Fixed Bunsen's dissimilarity for managingOrganization identifier. (#634)

* Fixed Bunsen's dissimilarity for managingOrganization identifier.

* Removed wildcard import.

* Addressed review comments.

* Modified java docs for DefinitionVisitor visitReference method.

* Modified java docs for DefinitionVisitor visitReference method.

Author: atulai-sg

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

@@ -555,8 +555,10 @@ public HapiConverter<Schema> visitReference(String elementName,
       List<String> referenceTypes,
       List<StructureField<HapiConverter<Schema>>> children) {
 
-    // Generate a record name based on the type of references it can contain.
-    String recordName = referenceTypes.stream().collect(Collectors.joining()) + "Reference";
+    // Generate a record name based on the element name.
+    String recordName = elementName + "Reference";
+    // Remove extension type [x] as this creates issue while identifying schema.
+    recordName = recordName.replaceAll("\\[x\\]", "");
 
     String fullName = basePackage + "." + recordName;
 

bunsen/bunsen-avro/src/test/java/com/cerner/bunsen/avro/R4AvroConverterTest.java

@@ -19,6 +19,7 @@
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.Condition;
 import org.hl7.fhir.r4.model.Extension;
+import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.r4.model.IntegerType;
 import org.hl7.fhir.r4.model.Medication;
 import org.hl7.fhir.r4.model.MedicationRequest;
@@ -285,6 +286,15 @@ public void testSingleReference() {
         testConditionDecoded.getSubject().getReference());
   }
 
+  @Test
+  public void testManagingOrganizationIdentifier() {
+
+    Identifier identifier = testPatientDecoded.getManagingOrganization().getIdentifier();
+
+    Assert.assertNotNull(identifier);
+    Assert.assertEquals(identifier.getAssigner().getReference(), "Organization/234");
+  }
+
   @Test
   public void testMultiReferenceTypes() {
 

bunsen/bunsen-avro/src/test/java/com/cerner/bunsen/avro/Stu3AvroConverterTest.java

@@ -21,6 +21,7 @@
 import org.hl7.fhir.dstu3.model.Coding;
 import org.hl7.fhir.dstu3.model.Condition;
 import org.hl7.fhir.dstu3.model.Extension;
+import org.hl7.fhir.dstu3.model.Identifier;
 import org.hl7.fhir.dstu3.model.IntegerType;
 import org.hl7.fhir.dstu3.model.Medication;
 import org.hl7.fhir.dstu3.model.MedicationRequest;
@@ -282,6 +283,15 @@ public void testSingleReference() {
         testConditionDecoded.getSubject().getReference());
   }
 
+  @Test
+  public void testManagingOrganizationIdentifier() {
+
+    Identifier identifier = testPatientDecoded.getManagingOrganization().getIdentifier();
+
+    Assert.assertNotNull(identifier);
+    Assert.assertEquals(identifier.getAssigner().getReference(), "Organization/234");
+  }
+
   @Test
   public void testMultiReferenceTypes() {
 

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

@@ -620,7 +620,7 @@ private <T> T transform(DefinitionVisitor<T> visitor,
           .sorted()
           .collect(Collectors.toList());
 
-      return visitor.visitReference(rootName, referenceTypes, childElements);
+      return visitor.visitReference(parentElement.toString(), referenceTypes, childElements);
 
     } else {
 

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

@@ -203,6 +203,13 @@ public static Patient newPatient() {
     patient.setActive(true);
     patient.setMultipleBirth(new IntegerType(1));
 
+    // This is to introduce conflict with managingOrganization identifier
+    // and make sure conflict is resolved.
+    Identifier patientIdentifier = new Identifier();
+    patientIdentifier.setId("patient123");
+    patientIdentifier.getAssigner().setReference("Organization/123");
+    patient.setIdentifier(List.of(patientIdentifier));
+
     patient.setBirthDateElement(new DateType("1945-01-02"));
 
     patient.addGeneralPractitioner().setReference("Practitioner/12345");
@@ -212,6 +219,11 @@ public static Patient newPatient() {
     practitionerIdentifier.getAssigner().setReference("Organization/123456");
     patient.getGeneralPractitionerFirstRep().setIdentifier(practitionerIdentifier);
 
+    Identifier managingOrganisationIdentifier = new Identifier();
+    managingOrganisationIdentifier.setId("O123456");
+    managingOrganisationIdentifier.getAssigner().setReference("Organization/234");
+    patient.getManagingOrganization().setIdentifier(managingOrganisationIdentifier);
+
     Address address = patient.addAddress();
     address.addLine("123 Fake Street");
     address.setCity("Chicago");

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

@@ -586,7 +586,7 @@ private <T> T transform(DefinitionVisitor<T> visitor,
           .sorted()
           .collect(Collectors.toList());
 
-      return visitor.visitReference(rootName, referenceTypes, childElements);
+      return visitor.visitReference(parentElement.toString(), referenceTypes, childElements);
 
     } else {
 

bunsen/bunsen-core-stu3/src/test/java/com/cerner/bunsen/stu3/TestData.java

@@ -198,6 +198,13 @@ public static Patient newPatient() {
     patient.setActive(true);
     patient.setMultipleBirth(new IntegerType(1));
 
+    // This is to introduce conflict with managingOrganization identifier
+    // and make sure conflict is resolved.
+    Identifier patientIdentifier = new Identifier();
+    patientIdentifier.setId("patient123");
+    patientIdentifier.getAssigner().setReference("Organization/123");
+    patient.setIdentifier(List.of(patientIdentifier));
+
     patient.setBirthDateElement(new DateType("1945-01-02"));
 
     patient.addGeneralPractitioner().setReference("Practitioner/12345");
@@ -207,6 +214,11 @@ public static Patient newPatient() {
     practitionerIdentifier.getAssigner().setReference("Organization/123456");
     patient.getGeneralPractitionerFirstRep().setIdentifier(practitionerIdentifier);
 
+    Identifier managingOrganisationIdentifier = new Identifier();
+    managingOrganisationIdentifier.setId("O123456");
+    managingOrganisationIdentifier.getAssigner().setReference("Organization/234");
+    patient.getManagingOrganization().setIdentifier(managingOrganisationIdentifier);
+
     Address address = patient.addAddress();
     address.addLine("123 Fake Street");
     address.setId("address123");

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

@@ -50,8 +50,11 @@ T visitContained(String elementPath,
 
   /**
    * Visits a reference type.
+   * The element name in itself is not sufficient as similar element names at
+   * different places cause conflict and hence we would need full schema path
+   * to differentiate between such conflicting reference names.
    *
-   * @param elementName the element to visit.
+   * @param elementName the full schema path of element which needs to be visited.
    * @param referenceTypes the types of resource that can be referenced
    * @param children the child fields of the reference
    * @return the visitor result.

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

@@ -167,6 +167,9 @@ public Object fromHapi(Object input) {
       StructureField<HapiConverter<T>> schemaEntry = schemaIterator.next();
       // We do not want id in nested elements or sub-elements.
       // https://github.com/FHIR/sql-on-fhir/blob/master/sql-on-fhir.md#id-fields-omitted
+      // So, there can be schema elements where id is not present in which case we should
+      // check whether field name is id; if yes, proceed accordingly and set the iterator
+      // for meta element and if not then the field is going to be meta element.
       if (schemaEntry.fieldName().equals("id")) {
         // Id element.
         values[0] = schemaEntry.result().fromHapi(((IAnyResource) composite).getIdElement());

pipelines/controller/pom.xml

@@ -124,6 +124,12 @@
           <groupId>org.apache.parquet</groupId>
           <artifactId>parquet-hadoop-bundle</artifactId>
         </exclusion>
+        <!-- This exclusion is required as it fails to read artifact descriptor for
+             org.glassfish:javax.el:jar:3.0.1-b06-SNAPSHOT when built project at root level. -->
+        <exclusion>
+          <groupId>org.glassfish</groupId>
+          <artifactId>javax.el</artifactId>
+        </exclusion>
       </exclusions>
     </dependency>
   </dependencies>