Merge branch 'main' into chores/add-more-ca-test-files

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

@@ -8,10 +8,11 @@
 import org.hl7.fhir.r4.model.ServiceRequest;
 
 /**
- * Updates Placer Order Number (ORC-2) with content from Placer Group Number (ORC-4). It also
- * replaces Placer Order Number's Entity Identifier (ORC-2.1) and Namespace Id (ORC-2.2) with Placer
- * Group Number's Entity Identifier (ORC-4.1) and Namespace Id (ORC-4.2) respectively. Effectively,
- * we're swapping ORC-2 for ORC-4 and vice versa.
+ * Updates Placer Order Number in ORC and OBR (ORC-2 and OBR-4) with content from Placer Group
+ * Number (ORC-4). Specifically, it updated ORC-2.1/OBR-2.1 with OBR-4.1, and ORC-2.2/OBR-2.2 with
+ * OBR-4.2. It also updates Placer Group Number (ORC-4) with the original value for Placer Order
+ * Number (ORC-2). Specifically, it updates ORC-4.1 and ORC-4.2 with the original values in ORC-2.1
+ * and ORC-2.2 respectively.
  */
 public class SwapPlacerOrderAndGroupNumbers implements CustomFhirTransformation {
 
@@ -28,6 +29,8 @@ public void transform(FhirResource<?> resource, Map<String, String> args) {
 
             HapiHelper.setORC2_1Value(serviceRequest, orc4_1);
             HapiHelper.setORC2_2Value(serviceRequest, orc4_2);
+            HapiHelper.setOBR2_1Value(serviceRequest, orc4_1);
+            HapiHelper.setOBR2_2Value(serviceRequest, orc4_2);
             HapiHelper.setORC4_1Value(serviceRequest, orc2_1);
             HapiHelper.setORC4_2Value(serviceRequest, orc2_2);
         }

etor/src/main/java/gov/hhs/cdc/trustedintermediary/external/hapi/HapiMessageHelper.java

@@ -23,8 +23,11 @@ public static HapiMessageHelper getInstance() {
     private HapiMessageHelper() {}
 
     public String extractPlacerOrderNumber(Bundle messageBundle) {
+        // Placer Order Number can be extracted from ORC-2 and OBR-2, but the value is always the
+        // same
+        // if available on both
         return fhirEngine.getStringFromFhirPath(
-                messageBundle, Hl7FhirMappingPath.PLACER_ORDER_NUMBER.getFhirPath());
+                messageBundle, Hl7FhirMappingPath.PLACER_ORDER_NUMBER_ORC_2.getFhirPath());
     }
 
     public String extractSendingApplicationNamespace(Bundle messageBundle) {

etor/src/main/java/gov/hhs/cdc/trustedintermediary/plugin/path/Hl7FhirMappingPath.java

@@ -7,11 +7,16 @@
  * defines the HL7 field names.
  */
 public enum Hl7FhirMappingPath {
-    PLACER_ORDER_NUMBER(
+    PLACER_ORDER_NUMBER_ORC_2(
             "ORC.2",
             """
      Bundle.entry.resource.ofType(ServiceRequest).identifier.where(type.coding.code = 'PLAC').value
      """),
+    PLACER_ORDER_NUMBER_OBR_2(
+            "OBR.2",
+            """
+     Bundle.entry.resource.ofType(ServiceRequest).extension.where(url = 'https://reportstream.cdc.gov/fhir/StructureDefinition/obr-observation-request').extension.where(url = 'OBR.2').value
+     """),
     SENDING_FACILITY_NAMESPACE(
             "",
             """

etor/src/main/resources/transformation_definitions.json

@@ -106,7 +106,7 @@
     },
     {
       "name": "ucsdOruSwapPlacerOrderAndGroupNumbers",
-      "description": "Swaps UCSD ORU's Placer Order Number (ORC-2) and Placer Group Number (ORC-4)",
+      "description": "Swaps UCSD ORU's Placer Order Number (ORC-2) and Placer Group Number (ORC-4). It also update OBR-2 with the original value for ORC-4",
       "message": "",
       "conditions": [
         "Bundle.entry.resource.ofType(MessageHeader).destination.receiver.resolve().identifier.where(extension.value = 'HD.1').value in ('R797' | 'R508')",

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

@@ -20,33 +20,41 @@ class SwapPlacerOrderAndGroupNumbersTest extends Specification {
         transformClass = new SwapPlacerOrderAndGroupNumbers()
     }
 
-    def "swap ORC-2.1 with ORC-4.1 and ORC-2.2 with ORC-4.2"() {
+    def "swap ORC-2.1 + OBR-2.1 with ORC-4.1 and ORC-2.2 + OBR-2.2 with ORC-4.2"() {
         given:
         def fhirResource = ExamplesHelper.getExampleFhirResource("../MN/004_MN_ORU_R01_NBS_1_hl7_translation.fhir")
         def bundle = fhirResource.getUnderlyingResource() as Bundle
 
         def serviceRequest = HapiHelper.resourceInBundle(bundle, ServiceRequest)
         def orc2_1 = HapiHelper.getORC2_1Value(serviceRequest)
+        def obr2_1 = HapiHelper.getOBR2_1Value(serviceRequest)
         def orc2_2 = HapiHelper.getORC2_2Value(serviceRequest)
+        def obr2_2 = HapiHelper.getOBR2_2Value(serviceRequest)
         def orc4_1 = HapiHelper.getORC4_1Value(serviceRequest)
         def orc4_2 = HapiHelper.getORC4_2Value(serviceRequest)
 
         expect:
         orc2_1 == "423787478"
+        obr2_1 == "423787478"
         orc2_2 == "EPIC"
+        obr2_2 == "EPIC"
         orc4_1 == null
         orc4_2 == null
 
         when:
         transformClass.transform(fhirResource, null)
         def actualOrc2_1 = HapiHelper.getORC2_1Value(serviceRequest)
+        def actualObr2_1 = HapiHelper.getOBR2_1Value(serviceRequest)
         def actualOrc2_2 = HapiHelper.getORC2_2Value(serviceRequest)
+        def actualObr2_2 = HapiHelper.getOBR2_2Value(serviceRequest)
         def actualOrc4_1 = HapiHelper.getORC4_1Value(serviceRequest)
         def actualOrc4_2 = HapiHelper.getORC4_2Value(serviceRequest)
 
         then:
         actualOrc2_1 == orc4_1
+        actualObr2_1 == orc4_1
         actualOrc2_2 == orc4_2
+        actualObr2_2 == orc4_2
         actualOrc4_1 == orc2_1
         actualOrc4_2 == orc2_2
     }

shared/build.gradle

@@ -19,7 +19,7 @@ dependencies {
     //logging
     implementation 'org.slf4j:slf4j-api:2.0.13'
     implementation 'ch.qos.logback:logback-classic:1.5.6'
-    implementation 'net.logstash.logback:logstash-logback-encoder:7.4'
+    implementation 'net.logstash.logback:logstash-logback-encoder:8.0'
 
     //jackson
     implementation 'com.fasterxml.jackson.core:jackson-core:2.17.2'

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

@@ -47,6 +47,7 @@ private HapiHelper() {}
     public static final StringType EXTENSION_HD2_HD3_DATA_TYPE = new StringType("HD.2,HD.3");
     public static final StringType EXTENSION_ORC2_DATA_TYPE = new StringType("ORC.2");
     public static final StringType EXTENSION_ORC4_DATA_TYPE = new StringType("ORC.4");
+    public static final StringType EXTENSION_OBR2_DATA_TYPE = new StringType("OBR.2");
 
     public static final String EXTENSION_CODING_SYSTEM =
             "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system";
@@ -61,6 +62,9 @@ private HapiHelper() {}
                     "O21",
                     "OML - Laboratory order");
 
+    public static final String EXTENSION_OBR_URL =
+            "https://reportstream.cdc.gov/fhir/StructureDefinition/obr-observation-request";
+
     /**
      * Returns a {@link Stream} of FHIR resources inside the provided {@link Bundle} that match the
      * given resource type.
@@ -411,6 +415,53 @@ public static String getORC21Value(ServiceRequest serviceRequest) {
 
     // OBR - Observation Request
 
+    // OBR-2 - Placer Order Number
+    public static Identifier getOBR2Identifier(ServiceRequest serviceRequest) {
+        if (!serviceRequest.hasExtension(EXTENSION_OBR_URL)
+                || !serviceRequest
+                        .getExtensionByUrl(EXTENSION_OBR_URL)
+                        .hasExtension(EXTENSION_OBR2_DATA_TYPE.toString())) {
+            return null;
+        }
+        var extension =
+                serviceRequest
+                        .getExtensionByUrl(EXTENSION_OBR_URL)
+                        .getExtensionByUrl(EXTENSION_OBR2_DATA_TYPE.toString());
+        return extension.castToIdentifier(extension.getValue());
+    }
+
+    // OBR-2.1 - Entity Identifier
+    public static String getOBR2_1Value(ServiceRequest serviceRequest) {
+        var identifier = getOBR2Identifier(serviceRequest);
+        if (identifier == null) {
+            return null;
+        }
+        return getEI1Value(identifier);
+    }
+
+    public static void setOBR2_1Value(ServiceRequest serviceRequest, String value) {
+        var identifier = getOBR2Identifier(serviceRequest);
+        if (identifier != null) {
+            setEI1Value(identifier, value);
+        }
+    }
+
+    // OBR-2.2 - Namespace ID
+    public static String getOBR2_2Value(ServiceRequest serviceRequest) {
+        var identifier = getOBR2Identifier(serviceRequest);
+        if (identifier == null) {
+            return null;
+        }
+        return getEI2Value(identifier);
+    }
+
+    public static void setOBR2_2Value(ServiceRequest serviceRequest, String value) {
+        var identifier = getOBR2Identifier(serviceRequest);
+        if (identifier != null) {
+            setEI2Value(identifier, value);
+        }
+    }
+
     // OBR-4 - Universal Service Identifier
 
     // OBR-4.1 - Identifier

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

@@ -601,6 +601,38 @@ class HapiHelperTest extends Specification {
         HapiHelper.getORC21Value(sr) == null
     }
 
+    // OBR-2 - Placer Order Number
+    def "obr-2 getter and setter methods work as expected"() {
+        given:
+        def obr2_1 = "obr2_1"
+        def obr2_2 = "obr2_2"
+        def bundle = new Bundle()
+        def serviceRequest = new ServiceRequest()
+        bundle.addEntry(new Bundle.BundleEntryComponent().setResource(serviceRequest))
+
+        expect:
+        HapiHelper.getOBR2Identifier(serviceRequest) == null
+        HapiHelper.getOBR2_1Value(serviceRequest) == null
+        HapiHelper.getOBR2_2Value(serviceRequest) == null
+
+        when:
+        HapiFhirHelper.setOBR2Extension(serviceRequest, new Identifier())
+
+        then:
+        HapiHelper.getOBR2Identifier(serviceRequest) != null
+        HapiHelper.getOBR2_1Value(serviceRequest) == null
+        HapiHelper.getOBR2_2Value(serviceRequest) == null
+
+        when:
+        HapiHelper.setOBR2_1Value(serviceRequest, obr2_1)
+        HapiHelper.setOBR2_2Value(serviceRequest, obr2_2)
+
+
+        then:
+        HapiHelper.getOBR2_1Value(serviceRequest) == obr2_1
+        HapiHelper.getOBR2_2Value(serviceRequest) == obr2_2
+    }
+
     // OBR-4.1 - Observation Identifier
     def "getOBR4_1Value returns the correct value"() {
         given:

shared/src/testFixtures/groovy/gov/hhs/cdc/trustedintermediary/external/hapi/HapiFhirHelper.groovy

@@ -237,6 +237,11 @@ class HapiFhirHelper {
         organization.addExtension().setUrl(HapiHelper.EXTENSION_XON_ORGANIZATION_URL).addExtension(HapiHelper.EXTENSION_XON10_URL, new StringType(value))
     }
 
+    // OBR - Placer Order Number
+    static void setOBR2Extension(ServiceRequest serviceRequest, Identifier identifier) {
+        serviceRequest.addExtension().setUrl(HapiHelper.EXTENSION_OBR_URL).addExtension(HapiHelper.EXTENSION_OBR2_DATA_TYPE.toString(), identifier)
+    }
+
     // OBR-4 - Universal Service Identifier
     static void setOBR4_1Value(ServiceRequest serviceRequest, String value) {
         serviceRequest.setCode(new CodeableConcept().addCoding(new Coding().setCode(value)))