-    return fhirBaseUrl + "/Library/" + libraryName;
-  }
-
-  public static String getFullUrl(Resource resource) {
-    String resourceType = String.valueOf(resource.getResourceType());
-    if ("Measure".equals(resourceType)) {
-      return buildMeasureUrl(resource.getIdPart());
-    } else if ("Library".equals(resourceType)) {
-      return buildLibraryUrl(resource.getIdPart());
-    } else {
-      return null;
-    }
+  public static String buildResourceFullUrl(String resourceType, String resourceName) {
+    return madieUrl + "/" + resourceType + "/" + resourceName;
   }
 }

src/main/resources/application.yml

@@ -3,8 +3,6 @@ server:
   servlet:
     context-path: /api
 
-fhir-base-url: ${FHIR_BASE_URL:http://ecqi.healthit.gov/ecqms}
-
 madie:
   cql-elm:
     service:

src/test/java/gov/cms/madie/madiefhirservice/services/HumanReadableServiceTest.java

@@ -60,19 +60,20 @@ class HumanReadableServiceTest implements ResourceFileUtil {
 
   @BeforeEach
   void setUp() {
-    Group measureGroup1 = Group.builder()
+    Group measureGroup1 =
+        Group.builder()
             .id("GroupId1")
             .groupDescription("some random group")
             .measureGroupTypes(List.of(MeasureGroupTypes.OUTCOME))
             .scoring(MeasureScoring.COHORT.toString())
-            .populations(List.of(
+            .populations(
+                List.of(
                     Population.builder()
-                            .id("PopId1")
-                            .name(PopulationType.INITIAL_POPULATION)
-                            .definition("Initial Population")
-                            .description(null)
-                            .build()
-            ))
+                        .id("PopId1")
+                        .name(PopulationType.INITIAL_POPULATION)
+                        .definition("Initial Population")
+                        .description(null)
+                        .build()))
             .build();
     measureGroup1.setStratifications(null);
 
@@ -98,7 +99,7 @@ void setUp() {
             .setName(madieMeasure.getCqlLibraryName())
             .setTitle(madieMeasure.getMeasureName())
             .setExperimental(true)
-            .setUrl("fhirBaseUrl/Measure/" + madieMeasure.getCqlLibraryName())
+            .setUrl("baseUrl/Measure/" + madieMeasure.getCqlLibraryName())
             .setVersion(madieMeasure.getVersion().toString())
             .setEffectivePeriod(
                 getPeriodFromDates(

src/test/java/gov/cms/madie/madiefhirservice/services/MeasureBundleServiceTest.java

@@ -29,8 +29,6 @@
 import static org.hamcrest.CoreMatchers.is;
 import static org.hamcrest.CoreMatchers.notNullValue;
 import static org.hamcrest.MatcherAssert.assertThat;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.ArgumentMatchers.anyMap;
 import static org.mockito.ArgumentMatchers.anyString;
@@ -120,12 +118,12 @@ public void testCreateMeasureBundle() {
     Bundle.BundleEntryRequestComponent measureEntryRequest = bundle.getEntry().get(0).getRequest();
     assertThat(
         measureEntryRequest.getUrl(), is(equalTo("Measure/" + madieMeasure.getCqlLibraryName())));
-    assertThat(measureEntryRequest.getMethod(), is(equalTo(Bundle.HTTPVerb.PUT)));
+    assertThat(measureEntryRequest.getMethod(), is(equalTo(Bundle.HTTPVerb.POST)));
 
     Bundle.BundleEntryRequestComponent libraryEntryRequest = bundle.getEntry().get(1).getRequest();
     assertThat(
         libraryEntryRequest.getUrl(), is(equalTo("Library/" + madieMeasure.getCqlLibraryName())));
-    assertThat(libraryEntryRequest.getMethod(), is(equalTo(Bundle.HTTPVerb.PUT)));
+    assertThat(libraryEntryRequest.getMethod(), is(equalTo(Bundle.HTTPVerb.POST)));
   }
 
   @Test

src/test/java/gov/cms/madie/madiefhirservice/services/MeasureTranslatorServiceTest.java

@@ -81,7 +81,6 @@ public void setUp() throws JsonProcessingException {
     String cvMeasureJson =
         getStringFromTestResource("/measures/SimpleFhirMeasureLib/madie_cv_measure.json");
     madieCVMeasure = MeasureTestHelper.createMadieMeasureFromJson(cvMeasureJson);
-    ReflectionTestUtils.setField(fhirResourceHelpers, "fhirBaseUrl", "cms.gov");
     ReflectionTestUtils.setField(fhirResourceHelpers, "madieUrl", "madie.cms.gov");
   }