Eliminate warnings for missing fields

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

@@ -28,16 +28,11 @@ public void transform(HealthData<?> resource, Map<String, Object> args) {
             return;
         }
 
-        // Extract or create the OBR-16 extension from the ServiceRequest
+        // Extract or create the OBR 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

@@ -5,6 +5,7 @@
 import gov.hhs.cdc.trustedintermediary.wrappers.HealthData;
 import java.util.Map;
 import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Identifier;
 
 /**
  * Removes Assigning Authority (PID-3.4) and Identifier Type Code (PID-3.5) from Patient Identifier
@@ -15,7 +16,12 @@ 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
+
+        Identifier patientIdentifier = HapiHelper.getPID3Identifier(bundle);
+        if (patientIdentifier == null) {
+            return;
+        }
+        patientIdentifier.setAssigner(null);
+        HapiHelper.removePID3_5Value(patientIdentifier);
     }
 }

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
@@ -214,6 +215,7 @@ class CopyOrcOrderProviderToObrOrderProviderTest extends Specification{
     }
 
     void evaluateObr16IsNull(ServiceRequest serviceRequest) {
+        assert getObr16Extension(serviceRequest) == null
         assert getObr16ExtensionPractitioner(serviceRequest) == null
     }
 
@@ -235,18 +237,18 @@ class CopyOrcOrderProviderToObrOrderProviderTest extends Specification{
         assert codingSystem == null || codingSystem[0]?.code == expectedIdentifierTypeCode
     }
 
+    Extension getObr16Extension(serviceRequest) {
+        def obrExtension =  serviceRequest.getExtensionByUrl(HapiHelper.EXTENSION_OBR_URL)
+        def obr16Extension = obrExtension.getExtensionByUrl(HapiHelper.EXTENSION_OBR16_DATA_TYPE.toString())
+        return obr16Extension
+    }
+
     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
+        def obr16Extension = getObr16Extension(serviceRequest)
+        if (obr16Extension == null) {
+            return null
         }
+        return obr16Extension.value.getResource()
     }
 
     Practitioner getOrc12ExtensionPractitioner(Bundle bundle) {

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

@@ -22,18 +22,26 @@ 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 pid_5_initial = HapiHelper.getPID5Extension(bundle)
+        def xpn_7_initial = pid_5_initial.getExtensionByUrl(HapiHelper.EXTENSION_XPN7_URL)
+        def patientName = HapiHelper.getPIDPatient(bundle).getNameFirstRep()
+        def patientNameUse = patientName.getUse()
 
         expect:
-        pid5_7 != null
+        xpn_7_initial != null
+        patientNameUse.toString() == "OFFICIAL"
 
         when:
         transformClass.transform(fhirResource, null)
 
         then:
-        HapiFhirHelper.getPID5_7Value(bundle) == null
+        def pid_5_transformed = HapiHelper.getPID5Extension(bundle)
+        def xpn_7_transformed = pid_5_transformed.getExtensionByUrl(HapiHelper.EXTENSION_XPN7_URL)
+        xpn_7_transformed == 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

@@ -268,6 +268,9 @@ public static Identifier getPID3_4Identifier(Bundle bundle) {
             return null;
         }
         Organization organization = (Organization) identifier.getAssigner().getResource();
+        if (organization == null) {
+            return null;
+        }
         return organization.getIdentifierFirstRep();
     }
 
@@ -288,6 +291,29 @@ public static void setPID3_5Value(Bundle bundle, String value) {
         setCX5Value(identifier, value);
     }
 
+    public static void removePID3_5Value(Identifier patientIdentifier) {
+        if (patientIdentifier == null) {
+            return;
+        }
+
+        patientIdentifier.setType(null);
+
+        Extension cxExtension =
+                patientIdentifier.getExtensionByUrl(HapiHelper.EXTENSION_CX_IDENTIFIER_URL);
+        if (cxExtension == null) {
+            return;
+        }
+
+        if (cxExtension.hasExtension(HapiHelper.EXTENSION_CX5_URL)) {
+            cxExtension.removeExtension(HapiHelper.EXTENSION_CX5_URL);
+        }
+
+        // The cx-identifier extension can be removed if it has no more sub-extensions
+        if (cxExtension.getExtension().isEmpty()) {
+            patientIdentifier.removeExtension(HapiHelper.EXTENSION_CX_IDENTIFIER_URL);
+        }
+    }
+
     // PID-5 - Patient Name
     public static Extension getPID5Extension(Bundle bundle) {
         Patient patient = getPIDPatient(bundle);
@@ -307,6 +333,24 @@ public static void setPID5_7ExtensionValue(Bundle bundle, String value) {
         }
     }
 
+    public static void removePID5_7Value(Bundle bundle) {
+        Patient patient = HapiHelper.getPIDPatient(bundle);
+        if (patient == null) {
+            return;
+        }
+        HumanName patientName = patient.getNameFirstRep();
+        patientName.setUse(null);
+
+        Extension pid5Extension = HapiHelper.getPID5Extension(bundle);
+        if (pid5Extension == null) {
+            return;
+        }
+        Extension xpn7Extension = pid5Extension.getExtensionByUrl(HapiHelper.EXTENSION_XPN7_URL);
+        if (xpn7Extension != null) {
+            pid5Extension.removeExtension(HapiHelper.EXTENSION_XPN7_URL);
+        }
+    }
+
     // ORC - Common Order
 
     // Diagnostic Report
@@ -500,13 +544,16 @@ public static String getOBR4_1Value(ServiceRequest serviceRequest) {
     }
 
     // OBR16 - Ordering Provider
-
-    // OBR16 -
     public static void setOBR16WithPractitioner(
-            Extension obr16Extension, PractitionerRole practitionerRole) {
-        if (practitionerRole == null) {
+            Extension obrExtension, PractitionerRole practitionerRole) {
+        if (practitionerRole == null || !practitionerRole.getPractitioner().hasReference()) {
             return;
         }
+
+        Extension obr16Extension =
+                HapiHelper.ensureSubExtensionExists(
+                        obrExtension, HapiHelper.EXTENSION_OBR16_DATA_TYPE.toString());
+
         obr16Extension.setValue(practitionerRole.getPractitioner());
     }
 

shared/src/test/groovy/gov/hhs/cdc/trustedintermediary/external/hapi/HapiHelperTest.groovy

@@ -477,6 +477,52 @@ class HapiHelperTest extends Specification {
         HapiFhirHelper.getPID3_5Value(bundle) == pid3_5
     }
 
+    // PID-3.5 - Removing Identifier Type Code
+    def "null patientIdentifier remains null"() {
+        given:
+        Identifier patientIdentifier = null
+
+        when:
+        HapiHelper.removePID3_5Value(patientIdentifier)
+
+        then:
+        patientIdentifier == null
+    }
+
+    def "patientIdentifier with no extensions leaves extensions as-is"() {
+        given:
+        Identifier patientIdentifier = new Identifier()
+
+        expect:
+        !patientIdentifier.hasExtension()
+
+        when:
+        HapiHelper.removePID3_5Value(patientIdentifier)
+
+        then:
+        !patientIdentifier.hasExtension()
+    }
+
+    def "removing of the patient assigning identifier clears extensions and type coding"() {
+        given:
+        def pid3_5 = "pid3_5"
+        def bundle = new Bundle()
+        def patientIdentifier = new Identifier()
+
+        HapiFhirHelper.createPIDPatient(bundle)
+        HapiFhirHelper.setPID3Identifier(bundle, patientIdentifier)
+        HapiHelper.setPID3_5Value(bundle, pid3_5)
+
+        patientIdentifier.type.addCoding(new Coding(code: pid3_5))
+
+        when:
+        HapiHelper.removePID3_5Value(patientIdentifier)
+
+        then:
+        patientIdentifier.extension.isEmpty()
+        patientIdentifier.type.isEmpty()
+    }
+
     // PID-5 - Patient Name
     def "patient name methods work as expected"() {
         given:
@@ -531,6 +577,45 @@ class HapiHelperTest extends Specification {
         HapiFhirHelper.getPID5_7Value(bundle) == null
     }
 
+    // PID-5.7 - Removing Name Type Code
+    def "bundle without patient remains empty"() {
+        given:
+        def bundle = new Bundle()
+
+        when:
+        HapiHelper.removePID5_7Value(bundle)
+
+        then:
+        bundle.getEntry().size() == 0
+    }
+
+    def "bundle with patient but no extensions remains empty"() {
+        given:
+        def bundle = new Bundle()
+        HapiFhirHelper.createPIDPatient(bundle)
+
+        when:
+        HapiHelper.removePID5_7Value(bundle)
+
+        then:
+        HapiHelper.getPID5Extension(bundle) == null
+    }
+
+    def "bundle with patient and pid5 extensions but no xpn7 extension remains empty"() {
+        given:
+        def bundle = new Bundle()
+        HapiFhirHelper.createPIDPatient(bundle)
+        HapiFhirHelper.setPID5Extension(bundle)
+
+        when:
+        HapiHelper.removePID5_7Value(bundle)
+
+        then:
+        Extension pid5Extension = HapiHelper.getPID5Extension(bundle)
+        !pid5Extension.hasExtension()
+    }
+
+
     // ORC-2 - Placer Order Number
     def "orc-2.1 methods work as expected"() {
         given:
@@ -863,21 +948,19 @@ class HapiHelperTest extends Specification {
 
     def "setOBR16WithPractitioner sets the expected value on an extension"() {
         given:
-        def ext = new Extension()
+        Extension obrExtension = new Extension()
         def role = new PractitionerRole()
         def practitioner = new Practitioner()
         practitioner.setId("test123")
         def ref = new Reference(practitioner.getId())
         role.setPractitioner(ref)
 
-        expect:
-        ext.getValue() == null
-
         when:
-        HapiHelper.setOBR16WithPractitioner(ext, role)
+        HapiHelper.setOBR16WithPractitioner(obrExtension, role)
 
         then:
-        ext.getValue().getReference() == "test123"
+        def obr16Extension = obrExtension.getExtensionByUrl(HapiHelper.EXTENSION_OBR16_DATA_TYPE.toString())
+        obr16Extension.getValue().getReference() == "test123"
     }
 
     def "setOBR16WithPractitioner does nothing if the provided PractitionerRole is null"() {
@@ -892,7 +975,8 @@ class HapiHelperTest extends Specification {
         HapiHelper.setOBR16WithPractitioner(ext, role)
 
         then:
-        ext.getValue() == null
+        def obr16Extension = ext.getExtensionByUrl(HapiHelper.EXTENSION_OBR16_DATA_TYPE.toString())
+        obr16Extension == null
     }
 
     def "urlForCodeType should return expected values"() {