Merge pull request #1378 from CDCgov/story/1299-1-refactor2-remove-ac…

…cession-number

1299 Refactor common matching methods in transforms

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

@@ -42,7 +42,8 @@ public void transform(FhirResource<?> resource, Map<String, Object> args) {
             }
 
             var coding = codingList.get(0);
-            if (!HapiHelper.hasDefinedAlternateCoding(coding, HapiHelper.LOCAL_CODE_URL)) {
+            if (!HapiHelper.hasDefinedCoding(
+                    coding, HapiHelper.EXTENSION_ALT_CODING, HapiHelper.LOCAL_CODE)) {
                 continue;
             }
 

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

@@ -5,10 +5,8 @@
 import gov.hhs.cdc.trustedintermediary.external.hapi.HapiHelper;
 import java.util.HashSet;
 import java.util.Map;
-import java.util.Objects;
 import java.util.Set;
 import org.hl7.fhir.r4.model.Bundle;
-import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Resource;
 
@@ -26,35 +24,17 @@ public void transform(FhirResource<?> resource, Map<String, Object> args) {
             Resource resourceEntry = entry.getResource();
 
             if (resourceEntry instanceof Observation observation) {
-                removeMatchingObservation(observation, resourcesToRemove, args);
-            }
-        }
 
-        bundle.getEntry().removeIf(entry -> resourcesToRemove.contains(entry.getResource()));
-    }
-
-    private void removeMatchingObservation(
-            Observation observation, Set<Resource> resourcesToRemove, Map<String, Object> args) {
-        for (Coding coding : observation.getCode().getCoding()) {
-            if (isMatchingCode(coding, args)) {
-                resourcesToRemove.add(observation);
-                break;
+                if (HapiHelper.hasMatchingCoding(
+                        observation,
+                        args.get(CODE_NAME).toString(),
+                        args.get(CODING_NAME).toString(),
+                        args.get(CODING_SYSTEM_NAME).toString())) {
+                    resourcesToRemove.add(observation);
+                }
             }
         }
-    }
 
-    // TODO: Need to refactor this to handle missing extensions, etc. and determine if we can
-    // generalize it
-    private Boolean isMatchingCode(Coding coding, Map<String, Object> args) {
-        // Let it fail if args.get(<property>) is not a string
-        return Objects.equals(coding.getCode(), args.get(CODE_NAME))
-                && coding.getExtensionByUrl(HapiHelper.EXTENSION_CODING_SYSTEM)
-                        .getValue()
-                        .toString()
-                        .equals(args.get(CODING_SYSTEM_NAME))
-                && coding.getExtensionByUrl(HapiHelper.EXTENSION_CWE_CODING)
-                        .getValue()
-                        .toString()
-                        .equals(args.get(CODING_NAME));
+        bundle.getEntry().removeIf(entry -> resourcesToRemove.contains(entry.getResource()));
     }
 }

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

@@ -13,6 +13,7 @@
 import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.r4.model.MessageHeader;
 import org.hl7.fhir.r4.model.Meta;
+import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Organization;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Practitioner;
@@ -684,25 +685,55 @@ public static String urlForCodeType(String code) {
     }
 
     /**
-     * Check if a given Coding resource has alternate coding, and if it has a value of the expected
-     * type.
+     * Check if a given Coding resource has a coding extension and coding system extension with the
+     * specified type.
      *
      * @param coding the resource to check. Expected to be converted from an HL7 CWE format field.
-     * @param codingSystem Name of coding system to look for (e.g. Local code, LOINC...)
+     * @param codingExt Name of coding extension (e.g. "coding", "alt-coding")
+     * @param codingSystemExt Name of coding system to look for (e.g. Local code "L", LOINC "LN"...)
      * @return True if the Coding is formatted correctly and has the expected code type, else false
      */
-    public static Boolean hasDefinedAlternateCoding(Coding coding, String codingSystem) {
-        if (!HapiHelper.hasCodingSystem(coding)
-                || !HapiHelper.hasCodingExtensionWithUrl(coding, HapiHelper.EXTENSION_CWE_CODING)) {
+    public static boolean hasDefinedCoding(
+            Coding coding, String codingExt, String codingSystemExt) {
+        var codingExtMatch =
+                hasMatchingCodingExtension(coding, HapiHelper.EXTENSION_CWE_CODING, codingExt);
+        var codingSystemExtMatch =
+                hasMatchingCodingExtension(
+                        coding, HapiHelper.EXTENSION_CODING_SYSTEM, codingSystemExt);
+        return codingExtMatch && codingSystemExtMatch;
+    }
+
+    private static boolean hasMatchingCodingExtension(
+            Coding coding, String extensionUrl, String valueToMatch) {
+        if (!HapiHelper.hasCodingExtensionWithUrl(coding, extensionUrl)) {
             return false;
         }
 
-        var cwe =
-                HapiHelper.getCodingExtensionByUrl(coding, HapiHelper.EXTENSION_CWE_CODING)
-                        .getValue()
-                        .toString();
+        var extensionValue =
+                HapiHelper.getCodingExtensionByUrl(coding, extensionUrl).getValue().toString();
+        return Objects.equals(valueToMatch, extensionValue);
+    }
 
-        return Objects.equals(cwe, HapiHelper.EXTENSION_ALT_CODING)
-                && HapiHelper.getCodingSystem(coding).equals(codingSystem);
+    /**
+     * Check if an observation has a Coding resource with the given code, coding, and coding system
+     *
+     * @param codeToMatch The code to look for.
+     * @param codingExtToMatch Name of coding extension (e.g. "coding", "alt-coding")
+     * @param codingSystemToMatch Name of coding system to look for (e.g. Local code "L", LOINC
+     *     "LN"...)
+     * @return True if the Coding is present in the observation, else false
+     */
+    public static boolean hasMatchingCoding(
+            Observation observation,
+            String codeToMatch,
+            String codingExtToMatch,
+            String codingSystemToMatch) {
+        for (Coding coding : observation.getCode().getCoding()) {
+            if (Objects.equals(coding.getCode(), codeToMatch)
+                    && hasDefinedCoding(coding, codingExtToMatch, codingSystemToMatch)) {
+                return true;
+            }
+        }
+        return false;
     }
 }

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

@@ -931,4 +931,24 @@ class HapiHelperTest extends Specification {
         def pr = HapiHelper.getPractitioner(role)
         pr.id == practitioner.id
     }
+
+    def "hasDefinedCoding returns the correct result"() {
+        given:
+        def coding = new Coding()
+        coding.code = "SOME_CODE"
+        coding.addExtension(HapiHelper.EXTENSION_CWE_CODING, new StringType("coding"))
+        coding.addExtension(HapiHelper.EXTENSION_CODING_SYSTEM, new StringType("L"))
+
+        when:
+        def actualResult = HapiHelper.hasDefinedCoding(coding, codingExt, codingSystemExt)
+
+        then:
+        actualResult == expectedResult
+
+        where:
+        codingExt     | codingSystemExt || expectedResult
+        "coding"      | "L"             || true
+        "alt-coding"  | "L"             || false
+        "coding"      | "LN"            || false
+    }
 }