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https://github.com/pcvolkmer/onco-analytics-monitor.git
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test: check handling of incoming kafka records
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package dev.pcvolkmer.oncoanalytics.monitor.topiclisteners
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import dev.pcvolkmer.oncoanalytics.monitor.StatisticsSink
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import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionRepository
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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.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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import java.time.Instant
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import kotlin.time.Duration.Companion.seconds
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import kotlin.time.toJavaDuration
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@ExtendWith(MockitoExtension::class)
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class FhirObdsTopicMonitorTest {
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private lateinit var topicMonitor: FhirObdsTopicMonitor
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private lateinit var statisticsEventProducer: StatisticsSink
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private fun payload(): String {
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return ClassPathResource("testfhir.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.statisticsEventProducer = Sinks.many().multicast().directBestEffort()
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this.topicMonitor = FhirObdsTopicMonitor(conditionRepository, statisticsEventProducer)
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whenever(conditionRepository.save(any())).thenReturn(true)
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}
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@Test
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fun shouldHandleKafkaRecordAndEmitEvent() {
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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(
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"test",
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Instant.now().toEpochMilli(),
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"Struct{REFERENZ_NUMMER=00001234,TUMOR_ID=1}",
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payload()
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)
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stepVerifier.verify()
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}
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}
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package dev.pcvolkmer.oncoanalytics.monitor.topiclisteners
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import dev.pcvolkmer.oncoanalytics.monitor.StatisticsSink
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import dev.pcvolkmer.oncoanalytics.monitor.conditions.ConditionRepository
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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.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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import java.time.Instant
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import kotlin.time.Duration.Companion.seconds
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import kotlin.time.toJavaDuration
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@ExtendWith(MockitoExtension::class)
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class FhirPseudonymizedTopicMonitorTest {
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private lateinit var topicMonitor: FhirPseudonymizedTopicMonitor
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private lateinit var statisticsEventProducer: StatisticsSink
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private fun payload(): String {
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return ClassPathResource("testfhir.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.statisticsEventProducer = Sinks.many().multicast().directBestEffort()
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this.topicMonitor = FhirPseudonymizedTopicMonitor(conditionRepository, statisticsEventProducer)
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whenever(conditionRepository.save(any())).thenReturn(true)
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}
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@Test
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fun shouldHandleKafkaRecordAndEmitEvent() {
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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(
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"test",
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Instant.now().toEpochMilli(),
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"Struct{REFERENZ_NUMMER=00001234,TUMOR_ID=1}",
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payload()
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)
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stepVerifier.verify()
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}
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}
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package dev.pcvolkmer.oncoanalytics.monitor.topiclisteners
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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.ConditionRepository
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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.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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import java.time.Instant
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import kotlin.time.Duration.Companion.seconds
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import kotlin.time.toJavaDuration
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@ExtendWith(MockitoExtension::class)
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class ObdsXmlTopicMonitorTest {
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private lateinit var topicMonitor: ObdsXmlTopicMonitor
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private lateinit var statisticsEventProducer: StatisticsSink
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private val objectMapper = JsonMapper.builder()
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.addModules(ParameterNamesModule())
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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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return ClassPathResource("testobds.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.statisticsEventProducer = Sinks.many().multicast().directBestEffort()
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this.topicMonitor = ObdsXmlTopicMonitor(conditionRepository, objectMapper, statisticsEventProducer)
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whenever(conditionRepository.saveIfNewerVersion(any())).thenReturn(true)
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}
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@Test
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fun shouldHandleKafkaRecordAndEmitEvent() {
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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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stepVerifier.verify()
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}
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}
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48
src/test/resources/testfhir.json
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48
src/test/resources/testfhir.json
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{
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"resourceType": "Bundle",
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"type": "transaction",
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"entry": [
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{
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"fullUrl": "Condition/test123",
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"resource": {
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"resourceType": "Condition",
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"id": "test123",
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"meta": {
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"source": "TEST.ONKOSTAR:obds-to-fhir:0.0.0",
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"profile": [
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"http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Condition-Primaerdiagnose"
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]
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},
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"code": {
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"coding": [
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{
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"system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
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"version": "2015",
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"code": "C17.1"
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}
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]
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},
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"subject": {
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"reference": "Patient/test123",
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"identifier": {
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"type": {
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"coding": [
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{
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"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
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"code": "MR"
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}
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]
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},
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"system": "https://fhir.diz.uk-erlangen.de/identifiers/patient-id",
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"value": "00001234"
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}
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},
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"onsetDateTime": "2024-01-01"
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},
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"request": {
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"method": "PUT",
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"url": "Condition/test123"
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}
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}
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]
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}
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1
src/test/resources/testobds.json
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1
src/test/resources/testobds.json
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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\"?><ADT_GEKID xmlns=\"http://www.gekid.de/namespace\" Schema_Version=\"2.2.3\"><Absender Absender_ID=\"TEST\" Software_ID=\"ONKOSTAR\" Installations_ID=\"2011\"><Absender_Bezeichnung>TEST</Absender_Bezeichnung><Absender_Anschrift>Musterstraße 1, 012345 Musterhausen</Absender_Anschrift></Absender><Menge_Patient><Patient><Patienten_Stammdaten Patient_ID=\"00001234\"><KrankenversichertenNr>E123456789</KrankenversichertenNr><KrankenkassenNr>123456789</KrankenkassenNr><Patienten_Nachname>Tester</Patienten_Nachname><Patienten_Titel></Patienten_Titel><Patienten_Vornamen>Patrick</Patienten_Vornamen><Patienten_Geburtsname>Tester</Patienten_Geburtsname><Patienten_Geschlecht>M</Patienten_Geschlecht><Patienten_Geburtsdatum>01.01.1980</Patienten_Geburtsdatum><Menge_Adresse><Adresse><Patienten_Strasse>Testweg</Patienten_Strasse><Patienten_Hausnummer>1</Patienten_Hausnummer><Patienten_Land>DE</Patienten_Land><Patienten_PLZ>01234</Patienten_PLZ><Patienten_Ort>Musterhausen</Patienten_Ort></Adresse></Menge_Adresse></Patienten_Stammdaten><Menge_Meldung><Meldung Meldung_ID=\"TEST123456\" Melder_ID=\"TEST\"><Meldedatum>11.06.2024</Meldedatum><Meldebegruendung>I</Meldebegruendung><Meldeanlass>statusaenderung</Meldeanlass><Tumorzuordnung Tumor_ID=\"1\"><Primaertumor_ICD_Code>C17.1</Primaertumor_ICD_Code><Primaertumor_ICD_Version>10 2015 GM</Primaertumor_ICD_Version><Diagnosedatum>10.06.2024</Diagnosedatum><Seitenlokalisation>T</Seitenlokalisation></Tumorzuordnung><Menge_Tumorkonferenz><Tumorkonferenz Tumorkonferenz_ID=\"1234567\"><Tumorkonferenz_Datum>11.06.2024</Tumorkonferenz_Datum><Tumorkonferenz_Typ>praeth</Tumorkonferenz_Typ></Tumorkonferenz></Menge_Tumorkonferenz></Meldung></Menge_Meldung></Patient></Menge_Patient></ADT_GEKID>"}}
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