Changes to fix issues of missing extensions and others (#1050)

* Changes to fix issues of missing extensions and others

* Resolving parquet-tools memory error

* Addressing review comments

* Addressing review comments

* Increasing the sleep time during e2e tests before triggering incremental runs

bunsen/bunsen-avro/src/main/java/com/cerner/bunsen/avro/converters/DefinitionToAvroVisitor.java

@@ -102,7 +102,7 @@ public Schema getDataType() {
   // FHIR (Double and BigDecimal are not assignable to each other hence explicit conversions).
   // Note with this approach we are loosing some precision!
   private static final HapiConverter<Schema> DOUBLE_CONVERTER =
-      new PrimitiveConverter<Schema>("Double") {
+      new PrimitiveConverter<Schema>("Decimal") {
         @Override
         public void toHapi(Object input, IPrimitiveType primitive) {
           Preconditions.checkArgument((input instanceof BigDecimal) || (input instanceof Double));

bunsen/bunsen-avro/src/test/java/com/cerner/bunsen/avro/R4AvroConverterUsCoreTest.java

@@ -37,6 +37,7 @@
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Provenance;
 import org.hl7.fhir.r4.model.Quantity;
+import org.hl7.fhir.r4.model.QuestionnaireResponse;
 import org.hl7.fhir.r4.model.Task;
 import org.junit.Assert;
 import org.junit.BeforeClass;
@@ -101,6 +102,13 @@ public class R4AvroConverterUsCoreTest {
 
   private static Encounter testEncounterDecoded;
 
+  private static QuestionnaireResponse testQuestionnaireResponse =
+      TestData.newQuestionnaireResponse();
+
+  private static Record avroQuestionnaireResponse;
+
+  private static QuestionnaireResponse testQuestionnaireResponseDecoded;
+
   private static FhirContext fhirContext;
 
   /** Initialize test data. */
@@ -175,6 +183,15 @@ public static void convertTestData() throws ProfileException {
         AvroConverter.forResources(fhirContext, R4UsCoreProfileData.US_CORE_ENCOUNTER_PROFILES, 1);
     avroEncounter = (Record) encounterConverter.resourceToAvro(testEncounter);
     testEncounterDecoded = (Encounter) encounterConverter.avroToResource(avroEncounter);
+
+    AvroConverter questionnaireResponseConverter =
+        AvroConverter.forResources(
+            fhirContext, R4UsCoreProfileData.US_CORE_QUESTIONNAIRE_RESPONSE_PROFILES, 1);
+    avroQuestionnaireResponse =
+        (Record) questionnaireResponseConverter.resourceToAvro(testQuestionnaireResponse);
+    testQuestionnaireResponseDecoded =
+        (QuestionnaireResponse)
+            questionnaireResponseConverter.avroToResource(avroQuestionnaireResponse);
   }
 
   @Test
@@ -588,4 +605,9 @@ public void testEncounterConversions() {
     Assert.assertEquals(
         testEncounter.getParticipant().size(), testEncounterDecoded.getParticipant().size());
   }
+
+  @Test
+  public void setTestQuestionnaireResponseConversions() {
+    Assert.assertTrue(testQuestionnaireResponse.equalsDeep(testQuestionnaireResponseDecoded));
+  }
 }

bunsen/bunsen-core-r4/src/main/java/com/cerner/bunsen/definitions/r4/R4StructureDefinitions.java

@@ -8,6 +8,8 @@
 import java.util.Collection;
 import java.util.List;
 import java.util.stream.Collectors;
+import javax.annotation.Nonnull;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.CanonicalType;
 import org.hl7.fhir.r4.model.ElementDefinition;
 import org.hl7.fhir.r4.model.StructureDefinition;
@@ -37,9 +39,16 @@ public FhirConversionSupport conversionSupport() {
   }
 
   @Override
-  protected IStructureDefinition getStructureDefinition(String resourceUrl) {
-    return new StructureDefinitionWrapper(
-        (StructureDefinition) context.getValidationSupport().fetchStructureDefinition(resourceUrl));
+  @Nonnull
+  protected IStructureDefinition getStructureDefinition(String resourceUrl)
+      throws IllegalArgumentException {
+    IBaseResource baseResource =
+        context.getValidationSupport().fetchStructureDefinition(resourceUrl);
+    if (baseResource == null) {
+      throw new IllegalArgumentException(
+          String.format("Unable to find definition for %s", resourceUrl));
+    }
+    return new StructureDefinitionWrapper((StructureDefinition) baseResource);
   }
 
   // FHIR version specific interface implementations

bunsen/bunsen-core-r4/src/test/java/com/cerner/bunsen/r4/TestData.java

@@ -32,6 +32,10 @@
 import org.hl7.fhir.r4.model.Period;
 import org.hl7.fhir.r4.model.Provenance;
 import org.hl7.fhir.r4.model.Quantity;
+import org.hl7.fhir.r4.model.QuestionnaireResponse;
+import org.hl7.fhir.r4.model.QuestionnaireResponse.QuestionnaireResponseItemAnswerComponent;
+import org.hl7.fhir.r4.model.QuestionnaireResponse.QuestionnaireResponseItemComponent;
+import org.hl7.fhir.r4.model.QuestionnaireResponse.QuestionnaireResponseStatus;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.Task;
@@ -438,6 +442,26 @@ public static Provenance newProvenance() {
     return provenance;
   }
 
+  /**
+   * Returns a new QuestionnaireResponse for testing.
+   *
+   * @return a FHIR QuestionnaireResponse for testing.
+   */
+  public static QuestionnaireResponse newQuestionnaireResponse() {
+    QuestionnaireResponse response = new QuestionnaireResponse();
+    response.setId("test-questionnaire-response-id");
+    response.setStatus(QuestionnaireResponseStatus.COMPLETED);
+    response.setSubject(new Reference("Patient/12345").setDisplay("Here is a display for you."));
+    QuestionnaireResponseItemComponent component = new QuestionnaireResponseItemComponent();
+    component.setText("What is your Gender?");
+    QuestionnaireResponseItemAnswerComponent answerComponent =
+        new QuestionnaireResponseItemAnswerComponent();
+    answerComponent.setValue(new StringType("Male"));
+    component.addAnswer(answerComponent);
+    response.addItem(component);
+    return response;
+  }
+
   /**
    * Returns a new Patient from Bunsen Test profile for testing.
    *

bunsen/bunsen-core-stu3/src/main/java/com/cerner/bunsen/definitions/stu3/Stu3StructureDefinitions.java

@@ -7,8 +7,10 @@
 import com.cerner.bunsen.definitions.StructureDefinitions;
 import java.util.List;
 import java.util.stream.Collectors;
+import javax.annotation.Nonnull;
 import org.hl7.fhir.dstu3.model.ElementDefinition;
 import org.hl7.fhir.dstu3.model.StructureDefinition;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -31,9 +33,16 @@ public FhirConversionSupport conversionSupport() {
   }
 
   @Override
-  protected IStructureDefinition getStructureDefinition(String resourceUrl) {
-    return new StructureDefinitionWrapper(
-        (StructureDefinition) context.getValidationSupport().fetchStructureDefinition(resourceUrl));
+  @Nonnull
+  protected IStructureDefinition getStructureDefinition(String resourceUrl)
+      throws IllegalArgumentException {
+    IBaseResource baseResource =
+        context.getValidationSupport().fetchStructureDefinition(resourceUrl);
+    if (baseResource == null) {
+      throw new IllegalArgumentException(
+          String.format("Unable to find definition for %s", resourceUrl));
+    }
+    return new StructureDefinitionWrapper((StructureDefinition) baseResource);
   }
 
   // FHIR version specific interface implementations

bunsen/bunsen-core/src/main/java/com/cerner/bunsen/definitions/HapiConverter.java

@@ -76,7 +76,7 @@ public String extensionUrl() {
 
   /**
    * The FHIR type of the element to be converted, or null if there is no FHIR type, such as within
-   * a FHIR backbone element.
+   * a FHIR backbone element. The return value should be a valid FHIR type.
    *
    * @return FHIR type of the element to be converted.
    */

bunsen/bunsen-core/src/main/java/com/cerner/bunsen/definitions/StructureDefinitions.java

@@ -16,6 +16,7 @@
 import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
+import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 
 /** Abstract base class to visit FHIR structure definitions. */
@@ -494,24 +495,9 @@ public <T> T transform(
 
     IStructureDefinition definition = getStructureDefinition(resourceTypeUrl);
 
-    if (definition == null) {
-      throw new IllegalArgumentException("Unable to find definition for " + resourceTypeUrl);
-    }
-
     List<IStructureDefinition> containedDefinitions =
         containedResourceTypeUrls.stream()
-            .map(
-                containedResourceTypeUrl -> {
-                  IStructureDefinition containedDefinition =
-                      getStructureDefinition(containedResourceTypeUrl);
-
-                  if (containedDefinition == null) {
-                    throw new IllegalArgumentException(
-                        "Unable to find definition for " + containedResourceTypeUrl);
-                  }
-
-                  return containedDefinition;
-                })
+            .map(containedResourceTypeUrl -> getStructureDefinition(containedResourceTypeUrl))
             .collect(Collectors.toList());
 
     return transformRoot(visitor, definition, containedDefinitions);
@@ -550,7 +536,11 @@ private <T> T transform(
               // Retrieve only the unique reference types
               .distinct()
               .collect(Collectors.toList());
-      return visitor.visitReference(parentElement.toString(), referenceTypes, childElements);
+
+      String elementName = DefinitionVisitorsUtil.elementName(parentElement.getPath());
+      String elementFullPath = DefinitionVisitorsUtil.pathFromStack(elementName, stack);
+      return visitor.visitReference(
+          DefinitionVisitorsUtil.recordNameFor(elementFullPath), referenceTypes, childElements);
     } else {
       String rootName = DefinitionVisitorsUtil.elementName(root.getPath());
 
@@ -600,12 +590,16 @@ private <T> T transformRoot(
   }
 
   /**
-   * Returns the structure definition interface corresponding to the given URL.
+   * Returns the structure definition interface corresponding to the given resourceUrl.
    *
    * @param resourceUrl it can be a resource type like `Patient` or a profile URL.
-   * @return the {@link IStructureDefinition} corresponding to the `resourceUrl`.
+   * @return the {@link IStructureDefinition} corresponding to the `resourceUrl`
+   * @throws IllegalArgumentException if the structure definition cannot be found for the given
+   *     resourceUrl.
    */
-  protected abstract IStructureDefinition getStructureDefinition(String resourceUrl);
+  @Nonnull
+  protected abstract IStructureDefinition getStructureDefinition(String resourceUrl)
+      throws IllegalArgumentException;
 
   /**
    * Returns the structure definition interface corresponding to the given element.

bunsen/extension-structure-definitions/src/main/java/com/cerner/bunsen/common/R4UsCoreProfileData.java

@@ -50,4 +50,9 @@ public class R4UsCoreProfileData {
       Arrays.asList(
           "http://hl7.org/fhir/StructureDefinition/Medication",
           "http://hl7.org/fhir/us/core/StructureDefinition/us-core-medication");
+
+  public static final List<String> US_CORE_QUESTIONNAIRE_RESPONSE_PROFILES =
+      Arrays.asList(
+          "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse",
+          "http://hl7.org/fhir/us/core/StructureDefinition/us-core-questionnaireresponse");
 }