Merge pull request #1288 from CDCgov/task/1243-ca_transform_obr4.3_mo…

…dication Transformation: Modified OBR-4.3 codingSystem
CDCgov · Sep 10, 2024 · 6c599da · 6c599da
2 parents 1ce5113 + 684ee83
commit 6c599da
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Showing 4 changed files with 53 additions and 15 deletions.
diff --git a/...dintermediary/etor/ruleengine/transformation/custom/UpdateUniversalServiceIdentifier.java b/...dintermediary/etor/ruleengine/transformation/custom/UpdateUniversalServiceIdentifier.java
@@ -17,6 +17,11 @@
  * Service Identifier (OBR-4)
  */
 public class UpdateUniversalServiceIdentifier implements CustomFhirTransformation {
+
+    public static final String CHECK_VALUE_NAME = "checkValue";
+    public static final String CODING_SYSTEM_NAME = "codingSystem";
+    public static final String ALTERNATE_ID_NAME = "alternateId";
+
     @Override
     public void transform(FhirResource<?> resource, Map<String, String> args) {
         Bundle bundle = (Bundle) resource.getUnderlyingResource();
@@ -26,19 +31,22 @@ public void transform(FhirResource<?> resource, Map<String, String> args) {
                 it -> {
                     var allCodings = it.getCode().getCoding();
                     var codingSystemContainer =
-                            getCodingSystemContainer(allCodings, args.get("checkValue"));
+                            getCodingSystemContainer(allCodings, args.get(CHECK_VALUE_NAME));
 
                     if (codingSystemContainer == null) {
                         // we're only interested in coding that matches the checkValue argument
                         return;
                     }
 
                     // check for the coding system label and create or override it
-                    updateCodingSystemLabel(codingSystemContainer, args.get("codingSystem"));
+                    updateCodingSystemLabel(codingSystemContainer, args.get(CODING_SYSTEM_NAME));
 
                     // the alt id is stored on a separate coding object, so we need to filter
                     // for it
-                    updateAlternateCodingId(allCodings, args);
+                    String alternateId = args.get(ALTERNATE_ID_NAME);
+                    if (alternateId != null) {
+                        updateAlternateCodingId(allCodings, alternateId);
+                    }
                 });
     }
 
@@ -81,7 +89,7 @@ private Coding getAltCodingContainer(List<Coding> allCodings) {
     }
 
     /** Find and create or update the "Alternate Id" object in a given List */
-    private void updateAlternateCodingId(List<Coding> allCodings, Map<String, String> args) {
+    private void updateAlternateCodingId(List<Coding> allCodings, String alternateId) {
         var altCodingContainer = getAltCodingContainer(allCodings);
 
         if (altCodingContainer == null) {
@@ -93,6 +101,6 @@ private void updateAlternateCodingId(List<Coding> allCodings, Map<String, String
             altCodingContainer.addExtension(altCodingExtension);
             allCodings.add(altCodingContainer);
         }
-        altCodingContainer.setCode(args.get("alternateId"));
+        altCodingContainer.setCode(alternateId);
     }
 }
diff --git a/etor/src/main/resources/transformation_definitions.json b/etor/src/main/resources/transformation_definitions.json
@@ -181,8 +181,7 @@
           "name": "UpdateUniversalServiceIdentifier",
           "args": {
             "checkValue": "54089-8",
-            "codingSystem": "LN",
-            "alternateId": "CDPHGSPEAP"
+            "codingSystem": "CDPHGSPEAP"
           }
         }
       ]

diff --git a/...mediary/etor/ruleengine/transformation/custom/UpdateUniversalServiceIdentifierTest.groovy b/...mediary/etor/ruleengine/transformation/custom/UpdateUniversalServiceIdentifierTest.groovy
@@ -12,9 +12,12 @@ class UpdateUniversalServiceIdentifierTest extends Specification {
     def fhirResource
     def args = Map.of(
     "checkValue", "54089-8",
-    "codingSystem", "LN",
-    "alternateId", "CDPHGSPEAP"
-    )
+    "codingSystem", "CDPHGSPEAP",
+    "alternateId", "CDPHGSPEAP")
+    def argsNoAlternateId = [
+        "checkValue": "54089-8",
+        "codingSystem": "CDPHGSPEAP",
+        "alternateId": null] as Map
 
     def setup() {
         TestApplicationContext.reset()
@@ -102,10 +105,38 @@ class UpdateUniversalServiceIdentifierTest extends Specification {
 
         then:
         transformedObr4_1 == obr4_1
-        transformedObr4_3 == "LN"
+        transformedObr4_3 == "CDPHGSPEAP"
         transformedObr4_4 == "CDPHGSPEAP"
     }
 
+
+    def "update only obr4-1 through obr4-3 values when the code matches and alternate id is null"() {
+        given:
+        def bundle = fhirResource.getUnderlyingResource() as Bundle
+        def result = getObrSections(bundle)[2]
+        def obr4_1 = result[0]
+        def obr4_3 = result[1]
+        def obr4_4 = result[2]
+
+        expect:
+        obr4_1 == "54089-8"
+        obr4_3 == "NA"
+        obr4_4 == "This value should change"
+
+        when:
+        transformClass.transform(fhirResource, argsNoAlternateId)
+        bundle = fhirResource.getUnderlyingResource() as Bundle
+        def transformedResult = getObrSections(bundle)[2]
+        def transformedObr4_1 = transformedResult[0]
+        def transformedObr4_3 = transformedResult[1]
+        def transformedObr4_4 = transformedResult[2]
+
+        then:
+        transformedObr4_1 == obr4_1
+        transformedObr4_3 == "CDPHGSPEAP"
+        transformedObr4_4 == obr4_4
+    }
+
     def "leave obr4 values unchanged if the code matches and they're already correct"() {
         given:
         def bundle = fhirResource.getUnderlyingResource() as Bundle
@@ -116,7 +147,7 @@ class UpdateUniversalServiceIdentifierTest extends Specification {
 
         expect:
         obr4_1 == "54089-8"
-        obr4_3 == "LN"
+        obr4_3 == "CDPHGSPEAP"
         obr4_4 == "CDPHGSPEAP"
 
         when:
@@ -156,7 +187,7 @@ class UpdateUniversalServiceIdentifierTest extends Specification {
 
         then:
         transformedObr4_1 == obr4_1
-        transformedObr4_3 == "LN"
+        transformedObr4_3 == "CDPHGSPEAP"
         transformedObr4_4 == "CDPHGSPEAP"
     }
 

diff --git a/examples/Test/Results/005_AL_ORU_R01_NBS_Simplified_1_hl7_translation.fhir b/examples/Test/Results/005_AL_ORU_R01_NBS_Simplified_1_hl7_translation.fhir
@@ -3090,7 +3090,7 @@
                 },
                 {
                   "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system",
-                  "valueString": "LN"
+                  "valueString": "CDPHGSPEAP"
                 }
               ],
               "system": "http://loinc.org",
@@ -4267,7 +4267,7 @@
                 },
                 {
                   "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system",
-                  "valueString": "LN"
+                  "valueString": "CDPHGSPEAP"
                 }
               ],
               "system": "http://loinc.org",