summaryrefslogtreecommitdiff
path: root/src/main/kotlin
diff options
context:
space:
mode:
Diffstat (limited to 'src/main/kotlin')
-rw-r--r--src/main/kotlin/dev/dnpm/etl/processor/config/AppConfiguration.kt1
-rw-r--r--src/main/kotlin/dev/dnpm/etl/processor/consent/ConsentEvaluator.kt12
-rw-r--r--src/main/kotlin/dev/dnpm/etl/processor/input/KafkaInputListener.kt8
-rw-r--r--src/main/kotlin/dev/dnpm/etl/processor/input/MtbFileRestController.kt7
-rw-r--r--src/main/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSender.kt8
-rw-r--r--src/main/kotlin/dev/dnpm/etl/processor/output/MtbRequest.kt8
-rw-r--r--src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt36
-rw-r--r--src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt48
-rw-r--r--src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt14
-rw-r--r--src/main/kotlin/dev/dnpm/etl/processor/services/TransformationService.kt6
10 files changed, 76 insertions, 72 deletions
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfiguration.kt b/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfiguration.kt
index 3e88ffd..d780642 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfiguration.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfiguration.kt
@@ -20,7 +20,6 @@
package dev.dnpm.etl.processor.config
-import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.consent.GicsConsentService
import dev.dnpm.etl.processor.consent.GicsGetBroadConsentService
import dev.dnpm.etl.processor.consent.IConsentService
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/consent/ConsentEvaluator.kt b/src/main/kotlin/dev/dnpm/etl/processor/consent/ConsentEvaluator.kt
index a8b8fdb..1f867e8 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/consent/ConsentEvaluator.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/consent/ConsentEvaluator.kt
@@ -20,9 +20,9 @@
package dev.dnpm.etl.processor.consent
-import dev.pcvolkmer.mv64e.mtb.ConsentProvision
-import dev.pcvolkmer.mv64e.mtb.ModelProjectConsentPurpose
-import dev.pcvolkmer.mv64e.mtb.Mtb
+import dev.pcvolkmer.mv64e.model.ConsentProvisionType
+import dev.pcvolkmer.mv64e.model.ModelProjectConsentPurpose
+import dev.pcvolkmer.mv64e.model.PatientRecord
import org.springframework.stereotype.Service
/** Evaluates consent using provided consent service and file based consent information */
@@ -30,8 +30,8 @@ import org.springframework.stereotype.Service
class ConsentEvaluator(
private val consentService: IConsentService,
) {
- fun check(mtbFile: Mtb): ConsentEvaluation {
- val ttpConsentStatus = consentService.getTtpBroadConsentStatus(mtbFile.patient.id)
+ fun check(mtbFile: PatientRecord): ConsentEvaluation {
+ val ttpConsentStatus = consentService.getTtpBroadConsentStatus(mtbFile.patient!!.id)
val consentGiven =
ttpConsentStatus == TtpConsentStatus.BROAD_CONSENT_GIVEN ||
ttpConsentStatus == TtpConsentStatus.GENOM_DE_CONSENT_SEQUENCING_PERMIT ||
@@ -39,7 +39,7 @@ class ConsentEvaluator(
ttpConsentStatus == TtpConsentStatus.UNKNOWN_CHECK_FILE &&
mtbFile.metadata?.modelProjectConsent?.provisions?.any {
it.purpose == ModelProjectConsentPurpose.SEQUENCING &&
- it.type == ConsentProvision.PERMIT
+ it.type == ConsentProvisionType.PERMIT
} == true
return ConsentEvaluation(ttpConsentStatus, consentGiven)
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/input/KafkaInputListener.kt b/src/main/kotlin/dev/dnpm/etl/processor/input/KafkaInputListener.kt
index a126e07..51d093b 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/input/KafkaInputListener.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/input/KafkaInputListener.kt
@@ -26,7 +26,7 @@ import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.consent.ConsentEvaluator
import dev.dnpm.etl.processor.consent.TtpConsentStatus
import dev.dnpm.etl.processor.services.RequestProcessor
-import dev.pcvolkmer.mv64e.mtb.Mtb
+import dev.pcvolkmer.mv64e.model.PatientRecord
import org.apache.kafka.clients.consumer.ConsumerRecord
import org.slf4j.LoggerFactory
import org.springframework.http.MediaType
@@ -72,8 +72,8 @@ class KafkaInputListener(
private fun handleDnpmV2Message(record: ConsumerRecord<String, String>) {
try {
- val mtbFile = jsonMapper.readValue(record.value(), Mtb::class.java)
- val patientId = PatientId(mtbFile.patient.id)
+ val mtbFile = jsonMapper.readValue(record.value(), PatientRecord::class.java)
+ val patientId = PatientId(mtbFile.patient!!.id)
val firstRequestIdHeader = record.headers().headers("requestId")?.firstOrNull()
val requestId =
if (null != firstRequestIdHeader) {
@@ -106,7 +106,7 @@ class KafkaInputListener(
}
} catch (e: Exception) {
logger.error("Error while processing MtbFile", e)
- requestProcessor.processMtbFile(Mtb.builder().build())
+ requestProcessor.processMtbFile(PatientRecord.builder().build())
}
}
}
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/input/MtbFileRestController.kt b/src/main/kotlin/dev/dnpm/etl/processor/input/MtbFileRestController.kt
index 47f0766..7ab846a 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/input/MtbFileRestController.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/input/MtbFileRestController.kt
@@ -22,10 +22,9 @@ package dev.dnpm.etl.processor.input
import dev.dnpm.etl.processor.CustomMediaType
import dev.dnpm.etl.processor.PatientId
-import dev.dnpm.etl.processor.consent.ConsentEvaluator
import dev.dnpm.etl.processor.consent.TtpConsentStatus
import dev.dnpm.etl.processor.services.RequestProcessor
-import dev.pcvolkmer.mv64e.mtb.Mtb
+import dev.pcvolkmer.mv64e.model.PatientRecord
import org.slf4j.LoggerFactory
import org.springframework.http.MediaType
import org.springframework.http.ResponseEntity
@@ -52,7 +51,7 @@ class MtbFileRestController(
CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE,
],
)
- fun mtbFile(@RequestBody mtbFile: Mtb): ResponseEntity<Unit> {
+ fun mtbFile(@RequestBody mtbFile: PatientRecord): ResponseEntity<Unit> {
logger.debug("Accepted MTB File (DNPM V2) for processing")
if (requestProcessor.processMtbFile(mtbFile)) {
return ResponseEntity.accepted().build()
@@ -80,7 +79,7 @@ class MtbFileRestControllerAdvice(
@ExceptionHandler(HttpMessageNotReadableException::class)
fun handleMessageNotReadableException(e: Exception): ResponseEntity<Unit> {
logger.error("Error while processing MtbFile", e)
- requestProcessor.processMtbFile(Mtb.builder().build())
+ requestProcessor.processMtbFile(PatientRecord.builder().build())
return ResponseEntity.badRequest().build()
}
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSender.kt b/src/main/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSender.kt
index 8c20b7c..e198952 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSender.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSender.kt
@@ -23,8 +23,8 @@ package dev.dnpm.etl.processor.output
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 dev.pcvolkmer.mv64e.model.MvhMetadata
+import dev.pcvolkmer.mv64e.model.PatientRecord
import org.apache.kafka.clients.producer.ProducerRecord
import org.slf4j.LoggerFactory
import org.springframework.kafka.core.KafkaTemplate
@@ -75,7 +75,7 @@ class KafkaMtbFileSender(
}
override fun send(request: DeleteRequest): MtbFileSender.Response {
- val dummyMtbFile = Mtb.builder().metadata(MvhMetadata()).build()
+ val dummyMtbFile = PatientRecord.builder().metadata(MvhMetadata()).build()
return try {
return retryTemplate.execute<MtbFileSender.Response, Exception> {
@@ -114,7 +114,7 @@ class KafkaMtbFileSender(
private fun key(request: MtbRequest): String =
when (request) {
- is DnpmV2MtbFileRequest -> "{\"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}")
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/output/MtbRequest.kt b/src/main/kotlin/dev/dnpm/etl/processor/output/MtbRequest.kt
index 75401e6..e066d54 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/output/MtbRequest.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/output/MtbRequest.kt
@@ -22,7 +22,7 @@ package dev.dnpm.etl.processor.output
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.RequestId
-import dev.pcvolkmer.mv64e.mtb.Mtb
+import dev.pcvolkmer.mv64e.model.PatientRecord
interface MtbRequest {
val requestId: RequestId
@@ -37,9 +37,9 @@ sealed interface MtbFileRequest<out T> : MtbRequest {
data class DnpmV2MtbFileRequest(
override val requestId: RequestId,
- override val content: Mtb,
-) : MtbFileRequest<Mtb> {
- override fun patientPseudonym(): PatientPseudonym = PatientPseudonym(content.patient.id)
+ override val content: PatientRecord,
+) : MtbFileRequest<PatientRecord> {
+ override fun patientPseudonym(): PatientPseudonym = PatientPseudonym(content.patient!!.id)
}
data class DeleteRequest(
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
index 6615b35..21f3a7f 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
@@ -21,9 +21,9 @@
package dev.dnpm.etl.processor.pseudonym
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 dev.pcvolkmer.mv64e.model.MvhMetadata
+import dev.pcvolkmer.mv64e.model.MvhMetadataModelProjectConsent
+import dev.pcvolkmer.mv64e.model.PatientRecord
import org.apache.commons.codec.digest.DigestUtils
/**
@@ -33,8 +33,8 @@ import org.apache.commons.codec.digest.DigestUtils
* @return The MTB file containing patient pseudonymes
* @since 0.11.0
*/
-infix fun Mtb.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
- val patientPseudonym = pseudonymizeService.patientPseudonym(PatientId(this.patient.id)).value
+infix fun PatientRecord.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
+ val patientPseudonym = pseudonymizeService.patientPseudonym(PatientId(this.patient!!.id)).value
this.episodesOfCare?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym }
this.carePlans?.filterNotNull()?.forEach { carePlan ->
@@ -57,7 +57,7 @@ infix fun Mtb.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
this.diagnoses?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym }
this.guidelineTherapies?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym }
this.guidelineProcedures?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym }
- this.patient.id = patientPseudonym
+ this.patient?.id = patientPseudonym
this.claims?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym }
this.claimResponses?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym }
this.familyMemberHistories?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym }
@@ -116,7 +116,7 @@ infix fun Mtb.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
* @return The MTB file containing rehashed content IDs
* @since 0.11.0
*/
-infix fun Mtb.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
+infix fun PatientRecord.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
val prefix = pseudonymizeService.prefix()
fun anonymize(id: String): String {
@@ -280,25 +280,25 @@ infix fun Mtb.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
}
}
-fun Mtb.ensureMetaDataIsInitialized() {
+fun PatientRecord.ensureMetaDataIsInitialized() {
// init metadata if necessary
if (this.metadata == null) {
val mvhMetadata = MvhMetadata.builder().build()
this.metadata = mvhMetadata
}
- if (this.metadata.researchConsents == null) {
- this.metadata.researchConsents = mutableListOf()
+ if (this.metadata?.researchConsents == null) {
+ this.metadata?.researchConsents = mutableListOf()
}
- if (this.metadata.modelProjectConsent == null) {
- this.metadata.modelProjectConsent = ModelProjectConsent()
- this.metadata.modelProjectConsent.provisions = mutableListOf()
- } else if (this.metadata.modelProjectConsent.provisions != null) {
+ if (this.metadata?.modelProjectConsent == null) {
+ this.metadata?.modelProjectConsent = MvhMetadataModelProjectConsent()
+ this.metadata?.modelProjectConsent?.provisions = mutableListOf()
+ } else if (this.metadata?.modelProjectConsent?.provisions != null) {
// make sure list can be changed
- this.metadata.modelProjectConsent.provisions =
- this.metadata.modelProjectConsent.provisions.toMutableList()
+ this.metadata?.modelProjectConsent?.provisions =
+ this.metadata?.modelProjectConsent?.provisions?.toMutableList()
}
}
-infix fun Mtb.addGenomDeTan(pseudonymizeService: PseudonymizeService) {
- this.metadata?.transferTan = pseudonymizeService.genomDeTan(PatientId(this.patient.id))
+infix fun PatientRecord.addGenomDeTan(pseudonymizeService: PseudonymizeService) {
+ this.metadata?.transferTAN = pseudonymizeService.genomDeTan(PatientId(this.patient!!.id))
}
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt b/src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt
index a95420a..15ccdc4 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt
@@ -28,7 +28,13 @@ import dev.dnpm.etl.processor.consent.ConsentDomain
import dev.dnpm.etl.processor.consent.IConsentService
import dev.dnpm.etl.processor.consent.MtbFileConsentService
import dev.dnpm.etl.processor.pseudonym.ensureMetaDataIsInitialized
-import dev.pcvolkmer.mv64e.mtb.*
+import dev.pcvolkmer.mv64e.model.ConsentProvisionType
+import dev.pcvolkmer.mv64e.model.ModelProjectConsentPurpose
+import dev.pcvolkmer.mv64e.model.MvhMetadata
+import dev.pcvolkmer.mv64e.model.MvhMetadataModelProjectConsentProvisionsInner
+import dev.pcvolkmer.mv64e.model.MvhSubmissionType
+import dev.pcvolkmer.mv64e.model.PatientRecord
+import dev.pcvolkmer.mv64e.model.ResearchConsent
import org.apache.commons.lang3.NotImplementedException
import org.hl7.fhir.r4.model.*
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent
@@ -65,7 +71,7 @@ class ConsentProcessor(
* @param mtbFile File v2 (will be enriched with consent data)
* @return true if consent is given
*/
- fun consentGatedCheckAndTryEmbedding(mtbFile: Mtb): Boolean {
+ fun consentGatedCheckAndTryEmbedding(mtbFile: PatientRecord): Boolean {
mtbFile.ensureMetaDataIsInitialized()
if (consentService is MtbFileConsentService) {
@@ -73,7 +79,7 @@ class ConsentProcessor(
return true
}
- val personIdentifierValue = mtbFile.patient.id
+ val personIdentifierValue = mtbFile.patient!!.id
val requestDate = Date.from(Instant.now(Clock.systemUTC()))
// 1. Broad consent Entry exists?
@@ -129,7 +135,7 @@ class ConsentProcessor(
return false
}
- fun embedBroadConsentResources(mtbFile: Mtb, broadConsent: Bundle) {
+ fun embedBroadConsentResources(mtbFile: PatientRecord, broadConsent: Bundle) {
for (entry in broadConsent.entry) {
val resource = entry.resource
if (resource is Consent) {
@@ -137,12 +143,12 @@ class ConsentProcessor(
// we need another step to back to string, before we convert to object map
val asJsonString = fhirContext.newJsonParser().encodeResourceToString(resource)
try {
- val mapOfJson: MvhMetadata.ResearchConsent? =
+ val mapOfJson: ResearchConsent? =
jsonMapper.readValue(
asJsonString,
- MvhMetadata.ResearchConsent::class.java,
+ ResearchConsent::class.java,
)
- mtbFile.metadata.researchConsents.add(mapOfJson)
+ mtbFile.metadata?.researchConsents?.add(mapOfJson)
} catch (e: JsonProcessingException) {
throw RuntimeException(e)
}
@@ -150,7 +156,7 @@ class ConsentProcessor(
}
}
- fun addGenomeDbProvisions(mtbFile: Mtb, consentGnomeDe: Bundle) {
+ fun addGenomeDbProvisions(mtbFile: PatientRecord, consentGnomeDe: Bundle) {
for (entry in consentGnomeDe.entry) {
val resource = entry.resource
if (resource !is Consent) {
@@ -167,22 +173,22 @@ class ConsentProcessor(
val provisionCode = getProvisionCode(provisionComponent)
if (provisionCode != null) {
try {
- val modelProjectConsentPurpose = ModelProjectConsentPurpose.forValue(provisionCode)
+ val modelProjectConsentPurpose = ModelProjectConsentPurpose.fromValue(provisionCode)
if (ModelProjectConsentPurpose.SEQUENCING == modelProjectConsentPurpose) {
// CONVENTION: wrapping date is date of SEQUENCING consent
- mtbFile.metadata.modelProjectConsent.date = resource.dateTime
+ mtbFile.metadata?.modelProjectConsent?.date = resource.dateTime
}
val provision =
- Provision.builder()
- .type(ConsentProvision.valueOf(provisionComponent.type.name))
+ MvhMetadataModelProjectConsentProvisionsInner.builder()
+ .type(ConsentProvisionType.valueOf(provisionComponent.type.name))
.date(provisionComponent.period.start)
.purpose(modelProjectConsentPurpose)
.build()
- mtbFile.metadata.modelProjectConsent.provisions.add(provision)
- } catch (ioe: IOException) {
+ mtbFile.metadata?.modelProjectConsent?.provisions?.add(provision)
+ } catch (ioe: IllegalArgumentException) {
logger.error(
"Provision code '$provisionCode' is unknown and cannot be mapped.",
ioe.toString(),
@@ -190,8 +196,8 @@ class ConsentProcessor(
}
}
- if (mtbFile.metadata.modelProjectConsent.provisions.isNotEmpty()) {
- mtbFile.metadata.modelProjectConsent.version = gIcsConfigProperties.genomeDeConsentVersion
+ if (mtbFile.metadata?.modelProjectConsent?.provisions?.isNotEmpty() == true) {
+ mtbFile.metadata?.modelProjectConsent?.version = gIcsConfigProperties.genomeDeConsentVersion
}
}
}
@@ -207,15 +213,15 @@ class ConsentProcessor(
return provisionCode
}
- private fun setGenomDeSubmissionType(mtbFile: Mtb) {
+ private fun setGenomDeSubmissionType(mtbFile: PatientRecord) {
if (appConfigProperties.genomDeTestSubmission) {
- mtbFile.metadata.type = MvhSubmissionType.TEST
+ mtbFile.metadata?.type = MvhSubmissionType.TEST
logger.info("genomeDe submission mit TEST")
} else {
- mtbFile.metadata.type =
- when (mtbFile.metadata.type) {
+ mtbFile.metadata?.type =
+ when (mtbFile.metadata?.type) {
null -> MvhSubmissionType.INITIAL
- else -> mtbFile.metadata.type
+ else -> mtbFile.metadata?.type
}
}
}
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt b/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
index 4b7afff..c152d0f 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
@@ -32,8 +32,8 @@ import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
import dev.dnpm.etl.processor.pseudonym.addGenomDeTan
import dev.dnpm.etl.processor.pseudonym.anonymizeContentWith
import dev.dnpm.etl.processor.pseudonym.pseudonymizeWith
-import dev.pcvolkmer.mv64e.mtb.Mtb
-import dev.pcvolkmer.mv64e.mtb.MvhSubmissionType
+import dev.pcvolkmer.mv64e.model.MvhSubmissionType
+import dev.pcvolkmer.mv64e.model.PatientRecord
import org.apache.commons.codec.binary.Base32
import org.apache.commons.codec.digest.DigestUtils
import org.slf4j.Logger
@@ -58,11 +58,11 @@ class RequestProcessor(
private var logger: Logger = LoggerFactory.getLogger("RequestProcessor")
- fun processMtbFile(mtbFile: Mtb): Boolean {
+ fun processMtbFile(mtbFile: PatientRecord): Boolean {
return processMtbFile(mtbFile, randomRequestId())
}
- fun processMtbFile(mtbFile: Mtb, requestId: RequestId): Boolean {
+ fun processMtbFile(mtbFile: PatientRecord, requestId: RequestId): Boolean {
val isConsentOk =
consentProcessor != null && consentProcessor.consentGatedCheckAndTryEmbedding(mtbFile) ||
consentProcessor == null
@@ -127,7 +127,7 @@ class RequestProcessor(
RequestType.MTB_FILE,
submissionType,
RequestStatus.BLOCKED_INITIAL,
- Tan(request.content.metadata?.transferTan.orEmpty())
+ Tan(request.content.metadata?.transferTAN.orEmpty())
)
)
// Exit - no further processing
@@ -164,7 +164,7 @@ class RequestProcessor(
RequestType.MTB_FILE,
submissionType,
RequestStatus.UNKNOWN,
- Tan(request.content.metadata?.transferTan.orEmpty()),
+ Tan(request.content.metadata?.transferTAN.orEmpty()),
)
)
@@ -229,7 +229,7 @@ class RequestProcessor(
val patientPseudonym =
when (pseudonymizedMtbFileRequest) {
is DnpmV2MtbFileRequest ->
- PatientPseudonym(pseudonymizedMtbFileRequest.content.patient.id)
+ PatientPseudonym(pseudonymizedMtbFileRequest.content.patient!!.id)
}
val lastMtbFileRequestForPatient =
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/services/TransformationService.kt b/src/main/kotlin/dev/dnpm/etl/processor/services/TransformationService.kt
index 755e6b3..d6318ce 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/services/TransformationService.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/services/TransformationService.kt
@@ -22,16 +22,16 @@ package dev.dnpm.etl.processor.services
import com.jayway.jsonpath.JsonPath
import com.jayway.jsonpath.PathNotFoundException
-import dev.pcvolkmer.mv64e.mtb.Mtb
+import dev.pcvolkmer.mv64e.model.PatientRecord
import tools.jackson.databind.json.JsonMapper
class TransformationService(
private val jsonMapper: JsonMapper,
private val transformations: List<Transformation>,
) {
- fun transform(mtbFile: Mtb): Mtb {
+ fun transform(mtbFile: PatientRecord): PatientRecord {
val json = transform(jsonMapper.writeValueAsString(mtbFile))
- return jsonMapper.readValue(json, Mtb::class.java)
+ return jsonMapper.readValue(json, PatientRecord::class.java)
}
private fun transform(content: String): String {
generated by cgit v1.2.3 (git 2.25.1) at 2026-06-03 20:44:43 +0000