diff options
| author | Paul-Christian Volkmer | 2025-08-12 23:11:50 +0200 |
|---|---|---|
| committer | GitHub | 2025-08-12 23:11:50 +0200 |
| commit | 2e881578937ee39bab3cacff9ee09328658341c2 (patch) | |
| tree | 74e408d8c943ff0ba54df3ff6d4d3bb63a9d236a | |
| parent | bf898e5c25da311d90c0d30b0c5ebfd672781d92 (diff) | |
refactor: remove obsolete bwHC data model V1.0 (#129)
27 files changed, 286 insertions, 1596 deletions
@@ -1,6 +1,6 @@ # ETL-Processor for DNPM:DIP [](https://github.com/pcvolkmer/etl-processor/actions/workflows/test.yml) -Diese Anwendung versendet ein bwHC-MTB-File im bwHC-Datenmodell 1.0 an DNPM:DIP und pseudonymisiert +Diese Anwendung versendet ein MTB-File im DNPM-Datenmodell 2.1 an DNPM:DIP und pseudonymisiert die Patienten-ID. ## Einordnung innerhalb einer DNPM-ETL-Strecke @@ -8,7 +8,7 @@ die Patienten-ID. Diese Anwendung erlaubt das Entgegennehmen von HTTP/REST-Anfragen aus dem Onkostar-Plugin * *[onkostar-plugin-dnpmexport](https://github.com/CCC-MF/onkostar-plugin-dnpmexport)**. -Der Inhalt einer Anfrage, wenn ein bwHC-MTBFile, wird pseudonymisiert und auf Duplikate geprüft. +Der Inhalt einer Anfrage, wenn ein MTB-File, wird pseudonymisiert und auf Duplikate geprüft. Duplikate werden verworfen, Änderungen werden weitergeleitet. Löschanfragen werden immer als Löschanfrage an DNPM:DIP weitergeleitet. @@ -72,24 +72,9 @@ Siehe hierzu auch: https://github.com/CCC-MF/kafka-to-bwhc ## Konfiguration -### 🔥 Wichtige Änderungen in Version 0.10 +### 🔥 Wichtige Änderungen in Version 0.11 -Ab Version 0.10 wird [DNPM:DIP](https://github.com/dnpm-dip) unterstützt und als Standardendpunkt -verwendet. -Soll noch das alte bwHC-Backend verwendet werden, so ist die Umgebungsvariable `APP_REST_IS_BWHC` -auf `true` zu setzen. - -### 🔥 Breaking Changes nach Version 0.10 - -In Versionen des ETL-Processors **nach Version 0.10** werden die folgenden Konfigurationsoptionen -entfernt: - -* `APP_KAFKA_TOPIC`: Nutzen Sie nun die Konfigurationsoption `APP_KAFKA_OUTPUT_TOPIC` -* `APP_KAFKA_RESPONSE_TOPIC`: Nutzen Sie nun die Konfigurationsoption - `APP_KAFKA_OUTPUT_RESPONSE_TOPIC` - -Der Pfad zum Versenden von MTB-Daten ist nun offiziell `/mtb`. -In Versionen **nach Version 0.10** wird die Unterstützung des Pfads `/mtbfile` entfernt. +Ab Version 0.11 wird ausschließlich [DNPM:DIP](https://github.com/dnpm-dip) unterstützt. ### Pseudonymisierung der Patienten-ID @@ -316,18 +301,15 @@ Werden sowohl REST als auch Kafka-Endpunkt konfiguriert, wird nur der REST-Endpu #### REST -Folgende Umgebungsvariablen müssen gesetzt sein, damit ein bwHC-MTB-File an DNPM:DIP gesendet wird: +Folgende Umgebungsvariablen müssen gesetzt sein, damit ein MTB-File an DNPM:DIP gesendet wird: -* `APP_REST_URI`: URI der zu benutzenden API der Backend-Instanz. Zum Beispiel: - * `http://localhost:9000/bwhc/etl/api` für **bwHC Backend** - * `http://localhost:9000/api` für **dnpm:dip** +* `APP_REST_URI`: URI der zu benutzenden API der Backend-Instanz. Zum Beispiel `http://localhost:9000/api` * `APP_REST_USERNAME`: Basic-Auth-Benutzername für den REST-Endpunkt * `APP_REST_PASSWORD`: Basic-Auth-Passwort für den REST-Endpunkt -* `APP_REST_IS_BWHC`: `true` für **bwHC Backend**, weglassen oder `false` für **dnpm:dip** #### Kafka-Topics -Folgende Umgebungsvariablen müssen gesetzt sein, damit ein bwHC-MTB-File an ein Kafka-Topic +Folgende Umgebungsvariablen müssen gesetzt sein, damit ein MTB-File an ein Kafka-Topic übermittelt wird: * `APP_KAFKA_OUTPUT_TOPIC`: Zu verwendendes Topic zum Versenden von Anfragen. @@ -402,19 +384,7 @@ verwenden möchten. ### Antworten und Statusauswertung -Anfragen an das bwHC-Backend aus Versionen bis 0.9.x wurden wie folgt behandelt: - -| HTTP-Response | Status | -|----------------|-----------| -| `HTTP 200` | `SUCCESS` | -| `HTTP 201` | `WARNING` | -| `HTTP 400-...` | `ERROR` | - -Dies konnte dazu führen, dass zwar mit einem `HTTP 201` geantwortet wurde, aber dennoch in der -Issue-Liste die -Severity `error` aufgetaucht ist. - -Ab Version 0.10 wird die Issue-Liste der Antwort verwendet und die darion enthaltene höchste +Seit Version 0.10 wird die Issue-Liste der Antwort verwendet und die darion enthaltene höchste Severity-Stufe als Ergebnis verwendet. | Höchste Severity | Status | diff --git a/build.gradle.kts b/build.gradle.kts index f451edf..d9f01be 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -16,7 +16,6 @@ group = "dev.dnpm" version = "0.11.0-SNAPSHOT" var versions = mapOf( - "bwhc-dto-java" to "0.4.0", "mtb-dto" to "0.1.0-SNAPSHOT", "hapi-fhir" to "7.6.1", "mockito-kotlin" to "5.4.0", @@ -81,7 +80,6 @@ dependencies { implementation("org.flywaydb:flyway-mysql") implementation("commons-codec:commons-codec") implementation("io.projectreactor.kotlin:reactor-kotlin-extensions") - implementation("de.ukw.ccc:bwhc-dto-java:${versions["bwhc-dto-java"]}") implementation("dev.pcvolkmer.mv64e:mtb-dto:${versions["mtb-dto"]}") { isChanging = true } implementation("ca.uhn.hapi.fhir:hapi-fhir-base:${versions["hapi-fhir"]}") implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${versions["hapi-fhir"]}") diff --git a/src/integrationTest/kotlin/dev/dnpm/etl/processor/EtlProcessorApplicationTests.kt b/src/integrationTest/kotlin/dev/dnpm/etl/processor/EtlProcessorApplicationTests.kt index 7e48e62..130fea7 100644 --- a/src/integrationTest/kotlin/dev/dnpm/etl/processor/EtlProcessorApplicationTests.kt +++ b/src/integrationTest/kotlin/dev/dnpm/etl/processor/EtlProcessorApplicationTests.kt @@ -20,11 +20,11 @@ package dev.dnpm.etl.processor import com.fasterxml.jackson.databind.ObjectMapper -import de.ukw.ccc.bwhc.dto.* import dev.dnpm.etl.processor.monitoring.RequestRepository import dev.dnpm.etl.processor.monitoring.RequestStatus -import dev.dnpm.etl.processor.output.BwhcV1MtbFileRequest +import dev.dnpm.etl.processor.output.DnpmV2MtbFileRequest import dev.dnpm.etl.processor.output.MtbFileSender +import dev.pcvolkmer.mv64e.mtb.* import org.assertj.core.api.Assertions.assertThat import org.junit.jupiter.api.BeforeEach import org.junit.jupiter.api.Nested @@ -69,7 +69,7 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() { properties = [ "app.pseudonymize.generator=buildin", "app.consent.service=none", - "app.transformations[0].path=diagnoses[*].icd10.version", + "app.transformations[0].path=diagnoses[*].code.version", "app.transformations[0].from=2013", "app.transformations[0].to=2014", ] @@ -94,36 +94,21 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() { fun mtbFileIsTransformed() { doAnswer { MtbFileSender.Response(RequestStatus.SUCCESS) - }.whenever(mtbFileSender).send(any<BwhcV1MtbFileRequest>()) + }.whenever(mtbFileSender).send(any<DnpmV2MtbFileRequest>()) - val mtbFile = MtbFile.builder() - .withPatient( + val mtbFile = Mtb.builder() + .patient( Patient.builder() - .withId("TEST_12345678") - .withBirthDate("2000-08-08") - .withGender(Patient.Gender.MALE) + .id("TEST_12345678") .build() ) - .withConsent( - Consent.builder() - .withId("1") - .withStatus(Consent.Status.ACTIVE) - .withPatient("TEST_12345678") - .build() - ) - .withEpisode( - Episode.builder() - .withId("1") - .withPatient("TEST_12345678") - .withPeriod(PeriodStart("2023-08-08")) - .build() - ) - .withDiagnoses( + .diagnoses( listOf( - Diagnosis.builder() - .withId("1234") - .withIcd10(Icd10.builder().withCode("F79.9").withVersion("2013").build()) - .build() + MtbDiagnosis.builder() + .id("1234") + .patient(Reference.builder().id("TEST_12345678").build()) + .code(Coding.builder().code("F79.9").version("2013").build()) + .build(), ) ) .build() @@ -137,10 +122,10 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() { } } - val captor = argumentCaptor<BwhcV1MtbFileRequest>() + val captor = argumentCaptor<DnpmV2MtbFileRequest>() verify(mtbFileSender).send(captor.capture()) assertThat(captor.firstValue.content.diagnoses).hasSize(1).allMatch { diagnosis -> - diagnosis.icd10.version == "2014" + diagnosis.code.version == "2014" } } } diff --git a/src/integrationTest/kotlin/dev/dnpm/etl/processor/input/MtbFileRestControllerTest.kt b/src/integrationTest/kotlin/dev/dnpm/etl/processor/input/MtbFileRestControllerTest.kt index 8aa8ba0..78bdc8f 100644 --- a/src/integrationTest/kotlin/dev/dnpm/etl/processor/input/MtbFileRestControllerTest.kt +++ b/src/integrationTest/kotlin/dev/dnpm/etl/processor/input/MtbFileRestControllerTest.kt @@ -20,7 +20,6 @@ package dev.dnpm.etl.processor.input import com.fasterxml.jackson.databind.ObjectMapper -import de.ukw.ccc.bwhc.dto.* import dev.dnpm.etl.processor.anyValueClass import dev.dnpm.etl.processor.config.AppSecurityConfiguration import dev.dnpm.etl.processor.consent.ConsentByMtbFile @@ -29,6 +28,7 @@ import dev.dnpm.etl.processor.consent.IGetConsent import dev.dnpm.etl.processor.security.TokenRepository import dev.dnpm.etl.processor.security.UserRoleRepository import dev.dnpm.etl.processor.services.RequestProcessor +import dev.pcvolkmer.mv64e.mtb.* import org.junit.jupiter.api.BeforeEach import org.junit.jupiter.api.Nested import org.junit.jupiter.api.Test @@ -48,6 +48,8 @@ import org.springframework.test.context.junit.jupiter.SpringExtension import org.springframework.test.web.servlet.MockMvc import org.springframework.test.web.servlet.delete import org.springframework.test.web.servlet.post +import java.time.Instant +import java.util.* @WebMvcTest(controllers = [MtbFileRestController::class]) @ExtendWith(value = [MockitoExtension::class, SpringExtension::class]) @@ -93,7 +95,7 @@ class MtbFileRestControllerTest { status { isAccepted() } } - verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>()) + verify(requestProcessor, times(1)).processMtbFile(any<Mtb>()) } @Test @@ -106,7 +108,7 @@ class MtbFileRestControllerTest { status { isAccepted() } } - verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>()) + verify(requestProcessor, times(1)).processMtbFile(any<Mtb>()) } @Test @@ -119,7 +121,7 @@ class MtbFileRestControllerTest { status { isUnauthorized() } } - verify(requestProcessor, never()).processMtbFile(any<MtbFile>()) + verify(requestProcessor, never()).processMtbFile(any<Mtb>()) } @Test @@ -132,7 +134,7 @@ class MtbFileRestControllerTest { status { isForbidden() } } - verify(requestProcessor, never()).processMtbFile(any<MtbFile>()) + verify(requestProcessor, never()).processMtbFile(any<Mtb>()) } @Test @@ -180,7 +182,7 @@ class MtbFileRestControllerTest { status { isAccepted() } } - verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>()) + verify(requestProcessor, times(1)).processMtbFile(any<Mtb>()) } @Test @@ -193,33 +195,26 @@ class MtbFileRestControllerTest { status { isAccepted() } } - verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>()) + verify(requestProcessor, times(1)).processMtbFile(any<Mtb>()) } } companion object { - val mtbFile: MtbFile = MtbFile.builder() - .withPatient( + val mtbFile = Mtb.builder() + .patient( Patient.builder() - .withId("PID") - .withBirthDate("2000-08-08") - .withGender(Patient.Gender.MALE) + .id("PID") .build() ) - .withConsent( - Consent.builder() - .withId("1") - .withStatus(Consent.Status.ACTIVE) - .withPatient("PID") - .build() - ) - .withEpisode( - Episode.builder() - .withId("1") - .withPatient("PID") - .withPeriod(PeriodStart("2023-08-08")) - .build() + .episodesOfCare( + listOf( + MtbEpisodeOfCare.builder() + .id("1") + .patient(Reference.builder().id("PID").build()) + .period(PeriodDate.builder().start(Date.from(Instant.parse("2023-08-08T02:00:00.00Z"))).build()) + .build() + ) ) .build() diff --git a/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt b/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt index 207785e..1f3c650 100644 --- 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" diff --git a/src/main/kotlin/dev/dnpm/etl/processor/config/AppRestConfiguration.kt b/src/main/kotlin/dev/dnpm/etl/processor/config/AppRestConfiguration.kt index 1a18924..62c25bc 100644 --- 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) } 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 415a68f..47615be 100644 --- 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") - } - } 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 ca64fc9..d00ad25 100644 --- 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) - } - } diff --git a/src/main/kotlin/dev/dnpm/etl/processor/monitoring/ConnectionCheckService.kt b/src/main/kotlin/dev/dnpm/etl/processor/monitoring/ConnectionCheckService.kt index fe02b69..37cd5de 100644 --- 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 } -}
\ No newline at end of file +} 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 1f2743e..8be0a1c 100644 --- 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}") 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 9b500f0..7512200 100644 --- 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 diff --git a/src/main/kotlin/dev/dnpm/etl/processor/output/RestBwhcMtbFileSender.kt b/src/main/kotlin/dev/dnpm/etl/processor/output/RestBwhcMtbFileSender.kt deleted file mode 100644 index fbe6d0d..0000000 --- a/src/main/kotlin/dev/dnpm/etl/processor/output/RestBwhcMtbFileSender.kt +++ /dev/null @@ -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() - } - -}
\ No newline at end of file diff --git a/src/main/kotlin/dev/dnpm/etl/processor/output/RestMtbFileSender.kt b/src/main/kotlin/dev/dnpm/etl/processor/output/RestMtbFileSender.kt index 78222b2..ec6ff85 100644 --- 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 } 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 50d5b20..28a7d3c 100644 --- a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt +++ b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt @@ -19,7 +19,6 @@ 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 @@ -28,210 +27,6 @@ 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 * * @param pseudonymizeService The pseudonymizeService to be used @@ -353,4 +148,4 @@ fun Mtb.ensureMetaDataIsInitialized() { infix fun Mtb.addGenomDeTan(pseudonymizeService: PseudonymizeService) { this.metadata.transferTan = pseudonymizeService.genomDeTan(PatientId(this.patient.id)) -}
\ No newline at end of file +} 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 f2e8390..07d8a8d 100644 --- 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)) } } 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 9447a84..8f1081e 100644 --- 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)) diff --git a/src/main/resources/application-dev.yml b/src/main/resources/application-dev.yml index 895f026..ed57ec8 100644 --- a/src/main/resources/application-dev.yml +++ b/src/main/resources/application-dev.yml @@ -20,7 +20,7 @@ spring: app: rest: - uri: http://localhost:9000/bwhc/etl/api + uri: http://localhost/api #kafka: # topic: test # response-topic: test_response diff --git a/src/test/kotlin/dev/dnpm/etl/processor/input/KafkaInputListenerTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/input/KafkaInputListenerTest.kt index fbcfb3f..1239cdf 100644 --- a/src/test/kotlin/dev/dnpm/etl/processor/input/KafkaInputListenerTest.kt +++ b/src/test/kotlin/dev/dnpm/etl/processor/input/KafkaInputListenerTest.kt @@ -20,12 +20,10 @@ 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 de.ukw.ccc.bwhc.dto.Patient import dev.dnpm.etl.processor.consent.TtpConsentStatus import dev.dnpm.etl.processor.CustomMediaType import dev.dnpm.etl.processor.services.RequestProcessor +import dev.pcvolkmer.mv64e.mtb.* import org.apache.kafka.clients.consumer.ConsumerRecord import org.apache.kafka.common.header.internals.RecordHeader import org.apache.kafka.common.header.internals.RecordHeaders @@ -57,9 +55,20 @@ class KafkaInputListenerTest { @Test fun shouldProcessMtbFileRequest() { - val mtbFile = MtbFile.builder() - .withPatient(Patient.builder().withId("DUMMY_12345678").build()) - .withConsent(Consent.builder().withStatus(Consent.Status.ACTIVE).build()) + val mtbFile = Mtb.builder() + .patient(Patient.builder().id("DUMMY_12345678").build()) + .metadata( + MvhMetadata + .builder() + .modelProjectConsent( + ModelProjectConsent + .builder() + .provisions( + listOf(Provision.builder().type(ConsentProvision.PERMIT).purpose(ModelProjectConsentPurpose.SEQUENCING).build()) + ).build() + ) + .build() + ) .build() kafkaInputListener.onMessage( @@ -72,14 +81,25 @@ class KafkaInputListenerTest { ) ) - verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>()) + verify(requestProcessor, times(1)).processMtbFile(any<Mtb>()) } @Test fun shouldProcessDeleteRequest() { - val mtbFile = MtbFile.builder() - .withPatient(Patient.builder().withId("DUMMY_12345678").build()) - .withConsent(Consent.builder().withStatus(Consent.Status.REJECTED).build()) + val mtbFile = Mtb.builder() + .patient(Patient.builder().id("DUMMY_12345678").build()) + .metadata( + MvhMetadata + .builder() + .modelProjectConsent( + ModelProjectConsent + .builder() + .provisions( + listOf(Provision.builder().type(ConsentProvision.DENY).purpose(ModelProjectConsentPurpose.SEQUENCING).build()) + ).build() + ) + .build() + ) .build() kafkaInputListener.onMessage( @@ -100,9 +120,20 @@ class KafkaInputListenerTest { @Test fun shouldProcessMtbFileRequestWithExistingRequestId() { - val mtbFile = MtbFile.builder() - .withPatient(Patient.builder().withId("DUMMY_12345678").build()) - .withConsent(Consent.builder().withStatus(Consent.Status.ACTIVE).build()) + val mtbFile = Mtb.builder() + .patient(Patient.builder().id("DUMMY_12345678").build()) + .metadata( + MvhMetadata + .builder() + .modelProjectConsent( + ModelProjectConsent + .builder() + .provisions( + listOf(Provision.builder().type(ConsentProvision.PERMIT).purpose(ModelProjectConsentPurpose.SEQUENCING).build()) + ).build() + ) + .build() + ) .build() val headers = RecordHeaders(listOf(RecordHeader("requestId", UUID.randomUUID().toString().toByteArray()))) @@ -122,14 +153,25 @@ class KafkaInputListenerTest { ) ) - verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>(), anyValueClass()) + verify(requestProcessor, times(1)).processMtbFile(any<Mtb>(), anyValueClass()) } @Test fun shouldProcessDeleteRequestWithExistingRequestId() { - val mtbFile = MtbFile.builder() - .withPatient(Patient.builder().withId("DUMMY_12345678").build()) - .withConsent(Consent.builder().withStatus(Consent.Status.REJECTED).build()) + val mtbFile = Mtb.builder() + .patient(Patient.builder().id("DUMMY_12345678").build()) + .metadata( + MvhMetadata + .builder() + .modelProjectConsent( + ModelProjectConsent + .builder() + .provisions( + listOf(Provision.builder().type(ConsentProvision.DENY).purpose(ModelProjectConsentPurpose.SEQUENCING).build()) + ).build() + ) + .build() + ) .build() val headers = RecordHeaders(listOf(RecordHeader("requestId", UUID.randomUUID().toString().toByteArray()))) @@ -148,15 +190,29 @@ class KafkaInputListenerTest { Optional.empty() ) ) - verify(requestProcessor, times(1)).processDeletion(anyValueClass(), anyValueClass(), eq( - TtpConsentStatus.UNKNOWN_CHECK_FILE)) + verify(requestProcessor, times(1)).processDeletion( + anyValueClass(), anyValueClass(), eq( + TtpConsentStatus.UNKNOWN_CHECK_FILE + ) + ) } @Test fun shouldNotProcessDnpmV2Request() { - val mtbFile = MtbFile.builder() - .withPatient(Patient.builder().withId("DUMMY_12345678").build()) - .withConsent(Consent.builder().withStatus(Consent.Status.REJECTED).build()) + val mtbFile = Mtb.builder() + .patient(Patient.builder().id("DUMMY_12345678").build()) + .metadata( + MvhMetadata + .builder() + .modelProjectConsent( + ModelProjectConsent + .builder() + .provisions( + listOf(Provision.builder().type(ConsentProvision.DENY).purpose(ModelProjectConsentPurpose.SEQUENCING).build()) + ).build() + ) + .build() + ) .build() val headers = RecordHeaders( @@ -180,8 +236,11 @@ class KafkaInputListenerTest { Optional.empty() ) ) - verify(requestProcessor, times(0)).processDeletion(anyValueClass(), anyValueClass(), eq( - TtpConsentStatus.UNKNOWN_CHECK_FILE)) + verify(requestProcessor, times(0)).processDeletion( + anyValueClass(), anyValueClass(), eq( + TtpConsentStatus.UNKNOWN_CHECK_FILE + ) + ) } } diff --git a/src/test/kotlin/dev/dnpm/etl/processor/input/MtbFileRestControllerTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/input/MtbFileRestControllerTest.kt index 7a91ed1..845f325 100644 --- a/src/test/kotlin/dev/dnpm/etl/processor/input/MtbFileRestControllerTest.kt +++ b/src/test/kotlin/dev/dnpm/etl/processor/input/MtbFileRestControllerTest.kt @@ -20,31 +20,21 @@ package dev.dnpm.etl.processor.input import com.fasterxml.jackson.databind.ObjectMapper -import de.ukw.ccc.bwhc.dto.* -import de.ukw.ccc.bwhc.dto.Consent.Status import dev.dnpm.etl.processor.CustomMediaType -import dev.dnpm.etl.processor.consent.ConsentByMtbFile import dev.dnpm.etl.processor.consent.GicsConsentService -import dev.dnpm.etl.processor.consent.TtpConsentStatus import dev.dnpm.etl.processor.services.RequestProcessor import dev.pcvolkmer.mv64e.mtb.Mtb import org.junit.jupiter.api.BeforeEach import org.junit.jupiter.api.Nested import org.junit.jupiter.api.Test import org.junit.jupiter.api.extension.ExtendWith -import org.junit.jupiter.params.ParameterizedTest -import org.junit.jupiter.params.provider.ValueSource import org.mockito.Mock import org.mockito.Mockito.times import org.mockito.Mockito.verify import org.mockito.junit.jupiter.MockitoExtension import org.mockito.kotlin.any -import org.mockito.kotlin.anyValueClass -import org.mockito.kotlin.whenever import org.springframework.core.io.ClassPathResource -import org.springframework.http.MediaType import org.springframework.test.web.servlet.MockMvc -import org.springframework.test.web.servlet.delete import org.springframework.test.web.servlet.post import org.springframework.test.web.servlet.setup.MockMvcBuilders @@ -54,219 +44,6 @@ class MtbFileRestControllerTest { private val objectMapper = ObjectMapper() @Nested - inner class BwhcRequests { - - private lateinit var mockMvc: MockMvc - - private lateinit var requestProcessor: RequestProcessor - - - @BeforeEach - fun setup( - @Mock requestProcessor: RequestProcessor - ) { - this.requestProcessor = requestProcessor - val controller = MtbFileRestController( - requestProcessor, - ConsentByMtbFile() - ) - this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build() - } - - @Test - fun shouldProcessPostRequest() { - mockMvc.post("/mtbfile") { - content = objectMapper.writeValueAsString(bwhcMtbFileContent(Status.ACTIVE)) - contentType = MediaType.APPLICATION_JSON - }.andExpect { - status { - isAccepted() - } - } - - verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>()) - } - - @Test - fun shouldProcessPostRequestWithRejectedConsent() { - mockMvc.post("/mtbfile") { - content = objectMapper.writeValueAsString(bwhcMtbFileContent(Status.REJECTED)) - contentType = MediaType.APPLICATION_JSON - }.andExpect { - status { - isAccepted() - } - } - - verify(requestProcessor, times(1)).processDeletion( - anyValueClass(), - org.mockito.kotlin.eq(TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED) - ) - } - - @Test - fun shouldProcessDeleteRequest() { - mockMvc.delete("/mtbfile/TEST_12345678").andExpect { - status { - isAccepted() - } - } - - verify(requestProcessor, times(1)).processDeletion( - anyValueClass(), - org.mockito.kotlin.eq(TtpConsentStatus.UNKNOWN_CHECK_FILE) - ) - } - } - - @Nested - inner class BwhcRequestsCheckConsentViaTtp { - - private lateinit var mockMvc: MockMvc - - private lateinit var requestProcessor: RequestProcessor - - private lateinit var gicsConsentService: GicsConsentService - - @BeforeEach - fun setup( - @Mock requestProcessor: RequestProcessor, - @Mock gicsConsentService: GicsConsentService - ) { - this.requestProcessor = requestProcessor - val controller = MtbFileRestController(requestProcessor, gicsConsentService) - this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build() - this.gicsConsentService = gicsConsentService - } - - @ParameterizedTest - @ValueSource(strings = ["ACTIVE", "REJECTED"]) - fun shouldProcessPostRequest(status: String) { - - whenever(gicsConsentService.getTtpBroadConsentStatus(any())).thenReturn(TtpConsentStatus.BROAD_CONSENT_GIVEN) - - mockMvc.post("/mtbfile") { - content = objectMapper.writeValueAsString(bwhcMtbFileContent(Status.valueOf(status))) - contentType = MediaType.APPLICATION_JSON - }.andExpect { - status { - isAccepted() - } - } - - verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>()) - } - - - @ParameterizedTest - @ValueSource(strings = ["ACTIVE", "REJECTED"]) - fun shouldProcessPostRequestWithRejectedConsent(status: String) { - - whenever(gicsConsentService.getTtpBroadConsentStatus(any())).thenReturn(TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED) - - mockMvc.post("/mtbfile") { - content = objectMapper.writeValueAsString(bwhcMtbFileContent(Status.valueOf(status))) - contentType = MediaType.APPLICATION_JSON - }.andExpect { - status { - isAccepted() - } - } - - // consent status from ttp should override file consent value - verify(requestProcessor, times(1)).processDeletion( - anyValueClass(), - org.mockito.kotlin.eq(TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED) - ) - } - - @Test - fun shouldProcessDeleteRequest() { - - mockMvc.delete("/mtbfile/TEST_12345678").andExpect { - status { - isAccepted() - } - } - - verify(requestProcessor, times(1)).processDeletion( - anyValueClass(), - org.mockito.kotlin.eq(TtpConsentStatus.UNKNOWN_CHECK_FILE) - ) - verify(gicsConsentService, times(0)).getTtpBroadConsentStatus(any()) - - } - } - - - @Nested - inner class BwhcRequestsWithAlias { - - private lateinit var mockMvc: MockMvc - - private lateinit var requestProcessor: RequestProcessor - - @BeforeEach - fun setup( - @Mock requestProcessor: RequestProcessor - ) { - this.requestProcessor = requestProcessor - val controller = MtbFileRestController( - requestProcessor, - ConsentByMtbFile() - ) - this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build() - } - - @Test - fun shouldProcessPostRequest() { - mockMvc.post("/mtb") { - content = objectMapper.writeValueAsString(bwhcMtbFileContent(Status.ACTIVE)) - contentType = MediaType.APPLICATION_JSON - }.andExpect { - status { - isAccepted() - } - } - - verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>()) - } - - @Test - fun shouldProcessPostRequestWithRejectedConsent() { - mockMvc.post("/mtb") { - content = objectMapper.writeValueAsString(bwhcMtbFileContent(Status.REJECTED)) - contentType = MediaType.APPLICATION_JSON - }.andExpect { - status { - isAccepted() - } - } - - verify(requestProcessor, times(1)).processDeletion( - anyValueClass(), org.mockito.kotlin.eq( - TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED - ) - ) - } - - @Test - fun shouldProcessDeleteRequest() { - mockMvc.delete("/mtb/TEST_12345678").andExpect { - status { - isAccepted() - } - } - - verify(requestProcessor, times(1)).processDeletion( - anyValueClass(), org.mockito.kotlin.eq( - TtpConsentStatus.UNKNOWN_CHECK_FILE - ) - ) - } - } - - @Nested inner class RequestsForDnpmDataModel21 { private lateinit var mockMvc: MockMvc @@ -304,15 +81,4 @@ class MtbFileRestControllerTest { } } - - companion object { - fun bwhcMtbFileContent(consentStatus: Status) = MtbFile.builder().withPatient( - Patient.builder().withId("TEST_12345678").withBirthDate("2000-08-08").withGender(Patient.Gender.MALE) - .build() - ).withConsent( - Consent.builder().withId("1").withStatus(consentStatus).withPatient("TEST_12345678").build() - ).withEpisode( - Episode.builder().withId("1").withPatient("TEST_12345678").withPeriod(PeriodStart("2023-08-08")).build() - ).build() - } } diff --git a/src/test/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSenderTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSenderTest.kt index f1185ef..1e9c853 100644 --- a/src/test/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSenderTest.kt +++ b/src/test/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSenderTest.kt @@ -20,8 +20,6 @@ package dev.dnpm.etl.processor.output import com.fasterxml.jackson.databind.ObjectMapper -import de.ukw.ccc.bwhc.dto.* -import de.ukw.ccc.bwhc.dto.Patient import dev.dnpm.etl.processor.CustomMediaType import dev.dnpm.etl.processor.PatientPseudonym import dev.dnpm.etl.processor.RequestId @@ -39,7 +37,6 @@ import org.junit.jupiter.params.provider.MethodSource import org.mockito.Mock import org.mockito.junit.jupiter.MockitoExtension import org.mockito.kotlin.* -import org.springframework.http.MediaType import org.springframework.kafka.core.KafkaTemplate import org.springframework.kafka.support.SendResult import org.springframework.retry.policy.SimpleRetryPolicy @@ -76,20 +73,6 @@ class KafkaMtbFileSenderTest { @ParameterizedTest @MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource") - fun shouldSendMtbFileRequestAndReturnExpectedState(testData: TestData) { - doAnswer { - if (null != testData.exception) { - throw testData.exception - } - completedFuture(SendResult<String, String>(null, null)) - }.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>()) - - val response = kafkaMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1MtbFile(Consent.Status.ACTIVE))) - assertThat(response.status).isEqualTo(testData.requestStatus) - } - - @ParameterizedTest - @MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource") fun shouldSendDeleteRequestAndReturnExpectedState(testData: TestData) { doAnswer { if (null != testData.exception) { @@ -102,66 +85,6 @@ class KafkaMtbFileSenderTest { assertThat(response.status).isEqualTo(testData.requestStatus) } - @Test - fun shouldSendMtbFileRequestWithCorrectKeyAndHeaderAndBody() { - doAnswer { - completedFuture(SendResult<String, String>(null, null)) - }.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>()) - - kafkaMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1MtbFile(Consent.Status.ACTIVE))) - - val captor = argumentCaptor<ProducerRecord<String, String>>() - verify(kafkaTemplate, times(1)).send(captor.capture()) - assertThat(captor.firstValue.key()).isNotNull - assertThat(captor.firstValue.key()).isEqualTo("{\"pid\": \"PID\"}") - assertThat(captor.firstValue.headers().headers("contentType")).isNotNull - assertThat(captor.firstValue.headers().headers("contentType")?.firstOrNull()?.value()).isEqualTo(MediaType.APPLICATION_JSON_VALUE.toByteArray()) - assertThat(captor.firstValue.value()).isNotNull - assertThat(captor.firstValue.value()).isEqualTo(objectMapper.writeValueAsString(bwhcV1kafkaRecordData(TEST_REQUEST_ID, Consent.Status.ACTIVE))) - } - - @Test - fun shouldSendDeleteRequestWithCorrectKeyAndBody() { - doAnswer { - completedFuture(SendResult<String, String>(null, null)) - }.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>()) - - kafkaMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM)) - - val captor = argumentCaptor<ProducerRecord<String, String>>() - verify(kafkaTemplate, times(1)).send(captor.capture()) - assertThat(captor.firstValue.key()).isNotNull - assertThat(captor.firstValue.key()).isEqualTo("{\"pid\": \"PID\"}") - assertThat(captor.firstValue.value()).isNotNull - assertThat(captor.firstValue.value()).isEqualTo(objectMapper.writeValueAsString(bwhcV1kafkaRecordData(TEST_REQUEST_ID, Consent.Status.REJECTED))) - } - - @ParameterizedTest - @MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource") - fun shouldRetryOnMtbFileKafkaSendError(testData: TestData) { - val kafkaProperties = KafkaProperties("testtopic") - val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build() - this.kafkaMtbFileSender = KafkaMtbFileSender(this.kafkaTemplate, kafkaProperties, retryTemplate, this.objectMapper) - - doAnswer { - if (null != testData.exception) { - throw testData.exception - } - completedFuture(SendResult<String, String>(null, null)) - }.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>()) - - kafkaMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1MtbFile(Consent.Status.ACTIVE))) - - val expectedCount = when (testData.exception) { - // OK - No Retry - null -> times(1) - // Request failed - Retry max 3 times - else -> times(3) - } - - verify(kafkaTemplate, expectedCount).send(any<ProducerRecord<String, String>>()) - } - @ParameterizedTest @MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource") fun shouldRetryOnDeleteKafkaSendError(testData: TestData) { @@ -276,41 +199,6 @@ class KafkaMtbFileSenderTest { val TEST_REQUEST_ID = RequestId("TestId") val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID") - fun bwhcV1MtbFile(consentStatus: Consent.Status): MtbFile { - return if (consentStatus == Consent.Status.ACTIVE) { - MtbFile.builder() - .withPatient( - Patient.builder() - .withId("PID") - .withBirthDate("2000-08-08") - .withGender(Patient.Gender.MALE) - .build() - ) - .withConsent( - Consent.builder() - .withId("1") - .withStatus(consentStatus) - .withPatient("PID") - .build() - ) - .withEpisode( - Episode.builder() - .withId("1") - .withPatient("PID") - .withPeriod(PeriodStart("2023-08-08")) - .build() - ) - } else { - MtbFile.builder() - .withConsent( - Consent.builder() - .withStatus(consentStatus) - .withPatient("PID") - .build() - ) - }.build() - } - fun dnpmV2MtbFile(): Mtb { return Mtb().apply { this.patient = dev.pcvolkmer.mv64e.mtb.Patient().apply { @@ -334,10 +222,6 @@ class KafkaMtbFileSenderTest { } } - fun bwhcV1kafkaRecordData(requestId: RequestId, consentStatus: Consent.Status): MtbRequest { - return BwhcV1MtbFileRequest(requestId, bwhcV1MtbFile(consentStatus)) - } - fun dnmpV2kafkaRecordData(requestId: RequestId): MtbRequest { return DnpmV2MtbFileRequest(requestId, dnpmV2MtbFile()) } diff --git a/src/test/kotlin/dev/dnpm/etl/processor/output/RestBwhcMtbFileSenderTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/output/RestBwhcMtbFileSenderTest.kt deleted file mode 100644 index ead2496..0000000 --- a/src/test/kotlin/dev/dnpm/etl/processor/output/RestBwhcMtbFileSenderTest.kt +++ /dev/null @@ -1,313 +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 com.fasterxml.jackson.databind.ObjectMapper -import com.fasterxml.jackson.module.kotlin.KotlinModule -import de.ukw.ccc.bwhc.dto.* -import dev.dnpm.etl.processor.PatientPseudonym -import dev.dnpm.etl.processor.RequestId -import dev.dnpm.etl.processor.config.RestTargetProperties -import dev.dnpm.etl.processor.monitoring.ReportService -import dev.dnpm.etl.processor.monitoring.RequestStatus -import org.assertj.core.api.Assertions.assertThat -import org.junit.jupiter.api.BeforeEach -import org.junit.jupiter.params.ParameterizedTest -import org.junit.jupiter.params.provider.MethodSource -import org.springframework.http.HttpHeaders -import org.springframework.http.HttpMethod -import org.springframework.http.HttpStatus -import org.springframework.http.MediaType -import org.springframework.retry.policy.SimpleRetryPolicy -import org.springframework.retry.support.RetryTemplateBuilder -import org.springframework.test.web.client.ExpectedCount -import org.springframework.test.web.client.MockRestServiceServer -import org.springframework.test.web.client.match.MockRestRequestMatchers.* -import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus -import org.springframework.web.client.RestTemplate - -class RestBwhcMtbFileSenderTest { - - private lateinit var mockRestServiceServer: MockRestServiceServer - - private lateinit var restMtbFileSender: RestMtbFileSender - - private var reportService = ReportService(ObjectMapper().registerModule(KotlinModule.Builder().build())) - - @BeforeEach - fun setup() { - val restTemplate = RestTemplate() - val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile", null, null) - val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build() - - this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate) - - this.restMtbFileSender = - RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService) - } - - @ParameterizedTest - @MethodSource("deleteRequestWithResponseSource") - fun shouldReturnExpectedResponseForDelete(requestWithResponse: RequestWithResponse) { - this.mockRestServiceServer - .expect(method(HttpMethod.DELETE)) - .andExpect(requestTo("http://localhost:9000/mtbfile/Patient/${TEST_PATIENT_PSEUDONYM.value}")) - .andRespond { - withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it) - } - - val response = restMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM)) - assertThat(response.status).isEqualTo(requestWithResponse.response.status) - assertThat(response.body).isEqualTo(requestWithResponse.response.body) - } - - @ParameterizedTest - @MethodSource("mtbFileRequestWithResponseSource") - fun shouldReturnExpectedResponseForMtbFilePost(requestWithResponse: RequestWithResponse) { - this.mockRestServiceServer - .expect(method(HttpMethod.POST)) - .andExpect(requestTo("http://localhost:9000/mtbfile/MTBFile")) - .andExpect(header(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE)) - .andRespond { - withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it) - } - - val response = restMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, mtbFile)) - assertThat(response.status).isEqualTo(requestWithResponse.response.status) - assertThat(response.body).isEqualTo(requestWithResponse.response.body) - } - - @ParameterizedTest - @MethodSource("mtbFileRequestWithResponseSource") - fun shouldRetryOnMtbFileHttpRequestError(requestWithResponse: RequestWithResponse) { - val restTemplate = RestTemplate() - val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile", null, null) - val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build() - - this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate) - this.restMtbFileSender = - RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService) - - val expectedCount = when (requestWithResponse.httpStatus) { - // OK - No Retry - HttpStatus.OK, HttpStatus.CREATED -> ExpectedCount.max(1) - // Request failed - Retry max 3 times - else -> ExpectedCount.max(3) - } - - this.mockRestServiceServer - .expect(expectedCount, method(HttpMethod.POST)) - .andExpect(requestTo("http://localhost:9000/mtbfile/MTBFile")) - .andRespond { - withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it) - } - - val response = restMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, mtbFile)) - assertThat(response.status).isEqualTo(requestWithResponse.response.status) - assertThat(response.body).isEqualTo(requestWithResponse.response.body) - } - - @ParameterizedTest - @MethodSource("deleteRequestWithResponseSource") - fun shouldRetryOnDeleteHttpRequestError(requestWithResponse: RequestWithResponse) { - val restTemplate = RestTemplate() - val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile", null, null) - val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build() - - this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate) - this.restMtbFileSender = - RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService) - - val expectedCount = when (requestWithResponse.httpStatus) { - // OK - No Retry - HttpStatus.OK, HttpStatus.CREATED -> ExpectedCount.max(1) - // Request failed - Retry max 3 times - else -> ExpectedCount.max(3) - } - - this.mockRestServiceServer - .expect(expectedCount, method(HttpMethod.DELETE)) - .andExpect(requestTo("http://localhost:9000/mtbfile/Patient/${TEST_PATIENT_PSEUDONYM.value}")) - .andRespond { - withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it) - } - - val response = restMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM)) - assertThat(response.status).isEqualTo(requestWithResponse.response.status) - assertThat(response.body).isEqualTo(requestWithResponse.response.body) - } - - companion object { - data class RequestWithResponse( - val httpStatus: HttpStatus, - val body: String, - val response: MtbFileSender.Response - ) - - val TEST_REQUEST_ID = RequestId("TestId") - val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID") - - val mtbFile: MtbFile = MtbFile.builder() - .withPatient( - Patient.builder() - .withId("PID") - .withBirthDate("2000-08-08") - .withGender(Patient.Gender.MALE) - .build() - ) - .withConsent( - Consent.builder() - .withId("1") - .withStatus(Consent.Status.ACTIVE) - .withPatient("PID") - .build() - ) - .withEpisode( - Episode.builder() - .withId("1") - .withPatient("PID") - .withPeriod(PeriodStart("2023-08-08")) - .build() - ) - .build() - - private const val ERROR_RESPONSE_BODY = "Sonstiger Fehler bei der Übertragung" - - /** - * Synthetic http responses with related request status - * Also see: https://ibmi-intra.cs.uni-tuebingen.de/display/ZPM/bwHC+REST+API - */ - @JvmStatic - fun mtbFileRequestWithResponseSource(): Set<RequestWithResponse> { - return setOf( - RequestWithResponse( - HttpStatus.OK, - responseBodyWithMaxSeverity(ReportService.Severity.INFO), - MtbFileSender.Response( - RequestStatus.SUCCESS, - responseBodyWithMaxSeverity(ReportService.Severity.INFO) - ) - ), - RequestWithResponse( - HttpStatus.CREATED, - responseBodyWithMaxSeverity(ReportService.Severity.WARNING), - MtbFileSender.Response( - RequestStatus.WARNING, - responseBodyWithMaxSeverity(ReportService.Severity.WARNING) - ) - ), - RequestWithResponse( - HttpStatus.BAD_REQUEST, - responseBodyWithMaxSeverity(ReportService.Severity.ERROR), - MtbFileSender.Response(RequestStatus.ERROR, responseBodyWithMaxSeverity(ReportService.Severity.ERROR)) - ), - RequestWithResponse( - HttpStatus.UNPROCESSABLE_ENTITY, - responseBodyWithMaxSeverity(ReportService.Severity.FATAL), - MtbFileSender.Response( - RequestStatus.ERROR, - responseBodyWithMaxSeverity(ReportService.Severity.FATAL) - ) - ), - // Some more errors not mentioned in documentation - RequestWithResponse( - HttpStatus.NOT_FOUND, - ERROR_RESPONSE_BODY, - MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY) - ), - RequestWithResponse( - HttpStatus.INTERNAL_SERVER_ERROR, - ERROR_RESPONSE_BODY, - MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY) - ) - ) - } - - /** - * Synthetic http responses with related request status - * Also see: https://ibmi-intra.cs.uni-tuebingen.de/display/ZPM/bwHC+REST+API - */ - @JvmStatic - fun deleteRequestWithResponseSource(): Set<RequestWithResponse> { - return setOf( - RequestWithResponse(HttpStatus.OK, "", MtbFileSender.Response(RequestStatus.SUCCESS)), - // Some more errors not mentioned in documentation - RequestWithResponse( - HttpStatus.NOT_FOUND, - "what????", - MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY) - ), - RequestWithResponse( - HttpStatus.INTERNAL_SERVER_ERROR, - "what????", - MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY) - ) - ) - } - - fun responseBodyWithMaxSeverity(severity: ReportService.Severity): String { - return when (severity) { - ReportService.Severity.INFO -> """ - { - "patient": "PID", - "issues": [ - { "severity": "info", "message": "Info Message" } - ] - } - """ - - ReportService.Severity.WARNING -> """ - { - "patient": "PID", - "issues": [ - { "severity": "info", "message": "Info Message" }, - { "severity": "warning", "message": "Warning Message" } - ] - } - """ - - ReportService.Severity.ERROR -> """ - { - "patient": "PID", - "issues": [ - { "severity": "info", "message": "Info Message" }, - { "severity": "warning", "message": "Warning Message" }, - { "severity": "error", "message": "Error Message" } - ] - } - """ - - ReportService.Severity.FATAL -> """ - { - "patient": "PID", - "issues": [ - { "severity": "info", "message": "Info Message" }, - { "severity": "warning", "message": "Warning Message" }, - { "severity": "error", "message": "Error Message" }, - { "severity": "fatal", "message": "Fatal Message" } - ] - } - """ - } - } - } - - -} diff --git a/src/test/kotlin/dev/dnpm/etl/processor/output/RestDipMtbFileSenderTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/output/RestDipMtbFileSenderTest.kt index 8395518..1b27a62 100644 --- a/src/test/kotlin/dev/dnpm/etl/processor/output/RestDipMtbFileSenderTest.kt +++ b/src/test/kotlin/dev/dnpm/etl/processor/output/RestDipMtbFileSenderTest.kt @@ -21,8 +21,6 @@ package dev.dnpm.etl.processor.output import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.module.kotlin.KotlinModule -import de.ukw.ccc.bwhc.dto.* -import de.ukw.ccc.bwhc.dto.Patient import dev.dnpm.etl.processor.CustomMediaType import dev.dnpm.etl.processor.PatientPseudonym import dev.dnpm.etl.processor.RequestId @@ -55,78 +53,6 @@ import java.util.* class RestDipMtbFileSenderTest { @Nested - inner class BwhcV1ContentRequest { - - private lateinit var mockRestServiceServer: MockRestServiceServer - - private lateinit var restMtbFileSender: RestMtbFileSender - - private var reportService = ReportService(ObjectMapper().registerModule(KotlinModule.Builder().build())) - - @BeforeEach - fun setup() { - val restTemplate = RestTemplate() - val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false) - val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build() - - this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate) - - this.restMtbFileSender = - RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService) - } - - @ParameterizedTest - @MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#mtbFileRequestWithResponseSource") - fun shouldReturnExpectedResponseForMtbFilePost(requestWithResponse: RequestWithResponse) { - this.mockRestServiceServer - .expect(method(HttpMethod.POST)) - .andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient-record")) - .andExpect(header(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE)) - .andRespond { - withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it) - } - - val response = restMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1mtbFile)) - assertThat(response.status).isEqualTo(requestWithResponse.response.status) - assertThat(response.body).isEqualTo(requestWithResponse.response.body) - } - - @ParameterizedTest - @MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#mtbFileRequestWithResponseSource") - fun shouldRetryOnMtbFileHttpRequestError(requestWithResponse: RequestWithResponse) { - val restTemplate = RestTemplate() - val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false) - val retryTemplate = AppConfiguration().retryTemplate(AppConfigProperties("http://localhost:9000")) - retryTemplate.setBackOffPolicy(NoBackOffPolicy()) - - this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate) - this.restMtbFileSender = - RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService) - - val expectedCount = when (requestWithResponse.httpStatus) { - // OK - No Retry - HttpStatus.OK, HttpStatus.CREATED, HttpStatus.UNPROCESSABLE_ENTITY, HttpStatus.BAD_REQUEST -> ExpectedCount.max( - 1 - ) - // Request failed - Retry max 3 times - else -> ExpectedCount.max(3) - } - - this.mockRestServiceServer - .expect(expectedCount, method(HttpMethod.POST)) - .andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient-record")) - .andRespond { - withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it) - } - - val response = restMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1mtbFile)) - assertThat(response.status).isEqualTo(requestWithResponse.response.status) - assertThat(response.body).isEqualTo(requestWithResponse.response.body) - } - - } - - @Nested inner class DnpmV2ContentRequest { private lateinit var mockRestServiceServer: MockRestServiceServer @@ -138,7 +64,7 @@ class RestDipMtbFileSenderTest { @BeforeEach fun setup() { val restTemplate = RestTemplate() - val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false) + val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null) val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build() this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate) @@ -176,7 +102,7 @@ class RestDipMtbFileSenderTest { @BeforeEach fun setup() { val restTemplate = RestTemplate() - val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false) + val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null) val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build() this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate) @@ -204,8 +130,8 @@ class RestDipMtbFileSenderTest { @MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#deleteRequestWithResponseSource") fun shouldRetryOnDeleteHttpRequestError(requestWithResponse: RequestWithResponse) { val restTemplate = RestTemplate() - val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false) - val retryTemplate = AppConfiguration().retryTemplate(AppConfigProperties("http://localhost:9000")) + val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null) + val retryTemplate = AppConfiguration().retryTemplate(AppConfigProperties()) retryTemplate.setBackOffPolicy(NoBackOffPolicy()) this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate) @@ -245,30 +171,6 @@ class RestDipMtbFileSenderTest { val TEST_REQUEST_ID = RequestId("TestId") val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID") - val bwhcV1mtbFile: MtbFile = MtbFile.builder() - .withPatient( - Patient.builder() - .withId("PID") - .withBirthDate("2000-08-08") - .withGender(Patient.Gender.MALE) - .build() - ) - .withConsent( - Consent.builder() - .withId("1") - .withStatus(Consent.Status.ACTIVE) - .withPatient("PID") - .build() - ) - .withEpisode( - Episode.builder() - .withId("1") - .withPatient("PID") - .withPeriod(PeriodStart("2023-08-08")) - .build() - ) - .build() - fun dnpmV2MtbFile(): Mtb { return Mtb().apply { this.patient = dev.pcvolkmer.mv64e.mtb.Patient().apply { diff --git a/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt index b6baec9..5955263 100644 --- a/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt +++ b/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt @@ -21,8 +21,6 @@ package dev.dnpm.etl.processor.pseudonym import ca.uhn.fhir.context.FhirContext import com.fasterxml.jackson.databind.ObjectMapper -import de.ukw.ccc.bwhc.dto.* -import de.ukw.ccc.bwhc.dto.Patient import dev.dnpm.etl.processor.config.AppConfigProperties import dev.dnpm.etl.processor.config.GIcsConfigProperties import dev.dnpm.etl.processor.config.JacksonConfig @@ -52,172 +50,6 @@ class ExtensionsTest { } @Nested - inner class UsingBwhcDatamodel { - - val FAKE_MTB_FILE_PATH = "fake_MTBFile.json" - val CLEAN_PATIENT_ID = "5dad2f0b-49c6-47d8-a952-7b9e9e0f7549" - - - private fun fakeMtbFile(): MtbFile { - val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream - return getObjectMapper().readValue(mtbFile, MtbFile::class.java) - } - - private fun MtbFile.serialized(): String { - return getObjectMapper().writeValueAsString(this) - } - - @Test - fun shouldNotContainCleanPatientId(@Mock pseudonymizeService: PseudonymizeService) { - doAnswer { - it.arguments[0] - "PSEUDO-ID" - }.whenever(pseudonymizeService).patientPseudonym(anyValueClass()) - - val mtbFile = fakeMtbFile() - - mtbFile.pseudonymizeWith(pseudonymizeService) - - assertThat(mtbFile.patient.id).isEqualTo("PSEUDO-ID") - assertThat(mtbFile.serialized()).doesNotContain(CLEAN_PATIENT_ID) - } - - @Test - fun shouldNotContainAnyUuidAfterRehashingOfIds(@Mock pseudonymizeService: PseudonymizeService) { - doAnswer { - it.arguments[0] - "PSEUDO-ID" - }.whenever(pseudonymizeService).patientPseudonym(anyValueClass()) - - doAnswer { - "TESTDOMAIN" - }.whenever(pseudonymizeService).prefix() - - val mtbFile = fakeMtbFile() - - mtbFile.pseudonymizeWith(pseudonymizeService) - mtbFile.anonymizeContentWith(pseudonymizeService) - - val pattern = - "\"[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}\"".toRegex() - .toPattern() - val matcher = pattern.matcher(mtbFile.serialized()) - - assertThrows<IllegalStateException> { - matcher.find() - matcher.group() - }.also { - assertThat(it.message).isEqualTo("No match found") - } - - } - - @Test - fun shouldRehashIdsWithPrefix(@Mock pseudonymizeService: PseudonymizeService) { - doAnswer { - it.arguments[0] - "PSEUDO-ID" - }.whenever(pseudonymizeService).patientPseudonym(anyValueClass()) - - doAnswer { - "TESTDOMAIN" - }.whenever(pseudonymizeService).prefix() - - val mtbFile = MtbFile.builder() - .withPatient( - Patient.builder() - .withId("1") - .withBirthDate("2000-08-08") - .withGender(Patient.Gender.MALE) - .build() - ) - .withConsent( - Consent.builder() - .withId("1") - .withStatus(Consent.Status.ACTIVE) - .withPatient("123") - .build() - ) - .withEpisode( - Episode.builder() - .withId("1") - .withPatient("1") - .withPeriod(PeriodStart("2023-08-08")) - .build() - ) - .build() - - mtbFile.pseudonymizeWith(pseudonymizeService) - mtbFile.anonymizeContentWith(pseudonymizeService) - - - assertThat(mtbFile.episode.id) - // TESTDOMAIN<sha256(TESTDOMAIN-1)[0-41]> - .isEqualTo("TESTDOMAIN44e20a53bbbf9f3ae39626d05df7014dcd77d6098") - } - - @Test - fun shouldNotThrowExceptionOnNullValues(@Mock pseudonymizeService: PseudonymizeService) { - doAnswer { - it.arguments[0] - "PSEUDO-ID" - }.whenever(pseudonymizeService).patientPseudonym(anyValueClass()) - - doAnswer { - "TESTDOMAIN" - }.whenever(pseudonymizeService).prefix() - - val mtbFile = MtbFile.builder() - .withPatient( - Patient.builder() - .withId("1") - .withBirthDate("2000-08-08") - .withGender(Patient.Gender.MALE) - .build() - ) - .withConsent( - Consent.builder() - .withId("1") - .withStatus(Consent.Status.ACTIVE) - .withPatient("123") - .build() - ) - .withEpisode( - Episode.builder() - .withId("1") - .withPatient("1") - .withPeriod(PeriodStart("2023-08-08")) - .build() - ) - .withClaims(null) - .withDiagnoses(null) - .withCarePlans(null) - .withClaimResponses(null) - .withEcogStatus(null) - .withFamilyMemberDiagnoses(null) - .withGeneticCounsellingRequests(null) - .withHistologyReevaluationRequests(null) - .withHistologyReports(null) - .withLastGuidelineTherapies(null) - .withMolecularPathologyFindings(null) - .withMolecularTherapies(null) - .withNgsReports(null) - .withPreviousGuidelineTherapies(null) - .withRebiopsyRequests(null) - .withRecommendations(null) - .withResponses(null) - .withStudyInclusionRequests(null) - .withSpecimens(null) - .build() - - mtbFile.pseudonymizeWith(pseudonymizeService) - mtbFile.anonymizeContentWith(pseudonymizeService) - - assertThat(mtbFile.episode.id).isNotNull() - } - } - - @Nested inner class UsingDnpmV2Datamodel { val FAKE_MTB_FILE_PATH = "mv64e-mtb-fake-patient.json" @@ -251,7 +83,7 @@ class ExtensionsTest { private fun addConsentData(mtbFile: Mtb) { val gIcsConfigProperties = GIcsConfigProperties("", "", "") - val appConfigProperties = AppConfigProperties(null, emptyList()) + val appConfigProperties = AppConfigProperties(emptyList()) val bundle = Bundle() val dummyConsent = ConsentProcessorTest.getDummyGenomDeConsent() diff --git a/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeServiceTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeServiceTest.kt index 819454f..8ee19bc 100644 --- a/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeServiceTest.kt +++ b/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeServiceTest.kt @@ -19,8 +19,8 @@ package dev.dnpm.etl.processor.pseudonym -import de.ukw.ccc.bwhc.dto.* import dev.dnpm.etl.processor.config.PseudonymizeConfigProperties +import dev.pcvolkmer.mv64e.mtb.* import org.assertj.core.api.Assertions.assertThat import org.junit.jupiter.api.Test import org.junit.jupiter.api.extension.ExtendWith @@ -29,31 +29,26 @@ import org.mockito.Mock import org.mockito.junit.jupiter.MockitoExtension import org.mockito.kotlin.doAnswer import org.mockito.kotlin.whenever +import java.time.Instant +import java.util.* @ExtendWith(MockitoExtension::class) class PseudonymizeServiceTest { - private val mtbFile = MtbFile.builder() - .withPatient( + private val mtbFile = Mtb.builder() + .patient( Patient.builder() - .withId("123") - .withBirthDate("2000-08-08") - .withGender(Patient.Gender.MALE) + .id("123") .build() ) - .withConsent( - Consent.builder() - .withId("1") - .withStatus(Consent.Status.ACTIVE) - .withPatient("123") - .build() - ) - .withEpisode( - Episode.builder() - .withId("1") - .withPatient("123") - .withPeriod(PeriodStart("2023-08-08")) - .build() + .episodesOfCare( + listOf( + MtbEpisodeOfCare.builder() + .id("1") + .patient(Reference.builder().id("123").build()) + .period(PeriodDate.builder().start(Date.from(Instant.parse("2021-01-01T00:00:00.00Z"))).build()) + .build() + ) ) .build() @@ -102,4 +97,4 @@ class PseudonymizeServiceTest { assertThat(tans.add(tan)).`as`("never the same result!").isTrue } } -}
\ No newline at end of file +} diff --git a/src/test/kotlin/dev/dnpm/etl/processor/services/ConsentProcessorTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/services/ConsentProcessorTest.kt index 38ce0b3..af93f7b 100644 --- a/src/test/kotlin/dev/dnpm/etl/processor/services/ConsentProcessorTest.kt +++ b/src/test/kotlin/dev/dnpm/etl/processor/services/ConsentProcessorTest.kt @@ -51,7 +51,7 @@ class ConsentProcessorTest { this.objectMapper = jacksonConfig.objectMapper() this.fhirContext = JacksonConfig.fhirContext() this.gicsConsentService = gicsConsentService - this.appConfigProperties = AppConfigProperties(null, emptyList()) + this.appConfigProperties = AppConfigProperties(emptyList()) this.consentProcessor = ConsentProcessor( appConfigProperties, @@ -168,4 +168,4 @@ class ConsentProcessorTest { .parseResource<Bundle>(Bundle::class.java, bundle) } -}
\ No newline at end of file +} diff --git a/src/test/kotlin/dev/dnpm/etl/processor/services/RequestProcessorTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/services/RequestProcessorTest.kt index b36c696..0a42b9b 100644 --- a/src/test/kotlin/dev/dnpm/etl/processor/services/RequestProcessorTest.kt +++ b/src/test/kotlin/dev/dnpm/etl/processor/services/RequestProcessorTest.kt @@ -20,22 +20,21 @@ package dev.dnpm.etl.processor.services import com.fasterxml.jackson.databind.ObjectMapper -import de.ukw.ccc.bwhc.dto.* import dev.dnpm.etl.processor.Fingerprint import dev.dnpm.etl.processor.PatientId import dev.dnpm.etl.processor.PatientPseudonym import dev.dnpm.etl.processor.config.AppConfigProperties -import dev.dnpm.etl.processor.consent.GicsConsentService import dev.dnpm.etl.processor.consent.TtpConsentStatus 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.BwhcV1MtbFileRequest import dev.dnpm.etl.processor.output.DeleteRequest +import dev.dnpm.etl.processor.output.DnpmV2MtbFileRequest import dev.dnpm.etl.processor.output.MtbFileSender import dev.dnpm.etl.processor.output.RestMtbFileSender import dev.dnpm.etl.processor.pseudonym.PseudonymizeService import dev.dnpm.etl.processor.randomRequestId +import dev.pcvolkmer.mv64e.mtb.* import org.assertj.core.api.Assertions.assertThat import org.junit.jupiter.api.BeforeEach import org.junit.jupiter.api.Test @@ -49,6 +48,7 @@ import org.mockito.kotlin.argumentCaptor import org.mockito.kotlin.whenever import org.springframework.context.ApplicationEventPublisher import java.time.Instant +import java.util.* @ExtendWith(MockitoExtension::class) @@ -77,7 +77,7 @@ class RequestProcessorTest { this.sender = sender this.requestService = requestService this.applicationEventPublisher = applicationEventPublisher - this.appConfigProperties = AppConfigProperties(null) + this.appConfigProperties = AppConfigProperties() this.consentProcessor = consentProcessor val objectMapper = ObjectMapper() @@ -102,7 +102,7 @@ class RequestProcessorTest { randomRequestId(), PatientPseudonym("TEST_12345678901"), PatientId("P1"), - Fingerprint("zdlzv5s5ydmd4ktw2v5piohegc4jcyrm6j66bq6tv2uxuerndmga"), + Fingerprint("6vkiti5bk6ikwifpajpt7cygmd3dvw54d6lwfhzlynb3pqtzferq"), RequestType.MTB_FILE, RequestStatus.SUCCESS, Instant.parse("2023-08-08T02:00:00Z") @@ -119,29 +119,24 @@ class RequestProcessorTest { doAnswer { it.arguments[0] - }.whenever(transformationService).transform(any<MtbFile>()) + }.whenever(transformationService).transform(any<Mtb>()) - val mtbFile = MtbFile.builder() - .withPatient( + whenever(consentProcessor.consentGatedCheckAndTryEmbedding(any())).thenReturn(true) + + val mtbFile = Mtb.builder() + .patient( Patient.builder() - .withId("1") - .withBirthDate("2000-08-08") - .withGender(Patient.Gender.MALE) + .id("123") .build() ) - .withConsent( - Consent.builder() - .withId("1") - .withStatus(Consent.Status.ACTIVE) - .withPatient("123") - .build() - ) - .withEpisode( - Episode.builder() - .withId("1") - .withPatient("1") - .withPeriod(PeriodStart("2023-08-08")) - .build() + .episodesOfCare( + listOf( + MtbEpisodeOfCare.builder() + .id("1") + .patient(Reference.builder().id("123").build()) + .period(PeriodDate.builder().start(Date.from(Instant.parse("2023-08-08T02:00:00.00Z"))).build()) + .build() + ) ) .build() @@ -161,7 +156,7 @@ class RequestProcessorTest { randomRequestId(), PatientPseudonym("TEST_12345678901"), PatientId("P1"), - Fingerprint("zdlzv5s5ydmd4ktw2v5piohegc4jcyrm6j66bq6tv2uxuerndmga"), + Fingerprint("4gcjwtjjtcczybsljxepdfpkaeusvd7g3vogfqpmphyffyzfx7dq"), RequestType.MTB_FILE, RequestStatus.SUCCESS, Instant.parse("2023-08-08T02:00:00Z") @@ -178,29 +173,24 @@ class RequestProcessorTest { doAnswer { it.arguments[0] - }.whenever(transformationService).transform(any<MtbFile>()) + }.whenever(transformationService).transform(any<Mtb>()) + + whenever(consentProcessor.consentGatedCheckAndTryEmbedding(any())).thenReturn(true) - val mtbFile = MtbFile.builder() - .withPatient( + val mtbFile = Mtb.builder() + .patient( Patient.builder() - .withId("1") - .withBirthDate("2000-08-08") - .withGender(Patient.Gender.MALE) + .id("123") .build() ) - .withConsent( - Consent.builder() - .withId("1") - .withStatus(Consent.Status.ACTIVE) - .withPatient("123") - .build() - ) - .withEpisode( - Episode.builder() - .withId("1") - .withPatient("1") - .withPeriod(PeriodStart("2023-08-08")) - .build() + .episodesOfCare( + listOf( + MtbEpisodeOfCare.builder() + .id("1") + .patient(Reference.builder().id("123").build()) + .period(PeriodDate.builder().start(Date.from(Instant.parse("2021-01-01T00:00:00.00Z"))).build()) + .build() + ) ) .build() @@ -233,7 +223,7 @@ class RequestProcessorTest { doAnswer { MtbFileSender.Response(status = RequestStatus.SUCCESS) - }.whenever(sender).send(any<BwhcV1MtbFileRequest>()) + }.whenever(sender).send(any<DnpmV2MtbFileRequest>()) doAnswer { it.arguments[0] as String @@ -241,29 +231,24 @@ class RequestProcessorTest { doAnswer { it.arguments[0] - }.whenever(transformationService).transform(any<MtbFile>()) + }.whenever(transformationService).transform(any<Mtb>()) + + whenever(consentProcessor.consentGatedCheckAndTryEmbedding(any())).thenReturn(true) - val mtbFile = MtbFile.builder() - .withPatient( + val mtbFile = Mtb.builder() + .patient( Patient.builder() - .withId("1") - .withBirthDate("2000-08-08") - .withGender(Patient.Gender.MALE) + .id("123") .build() ) - .withConsent( - Consent.builder() - .withId("1") - .withStatus(Consent.Status.ACTIVE) - .withPatient("123") - .build() - ) - .withEpisode( - Episode.builder() - .withId("1") - .withPatient("1") - .withPeriod(PeriodStart("2023-08-08")) - .build() + .episodesOfCare( + listOf( + MtbEpisodeOfCare.builder() + .id("1") + .patient(Reference.builder().id("123").build()) + .period(PeriodDate.builder().start(Date.from(Instant.parse("2021-01-01T00:00:00.00Z"))).build()) + .build() + ) ) .build() @@ -296,7 +281,7 @@ class RequestProcessorTest { doAnswer { MtbFileSender.Response(status = RequestStatus.ERROR) - }.whenever(sender).send(any<BwhcV1MtbFileRequest>()) + }.whenever(sender).send(any<DnpmV2MtbFileRequest>()) doAnswer { it.arguments[0] as String @@ -304,29 +289,36 @@ class RequestProcessorTest { doAnswer { it.arguments[0] - }.whenever(transformationService).transform(any<MtbFile>()) + }.whenever(transformationService).transform(any<Mtb>()) - val mtbFile = MtbFile.builder() - .withPatient( + whenever(consentProcessor.consentGatedCheckAndTryEmbedding(any())).thenReturn(true) + + val mtbFile = Mtb.builder() + .patient( Patient.builder() - .withId("1") - .withBirthDate("2000-08-08") - .withGender(Patient.Gender.MALE) + .id("123") .build() ) - .withConsent( - Consent.builder() - .withId("1") - .withStatus(Consent.Status.ACTIVE) - .withPatient("123") + .metadata( + MvhMetadata + .builder() + .modelProjectConsent( + ModelProjectConsent + .builder() + .provisions( + listOf(Provision.builder().type(ConsentProvision.PERMIT).purpose(ModelProjectConsentPurpose.SEQUENCING).build()) + ).build() + ) .build() ) - .withEpisode( - Episode.builder() - .withId("1") - .withPatient("1") - .withPeriod(PeriodStart("2023-08-08")) - .build() + .episodesOfCare( + listOf( + MtbEpisodeOfCare.builder() + .id("1") + .patient(Reference.builder().id("123").build()) + .period(PeriodDate.builder().start(Date.from(Instant.parse("2021-01-01T00:00:00.00Z"))).build()) + .build() + ) ) .build() @@ -426,33 +418,28 @@ class RequestProcessorTest { doAnswer { it.arguments[0] - }.whenever(transformationService).transform(any<MtbFile>()) + }.whenever(transformationService).transform(any<Mtb>()) doAnswer { MtbFileSender.Response(status = RequestStatus.SUCCESS) - }.whenever(sender).send(any<BwhcV1MtbFileRequest>()) + }.whenever(sender).send(any<DnpmV2MtbFileRequest>()) - val mtbFile = MtbFile.builder() - .withPatient( + whenever(consentProcessor.consentGatedCheckAndTryEmbedding(any())).thenReturn(true) + + val mtbFile = Mtb.builder() + .patient( Patient.builder() - .withId("1") - .withBirthDate("2000-08-08") - .withGender(Patient.Gender.MALE) - .build() - ) - .withConsent( - Consent.builder() - .withId("1") - .withStatus(Consent.Status.ACTIVE) - .withPatient("123") + .id("123") .build() ) - .withEpisode( - Episode.builder() - .withId("1") - .withPatient("1") - .withPeriod(PeriodStart("2023-08-08")) - .build() + .episodesOfCare( + listOf( + MtbEpisodeOfCare.builder() + .id("1") + .patient(Reference.builder().id("123").build()) + .period(PeriodDate.builder().start(Date.from(Instant.parse("2021-01-01T00:00:00.00Z"))).build()) + .build() + ) ) .build() diff --git a/src/test/kotlin/dev/dnpm/etl/processor/services/TransformationServiceTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/services/TransformationServiceTest.kt index 113245a..4a2d2d3 100644 --- a/src/test/kotlin/dev/dnpm/etl/processor/services/TransformationServiceTest.kt +++ b/src/test/kotlin/dev/dnpm/etl/processor/services/TransformationServiceTest.kt @@ -19,20 +19,11 @@ package dev.dnpm.etl.processor.services -import de.ukw.ccc.bwhc.dto.Consent -import de.ukw.ccc.bwhc.dto.Diagnosis -import de.ukw.ccc.bwhc.dto.Icd10 -import de.ukw.ccc.bwhc.dto.MtbFile import dev.dnpm.etl.processor.config.JacksonConfig -import dev.pcvolkmer.mv64e.mtb.ConsentProvision -import dev.pcvolkmer.mv64e.mtb.ModelProjectConsent -import dev.pcvolkmer.mv64e.mtb.ModelProjectConsentPurpose +import dev.pcvolkmer.mv64e.mtb.* import org.assertj.core.api.Assertions.assertThat import org.junit.jupiter.api.BeforeEach import org.junit.jupiter.api.Test -import dev.pcvolkmer.mv64e.mtb.Mtb -import dev.pcvolkmer.mv64e.mtb.MvhMetadata -import dev.pcvolkmer.mv64e.mtb.Provision import org.hl7.fhir.instance.model.api.IBaseResource import java.time.Instant import java.util.Date @@ -45,82 +36,59 @@ class TransformationServiceTest { fun setup() { this.service = TransformationService( JacksonConfig().objectMapper(), listOf( - Transformation.of("consent.status") from Consent.Status.ACTIVE to Consent.Status.REJECTED, - Transformation.of("diagnoses[*].icd10.version") from "2013" to "2014", + Transformation.of("diagnoses[*].code.version") from "2013" to "2014", ) ) } @Test fun shouldTransformMtbFile() { - val mtbFile = MtbFile.builder().withDiagnoses( + val mtbFile = Mtb.builder().diagnoses( listOf( - Diagnosis.builder().withId("1234").withIcd10(Icd10("F79.9").also { - it.version = "2013" - }).build() + MtbDiagnosis.builder().id("1234").code(Coding.builder().code("F79.9").version("2013").build()).build() ) ).build() val actual = this.service.transform(mtbFile) assertThat(actual).isNotNull - assertThat(actual.diagnoses[0].icd10.version).isEqualTo("2014") + assertThat(actual.diagnoses[0].code.version).isEqualTo("2014") } @Test fun shouldOnlyTransformGivenValues() { - val mtbFile = MtbFile.builder().withDiagnoses( + val mtbFile = Mtb.builder().diagnoses( listOf( - Diagnosis.builder().withId("1234").withIcd10(Icd10("F79.9").also { - it.version = "2013" - }).build(), - Diagnosis.builder().withId("5678").withIcd10(Icd10("F79.8").also { - it.version = "2019" - }).build() + MtbDiagnosis.builder().id("1234").code(Coding.builder().code("F79.9").version("2013").build()).build(), + MtbDiagnosis.builder().id("1234").code(Coding.builder().code("F79.8").version("2019").build()).build() ) ).build() val actual = this.service.transform(mtbFile) assertThat(actual).isNotNull - assertThat(actual.diagnoses[0].icd10.code).isEqualTo("F79.9") - assertThat(actual.diagnoses[0].icd10.version).isEqualTo("2014") - assertThat(actual.diagnoses[1].icd10.code).isEqualTo("F79.8") - assertThat(actual.diagnoses[1].icd10.version).isEqualTo("2019") - } - - @Test - fun shouldTransformMtbFileWithConsentEnum() { - val mtbFile = MtbFile.builder().withConsent( - Consent("123", "456", Consent.Status.ACTIVE) - ).build() - - val actual = this.service.transform(mtbFile) - - assertThat(actual.consent).isNotNull - assertThat(actual.consent.status).isEqualTo(Consent.Status.REJECTED) + assertThat(actual.diagnoses[0].code.code).isEqualTo("F79.9") + assertThat(actual.diagnoses[0].code.version).isEqualTo("2014") + assertThat(actual.diagnoses[1].code.code).isEqualTo("F79.8") + assertThat(actual.diagnoses[1].code.version).isEqualTo("2019") } @Test fun shouldTransformConsentValues() { - val mtbFile = MtbFile.builder().withDiagnoses( + val mtbFile = Mtb.builder().diagnoses( listOf( - Diagnosis.builder().withId("1234").withIcd10(Icd10("F79.9").also { - it.version = "2013" - }).build(), - Diagnosis.builder().withId("5678").withIcd10(Icd10("F79.8").also { - it.version = "2019" - }).build() + MtbDiagnosis.builder().id("1234").code(Coding.builder().code("F79.9").version("2013").build()).build(), + MtbDiagnosis.builder().id("1234").code(Coding.builder().code("F79.8").version("2019").build()).build() ) ).build() val actual = this.service.transform(mtbFile) assertThat(actual).isNotNull - assertThat(actual.diagnoses[0].icd10.code).isEqualTo("F79.9") - assertThat(actual.diagnoses[0].icd10.version).isEqualTo("2014") - assertThat(actual.diagnoses[1].icd10.code).isEqualTo("F79.8") - assertThat(actual.diagnoses[1].icd10.version).isEqualTo("2019") + assertThat(actual.diagnoses[0].code.code).isEqualTo("F79.9") + assertThat(actual.diagnoses[0].code.version).isEqualTo("2014") + assertThat(actual.diagnoses[1].code.code).isEqualTo("F79.8") + assertThat(actual.diagnoses[1].code.version).isEqualTo("2019") } @Test @@ -155,5 +123,4 @@ class TransformationServiceTest { } - -}
\ No newline at end of file +} |