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Code Issues Releases Activity

refactor: add types for patient id and pseudonym

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This commit is contained in:
Paul-Christian Volkmer
2024-07-15 10:27:51 +02:00
parent c949ec07e5
commit c8f6e6efc8
25 changed files with 216 additions and 180 deletions
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6
src/main/kotlin/dev/dnpm/etl/processor/input/KafkaInputListener.kt
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@ -22,6 +22,7 @@ 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.PatientId
import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.services.RequestProcessor
import org.apache.kafka.clients.consumer.ConsumerRecord
@ -36,6 +37,7 @@ class KafkaInputListener(
override fun onMessage(data: ConsumerRecord<String, String>) {
val mtbFile = objectMapper.readValue(data.value(), MtbFile::class.java)
val patientId = PatientId(mtbFile.patient.id)
val firstRequestIdHeader = data.headers().headers("requestId")?.firstOrNull()
val requestId = if (null != firstRequestIdHeader) {
RequestId(String(firstRequestIdHeader.value()))
@ -53,9 +55,9 @@ class KafkaInputListener(
} else {
logger.debug("Accepted MTB File and process deletion")
if (requestId.isBlank()) {
requestProcessor.processDeletion(mtbFile.patient.id)
requestProcessor.processDeletion(patientId)
} else {
requestProcessor.processDeletion(mtbFile.patient.id, requestId)
requestProcessor.processDeletion(patientId, requestId)
}
}
}

6
src/main/kotlin/dev/dnpm/etl/processor/input/MtbFileRestController.kt
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@ -21,6 +21,7 @@ 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.PatientId
import dev.dnpm.etl.processor.services.RequestProcessor
import org.slf4j.LoggerFactory
import org.springframework.http.ResponseEntity
@ -46,7 +47,8 @@ class MtbFileRestController(
requestProcessor.processMtbFile(mtbFile)
} else {
logger.debug("Accepted MTB File and process deletion")
requestProcessor.processDeletion(mtbFile.patient.id)
val patientId = PatientId(mtbFile.patient.id)
requestProcessor.processDeletion(patientId)
}
return ResponseEntity.accepted().build()
}
@ -54,7 +56,7 @@ class MtbFileRestController(
@DeleteMapping(path = ["{patientId}"])
fun deleteData(@PathVariable patientId: String): ResponseEntity<Void> {
logger.debug("Accepted patient ID to process deletion")
requestProcessor.processDeletion(patientId)
requestProcessor.processDeletion(PatientId(patientId))
return ResponseEntity.accepted().build()
}

20
src/main/kotlin/dev/dnpm/etl/processor/monitoring/Request.kt
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@ -19,9 +19,7 @@
package dev.dnpm.etl.processor.monitoring
import dev.dnpm.etl.processor.Fingerprint
import dev.dnpm.etl.processor.randomRequestId
import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.*
import org.springframework.data.annotation.Id
import org.springframework.data.domain.Page
import org.springframework.data.domain.Pageable
@ -38,8 +36,8 @@ import java.util.*
data class Request(
@Id val id: Long? = null,
val uuid: RequestId = randomRequestId(),
val patientId: String,
val pid: String,
val patientId: PatientPseudonym,
val pid: PatientId,
@Column("fingerprint")
val fingerprint: Fingerprint,
val type: RequestType,
@ -49,8 +47,8 @@ data class Request(
) {
constructor(
uuid: RequestId,
patientId: String,
pid: String,
patientId: PatientPseudonym,
pid: PatientId,
fingerprint: Fingerprint,
type: RequestType,
status: RequestStatus
@ -59,8 +57,8 @@ data class Request(
constructor(
uuid: RequestId,
patientId: String,
pid: String,
patientId: PatientPseudonym,
pid: PatientId,
fingerprint: Fingerprint,
type: RequestType,
status: RequestStatus,
@ -83,11 +81,11 @@ data class CountedState(
interface RequestRepository : CrudRepository<Request, Long>, PagingAndSortingRepository<Request, Long> {
fun findAllByPatientIdOrderByProcessedAtDesc(patientId: String): List<Request>
fun findAllByPatientIdOrderByProcessedAtDesc(patientId: PatientPseudonym): List<Request>
fun findByUuidEquals(uuid: RequestId): Optional<Request>
fun findRequestByPatientId(patientId: String, pageable: Pageable): Page<Request>
fun findRequestByPatientId(patientId: PatientPseudonym, pageable: Pageable): Page<Request>
@Query("SELECT count(*) AS count, status FROM request WHERE type = 'MTB_FILE' GROUP BY status ORDER BY status, count DESC;")
fun countStates(): List<CountedState>

4
src/main/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSender.kt
View File

@ -63,7 +63,7 @@ class KafkaMtbFileSender(
val dummyMtbFile = MtbFile.builder()
.withConsent(
Consent.builder()
.withPatient(request.patientId)
.withPatient(request.patientId.value)
.withStatus(Consent.Status.REJECTED)
.build()
)
@ -99,7 +99,7 @@ class KafkaMtbFileSender(
}
private fun key(request: MtbFileSender.DeleteRequest): String {
return "{\"pid\": \"${request.patientId}\"}"
return "{\"pid\": \"${request.patientId.value}\"}"
}
data class Data(val requestId: RequestId, val content: MtbFile)

3
src/main/kotlin/dev/dnpm/etl/processor/output/MtbFileSender.kt
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@ -20,6 +20,7 @@
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.dnpm.etl.processor.monitoring.RequestStatus
import org.springframework.http.HttpStatusCode
@ -35,7 +36,7 @@ interface MtbFileSender {
data class MtbFileRequest(val requestId: RequestId, val mtbFile: MtbFile)
data class DeleteRequest(val requestId: RequestId, val patientId: String)
data class DeleteRequest(val requestId: RequestId, val patientId: PatientPseudonym)
}

8
src/main/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeService.kt
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@ -19,6 +19,8 @@
package dev.dnpm.etl.processor.pseudonym
import dev.dnpm.etl.processor.PatientId
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.config.PseudonymizeConfigProperties
class PseudonymizeService(
@ -26,10 +28,10 @@ class PseudonymizeService(
private val configProperties: PseudonymizeConfigProperties
) {
fun patientPseudonym(patientId: String): String {
fun patientPseudonym(patientId: PatientId): PatientPseudonym {
return when (generator) {
is GpasPseudonymGenerator -> generator.generate(patientId)
else -> "${configProperties.prefix}_${generator.generate(patientId)}"
is GpasPseudonymGenerator -> PatientPseudonym(generator.generate(patientId.value))
else -> PatientPseudonym("${configProperties.prefix}_${generator.generate(patientId.value)}")
}
}

3
src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
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@ -20,6 +20,7 @@
package dev.dnpm.etl.processor.pseudonym
import de.ukw.ccc.bwhc.dto.MtbFile
import dev.dnpm.etl.processor.PatientId
import org.apache.commons.codec.digest.DigestUtils
/** Replaces patient ID with generated patient pseudonym
@ -29,7 +30,7 @@ import org.apache.commons.codec.digest.DigestUtils
* @return The MTB file containing patient pseudonymes
*/
infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
val patientPseudonym = pseudonymizeService.patientPseudonym(this.patient.id)
val patientPseudonym = pseudonymizeService.patientPseudonym(PatientId(this.patient.id)).value
this.episode?.patient = patientPseudonym
this.carePlans?.forEach { it.patient = patientPseudonym }

24
src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
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@ -21,9 +21,7 @@ package dev.dnpm.etl.processor.services
import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.MtbFile
import dev.dnpm.etl.processor.Fingerprint
import dev.dnpm.etl.processor.randomRequestId
import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.*
import dev.dnpm.etl.processor.config.AppConfigProperties
import dev.dnpm.etl.processor.monitoring.Report
import dev.dnpm.etl.processor.monitoring.Request
@ -56,17 +54,19 @@ class RequestProcessor(
}
fun processMtbFile(mtbFile: MtbFile, requestId: RequestId) {
val pid = mtbFile.patient.id
val pid = PatientId(mtbFile.patient.id)
mtbFile pseudonymizeWith pseudonymizeService
mtbFile anonymizeContentWith pseudonymizeService
val request = MtbFileSender.MtbFileRequest(requestId, transformationService.transform(mtbFile))
val patientPseudonym = PatientPseudonym(request.mtbFile.patient.id)
requestService.save(
Request(
requestId,
request.mtbFile.patient.id,
patientPseudonym,
pid,
fingerprint(request.mtbFile),
RequestType.MTB_FILE,
@ -101,20 +101,22 @@ class RequestProcessor(
}
private fun isDuplication(pseudonymizedMtbFile: MtbFile): Boolean {
val patientPseudonym = PatientPseudonym(pseudonymizedMtbFile.patient.id)
val lastMtbFileRequestForPatient =
requestService.lastMtbFileRequestForPatientPseudonym(pseudonymizedMtbFile.patient.id)
val isLastRequestDeletion = requestService.isLastRequestWithKnownStatusDeletion(pseudonymizedMtbFile.patient.id)
requestService.lastMtbFileRequestForPatientPseudonym(patientPseudonym)
val isLastRequestDeletion = requestService.isLastRequestWithKnownStatusDeletion(patientPseudonym)
return null != lastMtbFileRequestForPatient
&& !isLastRequestDeletion
&& lastMtbFileRequestForPatient.fingerprint == fingerprint(pseudonymizedMtbFile)
}
fun processDeletion(patientId: String) {
fun processDeletion(patientId: PatientId) {
processDeletion(patientId, randomRequestId())
}
fun processDeletion(patientId: String, requestId: RequestId) {
fun processDeletion(patientId: PatientId, requestId: RequestId) {
try {
val patientPseudonym = pseudonymizeService.patientPseudonym(patientId)
@ -123,7 +125,7 @@ class RequestProcessor(
requestId,
patientPseudonym,
patientId,
fingerprint(patientPseudonym),
fingerprint(patientPseudonym.value),
RequestType.DELETE,
RequestStatus.UNKNOWN
)
@ -147,7 +149,7 @@ class RequestProcessor(
requestService.save(
Request(
uuid = requestId,
patientId = "???",
patientId = emptyPatientPseudonym(),
pid = patientId,
fingerprint = Fingerprint.empty(),
status = RequestStatus.ERROR,

9
src/main/kotlin/dev/dnpm/etl/processor/services/RequestService.kt
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@ -19,6 +19,7 @@
package dev.dnpm.etl.processor.services
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.monitoring.*
import org.springframework.data.domain.Page
@ -40,15 +41,15 @@ class RequestService(
fun findByUuid(uuid: RequestId): Optional<Request> =
requestRepository.findByUuidEquals(uuid)
fun findRequestByPatientId(patientId: String, pageable: Pageable): Page<Request> = requestRepository.findRequestByPatientId(patientId, pageable)
fun findRequestByPatientId(patientId: PatientPseudonym, pageable: Pageable): Page<Request> = requestRepository.findRequestByPatientId(patientId, pageable)
fun allRequestsByPatientPseudonym(patientPseudonym: String) = requestRepository
fun allRequestsByPatientPseudonym(patientPseudonym: PatientPseudonym) = requestRepository
.findAllByPatientIdOrderByProcessedAtDesc(patientPseudonym)
fun lastMtbFileRequestForPatientPseudonym(patientPseudonym: String) =
fun lastMtbFileRequestForPatientPseudonym(patientPseudonym: PatientPseudonym) =
Companion.lastMtbFileRequestForPatientPseudonym(allRequestsByPatientPseudonym(patientPseudonym))
fun isLastRequestWithKnownStatusDeletion(patientPseudonym: String) =
fun isLastRequestWithKnownStatusDeletion(patientPseudonym: PatientPseudonym) =
Companion.isLastRequestWithKnownStatusDeletion(allRequestsByPatientPseudonym(patientPseudonym))
fun countStates(): Iterable<CountedState> = requestRepository.countStates()

10
src/main/kotlin/dev/dnpm/etl/processor/types.kt
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@ -38,4 +38,12 @@ value class RequestId(val value: String) {
}
fun randomRequestId() = RequestId(UUID.randomUUID().toString())
fun randomRequestId() = RequestId(UUID.randomUUID().toString())
@JvmInline
value class PatientId(val value: String)
@JvmInline
value class PatientPseudonym(val value: String)
fun emptyPatientPseudonym() = PatientPseudonym("")

3
src/main/kotlin/dev/dnpm/etl/processor/web/HomeController.kt
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@ -20,6 +20,7 @@
package dev.dnpm.etl.processor.web
import dev.dnpm.etl.processor.NotFoundException
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.monitoring.ReportService
import dev.dnpm.etl.processor.services.RequestService
@ -56,7 +57,7 @@ class HomeController(
@PageableDefault(page = 0, size = 20, sort = ["processedAt"], direction = Sort.Direction.DESC) pageable: Pageable,
model: Model
): String {
val requests = requestService.findRequestByPatientId(patientId, pageable)
val requests = requestService.findRequestByPatientId(PatientPseudonym(patientId), pageable)
model.addAttribute("patientId", patientId)
model.addAttribute("requests", requests)