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refactor: put FHIR data extraction into abstract class
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@ -0,0 +1,44 @@
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package dev.pcvolkmer.oncoanalytics.monitor.topiclisteners
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import ca.uhn.fhir.context.FhirContext
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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.Statistics
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import org.hl7.fhir.r4.model.Bundle
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import reactor.core.publisher.Sinks
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/**
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* Abstract class with common methods for FHIR TopicMonitors
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*
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* @property statisticsEventProducer The event producer/sink to notify about saved condition
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*
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* @author Paul-Christian Volkmer
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* @since 0.1.0
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*/
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abstract class AbstractFhirTopicMonitor(statisticsEventProducer: Sinks.Many<Statistics>) :
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AbstractTopicMonitor(statisticsEventProducer) {
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private val fhirContext = FhirContext.forR4()
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/**
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* Handle parsable FHIR resource
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*
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* @param payload The string representation of the FHIR resource
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* @param handler The handler function to define what to do if payload contains usable FHIR condition
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*/
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fun handleUsableFhirPayload(payload: String, handler: (condition: Condition) -> Unit) {
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val bundle = fhirContext.newJsonParser().parseResource(Bundle::class.java, payload)
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val firstEntry = bundle.entry.firstOrNull() ?: return
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if (firstEntry.resource.fhirType() == "Condition") {
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val condition = firstEntry.resource as org.hl7.fhir.r4.model.Condition
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handler(
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Condition(
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ConditionId(condition.id),
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condition.code.coding.first { "http://fhir.de/CodeSystem/bfarm/icd-10-gm" == it.system }.code
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)
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)
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}
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}
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}
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@ -0,0 +1,40 @@
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package dev.pcvolkmer.oncoanalytics.monitor.topiclisteners
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import dev.pcvolkmer.oncoanalytics.monitor.conditions.Statistics
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import org.apache.kafka.common.TopicPartition
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import org.springframework.kafka.listener.ConsumerSeekAware
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import org.springframework.kafka.listener.ConsumerSeekAware.ConsumerSeekCallback
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import reactor.core.publisher.Sinks
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/**
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* Abstract class with common methods for all TopicMonitors
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*
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* This implements ConsumerSeekAware to seek any topic to the beginning and load all available topic records from start.
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*
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* @property statisticsEventProducer The event producer/sink to notify about saved condition
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*
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* @author Paul-Christian Volkmer
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* @since 0.1.0
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*
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* @see ConsumerSeekAware
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*/
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abstract class AbstractTopicMonitor(private val statisticsEventProducer: Sinks.Many<Statistics>) : TopicMonitor,
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ConsumerSeekAware {
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/**
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* This will send new/updated statistics
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*
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* @param statistics The statistics to be sent/updated
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*/
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fun sendUpdatedStatistics(statistics: Statistics) {
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statisticsEventProducer.emitNext(statistics) { _, _ -> false }
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}
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/**
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* This will seek assigned Kafka Partitions back to the beginning for all inheriting classes
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*/
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override fun onPartitionsAssigned(assignments: MutableMap<TopicPartition, Long>, callback: ConsumerSeekCallback) {
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callback.seekToBeginning(assignments.keys)
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}
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}
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@ -1,12 +1,8 @@
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package dev.pcvolkmer.oncoanalytics.monitor.topiclisteners
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import ca.uhn.fhir.context.FhirContext
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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 dev.pcvolkmer.oncoanalytics.monitor.fetchStatistics
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import org.hl7.fhir.r4.model.Bundle
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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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@ -14,12 +10,20 @@ import org.springframework.messaging.handler.annotation.Header
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import org.springframework.messaging.handler.annotation.Payload
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import org.springframework.stereotype.Component
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/**
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* FHIR TopicMonitor to listen to Kafka Topics matching 'fhir.obds.Condition.*'
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*
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* @property statisticsEventProducer The event producer/sink to notify about saved condition
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*
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* @author Paul-Christian Volkmer
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* @since 0.1.0
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*/
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@Component
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class FhirObdsTopicMonitor(
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@Qualifier("fhirObdsConditionRepository")
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private val conditionRepository: ConditionRepository,
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statisticsEventProducer: StatisticsSink,
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) : TopicMonitor(statisticsEventProducer) {
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) : AbstractFhirTopicMonitor(statisticsEventProducer) {
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@KafkaListener(topicPattern = "fhir.obds.Condition.*")
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override fun handleTopicRecord(
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@ -29,22 +33,8 @@ class FhirObdsTopicMonitor(
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@Payload payload: String,
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) {
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try {
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val ctx = FhirContext.forR4()
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val parser = ctx.newJsonParser()
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val bundle = parser.parseResource(Bundle::class.java, payload)
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val firstEntry = bundle.entry.firstOrNull() ?: return
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if (firstEntry.resource.fhirType() == "Condition") {
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val condition = firstEntry.resource as org.hl7.fhir.r4.model.Condition
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val updated = conditionRepository.save(
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Condition(
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ConditionId(condition.id),
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condition.code.coding.first { "http://fhir.de/CodeSystem/bfarm/icd-10-gm" == it.system }.code
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)
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)
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if (updated) {
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this.handleUsableFhirPayload(payload) { condition ->
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if (conditionRepository.save(condition)) {
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sendUpdatedStatistics(fetchStatistics("fhirobds", conditionRepository))
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}
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}
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@ -1,12 +1,8 @@
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package dev.pcvolkmer.oncoanalytics.monitor.topiclisteners
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import ca.uhn.fhir.context.FhirContext
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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 dev.pcvolkmer.oncoanalytics.monitor.fetchStatistics
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import org.hl7.fhir.r4.model.Bundle
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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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@ -14,12 +10,20 @@ import org.springframework.messaging.handler.annotation.Header
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import org.springframework.messaging.handler.annotation.Payload
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import org.springframework.stereotype.Component
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/**
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* FHIR TopicMonitor to listen to Kafka Topics matching 'fhir.pseudonymized.*'
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*
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* @property statisticsEventProducer The event producer/sink to notify about saved condition
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*
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* @author Paul-Christian Volkmer
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* @since 0.1.0
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*/
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@Component
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class FhirPseudonymizedTopicMonitor(
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@Qualifier("fhirPseudonymizedConditionRepository")
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private val conditionRepository: ConditionRepository,
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statisticsEventProducer: StatisticsSink,
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) : TopicMonitor(statisticsEventProducer) {
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) : AbstractFhirTopicMonitor(statisticsEventProducer) {
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@KafkaListener(topicPattern = "fhir.pseudonymized.*")
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override fun handleTopicRecord(
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@ -29,22 +33,8 @@ class FhirPseudonymizedTopicMonitor(
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@Payload payload: String,
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) {
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try {
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val ctx = FhirContext.forR4()
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val parser = ctx.newJsonParser()
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val bundle = parser.parseResource(Bundle::class.java, payload)
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val firstEntry = bundle.entry.firstOrNull() ?: return
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if (firstEntry.resource.fhirType() == "Condition") {
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val condition = firstEntry.resource as org.hl7.fhir.r4.model.Condition
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val updated = conditionRepository.save(
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Condition(
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ConditionId(condition.id),
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condition.code.coding.first { "http://fhir.de/CodeSystem/bfarm/icd-10-gm" == it.system }.code
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)
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)
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if (updated) {
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this.handleUsableFhirPayload(payload) { condition ->
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if (conditionRepository.save(condition)) {
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sendUpdatedStatistics(fetchStatistics("fhirpseudonymized", conditionRepository))
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}
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}
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@ -19,13 +19,21 @@ import org.xml.sax.InputSource
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import java.io.StringReader
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import javax.xml.xpath.XPathFactory
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/**
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* oBDS TopicMonitor to listen to Kafka Topics matching 'onkostar.MELDUNG_EXPORT.*'
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*
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* @property statisticsEventProducer The event producer/sink to notify about saved condition
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*
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* @author Paul-Christian Volkmer
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* @since 0.1.0
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*/
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@Component
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class ObdsXmlTopicMonitor(
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@Qualifier("obdsXmlConditionRepository")
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private val conditionRepository: ConditionRepository,
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private val objectMapper: ObjectMapper,
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statisticsEventProducer: StatisticsSink,
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) : TopicMonitor(statisticsEventProducer) {
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) : AbstractTopicMonitor(statisticsEventProducer) {
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@KafkaListener(topicPattern = "onkostar.MELDUNG_EXPORT.*")
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override fun handleTopicRecord(
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@ -1,21 +1,19 @@
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package dev.pcvolkmer.oncoanalytics.monitor.topiclisteners
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import dev.pcvolkmer.oncoanalytics.monitor.conditions.Statistics
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import org.apache.kafka.common.TopicPartition
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import org.springframework.kafka.listener.ConsumerSeekAware
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import org.springframework.kafka.listener.ConsumerSeekAware.ConsumerSeekCallback
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import reactor.core.publisher.Sinks
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abstract class TopicMonitor(private val statisticsEventProducer: Sinks.Many<Statistics>) : ConsumerSeekAware {
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abstract fun handleTopicRecord(topic: String, timestamp: Long, key: String, payload: String)
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fun sendUpdatedStatistics(statistics: Statistics) {
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statisticsEventProducer.emitNext(statistics) { _, _ -> false }
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}
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override fun onPartitionsAssigned(assignments: MutableMap<TopicPartition, Long>, callback: ConsumerSeekCallback) {
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callback.seekToBeginning(assignments.keys)
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}
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/**
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* TopicMonitor to listen to Kafka Topics
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*
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* @author Paul-Christian Volkmer
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* @since 0.1.0
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*/
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interface TopicMonitor {
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/**
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* Handle incoming Kafka Record
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*
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* @param topic The exact name of the topic
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* @param timestamp The timestamp the record has been published
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* @param key The records key
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* @param payload The records payload
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*/
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fun handleTopicRecord(topic: String, timestamp: Long, key: String, payload: String)
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}
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