Cherry-Pick Eliminate Warning Messages

etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/ruleengine/transformation/custom/CopyOrcOrderProviderToObrOrderProvider.java

@@ -28,16 +28,8 @@ public void transform(HealthData<?> resource, Map<String, Object> args) {
             return;
         }
 
-        // Extract or create the OBR-16 extension from the ServiceRequest
         Extension obrExtension =
                 HapiHelper.ensureExtensionExists(serviceRequest, HapiHelper.EXTENSION_OBR_URL);
-
-        // Extract or create the OBR-16 data type extension
-        Extension obr16Extension =
-                HapiHelper.ensureSubExtensionExists(
-                        obrExtension, HapiHelper.EXTENSION_OBR16_DATA_TYPE.toString());
-
-        // Set the ORC-12 Practitioner in the OBR-16 extension
-        HapiHelper.setOBR16WithPractitioner(obr16Extension, practitionerRole);
+        HapiHelper.setOBR16WithPractitioner(obrExtension, practitionerRole);
     }
 }

etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/ruleengine/transformation/custom/RemovePatientIdentifiers.java

@@ -15,7 +15,8 @@ public class RemovePatientIdentifiers implements CustomFhirTransformation {
     @Override
     public void transform(HealthData<?> resource, Map<String, Object> args) {
         Bundle bundle = (Bundle) resource.getUnderlyingData();
-        HapiHelper.setPID3_4Value(bundle, ""); // remove PID.3-4
-        HapiHelper.setPID3_5Value(bundle, ""); // remove PID.3-5
+
+        HapiHelper.setPID3_4Value(bundle, null);
+        HapiHelper.removePID3_5Value(bundle);
     }
 }

etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/ruleengine/transformation/custom/RemovePatientNameTypeCode.java

@@ -12,8 +12,6 @@ public class RemovePatientNameTypeCode implements CustomFhirTransformation {
     @Override
     public void transform(final HealthData<?> resource, final Map<String, Object> args) {
         Bundle bundle = (Bundle) resource.getUnderlyingData();
-        // Need to set the value for extension to empty instead of removing the extension,
-        // otherwise RS will set its own value in its place
-        HapiHelper.setPID5_7ExtensionValue(bundle, null);
+        HapiHelper.removePID5_7Value(bundle);
     }
 }

etor/src/test/groovy/gov/hhs/cdc/trustedintermediary/etor/ruleengine/transformation/custom/CopyOrcOrderProviderToObrOrderProviderTest.groovy

@@ -7,6 +7,7 @@ import gov.hhs.cdc.trustedintermediary.external.hapi.HapiHelper
 import gov.hhs.cdc.trustedintermediary.wrappers.MetricMetadata
 import org.hl7.fhir.r4.model.Bundle
 import org.hl7.fhir.r4.model.DiagnosticReport
+import org.hl7.fhir.r4.model.Extension
 import org.hl7.fhir.r4.model.Practitioner
 import org.hl7.fhir.r4.model.Reference
 import org.hl7.fhir.r4.model.ServiceRequest
@@ -119,7 +120,7 @@ class CopyOrcOrderProviderToObrOrderProviderTest extends Specification{
         evaluateOrc12Values(bundle, EXPECTED_NPI, EXPECTED_FIRST_NAME, EXPECTED_LAST_NAME, EXPECTED_NAME_TYPE_CODE, EXPECTED_IDENTIFIER_TYPE_CODE)
 
         // OBR16 should not exist initially
-        def obr16Practitioner = getObr16ExtensionPractitioner(serviceRequest)
+        def obr16Practitioner = HapiHelper.getObr16ExtensionPractitioner(serviceRequest)
         obr16Practitioner == null
 
         when:
@@ -191,7 +192,7 @@ class CopyOrcOrderProviderToObrOrderProviderTest extends Specification{
     }
 
     void evaluateOrc12IsNull(Bundle bundle) {
-        assert getOrc12ExtensionPractitioner(bundle) == null
+        assert HapiHelper.getOrc12ExtensionPractitioner(bundle) == null
     }
 
     void evaluateOrc12Values(
@@ -201,7 +202,7 @@ class CopyOrcOrderProviderToObrOrderProviderTest extends Specification{
             String expectedLastName,
             String expectedNameTypeCode,
             String expectedIdentifierTypeCode) {
-        def practitioner = getOrc12ExtensionPractitioner(bundle)
+        def practitioner = HapiHelper.getOrc12ExtensionPractitioner(bundle)
         def xcnExtension = practitioner.getExtensionByUrl(PRACTITIONER_EXTENSION_URL)
 
         assert practitioner.identifier[0]?.value == expectedNpi
@@ -214,7 +215,8 @@ class CopyOrcOrderProviderToObrOrderProviderTest extends Specification{
     }
 
     void evaluateObr16IsNull(ServiceRequest serviceRequest) {
-        assert getObr16ExtensionPractitioner(serviceRequest) == null
+        assert HapiHelper.getObr16Extension(serviceRequest) == null
+        assert HapiHelper.getObr16ExtensionPractitioner(serviceRequest) == null
     }
 
     void evaluateObr16Values(
@@ -224,7 +226,7 @@ class CopyOrcOrderProviderToObrOrderProviderTest extends Specification{
             String expectedLastName,
             String expectedNameTypeCode,
             String expectedIdentifierTypeCode) {
-        def practitioner = getObr16ExtensionPractitioner(serviceRequest)
+        def practitioner = HapiHelper.getObr16ExtensionPractitioner(serviceRequest)
         def xcnExtension = practitioner.getExtensionByUrl(PRACTITIONER_EXTENSION_URL)
 
         assert practitioner.identifier[0]?.value == expectedNpi
@@ -234,40 +236,4 @@ class CopyOrcOrderProviderToObrOrderProviderTest extends Specification{
         def codingSystem = practitioner.identifier[0]?.type?.coding
         assert codingSystem == null || codingSystem[0]?.code == expectedIdentifierTypeCode
     }
-
-    Practitioner getObr16ExtensionPractitioner (serviceRequest) {
-        def resource
-        try {
-            def extensionByUrl1 =  serviceRequest.getExtensionByUrl(HapiHelper.EXTENSION_OBR_URL)
-            def extensionByUrl2 = extensionByUrl1.getExtensionByUrl(HapiHelper.EXTENSION_OBR16_DATA_TYPE.toString())
-            def value = extensionByUrl2.value
-            resource = value.getResource()
-            return resource
-        } catch(Exception ignored) {
-            resource = null
-            return resource
-        }
-    }
-
-    Practitioner getOrc12ExtensionPractitioner(Bundle bundle) {
-        def diagnosticReport = HapiHelper.getDiagnosticReport(bundle)
-        def serviceRequest = HapiHelper.getServiceRequest(diagnosticReport)
-
-        def orcExtension = serviceRequest.getExtensionByUrl(HapiHelper.EXTENSION_ORC_URL)
-        def orc12Extension = orcExtension.getExtensionByUrl(HapiHelper.EXTENSION_ORC12_URL)
-
-        if (orc12Extension == null) {
-            return null
-        }
-
-        def practitionerReference = (Reference) orc12Extension.getValue()
-        def practitionerUrl = practitionerReference.getReference()
-
-        for (Bundle.BundleEntryComponent entry : bundle.getEntry()) {
-            if (Objects.equals(entry.getFullUrl(), practitionerUrl) && entry.getResource() instanceof Practitioner)
-                return (Practitioner) entry.getResource()
-        }
-
-        return null
-    }
 }

etor/src/test/groovy/gov/hhs/cdc/trustedintermediary/etor/ruleengine/transformation/custom/RemovePatientIdentifierTest.groovy

@@ -33,10 +33,10 @@ class RemovePatientIdentifierTest extends Specification {
 
         when:
         transformClass.transform(fhirResource, null)
-        def actualPid3_4 = HapiFhirHelper.getPID3_4Value(bundle)
-        def actualPid3_5 = HapiFhirHelper.getPID3_5Value(bundle)
 
         then:
+        def actualPid3_4 = HapiFhirHelper.getPID3_4Value(bundle)
+        def actualPid3_5 = HapiFhirHelper.getPID3_5Value(bundle)
         actualPid3_4 == null || actualPid3_4.isEmpty()
         actualPid3_5 == null || actualPid3_5.isEmpty()
     }

etor/src/test/groovy/gov/hhs/cdc/trustedintermediary/etor/ruleengine/transformation/custom/RemovePatientNameTypeCodeTest.groovy

@@ -22,18 +22,22 @@ class RemovePatientNameTypeCodeTest extends Specification {
 
     def "remove PID.5-7 from Bundle"() {
         given:
-        def fhirResource = ExamplesHelper.getExampleFhirResource("../CA/002_CA_ORU_R01_initial_translation.fhir")
+        def fhirResource = ExamplesHelper.getExampleFhirResource("../CA/007_CA_ORU_R01_CDPH_produced_UCSD2024-07-11-16-02-17-749_1_hl7_translation.fhir")
         def bundle = fhirResource.getUnderlyingData() as Bundle
-        def pid5_7 = HapiFhirHelper.getPID5_7Value(bundle)
+        def pid5Extension = HapiHelper.getPID5Extension(bundle)
+        def patientName = HapiHelper.getPIDPatient(bundle).getNameFirstRep()
+        def patientNameUse = patientName.getUse()
 
         expect:
-        pid5_7 != null
+        pid5Extension.getExtensionByUrl(HapiHelper.EXTENSION_XPN7_URL) != null
+        patientNameUse.toString() == "OFFICIAL"
 
         when:
         transformClass.transform(fhirResource, null)
 
         then:
-        HapiFhirHelper.getPID5_7Value(bundle) == null
+        pid5Extension.getExtensionByUrl(HapiHelper.EXTENSION_XPN7_URL) == null
+        !patientName.hasUse()
     }
 
     def "don't throw exception if patient resource not present"() {

shared/src/main/java/gov/hhs/cdc/trustedintermediary/external/hapi/HapiHelper.java

@@ -18,6 +18,7 @@
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Practitioner;
 import org.hl7.fhir.r4.model.PractitionerRole;
+import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.r4.model.ServiceRequest;
 import org.hl7.fhir.r4.model.StringType;
@@ -268,15 +269,27 @@ public static Identifier getPID3_4Identifier(Bundle bundle) {
             return null;
         }
         Organization organization = (Organization) identifier.getAssigner().getResource();
+        if (organization == null) {
+            return null;
+        }
         return organization.getIdentifierFirstRep();
     }
 
     public static void setPID3_4Value(Bundle bundle, String value) {
-        Identifier identifier = getPID3_4Identifier(bundle);
-        if (identifier == null) {
+        if (value == null) {
+            Identifier pid3Identifier = getPID3Identifier(bundle);
+            if (pid3Identifier == null) {
+                return;
+            }
+            pid3Identifier.setAssigner(null);
             return;
         }
-        identifier.setValue(value);
+
+        Identifier pid3_4Identifier = getPID3_4Identifier(bundle);
+        if (pid3_4Identifier == null) {
+            return;
+        }
+        pid3_4Identifier.setValue(value);
     }
 
     // PID-3.5 - Identifier Type Code
@@ -288,22 +301,61 @@ public static void setPID3_5Value(Bundle bundle, String value) {
         setCX5Value(identifier, value);
     }
 
+    public static void removePID3_5Value(Bundle bundle) {
+        Identifier patientIdentifier = getPID3Identifier(bundle);
+        if (patientIdentifier == null) {
+            return;
+        }
+
+        patientIdentifier.setType(null);
+
+        Extension cxExtension = patientIdentifier.getExtensionByUrl(EXTENSION_CX_IDENTIFIER_URL);
+        if (cxExtension == null) {
+            return;
+        }
+
+        if (cxExtension.hasExtension(EXTENSION_CX5_URL)) {
+            cxExtension.removeExtension(EXTENSION_CX5_URL);
+        }
+
+        // The cx-identifier extension can be removed if it has no more sub-extensions
+        if (cxExtension.getExtension().isEmpty()) {
+            patientIdentifier.removeExtension(EXTENSION_CX_IDENTIFIER_URL);
+        }
+    }
+
     // PID-5 - Patient Name
     public static Extension getPID5Extension(Bundle bundle) {
         Patient patient = getPIDPatient(bundle);
         if (patient == null) {
             return null;
         }
         HumanName name = patient.getNameFirstRep();
-        return name.getExtensionByUrl(HapiHelper.EXTENSION_XPN_HUMAN_NAME_URL);
+        return name.getExtensionByUrl(EXTENSION_XPN_HUMAN_NAME_URL);
     }
 
     public static void setPID5_7ExtensionValue(Bundle bundle, String value) {
         Extension extension = getPID5Extension(bundle);
-        if (extension != null && extension.hasExtension(HapiHelper.EXTENSION_XPN7_URL)) {
-            extension
-                    .getExtensionByUrl(HapiHelper.EXTENSION_XPN7_URL)
-                    .setValue(new StringType(value));
+        if (extension != null && extension.hasExtension(EXTENSION_XPN7_URL)) {
+            extension.getExtensionByUrl(EXTENSION_XPN7_URL).setValue(new StringType(value));
+        }
+    }
+
+    public static void removePID5_7Value(Bundle bundle) {
+        Patient patient = getPIDPatient(bundle);
+        if (patient == null) {
+            return;
+        }
+        HumanName patientName = patient.getNameFirstRep();
+        patientName.setUse(null);
+
+        Extension pid5Extension = getPID5Extension(bundle);
+        if (pid5Extension == null) {
+            return;
+        }
+        Extension xpn7Extension = pid5Extension.getExtensionByUrl(EXTENSION_XPN7_URL);
+        if (xpn7Extension != null) {
+            pid5Extension.removeExtension(EXTENSION_XPN7_URL);
         }
     }
 
@@ -499,17 +551,69 @@ public static String getOBR4_1Value(ServiceRequest serviceRequest) {
         return getCWE1Value(cc.getCoding().get(0));
     }
 
-    // OBR16 - Ordering Provider
-
-    // OBR16 -
+    // OBR-16 - Ordering Provider
     public static void setOBR16WithPractitioner(
-            Extension obr16Extension, PractitionerRole practitionerRole) {
-        if (practitionerRole == null) {
+            Extension obrExtension, PractitionerRole practitionerRole) {
+        if (practitionerRole == null || !practitionerRole.getPractitioner().hasReference()) {
             return;
         }
+
+        Extension obr16Extension =
+                ensureSubExtensionExists(obrExtension, EXTENSION_OBR16_DATA_TYPE.toString());
+
         obr16Extension.setValue(practitionerRole.getPractitioner());
     }
 
+    public static Extension getObr16Extension(ServiceRequest serviceRequest) {
+        Extension obrExtension = serviceRequest.getExtensionByUrl(EXTENSION_OBR_URL);
+        if (obrExtension == null) {
+            return null;
+        }
+        return obrExtension.getExtensionByUrl(EXTENSION_OBR16_DATA_TYPE.toString());
+    }
+
+    public static Practitioner getObr16ExtensionPractitioner(ServiceRequest serviceRequest) {
+        Extension obr16Extension = getObr16Extension(serviceRequest);
+        if (obr16Extension == null || obr16Extension.getValue() == null) {
+            return null;
+        }
+
+        if (obr16Extension.getValue() instanceof Reference reference
+                && reference.getResource() instanceof Practitioner practitioner) {
+            return practitioner;
+        }
+        return null;
+    }
+
+    // ORC-12 - Ordering Provider
+    public static Practitioner getOrc12ExtensionPractitioner(Bundle bundle) {
+        DiagnosticReport diagnosticReport = getDiagnosticReport(bundle);
+        if (diagnosticReport == null) return null;
+
+        ServiceRequest serviceRequest = getServiceRequest(diagnosticReport);
+        if (serviceRequest == null) return null;
+
+        Extension orcExtension = serviceRequest.getExtensionByUrl(EXTENSION_ORC_URL);
+        if (orcExtension == null) return null;
+
+        Extension orc12Extension = orcExtension.getExtensionByUrl(EXTENSION_ORC12_URL);
+        if (orc12Extension == null) return null;
+
+        Reference practitionerReference = (Reference) orc12Extension.getValue();
+        if (practitionerReference == null) return null;
+
+        String practitionerUrl = practitionerReference.getReference();
+        if (practitionerUrl == null) return null;
+
+        for (Bundle.BundleEntryComponent entry : bundle.getEntry()) {
+            if (Objects.equals(entry.getFullUrl(), practitionerUrl)
+                    && entry.getResource() instanceof Practitioner practitioner)
+                return practitioner;
+        }
+
+        return null;
+    }
+
     /**
      * Ensures that the extension exists for a given serviceRequest. If the extension does not
      * exist, it will create it.
@@ -678,9 +782,9 @@ public static void removeHl7FieldIdentifier(List<Identifier> identifiers, String
 
     public static String urlForCodeType(String code) {
         return switch (code) {
-            case HapiHelper.LOINC_CODE -> HapiHelper.LOINC_URL;
-            case HapiHelper.PLT_CODE -> null;
-            default -> HapiHelper.LOCAL_CODE_URL;
+            case LOINC_CODE -> LOINC_URL;
+            case PLT_CODE -> null;
+            default -> LOCAL_CODE_URL;
         };
     }
 
@@ -695,22 +799,19 @@ public static String urlForCodeType(String code) {
      */
     public static boolean hasDefinedCoding(
             Coding coding, String codingExt, String codingSystemExt) {
-        var codingExtMatch =
-                hasMatchingCodingExtension(coding, HapiHelper.EXTENSION_CWE_CODING, codingExt);
+        var codingExtMatch = hasMatchingCodingExtension(coding, EXTENSION_CWE_CODING, codingExt);
         var codingSystemExtMatch =
-                hasMatchingCodingExtension(
-                        coding, HapiHelper.EXTENSION_CODING_SYSTEM, codingSystemExt);
+                hasMatchingCodingExtension(coding, EXTENSION_CODING_SYSTEM, codingSystemExt);
         return codingExtMatch && codingSystemExtMatch;
     }
 
     private static boolean hasMatchingCodingExtension(
             Coding coding, String extensionUrl, String valueToMatch) {
-        if (!HapiHelper.hasCodingExtensionWithUrl(coding, extensionUrl)) {
+        if (!hasCodingExtensionWithUrl(coding, extensionUrl)) {
             return false;
         }
 
-        var extensionValue =
-                HapiHelper.getCodingExtensionByUrl(coding, extensionUrl).getValue().toString();
+        var extensionValue = getCodingExtensionByUrl(coding, extensionUrl).getValue().toString();
         return Objects.equals(valueToMatch, extensionValue);
     }