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21
README.md
21
README.md
@ -52,8 +52,6 @@ Soll noch das alte bwHC-Backend verwendet werden, so ist die Umgebungsvariable
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In Versionen des ETL-Processors **nach Version 0.10** werden die folgenden Konfigurationsoptionen entfernt:
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In Versionen des ETL-Processors **nach Version 0.10** werden die folgenden Konfigurationsoptionen entfernt:
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* `APP_PSEUDONYMIZE_GPAS_SSLCALOCATION`: Nutzen Sie hier, wie unter [_Integration eines eigenen Root CA
|
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Zertifikats_](#integration-eines-eigenen-root-ca-zertifikats) beschrieben, das Einbinden eigener Zertifikate.
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* `APP_KAFKA_TOPIC`: Nutzen Sie nun die Konfigurationsoption `APP_KAFKA_OUTPUT_TOPIC`
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* `APP_KAFKA_TOPIC`: Nutzen Sie nun die Konfigurationsoption `APP_KAFKA_OUTPUT_TOPIC`
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* `APP_KAFKA_RESPONSE_TOPIC`: Nutzen Sie nun die Konfigurationsoption `APP_KAFKA_OUTPUT_RESPONSE_TOPIC`
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* `APP_KAFKA_RESPONSE_TOPIC`: Nutzen Sie nun die Konfigurationsoption `APP_KAFKA_OUTPUT_RESPONSE_TOPIC`
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@ -68,13 +66,11 @@ Ist diese nicht gesetzt. wird intern eine Anonymisierung der Patienten-ID vorgen
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* `APP_PSEUDONYMIZE_PREFIX`: Standortbezogenes Präfix - `UNKNOWN`, wenn nicht gesetzt
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* `APP_PSEUDONYMIZE_PREFIX`: Standortbezogenes Präfix - `UNKNOWN`, wenn nicht gesetzt
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* `APP_PSEUDONYMIZE_GENERATOR`: `BUILDIN` oder `GPAS` - `BUILDIN`, wenn nicht gesetzt
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* `APP_PSEUDONYMIZE_GENERATOR`: `BUILDIN` oder `GPAS` - `BUILDIN`, wenn nicht gesetzt
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**Hinweise**:
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**Hinweis**
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* Der alte Konfigurationsparameter `APP_PSEUDONYMIZER` mit den Werten `GPAS` oder `BUILDIN` sollte nicht mehr verwendet
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Die Pseudonymisierung erfolgt im ETL-Prozessor nur für die Patienten-ID.
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werden.
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Andere IDs werden mithilfe des standortbezogenen Präfixes (erneut) anonymisiert, um für den aktuellen Kontext nicht
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* Die Pseudonymisierung erfolgt im ETL-Prozessor nur für die Patienten-ID.
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vergleichbare IDs bereitzustellen.
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Andere IDs werden mithilfe des standortbezogenen Präfixes (erneut) anonymisiert, um für den aktuellen Kontext nicht
|
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vergleichbare IDs bereitzustellen.
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#### Eingebaute Anonymisierung
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#### Eingebaute Anonymisierung
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@ -90,13 +86,6 @@ Wurde die Verwendung von gPAS konfiguriert, so sind weitere Angaben zu konfiguri
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* `APP_PSEUDONYMIZE_GPAS_TARGET`: gPas Domänenname
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* `APP_PSEUDONYMIZE_GPAS_TARGET`: gPas Domänenname
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* `APP_PSEUDONYMIZE_GPAS_USERNAME`: gPas Basic-Auth Benutzername
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* `APP_PSEUDONYMIZE_GPAS_USERNAME`: gPas Basic-Auth Benutzername
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* `APP_PSEUDONYMIZE_GPAS_PASSWORD`: gPas Basic-Auth Passwort
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* `APP_PSEUDONYMIZE_GPAS_PASSWORD`: gPas Basic-Auth Passwort
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* ~~`APP_PSEUDONYMIZE_GPAS_SSLCALOCATION`~~: **Veraltet** - Root Zertifikat für gPas, falls es dediziert hinzugefügt werden muss.
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**Wird in nach Version 0.10 entfernt**
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Der Konfigurationsparameter `APP_PSEUDONYMIZE_GPAS_SSLCALOCATION` sollte nicht mehr verwendet werden und wird nach
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Version 0.10 entfernt.
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Stattdessen sollte das Root Zertifikat wie unter [_Integration eines eigenen Root CA
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Zertifikats_](#integration-eines-eigenen-root-ca-zertifikats) beschrieben eingebunden werden.
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### Anmeldung mit einem Passwort
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### Anmeldung mit einem Passwort
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@ -226,9 +215,7 @@ Folgende Umgebungsvariablen müssen gesetzt sein, damit ein bwHC-MTB-File an DNP
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Folgende Umgebungsvariablen müssen gesetzt sein, damit ein bwHC-MTB-File an ein Kafka-Topic übermittelt wird:
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Folgende Umgebungsvariablen müssen gesetzt sein, damit ein bwHC-MTB-File an ein Kafka-Topic übermittelt wird:
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* `APP_KAFKA_OUTPUT_TOPIC`: Zu verwendendes Topic zum Versenden von Anfragen.
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* `APP_KAFKA_OUTPUT_TOPIC`: Zu verwendendes Topic zum Versenden von Anfragen.
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Ersetzt ~~`APP_KAFKA_TOPIC`~~, **welches nach Version 0.10 entfernt wird**.
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* `APP_KAFKA_OUTPUT_RESPONSE_TOPIC`: Topic mit Antworten über den Erfolg des Versendens. Standardwert: `APP_KAFKA_TOPIC` mit Anhang "_response".
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* `APP_KAFKA_OUTPUT_RESPONSE_TOPIC`: Topic mit Antworten über den Erfolg des Versendens. Standardwert: `APP_KAFKA_TOPIC` mit Anhang "_response".
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Ersetzt ~~`APP_KAFKA_RESPONSE_TOPIC`~~, **welches nach Version 0.10 entfernt wird**.
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* `APP_KAFKA_GROUP_ID`: Kafka GroupID des Consumers. Standardwert: `APP_KAFKA_TOPIC` mit Anhang "_group".
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* `APP_KAFKA_GROUP_ID`: Kafka GroupID des Consumers. Standardwert: `APP_KAFKA_TOPIC` mit Anhang "_group".
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* `APP_KAFKA_SERVERS`: Zu verwendende Kafka-Bootstrap-Server als kommagetrennte Liste
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* `APP_KAFKA_SERVERS`: Zu verwendende Kafka-Bootstrap-Server als kommagetrennte Liste
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@ -5,7 +5,7 @@ import org.springframework.boot.gradle.tasks.bundling.BootBuildImage
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plugins {
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plugins {
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war
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war
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id("org.springframework.boot") version "3.3.10"
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id("org.springframework.boot") version "3.4.4"
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id("io.spring.dependency-management") version "1.1.7"
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id("io.spring.dependency-management") version "1.1.7"
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kotlin("jvm") version "1.9.25"
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kotlin("jvm") version "1.9.25"
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kotlin("plugin.spring") version "1.9.25"
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kotlin("plugin.spring") version "1.9.25"
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@ -13,12 +13,12 @@ plugins {
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}
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}
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group = "dev.dnpm"
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group = "dev.dnpm"
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version = "0.10.0-SNAPSHOT"
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version = "0.11.0-SNAPSHOT"
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var versions = mapOf(
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var versions = mapOf(
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"bwhc-dto-java" to "0.4.0",
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"bwhc-dto-java" to "0.4.0",
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"mtb-dto" to "0.1.0-SNAPSHOT",
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"hapi-fhir" to "7.6.0",
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"hapi-fhir" to "7.6.0",
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"commons-compress" to "1.26.2",
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"mockito-kotlin" to "5.4.0",
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"mockito-kotlin" to "5.4.0",
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"archunit" to "1.3.0",
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"archunit" to "1.3.0",
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// Webjars
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// Webjars
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@ -49,9 +49,18 @@ configurations {
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compileOnly {
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compileOnly {
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extendsFrom(configurations.annotationProcessor.get())
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extendsFrom(configurations.annotationProcessor.get())
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}
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}
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all {
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resolutionStrategy {
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cacheChangingModulesFor(5, "minutes")
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}
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}
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}
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}
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repositories {
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repositories {
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maven {
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url = uri("https://git.dnpm.dev/api/packages/public-snapshots/maven")
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||||||
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}
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||||||
maven {
|
maven {
|
||||||
url = uri("https://git.dnpm.dev/api/packages/public/maven")
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url = uri("https://git.dnpm.dev/api/packages/public/maven")
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||||||
}
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}
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@ -73,6 +82,7 @@ dependencies {
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implementation("commons-codec:commons-codec")
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implementation("commons-codec:commons-codec")
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implementation("io.projectreactor.kotlin:reactor-kotlin-extensions")
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implementation("io.projectreactor.kotlin:reactor-kotlin-extensions")
|
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implementation("de.ukw.ccc:bwhc-dto-java:${versions["bwhc-dto-java"]}")
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implementation("de.ukw.ccc:bwhc-dto-java:${versions["bwhc-dto-java"]}")
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implementation("dev.pcvolkmer.mv64e:mtb-dto:${versions["mtb-dto"]}") { isChanging = true }
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||||||
implementation("ca.uhn.hapi.fhir:hapi-fhir-base:${versions["hapi-fhir"]}")
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implementation("ca.uhn.hapi.fhir:hapi-fhir-base:${versions["hapi-fhir"]}")
|
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implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${versions["hapi-fhir"]}")
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implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${versions["hapi-fhir"]}")
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implementation("org.apache.httpcomponents.client5:httpclient5")
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implementation("org.apache.httpcomponents.client5:httpclient5")
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@ -99,10 +109,8 @@ dependencies {
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|||||||
integrationTestImplementation("org.testcontainers:junit-jupiter")
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integrationTestImplementation("org.testcontainers:junit-jupiter")
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integrationTestImplementation("org.testcontainers:postgresql")
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integrationTestImplementation("org.testcontainers:postgresql")
|
||||||
integrationTestImplementation("com.tngtech.archunit:archunit:${versions["archunit"]}")
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integrationTestImplementation("com.tngtech.archunit:archunit:${versions["archunit"]}")
|
||||||
integrationTestImplementation("net.sourceforge.htmlunit:htmlunit")
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integrationTestImplementation("org.htmlunit:htmlunit")
|
||||||
integrationTestImplementation("org.springframework:spring-webflux")
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integrationTestImplementation("org.springframework:spring-webflux")
|
||||||
// Override dependency version from org.testcontainers:junit-jupiter - CVE-2024-26308, CVE-2024-25710
|
|
||||||
integrationTestImplementation("org.apache.commons:commons-compress:${versions["commons-compress"]}")
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|
||||||
}
|
}
|
||||||
|
|
||||||
tasks.withType<KotlinCompile> {
|
tasks.withType<KotlinCompile> {
|
||||||
@ -119,8 +127,9 @@ tasks.withType<Test> {
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
task<Test>("integrationTest") {
|
tasks.register<Test>("integrationTest") {
|
||||||
description = "Runs integration tests"
|
description = "Runs integration tests"
|
||||||
|
group = "verification"
|
||||||
|
|
||||||
testClassesDirs = sourceSets["integrationTest"].output.classesDirs
|
testClassesDirs = sourceSets["integrationTest"].output.classesDirs
|
||||||
classpath = sourceSets["integrationTest"].runtimeClasspath
|
classpath = sourceSets["integrationTest"].runtimeClasspath
|
||||||
|
@ -23,6 +23,7 @@ import com.fasterxml.jackson.databind.ObjectMapper
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|||||||
import de.ukw.ccc.bwhc.dto.*
|
import de.ukw.ccc.bwhc.dto.*
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestRepository
|
import dev.dnpm.etl.processor.monitoring.RequestRepository
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||||
|
import dev.dnpm.etl.processor.output.BwhcV1MtbFileRequest
|
||||||
import dev.dnpm.etl.processor.output.MtbFileSender
|
import dev.dnpm.etl.processor.output.MtbFileSender
|
||||||
import org.assertj.core.api.Assertions.assertThat
|
import org.assertj.core.api.Assertions.assertThat
|
||||||
import org.junit.jupiter.api.BeforeEach
|
import org.junit.jupiter.api.BeforeEach
|
||||||
@ -33,10 +34,10 @@ import org.mockito.kotlin.*
|
|||||||
import org.springframework.beans.factory.annotation.Autowired
|
import org.springframework.beans.factory.annotation.Autowired
|
||||||
import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc
|
import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc
|
||||||
import org.springframework.boot.test.context.SpringBootTest
|
import org.springframework.boot.test.context.SpringBootTest
|
||||||
import org.springframework.boot.test.mock.mockito.MockBean
|
|
||||||
import org.springframework.context.ApplicationContext
|
import org.springframework.context.ApplicationContext
|
||||||
import org.springframework.http.MediaType
|
import org.springframework.http.MediaType
|
||||||
import org.springframework.test.context.TestPropertySource
|
import org.springframework.test.context.TestPropertySource
|
||||||
|
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||||
import org.springframework.test.context.junit.jupiter.SpringExtension
|
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||||
import org.springframework.test.web.servlet.MockMvc
|
import org.springframework.test.web.servlet.MockMvc
|
||||||
import org.springframework.test.web.servlet.post
|
import org.springframework.test.web.servlet.post
|
||||||
@ -45,7 +46,7 @@ import org.testcontainers.junit.jupiter.Testcontainers
|
|||||||
@Testcontainers
|
@Testcontainers
|
||||||
@ExtendWith(SpringExtension::class)
|
@ExtendWith(SpringExtension::class)
|
||||||
@SpringBootTest
|
@SpringBootTest
|
||||||
@MockBean(MtbFileSender::class)
|
@MockitoBean(types = [MtbFileSender::class])
|
||||||
@TestPropertySource(
|
@TestPropertySource(
|
||||||
properties = [
|
properties = [
|
||||||
"app.rest.uri=http://example.com",
|
"app.rest.uri=http://example.com",
|
||||||
@ -73,7 +74,7 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
|
|||||||
)
|
)
|
||||||
inner class TransformationTest {
|
inner class TransformationTest {
|
||||||
|
|
||||||
@MockBean
|
@MockitoBean
|
||||||
private lateinit var mtbFileSender: MtbFileSender
|
private lateinit var mtbFileSender: MtbFileSender
|
||||||
|
|
||||||
@Autowired
|
@Autowired
|
||||||
@ -91,7 +92,7 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
|
|||||||
fun mtbFileIsTransformed() {
|
fun mtbFileIsTransformed() {
|
||||||
doAnswer {
|
doAnswer {
|
||||||
MtbFileSender.Response(RequestStatus.SUCCESS)
|
MtbFileSender.Response(RequestStatus.SUCCESS)
|
||||||
}.whenever(mtbFileSender).send(any<MtbFileSender.MtbFileRequest>())
|
}.whenever(mtbFileSender).send(any<BwhcV1MtbFileRequest>())
|
||||||
|
|
||||||
val mtbFile = MtbFile.builder()
|
val mtbFile = MtbFile.builder()
|
||||||
.withPatient(
|
.withPatient(
|
||||||
@ -134,9 +135,9 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
val captor = argumentCaptor<MtbFileSender.MtbFileRequest>()
|
val captor = argumentCaptor<BwhcV1MtbFileRequest>()
|
||||||
verify(mtbFileSender).send(captor.capture())
|
verify(mtbFileSender).send(captor.capture())
|
||||||
assertThat(captor.firstValue.mtbFile.diagnoses).hasSize(1).allMatch { diagnosis ->
|
assertThat(captor.firstValue.content.diagnoses).hasSize(1).allMatch { diagnosis ->
|
||||||
diagnosis.icd10.version == "2014"
|
diagnosis.icd10.version == "2014"
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
@ -26,9 +26,9 @@ import dev.dnpm.etl.processor.output.KafkaMtbFileSender
|
|||||||
import dev.dnpm.etl.processor.output.RestMtbFileSender
|
import dev.dnpm.etl.processor.output.RestMtbFileSender
|
||||||
import dev.dnpm.etl.processor.pseudonym.AnonymizingGenerator
|
import dev.dnpm.etl.processor.pseudonym.AnonymizingGenerator
|
||||||
import dev.dnpm.etl.processor.pseudonym.GpasPseudonymGenerator
|
import dev.dnpm.etl.processor.pseudonym.GpasPseudonymGenerator
|
||||||
import dev.dnpm.etl.processor.services.RequestProcessor
|
|
||||||
import dev.dnpm.etl.processor.security.TokenRepository
|
import dev.dnpm.etl.processor.security.TokenRepository
|
||||||
import dev.dnpm.etl.processor.security.TokenService
|
import dev.dnpm.etl.processor.security.TokenService
|
||||||
|
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||||
import org.assertj.core.api.Assertions.assertThat
|
import org.assertj.core.api.Assertions.assertThat
|
||||||
import org.junit.jupiter.api.Nested
|
import org.junit.jupiter.api.Nested
|
||||||
import org.junit.jupiter.api.Test
|
import org.junit.jupiter.api.Test
|
||||||
@ -36,24 +36,25 @@ import org.junit.jupiter.api.assertThrows
|
|||||||
import org.springframework.beans.factory.NoSuchBeanDefinitionException
|
import org.springframework.beans.factory.NoSuchBeanDefinitionException
|
||||||
import org.springframework.boot.autoconfigure.kafka.KafkaAutoConfiguration
|
import org.springframework.boot.autoconfigure.kafka.KafkaAutoConfiguration
|
||||||
import org.springframework.boot.test.context.SpringBootTest
|
import org.springframework.boot.test.context.SpringBootTest
|
||||||
import org.springframework.boot.test.mock.mockito.MockBean
|
|
||||||
import org.springframework.boot.test.mock.mockito.MockBeans
|
|
||||||
import org.springframework.context.ApplicationContext
|
import org.springframework.context.ApplicationContext
|
||||||
import org.springframework.retry.support.RetryTemplate
|
import org.springframework.retry.support.RetryTemplate
|
||||||
import org.springframework.security.crypto.password.PasswordEncoder
|
import org.springframework.security.crypto.password.PasswordEncoder
|
||||||
import org.springframework.security.provisioning.InMemoryUserDetailsManager
|
import org.springframework.security.provisioning.InMemoryUserDetailsManager
|
||||||
import org.springframework.test.context.ContextConfiguration
|
import org.springframework.test.context.ContextConfiguration
|
||||||
import org.springframework.test.context.TestPropertySource
|
import org.springframework.test.context.TestPropertySource
|
||||||
|
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||||
|
|
||||||
@SpringBootTest
|
@SpringBootTest
|
||||||
@ContextConfiguration(classes = [
|
@ContextConfiguration(
|
||||||
|
classes = [
|
||||||
AppConfiguration::class,
|
AppConfiguration::class,
|
||||||
AppSecurityConfiguration::class,
|
AppSecurityConfiguration::class,
|
||||||
KafkaAutoConfiguration::class,
|
KafkaAutoConfiguration::class,
|
||||||
AppKafkaConfiguration::class,
|
AppKafkaConfiguration::class,
|
||||||
AppRestConfiguration::class
|
AppRestConfiguration::class
|
||||||
])
|
]
|
||||||
@MockBean(ObjectMapper::class)
|
)
|
||||||
|
@MockitoBean(types = [ObjectMapper::class])
|
||||||
@TestPropertySource(
|
@TestPropertySource(
|
||||||
properties = [
|
properties = [
|
||||||
"app.pseudonymize.generator=BUILDIN",
|
"app.pseudonymize.generator=BUILDIN",
|
||||||
@ -86,7 +87,7 @@ class AppConfigurationTest {
|
|||||||
"app.kafka.group-id=test"
|
"app.kafka.group-id=test"
|
||||||
]
|
]
|
||||||
)
|
)
|
||||||
@MockBean(RequestRepository::class)
|
@MockitoBean(types = [RequestRepository::class])
|
||||||
inner class AppConfigurationKafkaTest(private val context: ApplicationContext) {
|
inner class AppConfigurationKafkaTest(private val context: ApplicationContext) {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
@ -145,7 +146,7 @@ class AppConfigurationTest {
|
|||||||
"app.kafka.group-id=test"
|
"app.kafka.group-id=test"
|
||||||
]
|
]
|
||||||
)
|
)
|
||||||
@MockBean(RequestProcessor::class)
|
@MockitoBean(types = [RequestProcessor::class])
|
||||||
inner class AppConfigurationUsingKafkaInputTest(private val context: ApplicationContext) {
|
inner class AppConfigurationUsingKafkaInputTest(private val context: ApplicationContext) {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
@ -181,40 +182,7 @@ class AppConfigurationTest {
|
|||||||
@Nested
|
@Nested
|
||||||
@TestPropertySource(
|
@TestPropertySource(
|
||||||
properties = [
|
properties = [
|
||||||
"app.pseudonymize.generator=",
|
"app.pseudonymize.generator=buildin"
|
||||||
"app.pseudonymizer=buildin",
|
|
||||||
]
|
|
||||||
)
|
|
||||||
inner class AppConfigurationPseudonymizerBuildinTest(private val context: ApplicationContext) {
|
|
||||||
|
|
||||||
@Test
|
|
||||||
fun shouldUseConfiguredGenerator() {
|
|
||||||
assertThat(context.getBean(AnonymizingGenerator::class.java)).isNotNull
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
@Nested
|
|
||||||
@TestPropertySource(
|
|
||||||
properties = [
|
|
||||||
"app.pseudonymize.generator=",
|
|
||||||
"app.pseudonymizer=gpas",
|
|
||||||
]
|
|
||||||
)
|
|
||||||
inner class AppConfigurationPseudonymizerGpasTest(private val context: ApplicationContext) {
|
|
||||||
|
|
||||||
@Test
|
|
||||||
fun shouldUseConfiguredGenerator() {
|
|
||||||
assertThat(context.getBean(GpasPseudonymGenerator::class.java)).isNotNull
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
@Nested
|
|
||||||
@TestPropertySource(
|
|
||||||
properties = [
|
|
||||||
"app.pseudonymize.generator=buildin",
|
|
||||||
"app.pseudonymizer=",
|
|
||||||
]
|
]
|
||||||
)
|
)
|
||||||
inner class AppConfigurationPseudonymizeGeneratorBuildinTest(private val context: ApplicationContext) {
|
inner class AppConfigurationPseudonymizeGeneratorBuildinTest(private val context: ApplicationContext) {
|
||||||
@ -229,8 +197,7 @@ class AppConfigurationTest {
|
|||||||
@Nested
|
@Nested
|
||||||
@TestPropertySource(
|
@TestPropertySource(
|
||||||
properties = [
|
properties = [
|
||||||
"app.pseudonymize.generator=gpas",
|
"app.pseudonymize.generator=gpas"
|
||||||
"app.pseudonymizer=",
|
|
||||||
]
|
]
|
||||||
)
|
)
|
||||||
inner class AppConfigurationPseudonymizeGeneratorGpasTest(private val context: ApplicationContext) {
|
inner class AppConfigurationPseudonymizeGeneratorGpasTest(private val context: ApplicationContext) {
|
||||||
@ -248,11 +215,13 @@ class AppConfigurationTest {
|
|||||||
"app.security.enable-tokens=true"
|
"app.security.enable-tokens=true"
|
||||||
]
|
]
|
||||||
)
|
)
|
||||||
@MockBeans(value = [
|
@MockitoBean(
|
||||||
MockBean(InMemoryUserDetailsManager::class),
|
types = [
|
||||||
MockBean(PasswordEncoder::class),
|
InMemoryUserDetailsManager::class,
|
||||||
MockBean(TokenRepository::class)
|
PasswordEncoder::class,
|
||||||
])
|
TokenRepository::class
|
||||||
|
]
|
||||||
|
)
|
||||||
inner class AppConfigurationTokenEnabledTest(private val context: ApplicationContext) {
|
inner class AppConfigurationTokenEnabledTest(private val context: ApplicationContext) {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
@ -263,11 +232,13 @@ class AppConfigurationTest {
|
|||||||
}
|
}
|
||||||
|
|
||||||
@Nested
|
@Nested
|
||||||
@MockBeans(value = [
|
@MockitoBean(
|
||||||
MockBean(InMemoryUserDetailsManager::class),
|
types = [
|
||||||
MockBean(PasswordEncoder::class),
|
InMemoryUserDetailsManager::class,
|
||||||
MockBean(TokenRepository::class)
|
PasswordEncoder::class,
|
||||||
])
|
TokenRepository::class
|
||||||
|
]
|
||||||
|
)
|
||||||
inner class AppConfigurationTokenDisabledTest(private val context: ApplicationContext) {
|
inner class AppConfigurationTokenDisabledTest(private val context: ApplicationContext) {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
|
@ -37,13 +37,13 @@ import org.mockito.kotlin.times
|
|||||||
import org.mockito.kotlin.verify
|
import org.mockito.kotlin.verify
|
||||||
import org.springframework.beans.factory.annotation.Autowired
|
import org.springframework.beans.factory.annotation.Autowired
|
||||||
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
||||||
import org.springframework.boot.test.mock.mockito.MockBean
|
|
||||||
import org.springframework.http.MediaType
|
import org.springframework.http.MediaType
|
||||||
import org.springframework.security.oauth2.client.registration.ClientRegistrationRepository
|
import org.springframework.security.oauth2.client.registration.ClientRegistrationRepository
|
||||||
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.anonymous
|
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.anonymous
|
||||||
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user
|
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user
|
||||||
import org.springframework.test.context.ContextConfiguration
|
import org.springframework.test.context.ContextConfiguration
|
||||||
import org.springframework.test.context.TestPropertySource
|
import org.springframework.test.context.TestPropertySource
|
||||||
|
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||||
import org.springframework.test.context.junit.jupiter.SpringExtension
|
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||||
import org.springframework.test.web.servlet.MockMvc
|
import org.springframework.test.web.servlet.MockMvc
|
||||||
import org.springframework.test.web.servlet.delete
|
import org.springframework.test.web.servlet.delete
|
||||||
@ -57,7 +57,7 @@ import org.springframework.test.web.servlet.post
|
|||||||
AppSecurityConfiguration::class
|
AppSecurityConfiguration::class
|
||||||
]
|
]
|
||||||
)
|
)
|
||||||
@MockBean(TokenRepository::class, RequestProcessor::class)
|
@MockitoBean(types = [TokenRepository::class, RequestProcessor::class])
|
||||||
@TestPropertySource(
|
@TestPropertySource(
|
||||||
properties = [
|
properties = [
|
||||||
"app.pseudonymize.generator=BUILDIN",
|
"app.pseudonymize.generator=BUILDIN",
|
||||||
@ -91,7 +91,7 @@ class MtbFileRestControllerTest {
|
|||||||
status { isAccepted() }
|
status { isAccepted() }
|
||||||
}
|
}
|
||||||
|
|
||||||
verify(requestProcessor, times(1)).processMtbFile(any())
|
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
@ -104,7 +104,7 @@ class MtbFileRestControllerTest {
|
|||||||
status { isAccepted() }
|
status { isAccepted() }
|
||||||
}
|
}
|
||||||
|
|
||||||
verify(requestProcessor, times(1)).processMtbFile(any())
|
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
@ -117,7 +117,7 @@ class MtbFileRestControllerTest {
|
|||||||
status { isUnauthorized() }
|
status { isUnauthorized() }
|
||||||
}
|
}
|
||||||
|
|
||||||
verify(requestProcessor, never()).processMtbFile(any())
|
verify(requestProcessor, never()).processMtbFile(any<MtbFile>())
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
@ -130,7 +130,7 @@ class MtbFileRestControllerTest {
|
|||||||
status { isForbidden() }
|
status { isForbidden() }
|
||||||
}
|
}
|
||||||
|
|
||||||
verify(requestProcessor, never()).processMtbFile(any())
|
verify(requestProcessor, never()).processMtbFile(any<MtbFile>())
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
@ -156,7 +156,7 @@ class MtbFileRestControllerTest {
|
|||||||
}
|
}
|
||||||
|
|
||||||
@Nested
|
@Nested
|
||||||
@MockBean(UserRoleRepository::class, ClientRegistrationRepository::class)
|
@MockitoBean(types = [UserRoleRepository::class, ClientRegistrationRepository::class])
|
||||||
@TestPropertySource(
|
@TestPropertySource(
|
||||||
properties = [
|
properties = [
|
||||||
"app.pseudonymize.generator=BUILDIN",
|
"app.pseudonymize.generator=BUILDIN",
|
||||||
@ -177,7 +177,7 @@ class MtbFileRestControllerTest {
|
|||||||
status { isAccepted() }
|
status { isAccepted() }
|
||||||
}
|
}
|
||||||
|
|
||||||
verify(requestProcessor, times(1)).processMtbFile(any())
|
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
@ -190,7 +190,7 @@ class MtbFileRestControllerTest {
|
|||||||
status { isAccepted() }
|
status { isAccepted() }
|
||||||
}
|
}
|
||||||
|
|
||||||
verify(requestProcessor, times(1)).processMtbFile(any())
|
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -27,8 +27,8 @@ import org.junit.jupiter.api.extension.ExtendWith
|
|||||||
import org.springframework.beans.factory.annotation.Autowired
|
import org.springframework.beans.factory.annotation.Autowired
|
||||||
import org.springframework.boot.test.autoconfigure.data.jdbc.DataJdbcTest
|
import org.springframework.boot.test.autoconfigure.data.jdbc.DataJdbcTest
|
||||||
import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase
|
import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase
|
||||||
import org.springframework.boot.test.mock.mockito.MockBean
|
|
||||||
import org.springframework.test.context.TestPropertySource
|
import org.springframework.test.context.TestPropertySource
|
||||||
|
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||||
import org.springframework.test.context.junit.jupiter.SpringExtension
|
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||||
import org.springframework.transaction.annotation.Transactional
|
import org.springframework.transaction.annotation.Transactional
|
||||||
import org.testcontainers.junit.jupiter.Testcontainers
|
import org.testcontainers.junit.jupiter.Testcontainers
|
||||||
@ -39,7 +39,7 @@ import java.time.Instant
|
|||||||
@DataJdbcTest
|
@DataJdbcTest
|
||||||
@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE)
|
@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE)
|
||||||
@Transactional
|
@Transactional
|
||||||
@MockBean(MtbFileSender::class)
|
@MockitoBean(types = [MtbFileSender::class])
|
||||||
@TestPropertySource(
|
@TestPropertySource(
|
||||||
properties = [
|
properties = [
|
||||||
"app.pseudonymize.generator=buildin",
|
"app.pseudonymize.generator=buildin",
|
||||||
|
@ -1,7 +1,7 @@
|
|||||||
/*
|
/*
|
||||||
* This file is part of ETL-Processor
|
* This file is part of ETL-Processor
|
||||||
*
|
*
|
||||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
* 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
|
* 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
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
@ -47,10 +47,9 @@ class GpasPseudonymGeneratorTest {
|
|||||||
fun setup() {
|
fun setup() {
|
||||||
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
|
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
|
||||||
val gPasConfigProperties = GPasConfigProperties(
|
val gPasConfigProperties = GPasConfigProperties(
|
||||||
"http://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate",
|
"https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate",
|
||||||
"test",
|
"test",
|
||||||
null,
|
null,
|
||||||
null,
|
|
||||||
null
|
null
|
||||||
)
|
)
|
||||||
|
|
||||||
@ -63,7 +62,7 @@ class GpasPseudonymGeneratorTest {
|
|||||||
fun shouldReturnExpectedPseudonym() {
|
fun shouldReturnExpectedPseudonym() {
|
||||||
this.mockRestServiceServer.expect {
|
this.mockRestServiceServer.expect {
|
||||||
method(HttpMethod.POST)
|
method(HttpMethod.POST)
|
||||||
requestTo("http://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
|
requestTo("https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
|
||||||
}.andRespond {
|
}.andRespond {
|
||||||
withStatus(HttpStatus.OK).body(getDummyResponseBody("1234", "test", "test1234ABCDEF567890"))
|
withStatus(HttpStatus.OK).body(getDummyResponseBody("1234", "test", "test1234ABCDEF567890"))
|
||||||
.createResponse(it)
|
.createResponse(it)
|
||||||
@ -76,7 +75,7 @@ class GpasPseudonymGeneratorTest {
|
|||||||
fun shouldThrowExceptionIfGpasNotAvailable() {
|
fun shouldThrowExceptionIfGpasNotAvailable() {
|
||||||
this.mockRestServiceServer.expect {
|
this.mockRestServiceServer.expect {
|
||||||
method(HttpMethod.POST)
|
method(HttpMethod.POST)
|
||||||
requestTo("http://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
|
requestTo("https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
|
||||||
}.andRespond {
|
}.andRespond {
|
||||||
withException(IOException("Simulated IO error")).createResponse(it)
|
withException(IOException("Simulated IO error")).createResponse(it)
|
||||||
}
|
}
|
||||||
@ -88,7 +87,7 @@ class GpasPseudonymGeneratorTest {
|
|||||||
fun shouldThrowExceptionIfGpasDoesNotReturn2xxResponse() {
|
fun shouldThrowExceptionIfGpasDoesNotReturn2xxResponse() {
|
||||||
this.mockRestServiceServer.expect {
|
this.mockRestServiceServer.expect {
|
||||||
method(HttpMethod.POST)
|
method(HttpMethod.POST)
|
||||||
requestTo("http://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
|
requestTo("https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
|
||||||
}.andRespond {
|
}.andRespond {
|
||||||
withStatus(HttpStatus.FOUND)
|
withStatus(HttpStatus.FOUND)
|
||||||
.header(HttpHeaders.LOCATION, "https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
|
.header(HttpHeaders.LOCATION, "https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
|
||||||
|
@ -31,8 +31,8 @@ import org.junit.jupiter.api.Test
|
|||||||
import org.junit.jupiter.api.extension.ExtendWith
|
import org.junit.jupiter.api.extension.ExtendWith
|
||||||
import org.springframework.beans.factory.annotation.Autowired
|
import org.springframework.beans.factory.annotation.Autowired
|
||||||
import org.springframework.boot.test.context.SpringBootTest
|
import org.springframework.boot.test.context.SpringBootTest
|
||||||
import org.springframework.boot.test.mock.mockito.MockBean
|
|
||||||
import org.springframework.test.context.TestPropertySource
|
import org.springframework.test.context.TestPropertySource
|
||||||
|
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||||
import org.springframework.test.context.junit.jupiter.SpringExtension
|
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||||
import org.springframework.transaction.annotation.Transactional
|
import org.springframework.transaction.annotation.Transactional
|
||||||
import org.testcontainers.junit.jupiter.Testcontainers
|
import org.testcontainers.junit.jupiter.Testcontainers
|
||||||
@ -42,7 +42,7 @@ import java.time.Instant
|
|||||||
@ExtendWith(SpringExtension::class)
|
@ExtendWith(SpringExtension::class)
|
||||||
@SpringBootTest
|
@SpringBootTest
|
||||||
@Transactional
|
@Transactional
|
||||||
@MockBean(MtbFileSender::class)
|
@MockitoBean(types = [MtbFileSender::class])
|
||||||
@TestPropertySource(
|
@TestPropertySource(
|
||||||
properties = [
|
properties = [
|
||||||
"app.pseudonymize.generator=buildin",
|
"app.pseudonymize.generator=buildin",
|
||||||
|
@ -19,8 +19,6 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.web
|
package dev.dnpm.etl.processor.web
|
||||||
|
|
||||||
import com.gargoylesoftware.htmlunit.WebClient
|
|
||||||
import com.gargoylesoftware.htmlunit.html.HtmlPage
|
|
||||||
import dev.dnpm.etl.processor.config.AppConfiguration
|
import dev.dnpm.etl.processor.config.AppConfiguration
|
||||||
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||||
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
|
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
|
||||||
@ -29,11 +27,13 @@ import dev.dnpm.etl.processor.monitoring.RestConnectionCheckService
|
|||||||
import dev.dnpm.etl.processor.output.MtbFileSender
|
import dev.dnpm.etl.processor.output.MtbFileSender
|
||||||
import dev.dnpm.etl.processor.pseudonym.Generator
|
import dev.dnpm.etl.processor.pseudonym.Generator
|
||||||
import dev.dnpm.etl.processor.security.Role
|
import dev.dnpm.etl.processor.security.Role
|
||||||
import dev.dnpm.etl.processor.services.RequestProcessor
|
|
||||||
import dev.dnpm.etl.processor.security.TokenService
|
import dev.dnpm.etl.processor.security.TokenService
|
||||||
import dev.dnpm.etl.processor.services.TransformationService
|
|
||||||
import dev.dnpm.etl.processor.security.UserRoleService
|
import dev.dnpm.etl.processor.security.UserRoleService
|
||||||
|
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||||
|
import dev.dnpm.etl.processor.services.TransformationService
|
||||||
import org.assertj.core.api.Assertions.assertThat
|
import org.assertj.core.api.Assertions.assertThat
|
||||||
|
import org.htmlunit.WebClient
|
||||||
|
import org.htmlunit.html.HtmlPage
|
||||||
import org.junit.jupiter.api.BeforeEach
|
import org.junit.jupiter.api.BeforeEach
|
||||||
import org.junit.jupiter.api.Nested
|
import org.junit.jupiter.api.Nested
|
||||||
import org.junit.jupiter.api.Test
|
import org.junit.jupiter.api.Test
|
||||||
@ -46,7 +46,6 @@ import org.mockito.kotlin.verify
|
|||||||
import org.mockito.kotlin.whenever
|
import org.mockito.kotlin.whenever
|
||||||
import org.springframework.beans.factory.annotation.Autowired
|
import org.springframework.beans.factory.annotation.Autowired
|
||||||
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
||||||
import org.springframework.boot.test.mock.mockito.MockBean
|
|
||||||
import org.springframework.http.HttpHeaders
|
import org.springframework.http.HttpHeaders
|
||||||
import org.springframework.http.MediaType
|
import org.springframework.http.MediaType
|
||||||
import org.springframework.http.MediaType.TEXT_EVENT_STREAM
|
import org.springframework.http.MediaType.TEXT_EVENT_STREAM
|
||||||
@ -55,6 +54,7 @@ import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequ
|
|||||||
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user
|
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user
|
||||||
import org.springframework.test.context.ContextConfiguration
|
import org.springframework.test.context.ContextConfiguration
|
||||||
import org.springframework.test.context.TestPropertySource
|
import org.springframework.test.context.TestPropertySource
|
||||||
|
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||||
import org.springframework.test.context.junit.jupiter.SpringExtension
|
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||||
import org.springframework.test.web.reactive.server.WebTestClient
|
import org.springframework.test.web.reactive.server.WebTestClient
|
||||||
import org.springframework.test.web.servlet.*
|
import org.springframework.test.web.servlet.*
|
||||||
@ -81,14 +81,16 @@ abstract class MockSink : Sinks.Many<Boolean>
|
|||||||
"app.pseudonymize.generator=BUILDIN"
|
"app.pseudonymize.generator=BUILDIN"
|
||||||
]
|
]
|
||||||
)
|
)
|
||||||
@MockBean(name = "configsUpdateProducer", classes = [MockSink::class])
|
@MockitoBean(name = "configsUpdateProducer", types = [MockSink::class])
|
||||||
@MockBean(
|
@MockitoBean(
|
||||||
|
types = [
|
||||||
Generator::class,
|
Generator::class,
|
||||||
MtbFileSender::class,
|
MtbFileSender::class,
|
||||||
RequestProcessor::class,
|
RequestProcessor::class,
|
||||||
TransformationService::class,
|
TransformationService::class,
|
||||||
GPasConnectionCheckService::class,
|
GPasConnectionCheckService::class,
|
||||||
RestConnectionCheckService::class,
|
RestConnectionCheckService::class
|
||||||
|
]
|
||||||
)
|
)
|
||||||
class ConfigControllerTest {
|
class ConfigControllerTest {
|
||||||
|
|
||||||
@ -143,8 +145,10 @@ class ConfigControllerTest {
|
|||||||
"app.security.admin-user=admin"
|
"app.security.admin-user=admin"
|
||||||
]
|
]
|
||||||
)
|
)
|
||||||
@MockBean(
|
@MockitoBean(
|
||||||
|
types = [
|
||||||
TokenService::class
|
TokenService::class
|
||||||
|
]
|
||||||
)
|
)
|
||||||
inner class WithTokensEnabled {
|
inner class WithTokensEnabled {
|
||||||
private lateinit var tokenService: TokenService
|
private lateinit var tokenService: TokenService
|
||||||
@ -252,8 +256,10 @@ class ConfigControllerTest {
|
|||||||
"app.security.admin-password={noop}very-secret"
|
"app.security.admin-password={noop}very-secret"
|
||||||
]
|
]
|
||||||
)
|
)
|
||||||
@MockBean(
|
@MockitoBean(
|
||||||
|
types = [
|
||||||
UserRoleService::class
|
UserRoleService::class
|
||||||
|
]
|
||||||
)
|
)
|
||||||
inner class WithUserRolesEnabled {
|
inner class WithUserRolesEnabled {
|
||||||
private lateinit var userRoleService: UserRoleService
|
private lateinit var userRoleService: UserRoleService
|
||||||
|
@ -19,8 +19,6 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.web
|
package dev.dnpm.etl.processor.web
|
||||||
|
|
||||||
import com.gargoylesoftware.htmlunit.WebClient
|
|
||||||
import com.gargoylesoftware.htmlunit.html.HtmlPage
|
|
||||||
import dev.dnpm.etl.processor.*
|
import dev.dnpm.etl.processor.*
|
||||||
import dev.dnpm.etl.processor.config.AppConfiguration
|
import dev.dnpm.etl.processor.config.AppConfiguration
|
||||||
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||||
@ -30,6 +28,8 @@ import dev.dnpm.etl.processor.monitoring.RequestStatus
|
|||||||
import dev.dnpm.etl.processor.monitoring.RequestType
|
import dev.dnpm.etl.processor.monitoring.RequestType
|
||||||
import dev.dnpm.etl.processor.services.RequestService
|
import dev.dnpm.etl.processor.services.RequestService
|
||||||
import org.assertj.core.api.Assertions.assertThat
|
import org.assertj.core.api.Assertions.assertThat
|
||||||
|
import org.htmlunit.WebClient
|
||||||
|
import org.htmlunit.html.HtmlPage
|
||||||
import org.junit.jupiter.api.BeforeEach
|
import org.junit.jupiter.api.BeforeEach
|
||||||
import org.junit.jupiter.api.Nested
|
import org.junit.jupiter.api.Nested
|
||||||
import org.junit.jupiter.api.Test
|
import org.junit.jupiter.api.Test
|
||||||
@ -40,13 +40,13 @@ import org.mockito.kotlin.any
|
|||||||
import org.mockito.kotlin.whenever
|
import org.mockito.kotlin.whenever
|
||||||
import org.springframework.beans.factory.annotation.Autowired
|
import org.springframework.beans.factory.annotation.Autowired
|
||||||
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
||||||
import org.springframework.boot.test.mock.mockito.MockBean
|
|
||||||
import org.springframework.data.domain.Page
|
import org.springframework.data.domain.Page
|
||||||
import org.springframework.data.domain.PageImpl
|
import org.springframework.data.domain.PageImpl
|
||||||
import org.springframework.data.domain.Pageable
|
import org.springframework.data.domain.Pageable
|
||||||
import org.springframework.security.test.context.support.WithMockUser
|
import org.springframework.security.test.context.support.WithMockUser
|
||||||
import org.springframework.test.context.ContextConfiguration
|
import org.springframework.test.context.ContextConfiguration
|
||||||
import org.springframework.test.context.TestPropertySource
|
import org.springframework.test.context.TestPropertySource
|
||||||
|
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||||
import org.springframework.test.context.junit.jupiter.SpringExtension
|
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||||
import org.springframework.test.web.servlet.MockMvc
|
import org.springframework.test.web.servlet.MockMvc
|
||||||
import org.springframework.test.web.servlet.get
|
import org.springframework.test.web.servlet.get
|
||||||
@ -71,8 +71,8 @@ import java.util.*
|
|||||||
"app.security.admin-password={noop}very-secret"
|
"app.security.admin-password={noop}very-secret"
|
||||||
]
|
]
|
||||||
)
|
)
|
||||||
@MockBean(
|
@MockitoBean(
|
||||||
RequestService::class
|
types = [RequestService::class]
|
||||||
)
|
)
|
||||||
class HomeControllerTest {
|
class HomeControllerTest {
|
||||||
|
|
||||||
|
@ -19,21 +19,21 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.web
|
package dev.dnpm.etl.processor.web
|
||||||
|
|
||||||
import com.gargoylesoftware.htmlunit.WebClient
|
|
||||||
import com.gargoylesoftware.htmlunit.html.HtmlPage
|
|
||||||
import dev.dnpm.etl.processor.config.AppConfiguration
|
import dev.dnpm.etl.processor.config.AppConfiguration
|
||||||
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||||
import dev.dnpm.etl.processor.security.TokenService
|
import dev.dnpm.etl.processor.security.TokenService
|
||||||
import org.assertj.core.api.Assertions.assertThat
|
import org.assertj.core.api.Assertions.assertThat
|
||||||
|
import org.htmlunit.WebClient
|
||||||
|
import org.htmlunit.html.HtmlPage
|
||||||
import org.junit.jupiter.api.BeforeEach
|
import org.junit.jupiter.api.BeforeEach
|
||||||
import org.junit.jupiter.api.Test
|
import org.junit.jupiter.api.Test
|
||||||
import org.junit.jupiter.api.extension.ExtendWith
|
import org.junit.jupiter.api.extension.ExtendWith
|
||||||
import org.mockito.junit.jupiter.MockitoExtension
|
import org.mockito.junit.jupiter.MockitoExtension
|
||||||
import org.springframework.beans.factory.annotation.Autowired
|
import org.springframework.beans.factory.annotation.Autowired
|
||||||
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
||||||
import org.springframework.boot.test.mock.mockito.MockBean
|
|
||||||
import org.springframework.test.context.ContextConfiguration
|
import org.springframework.test.context.ContextConfiguration
|
||||||
import org.springframework.test.context.TestPropertySource
|
import org.springframework.test.context.TestPropertySource
|
||||||
|
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||||
import org.springframework.test.context.junit.jupiter.SpringExtension
|
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||||
import org.springframework.test.web.servlet.MockMvc
|
import org.springframework.test.web.servlet.MockMvc
|
||||||
import org.springframework.test.web.servlet.get
|
import org.springframework.test.web.servlet.get
|
||||||
@ -56,8 +56,8 @@ import org.springframework.test.web.servlet.htmlunit.MockMvcWebClientBuilder
|
|||||||
"app.security.enable-tokens=true"
|
"app.security.enable-tokens=true"
|
||||||
]
|
]
|
||||||
)
|
)
|
||||||
@MockBean(
|
@MockitoBean(
|
||||||
TokenService::class,
|
types = [TokenService::class]
|
||||||
)
|
)
|
||||||
class LoginControllerTest {
|
class LoginControllerTest {
|
||||||
|
|
||||||
|
@ -19,9 +19,9 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.web
|
package dev.dnpm.etl.processor.web
|
||||||
|
|
||||||
import com.gargoylesoftware.htmlunit.WebClient
|
|
||||||
import dev.dnpm.etl.processor.config.AppConfiguration
|
import dev.dnpm.etl.processor.config.AppConfiguration
|
||||||
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||||
|
import org.htmlunit.WebClient
|
||||||
import org.junit.jupiter.api.BeforeEach
|
import org.junit.jupiter.api.BeforeEach
|
||||||
import org.junit.jupiter.api.Test
|
import org.junit.jupiter.api.Test
|
||||||
import org.junit.jupiter.api.extension.ExtendWith
|
import org.junit.jupiter.api.extension.ExtendWith
|
||||||
|
@ -41,10 +41,10 @@ import org.mockito.kotlin.doAnswer
|
|||||||
import org.mockito.kotlin.whenever
|
import org.mockito.kotlin.whenever
|
||||||
import org.springframework.beans.factory.annotation.Autowired
|
import org.springframework.beans.factory.annotation.Autowired
|
||||||
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
||||||
import org.springframework.boot.test.mock.mockito.MockBean
|
|
||||||
import org.springframework.http.MediaType.TEXT_EVENT_STREAM
|
import org.springframework.http.MediaType.TEXT_EVENT_STREAM
|
||||||
import org.springframework.test.context.ContextConfiguration
|
import org.springframework.test.context.ContextConfiguration
|
||||||
import org.springframework.test.context.TestPropertySource
|
import org.springframework.test.context.TestPropertySource
|
||||||
|
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||||
import org.springframework.test.context.junit.jupiter.SpringExtension
|
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||||
import org.springframework.test.web.reactive.server.WebTestClient
|
import org.springframework.test.web.reactive.server.WebTestClient
|
||||||
import org.springframework.test.web.servlet.MockMvc
|
import org.springframework.test.web.servlet.MockMvc
|
||||||
@ -74,8 +74,8 @@ import java.time.temporal.ChronoUnit
|
|||||||
"app.security.admin-password={noop}very-secret"
|
"app.security.admin-password={noop}very-secret"
|
||||||
]
|
]
|
||||||
)
|
)
|
||||||
@MockBean(
|
@MockitoBean(
|
||||||
RequestService::class
|
types = [RequestService::class]
|
||||||
)
|
)
|
||||||
class StatisticsRestControllerTest {
|
class StatisticsRestControllerTest {
|
||||||
|
|
||||||
|
@ -1,7 +1,7 @@
|
|||||||
/*
|
/*
|
||||||
* This file is part of ETL-Processor
|
* This file is part of ETL-Processor
|
||||||
*
|
*
|
||||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
* 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
|
* 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
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
@ -21,16 +21,10 @@ package dev.dnpm.etl.processor.config
|
|||||||
|
|
||||||
import dev.dnpm.etl.processor.security.Role
|
import dev.dnpm.etl.processor.security.Role
|
||||||
import org.springframework.boot.context.properties.ConfigurationProperties
|
import org.springframework.boot.context.properties.ConfigurationProperties
|
||||||
import org.springframework.boot.context.properties.DeprecatedConfigurationProperty
|
|
||||||
|
|
||||||
@ConfigurationProperties(AppConfigProperties.NAME)
|
@ConfigurationProperties(AppConfigProperties.NAME)
|
||||||
data class AppConfigProperties(
|
data class AppConfigProperties(
|
||||||
var bwhcUri: String?,
|
var bwhcUri: String?,
|
||||||
@get:DeprecatedConfigurationProperty(
|
|
||||||
reason = "Deprecated in favor of 'app.pseudonymize.generator'",
|
|
||||||
replacement = "app.pseudonymize.generator"
|
|
||||||
)
|
|
||||||
var pseudonymizer: PseudonymGenerator = PseudonymGenerator.BUILDIN,
|
|
||||||
var transformations: List<TransformationProperties> = listOf(),
|
var transformations: List<TransformationProperties> = listOf(),
|
||||||
var maxRetryAttempts: Int = 3,
|
var maxRetryAttempts: Int = 3,
|
||||||
var duplicationDetection: Boolean = true
|
var duplicationDetection: Boolean = true
|
||||||
@ -56,10 +50,6 @@ data class GPasConfigProperties(
|
|||||||
val target: String = "etl-processor",
|
val target: String = "etl-processor",
|
||||||
val username: String?,
|
val username: String?,
|
||||||
val password: String?,
|
val password: String?,
|
||||||
@get:DeprecatedConfigurationProperty(
|
|
||||||
reason = "Deprecated in favor of including Root CA"
|
|
||||||
)
|
|
||||||
val sslCaLocation: String?
|
|
||||||
) {
|
) {
|
||||||
companion object {
|
companion object {
|
||||||
const val NAME = "app.pseudonymize.gpas"
|
const val NAME = "app.pseudonymize.gpas"
|
||||||
@ -82,18 +72,8 @@ data class RestTargetProperties(
|
|||||||
data class KafkaProperties(
|
data class KafkaProperties(
|
||||||
val inputTopic: String?,
|
val inputTopic: String?,
|
||||||
val outputTopic: String = "etl-processor",
|
val outputTopic: String = "etl-processor",
|
||||||
@get:DeprecatedConfigurationProperty(
|
|
||||||
reason = "Deprecated",
|
|
||||||
replacement = "outputTopic"
|
|
||||||
)
|
|
||||||
val topic: String = outputTopic,
|
|
||||||
val outputResponseTopic: String = "${outputTopic}_response",
|
val outputResponseTopic: String = "${outputTopic}_response",
|
||||||
@get:DeprecatedConfigurationProperty(
|
val groupId: String = "${outputTopic}_group",
|
||||||
reason = "Deprecated",
|
|
||||||
replacement = "outputResponseTopic"
|
|
||||||
)
|
|
||||||
val responseTopic: String = outputResponseTopic,
|
|
||||||
val groupId: String = "${topic}_group",
|
|
||||||
val servers: String = ""
|
val servers: String = ""
|
||||||
) {
|
) {
|
||||||
companion object {
|
companion object {
|
||||||
|
@ -1,7 +1,7 @@
|
|||||||
/*
|
/*
|
||||||
* This file is part of ETL-Processor
|
* This file is part of ETL-Processor
|
||||||
*
|
*
|
||||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
* 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
|
* 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
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
@ -32,12 +32,6 @@ import dev.dnpm.etl.processor.security.TokenRepository
|
|||||||
import dev.dnpm.etl.processor.security.TokenService
|
import dev.dnpm.etl.processor.security.TokenService
|
||||||
import dev.dnpm.etl.processor.services.Transformation
|
import dev.dnpm.etl.processor.services.Transformation
|
||||||
import dev.dnpm.etl.processor.services.TransformationService
|
import dev.dnpm.etl.processor.services.TransformationService
|
||||||
import org.apache.hc.client5.http.impl.classic.HttpClients
|
|
||||||
import org.apache.hc.client5.http.impl.io.BasicHttpClientConnectionManager
|
|
||||||
import org.apache.hc.client5.http.socket.ConnectionSocketFactory
|
|
||||||
import org.apache.hc.client5.http.socket.PlainConnectionSocketFactory
|
|
||||||
import org.apache.hc.client5.http.ssl.SSLConnectionSocketFactory
|
|
||||||
import org.apache.hc.core5.http.config.RegistryBuilder
|
|
||||||
import org.slf4j.LoggerFactory
|
import org.slf4j.LoggerFactory
|
||||||
import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean
|
import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean
|
||||||
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty
|
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty
|
||||||
@ -45,7 +39,6 @@ import org.springframework.boot.context.properties.EnableConfigurationProperties
|
|||||||
import org.springframework.context.annotation.Bean
|
import org.springframework.context.annotation.Bean
|
||||||
import org.springframework.context.annotation.Configuration
|
import org.springframework.context.annotation.Configuration
|
||||||
import org.springframework.data.jdbc.repository.config.AbstractJdbcConfiguration
|
import org.springframework.data.jdbc.repository.config.AbstractJdbcConfiguration
|
||||||
import org.springframework.http.client.HttpComponentsClientHttpRequestFactory
|
|
||||||
import org.springframework.retry.RetryCallback
|
import org.springframework.retry.RetryCallback
|
||||||
import org.springframework.retry.RetryContext
|
import org.springframework.retry.RetryContext
|
||||||
import org.springframework.retry.RetryListener
|
import org.springframework.retry.RetryListener
|
||||||
@ -58,13 +51,6 @@ import org.springframework.security.provisioning.InMemoryUserDetailsManager
|
|||||||
import org.springframework.web.client.HttpClientErrorException
|
import org.springframework.web.client.HttpClientErrorException
|
||||||
import org.springframework.web.client.RestTemplate
|
import org.springframework.web.client.RestTemplate
|
||||||
import reactor.core.publisher.Sinks
|
import reactor.core.publisher.Sinks
|
||||||
import java.io.BufferedInputStream
|
|
||||||
import java.io.FileInputStream
|
|
||||||
import java.security.KeyStore
|
|
||||||
import java.security.cert.CertificateFactory
|
|
||||||
import java.security.cert.X509Certificate
|
|
||||||
import javax.net.ssl.SSLContext
|
|
||||||
import javax.net.ssl.TrustManagerFactory
|
|
||||||
import kotlin.time.Duration.Companion.seconds
|
import kotlin.time.Duration.Companion.seconds
|
||||||
import kotlin.time.toJavaDuration
|
import kotlin.time.toJavaDuration
|
||||||
|
|
||||||
@ -90,18 +76,6 @@ class AppConfiguration {
|
|||||||
@ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "GPAS")
|
@ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "GPAS")
|
||||||
@Bean
|
@Bean
|
||||||
fun gpasPseudonymGenerator(configProperties: GPasConfigProperties, retryTemplate: RetryTemplate, restTemplate: RestTemplate): Generator {
|
fun gpasPseudonymGenerator(configProperties: GPasConfigProperties, retryTemplate: RetryTemplate, restTemplate: RestTemplate): Generator {
|
||||||
try {
|
|
||||||
if (!configProperties.sslCaLocation.isNullOrBlank()) {
|
|
||||||
return GpasPseudonymGenerator(
|
|
||||||
configProperties,
|
|
||||||
retryTemplate,
|
|
||||||
createCustomGpasRestTemplate(configProperties)
|
|
||||||
)
|
|
||||||
}
|
|
||||||
} catch (e: Exception) {
|
|
||||||
throw RuntimeException(e)
|
|
||||||
}
|
|
||||||
|
|
||||||
return GpasPseudonymGenerator(configProperties, retryTemplate, restTemplate)
|
return GpasPseudonymGenerator(configProperties, retryTemplate, restTemplate)
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -111,92 +85,6 @@ class AppConfiguration {
|
|||||||
return AnonymizingGenerator()
|
return AnonymizingGenerator()
|
||||||
}
|
}
|
||||||
|
|
||||||
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS")
|
|
||||||
@ConditionalOnMissingBean
|
|
||||||
@Bean
|
|
||||||
fun gpasPseudonymGeneratorOnDeprecatedProperty(configProperties: GPasConfigProperties, retryTemplate: RetryTemplate, restTemplate: RestTemplate): Generator {
|
|
||||||
try {
|
|
||||||
if (!configProperties.sslCaLocation.isNullOrBlank()) {
|
|
||||||
return GpasPseudonymGenerator(
|
|
||||||
configProperties,
|
|
||||||
retryTemplate,
|
|
||||||
createCustomGpasRestTemplate(configProperties)
|
|
||||||
)
|
|
||||||
}
|
|
||||||
} catch (e: Exception) {
|
|
||||||
throw RuntimeException(e)
|
|
||||||
}
|
|
||||||
|
|
||||||
return GpasPseudonymGenerator(configProperties, retryTemplate, restTemplate)
|
|
||||||
}
|
|
||||||
|
|
||||||
private fun createCustomGpasRestTemplate(configProperties: GPasConfigProperties): RestTemplate {
|
|
||||||
fun getSslContext(certificateLocation: String): SSLContext? {
|
|
||||||
val ks = KeyStore.getInstance(KeyStore.getDefaultType())
|
|
||||||
|
|
||||||
val fis = FileInputStream(certificateLocation)
|
|
||||||
val ca = CertificateFactory.getInstance("X.509")
|
|
||||||
.generateCertificate(BufferedInputStream(fis)) as X509Certificate
|
|
||||||
|
|
||||||
ks.load(null, null)
|
|
||||||
ks.setCertificateEntry(1.toString(), ca)
|
|
||||||
|
|
||||||
val tmf = TrustManagerFactory.getInstance(
|
|
||||||
TrustManagerFactory.getDefaultAlgorithm()
|
|
||||||
)
|
|
||||||
tmf.init(ks)
|
|
||||||
|
|
||||||
val sslContext = SSLContext.getInstance("TLS")
|
|
||||||
sslContext.init(null, tmf.trustManagers, null)
|
|
||||||
|
|
||||||
return sslContext
|
|
||||||
}
|
|
||||||
|
|
||||||
fun getCustomRestTemplate(customSslContext: SSLContext): RestTemplate {
|
|
||||||
val sslsf = SSLConnectionSocketFactory(customSslContext)
|
|
||||||
val socketFactoryRegistry = RegistryBuilder.create<ConnectionSocketFactory>()
|
|
||||||
.register("https", sslsf).register("http", PlainConnectionSocketFactory()).build()
|
|
||||||
|
|
||||||
val connectionManager = BasicHttpClientConnectionManager(
|
|
||||||
socketFactoryRegistry
|
|
||||||
)
|
|
||||||
val httpClient = HttpClients.custom()
|
|
||||||
.setConnectionManager(connectionManager).build()
|
|
||||||
|
|
||||||
val requestFactory = HttpComponentsClientHttpRequestFactory(
|
|
||||||
httpClient
|
|
||||||
)
|
|
||||||
return RestTemplate(requestFactory)
|
|
||||||
}
|
|
||||||
|
|
||||||
try {
|
|
||||||
if (!configProperties.sslCaLocation.isNullOrBlank()) {
|
|
||||||
val customSslContext = getSslContext(configProperties.sslCaLocation)
|
|
||||||
logger.warn(
|
|
||||||
String.format(
|
|
||||||
"%s has been initialized with SSL certificate %s. This is deprecated in favor of including Root CA.",
|
|
||||||
this.javaClass.name, configProperties.sslCaLocation
|
|
||||||
)
|
|
||||||
)
|
|
||||||
|
|
||||||
if (customSslContext != null) {
|
|
||||||
return getCustomRestTemplate(customSslContext)
|
|
||||||
}
|
|
||||||
}
|
|
||||||
} catch (e: Exception) {
|
|
||||||
throw RuntimeException(e)
|
|
||||||
}
|
|
||||||
|
|
||||||
throw RuntimeException("Custom SSL configuration for gPAS not usable")
|
|
||||||
}
|
|
||||||
|
|
||||||
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "BUILDIN")
|
|
||||||
@ConditionalOnMissingBean
|
|
||||||
@Bean
|
|
||||||
fun buildinPseudonymGeneratorOnDeprecatedProperty(): Generator {
|
|
||||||
return AnonymizingGenerator()
|
|
||||||
}
|
|
||||||
|
|
||||||
@Bean
|
@Bean
|
||||||
fun pseudonymizeService(
|
fun pseudonymizeService(
|
||||||
generator: Generator,
|
generator: Generator,
|
||||||
|
@ -1,7 +1,7 @@
|
|||||||
/*
|
/*
|
||||||
* This file is part of ETL-Processor
|
* This file is part of ETL-Processor
|
||||||
*
|
*
|
||||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
* 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
|
* 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
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
@ -71,7 +71,7 @@ class AppKafkaConfiguration {
|
|||||||
kafkaProperties: KafkaProperties,
|
kafkaProperties: KafkaProperties,
|
||||||
kafkaResponseProcessor: KafkaResponseProcessor
|
kafkaResponseProcessor: KafkaResponseProcessor
|
||||||
): KafkaMessageListenerContainer<String, String> {
|
): KafkaMessageListenerContainer<String, String> {
|
||||||
val containerProperties = ContainerProperties(kafkaProperties.responseTopic)
|
val containerProperties = ContainerProperties(kafkaProperties.outputResponseTopic)
|
||||||
containerProperties.messageListener = kafkaResponseProcessor
|
containerProperties.messageListener = kafkaResponseProcessor
|
||||||
return KafkaMessageListenerContainer(consumerFactory, containerProperties)
|
return KafkaMessageListenerContainer(consumerFactory, containerProperties)
|
||||||
}
|
}
|
||||||
|
@ -1,7 +1,7 @@
|
|||||||
/*
|
/*
|
||||||
* This file is part of ETL-Processor
|
* This file is part of ETL-Processor
|
||||||
*
|
*
|
||||||
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
* 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
|
* 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
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
@ -87,9 +87,14 @@ class AppSecurityConfiguration(
|
|||||||
|
|
||||||
@Bean
|
@Bean
|
||||||
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "true")
|
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "true")
|
||||||
fun filterChainOidc(http: HttpSecurity, passwordEncoder: PasswordEncoder, userRoleRepository: UserRoleRepository, sessionRegistry: SessionRegistry): SecurityFilterChain {
|
fun filterChainOidc(
|
||||||
|
http: HttpSecurity,
|
||||||
|
passwordEncoder: PasswordEncoder,
|
||||||
|
userRoleRepository: UserRoleRepository,
|
||||||
|
sessionRegistry: SessionRegistry
|
||||||
|
): SecurityFilterChain {
|
||||||
http {
|
http {
|
||||||
authorizeRequests {
|
authorizeHttpRequests {
|
||||||
authorize("/configs/**", hasRole("ADMIN"))
|
authorize("/configs/**", hasRole("ADMIN"))
|
||||||
authorize("/mtbfile/**", hasAnyRole("MTBFILE", "ADMIN", "USER"))
|
authorize("/mtbfile/**", hasAnyRole("MTBFILE", "ADMIN", "USER"))
|
||||||
authorize("/report/**", hasAnyRole("ADMIN", "USER"))
|
authorize("/report/**", hasAnyRole("ADMIN", "USER"))
|
||||||
@ -127,13 +132,22 @@ class AppSecurityConfiguration(
|
|||||||
|
|
||||||
@Bean
|
@Bean
|
||||||
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "true")
|
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "true")
|
||||||
fun grantedAuthoritiesMapper(userRoleRepository: UserRoleRepository, appSecurityConfigProperties: SecurityConfigProperties): GrantedAuthoritiesMapper {
|
fun grantedAuthoritiesMapper(
|
||||||
|
userRoleRepository: UserRoleRepository,
|
||||||
|
appSecurityConfigProperties: SecurityConfigProperties
|
||||||
|
): GrantedAuthoritiesMapper {
|
||||||
return GrantedAuthoritiesMapper { grantedAuthority ->
|
return GrantedAuthoritiesMapper { grantedAuthority ->
|
||||||
grantedAuthority.filterIsInstance<OidcUserAuthority>()
|
grantedAuthority.filterIsInstance<OidcUserAuthority>()
|
||||||
.onEach {
|
.onEach {
|
||||||
val userRole = userRoleRepository.findByUsername(it.userInfo.preferredUsername)
|
val userRole = userRoleRepository.findByUsername(it.userInfo.preferredUsername)
|
||||||
if (userRole.isEmpty) {
|
if (userRole.isEmpty) {
|
||||||
userRoleRepository.save(UserRole(null, it.userInfo.preferredUsername, appSecurityConfigProperties.defaultNewUserRole))
|
userRoleRepository.save(
|
||||||
|
UserRole(
|
||||||
|
null,
|
||||||
|
it.userInfo.preferredUsername,
|
||||||
|
appSecurityConfigProperties.defaultNewUserRole
|
||||||
|
)
|
||||||
|
)
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
.map {
|
.map {
|
||||||
@ -147,7 +161,7 @@ class AppSecurityConfiguration(
|
|||||||
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "false", matchIfMissing = true)
|
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "false", matchIfMissing = true)
|
||||||
fun filterChain(http: HttpSecurity, passwordEncoder: PasswordEncoder): SecurityFilterChain {
|
fun filterChain(http: HttpSecurity, passwordEncoder: PasswordEncoder): SecurityFilterChain {
|
||||||
http {
|
http {
|
||||||
authorizeRequests {
|
authorizeHttpRequests {
|
||||||
authorize("/configs/**", hasRole("ADMIN"))
|
authorize("/configs/**", hasRole("ADMIN"))
|
||||||
authorize("/mtbfile/**", hasAnyRole("MTBFILE", "ADMIN"))
|
authorize("/mtbfile/**", hasAnyRole("MTBFILE", "ADMIN"))
|
||||||
authorize("/report/**", hasRole("ADMIN"))
|
authorize("/report/**", hasRole("ADMIN"))
|
||||||
|
@ -1,7 +1,7 @@
|
|||||||
/*
|
/*
|
||||||
* This file is part of ETL-Processor
|
* This file is part of ETL-Processor
|
||||||
*
|
*
|
||||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
* 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
|
* 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
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
@ -22,11 +22,13 @@ package dev.dnpm.etl.processor.input
|
|||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import de.ukw.ccc.bwhc.dto.Consent
|
import de.ukw.ccc.bwhc.dto.Consent
|
||||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||||
|
import dev.dnpm.etl.processor.CustomMediaType
|
||||||
import dev.dnpm.etl.processor.PatientId
|
import dev.dnpm.etl.processor.PatientId
|
||||||
import dev.dnpm.etl.processor.RequestId
|
import dev.dnpm.etl.processor.RequestId
|
||||||
import dev.dnpm.etl.processor.services.RequestProcessor
|
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||||
import org.apache.kafka.clients.consumer.ConsumerRecord
|
import org.apache.kafka.clients.consumer.ConsumerRecord
|
||||||
import org.slf4j.LoggerFactory
|
import org.slf4j.LoggerFactory
|
||||||
|
import org.springframework.http.MediaType
|
||||||
import org.springframework.kafka.listener.MessageListener
|
import org.springframework.kafka.listener.MessageListener
|
||||||
|
|
||||||
class KafkaInputListener(
|
class KafkaInputListener(
|
||||||
@ -35,10 +37,29 @@ class KafkaInputListener(
|
|||||||
) : MessageListener<String, String> {
|
) : MessageListener<String, String> {
|
||||||
private val logger = LoggerFactory.getLogger(KafkaInputListener::class.java)
|
private val logger = LoggerFactory.getLogger(KafkaInputListener::class.java)
|
||||||
|
|
||||||
override fun onMessage(data: ConsumerRecord<String, String>) {
|
override fun onMessage(record: ConsumerRecord<String, String>) {
|
||||||
val mtbFile = objectMapper.readValue(data.value(), MtbFile::class.java)
|
when (guessMimeType(record)) {
|
||||||
|
MediaType.APPLICATION_JSON_VALUE -> handleBwhcMessage(record)
|
||||||
|
CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE -> handleDnpmV2Message(record)
|
||||||
|
else -> {
|
||||||
|
/* ignore other messages */
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private fun guessMimeType(record: ConsumerRecord<String, String>): String {
|
||||||
|
if (record.headers().headers("contentType").toList().isEmpty()) {
|
||||||
|
// Fallback if no contentType set (old behavior)
|
||||||
|
return MediaType.APPLICATION_JSON_VALUE
|
||||||
|
}
|
||||||
|
|
||||||
|
return record.headers().headers("contentType")?.firstOrNull()?.value().contentToString()
|
||||||
|
}
|
||||||
|
|
||||||
|
private fun handleBwhcMessage(record: ConsumerRecord<String, String>) {
|
||||||
|
val mtbFile = objectMapper.readValue(record.value(), MtbFile::class.java)
|
||||||
val patientId = PatientId(mtbFile.patient.id)
|
val patientId = PatientId(mtbFile.patient.id)
|
||||||
val firstRequestIdHeader = data.headers().headers("requestId")?.firstOrNull()
|
val firstRequestIdHeader = record.headers().headers("requestId")?.firstOrNull()
|
||||||
val requestId = if (null != firstRequestIdHeader) {
|
val requestId = if (null != firstRequestIdHeader) {
|
||||||
RequestId(String(firstRequestIdHeader.value()))
|
RequestId(String(firstRequestIdHeader.value()))
|
||||||
} else {
|
} else {
|
||||||
@ -61,4 +82,10 @@ 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")
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
@ -21,9 +21,12 @@ package dev.dnpm.etl.processor.input
|
|||||||
|
|
||||||
import de.ukw.ccc.bwhc.dto.Consent
|
import de.ukw.ccc.bwhc.dto.Consent
|
||||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||||
|
import dev.dnpm.etl.processor.CustomMediaType
|
||||||
import dev.dnpm.etl.processor.PatientId
|
import dev.dnpm.etl.processor.PatientId
|
||||||
import dev.dnpm.etl.processor.services.RequestProcessor
|
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||||
|
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||||
import org.slf4j.LoggerFactory
|
import org.slf4j.LoggerFactory
|
||||||
|
import org.springframework.http.MediaType
|
||||||
import org.springframework.http.ResponseEntity
|
import org.springframework.http.ResponseEntity
|
||||||
import org.springframework.web.bind.annotation.*
|
import org.springframework.web.bind.annotation.*
|
||||||
|
|
||||||
@ -40,19 +43,26 @@ class MtbFileRestController(
|
|||||||
return ResponseEntity.ok("Test")
|
return ResponseEntity.ok("Test")
|
||||||
}
|
}
|
||||||
|
|
||||||
@PostMapping
|
@PostMapping( consumes = [ MediaType.APPLICATION_JSON_VALUE ] )
|
||||||
fun mtbFile(@RequestBody mtbFile: MtbFile): ResponseEntity<Unit> {
|
fun mtbFile(@RequestBody mtbFile: MtbFile): ResponseEntity<Unit> {
|
||||||
if (mtbFile.consent.status == Consent.Status.ACTIVE) {
|
if (mtbFile.consent.status == Consent.Status.ACTIVE) {
|
||||||
logger.debug("Accepted MTB File for processing")
|
logger.debug("Accepted MTB File (bwHC V1) for processing")
|
||||||
requestProcessor.processMtbFile(mtbFile)
|
requestProcessor.processMtbFile(mtbFile)
|
||||||
} else {
|
} else {
|
||||||
logger.debug("Accepted MTB File and process deletion")
|
logger.debug("Accepted MTB File (bwHC V1) and process deletion")
|
||||||
val patientId = PatientId(mtbFile.patient.id)
|
val patientId = PatientId(mtbFile.patient.id)
|
||||||
requestProcessor.processDeletion(patientId)
|
requestProcessor.processDeletion(patientId)
|
||||||
}
|
}
|
||||||
return ResponseEntity.accepted().build()
|
return ResponseEntity.accepted().build()
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@PostMapping( consumes = [ 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)
|
||||||
|
return ResponseEntity.accepted().build()
|
||||||
|
}
|
||||||
|
|
||||||
@DeleteMapping(path = ["{patientId}"])
|
@DeleteMapping(path = ["{patientId}"])
|
||||||
fun deleteData(@PathVariable patientId: String): ResponseEntity<Unit> {
|
fun deleteData(@PathVariable patientId: String): ResponseEntity<Unit> {
|
||||||
logger.debug("Accepted patient ID to process deletion")
|
logger.debug("Accepted patient ID to process deletion")
|
||||||
|
@ -1,7 +1,7 @@
|
|||||||
/*
|
/*
|
||||||
* This file is part of ETL-Processor
|
* This file is part of ETL-Processor
|
||||||
*
|
*
|
||||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
* 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
|
* 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
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
@ -22,10 +22,12 @@ package dev.dnpm.etl.processor.output
|
|||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import de.ukw.ccc.bwhc.dto.Consent
|
import de.ukw.ccc.bwhc.dto.Consent
|
||||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||||
import dev.dnpm.etl.processor.RequestId
|
import dev.dnpm.etl.processor.CustomMediaType
|
||||||
import dev.dnpm.etl.processor.config.KafkaProperties
|
import dev.dnpm.etl.processor.config.KafkaProperties
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||||
|
import org.apache.kafka.clients.producer.ProducerRecord
|
||||||
import org.slf4j.LoggerFactory
|
import org.slf4j.LoggerFactory
|
||||||
|
import org.springframework.http.MediaType
|
||||||
import org.springframework.kafka.core.KafkaTemplate
|
import org.springframework.kafka.core.KafkaTemplate
|
||||||
import org.springframework.retry.support.RetryTemplate
|
import org.springframework.retry.support.RetryTemplate
|
||||||
|
|
||||||
@ -38,14 +40,20 @@ class KafkaMtbFileSender(
|
|||||||
|
|
||||||
private val logger = LoggerFactory.getLogger(KafkaMtbFileSender::class.java)
|
private val logger = LoggerFactory.getLogger(KafkaMtbFileSender::class.java)
|
||||||
|
|
||||||
override fun send(request: MtbFileSender.MtbFileRequest): MtbFileSender.Response {
|
override fun <T> send(request: MtbFileRequest<T>): MtbFileSender.Response {
|
||||||
return try {
|
return try {
|
||||||
return retryTemplate.execute<MtbFileSender.Response, Exception> {
|
return retryTemplate.execute<MtbFileSender.Response, Exception> {
|
||||||
val result = kafkaTemplate.send(
|
val record =
|
||||||
kafkaProperties.topic,
|
ProducerRecord(kafkaProperties.outputTopic, key(request), objectMapper.writeValueAsString(request))
|
||||||
key(request),
|
when (request) {
|
||||||
objectMapper.writeValueAsString(Data(request.requestId, request.mtbFile))
|
is BwhcV1MtbFileRequest -> record.headers()
|
||||||
)
|
.add("contentType", MediaType.APPLICATION_JSON_VALUE.toByteArray())
|
||||||
|
|
||||||
|
is DnpmV2MtbFileRequest -> record.headers()
|
||||||
|
.add("contentType", CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE.toByteArray())
|
||||||
|
}
|
||||||
|
|
||||||
|
val result = kafkaTemplate.send(record)
|
||||||
if (result.get() != null) {
|
if (result.get() != null) {
|
||||||
logger.debug("Sent file via KafkaMtbFileSender")
|
logger.debug("Sent file via KafkaMtbFileSender")
|
||||||
MtbFileSender.Response(RequestStatus.UNKNOWN)
|
MtbFileSender.Response(RequestStatus.UNKNOWN)
|
||||||
@ -59,7 +67,7 @@ class KafkaMtbFileSender(
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
override fun send(request: MtbFileSender.DeleteRequest): MtbFileSender.Response {
|
override fun send(request: DeleteRequest): MtbFileSender.Response {
|
||||||
val dummyMtbFile = MtbFile.builder()
|
val dummyMtbFile = MtbFile.builder()
|
||||||
.withConsent(
|
.withConsent(
|
||||||
Consent.builder()
|
Consent.builder()
|
||||||
@ -71,12 +79,15 @@ class KafkaMtbFileSender(
|
|||||||
|
|
||||||
return try {
|
return try {
|
||||||
return retryTemplate.execute<MtbFileSender.Response, Exception> {
|
return retryTemplate.execute<MtbFileSender.Response, Exception> {
|
||||||
val result = kafkaTemplate.send(
|
val record =
|
||||||
kafkaProperties.topic,
|
ProducerRecord(
|
||||||
|
kafkaProperties.outputTopic,
|
||||||
key(request),
|
key(request),
|
||||||
objectMapper.writeValueAsString(Data(request.requestId, dummyMtbFile))
|
// Always use old BwhcV1FileRequest with Consent REJECT
|
||||||
|
objectMapper.writeValueAsString(BwhcV1MtbFileRequest(request.requestId, dummyMtbFile))
|
||||||
)
|
)
|
||||||
|
|
||||||
|
val result = kafkaTemplate.send(record)
|
||||||
if (result.get() != null) {
|
if (result.get() != null) {
|
||||||
logger.debug("Sent deletion request via KafkaMtbFileSender")
|
logger.debug("Sent deletion request via KafkaMtbFileSender")
|
||||||
MtbFileSender.Response(RequestStatus.UNKNOWN)
|
MtbFileSender.Response(RequestStatus.UNKNOWN)
|
||||||
@ -91,16 +102,15 @@ class KafkaMtbFileSender(
|
|||||||
}
|
}
|
||||||
|
|
||||||
override fun endpoint(): String {
|
override fun endpoint(): String {
|
||||||
return "${this.kafkaProperties.servers} (${this.kafkaProperties.topic}/${this.kafkaProperties.responseTopic})"
|
return "${this.kafkaProperties.servers} (${this.kafkaProperties.outputTopic}/${this.kafkaProperties.outputResponseTopic})"
|
||||||
}
|
}
|
||||||
|
|
||||||
private fun key(request: MtbFileSender.MtbFileRequest): String {
|
private fun key(request: MtbRequest): String {
|
||||||
return "{\"pid\": \"${request.mtbFile.patient.id}\"}"
|
return when (request) {
|
||||||
|
is BwhcV1MtbFileRequest -> "{\"pid\": \"${request.content.patient.id}\"}"
|
||||||
|
is DnpmV2MtbFileRequest -> "{\"pid\": \"${request.content.patient.id}\"}"
|
||||||
|
is DeleteRequest -> "{\"pid\": \"${request.patientId.value}\"}"
|
||||||
|
else -> throw IllegalArgumentException("Unsupported request type: ${request::class.simpleName}")
|
||||||
}
|
}
|
||||||
|
|
||||||
private fun key(request: MtbFileSender.DeleteRequest): String {
|
|
||||||
return "{\"pid\": \"${request.patientId.value}\"}"
|
|
||||||
}
|
}
|
||||||
|
|
||||||
data class Data(val requestId: RequestId, val content: MtbFile)
|
|
||||||
}
|
}
|
@ -19,25 +19,17 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.output
|
package dev.dnpm.etl.processor.output
|
||||||
|
|
||||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
|
||||||
import dev.dnpm.etl.processor.PatientPseudonym
|
|
||||||
import dev.dnpm.etl.processor.RequestId
|
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||||
import org.springframework.http.HttpStatusCode
|
import org.springframework.http.HttpStatusCode
|
||||||
|
|
||||||
interface MtbFileSender {
|
interface MtbFileSender {
|
||||||
fun send(request: MtbFileRequest): Response
|
fun <T> send(request: MtbFileRequest<T>): Response
|
||||||
|
|
||||||
fun send(request: DeleteRequest): Response
|
fun send(request: DeleteRequest): Response
|
||||||
|
|
||||||
fun endpoint(): String
|
fun endpoint(): String
|
||||||
|
|
||||||
data class Response(val status: RequestStatus, val body: String = "")
|
data class Response(val status: RequestStatus, val body: String = "")
|
||||||
|
|
||||||
data class MtbFileRequest(val requestId: RequestId, val mtbFile: MtbFile)
|
|
||||||
|
|
||||||
data class DeleteRequest(val requestId: RequestId, val patientId: PatientPseudonym)
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
fun Int.asRequestStatus(): RequestStatus {
|
fun Int.asRequestStatus(): RequestStatus {
|
||||||
|
59
src/main/kotlin/dev/dnpm/etl/processor/output/MtbRequest.kt
Normal file
59
src/main/kotlin/dev/dnpm/etl/processor/output/MtbRequest.kt
Normal file
@ -0,0 +1,59 @@
|
|||||||
|
/*
|
||||||
|
* 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 de.ukw.ccc.bwhc.dto.MtbFile
|
||||||
|
import dev.dnpm.etl.processor.PatientPseudonym
|
||||||
|
import dev.dnpm.etl.processor.RequestId
|
||||||
|
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||||
|
|
||||||
|
interface MtbRequest {
|
||||||
|
val requestId: RequestId
|
||||||
|
}
|
||||||
|
|
||||||
|
sealed interface MtbFileRequest<out T> : MtbRequest {
|
||||||
|
override val requestId: RequestId
|
||||||
|
val content: T
|
||||||
|
|
||||||
|
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
|
||||||
|
) : MtbFileRequest<Mtb> {
|
||||||
|
override fun patientPseudonym(): PatientPseudonym {
|
||||||
|
return PatientPseudonym(content.patient.id)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
data class DeleteRequest(
|
||||||
|
override val requestId: RequestId,
|
||||||
|
val patientId: PatientPseudonym
|
||||||
|
) : MtbRequest
|
@ -1,7 +1,7 @@
|
|||||||
/*
|
/*
|
||||||
* This file is part of ETL-Processor
|
* This file is part of ETL-Processor
|
||||||
*
|
*
|
||||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
* 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
|
* 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
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
@ -19,10 +19,11 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.output
|
package dev.dnpm.etl.processor.output
|
||||||
|
|
||||||
import dev.dnpm.etl.processor.config.RestTargetProperties
|
import dev.dnpm.etl.processor.CustomMediaType
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
|
||||||
import dev.dnpm.etl.processor.PatientPseudonym
|
import dev.dnpm.etl.processor.PatientPseudonym
|
||||||
|
import dev.dnpm.etl.processor.config.RestTargetProperties
|
||||||
import dev.dnpm.etl.processor.monitoring.ReportService
|
import dev.dnpm.etl.processor.monitoring.ReportService
|
||||||
|
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||||
import dev.dnpm.etl.processor.monitoring.asRequestStatus
|
import dev.dnpm.etl.processor.monitoring.asRequestStatus
|
||||||
import org.slf4j.LoggerFactory
|
import org.slf4j.LoggerFactory
|
||||||
import org.springframework.http.HttpEntity
|
import org.springframework.http.HttpEntity
|
||||||
@ -46,11 +47,11 @@ abstract class RestMtbFileSender(
|
|||||||
|
|
||||||
abstract fun deleteUrl(patientId: PatientPseudonym): String
|
abstract fun deleteUrl(patientId: PatientPseudonym): String
|
||||||
|
|
||||||
override fun send(request: MtbFileSender.MtbFileRequest): MtbFileSender.Response {
|
override fun <T> send(request: MtbFileRequest<T>): MtbFileSender.Response {
|
||||||
try {
|
try {
|
||||||
return retryTemplate.execute<MtbFileSender.Response, Exception> {
|
return retryTemplate.execute<MtbFileSender.Response, Exception> {
|
||||||
val headers = getHttpHeaders()
|
val headers = getHttpHeaders(request)
|
||||||
val entityReq = HttpEntity(request.mtbFile, headers)
|
val entityReq = HttpEntity(request.content, headers)
|
||||||
val response = restTemplate.postForEntity(
|
val response = restTemplate.postForEntity(
|
||||||
sendUrl(),
|
sendUrl(),
|
||||||
entityReq,
|
entityReq,
|
||||||
@ -76,10 +77,10 @@ abstract class RestMtbFileSender(
|
|||||||
return MtbFileSender.Response(RequestStatus.ERROR, "Sonstiger Fehler bei der Übertragung")
|
return MtbFileSender.Response(RequestStatus.ERROR, "Sonstiger Fehler bei der Übertragung")
|
||||||
}
|
}
|
||||||
|
|
||||||
override fun send(request: MtbFileSender.DeleteRequest): MtbFileSender.Response {
|
override fun send(request: DeleteRequest): MtbFileSender.Response {
|
||||||
try {
|
try {
|
||||||
return retryTemplate.execute<MtbFileSender.Response, Exception> {
|
return retryTemplate.execute<MtbFileSender.Response, Exception> {
|
||||||
val headers = getHttpHeaders()
|
val headers = getHttpHeaders(request)
|
||||||
val entityReq = HttpEntity(null, headers)
|
val entityReq = HttpEntity(null, headers)
|
||||||
restTemplate.delete(
|
restTemplate.delete(
|
||||||
deleteUrl(request.patientId),
|
deleteUrl(request.patientId),
|
||||||
@ -102,11 +103,15 @@ abstract class RestMtbFileSender(
|
|||||||
return this.restTargetProperties.uri.orEmpty()
|
return this.restTargetProperties.uri.orEmpty()
|
||||||
}
|
}
|
||||||
|
|
||||||
private fun getHttpHeaders(): HttpHeaders {
|
private fun getHttpHeaders(request: MtbRequest): HttpHeaders {
|
||||||
val username = restTargetProperties.username
|
val username = restTargetProperties.username
|
||||||
val password = restTargetProperties.password
|
val password = restTargetProperties.password
|
||||||
val headers = HttpHeaders()
|
val headers = HttpHeaders()
|
||||||
headers.contentType = MediaType.APPLICATION_JSON
|
headers.contentType = when (request) {
|
||||||
|
is BwhcV1MtbFileRequest -> MediaType.APPLICATION_JSON
|
||||||
|
is DnpmV2MtbFileRequest -> CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON
|
||||||
|
else -> MediaType.APPLICATION_JSON
|
||||||
|
}
|
||||||
|
|
||||||
if (username.isNullOrBlank() || password.isNullOrBlank()) {
|
if (username.isNullOrBlank() || password.isNullOrBlank()) {
|
||||||
return headers
|
return headers
|
||||||
|
@ -21,12 +21,12 @@ package dev.dnpm.etl.processor.pseudonym
|
|||||||
|
|
||||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||||
import dev.dnpm.etl.processor.PatientId
|
import dev.dnpm.etl.processor.PatientId
|
||||||
|
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||||
import org.apache.commons.codec.digest.DigestUtils
|
import org.apache.commons.codec.digest.DigestUtils
|
||||||
|
|
||||||
/** Replaces patient ID with generated patient pseudonym
|
/** Replaces patient ID with generated patient pseudonym
|
||||||
*
|
*
|
||||||
* @param pseudonymizeService The pseudonymizeService to be used
|
* @param pseudonymizeService The pseudonymizeService to be used
|
||||||
*
|
|
||||||
* @return The MTB file containing patient pseudonymes
|
* @return The MTB file containing patient pseudonymes
|
||||||
*/
|
*/
|
||||||
infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
|
infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
|
||||||
@ -49,7 +49,11 @@ infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
|
|||||||
}
|
}
|
||||||
this.lastGuidelineTherapies?.forEach { it.patient = patientPseudonym }
|
this.lastGuidelineTherapies?.forEach { it.patient = patientPseudonym }
|
||||||
this.molecularPathologyFindings?.forEach { it.patient = patientPseudonym }
|
this.molecularPathologyFindings?.forEach { it.patient = patientPseudonym }
|
||||||
this.molecularTherapies?.forEach { molecularTherapy -> molecularTherapy.history.forEach { it.patient = patientPseudonym } }
|
this.molecularTherapies?.forEach { molecularTherapy ->
|
||||||
|
molecularTherapy.history.forEach {
|
||||||
|
it.patient = patientPseudonym
|
||||||
|
}
|
||||||
|
}
|
||||||
this.ngsReports?.forEach { it.patient = patientPseudonym }
|
this.ngsReports?.forEach { it.patient = patientPseudonym }
|
||||||
this.previousGuidelineTherapies?.forEach { it.patient = patientPseudonym }
|
this.previousGuidelineTherapies?.forEach { it.patient = patientPseudonym }
|
||||||
this.rebiopsyRequests?.forEach { it.patient = patientPseudonym }
|
this.rebiopsyRequests?.forEach { it.patient = patientPseudonym }
|
||||||
@ -63,7 +67,6 @@ infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
|
|||||||
* Creates new hash of content IDs with given prefix except for patient IDs
|
* Creates new hash of content IDs with given prefix except for patient IDs
|
||||||
*
|
*
|
||||||
* @param pseudonymizeService The pseudonymizeService to be used
|
* @param pseudonymizeService The pseudonymizeService to be used
|
||||||
*
|
|
||||||
* @return The MTB file containing rehashed content IDs
|
* @return The MTB file containing rehashed content IDs
|
||||||
*/
|
*/
|
||||||
infix fun MtbFile.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
|
infix fun MtbFile.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
|
||||||
@ -224,3 +227,89 @@ infix fun MtbFile.anonymizeContentWith(pseudonymizeService: PseudonymizeService)
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/** Replaces patient ID with generated patient pseudonym
|
||||||
|
*
|
||||||
|
* @since 0.11.0
|
||||||
|
*
|
||||||
|
* @param pseudonymizeService The pseudonymizeService to be used
|
||||||
|
* @return The MTB file containing patient pseudonymes
|
||||||
|
*/
|
||||||
|
infix fun Mtb.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
|
||||||
|
val patientPseudonym = pseudonymizeService.patientPseudonym(PatientId(this.patient.id)).value
|
||||||
|
|
||||||
|
this.episodesOfCare?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
this.carePlans?.forEach {
|
||||||
|
it.patient.id = patientPseudonym
|
||||||
|
it.rebiopsyRequests?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
it.histologyReevaluationRequests?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
it.medicationRecommendations.forEach { it.patient.id = patientPseudonym }
|
||||||
|
it.studyEnrollmentRecommendations?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
it.procedureRecommendations?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
it.geneticCounselingRecommendation.patient.id = patientPseudonym
|
||||||
|
}
|
||||||
|
this.diagnoses?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
this.guidelineTherapies?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
this.guidelineProcedures?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
this.patient.id = patientPseudonym
|
||||||
|
this.claims?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
this.claimResponses?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
this.diagnoses?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
this.histologyReports?.forEach {
|
||||||
|
it.patient.id = patientPseudonym
|
||||||
|
it.results.tumorMorphology?.patient?.id = patientPseudonym
|
||||||
|
it.results.tumorCellContent?.patient?.id = patientPseudonym
|
||||||
|
}
|
||||||
|
this.ngsReports?.forEach {
|
||||||
|
it.patient.id = patientPseudonym
|
||||||
|
it.results.simpleVariants?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
it.results.copyNumberVariants?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
it.results.dnaFusions?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
it.results.rnaFusions?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
it.results.tumorCellContent?.patient?.id = patientPseudonym
|
||||||
|
it.results.brcaness?.patient?.id = patientPseudonym
|
||||||
|
it.results.tmb?.patient?.id = patientPseudonym
|
||||||
|
it.results.hrdScore?.patient?.id = patientPseudonym
|
||||||
|
}
|
||||||
|
this.ihcReports?.forEach {
|
||||||
|
it.patient.id = patientPseudonym
|
||||||
|
it.results.msiMmr?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
it.results.proteinExpression?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
}
|
||||||
|
this.responses?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
this.specimens?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
this.priorDiagnosticReports?.forEach { it.patient.id = patientPseudonym }
|
||||||
|
this.performanceStatus.forEach { it.patient.id = patientPseudonym }
|
||||||
|
this.systemicTherapies.forEach {
|
||||||
|
it.history?.forEach {
|
||||||
|
it.patient.id = patientPseudonym
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Creates new hash of content IDs with given prefix except for patient IDs
|
||||||
|
*
|
||||||
|
* @since 0.11.0
|
||||||
|
*
|
||||||
|
* @param pseudonymizeService The pseudonymizeService to be used
|
||||||
|
* @return The MTB file containing rehashed content IDs
|
||||||
|
*/
|
||||||
|
infix fun Mtb.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.episodesOfCare?.forEach {
|
||||||
|
it?.apply {
|
||||||
|
id = id?.let {
|
||||||
|
anonymize(it)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// TODO all other properties
|
||||||
|
}
|
||||||
|
@ -1,7 +1,7 @@
|
|||||||
/*
|
/*
|
||||||
* This file is part of ETL-Processor
|
* This file is part of ETL-Processor
|
||||||
*
|
*
|
||||||
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
* 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
|
* 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
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
@ -27,10 +27,11 @@ import dev.dnpm.etl.processor.monitoring.Report
|
|||||||
import dev.dnpm.etl.processor.monitoring.Request
|
import dev.dnpm.etl.processor.monitoring.Request
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestType
|
import dev.dnpm.etl.processor.monitoring.RequestType
|
||||||
import dev.dnpm.etl.processor.output.MtbFileSender
|
import dev.dnpm.etl.processor.output.*
|
||||||
import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
|
import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
|
||||||
import dev.dnpm.etl.processor.pseudonym.anonymizeContentWith
|
import dev.dnpm.etl.processor.pseudonym.anonymizeContentWith
|
||||||
import dev.dnpm.etl.processor.pseudonym.pseudonymizeWith
|
import dev.dnpm.etl.processor.pseudonym.pseudonymizeWith
|
||||||
|
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||||
import org.apache.commons.codec.binary.Base32
|
import org.apache.commons.codec.binary.Base32
|
||||||
import org.apache.commons.codec.digest.DigestUtils
|
import org.apache.commons.codec.digest.DigestUtils
|
||||||
import org.springframework.context.ApplicationEventPublisher
|
import org.springframework.context.ApplicationEventPublisher
|
||||||
@ -55,29 +56,40 @@ class RequestProcessor(
|
|||||||
|
|
||||||
fun processMtbFile(mtbFile: MtbFile, requestId: RequestId) {
|
fun processMtbFile(mtbFile: MtbFile, requestId: RequestId) {
|
||||||
val pid = PatientId(mtbFile.patient.id)
|
val pid = PatientId(mtbFile.patient.id)
|
||||||
|
|
||||||
mtbFile pseudonymizeWith pseudonymizeService
|
mtbFile pseudonymizeWith pseudonymizeService
|
||||||
mtbFile anonymizeContentWith pseudonymizeService
|
mtbFile anonymizeContentWith pseudonymizeService
|
||||||
|
val request = BwhcV1MtbFileRequest(requestId, transformationService.transform(mtbFile))
|
||||||
|
saveAndSend(request, pid)
|
||||||
|
}
|
||||||
|
|
||||||
val request = MtbFileSender.MtbFileRequest(requestId, transformationService.transform(mtbFile))
|
fun processMtbFile(mtbFile: Mtb) {
|
||||||
|
processMtbFile(mtbFile, randomRequestId())
|
||||||
|
}
|
||||||
|
|
||||||
val patientPseudonym = PatientPseudonym(request.mtbFile.patient.id)
|
fun processMtbFile(mtbFile: Mtb, requestId: RequestId) {
|
||||||
|
val pid = PatientId(mtbFile.patient.id)
|
||||||
|
mtbFile pseudonymizeWith pseudonymizeService
|
||||||
|
mtbFile anonymizeContentWith pseudonymizeService
|
||||||
|
val request = DnpmV2MtbFileRequest(requestId, transformationService.transform(mtbFile))
|
||||||
|
saveAndSend(request, pid)
|
||||||
|
}
|
||||||
|
|
||||||
|
private fun <T> saveAndSend(request: MtbFileRequest<T>, pid: PatientId) {
|
||||||
requestService.save(
|
requestService.save(
|
||||||
Request(
|
Request(
|
||||||
requestId,
|
request.requestId,
|
||||||
patientPseudonym,
|
request.patientPseudonym(),
|
||||||
pid,
|
pid,
|
||||||
fingerprint(request.mtbFile),
|
fingerprint(request),
|
||||||
RequestType.MTB_FILE,
|
RequestType.MTB_FILE,
|
||||||
RequestStatus.UNKNOWN
|
RequestStatus.UNKNOWN
|
||||||
)
|
)
|
||||||
)
|
)
|
||||||
|
|
||||||
if (appConfigProperties.duplicationDetection && isDuplication(mtbFile)) {
|
if (appConfigProperties.duplicationDetection && isDuplication(request)) {
|
||||||
applicationEventPublisher.publishEvent(
|
applicationEventPublisher.publishEvent(
|
||||||
ResponseEvent(
|
ResponseEvent(
|
||||||
requestId,
|
request.requestId,
|
||||||
Instant.now(),
|
Instant.now(),
|
||||||
RequestStatus.DUPLICATION
|
RequestStatus.DUPLICATION
|
||||||
)
|
)
|
||||||
@ -89,7 +101,7 @@ class RequestProcessor(
|
|||||||
|
|
||||||
applicationEventPublisher.publishEvent(
|
applicationEventPublisher.publishEvent(
|
||||||
ResponseEvent(
|
ResponseEvent(
|
||||||
requestId,
|
request.requestId,
|
||||||
Instant.now(),
|
Instant.now(),
|
||||||
responseStatus.status,
|
responseStatus.status,
|
||||||
when (responseStatus.status) {
|
when (responseStatus.status) {
|
||||||
@ -100,8 +112,11 @@ class RequestProcessor(
|
|||||||
)
|
)
|
||||||
}
|
}
|
||||||
|
|
||||||
private fun isDuplication(pseudonymizedMtbFile: MtbFile): Boolean {
|
private fun <T> isDuplication(pseudonymizedMtbFileRequest: MtbFileRequest<T>): Boolean {
|
||||||
val patientPseudonym = PatientPseudonym(pseudonymizedMtbFile.patient.id)
|
val patientPseudonym = when (pseudonymizedMtbFileRequest) {
|
||||||
|
is BwhcV1MtbFileRequest -> PatientPseudonym(pseudonymizedMtbFileRequest.content.patient.id)
|
||||||
|
is DnpmV2MtbFileRequest -> PatientPseudonym(pseudonymizedMtbFileRequest.content.patient.id)
|
||||||
|
}
|
||||||
|
|
||||||
val lastMtbFileRequestForPatient =
|
val lastMtbFileRequestForPatient =
|
||||||
requestService.lastMtbFileRequestForPatientPseudonym(patientPseudonym)
|
requestService.lastMtbFileRequestForPatientPseudonym(patientPseudonym)
|
||||||
@ -109,7 +124,7 @@ class RequestProcessor(
|
|||||||
|
|
||||||
return null != lastMtbFileRequestForPatient
|
return null != lastMtbFileRequestForPatient
|
||||||
&& !isLastRequestDeletion
|
&& !isLastRequestDeletion
|
||||||
&& lastMtbFileRequestForPatient.fingerprint == fingerprint(pseudonymizedMtbFile)
|
&& lastMtbFileRequestForPatient.fingerprint == fingerprint(pseudonymizedMtbFileRequest)
|
||||||
}
|
}
|
||||||
|
|
||||||
fun processDeletion(patientId: PatientId) {
|
fun processDeletion(patientId: PatientId) {
|
||||||
@ -131,7 +146,7 @@ class RequestProcessor(
|
|||||||
)
|
)
|
||||||
)
|
)
|
||||||
|
|
||||||
val responseStatus = sender.send(MtbFileSender.DeleteRequest(requestId, patientPseudonym))
|
val responseStatus = sender.send(DeleteRequest(requestId, patientPseudonym))
|
||||||
|
|
||||||
applicationEventPublisher.publishEvent(
|
applicationEventPublisher.publishEvent(
|
||||||
ResponseEvent(
|
ResponseEvent(
|
||||||
@ -160,8 +175,11 @@ class RequestProcessor(
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
private fun fingerprint(mtbFile: MtbFile): Fingerprint {
|
private fun <T> fingerprint(request: MtbFileRequest<T>): Fingerprint {
|
||||||
return fingerprint(objectMapper.writeValueAsString(mtbFile))
|
return when (request) {
|
||||||
|
is BwhcV1MtbFileRequest -> fingerprint(objectMapper.writeValueAsString(request.content))
|
||||||
|
is DnpmV2MtbFileRequest -> fingerprint(objectMapper.writeValueAsString(request.content))
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
private fun fingerprint(s: String): Fingerprint {
|
private fun fingerprint(s: String): Fingerprint {
|
||||||
|
@ -23,10 +23,21 @@ import com.fasterxml.jackson.databind.ObjectMapper
|
|||||||
import com.jayway.jsonpath.JsonPath
|
import com.jayway.jsonpath.JsonPath
|
||||||
import com.jayway.jsonpath.PathNotFoundException
|
import com.jayway.jsonpath.PathNotFoundException
|
||||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||||
|
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||||
|
|
||||||
class TransformationService(private val objectMapper: ObjectMapper, private val transformations: List<Transformation>) {
|
class TransformationService(private val objectMapper: ObjectMapper, private val transformations: List<Transformation>) {
|
||||||
fun transform(mtbFile: MtbFile): MtbFile {
|
fun transform(mtbFile: MtbFile): MtbFile {
|
||||||
var json = objectMapper.writeValueAsString(mtbFile)
|
val json = transform(objectMapper.writeValueAsString(mtbFile))
|
||||||
|
return objectMapper.readValue(json, MtbFile::class.java)
|
||||||
|
}
|
||||||
|
|
||||||
|
fun transform(mtbFile: Mtb): Mtb {
|
||||||
|
val json = transform(objectMapper.writeValueAsString(mtbFile))
|
||||||
|
return objectMapper.readValue(json, Mtb::class.java)
|
||||||
|
}
|
||||||
|
|
||||||
|
private fun transform(content: String): String {
|
||||||
|
var json = content
|
||||||
|
|
||||||
transformations.forEach { transformation ->
|
transformations.forEach { transformation ->
|
||||||
val jsonPath = JsonPath.parse(json)
|
val jsonPath = JsonPath.parse(json)
|
||||||
@ -48,7 +59,7 @@ class TransformationService(private val objectMapper: ObjectMapper, private val
|
|||||||
json = jsonPath.jsonString()
|
json = jsonPath.jsonString()
|
||||||
}
|
}
|
||||||
|
|
||||||
return objectMapper.readValue(json, MtbFile::class.java)
|
return json
|
||||||
}
|
}
|
||||||
|
|
||||||
fun getTransformations(): List<Transformation> {
|
fun getTransformations(): List<Transformation> {
|
||||||
|
@ -1,7 +1,7 @@
|
|||||||
/*
|
/*
|
||||||
* This file is part of ETL-Processor
|
* This file is part of ETL-Processor
|
||||||
*
|
*
|
||||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
* 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
|
* 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
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
@ -19,6 +19,7 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor
|
package dev.dnpm.etl.processor
|
||||||
|
|
||||||
|
import org.springframework.http.MediaType
|
||||||
import java.util.*
|
import java.util.*
|
||||||
|
|
||||||
class Fingerprint(val value: String) {
|
class Fingerprint(val value: String) {
|
||||||
@ -47,3 +48,16 @@ value class PatientId(val value: String)
|
|||||||
value class PatientPseudonym(val value: String)
|
value class PatientPseudonym(val value: String)
|
||||||
|
|
||||||
fun emptyPatientPseudonym() = PatientPseudonym("")
|
fun emptyPatientPseudonym() = PatientPseudonym("")
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Custom MediaTypes
|
||||||
|
*
|
||||||
|
* @since 0.11.0
|
||||||
|
*/
|
||||||
|
object CustomMediaType {
|
||||||
|
val APPLICATION_VND_DNPM_V2_MTB_JSON = MediaType("application", "vnd.dnpm.v2.mtb+json")
|
||||||
|
const val APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE = "application/vnd.dnpm.v2.mtb+json"
|
||||||
|
|
||||||
|
val APPLICATION_VND_DNPM_V2_RD_JSON = MediaType("application", "vnd.dnpm.v2.rd+json")
|
||||||
|
const val APPLICATION_VND_DNPM_V2_RD_JSON_VALUE = "application/vnd.dnpm.v2.rd+json"
|
||||||
|
}
|
||||||
|
@ -1,7 +1,7 @@
|
|||||||
/*
|
/*
|
||||||
* This file is part of ETL-Processor
|
* This file is part of ETL-Processor
|
||||||
*
|
*
|
||||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
* 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
|
* 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
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
@ -23,6 +23,7 @@ import com.fasterxml.jackson.databind.ObjectMapper
|
|||||||
import de.ukw.ccc.bwhc.dto.Consent
|
import de.ukw.ccc.bwhc.dto.Consent
|
||||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||||
import de.ukw.ccc.bwhc.dto.Patient
|
import de.ukw.ccc.bwhc.dto.Patient
|
||||||
|
import dev.dnpm.etl.processor.CustomMediaType
|
||||||
import dev.dnpm.etl.processor.services.RequestProcessor
|
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||||
import org.apache.kafka.clients.consumer.ConsumerRecord
|
import org.apache.kafka.clients.consumer.ConsumerRecord
|
||||||
import org.apache.kafka.common.header.internals.RecordHeader
|
import org.apache.kafka.common.header.internals.RecordHeader
|
||||||
@ -63,9 +64,17 @@ class KafkaInputListenerTest {
|
|||||||
.withConsent(Consent.builder().withStatus(Consent.Status.ACTIVE).build())
|
.withConsent(Consent.builder().withStatus(Consent.Status.ACTIVE).build())
|
||||||
.build()
|
.build()
|
||||||
|
|
||||||
kafkaInputListener.onMessage(ConsumerRecord("testtopic", 0, 0, "", this.objectMapper.writeValueAsString(mtbFile)))
|
kafkaInputListener.onMessage(
|
||||||
|
ConsumerRecord(
|
||||||
|
"testtopic",
|
||||||
|
0,
|
||||||
|
0,
|
||||||
|
"",
|
||||||
|
this.objectMapper.writeValueAsString(mtbFile)
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
verify(requestProcessor, times(1)).processMtbFile(any())
|
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
@ -75,7 +84,15 @@ class KafkaInputListenerTest {
|
|||||||
.withConsent(Consent.builder().withStatus(Consent.Status.REJECTED).build())
|
.withConsent(Consent.builder().withStatus(Consent.Status.REJECTED).build())
|
||||||
.build()
|
.build()
|
||||||
|
|
||||||
kafkaInputListener.onMessage(ConsumerRecord("testtopic", 0, 0, "", this.objectMapper.writeValueAsString(mtbFile)))
|
kafkaInputListener.onMessage(
|
||||||
|
ConsumerRecord(
|
||||||
|
"testtopic",
|
||||||
|
0,
|
||||||
|
0,
|
||||||
|
"",
|
||||||
|
this.objectMapper.writeValueAsString(mtbFile)
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
|
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
|
||||||
}
|
}
|
||||||
@ -89,10 +106,22 @@ class KafkaInputListenerTest {
|
|||||||
|
|
||||||
val headers = RecordHeaders(listOf(RecordHeader("requestId", UUID.randomUUID().toString().toByteArray())))
|
val headers = RecordHeaders(listOf(RecordHeader("requestId", UUID.randomUUID().toString().toByteArray())))
|
||||||
kafkaInputListener.onMessage(
|
kafkaInputListener.onMessage(
|
||||||
ConsumerRecord("testtopic", 0, 0, -1L, TimestampType.NO_TIMESTAMP_TYPE, -1, -1, "", this.objectMapper.writeValueAsString(mtbFile), headers, Optional.empty())
|
ConsumerRecord(
|
||||||
|
"testtopic",
|
||||||
|
0,
|
||||||
|
0,
|
||||||
|
-1L,
|
||||||
|
TimestampType.NO_TIMESTAMP_TYPE,
|
||||||
|
-1,
|
||||||
|
-1,
|
||||||
|
"",
|
||||||
|
this.objectMapper.writeValueAsString(mtbFile),
|
||||||
|
headers,
|
||||||
|
Optional.empty()
|
||||||
|
)
|
||||||
)
|
)
|
||||||
|
|
||||||
verify(requestProcessor, times(1)).processMtbFile(any(), anyValueClass())
|
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>(), anyValueClass())
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
@ -104,9 +133,52 @@ class KafkaInputListenerTest {
|
|||||||
|
|
||||||
val headers = RecordHeaders(listOf(RecordHeader("requestId", UUID.randomUUID().toString().toByteArray())))
|
val headers = RecordHeaders(listOf(RecordHeader("requestId", UUID.randomUUID().toString().toByteArray())))
|
||||||
kafkaInputListener.onMessage(
|
kafkaInputListener.onMessage(
|
||||||
ConsumerRecord("testtopic", 0, 0, -1L, TimestampType.NO_TIMESTAMP_TYPE, -1, -1, "", this.objectMapper.writeValueAsString(mtbFile), headers, Optional.empty())
|
ConsumerRecord(
|
||||||
|
"testtopic",
|
||||||
|
0,
|
||||||
|
0,
|
||||||
|
-1L,
|
||||||
|
TimestampType.NO_TIMESTAMP_TYPE,
|
||||||
|
-1,
|
||||||
|
-1,
|
||||||
|
"",
|
||||||
|
this.objectMapper.writeValueAsString(mtbFile),
|
||||||
|
headers,
|
||||||
|
Optional.empty()
|
||||||
|
)
|
||||||
)
|
)
|
||||||
verify(requestProcessor, times(1)).processDeletion(anyValueClass(), anyValueClass())
|
verify(requestProcessor, times(1)).processDeletion(anyValueClass(), anyValueClass())
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun shouldNotProcessDnpmV2Request() {
|
||||||
|
val mtbFile = MtbFile.builder()
|
||||||
|
.withPatient(Patient.builder().withId("DUMMY_12345678").build())
|
||||||
|
.withConsent(Consent.builder().withStatus(Consent.Status.REJECTED).build())
|
||||||
|
.build()
|
||||||
|
|
||||||
|
val headers = RecordHeaders(
|
||||||
|
listOf(
|
||||||
|
RecordHeader("requestId", UUID.randomUUID().toString().toByteArray()),
|
||||||
|
RecordHeader("contentType", CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE.toByteArray())
|
||||||
|
)
|
||||||
|
)
|
||||||
|
kafkaInputListener.onMessage(
|
||||||
|
ConsumerRecord(
|
||||||
|
"testtopic",
|
||||||
|
0,
|
||||||
|
0,
|
||||||
|
-1L,
|
||||||
|
TimestampType.NO_TIMESTAMP_TYPE,
|
||||||
|
-1,
|
||||||
|
-1,
|
||||||
|
"",
|
||||||
|
this.objectMapper.writeValueAsString(mtbFile),
|
||||||
|
headers,
|
||||||
|
Optional.empty()
|
||||||
|
)
|
||||||
|
)
|
||||||
|
verify(requestProcessor, times(0)).processDeletion(anyValueClass(), anyValueClass())
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
@ -21,7 +21,9 @@ package dev.dnpm.etl.processor.input
|
|||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import de.ukw.ccc.bwhc.dto.*
|
import de.ukw.ccc.bwhc.dto.*
|
||||||
|
import dev.dnpm.etl.processor.CustomMediaType
|
||||||
import dev.dnpm.etl.processor.services.RequestProcessor
|
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||||
|
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||||
import org.junit.jupiter.api.BeforeEach
|
import org.junit.jupiter.api.BeforeEach
|
||||||
import org.junit.jupiter.api.Nested
|
import org.junit.jupiter.api.Nested
|
||||||
import org.junit.jupiter.api.Test
|
import org.junit.jupiter.api.Test
|
||||||
@ -32,6 +34,7 @@ import org.mockito.Mockito.verify
|
|||||||
import org.mockito.junit.jupiter.MockitoExtension
|
import org.mockito.junit.jupiter.MockitoExtension
|
||||||
import org.mockito.kotlin.any
|
import org.mockito.kotlin.any
|
||||||
import org.mockito.kotlin.anyValueClass
|
import org.mockito.kotlin.anyValueClass
|
||||||
|
import org.springframework.core.io.ClassPathResource
|
||||||
import org.springframework.http.MediaType
|
import org.springframework.http.MediaType
|
||||||
import org.springframework.test.web.servlet.MockMvc
|
import org.springframework.test.web.servlet.MockMvc
|
||||||
import org.springframework.test.web.servlet.delete
|
import org.springframework.test.web.servlet.delete
|
||||||
@ -70,7 +73,7 @@ class MtbFileRestControllerTest {
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
verify(requestProcessor, times(1)).processMtbFile(any())
|
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
@ -126,7 +129,7 @@ class MtbFileRestControllerTest {
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
verify(requestProcessor, times(1)).processMtbFile(any())
|
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
@ -155,6 +158,40 @@ class MtbFileRestControllerTest {
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
inner class RequestsForDnpmDataModel21 {
|
||||||
|
|
||||||
|
private lateinit var mockMvc: MockMvc
|
||||||
|
|
||||||
|
private lateinit var requestProcessor: RequestProcessor
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setup(
|
||||||
|
@Mock requestProcessor: RequestProcessor
|
||||||
|
) {
|
||||||
|
this.requestProcessor = requestProcessor
|
||||||
|
val controller = MtbFileRestController(requestProcessor)
|
||||||
|
this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build()
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun shouldRespondPostRequest() {
|
||||||
|
val mtbFileContent = ClassPathResource("mv64e-mtb-fake-patient.json").inputStream.readAllBytes().toString(Charsets.UTF_8)
|
||||||
|
|
||||||
|
mockMvc.post("/mtb") {
|
||||||
|
content = mtbFileContent
|
||||||
|
contentType = CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON
|
||||||
|
}.andExpect {
|
||||||
|
status {
|
||||||
|
isAccepted()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
companion object {
|
companion object {
|
||||||
fun bwhcMtbFileContent(consentStatus: Consent.Status) = MtbFile.builder()
|
fun bwhcMtbFileContent(consentStatus: Consent.Status) = MtbFile.builder()
|
||||||
.withPatient(
|
.withPatient(
|
||||||
|
@ -1,7 +1,7 @@
|
|||||||
/*
|
/*
|
||||||
* This file is part of ETL-Processor
|
* This file is part of ETL-Processor
|
||||||
*
|
*
|
||||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
* 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
|
* 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
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
@ -21,20 +21,25 @@ package dev.dnpm.etl.processor.output
|
|||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import de.ukw.ccc.bwhc.dto.*
|
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.PatientPseudonym
|
||||||
import dev.dnpm.etl.processor.RequestId
|
import dev.dnpm.etl.processor.RequestId
|
||||||
import dev.dnpm.etl.processor.config.KafkaProperties
|
import dev.dnpm.etl.processor.config.KafkaProperties
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||||
|
import dev.pcvolkmer.mv64e.mtb.*
|
||||||
|
import org.apache.kafka.clients.producer.ProducerRecord
|
||||||
import org.assertj.core.api.Assertions.assertThat
|
import org.assertj.core.api.Assertions.assertThat
|
||||||
import org.junit.jupiter.api.BeforeEach
|
import org.junit.jupiter.api.BeforeEach
|
||||||
|
import org.junit.jupiter.api.Nested
|
||||||
import org.junit.jupiter.api.Test
|
import org.junit.jupiter.api.Test
|
||||||
import org.junit.jupiter.api.extension.ExtendWith
|
import org.junit.jupiter.api.extension.ExtendWith
|
||||||
import org.junit.jupiter.params.ParameterizedTest
|
import org.junit.jupiter.params.ParameterizedTest
|
||||||
import org.junit.jupiter.params.provider.MethodSource
|
import org.junit.jupiter.params.provider.MethodSource
|
||||||
import org.mockito.ArgumentMatchers.anyString
|
|
||||||
import org.mockito.Mock
|
import org.mockito.Mock
|
||||||
import org.mockito.junit.jupiter.MockitoExtension
|
import org.mockito.junit.jupiter.MockitoExtension
|
||||||
import org.mockito.kotlin.*
|
import org.mockito.kotlin.*
|
||||||
|
import org.springframework.http.MediaType
|
||||||
import org.springframework.kafka.core.KafkaTemplate
|
import org.springframework.kafka.core.KafkaTemplate
|
||||||
import org.springframework.kafka.support.SendResult
|
import org.springframework.kafka.support.SendResult
|
||||||
import org.springframework.retry.policy.SimpleRetryPolicy
|
import org.springframework.retry.policy.SimpleRetryPolicy
|
||||||
@ -45,6 +50,9 @@ import java.util.concurrent.ExecutionException
|
|||||||
@ExtendWith(MockitoExtension::class)
|
@ExtendWith(MockitoExtension::class)
|
||||||
class KafkaMtbFileSenderTest {
|
class KafkaMtbFileSenderTest {
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
inner class BwhcV1Record {
|
||||||
|
|
||||||
private lateinit var kafkaTemplate: KafkaTemplate<String, String>
|
private lateinit var kafkaTemplate: KafkaTemplate<String, String>
|
||||||
|
|
||||||
private lateinit var kafkaMtbFileSender: KafkaMtbFileSender
|
private lateinit var kafkaMtbFileSender: KafkaMtbFileSender
|
||||||
@ -65,67 +73,69 @@ class KafkaMtbFileSenderTest {
|
|||||||
}
|
}
|
||||||
|
|
||||||
@ParameterizedTest
|
@ParameterizedTest
|
||||||
@MethodSource("requestWithResponseSource")
|
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
|
||||||
fun shouldSendMtbFileRequestAndReturnExpectedState(testData: TestData) {
|
fun shouldSendMtbFileRequestAndReturnExpectedState(testData: TestData) {
|
||||||
doAnswer {
|
doAnswer {
|
||||||
if (null != testData.exception) {
|
if (null != testData.exception) {
|
||||||
throw testData.exception
|
throw testData.exception
|
||||||
}
|
}
|
||||||
completedFuture(SendResult<String, String>(null, null))
|
completedFuture(SendResult<String, String>(null, null))
|
||||||
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
|
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
|
||||||
|
|
||||||
val response = kafkaMtbFileSender.send(MtbFileSender.MtbFileRequest(TEST_REQUEST_ID, mtbFile(Consent.Status.ACTIVE)))
|
val response = kafkaMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1MtbFile(Consent.Status.ACTIVE)))
|
||||||
assertThat(response.status).isEqualTo(testData.requestStatus)
|
assertThat(response.status).isEqualTo(testData.requestStatus)
|
||||||
}
|
}
|
||||||
|
|
||||||
@ParameterizedTest
|
@ParameterizedTest
|
||||||
@MethodSource("requestWithResponseSource")
|
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
|
||||||
fun shouldSendDeleteRequestAndReturnExpectedState(testData: TestData) {
|
fun shouldSendDeleteRequestAndReturnExpectedState(testData: TestData) {
|
||||||
doAnswer {
|
doAnswer {
|
||||||
if (null != testData.exception) {
|
if (null != testData.exception) {
|
||||||
throw testData.exception
|
throw testData.exception
|
||||||
}
|
}
|
||||||
completedFuture(SendResult<String, String>(null, null))
|
completedFuture(SendResult<String, String>(null, null))
|
||||||
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
|
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
|
||||||
|
|
||||||
val response = kafkaMtbFileSender.send(MtbFileSender.DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
val response = kafkaMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
||||||
assertThat(response.status).isEqualTo(testData.requestStatus)
|
assertThat(response.status).isEqualTo(testData.requestStatus)
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
fun shouldSendMtbFileRequestWithCorrectKeyAndBody() {
|
fun shouldSendMtbFileRequestWithCorrectKeyAndHeaderAndBody() {
|
||||||
doAnswer {
|
doAnswer {
|
||||||
completedFuture(SendResult<String, String>(null, null))
|
completedFuture(SendResult<String, String>(null, null))
|
||||||
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
|
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
|
||||||
|
|
||||||
kafkaMtbFileSender.send(MtbFileSender.MtbFileRequest(TEST_REQUEST_ID, mtbFile(Consent.Status.ACTIVE)))
|
kafkaMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1MtbFile(Consent.Status.ACTIVE)))
|
||||||
|
|
||||||
val captor = argumentCaptor<String>()
|
val captor = argumentCaptor<ProducerRecord<String, String>>()
|
||||||
verify(kafkaTemplate, times(1)).send(anyString(), captor.capture(), captor.capture())
|
verify(kafkaTemplate, times(1)).send(captor.capture())
|
||||||
assertThat(captor.firstValue).isNotNull
|
assertThat(captor.firstValue.key()).isNotNull
|
||||||
assertThat(captor.firstValue).isEqualTo("{\"pid\": \"PID\"}")
|
assertThat(captor.firstValue.key()).isEqualTo("{\"pid\": \"PID\"}")
|
||||||
assertThat(captor.secondValue).isNotNull
|
assertThat(captor.firstValue.headers().headers("contentType")).isNotNull
|
||||||
assertThat(captor.secondValue).isEqualTo(objectMapper.writeValueAsString(kafkaRecordData(TEST_REQUEST_ID, Consent.Status.ACTIVE)))
|
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
|
@Test
|
||||||
fun shouldSendDeleteRequestWithCorrectKeyAndBody() {
|
fun shouldSendDeleteRequestWithCorrectKeyAndBody() {
|
||||||
doAnswer {
|
doAnswer {
|
||||||
completedFuture(SendResult<String, String>(null, null))
|
completedFuture(SendResult<String, String>(null, null))
|
||||||
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
|
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
|
||||||
|
|
||||||
kafkaMtbFileSender.send(MtbFileSender.DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
kafkaMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
||||||
|
|
||||||
val captor = argumentCaptor<String>()
|
val captor = argumentCaptor<ProducerRecord<String, String>>()
|
||||||
verify(kafkaTemplate, times(1)).send(anyString(), captor.capture(), captor.capture())
|
verify(kafkaTemplate, times(1)).send(captor.capture())
|
||||||
assertThat(captor.firstValue).isNotNull
|
assertThat(captor.firstValue.key()).isNotNull
|
||||||
assertThat(captor.firstValue).isEqualTo("{\"pid\": \"PID\"}")
|
assertThat(captor.firstValue.key()).isEqualTo("{\"pid\": \"PID\"}")
|
||||||
assertThat(captor.secondValue).isNotNull
|
assertThat(captor.firstValue.value()).isNotNull
|
||||||
assertThat(captor.secondValue).isEqualTo(objectMapper.writeValueAsString(kafkaRecordData(TEST_REQUEST_ID, Consent.Status.REJECTED)))
|
assertThat(captor.firstValue.value()).isEqualTo(objectMapper.writeValueAsString(bwhcV1kafkaRecordData(TEST_REQUEST_ID, Consent.Status.REJECTED)))
|
||||||
}
|
}
|
||||||
|
|
||||||
@ParameterizedTest
|
@ParameterizedTest
|
||||||
@MethodSource("requestWithResponseSource")
|
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
|
||||||
fun shouldRetryOnMtbFileKafkaSendError(testData: TestData) {
|
fun shouldRetryOnMtbFileKafkaSendError(testData: TestData) {
|
||||||
val kafkaProperties = KafkaProperties("testtopic")
|
val kafkaProperties = KafkaProperties("testtopic")
|
||||||
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
|
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
|
||||||
@ -136,9 +146,9 @@ class KafkaMtbFileSenderTest {
|
|||||||
throw testData.exception
|
throw testData.exception
|
||||||
}
|
}
|
||||||
completedFuture(SendResult<String, String>(null, null))
|
completedFuture(SendResult<String, String>(null, null))
|
||||||
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
|
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
|
||||||
|
|
||||||
kafkaMtbFileSender.send(MtbFileSender.MtbFileRequest(TEST_REQUEST_ID, mtbFile(Consent.Status.ACTIVE)))
|
kafkaMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1MtbFile(Consent.Status.ACTIVE)))
|
||||||
|
|
||||||
val expectedCount = when (testData.exception) {
|
val expectedCount = when (testData.exception) {
|
||||||
// OK - No Retry
|
// OK - No Retry
|
||||||
@ -147,11 +157,11 @@ class KafkaMtbFileSenderTest {
|
|||||||
else -> times(3)
|
else -> times(3)
|
||||||
}
|
}
|
||||||
|
|
||||||
verify(kafkaTemplate, expectedCount).send(anyString(), anyString(), anyString())
|
verify(kafkaTemplate, expectedCount).send(any<ProducerRecord<String, String>>())
|
||||||
}
|
}
|
||||||
|
|
||||||
@ParameterizedTest
|
@ParameterizedTest
|
||||||
@MethodSource("requestWithResponseSource")
|
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
|
||||||
fun shouldRetryOnDeleteKafkaSendError(testData: TestData) {
|
fun shouldRetryOnDeleteKafkaSendError(testData: TestData) {
|
||||||
val kafkaProperties = KafkaProperties("testtopic")
|
val kafkaProperties = KafkaProperties("testtopic")
|
||||||
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
|
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
|
||||||
@ -162,9 +172,9 @@ class KafkaMtbFileSenderTest {
|
|||||||
throw testData.exception
|
throw testData.exception
|
||||||
}
|
}
|
||||||
completedFuture(SendResult<String, String>(null, null))
|
completedFuture(SendResult<String, String>(null, null))
|
||||||
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
|
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
|
||||||
|
|
||||||
kafkaMtbFileSender.send(MtbFileSender.DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
kafkaMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
||||||
|
|
||||||
val expectedCount = when (testData.exception) {
|
val expectedCount = when (testData.exception) {
|
||||||
// OK - No Retry
|
// OK - No Retry
|
||||||
@ -173,14 +183,98 @@ class KafkaMtbFileSenderTest {
|
|||||||
else -> times(3)
|
else -> times(3)
|
||||||
}
|
}
|
||||||
|
|
||||||
verify(kafkaTemplate, expectedCount).send(anyString(), anyString(), anyString())
|
verify(kafkaTemplate, expectedCount).send(any<ProducerRecord<String, String>>())
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
inner class DnpmV2Record {
|
||||||
|
|
||||||
|
private lateinit var kafkaTemplate: KafkaTemplate<String, String>
|
||||||
|
|
||||||
|
private lateinit var kafkaMtbFileSender: KafkaMtbFileSender
|
||||||
|
|
||||||
|
private lateinit var objectMapper: ObjectMapper
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setup(
|
||||||
|
@Mock kafkaTemplate: KafkaTemplate<String, String>
|
||||||
|
) {
|
||||||
|
val kafkaProperties = KafkaProperties("testtopic")
|
||||||
|
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
|
||||||
|
|
||||||
|
this.objectMapper = ObjectMapper()
|
||||||
|
this.kafkaTemplate = kafkaTemplate
|
||||||
|
|
||||||
|
this.kafkaMtbFileSender = KafkaMtbFileSender(kafkaTemplate, kafkaProperties, retryTemplate, objectMapper)
|
||||||
|
}
|
||||||
|
|
||||||
|
@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(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile()))
|
||||||
|
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(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile()))
|
||||||
|
|
||||||
|
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(CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE.toByteArray())
|
||||||
|
assertThat(captor.firstValue.value()).isNotNull
|
||||||
|
assertThat(captor.firstValue.value()).isEqualTo(objectMapper.writeValueAsString(dnmpV2kafkaRecordData(TEST_REQUEST_ID)))
|
||||||
|
}
|
||||||
|
|
||||||
|
@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(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile()))
|
||||||
|
|
||||||
|
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>>())
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
companion object {
|
companion object {
|
||||||
val TEST_REQUEST_ID = RequestId("TestId")
|
val TEST_REQUEST_ID = RequestId("TestId")
|
||||||
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID")
|
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID")
|
||||||
|
|
||||||
fun mtbFile(consentStatus: Consent.Status): MtbFile {
|
fun bwhcV1MtbFile(consentStatus: Consent.Status): MtbFile {
|
||||||
return if (consentStatus == Consent.Status.ACTIVE) {
|
return if (consentStatus == Consent.Status.ACTIVE) {
|
||||||
MtbFile.builder()
|
MtbFile.builder()
|
||||||
.withPatient(
|
.withPatient(
|
||||||
@ -215,8 +309,31 @@ class KafkaMtbFileSenderTest {
|
|||||||
}.build()
|
}.build()
|
||||||
}
|
}
|
||||||
|
|
||||||
fun kafkaRecordData(requestId: RequestId, consentStatus: Consent.Status): KafkaMtbFileSender.Data {
|
fun dnpmV2MtbFile(): Mtb = Mtb.builder()
|
||||||
return KafkaMtbFileSender.Data(requestId, mtbFile(consentStatus))
|
.withPatient(
|
||||||
|
dev.pcvolkmer.mv64e.mtb.Patient.builder()
|
||||||
|
.withId("PID")
|
||||||
|
.withBirthDate("2000-08-08")
|
||||||
|
.withGender(CodingGender.builder().withCode(CodingGender.Code.MALE).build())
|
||||||
|
.build()
|
||||||
|
)
|
||||||
|
.withEpisodesOfCare(
|
||||||
|
listOf(
|
||||||
|
MTBEpisodeOfCare.builder()
|
||||||
|
.withId("1")
|
||||||
|
.withPatient(Reference("PID"))
|
||||||
|
.withPeriod(PeriodDate.builder().withStart("2023-08-08").build())
|
||||||
|
.build()
|
||||||
|
)
|
||||||
|
)
|
||||||
|
.build()
|
||||||
|
|
||||||
|
fun bwhcV1kafkaRecordData(requestId: RequestId, consentStatus: Consent.Status): MtbRequest {
|
||||||
|
return BwhcV1MtbFileRequest(requestId, bwhcV1MtbFile(consentStatus))
|
||||||
|
}
|
||||||
|
|
||||||
|
fun dnmpV2kafkaRecordData(requestId: RequestId): MtbRequest {
|
||||||
|
return DnpmV2MtbFileRequest(requestId, dnpmV2MtbFile())
|
||||||
}
|
}
|
||||||
|
|
||||||
data class TestData(val requestStatus: RequestStatus, val exception: Throwable? = null)
|
data class TestData(val requestStatus: RequestStatus, val exception: Throwable? = null)
|
||||||
|
@ -30,16 +30,16 @@ import dev.dnpm.etl.processor.monitoring.RequestStatus
|
|||||||
import org.assertj.core.api.Assertions.assertThat
|
import org.assertj.core.api.Assertions.assertThat
|
||||||
import org.junit.jupiter.api.BeforeEach
|
import org.junit.jupiter.api.BeforeEach
|
||||||
import org.junit.jupiter.params.ParameterizedTest
|
import org.junit.jupiter.params.ParameterizedTest
|
||||||
import org.junit.jupiter.params.provider.Arguments
|
|
||||||
import org.junit.jupiter.params.provider.MethodSource
|
import org.junit.jupiter.params.provider.MethodSource
|
||||||
|
import org.springframework.http.HttpHeaders
|
||||||
import org.springframework.http.HttpMethod
|
import org.springframework.http.HttpMethod
|
||||||
import org.springframework.http.HttpStatus
|
import org.springframework.http.HttpStatus
|
||||||
|
import org.springframework.http.MediaType
|
||||||
import org.springframework.retry.policy.SimpleRetryPolicy
|
import org.springframework.retry.policy.SimpleRetryPolicy
|
||||||
import org.springframework.retry.support.RetryTemplateBuilder
|
import org.springframework.retry.support.RetryTemplateBuilder
|
||||||
import org.springframework.test.web.client.ExpectedCount
|
import org.springframework.test.web.client.ExpectedCount
|
||||||
import org.springframework.test.web.client.MockRestServiceServer
|
import org.springframework.test.web.client.MockRestServiceServer
|
||||||
import org.springframework.test.web.client.match.MockRestRequestMatchers.method
|
import org.springframework.test.web.client.match.MockRestRequestMatchers.*
|
||||||
import org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo
|
|
||||||
import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus
|
import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus
|
||||||
import org.springframework.web.client.RestTemplate
|
import org.springframework.web.client.RestTemplate
|
||||||
|
|
||||||
@ -73,7 +73,7 @@ class RestBwhcMtbFileSenderTest {
|
|||||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||||
}
|
}
|
||||||
|
|
||||||
val response = restMtbFileSender.send(MtbFileSender.DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
val response = restMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
||||||
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
||||||
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
||||||
}
|
}
|
||||||
@ -84,11 +84,12 @@ class RestBwhcMtbFileSenderTest {
|
|||||||
this.mockRestServiceServer
|
this.mockRestServiceServer
|
||||||
.expect(method(HttpMethod.POST))
|
.expect(method(HttpMethod.POST))
|
||||||
.andExpect(requestTo("http://localhost:9000/mtbfile/MTBFile"))
|
.andExpect(requestTo("http://localhost:9000/mtbfile/MTBFile"))
|
||||||
|
.andExpect(header(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE))
|
||||||
.andRespond {
|
.andRespond {
|
||||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||||
}
|
}
|
||||||
|
|
||||||
val response = restMtbFileSender.send(MtbFileSender.MtbFileRequest(TEST_REQUEST_ID, mtbFile))
|
val response = restMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, mtbFile))
|
||||||
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
||||||
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
||||||
}
|
}
|
||||||
@ -118,7 +119,7 @@ class RestBwhcMtbFileSenderTest {
|
|||||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||||
}
|
}
|
||||||
|
|
||||||
val response = restMtbFileSender.send(MtbFileSender.MtbFileRequest(TEST_REQUEST_ID, mtbFile))
|
val response = restMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, mtbFile))
|
||||||
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
||||||
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
||||||
}
|
}
|
||||||
@ -148,7 +149,7 @@ class RestBwhcMtbFileSenderTest {
|
|||||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||||
}
|
}
|
||||||
|
|
||||||
val response = restMtbFileSender.send(MtbFileSender.DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
val response = restMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
||||||
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
||||||
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
||||||
}
|
}
|
||||||
|
@ -22,6 +22,8 @@ package dev.dnpm.etl.processor.output
|
|||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import com.fasterxml.jackson.module.kotlin.KotlinModule
|
import com.fasterxml.jackson.module.kotlin.KotlinModule
|
||||||
import de.ukw.ccc.bwhc.dto.*
|
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.PatientPseudonym
|
||||||
import dev.dnpm.etl.processor.RequestId
|
import dev.dnpm.etl.processor.RequestId
|
||||||
import dev.dnpm.etl.processor.config.AppConfigProperties
|
import dev.dnpm.etl.processor.config.AppConfigProperties
|
||||||
@ -29,25 +31,30 @@ import dev.dnpm.etl.processor.config.AppConfiguration
|
|||||||
import dev.dnpm.etl.processor.config.RestTargetProperties
|
import dev.dnpm.etl.processor.config.RestTargetProperties
|
||||||
import dev.dnpm.etl.processor.monitoring.ReportService
|
import dev.dnpm.etl.processor.monitoring.ReportService
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||||
import dev.dnpm.etl.processor.output.RestBwhcMtbFileSenderTest.Companion
|
import dev.pcvolkmer.mv64e.mtb.*
|
||||||
import org.assertj.core.api.Assertions.assertThat
|
import org.assertj.core.api.Assertions.assertThat
|
||||||
import org.junit.jupiter.api.BeforeEach
|
import org.junit.jupiter.api.BeforeEach
|
||||||
|
import org.junit.jupiter.api.Nested
|
||||||
import org.junit.jupiter.params.ParameterizedTest
|
import org.junit.jupiter.params.ParameterizedTest
|
||||||
import org.junit.jupiter.params.provider.MethodSource
|
import org.junit.jupiter.params.provider.MethodSource
|
||||||
|
import org.springframework.http.HttpHeaders
|
||||||
import org.springframework.http.HttpMethod
|
import org.springframework.http.HttpMethod
|
||||||
import org.springframework.http.HttpStatus
|
import org.springframework.http.HttpStatus
|
||||||
|
import org.springframework.http.MediaType
|
||||||
import org.springframework.retry.backoff.NoBackOffPolicy
|
import org.springframework.retry.backoff.NoBackOffPolicy
|
||||||
import org.springframework.retry.policy.SimpleRetryPolicy
|
import org.springframework.retry.policy.SimpleRetryPolicy
|
||||||
import org.springframework.retry.support.RetryTemplateBuilder
|
import org.springframework.retry.support.RetryTemplateBuilder
|
||||||
import org.springframework.test.web.client.ExpectedCount
|
import org.springframework.test.web.client.ExpectedCount
|
||||||
import org.springframework.test.web.client.MockRestServiceServer
|
import org.springframework.test.web.client.MockRestServiceServer
|
||||||
import org.springframework.test.web.client.match.MockRestRequestMatchers.method
|
import org.springframework.test.web.client.match.MockRestRequestMatchers.*
|
||||||
import org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo
|
|
||||||
import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus
|
import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus
|
||||||
import org.springframework.web.client.RestTemplate
|
import org.springframework.web.client.RestTemplate
|
||||||
|
|
||||||
class RestDipMtbFileSenderTest {
|
class RestDipMtbFileSenderTest {
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
inner class BwhcV1ContentRequest {
|
||||||
|
|
||||||
private lateinit var mockRestServiceServer: MockRestServiceServer
|
private lateinit var mockRestServiceServer: MockRestServiceServer
|
||||||
|
|
||||||
private lateinit var restMtbFileSender: RestMtbFileSender
|
private lateinit var restMtbFileSender: RestMtbFileSender
|
||||||
@ -62,41 +69,28 @@ class RestDipMtbFileSenderTest {
|
|||||||
|
|
||||||
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
|
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
|
||||||
|
|
||||||
this.restMtbFileSender = RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
|
this.restMtbFileSender =
|
||||||
|
RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
|
||||||
}
|
}
|
||||||
|
|
||||||
@ParameterizedTest
|
@ParameterizedTest
|
||||||
@MethodSource("deleteRequestWithResponseSource")
|
@MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#mtbFileRequestWithResponseSource")
|
||||||
fun shouldReturnExpectedResponseForDelete(requestWithResponse: RequestWithResponse) {
|
|
||||||
this.mockRestServiceServer
|
|
||||||
.expect(method(HttpMethod.DELETE))
|
|
||||||
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient/${TEST_PATIENT_PSEUDONYM.value}"))
|
|
||||||
.andRespond {
|
|
||||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
|
||||||
}
|
|
||||||
|
|
||||||
val response = restMtbFileSender.send(MtbFileSender.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) {
|
fun shouldReturnExpectedResponseForMtbFilePost(requestWithResponse: RequestWithResponse) {
|
||||||
this.mockRestServiceServer
|
this.mockRestServiceServer
|
||||||
.expect(method(HttpMethod.POST))
|
.expect(method(HttpMethod.POST))
|
||||||
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient-record"))
|
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient-record"))
|
||||||
|
.andExpect(header(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE))
|
||||||
.andRespond {
|
.andRespond {
|
||||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||||
}
|
}
|
||||||
|
|
||||||
val response = restMtbFileSender.send(MtbFileSender.MtbFileRequest(TEST_REQUEST_ID, mtbFile))
|
val response = restMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1mtbFile))
|
||||||
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
||||||
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
||||||
}
|
}
|
||||||
|
|
||||||
@ParameterizedTest
|
@ParameterizedTest
|
||||||
@MethodSource("mtbFileRequestWithResponseSource")
|
@MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#mtbFileRequestWithResponseSource")
|
||||||
fun shouldRetryOnMtbFileHttpRequestError(requestWithResponse: RequestWithResponse) {
|
fun shouldRetryOnMtbFileHttpRequestError(requestWithResponse: RequestWithResponse) {
|
||||||
val restTemplate = RestTemplate()
|
val restTemplate = RestTemplate()
|
||||||
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false)
|
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false)
|
||||||
@ -123,13 +117,89 @@ class RestDipMtbFileSenderTest {
|
|||||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||||
}
|
}
|
||||||
|
|
||||||
val response = restMtbFileSender.send(MtbFileSender.MtbFileRequest(TEST_REQUEST_ID, mtbFile))
|
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
|
||||||
|
|
||||||
|
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 shouldReturnExpectedResponseForDnpmV2MtbFilePost(requestWithResponse: RequestWithResponse) {
|
||||||
|
this.mockRestServiceServer
|
||||||
|
.expect(method(HttpMethod.POST))
|
||||||
|
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient-record"))
|
||||||
|
.andExpect(header(HttpHeaders.CONTENT_TYPE, CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE))
|
||||||
|
.andRespond {
|
||||||
|
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||||
|
}
|
||||||
|
|
||||||
|
val response = restMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile))
|
||||||
|
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
||||||
|
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
inner class DeleteRequest {
|
||||||
|
|
||||||
|
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#deleteRequestWithResponseSource")
|
||||||
|
fun shouldReturnExpectedResponseForDelete(requestWithResponse: RequestWithResponse) {
|
||||||
|
this.mockRestServiceServer
|
||||||
|
.expect(method(HttpMethod.DELETE))
|
||||||
|
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/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.status).isEqualTo(requestWithResponse.response.status)
|
||||||
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
||||||
}
|
}
|
||||||
|
|
||||||
@ParameterizedTest
|
@ParameterizedTest
|
||||||
@MethodSource("deleteRequestWithResponseSource")
|
@MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#deleteRequestWithResponseSource")
|
||||||
fun shouldRetryOnDeleteHttpRequestError(requestWithResponse: RequestWithResponse) {
|
fun shouldRetryOnDeleteHttpRequestError(requestWithResponse: RequestWithResponse) {
|
||||||
val restTemplate = RestTemplate()
|
val restTemplate = RestTemplate()
|
||||||
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false)
|
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false)
|
||||||
@ -156,11 +226,13 @@ class RestDipMtbFileSenderTest {
|
|||||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||||
}
|
}
|
||||||
|
|
||||||
val response = restMtbFileSender.send(MtbFileSender.DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
val response = restMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
||||||
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
||||||
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
||||||
}
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
companion object {
|
companion object {
|
||||||
data class RequestWithResponse(
|
data class RequestWithResponse(
|
||||||
val httpStatus: HttpStatus,
|
val httpStatus: HttpStatus,
|
||||||
@ -171,7 +243,7 @@ class RestDipMtbFileSenderTest {
|
|||||||
val TEST_REQUEST_ID = RequestId("TestId")
|
val TEST_REQUEST_ID = RequestId("TestId")
|
||||||
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID")
|
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID")
|
||||||
|
|
||||||
val mtbFile: MtbFile = MtbFile.builder()
|
val bwhcV1mtbFile: MtbFile = MtbFile.builder()
|
||||||
.withPatient(
|
.withPatient(
|
||||||
Patient.builder()
|
Patient.builder()
|
||||||
.withId("PID")
|
.withId("PID")
|
||||||
@ -195,6 +267,25 @@ class RestDipMtbFileSenderTest {
|
|||||||
)
|
)
|
||||||
.build()
|
.build()
|
||||||
|
|
||||||
|
val dnpmV2MtbFile: Mtb = Mtb.builder()
|
||||||
|
.withPatient(
|
||||||
|
dev.pcvolkmer.mv64e.mtb.Patient.builder()
|
||||||
|
.withId("PID")
|
||||||
|
.withBirthDate("2000-08-08")
|
||||||
|
.withGender(CodingGender.builder().withCode(CodingGender.Code.MALE).build())
|
||||||
|
.build()
|
||||||
|
)
|
||||||
|
.withEpisodesOfCare(
|
||||||
|
listOf(
|
||||||
|
MTBEpisodeOfCare.builder()
|
||||||
|
.withId("1")
|
||||||
|
.withPatient(Reference("PID"))
|
||||||
|
.withPeriod(PeriodDate.builder().withStart("2023-08-08").build())
|
||||||
|
.build()
|
||||||
|
)
|
||||||
|
)
|
||||||
|
.build()
|
||||||
|
|
||||||
private const val ERROR_RESPONSE_BODY = "Sonstiger Fehler bei der Übertragung"
|
private const val ERROR_RESPONSE_BODY = "Sonstiger Fehler bei der Übertragung"
|
||||||
|
|
||||||
/**
|
/**
|
||||||
|
@ -1,7 +1,7 @@
|
|||||||
/*
|
/*
|
||||||
* This file is part of ETL-Processor
|
* This file is part of ETL-Processor
|
||||||
*
|
*
|
||||||
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
* 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
|
* 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
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
@ -21,7 +21,12 @@ package dev.dnpm.etl.processor.pseudonym
|
|||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import de.ukw.ccc.bwhc.dto.*
|
import de.ukw.ccc.bwhc.dto.*
|
||||||
|
import dev.pcvolkmer.mv64e.mtb.MTBEpisodeOfCare
|
||||||
|
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||||
|
import dev.pcvolkmer.mv64e.mtb.PeriodDate
|
||||||
|
import dev.pcvolkmer.mv64e.mtb.Reference
|
||||||
import org.assertj.core.api.Assertions.assertThat
|
import org.assertj.core.api.Assertions.assertThat
|
||||||
|
import org.junit.jupiter.api.Nested
|
||||||
import org.junit.jupiter.api.Test
|
import org.junit.jupiter.api.Test
|
||||||
import org.junit.jupiter.api.assertThrows
|
import org.junit.jupiter.api.assertThrows
|
||||||
import org.junit.jupiter.api.extension.ExtendWith
|
import org.junit.jupiter.api.extension.ExtendWith
|
||||||
@ -32,12 +37,15 @@ import org.mockito.kotlin.doAnswer
|
|||||||
import org.mockito.kotlin.whenever
|
import org.mockito.kotlin.whenever
|
||||||
import org.springframework.core.io.ClassPathResource
|
import org.springframework.core.io.ClassPathResource
|
||||||
|
|
||||||
const val FAKE_MTB_FILE_PATH = "fake_MTBFile.json"
|
|
||||||
const val CLEAN_PATIENT_ID = "5dad2f0b-49c6-47d8-a952-7b9e9e0f7549"
|
|
||||||
|
|
||||||
@ExtendWith(MockitoExtension::class)
|
@ExtendWith(MockitoExtension::class)
|
||||||
class ExtensionsTest {
|
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 {
|
private fun fakeMtbFile(): MtbFile {
|
||||||
val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
|
val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
|
||||||
return ObjectMapper().readValue(mtbFile, MtbFile::class.java)
|
return ObjectMapper().readValue(mtbFile, MtbFile::class.java)
|
||||||
@ -191,8 +199,83 @@ class ExtensionsTest {
|
|||||||
mtbFile.pseudonymizeWith(pseudonymizeService)
|
mtbFile.pseudonymizeWith(pseudonymizeService)
|
||||||
mtbFile.anonymizeContentWith(pseudonymizeService)
|
mtbFile.anonymizeContentWith(pseudonymizeService)
|
||||||
|
|
||||||
|
|
||||||
assertThat(mtbFile.episode.id).isNotNull()
|
assertThat(mtbFile.episode.id).isNotNull()
|
||||||
}
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
inner class UsingDnpmV2Datamodel {
|
||||||
|
|
||||||
|
val FAKE_MTB_FILE_PATH = "mv64e-mtb-fake-patient.json"
|
||||||
|
val CLEAN_PATIENT_ID = "63f8fd7b-8127-4f3c-8843-aa9199e21c29"
|
||||||
|
|
||||||
|
private fun fakeMtbFile(): Mtb {
|
||||||
|
val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
|
||||||
|
return ObjectMapper().readValue(mtbFile, Mtb::class.java)
|
||||||
|
}
|
||||||
|
|
||||||
|
private fun Mtb.serialized(): String {
|
||||||
|
return ObjectMapper().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 shouldNotThrowExceptionOnNullValues(@Mock pseudonymizeService: PseudonymizeService) {
|
||||||
|
doAnswer {
|
||||||
|
it.arguments[0]
|
||||||
|
"PSEUDO-ID"
|
||||||
|
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||||
|
|
||||||
|
doAnswer {
|
||||||
|
"TESTDOMAIN"
|
||||||
|
}.whenever(pseudonymizeService).prefix()
|
||||||
|
|
||||||
|
val mtbFile = Mtb.builder()
|
||||||
|
.withPatient(
|
||||||
|
dev.pcvolkmer.mv64e.mtb.Patient.builder()
|
||||||
|
.withId("1")
|
||||||
|
.withBirthDate("2000-08-08")
|
||||||
|
.withGender(null)
|
||||||
|
.build()
|
||||||
|
)
|
||||||
|
.withEpisodesOfCare(
|
||||||
|
listOf(
|
||||||
|
MTBEpisodeOfCare.builder()
|
||||||
|
.withId("1")
|
||||||
|
.withPatient(Reference("1"))
|
||||||
|
.withPeriod(PeriodDate.builder().withStart("2023-08-08").build())
|
||||||
|
.build()
|
||||||
|
)
|
||||||
|
)
|
||||||
|
.withClaims(null)
|
||||||
|
.withDiagnoses(null)
|
||||||
|
.withCarePlans(null)
|
||||||
|
.withClaimResponses(null)
|
||||||
|
.withHistologyReports(null)
|
||||||
|
.withNgsReports(null)
|
||||||
|
.withResponses(null)
|
||||||
|
.withSpecimens(null)
|
||||||
|
.build()
|
||||||
|
|
||||||
|
mtbFile.pseudonymizeWith(pseudonymizeService)
|
||||||
|
mtbFile.anonymizeContentWith(pseudonymizeService)
|
||||||
|
|
||||||
|
assertThat(mtbFile.episodesOfCare).hasSize(1)
|
||||||
|
assertThat(mtbFile.episodesOfCare.map { it.id }).isNotNull
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
@ -21,14 +21,19 @@ package dev.dnpm.etl.processor.services
|
|||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import de.ukw.ccc.bwhc.dto.*
|
import de.ukw.ccc.bwhc.dto.*
|
||||||
import dev.dnpm.etl.processor.*
|
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.config.AppConfigProperties
|
||||||
import dev.dnpm.etl.processor.monitoring.Request
|
import dev.dnpm.etl.processor.monitoring.Request
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestType
|
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.MtbFileSender
|
import dev.dnpm.etl.processor.output.MtbFileSender
|
||||||
import dev.dnpm.etl.processor.output.RestMtbFileSender
|
import dev.dnpm.etl.processor.output.RestMtbFileSender
|
||||||
import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
|
import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
|
||||||
|
import dev.dnpm.etl.processor.randomRequestId
|
||||||
import org.assertj.core.api.Assertions.assertThat
|
import org.assertj.core.api.Assertions.assertThat
|
||||||
import org.junit.jupiter.api.BeforeEach
|
import org.junit.jupiter.api.BeforeEach
|
||||||
import org.junit.jupiter.api.Test
|
import org.junit.jupiter.api.Test
|
||||||
@ -109,7 +114,7 @@ class RequestProcessorTest {
|
|||||||
|
|
||||||
doAnswer {
|
doAnswer {
|
||||||
it.arguments[0]
|
it.arguments[0]
|
||||||
}.whenever(transformationService).transform(any())
|
}.whenever(transformationService).transform(any<MtbFile>())
|
||||||
|
|
||||||
val mtbFile = MtbFile.builder()
|
val mtbFile = MtbFile.builder()
|
||||||
.withPatient(
|
.withPatient(
|
||||||
@ -168,7 +173,7 @@ class RequestProcessorTest {
|
|||||||
|
|
||||||
doAnswer {
|
doAnswer {
|
||||||
it.arguments[0]
|
it.arguments[0]
|
||||||
}.whenever(transformationService).transform(any())
|
}.whenever(transformationService).transform(any<MtbFile>())
|
||||||
|
|
||||||
val mtbFile = MtbFile.builder()
|
val mtbFile = MtbFile.builder()
|
||||||
.withPatient(
|
.withPatient(
|
||||||
@ -223,7 +228,7 @@ class RequestProcessorTest {
|
|||||||
|
|
||||||
doAnswer {
|
doAnswer {
|
||||||
MtbFileSender.Response(status = RequestStatus.SUCCESS)
|
MtbFileSender.Response(status = RequestStatus.SUCCESS)
|
||||||
}.whenever(sender).send(any<MtbFileSender.MtbFileRequest>())
|
}.whenever(sender).send(any<BwhcV1MtbFileRequest>())
|
||||||
|
|
||||||
doAnswer {
|
doAnswer {
|
||||||
it.arguments[0] as String
|
it.arguments[0] as String
|
||||||
@ -231,7 +236,7 @@ class RequestProcessorTest {
|
|||||||
|
|
||||||
doAnswer {
|
doAnswer {
|
||||||
it.arguments[0]
|
it.arguments[0]
|
||||||
}.whenever(transformationService).transform(any())
|
}.whenever(transformationService).transform(any<MtbFile>())
|
||||||
|
|
||||||
val mtbFile = MtbFile.builder()
|
val mtbFile = MtbFile.builder()
|
||||||
.withPatient(
|
.withPatient(
|
||||||
@ -286,7 +291,7 @@ class RequestProcessorTest {
|
|||||||
|
|
||||||
doAnswer {
|
doAnswer {
|
||||||
MtbFileSender.Response(status = RequestStatus.ERROR)
|
MtbFileSender.Response(status = RequestStatus.ERROR)
|
||||||
}.whenever(sender).send(any<MtbFileSender.MtbFileRequest>())
|
}.whenever(sender).send(any<BwhcV1MtbFileRequest>())
|
||||||
|
|
||||||
doAnswer {
|
doAnswer {
|
||||||
it.arguments[0] as String
|
it.arguments[0] as String
|
||||||
@ -294,7 +299,7 @@ class RequestProcessorTest {
|
|||||||
|
|
||||||
doAnswer {
|
doAnswer {
|
||||||
it.arguments[0]
|
it.arguments[0]
|
||||||
}.whenever(transformationService).transform(any())
|
}.whenever(transformationService).transform(any<MtbFile>())
|
||||||
|
|
||||||
val mtbFile = MtbFile.builder()
|
val mtbFile = MtbFile.builder()
|
||||||
.withPatient(
|
.withPatient(
|
||||||
@ -336,7 +341,7 @@ class RequestProcessorTest {
|
|||||||
|
|
||||||
doAnswer {
|
doAnswer {
|
||||||
MtbFileSender.Response(status = RequestStatus.UNKNOWN)
|
MtbFileSender.Response(status = RequestStatus.UNKNOWN)
|
||||||
}.whenever(sender).send(any<MtbFileSender.DeleteRequest>())
|
}.whenever(sender).send(any<DeleteRequest>())
|
||||||
|
|
||||||
this.requestProcessor.processDeletion(TEST_PATIENT_ID)
|
this.requestProcessor.processDeletion(TEST_PATIENT_ID)
|
||||||
|
|
||||||
@ -354,7 +359,7 @@ class RequestProcessorTest {
|
|||||||
|
|
||||||
doAnswer {
|
doAnswer {
|
||||||
MtbFileSender.Response(status = RequestStatus.SUCCESS)
|
MtbFileSender.Response(status = RequestStatus.SUCCESS)
|
||||||
}.whenever(sender).send(any<MtbFileSender.DeleteRequest>())
|
}.whenever(sender).send(any<DeleteRequest>())
|
||||||
|
|
||||||
this.requestProcessor.processDeletion(TEST_PATIENT_ID)
|
this.requestProcessor.processDeletion(TEST_PATIENT_ID)
|
||||||
|
|
||||||
@ -372,7 +377,7 @@ class RequestProcessorTest {
|
|||||||
|
|
||||||
doAnswer {
|
doAnswer {
|
||||||
MtbFileSender.Response(status = RequestStatus.ERROR)
|
MtbFileSender.Response(status = RequestStatus.ERROR)
|
||||||
}.whenever(sender).send(any<MtbFileSender.DeleteRequest>())
|
}.whenever(sender).send(any<DeleteRequest>())
|
||||||
|
|
||||||
this.requestProcessor.processDeletion(TEST_PATIENT_ID)
|
this.requestProcessor.processDeletion(TEST_PATIENT_ID)
|
||||||
|
|
||||||
@ -404,11 +409,11 @@ class RequestProcessorTest {
|
|||||||
|
|
||||||
doAnswer {
|
doAnswer {
|
||||||
it.arguments[0]
|
it.arguments[0]
|
||||||
}.whenever(transformationService).transform(any())
|
}.whenever(transformationService).transform(any<MtbFile>())
|
||||||
|
|
||||||
doAnswer {
|
doAnswer {
|
||||||
MtbFileSender.Response(status = RequestStatus.SUCCESS)
|
MtbFileSender.Response(status = RequestStatus.SUCCESS)
|
||||||
}.whenever(sender).send(any<MtbFileSender.MtbFileRequest>())
|
}.whenever(sender).send(any<BwhcV1MtbFileRequest>())
|
||||||
|
|
||||||
val mtbFile = MtbFile.builder()
|
val mtbFile = MtbFile.builder()
|
||||||
.withPatient(
|
.withPatient(
|
||||||
|
2243
src/test/resources/mv64e-mtb-fake-patient.json
Normal file
2243
src/test/resources/mv64e-mtb-fake-patient.json
Normal file
File diff suppressed because it is too large
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Reference in New Issue
Block a user