refactor: remove obsolete bwHC data model V1.0 (#129)

2025-09-13 17:02:52 +00:00 · 2025-08-12 23:11:50 +02:00
parent bf898e5c25
commit 2e88157893
27 changed files with 286 additions and 1596 deletions
--- a/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt
@@ -24,7 +24,6 @@ import org.springframework.boot.context.properties.ConfigurationProperties

@ConfigurationProperties(AppConfigProperties.NAME)
 data class AppConfigProperties(
-    var bwhcUri: String?,
    var transformations: List<TransformationProperties> = listOf(),
    var maxRetryAttempts: Int = 3,
    var duplicationDetection: Boolean = true,
@@ -128,8 +127,7 @@ data class GIcsConfigProperties(
 data class RestTargetProperties(
    val uri: String?,
    val username: String?,
-    val password: String?,
-    val isBwhc: Boolean = false,
+    val password: String?
 ) {
    companion object {
        const val NAME = "app.rest"
--- a/src/main/kotlin/dev/dnpm/etl/processor/config/AppRestConfiguration.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/config/AppRestConfiguration.kt
@@ -24,7 +24,6 @@ import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
 import dev.dnpm.etl.processor.monitoring.ReportService
 import dev.dnpm.etl.processor.monitoring.RestConnectionCheckService
 import dev.dnpm.etl.processor.output.MtbFileSender
-import dev.dnpm.etl.processor.output.RestBwhcMtbFileSender
 import dev.dnpm.etl.processor.output.RestDipMtbFileSender
 import org.slf4j.LoggerFactory
 import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean
@@ -57,11 +56,6 @@ class AppRestConfiguration {
        retryTemplate: RetryTemplate,
        reportService: ReportService,
    ): MtbFileSender {
-        if (restTargetProperties.isBwhc) {
-            logger.info("Selected 'RestBwhcMtbFileSender'")
-            return RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
-        }
-
        logger.info("Selected 'RestDipMtbFileSender'")
        return RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
    }
--- a/src/main/kotlin/dev/dnpm/etl/processor/input/KafkaInputListener.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/input/KafkaInputListener.kt
@@ -20,13 +20,13 @@
 package dev.dnpm.etl.processor.input

 import com.fasterxml.jackson.databind.ObjectMapper
-import de.ukw.ccc.bwhc.dto.Consent
-import de.ukw.ccc.bwhc.dto.MtbFile
 import dev.dnpm.etl.processor.CustomMediaType
 import dev.dnpm.etl.processor.PatientId
 import dev.dnpm.etl.processor.RequestId
 import dev.dnpm.etl.processor.consent.TtpConsentStatus
 import dev.dnpm.etl.processor.services.RequestProcessor
+import dev.pcvolkmer.mv64e.mtb.ConsentProvision
+import dev.pcvolkmer.mv64e.mtb.Mtb
 import org.apache.kafka.clients.consumer.ConsumerRecord
 import org.slf4j.LoggerFactory
 import org.springframework.http.MediaType
@@ -40,7 +40,7 @@ class KafkaInputListener(

    override fun onMessage(record: ConsumerRecord<String, String>) {
        when (guessMimeType(record)) {
-            MediaType.APPLICATION_JSON_VALUE -> handleBwhcMessage(record)
+            MediaType.APPLICATION_JSON_VALUE -> handleDnpmV2Message(record)
            CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE -> handleDnpmV2Message(record)
            else -> {
                /* ignore other messages */
@@ -57,8 +57,11 @@ class KafkaInputListener(
        return record.headers().headers("contentType")?.firstOrNull()?.value().contentToString()
    }

-    private fun handleBwhcMessage(record: ConsumerRecord<String, String>) {
-        val mtbFile = objectMapper.readValue(record.value(), MtbFile::class.java)
+    private fun handleDnpmV2Message(record: ConsumerRecord<String, String>) {
+        // Do not handle DNPM-V2 for now
+        logger.warn("Ignoring MTB File in DNPM V2 format: Not implemented yet")
+
+        val mtbFile = objectMapper.readValue(record.value(), Mtb::class.java)
        val patientId = PatientId(mtbFile.patient.id)
        val firstRequestIdHeader = record.headers().headers("requestId")?.firstOrNull()
        val requestId = if (null != firstRequestIdHeader) {
@@ -67,7 +70,8 @@ class KafkaInputListener(
            RequestId("")
        }

-        if (mtbFile.consent.status == Consent.Status.ACTIVE) {
+        // TODO: Use MV Consent for now - needs to be replaced with proper consent evaluation
+        if (mtbFile.metadata.modelProjectConsent.provisions.filter { it.type == ConsentProvision.PERMIT }.isNotEmpty()) {
            logger.debug("Accepted MTB File for processing")
            if (requestId.isBlank()) {
                requestProcessor.processMtbFile(mtbFile)
@@ -88,9 +92,4 @@ class KafkaInputListener(
        }
    }

-    private fun handleDnpmV2Message(record: ConsumerRecord<String, String>) {
-        // Do not handle DNPM-V2 for now
-        logger.warn("Ignoring MTB File in DNPM V2 format: Not implemented yet")
-    }
-
 }
--- a/src/main/kotlin/dev/dnpm/etl/processor/input/MtbFileRestController.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/input/MtbFileRestController.kt
@@ -19,8 +19,6 @@

 package dev.dnpm.etl.processor.input

-import de.ukw.ccc.bwhc.dto.Consent
-import de.ukw.ccc.bwhc.dto.MtbFile
 import dev.dnpm.etl.processor.CustomMediaType
 import dev.dnpm.etl.processor.PatientId
 import dev.dnpm.etl.processor.consent.IGetConsent
@@ -46,23 +44,7 @@ class MtbFileRestController(
        return ResponseEntity.ok("Test")
    }

-    @PostMapping(consumes = [MediaType.APPLICATION_JSON_VALUE])
-    fun mtbFile(@RequestBody mtbFile: MtbFile): ResponseEntity<Unit> {
-        val consentStatusBooleanPair = checkConsentStatus(mtbFile)
-        val ttpConsentStatus = consentStatusBooleanPair.first
-        val isConsentOK = consentStatusBooleanPair.second
-        if (isConsentOK) {
-            logger.debug("Accepted MTB File (bwHC V1) for processing")
-            requestProcessor.processMtbFile(mtbFile)
-        } else {
-            logger.debug("Accepted MTB File (bwHC V1) and process deletion")
-            val patientId = PatientId(mtbFile.patient.id)
-            requestProcessor.processDeletion(patientId, ttpConsentStatus)
-        }
-        return ResponseEntity.accepted().build()
-    }
-
-    @PostMapping(consumes = [CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE])
+    @PostMapping(consumes = [MediaType.APPLICATION_JSON_VALUE, CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE])
    fun mtbFile(@RequestBody mtbFile: Mtb): ResponseEntity<Unit> {
        logger.debug("Accepted MTB File (DNPM V2) for processing")
        requestProcessor.processMtbFile(mtbFile)
@@ -76,17 +58,4 @@ class MtbFileRestController(
        return ResponseEntity.accepted().build()
    }

-    private fun checkConsentStatus(mtbFile: MtbFile): Pair<TtpConsentStatus, Boolean> {
-        var ttpConsentStatus = iGetConsent.getTtpBroadConsentStatus(mtbFile.patient.id)
-
-        val isConsentOK = (ttpConsentStatus == TtpConsentStatus.UNKNOWN_CHECK_FILE && mtbFile.consent.status == Consent.Status.ACTIVE)
-                    || ttpConsentStatus == TtpConsentStatus.BROAD_CONSENT_GIVEN
-
-        if (ttpConsentStatus == TtpConsentStatus.UNKNOWN_CHECK_FILE && mtbFile.consent.status == Consent.Status.REJECTED) {
-            // in case ttp check is disabled - we propagate rejected status anyway
-            ttpConsentStatus = TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED
-        }
-        return Pair(ttpConsentStatus, isConsentOK)
-    }
-
 }
--- a/src/main/kotlin/dev/dnpm/etl/processor/monitoring/ConnectionCheckService.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/monitoring/ConnectionCheckService.kt
@@ -128,15 +128,11 @@ class RestConnectionCheckService(
    fun check() {
        result = try {
            val available = restTemplate.getForEntity(
-                if (restTargetProperties.isBwhc) {
-                    UriComponentsBuilder.fromUriString(restTargetProperties.uri.toString()).path("").toUriString()
-                } else {
-                    UriComponentsBuilder.fromUriString(restTargetProperties.uri.toString())
-                        .pathSegment("mtb")
-                        .pathSegment("kaplan-meier")
-                        .pathSegment("config")
-                        .toUriString()
-                },
+                UriComponentsBuilder.fromUriString(restTargetProperties.uri.toString())
+                    .pathSegment("mtb")
+                    .pathSegment("kaplan-meier")
+                    .pathSegment("config")
+                    .toUriString(),
                String::class.java
            ).statusCode == HttpStatus.OK

@@ -267,4 +263,4 @@ class GIcsConnectionCheckService(
    override fun connectionAvailable(): ConnectionCheckResult.GIcsConnectionCheckResult {
        return this.result
    }
-}
+}
--- a/src/main/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSender.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSender.kt
@@ -20,11 +20,11 @@
 package dev.dnpm.etl.processor.output

 import com.fasterxml.jackson.databind.ObjectMapper
-import de.ukw.ccc.bwhc.dto.Consent
-import de.ukw.ccc.bwhc.dto.MtbFile
 import dev.dnpm.etl.processor.CustomMediaType
 import dev.dnpm.etl.processor.config.KafkaProperties
 import dev.dnpm.etl.processor.monitoring.RequestStatus
+import dev.pcvolkmer.mv64e.mtb.Mtb
+import dev.pcvolkmer.mv64e.mtb.MvhMetadata
 import org.apache.kafka.clients.producer.ProducerRecord
 import org.slf4j.LoggerFactory
 import org.springframework.http.MediaType
@@ -50,9 +50,6 @@ class KafkaMtbFileSender(
                        objectMapper.writeValueAsString(request)
                    )
                when (request) {
-                    is BwhcV1MtbFileRequest -> record.headers()
-                        .add("contentType", MediaType.APPLICATION_JSON_VALUE.toByteArray())
-
                    is DnpmV2MtbFileRequest -> record.headers()
                        .add(
                            "contentType",
@@ -75,13 +72,8 @@ class KafkaMtbFileSender(
    }

    override fun send(request: DeleteRequest): MtbFileSender.Response {
-        val dummyMtbFile = MtbFile.builder()
-            .withConsent(
-                Consent.builder()
-                    .withPatient(request.patientId.value)
-                    .withStatus(Consent.Status.REJECTED)
-                    .build()
-            )
+        val dummyMtbFile = Mtb.builder()
+            .metadata(MvhMetadata())
            .build()

        return try {
@@ -92,7 +84,7 @@ class KafkaMtbFileSender(
                        key(request),
                        // Always use old BwhcV1FileRequest with Consent REJECT
                        objectMapper.writeValueAsString(
-                            BwhcV1MtbFileRequest(
+                            DnpmV2MtbFileRequest(
                                request.requestId,
                                dummyMtbFile
                            )
@@ -119,7 +111,6 @@ class KafkaMtbFileSender(

    private fun key(request: MtbRequest): String {
        return when (request) {
-            is BwhcV1MtbFileRequest -> "{\"pid\": \"${request.content.patient.id}\"}"
            is DnpmV2MtbFileRequest -> "{\"pid\": \"${request.content.patient.id}\"}"
            is DeleteRequest -> "{\"pid\": \"${request.patientId.value}\"}"
            else -> throw IllegalArgumentException("Unsupported request type: ${request::class.simpleName}")
--- a/src/main/kotlin/dev/dnpm/etl/processor/output/MtbRequest.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/output/MtbRequest.kt
@@ -19,7 +19,6 @@

 package dev.dnpm.etl.processor.output

-import de.ukw.ccc.bwhc.dto.MtbFile
 import dev.dnpm.etl.processor.PatientPseudonym
 import dev.dnpm.etl.processor.RequestId
 import dev.pcvolkmer.mv64e.mtb.Mtb
@@ -35,15 +34,6 @@ sealed interface MtbFileRequest<out T> : MtbRequest {
    fun patientPseudonym(): PatientPseudonym
 }

-data class BwhcV1MtbFileRequest(
-    override val requestId: RequestId,
-    override val content: MtbFile
-) : MtbFileRequest<MtbFile> {
-    override fun patientPseudonym(): PatientPseudonym {
-        return PatientPseudonym(content.patient.id)
-    }
-}
-
 data class DnpmV2MtbFileRequest(
    override val requestId: RequestId,
    override val content: Mtb
--- a/src/main/kotlin/dev/dnpm/etl/processor/output/RestBwhcMtbFileSender.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/output/RestBwhcMtbFileSender.kt
@@ -1,51 +0,0 @@
-/*
- * This file is part of ETL-Processor
- *
- * Copyright (c) 2025  Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as published
- * by the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program.  If not, see <https://www.gnu.org/licenses/>.
- */
-
-package dev.dnpm.etl.processor.output
-
-import dev.dnpm.etl.processor.PatientPseudonym
-import dev.dnpm.etl.processor.config.RestTargetProperties
-import dev.dnpm.etl.processor.monitoring.ReportService
-import org.springframework.retry.support.RetryTemplate
-import org.springframework.web.client.RestTemplate
-import org.springframework.web.util.UriComponentsBuilder
-
-class RestBwhcMtbFileSender(
-    restTemplate: RestTemplate,
-    private val restTargetProperties: RestTargetProperties,
-    retryTemplate: RetryTemplate,
-    reportService: ReportService,
-) : RestMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService) {
-
-    override fun sendUrl(): String {
-        return UriComponentsBuilder
-            .fromUriString(restTargetProperties.uri.toString())
-            .pathSegment("MTBFile")
-            .toUriString()
-    }
-
-    override fun deleteUrl(patientId: PatientPseudonym): String {
-        return UriComponentsBuilder
-            .fromUriString(restTargetProperties.uri.toString())
-            .pathSegment("Patient")
-            .pathSegment(patientId.value)
-            .toUriString()
-    }
-
-}
--- a/src/main/kotlin/dev/dnpm/etl/processor/output/RestMtbFileSender.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/output/RestMtbFileSender.kt
@@ -108,7 +108,6 @@ abstract class RestMtbFileSender(
        val password = restTargetProperties.password
        val headers = HttpHeaders()
        headers.contentType = when (request) {
-            is BwhcV1MtbFileRequest -> MediaType.APPLICATION_JSON
            is DnpmV2MtbFileRequest -> CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON
            else -> MediaType.APPLICATION_JSON
        }
--- a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
@@ -19,217 +19,12 @@

 package dev.dnpm.etl.processor.pseudonym

-import de.ukw.ccc.bwhc.dto.MtbFile
 import dev.dnpm.etl.processor.PatientId
 import dev.pcvolkmer.mv64e.mtb.ModelProjectConsent
 import dev.pcvolkmer.mv64e.mtb.Mtb
 import dev.pcvolkmer.mv64e.mtb.MvhMetadata
 import org.apache.commons.codec.digest.DigestUtils

-/** Replaces patient ID with generated patient pseudonym
- *
- * @param pseudonymizeService The pseudonymizeService to be used
- * @return The MTB file containing patient pseudonymes
- */
-infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
-    val patientPseudonym = pseudonymizeService.patientPseudonym(PatientId(this.patient.id)).value
-
-    this.episode?.patient = patientPseudonym
-    this.carePlans?.forEach { it.patient = patientPseudonym }
-    this.patient.id = patientPseudonym
-    this.claims?.forEach { it.patient = patientPseudonym }
-    this.consent?.patient = patientPseudonym
-    this.claimResponses?.forEach { it.patient = patientPseudonym }
-    this.diagnoses?.forEach { it.patient = patientPseudonym }
-    this.ecogStatus?.forEach { it.patient = patientPseudonym }
-    this.familyMemberDiagnoses?.forEach { it.patient = patientPseudonym }
-    this.geneticCounsellingRequests?.forEach { it.patient = patientPseudonym }
-    this.histologyReevaluationRequests?.forEach { it.patient = patientPseudonym }
-    this.histologyReports?.forEach {
-        it.patient = patientPseudonym
-        it.tumorMorphology?.patient = patientPseudonym
-    }
-    this.lastGuidelineTherapies?.forEach { it.patient = patientPseudonym }
-    this.molecularPathologyFindings?.forEach { it.patient = patientPseudonym }
-    this.molecularTherapies?.forEach { molecularTherapy ->
-        molecularTherapy.history.forEach {
-            it.patient = patientPseudonym
-        }
-    }
-    this.ngsReports?.forEach { it.patient = patientPseudonym }
-    this.previousGuidelineTherapies?.forEach { it.patient = patientPseudonym }
-    this.rebiopsyRequests?.forEach { it.patient = patientPseudonym }
-    this.recommendations?.forEach { it.patient = patientPseudonym }
-    this.responses?.forEach { it.patient = patientPseudonym }
-    this.studyInclusionRequests?.forEach { it.patient = patientPseudonym }
-    this.specimens?.forEach { it.patient = patientPseudonym }
-}
-
-/**
- * Creates new hash of content IDs with given prefix except for patient IDs
- *
- * @param pseudonymizeService The pseudonymizeService to be used
- * @return The MTB file containing rehashed content IDs
- */
-infix fun MtbFile.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
-    val prefix = pseudonymizeService.prefix()
-
-    fun anonymize(id: String): String {
-        val hash = DigestUtils.sha256Hex("$prefix-$id").substring(0, 41).lowercase()
-        return "$prefix$hash"
-    }
-
-    this.episode?.apply {
-        id = id?.let {
-            anonymize(it)
-        }
-    }
-    this.carePlans?.onEach { carePlan ->
-        carePlan?.apply {
-            id = id?.let { anonymize(it) }
-            diagnosis = diagnosis?.let { anonymize(it) }
-            geneticCounsellingRequest = geneticCounsellingRequest?.let { anonymize(it) }
-            rebiopsyRequests = rebiopsyRequests.map { it?.let { anonymize(it) } }
-            recommendations = recommendations.map { it?.let { anonymize(it) } }
-            studyInclusionRequests = studyInclusionRequests.map { it?.let { anonymize(it) } }
-        }
-    }
-    this.claims?.onEach { claim ->
-        claim?.apply {
-            id = id?.let { anonymize(it) }
-            therapy = therapy?.let { anonymize(it) }
-        }
-    }
-    this.claimResponses?.onEach { claimResponse ->
-        claimResponse?.apply {
-            id = id?.let { anonymize(it) }
-            claim = claim?.let { anonymize(it) }
-        }
-    }
-    this.consent?.apply {
-        id = id?.let { anonymize(it) }
-    }
-    this.diagnoses?.onEach { diagnosis ->
-        diagnosis?.apply {
-            id = id?.let { anonymize(it) }
-            histologyResults = histologyResults?.map { it?.let { anonymize(it) } }
-        }
-    }
-    this.ecogStatus?.onEach { ecogStatus ->
-        ecogStatus?.apply {
-            id = id?.let { anonymize(it) }
-        }
-    }
-    this.familyMemberDiagnoses?.onEach { familyMemberDiagnosis ->
-        familyMemberDiagnosis?.apply {
-            id = id?.let { anonymize(it) }
-        }
-    }
-    this.geneticCounsellingRequests?.onEach { geneticCounsellingRequest ->
-        geneticCounsellingRequest?.apply {
-            id = id?.let { anonymize(it) }
-        }
-    }
-    this.histologyReevaluationRequests?.onEach { histologyReevaluationRequest ->
-        histologyReevaluationRequest?.apply {
-            id = id?.let { anonymize(it) }
-            specimen = specimen?.let { anonymize(it) }
-        }
-    }
-    this.histologyReports?.onEach { histologyReport ->
-        histologyReport?.apply {
-            id = id?.let { anonymize(it) }
-            specimen = specimen?.let { anonymize(it) }
-            tumorMorphology?.apply {
-                id = id?.let { anonymize(it) }
-                specimen = specimen?.let { anonymize(it) }
-            }
-            tumorCellContent?.apply {
-                id = id?.let { anonymize(it) }
-                specimen = specimen?.let { anonymize(it) }
-            }
-        }
-    }
-    this.lastGuidelineTherapies?.onEach { lastGuidelineTherapy ->
-        lastGuidelineTherapy?.apply {
-            id = id?.let { anonymize(it) }
-            diagnosis = diagnosis?.let { anonymize(it) }
-        }
-    }
-    this.molecularPathologyFindings?.onEach { molecularPathologyFinding ->
-        molecularPathologyFinding?.apply {
-            id = id?.let { anonymize(it) }
-            specimen = specimen?.let { anonymize(it) }
-        }
-    }
-    this.molecularTherapies?.onEach { molecularTherapy ->
-        molecularTherapy?.apply {
-            history?.onEach { history ->
-                history?.apply {
-                    id = id?.let { anonymize(it) }
-                    basedOn = basedOn?.let { anonymize(it) }
-                }
-            }
-        }
-    }
-    this.ngsReports?.onEach { ngsReport ->
-        ngsReport?.apply {
-            id = id?.let { anonymize(it) }
-            specimen = specimen?.let { anonymize(it) }
-            tumorCellContent?.apply {
-                id = id?.let { anonymize(it) }
-                specimen = specimen?.let { anonymize(it) }
-            }
-            simpleVariants?.onEach { simpleVariant ->
-                simpleVariant?.apply {
-                    id = id?.let { anonymize(it) }
-                }
-            }
-        }
-    }
-    this.previousGuidelineTherapies?.onEach { previousGuidelineTherapy ->
-        previousGuidelineTherapy?.apply {
-            id = id?.let { anonymize(it) }
-            diagnosis = diagnosis?.let { anonymize(it) }
-            medication.forEach { medication ->
-                medication?.apply {
-                    id = id?.let { anonymize(it) }
-                }
-            }
-        }
-    }
-    this.rebiopsyRequests?.onEach { rebiopsyRequest ->
-        rebiopsyRequest?.apply {
-            id = id?.let { anonymize(it) }
-            specimen = specimen?.let { anonymize(it) }
-        }
-    }
-    this.recommendations?.onEach { recommendation ->
-        recommendation?.apply {
-            id = id?.let { anonymize(it) }
-            diagnosis = diagnosis?.let { anonymize(it) }
-            ngsReport = ngsReport?.let { anonymize(it) }
-        }
-    }
-    this.responses?.onEach { response ->
-        response?.apply {
-            id = id?.let { anonymize(it) }
-            therapy = therapy?.let { anonymize(it) }
-        }
-    }
-    this.studyInclusionRequests?.onEach { studyInclusionRequest ->
-        studyInclusionRequest?.apply {
-            id = id?.let { anonymize(it) }
-            reason = reason?.let { anonymize(it) }
-        }
-    }
-    this.specimens?.onEach { specimen ->
-        specimen?.apply {
-            id = id?.let { anonymize(it) }
-        }
-    }
-}
-
 /** Replaces patient ID with generated patient pseudonym
 *
 * @since 0.11.0
@@ -353,4 +148,4 @@ fun Mtb.ensureMetaDataIsInitialized() {
 infix fun Mtb.addGenomDeTan(pseudonymizeService: PseudonymizeService)
 {
    this.metadata.transferTan = pseudonymizeService.genomDeTan(PatientId(this.patient.id))
-}
+}
--- a/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
@@ -20,7 +20,6 @@
 package dev.dnpm.etl.processor.services

 import com.fasterxml.jackson.databind.ObjectMapper
-import de.ukw.ccc.bwhc.dto.MtbFile
 import dev.dnpm.etl.processor.*
 import dev.dnpm.etl.processor.config.AppConfigProperties
 import dev.dnpm.etl.processor.consent.TtpConsentStatus
@@ -28,7 +27,10 @@ import dev.dnpm.etl.processor.monitoring.Report
 import dev.dnpm.etl.processor.monitoring.Request
 import dev.dnpm.etl.processor.monitoring.RequestStatus
 import dev.dnpm.etl.processor.monitoring.RequestType
-import dev.dnpm.etl.processor.output.*
+import dev.dnpm.etl.processor.output.DeleteRequest
+import dev.dnpm.etl.processor.output.DnpmV2MtbFileRequest
+import dev.dnpm.etl.processor.output.MtbFileRequest
+import dev.dnpm.etl.processor.output.MtbFileSender
 import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
 import dev.dnpm.etl.processor.pseudonym.addGenomDeTan
 import dev.dnpm.etl.processor.pseudonym.anonymizeContentWith
@@ -42,7 +44,6 @@ import org.slf4j.Logger
 import org.slf4j.LoggerFactory
 import org.springframework.context.ApplicationEventPublisher
 import org.springframework.stereotype.Service
-import java.lang.RuntimeException
 import java.time.Instant
 import java.util.*

@@ -59,17 +60,6 @@ class RequestProcessor(
 ) {

    private var logger: Logger = LoggerFactory.getLogger("RequestProcessor")
-    fun processMtbFile(mtbFile: MtbFile) {
-        processMtbFile(mtbFile, randomRequestId())
-    }
-
-    fun processMtbFile(mtbFile: MtbFile, requestId: RequestId) {
-        val pid = PatientId(mtbFile.patient.id)
-        mtbFile pseudonymizeWith pseudonymizeService
-        mtbFile anonymizeContentWith pseudonymizeService
-        val request = BwhcV1MtbFileRequest(requestId, transformationService.transform(mtbFile))
-        saveAndSend(request, pid)
-    }

    fun processMtbFile(mtbFile: Mtb) {
        processMtbFile(mtbFile, randomRequestId())
@@ -144,7 +134,6 @@ class RequestProcessor(

    private fun <T> isDuplication(pseudonymizedMtbFileRequest: MtbFileRequest<T>): Boolean {
        val patientPseudonym = when (pseudonymizedMtbFileRequest) {
-            is BwhcV1MtbFileRequest -> PatientPseudonym(pseudonymizedMtbFileRequest.content.patient.id)
            is DnpmV2MtbFileRequest -> PatientPseudonym(pseudonymizedMtbFileRequest.content.patient.id)
        }

@@ -214,7 +203,6 @@ class RequestProcessor(

    private fun <T> fingerprint(request: MtbFileRequest<T>): Fingerprint {
        return when (request) {
-            is BwhcV1MtbFileRequest -> fingerprint(objectMapper.writeValueAsString(request.content))
            is DnpmV2MtbFileRequest -> fingerprint(objectMapper.writeValueAsString(request.content))
        }
    }
--- a/src/main/kotlin/dev/dnpm/etl/processor/services/TransformationService.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/services/TransformationService.kt
@@ -22,14 +22,9 @@ package dev.dnpm.etl.processor.services
 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 {
-        val json = transform(objectMapper.writeValueAsString(mtbFile))
-        return objectMapper.readValue(json, MtbFile::class.java)
-    }

    fun transform(mtbFile: Mtb): Mtb {
        val json = transform(objectMapper.writeValueAsString(mtbFile))