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https://github.com/pcvolkmer/onco-analytics-monitor.git
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feat: handle oBDS Version 3.x records
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b0dc82ed27
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@ -9,6 +9,7 @@ import dev.pcvolkmer.oncoanalytics.monitor.conditions.Condition
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import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionId
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import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionRepository
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import dev.pcvolkmer.oncoanalytics.monitor.fetchStatistics
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import org.slf4j.LoggerFactory
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import org.springframework.beans.factory.annotation.Qualifier
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import org.springframework.kafka.annotation.KafkaListener
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import org.springframework.kafka.support.KafkaHeaders
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@ -35,6 +36,9 @@ class ObdsXmlTopicMonitor(
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statisticsEventProducer: StatisticsSink,
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) : AbstractTopicMonitor(statisticsEventProducer) {
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private val logger = LoggerFactory.getLogger(javaClass)
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private val xPath = XPathFactory.newDefaultInstance().newXPath()
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@KafkaListener(topicPattern = "onkostar.MELDUNG_EXPORT.*")
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override fun handleTopicRecord(
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@Header(KafkaHeaders.RECEIVED_TOPIC) topic: String,
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@ -44,35 +48,69 @@ class ObdsXmlTopicMonitor(
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) {
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try {
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val p = objectMapper.readValue(payload, Record::class.java)
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val xPath = XPathFactory.newDefaultInstance().newXPath()
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when (xPath.evaluate("name(/*)", InputSource(StringReader(p.payload.data)))) {
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"ADT_GEKID" -> handleObds2Payload(p.payload)
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"oBDS" -> handleObds3Payload(p.payload)
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else -> logger.warn("Cannot handle a non oBDS 2.x/3.x record!")
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}
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} catch (e: Exception) {
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// Ignore
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}
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}
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private fun handleObds2Payload(payload: RecordPayload) {
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// Use local-name() due to XML namespace
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val patientId = xPath.evaluate(
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"//*[local-name()='Patienten_Stammdaten']/@Patient_ID",
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InputSource(StringReader(p.payload.data))
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InputSource(StringReader(payload.data))
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)
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val tumorId = xPath.evaluate(
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"//*[local-name()='Tumorzuordnung']/@Tumor_ID",
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InputSource(StringReader(p.payload.data))
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InputSource(StringReader(payload.data))
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)
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val icd10 = xPath.evaluate(
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"//*[local-name()='Primaertumor_ICD_Code']/text()",
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InputSource(StringReader(p.payload.data))
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InputSource(StringReader(payload.data))
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)
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val updated = conditionRepository.saveIfNewerVersion(
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Condition(
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ConditionId.fromPatientIdAndTumorId(patientId, tumorId),
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icd10,
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p.payload.version
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payload.version
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)
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)
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if (updated) {
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sendUpdatedStatistics(fetchStatistics("obdsxml", conditionRepository))
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}
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} catch (e: Exception) {
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// Ignore
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}
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private fun handleObds3Payload(payload: RecordPayload) {
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// Use local-name() due to XML namespace
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val patientId = xPath.evaluate(
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"//*[local-name()='Patient']/@Patient_ID",
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InputSource(StringReader(payload.data))
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)
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val tumorId = xPath.evaluate(
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"//*[local-name()='Tumorzuordnung']/@Tumor_ID",
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InputSource(StringReader(payload.data))
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)
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val icd10 = xPath.evaluate(
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"//*[local-name()='Primaertumor_ICD']/*[local-name()='Code']/text()",
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InputSource(StringReader(payload.data))
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)
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val updated = conditionRepository.saveIfNewerVersion(
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Condition(
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ConditionId.fromPatientIdAndTumorId(patientId, tumorId),
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icd10,
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payload.version
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)
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)
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if (updated) {
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sendUpdatedStatistics(fetchStatistics("obdsxml", conditionRepository))
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}
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}
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@ -4,14 +4,16 @@ import com.fasterxml.jackson.databind.MapperFeature
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import com.fasterxml.jackson.databind.json.JsonMapper
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import com.fasterxml.jackson.module.paramnames.ParameterNamesModule
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import dev.pcvolkmer.oncoanalytics.monitor.StatisticsSink
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import dev.pcvolkmer.oncoanalytics.monitor.conditions.Condition
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import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionId
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import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionRepository
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import org.assertj.core.api.Assertions.assertThat
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import org.junit.jupiter.api.BeforeEach
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import org.junit.jupiter.api.Test
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import org.junit.jupiter.api.extension.ExtendWith
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import org.mockito.Mock
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import org.mockito.junit.jupiter.MockitoExtension
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import org.mockito.kotlin.any
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import org.mockito.kotlin.whenever
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import org.mockito.kotlin.*
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import org.springframework.core.io.ClassPathResource
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import reactor.core.publisher.Sinks
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import reactor.test.StepVerifier
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@ -22,6 +24,8 @@ import kotlin.time.toJavaDuration
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@ExtendWith(MockitoExtension::class)
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class ObdsXmlTopicMonitorTest {
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private lateinit var conditionRepository: ConditionRepository
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private lateinit var topicMonitor: ObdsXmlTopicMonitor
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private lateinit var statisticsEventProducer: StatisticsSink
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@ -31,14 +35,19 @@ class ObdsXmlTopicMonitorTest {
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.enable(MapperFeature.AUTO_DETECT_CREATORS)
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.build()
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private fun payload(): String {
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private fun obds2Payload(): String {
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return ClassPathResource("testobds.json").getContentAsString(Charsets.UTF_8)
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}
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private fun obds3Payload(): String {
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return ClassPathResource("testobds3.json").getContentAsString(Charsets.UTF_8)
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}
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@BeforeEach
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fun setup(
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@Mock conditionRepository: ConditionRepository,
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) {
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this.conditionRepository = conditionRepository
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this.statisticsEventProducer = Sinks.many().multicast().directBestEffort()
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this.topicMonitor = ObdsXmlTopicMonitor(conditionRepository, objectMapper, statisticsEventProducer)
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@ -46,16 +55,59 @@ class ObdsXmlTopicMonitorTest {
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}
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@Test
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fun shouldHandleKafkaRecordAndEmitEvent() {
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fun shouldHandleObds2KafkaRecordAndEmitEvent() {
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val stepVerifier = StepVerifier
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.create(statisticsEventProducer.asFlux())
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.expectNextCount(1)
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.expectTimeout(3.seconds.toJavaDuration())
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.verifyLater()
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this.topicMonitor.handleTopicRecord("test", Instant.now().toEpochMilli(), "{\"ID\": 1}", payload())
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this.topicMonitor.handleTopicRecord("test", Instant.now().toEpochMilli(), "{\"ID\": 1}", obds2Payload())
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stepVerifier.verify()
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}
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@Test
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fun shouldHandleObds3KafkaRecordAndEmitEvent() {
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val stepVerifier = StepVerifier
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.create(statisticsEventProducer.asFlux())
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.expectNextCount(1)
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.expectTimeout(3.seconds.toJavaDuration())
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.verifyLater()
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this.topicMonitor.handleTopicRecord("test", Instant.now().toEpochMilli(), "{\"ID\": 1}", obds3Payload())
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stepVerifier.verify()
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}
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@Test
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fun shouldSaveConditionOnObds2Record() {
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this.topicMonitor.handleTopicRecord("test", Instant.now().toEpochMilli(), "{\"ID\": 1}", obds2Payload())
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val captor = argumentCaptor<Condition>()
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verify(conditionRepository, times(1)).saveIfNewerVersion(captor.capture())
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assertThat(captor.firstValue).isEqualTo(
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Condition(
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ConditionId.fromPatientIdAndTumorId("00001234", "1"),
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"C17.1",
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1
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)
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)
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}
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@Test
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fun shouldSaveConditionOnObds3Record() {
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this.topicMonitor.handleTopicRecord("test", Instant.now().toEpochMilli(), "{\"ID\": 1}", obds3Payload())
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val captor = argumentCaptor<Condition>()
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verify(conditionRepository, times(1)).saveIfNewerVersion(captor.capture())
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assertThat(captor.firstValue).isEqualTo(
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Condition(
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ConditionId.fromPatientIdAndTumorId("00001234", "1"),
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"C17.1",
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1
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)
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)
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}
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}
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1
src/test/resources/testobds3.json
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1
src/test/resources/testobds3.json
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@ -0,0 +1 @@
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{"schema":{"type":"struct","fields":[{"type":"int32","optional":true,"field":"YEAR"},{"type":"int32","optional":true,"field":"VERSIONSNUMMER"},{"type":"int32","optional":false,"field":"ID"},{"type":"string","optional":true,"field":"XML_DATEN"}],"optional":false},"payload":{"YEAR":2024,"VERSIONSNUMMER":1,"ID":123456,"XML_DATEN":"<?xml version=\"1.0\" encoding=\"utf-8\" ?><oBDS xmlns=\"http://www.basisdatensatz.de/oBDS/XML\" Schema_Version=\"3.0.2\"><Absender Absender_ID=\"TEST\" Software_ID=\"ONKOSTAR\" Software_Version=\"2.13.1\"><Bezeichnung>TEST</Bezeichnung><Anschrift>Musterstraße 1, 012345 Musterhausen</Anschrift></Absender><Meldedatum>2024-06-11</Meldedatum><Menge_Patient><Patient Patient_ID=\"00001234\"><Patienten_Stammdaten><Versichertendaten_GKV><IKNR>103456789</IKNR><GKV_Versichertennummer>E123456789</GKV_Versichertennummer></Versichertendaten_GKV><Nachname>Tester</Nachname><Vornamen>Patrick</Vornamen><Geschlecht>M</Geschlecht><Geburtsdatum Datumsgenauigkeit=\"T\">1980-01-01</Geburtsdatum><Adresse><Strasse>Testweg</Strasse><Hausnummer>1</Hausnummer><Land>DE</Land><PLZ>01234</PLZ><Ort>Musterhausen</Ort></Adresse></Patienten_Stammdaten><Menge_Meldung><Meldung Meldung_ID=\"TEST1727528\" Melder_ID=\"TEST\"><Meldebegruendung>I</Meldebegruendung><Eigene_Leistung>J</Eigene_Leistung><Tumorzuordnung Tumor_ID=\"1\"><Primaertumor_ICD><Code>C17.1</Code><Version>10 2015 GM</Version></Primaertumor_ICD><Diagnosedatum Datumsgenauigkeit=\"T\">2024-06-10</Diagnosedatum></Tumorzuordnung><Diagnose><Diagnosesicherung>1</Diagnosesicherung><Allgemeiner_Leistungszustand>0</Allgemeiner_Leistungszustand></Diagnose></Meldung></Menge_Meldung></Patient></Menge_Patient><Menge_Melder><Melder ID=\"TEST\"><Ident_Nummern><IKNR>103456789</IKNR></Ident_Nummern></Melder></Menge_Melder></oBDS>"}}
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