Added member oid extension for each observation

prime-router/src/main/kotlin/azure/ConditionMapper.kt

@@ -4,14 +4,22 @@ import gov.cdc.prime.router.Metadata
 import gov.cdc.prime.router.fhirengine.utils.getCodeSourcesMap
 import gov.cdc.prime.router.metadata.ObservationMappingConstants
 import org.hl7.fhir.r4.model.Coding
+import org.hl7.fhir.r4.model.Extension
 import org.hl7.fhir.r4.model.Observation
+import org.hl7.fhir.r4.model.StringType
 
 interface IConditionMapper {
     /**
      * Attempt to find diagnostic conditions for a series of test [codings]
      * @return a map associating test [codings] to their diagnostic conditions as Coding's
      */
     fun lookupConditions(codings: List<Coding>): Map<Coding, List<Coding>>
+
+    /**
+     * Lookup test code to Member OID mappings for the given [codings].
+     * @return a map associating test codes to their Member OIDs
+     */
+    fun lookupMemberOid(codings: List<Coding>): Map<String, String>
 }
 
 class LookupTableConditionMapper(metadata: Metadata) : IConditionMapper {
@@ -34,16 +42,32 @@ class LookupTableConditionMapper(metadata: Metadata) : IConditionMapper {
                 acc
             }
     }
+
+    override fun lookupMemberOid(codings: List<Coding>): Map<String, String> {
+        return mappingTable.FilterBuilder()
+            .isIn(ObservationMappingConstants.TEST_CODE_KEY, codings.map { it.code })
+            .filter().caseSensitiveDataRowsMap.fold(mutableMapOf()) { acc, condition ->
+                val testCode = condition[ObservationMappingConstants.TEST_CODE_KEY] ?: ""
+                val memberOid = condition[ObservationMappingConstants.TEST_OID_KEY] ?: ""
+                if (testCode.isNotEmpty() && memberOid.isNotEmpty()) {
+                    acc[testCode] = memberOid
+                }
+                acc
+            }
+    }
 }
 
 class ConditionStamper(private val conditionMapper: IConditionMapper) {
     companion object {
-        const val conditionCodeExtensionURL = "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code"
+        const val CONDITION_CODE_EXTENSION_URL = "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code"
+        const val MEMBER_OID_EXTENSION_URL =
+            "https://reportstream.cdc.gov/fhir/StructureDefinition/test-performed-member-oid"
 
         const val BUNDLE_CODE_IDENTIFIER = "observation.code.coding.code"
         const val BUNDLE_VALUE_IDENTIFIER = "observation.valueCodeableConcept.coding.code"
         const val MAPPING_CODES_IDENTIFIER = "observation.{code|valueCodeableConcept}.coding.code"
     }
+
     data class ObservationMappingFailure(val source: String, val failures: List<Coding>)
 
     data class ObservationStampingResult(
@@ -52,31 +76,47 @@ class ConditionStamper(private val conditionMapper: IConditionMapper) {
     )
 
     /**
-     * Lookup condition codes for an [observation] and add them as custom extensions
+     * Lookup condition codes and member OIDs for an [observation] and add them as custom extensions
      * @param observation the observation that will be stamped
      * @return a [ObservationStampingResult] including stamping success and any mapping failures
      */
     fun stampObservation(observation: Observation): ObservationStampingResult {
         val codeSourcesMap = observation.getCodeSourcesMap().filterValues { it.isNotEmpty() }
         if (codeSourcesMap.values.flatten().isEmpty()) return ObservationStampingResult(false)
 
+        // Lookup conditions and Member OIDs
         val conditionsToCode = conditionMapper.lookupConditions(codeSourcesMap.values.flatten())
+        val memberOidMap = conditionMapper.lookupMemberOid(codeSourcesMap.values.flatten())
+
         var mappedSomething = false
 
+        // Process condition mappings
         val failures = codeSourcesMap.mapNotNull { codes ->
             val unnmapped = codes.value.mapNotNull { code ->
                 val conditions = conditionsToCode.getOrDefault(code, emptyList())
                 if (conditions.isEmpty()) {
                     code
                 } else {
-                    conditions.forEach { code.addExtension(conditionCodeExtensionURL, it) }
+                    conditions.forEach { code.addExtension(CONDITION_CODE_EXTENSION_URL, it) }
                     mappedSomething = true
                     null
                 }
             }
             if (unnmapped.isEmpty()) null else ObservationMappingFailure(codes.key, unnmapped)
         }
 
+        // Add the Member OID extension to the observation, based on the lookup
+        observation.code.coding.forEach { coding ->
+            val testCode = coding.code
+            val memberOid = memberOidMap[testCode]
+            if (memberOid != null) {
+                val memberOidExtension = Extension(MEMBER_OID_EXTENSION_URL)
+                memberOidExtension.setValue(StringType(memberOid))
+                observation.addExtension(memberOidExtension)
+                mappedSomething = true
+            }
+        }
+
         return ObservationStampingResult(mappedSomething, failures)
     }
 }

prime-router/src/main/kotlin/azure/observability/event/TestSummary.kt

@@ -1,6 +1,6 @@
 package gov.cdc.prime.router.azure.observability.event
 
-import gov.cdc.prime.router.azure.ConditionStamper.Companion.conditionCodeExtensionURL
+import gov.cdc.prime.router.azure.ConditionStamper.Companion.CONDITION_CODE_EXTENSION_URL
 import org.hl7.fhir.r4.model.Coding
 
 data class TestSummary(
@@ -17,7 +17,7 @@ data class TestSummary(
          */
         fun fromCoding(coding: Coding): TestSummary {
             val conditions = coding.extension
-                .filter { it.url == conditionCodeExtensionURL }
+                .filter { it.url == CONDITION_CODE_EXTENSION_URL }
                 .map { it.castToCoding(it.value) }
                 .map(CodeSummary::fromCoding)
             return TestSummary(

prime-router/src/main/kotlin/fhirengine/utils/FHIRBundleHelpers.kt

@@ -7,7 +7,7 @@ import gov.cdc.prime.router.ReportStreamConditionFilter
 import gov.cdc.prime.router.ReportStreamFilter
 import gov.cdc.prime.router.azure.ConditionStamper.Companion.BUNDLE_CODE_IDENTIFIER
 import gov.cdc.prime.router.azure.ConditionStamper.Companion.BUNDLE_VALUE_IDENTIFIER
-import gov.cdc.prime.router.azure.ConditionStamper.Companion.conditionCodeExtensionURL
+import gov.cdc.prime.router.azure.ConditionStamper.Companion.CONDITION_CODE_EXTENSION_URL
 import gov.cdc.prime.router.codes
 import gov.cdc.prime.router.fhirengine.translation.hl7.utils.CustomContext
 import gov.cdc.prime.router.fhirengine.translation.hl7.utils.FhirPathUtils
@@ -63,7 +63,7 @@ fun Observation.getMappedConditionExtensions(): List<Extension> {
     return this.getCodeSourcesMap()
         .flatMap { it.value }
         .flatMap { it.extension }
-        .filter { it.url == conditionCodeExtensionURL }
+        .filter { it.url == CONDITION_CODE_EXTENSION_URL }
 }
 
 /**

prime-router/src/test/kotlin/azure/observability/bundleDigest/FhirPathBundleDigestExtractorStrategyTests.kt

@@ -3,7 +3,7 @@ package gov.cdc.prime.router.azure.observability.bundleDigest
 import assertk.assertThat
 import assertk.assertions.isDataClassEqualTo
 import fhirengine.engine.CustomFhirPathFunctions
-import gov.cdc.prime.router.azure.ConditionStamper.Companion.conditionCodeExtensionURL
+import gov.cdc.prime.router.azure.ConditionStamper.Companion.CONDITION_CODE_EXTENSION_URL
 import gov.cdc.prime.router.azure.observability.event.CodeSummary
 import gov.cdc.prime.router.azure.observability.event.ObservationSummary
 import gov.cdc.prime.router.azure.observability.event.TestSummary
@@ -152,7 +152,7 @@ class FhirPathBundleDigestExtractorStrategyTests {
         val observation = Observation()
         val coding = Coding()
         val extension = Extension()
-        extension.url = conditionCodeExtensionURL
+        extension.url = CONDITION_CODE_EXTENSION_URL
         extension.setValue(Coding())
         coding.extension = listOf(extension)
         observation.code.coding = listOf(coding)

prime-router/src/test/kotlin/fhirengine/engine/FhirConverterTests.kt

@@ -27,7 +27,9 @@ import gov.cdc.prime.router.SettingsProvider
 import gov.cdc.prime.router.Topic
 import gov.cdc.prime.router.azure.ActionHistory
 import gov.cdc.prime.router.azure.BlobAccess
+import gov.cdc.prime.router.azure.ConditionStamper
 import gov.cdc.prime.router.azure.DatabaseAccess
+import gov.cdc.prime.router.azure.LookupTableConditionMapper
 import gov.cdc.prime.router.azure.SubmissionTableService
 import gov.cdc.prime.router.azure.db.enums.TaskAction
 import gov.cdc.prime.router.azure.db.tables.pojos.Action
@@ -60,9 +62,12 @@ import io.mockk.verify
 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 org.jooq.tools.jdbc.MockConnection
 import org.jooq.tools.jdbc.MockDataProvider
 import org.jooq.tools.jdbc.MockResult
+import org.junit.Assert.assertEquals
+import org.junit.Assert.assertNotNull
 import org.junit.jupiter.api.AfterEach
 import org.junit.jupiter.api.BeforeEach
 import org.junit.jupiter.api.Nested
@@ -359,7 +364,7 @@ class FhirConverterTests {
                         ObservationMappingConstants.TEST_CODE_KEY,
                         ObservationMappingConstants.CONDITION_CODE_KEY,
                         ObservationMappingConstants.CONDITION_CODE_SYSTEM_KEY,
-                        ObservationMappingConstants.CONDITION_NAME_KEY
+                        ObservationMappingConstants.CONDITION_NAME_KEY,
                     ),
                     listOf(
                         "80382-5",
@@ -442,6 +447,67 @@ class FhirConverterTests {
         }
     }
 
+    @Test
+    fun `test condition code and member OID stamping`() {
+        @Suppress("ktlint:standard:max-line-length")
+        val fhirRecord =
+            """{"resourceType":"Bundle","id":"1667861767830636000.7db38d22-b713-49fc-abfa-2edba9c12347","meta":{"lastUpdated":"2022-11-07T22:56:07.832+00:00"},"identifier":{"value":"1234d1d1-95fe-462c-8ac6-46728dba581c"},"type":"message","timestamp":"2021-08-03T13:15:11.015+00:00","entry":[{"fullUrl":"Observation/d683b42a-bf50-45e8-9fce-6c0531994f09","resource":{"resourceType":"Observation","id":"d683b42a-bf50-45e8-9fce-6c0531994f09","status":"final","code":{"coding":[{"system":"http://loinc.org","code":"80382-5"}],"text":"Flu A"},"subject":{"reference":"Patient/9473889b-b2b9-45ac-a8d8-191f27132912"},"performer":[{"reference":"Organization/1a0139b9-fc23-450b-9b6c-cd081e5cea9d"}],"valueCodeableConcept":{"coding":[{"system":"http://snomed.info/sct","code":"260373001","display":"Detected"}]},"interpretation":[{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0078","code":"A","display":"Abnormal"}]}],"method":{"extension":[{"url":"https://reportstream.cdc.gov/fhir/StructureDefinition/testkit-name-id","valueCoding":{"code":"BD Veritor System for Rapid Detection of SARS-CoV-2 & Flu A+B_Becton, Dickinson and Company (BD)"}},{"url":"https://reportstream.cdc.gov/fhir/StructureDefinition/equipment-uid","valueCoding":{"code":"BD Veritor System for Rapid Detection of SARS-CoV-2 & Flu A+B_Becton, Dickinson and Company (BD)"}}],"coding":[{"display":"BD Veritor System for Rapid Detection of SARS-CoV-2 & Flu A+B*"}]},"specimen":{"reference":"Specimen/52a582e4-d389-42d0-b738-bee51cf5244d"},"device":{"reference":"Device/78dc4d98-2958-43a3-a445-76ceef8c0698"}}}]}"""
+
+        val memberOidExtensionURL = "https://reportstream.cdc.gov/fhir/StructureDefinition/test-performed-member-oid"
+
+        metadata.lookupTableStore += mapOf(
+            "observation-mapping" to LookupTable(
+                "observation-mapping",
+                listOf(
+                    listOf(
+                        ObservationMappingConstants.TEST_CODE_KEY,
+                        ObservationMappingConstants.CONDITION_CODE_KEY,
+                        ObservationMappingConstants.CONDITION_CODE_SYSTEM_KEY,
+                        ObservationMappingConstants.CONDITION_NAME_KEY,
+                        ObservationMappingConstants.TEST_OID_KEY
+                    ),
+                    listOf(
+                        "80382-5",
+                        "6142004",
+                        "SNOMEDCT",
+                        "Influenza (disorder)",
+                        "OID12345"
+                    ),
+                    listOf(
+                        "260373001",
+                        "Some Condition Code",
+                        "Condition Code System",
+                        "Condition Name",
+                        "OID67890"
+                    )
+                )
+            )
+        )
+
+        val bundle = FhirContext.forR4().newJsonParser().parseResource(Bundle::class.java, fhirRecord)
+
+        bundle.entry.filter { it.resource is Observation }.forEach {
+            val observation = (it.resource as Observation)
+
+            // Add Condition and Member OID extensions
+            ConditionStamper(LookupTableConditionMapper(metadata)).stampObservation(observation)
+
+            // Assert condition extensions
+            val conditionExtension = observation.code.coding[0].extension.find {
+                it.url == "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code"
+            }
+            assertNotNull(conditionExtension)
+            assertEquals("6142004", (conditionExtension!!.value as Coding).code)
+
+            // Assert Member OID extension
+            val memberOidExtension = observation.extension.find {
+                it.url == memberOidExtensionURL
+            }
+            assertNotNull(memberOidExtension)
+            assertEquals("OID12345", (memberOidExtension!!.value as StringType).value)
+        }
+    }
+
     @Test
     fun `test fully unmapped condition code stamping logs errors`() {
         val fhirData = File(BATCH_VALID_DATA_URL).readText()

prime-router/src/test/kotlin/fhirengine/engine/FhirReceiverFilterTests.kt

@@ -27,7 +27,7 @@ import gov.cdc.prime.router.TestSource
 import gov.cdc.prime.router.Topic
 import gov.cdc.prime.router.azure.ActionHistory
 import gov.cdc.prime.router.azure.BlobAccess
-import gov.cdc.prime.router.azure.ConditionStamper.Companion.conditionCodeExtensionURL
+import gov.cdc.prime.router.azure.ConditionStamper.Companion.CONDITION_CODE_EXTENSION_URL
 import gov.cdc.prime.router.azure.DatabaseAccess
 import gov.cdc.prime.router.azure.db.enums.TaskAction
 import gov.cdc.prime.router.azure.db.tables.pojos.ReportFile
@@ -508,7 +508,7 @@ class FhirReceiverFilterTests {
             val coding = it.code.coding.first()
             if (coding.extension.isEmpty()) {
                 coding.addExtension(
-                    conditionCodeExtensionURL,
+                    CONDITION_CODE_EXTENSION_URL,
                     Coding(
                         "system", "AOE", "name"
                     )
@@ -569,11 +569,11 @@ class FhirReceiverFilterTests {
         bundle.entry.filter { it.resource is Observation }.forEach {
             val observation = (it.resource as Observation)
             observation.code.coding[0].addExtension(
-                conditionCodeExtensionURL,
+                CONDITION_CODE_EXTENSION_URL,
                 Coding("SNOMEDCT", "6142004", "Influenza (disorder)")
             )
             observation.valueCodeableConcept.coding[0].addExtension(
-                conditionCodeExtensionURL,
+                CONDITION_CODE_EXTENSION_URL,
                 Coding("Condition Code System", "foobar", "Condition Name")
             )
         }
@@ -681,11 +681,11 @@ class FhirReceiverFilterTests {
         val bundle = FhirContext.forR4().newJsonParser().parseResource(Bundle::class.java, fhirRecord)
         bundle.getObservations().forEach { observation ->
             observation.code.coding[0].addExtension(
-                conditionCodeExtensionURL,
+                CONDITION_CODE_EXTENSION_URL,
                 Coding("SNOMEDCT", "6142004", "Influenza (disorder)")
             )
             observation.valueCodeableConcept.coding[0].addExtension(
-                conditionCodeExtensionURL,
+                CONDITION_CODE_EXTENSION_URL,
                 Coding("Condition Code System", "Some Condition Code", "Condition Name")
             )
         }

prime-router/src/test/kotlin/fhirengine/utils/FHIRBundleHelpersTests.kt

@@ -27,7 +27,7 @@ import gov.cdc.prime.router.Schema
 import gov.cdc.prime.router.Topic
 import gov.cdc.prime.router.azure.BlobAccess
 import gov.cdc.prime.router.azure.ConditionStamper
-import gov.cdc.prime.router.azure.ConditionStamper.Companion.conditionCodeExtensionURL
+import gov.cdc.prime.router.azure.ConditionStamper.Companion.CONDITION_CODE_EXTENSION_URL
 import gov.cdc.prime.router.azure.DatabaseAccess
 import gov.cdc.prime.router.azure.LookupTableConditionMapper
 import gov.cdc.prime.router.azure.QueueAccess
@@ -497,7 +497,7 @@ class FHIRBundleHelpersTests {
         val fhirRecord = File(VALID_ROUTING_DATA_URL).readText()
         val bundle = FhirContext.forR4().newJsonParser().parseResource(Bundle::class.java, fhirRecord)
         bundle.getObservations()[0].code.coding[0].addExtension(
-            conditionCodeExtensionURL, Coding("SOMESYSTEM", "840539006", "SOMECONDITION")
+            CONDITION_CODE_EXTENSION_URL, Coding("SOMESYSTEM", "840539006", "SOMECONDITION")
         )
 
         val filteredBundle = bundle.filterMappedObservations(
@@ -800,7 +800,7 @@ class FHIRBundleHelpersTests {
         assertThat(failure.failures.first().code).isEqualTo("some-unmapped-code")
 
         val extension = code.coding.first().extension.first()
-        assertThat(extension.url).isEqualTo(conditionCodeExtensionURL)
+        assertThat(extension.url).isEqualTo(CONDITION_CODE_EXTENSION_URL)
         assertThat((extension.value as? Coding)?.code).isEqualTo("6142004")
     }
 
@@ -853,7 +853,7 @@ class FHIRBundleHelpersTests {
         val extensions = entry.getMappedConditionExtensions()
         assertThat(extensions)
             .extracting { it.url }
-            .each { it.isEqualTo(conditionCodeExtensionURL) }
+            .each { it.isEqualTo(CONDITION_CODE_EXTENSION_URL) }
     }
 
     @Test
@@ -899,7 +899,7 @@ class FHIRBundleHelpersTests {
         assertThat(result.failures).isEmpty()
 
         val extension = code.coding.first().extension.first()
-        assertThat(extension.url).isEqualTo(conditionCodeExtensionURL)
+        assertThat(extension.url).isEqualTo(CONDITION_CODE_EXTENSION_URL)
         assertThat(extension.value)
             .isInstanceOf<Coding>()
             .transform { it.code }
@@ -947,7 +947,7 @@ class FHIRBundleHelpersTests {
         assertThat(result.failures).isEmpty()
 
         val extension = code.coding.first().extension.first()
-        assertThat(extension.url).isEqualTo(conditionCodeExtensionURL)
+        assertThat(extension.url).isEqualTo(CONDITION_CODE_EXTENSION_URL)
         assertThat(extension.value)
             .isInstanceOf<Coding>()
             .transform { it.code }