mirror of
https://github.com/pcvolkmer/etl-processor.git
synced 2025-07-06 00:12:53 +00:00
feat: support multiple request content types (#109)
This commit is contained in:
GitHub
@ -26,7 +26,6 @@ import dev.dnpm.etl.processor.PatientId
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import dev.dnpm.etl.processor.services.RequestProcessor
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import dev.pcvolkmer.mv64e.mtb.Mtb
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import org.slf4j.LoggerFactory
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import org.springframework.http.HttpStatus
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import org.springframework.http.MediaType
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import org.springframework.http.ResponseEntity
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import org.springframework.web.bind.annotation.*
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@ -47,10 +46,10 @@ class MtbFileRestController(
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@PostMapping( consumes = [ MediaType.APPLICATION_JSON_VALUE ] )
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fun mtbFile(@RequestBody mtbFile: MtbFile): ResponseEntity<Unit> {
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if (mtbFile.consent.status == Consent.Status.ACTIVE) {
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logger.debug("Accepted MTB File for processing")
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logger.debug("Accepted MTB File (bwHC V1) for processing")
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requestProcessor.processMtbFile(mtbFile)
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} else {
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logger.debug("Accepted MTB File and process deletion")
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logger.debug("Accepted MTB File (bwHC V1) and process deletion")
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val patientId = PatientId(mtbFile.patient.id)
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requestProcessor.processDeletion(patientId)
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}
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@ -59,7 +58,9 @@ class MtbFileRestController(
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@PostMapping( consumes = [ CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE] )
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fun mtbFile(@RequestBody mtbFile: Mtb): ResponseEntity<Unit> {
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return ResponseEntity.status(HttpStatus.NOT_IMPLEMENTED).build()
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logger.debug("Accepted MTB File (DNPM V2) for processing")
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requestProcessor.processMtbFile(mtbFile)
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return ResponseEntity.accepted().build()
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}
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@DeleteMapping(path = ["{patientId}"])
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@ -1,7 +1,7 @@
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/*
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* This file is part of ETL-Processor
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*
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* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
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* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
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*
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* This program is free software: you can redistribute it and/or modify
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* it under the terms of the GNU Affero General Public License as published
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@ -22,10 +22,12 @@ package dev.dnpm.etl.processor.output
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import com.fasterxml.jackson.databind.ObjectMapper
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import de.ukw.ccc.bwhc.dto.Consent
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import de.ukw.ccc.bwhc.dto.MtbFile
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import dev.dnpm.etl.processor.RequestId
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import dev.dnpm.etl.processor.CustomMediaType
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import dev.dnpm.etl.processor.config.KafkaProperties
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import dev.dnpm.etl.processor.monitoring.RequestStatus
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import org.apache.kafka.clients.producer.ProducerRecord
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import org.slf4j.LoggerFactory
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import org.springframework.http.MediaType
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import org.springframework.kafka.core.KafkaTemplate
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import org.springframework.retry.support.RetryTemplate
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@ -38,14 +40,20 @@ class KafkaMtbFileSender(
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private val logger = LoggerFactory.getLogger(KafkaMtbFileSender::class.java)
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override fun send(request: MtbFileSender.MtbFileRequest): MtbFileSender.Response {
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override fun <T> send(request: MtbFileRequest<T>): MtbFileSender.Response {
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return try {
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return retryTemplate.execute<MtbFileSender.Response, Exception> {
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val result = kafkaTemplate.send(
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kafkaProperties.outputTopic,
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key(request),
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objectMapper.writeValueAsString(Data(request.requestId, request.mtbFile))
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)
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val record =
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ProducerRecord(kafkaProperties.outputTopic, key(request), objectMapper.writeValueAsString(request))
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when (request) {
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is BwhcV1MtbFileRequest -> record.headers()
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.add("contentType", MediaType.APPLICATION_JSON_VALUE.toByteArray())
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is DnpmV2MtbFileRequest -> record.headers()
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.add("contentType", CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE.toByteArray())
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}
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val result = kafkaTemplate.send(record)
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if (result.get() != null) {
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logger.debug("Sent file via KafkaMtbFileSender")
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MtbFileSender.Response(RequestStatus.UNKNOWN)
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@ -59,7 +67,7 @@ class KafkaMtbFileSender(
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}
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}
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override fun send(request: MtbFileSender.DeleteRequest): MtbFileSender.Response {
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override fun send(request: DeleteRequest): MtbFileSender.Response {
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val dummyMtbFile = MtbFile.builder()
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.withConsent(
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Consent.builder()
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@ -71,12 +79,15 @@ class KafkaMtbFileSender(
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return try {
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return retryTemplate.execute<MtbFileSender.Response, Exception> {
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val result = kafkaTemplate.send(
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kafkaProperties.outputTopic,
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key(request),
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objectMapper.writeValueAsString(Data(request.requestId, dummyMtbFile))
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)
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val record =
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ProducerRecord(
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kafkaProperties.outputTopic,
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key(request),
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// Always use old BwhcV1FileRequest with Consent REJECT
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objectMapper.writeValueAsString(BwhcV1MtbFileRequest(request.requestId, dummyMtbFile))
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)
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val result = kafkaTemplate.send(record)
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if (result.get() != null) {
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logger.debug("Sent deletion request via KafkaMtbFileSender")
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MtbFileSender.Response(RequestStatus.UNKNOWN)
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@ -94,13 +105,12 @@ class KafkaMtbFileSender(
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return "${this.kafkaProperties.servers} (${this.kafkaProperties.outputTopic}/${this.kafkaProperties.outputResponseTopic})"
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}
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private fun key(request: MtbFileSender.MtbFileRequest): String {
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return "{\"pid\": \"${request.mtbFile.patient.id}\"}"
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private fun key(request: MtbRequest): String {
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return when (request) {
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is BwhcV1MtbFileRequest -> "{\"pid\": \"${request.content.patient.id}\"}"
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is DnpmV2MtbFileRequest -> "{\"pid\": \"${request.content.patient.id}\"}"
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is DeleteRequest -> "{\"pid\": \"${request.patientId.value}\"}"
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else -> throw IllegalArgumentException("Unsupported request type: ${request::class.simpleName}")
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}
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}
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private fun key(request: MtbFileSender.DeleteRequest): String {
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return "{\"pid\": \"${request.patientId.value}\"}"
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}
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data class Data(val requestId: RequestId, val content: MtbFile)
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}
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}
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@ -19,25 +19,17 @@
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package dev.dnpm.etl.processor.output
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import de.ukw.ccc.bwhc.dto.MtbFile
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import dev.dnpm.etl.processor.PatientPseudonym
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import dev.dnpm.etl.processor.RequestId
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import dev.dnpm.etl.processor.monitoring.RequestStatus
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import org.springframework.http.HttpStatusCode
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interface MtbFileSender {
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fun send(request: MtbFileRequest): Response
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fun <T> send(request: MtbFileRequest<T>): Response
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fun send(request: DeleteRequest): Response
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fun endpoint(): String
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data class Response(val status: RequestStatus, val body: String = "")
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data class MtbFileRequest(val requestId: RequestId, val mtbFile: MtbFile)
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data class DeleteRequest(val requestId: RequestId, val patientId: PatientPseudonym)
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}
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fun Int.asRequestStatus(): RequestStatus {
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@ -51,4 +43,4 @@ fun Int.asRequestStatus(): RequestStatus {
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fun HttpStatusCode.asRequestStatus(): RequestStatus {
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return this.value().asRequestStatus()
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}
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}
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59
src/main/kotlin/dev/dnpm/etl/processor/output/MtbRequest.kt
Normal file
59
src/main/kotlin/dev/dnpm/etl/processor/output/MtbRequest.kt
Normal file
@ -0,0 +1,59 @@
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/*
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* This file is part of ETL-Processor
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*
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* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
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*
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* This program is free software: you can redistribute it and/or modify
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* it under the terms of the GNU Affero General Public License as published
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* by the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Affero General Public License for more details.
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*
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* You should have received a copy of the GNU Affero General Public License
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* along with this program. If not, see <https://www.gnu.org/licenses/>.
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*/
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package dev.dnpm.etl.processor.output
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import de.ukw.ccc.bwhc.dto.MtbFile
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import dev.dnpm.etl.processor.PatientPseudonym
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import dev.dnpm.etl.processor.RequestId
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import dev.pcvolkmer.mv64e.mtb.Mtb
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interface MtbRequest {
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val requestId: RequestId
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}
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sealed interface MtbFileRequest<out T> : MtbRequest {
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override val requestId: RequestId
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val content: T
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fun patientPseudonym(): PatientPseudonym
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}
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data class BwhcV1MtbFileRequest(
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override val requestId: RequestId,
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override val content: MtbFile
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) : MtbFileRequest<MtbFile> {
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override fun patientPseudonym(): PatientPseudonym {
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return PatientPseudonym(content.patient.id)
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}
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}
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data class DnpmV2MtbFileRequest(
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override val requestId: RequestId,
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override val content: Mtb
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) : MtbFileRequest<Mtb> {
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override fun patientPseudonym(): PatientPseudonym {
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return PatientPseudonym(content.patient.id)
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}
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}
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data class DeleteRequest(
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override val requestId: RequestId,
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val patientId: PatientPseudonym
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) : MtbRequest
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@ -1,7 +1,7 @@
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/*
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* This file is part of ETL-Processor
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*
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* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
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* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
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*
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* This program is free software: you can redistribute it and/or modify
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* it under the terms of the GNU Affero General Public License as published
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@ -19,10 +19,11 @@
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package dev.dnpm.etl.processor.output
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import dev.dnpm.etl.processor.config.RestTargetProperties
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import dev.dnpm.etl.processor.monitoring.RequestStatus
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import dev.dnpm.etl.processor.CustomMediaType
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import dev.dnpm.etl.processor.PatientPseudonym
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import dev.dnpm.etl.processor.config.RestTargetProperties
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import dev.dnpm.etl.processor.monitoring.ReportService
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import dev.dnpm.etl.processor.monitoring.RequestStatus
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import dev.dnpm.etl.processor.monitoring.asRequestStatus
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import org.slf4j.LoggerFactory
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import org.springframework.http.HttpEntity
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@ -46,11 +47,11 @@ abstract class RestMtbFileSender(
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abstract fun deleteUrl(patientId: PatientPseudonym): String
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override fun send(request: MtbFileSender.MtbFileRequest): MtbFileSender.Response {
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override fun <T> send(request: MtbFileRequest<T>): MtbFileSender.Response {
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try {
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return retryTemplate.execute<MtbFileSender.Response, Exception> {
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val headers = getHttpHeaders()
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val entityReq = HttpEntity(request.mtbFile, headers)
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val headers = getHttpHeaders(request)
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val entityReq = HttpEntity(request.content, headers)
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val response = restTemplate.postForEntity(
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sendUrl(),
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entityReq,
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@ -76,10 +77,10 @@ abstract class RestMtbFileSender(
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return MtbFileSender.Response(RequestStatus.ERROR, "Sonstiger Fehler bei der Übertragung")
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}
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override fun send(request: MtbFileSender.DeleteRequest): MtbFileSender.Response {
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override fun send(request: DeleteRequest): MtbFileSender.Response {
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try {
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return retryTemplate.execute<MtbFileSender.Response, Exception> {
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val headers = getHttpHeaders()
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val headers = getHttpHeaders(request)
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val entityReq = HttpEntity(null, headers)
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restTemplate.delete(
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deleteUrl(request.patientId),
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@ -102,11 +103,15 @@ abstract class RestMtbFileSender(
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return this.restTargetProperties.uri.orEmpty()
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}
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private fun getHttpHeaders(): HttpHeaders {
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private fun getHttpHeaders(request: MtbRequest): HttpHeaders {
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val username = restTargetProperties.username
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val password = restTargetProperties.password
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val headers = HttpHeaders()
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headers.contentType = MediaType.APPLICATION_JSON
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headers.contentType = when (request) {
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is BwhcV1MtbFileRequest -> MediaType.APPLICATION_JSON
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is DnpmV2MtbFileRequest -> CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON
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else -> MediaType.APPLICATION_JSON
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}
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if (username.isNullOrBlank() || password.isNullOrBlank()) {
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return headers
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@ -116,4 +121,4 @@ abstract class RestMtbFileSender(
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return headers
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}
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}
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}
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@ -1,7 +1,7 @@
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/*
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* This file is part of ETL-Processor
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*
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* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
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* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
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*
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* This program is free software: you can redistribute it and/or modify
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* it under the terms of the GNU Affero General Public License as published
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@ -27,10 +27,11 @@ import dev.dnpm.etl.processor.monitoring.Report
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import dev.dnpm.etl.processor.monitoring.Request
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import dev.dnpm.etl.processor.monitoring.RequestStatus
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import dev.dnpm.etl.processor.monitoring.RequestType
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import dev.dnpm.etl.processor.output.MtbFileSender
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import dev.dnpm.etl.processor.output.*
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import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
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import dev.dnpm.etl.processor.pseudonym.anonymizeContentWith
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import dev.dnpm.etl.processor.pseudonym.pseudonymizeWith
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import dev.pcvolkmer.mv64e.mtb.Mtb
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import org.apache.commons.codec.binary.Base32
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import org.apache.commons.codec.digest.DigestUtils
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import org.springframework.context.ApplicationEventPublisher
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@ -55,29 +56,40 @@ class RequestProcessor(
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fun processMtbFile(mtbFile: MtbFile, requestId: RequestId) {
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val pid = PatientId(mtbFile.patient.id)
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mtbFile pseudonymizeWith pseudonymizeService
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mtbFile anonymizeContentWith pseudonymizeService
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val request = BwhcV1MtbFileRequest(requestId, transformationService.transform(mtbFile))
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saveAndSend(request, pid)
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}
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val request = MtbFileSender.MtbFileRequest(requestId, transformationService.transform(mtbFile))
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fun processMtbFile(mtbFile: Mtb) {
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processMtbFile(mtbFile, randomRequestId())
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}
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val patientPseudonym = PatientPseudonym(request.mtbFile.patient.id)
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fun processMtbFile(mtbFile: Mtb, requestId: RequestId) {
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val pid = PatientId(mtbFile.patient.id)
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mtbFile pseudonymizeWith pseudonymizeService
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mtbFile anonymizeContentWith pseudonymizeService
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val request = DnpmV2MtbFileRequest(requestId, transformationService.transform(mtbFile))
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saveAndSend(request, pid)
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}
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private fun <T> saveAndSend(request: MtbFileRequest<T>, pid: PatientId) {
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requestService.save(
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Request(
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requestId,
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patientPseudonym,
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request.requestId,
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request.patientPseudonym(),
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pid,
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fingerprint(request.mtbFile),
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fingerprint(request),
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RequestType.MTB_FILE,
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RequestStatus.UNKNOWN
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)
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)
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if (appConfigProperties.duplicationDetection && isDuplication(mtbFile)) {
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if (appConfigProperties.duplicationDetection && isDuplication(request)) {
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applicationEventPublisher.publishEvent(
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ResponseEvent(
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requestId,
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request.requestId,
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Instant.now(),
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RequestStatus.DUPLICATION
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)
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@ -89,7 +101,7 @@ class RequestProcessor(
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applicationEventPublisher.publishEvent(
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ResponseEvent(
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requestId,
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request.requestId,
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Instant.now(),
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responseStatus.status,
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when (responseStatus.status) {
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@ -100,8 +112,11 @@ class RequestProcessor(
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)
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}
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private fun isDuplication(pseudonymizedMtbFile: MtbFile): Boolean {
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val patientPseudonym = PatientPseudonym(pseudonymizedMtbFile.patient.id)
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private fun <T> isDuplication(pseudonymizedMtbFileRequest: MtbFileRequest<T>): Boolean {
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val patientPseudonym = when (pseudonymizedMtbFileRequest) {
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is BwhcV1MtbFileRequest -> PatientPseudonym(pseudonymizedMtbFileRequest.content.patient.id)
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is DnpmV2MtbFileRequest -> PatientPseudonym(pseudonymizedMtbFileRequest.content.patient.id)
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}
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val lastMtbFileRequestForPatient =
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requestService.lastMtbFileRequestForPatientPseudonym(patientPseudonym)
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@ -109,7 +124,7 @@ class RequestProcessor(
|
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return null != lastMtbFileRequestForPatient
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&& !isLastRequestDeletion
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&& lastMtbFileRequestForPatient.fingerprint == fingerprint(pseudonymizedMtbFile)
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&& lastMtbFileRequestForPatient.fingerprint == fingerprint(pseudonymizedMtbFileRequest)
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}
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fun processDeletion(patientId: PatientId) {
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@ -131,7 +146,7 @@ class RequestProcessor(
|
||||
)
|
||||
)
|
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val responseStatus = sender.send(MtbFileSender.DeleteRequest(requestId, patientPseudonym))
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val responseStatus = sender.send(DeleteRequest(requestId, patientPseudonym))
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applicationEventPublisher.publishEvent(
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||||
ResponseEvent(
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@ -160,8 +175,11 @@ class RequestProcessor(
|
||||
}
|
||||
}
|
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private fun fingerprint(mtbFile: MtbFile): Fingerprint {
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return fingerprint(objectMapper.writeValueAsString(mtbFile))
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private fun <T> fingerprint(request: MtbFileRequest<T>): Fingerprint {
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return when (request) {
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is BwhcV1MtbFileRequest -> fingerprint(objectMapper.writeValueAsString(request.content))
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is DnpmV2MtbFileRequest -> fingerprint(objectMapper.writeValueAsString(request.content))
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}
|
||||
}
|
||||
|
||||
private fun fingerprint(s: String): Fingerprint {
|
||||
@ -172,4 +190,4 @@ class RequestProcessor(
|
||||
)
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
@ -23,10 +23,21 @@ import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import com.jayway.jsonpath.JsonPath
|
||||
import com.jayway.jsonpath.PathNotFoundException
|
||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||
|
||||
class TransformationService(private val objectMapper: ObjectMapper, private val transformations: List<Transformation>) {
|
||||
fun transform(mtbFile: MtbFile): MtbFile {
|
||||
var json = objectMapper.writeValueAsString(mtbFile)
|
||||
val json = transform(objectMapper.writeValueAsString(mtbFile))
|
||||
return objectMapper.readValue(json, MtbFile::class.java)
|
||||
}
|
||||
|
||||
fun transform(mtbFile: Mtb): Mtb {
|
||||
val json = transform(objectMapper.writeValueAsString(mtbFile))
|
||||
return objectMapper.readValue(json, Mtb::class.java)
|
||||
}
|
||||
|
||||
private fun transform(content: String): String {
|
||||
var json = content
|
||||
|
||||
transformations.forEach { transformation ->
|
||||
val jsonPath = JsonPath.parse(json)
|
||||
@ -48,7 +59,7 @@ class TransformationService(private val objectMapper: ObjectMapper, private val
|
||||
json = jsonPath.jsonString()
|
||||
}
|
||||
|
||||
return objectMapper.readValue(json, MtbFile::class.java)
|
||||
return json
|
||||
}
|
||||
|
||||
fun getTransformations(): List<Transformation> {
|
||||
|
||||
Reference in New Issue
Block a user