Merge pull request #1371 from CDCgov/story/1299-1-remove-accession-nu…

…mber

CA Transform: Remove Accession Number

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

@@ -8,7 +8,6 @@
 import gov.hhs.cdc.trustedintermediary.wrappers.Logger;
 import java.util.HashMap;
 import java.util.Map;
-import java.util.Objects;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.Observation;
@@ -43,7 +42,8 @@ public void transform(FhirResource<?> resource, Map<String, Object> args) {
             }
 
             var coding = codingList.get(0);
-            if (!hasLocalCodeInAlternateCoding(coding)) {
+            if (!HapiHelper.hasDefinedCoding(
+                    coding, HapiHelper.EXTENSION_ALT_CODING, HapiHelper.LOCAL_CODE)) {
                 continue;
             }
 
@@ -60,24 +60,6 @@ public void transform(FhirResource<?> resource, Map<String, Object> args) {
         }
     }
 
-    private Boolean hasLocalCodeInAlternateCoding(Coding coding) {
-        if (!HapiHelper.hasCodingExtensionWithUrl(coding, HapiHelper.EXTENSION_CWE_CODING)) {
-            return false;
-        }
-
-        if (!HapiHelper.hasCodingSystem(coding)) {
-            return false;
-        }
-
-        var cwe =
-                HapiHelper.getCodingExtensionByUrl(coding, HapiHelper.EXTENSION_CWE_CODING)
-                        .getValue()
-                        .toString();
-        var codingSystem = HapiHelper.getCodingSystem(coding);
-
-        return Objects.equals(cwe, "alt-coding") && HapiHelper.LOCAL_CODE_URL.equals(codingSystem);
-    }
-
     private void logUnmappedLocalCode(Bundle bundle, Coding coding) {
         var msh41Identifier = HapiHelper.getMSH4_1Identifier(bundle);
         var msh41Value = msh41Identifier != null ? msh41Identifier.getValue() : null;
@@ -103,6 +85,12 @@ private Coding getMappedCoding(IdentifierCode identifierCode) {
         return mappedCoding;
     }
 
+    /**
+     * Initializes the local-to-LOINC/PLT hash map, customized for CDPH and UCSD. Currently, the
+     * mapping is hardcoded for simplicity. If expanded to support additional entities, the
+     * implementation may be updated to allow dynamic configuration via
+     * transformation_definitions.json or a database-driven mapping.
+     */
     private void initMap() {
         this.codingMap = new HashMap<>();
         // ALD

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

@@ -0,0 +1,41 @@
+package gov.hhs.cdc.trustedintermediary.etor.ruleengine.transformation.custom;
+
+import gov.hhs.cdc.trustedintermediary.etor.ruleengine.FhirResource;
+import gov.hhs.cdc.trustedintermediary.etor.ruleengine.transformation.CustomFhirTransformation;
+import gov.hhs.cdc.trustedintermediary.external.hapi.HapiHelper;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.Resource;
+
+public class RemoveObservationByCode implements CustomFhirTransformation {
+    public static final String CODE_NAME = "code";
+    public static final String CODING_SYSTEM_NAME = "codingSystemExtension";
+    public static final String CODING_NAME = "codingExtension";
+
+    @Override
+    public void transform(FhirResource<?> resource, Map<String, Object> args) {
+        var bundle = (Bundle) resource.getUnderlyingResource();
+        Set<Resource> resourcesToRemove = new HashSet<>();
+
+        for (Bundle.BundleEntryComponent entry : bundle.getEntry()) {
+            Resource resourceEntry = entry.getResource();
+
+            if (!(resourceEntry instanceof Observation observation)) {
+                continue;
+            }
+
+            if (HapiHelper.hasMatchingCoding(
+                    observation,
+                    args.get(CODE_NAME).toString(),
+                    args.get(CODING_NAME).toString(),
+                    args.get(CODING_SYSTEM_NAME).toString())) {
+                resourcesToRemove.add(resourceEntry);
+            }
+        }
+
+        bundle.getEntry().removeIf(entry -> resourcesToRemove.contains(entry.getResource()));
+    }
+}

etor/src/main/resources/transformation_definitions.json

@@ -216,6 +216,25 @@
           "args": {}
         }
       ]
+    },
+    {
+      "name": "ucsdOruRemoveAccessionNumberObservation",
+      "description": "Remove Observations for UCSD ORUs when their OBX-3.4 value is '99717-5' and OBX-3.6 is 'L'",
+      "message": "",
+      "conditions": [
+        "Bundle.entry.resource.ofType(MessageHeader).destination.receiver.resolve().identifier.where(extension.value = 'HD.1').value in ('R797' | 'R508')",
+        "Bundle.entry.resource.ofType(MessageHeader).event.code = 'R01'"
+      ],
+      "rules": [
+        {
+          "name": "RemoveObservationByCode",
+          "args": {
+            "code": "99717-5",
+            "codingSystemExtension": "L",
+            "codingExtension": "alt-coding"
+          }
+        }
+      ]
     }
   ]
 }

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

@@ -0,0 +1,193 @@
+package gov.hhs.cdc.trustedintermediary.etor.ruleengine.transformation.custom
+
+import gov.hhs.cdc.trustedintermediary.ExamplesHelper
+import gov.hhs.cdc.trustedintermediary.context.TestApplicationContext
+import gov.hhs.cdc.trustedintermediary.external.hapi.HapiFhirHelper
+import gov.hhs.cdc.trustedintermediary.external.hapi.HapiFhirResource
+import gov.hhs.cdc.trustedintermediary.external.hapi.HapiHelper
+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.StringType
+import spock.lang.Specification
+
+class RemoveObservationByCodeTest extends Specification {
+    def transformClass
+
+    def setup() {
+        TestApplicationContext.reset()
+        TestApplicationContext.init()
+        TestApplicationContext.injectRegisteredImplementations()
+
+        transformClass = new RemoveObservationByCode()
+    }
+
+    def "When an observation has the desired coding, it should be removed"() {
+        given:
+        def bundle = HapiFhirHelper.createMessageBundle(messageTypeCode: 'ORU_R01')
+        def observation = new Observation()
+        addCodingToObservation(observation, code, codingSystemExt, codingExt)
+        bundle.addEntry(new Bundle.BundleEntryComponent().setResource(observation))
+
+        def args = getArgs(code, codingSystemExt, codingExt)
+
+        expect:
+        HapiHelper.resourcesInBundle(bundle, Observation.class).count() == 1
+
+        when:
+        transformClass.transform(new HapiFhirResource(bundle), args)
+
+        then:
+        HapiHelper.resourcesInBundle(bundle, Observation.class).count() == 0
+
+        where:
+        code      | codingSystemExt | codingExt
+        "99717-5" | "L"             | "alt-coding"
+        "my_code" | "MY_SYS"        | "coding"
+    }
+
+    def "When an observation with >1 coding has the desired coding, it should be removed"() {
+        given:
+        final String MATCHING_CODE = "99717-5"
+        final String MATCHING_CODING_SYSTEM_EXT = "L"
+        final String MATCHING_CODING_EXT = "alt-coding"
+
+        def bundle = HapiFhirHelper.createMessageBundle(messageTypeCode: 'ORU_R01')
+        def observation = new Observation()
+
+        addCodingToObservation(observation, "ANOTHER_CODE", "ANOTHER_SYSTEM", "coding")
+        addCodingToObservation(observation, MATCHING_CODE, MATCHING_CODING_SYSTEM_EXT, MATCHING_CODING_EXT)
+        bundle.addEntry(new Bundle.BundleEntryComponent().setResource(observation))
+
+        def args = getArgs(MATCHING_CODE, MATCHING_CODING_SYSTEM_EXT, MATCHING_CODING_EXT)
+
+        expect:
+        HapiHelper.resourcesInBundle(bundle, Observation.class).count() == 1
+
+        when:
+        transformClass.transform(new HapiFhirResource(bundle), args)
+
+        then:
+        HapiHelper.resourcesInBundle(bundle, Observation.class).count() == 0
+    }
+
+    def "When an observation has coding that's only a partial match, it should NOT be removed"() {
+        given:
+        final String MATCHING_CODE = "99717-5"
+        final String MATCHING_CODING_SYSTEM_EXT = "L"
+        final String MATCHING_CODING_EXT = "alt-coding"
+
+        def bundle = HapiFhirHelper.createMessageBundle(messageTypeCode: 'ORU_R01')
+        def observation = new Observation()
+        addCodingToObservation(observation, code, codingSystemExt, codingExt)
+        bundle.addEntry(new Bundle.BundleEntryComponent().setResource(observation))
+
+        def args = getArgs(MATCHING_CODE, MATCHING_CODING_SYSTEM_EXT, MATCHING_CODING_EXT)
+
+        expect:
+        HapiHelper.resourcesInBundle(bundle, Observation.class).count() == 1
+
+        when:
+        transformClass.transform(new HapiFhirResource(bundle), args)
+
+        then:
+        HapiHelper.resourcesInBundle(bundle, Observation.class).count() == 1
+
+        where:
+        code      | codingSystemExt | codingExt
+        "11111-1" | "L"             | "alt-coding"
+        "99717-5" | "DIFFERENT_SYS" | "alt-coding"
+        "99717-5" | "L"             | "coding"
+    }
+
+    def "When an observation has no identifier OBX-3, it should NOT be removed"() {
+        given:
+        def bundle = HapiFhirHelper.createMessageBundle(messageTypeCode: 'ORU_R01')
+
+        // Add an observation with an observation value and a status, but no observation identifier
+        def observation = new Observation()
+        observation.status = Observation.ObservationStatus.FINAL
+        def valueCoding = new Coding()
+        valueCoding.code = "123456"
+        observation.valueCodeableConcept.coding.add(valueCoding)
+        bundle.addEntry(new Bundle.BundleEntryComponent().setResource(observation))
+
+        def args = getArgs("55555-5", "LN", "coding")
+
+        expect:
+        HapiHelper.resourcesInBundle(bundle, Observation.class).count() == 1
+
+        when:
+        transformClass.transform(new HapiFhirResource(bundle), args)
+
+        then:
+        HapiHelper.resourcesInBundle(bundle, Observation.class).count() == 1
+    }
+
+    def "When there is >1 matching observation, all matching observations should be removed"() {
+        given:
+        final String MATCHING_CODE = "99717-5"
+        final String MATCHING_CODING_SYSTEM_EXT = "L"
+        final String MATCHING_CODING_EXT = "alt-coding"
+
+        def bundle = HapiFhirHelper.createMessageBundle(messageTypeCode: 'ORU_R01')
+
+        def observation1 = new Observation()
+        def observation2 = new Observation()
+
+        addCodingToObservation(observation1, MATCHING_CODE, MATCHING_CODING_SYSTEM_EXT, MATCHING_CODING_EXT)
+        addCodingToObservation(observation2, MATCHING_CODE, MATCHING_CODING_SYSTEM_EXT, MATCHING_CODING_EXT)
+
+        bundle.addEntry(new Bundle.BundleEntryComponent().setResource(observation1))
+        bundle.addEntry(new Bundle.BundleEntryComponent().setResource(observation2))
+
+        def args = getArgs(MATCHING_CODE, MATCHING_CODING_SYSTEM_EXT, MATCHING_CODING_EXT)
+
+        expect:
+        HapiHelper.resourcesInBundle(bundle, Observation.class).count() == 2
+
+        when:
+        transformClass.transform(new HapiFhirResource(bundle), args)
+
+        then:
+        HapiHelper.resourcesInBundle(bundle, Observation.class).count() == 0
+    }
+
+    def "When message has multiple observations with only 1 matching, only 1 is removed"() {
+        given:
+        final String MATCHING_CODE = "99717-5"
+        final String MATCHING_CODING_SYSTEM_EXT = "L"
+        final String MATCHING_CODING_EXT = "alt-coding"
+
+        final String FHIR_ORU_PATH = "../CA/020_CA_ORU_R01_CDPH_OBX_to_LOINC_1_hl7_translation.fhir"
+        def fhirResource = ExamplesHelper.getExampleFhirResource(FHIR_ORU_PATH)
+        def bundle = fhirResource.getUnderlyingResource() as Bundle
+
+        def args = getArgs(MATCHING_CODE, MATCHING_CODING_SYSTEM_EXT, MATCHING_CODING_EXT)
+
+        expect:
+        HapiHelper.resourcesInBundle(bundle, Observation.class).count() == 114
+
+        when:
+        transformClass.transform(new HapiFhirResource(bundle), args)
+
+        then:
+        HapiHelper.resourcesInBundle(bundle, Observation.class).count() == 113
+    }
+
+    void addCodingToObservation(Observation observation, String code, String codingSystemExtension, String codingExtension) {
+        def coding = new Coding()
+
+        coding.code = code
+        coding.addExtension(HapiHelper.EXTENSION_CODING_SYSTEM, new StringType(codingSystemExtension))
+        coding.addExtension(HapiHelper.EXTENSION_CWE_CODING, new StringType(codingExtension))
+        observation.code.addCoding(coding)
+    }
+
+    Map<String, String> getArgs(String code, String codingSystem, String coding) {
+        return [
+            "code"                  : code,
+            "codingSystemExtension" : codingSystem,
+            codingExtension         : coding]
+    }
+}