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b5b6203f3a | |||
07508679e6 |
2
.gitignore
vendored
2
.gitignore
vendored
@ -39,5 +39,3 @@ out/
|
||||
.vscode/
|
||||
/dev/gpas*
|
||||
/deploy/.env
|
||||
/dev/gICS*
|
||||
/dev/gPAS*
|
||||
|
71
README.md
71
README.md
@ -26,12 +26,15 @@ Konfigurationsparameter
|
||||
|
||||
### Modelvorhaben genomDE §64e
|
||||
|
||||
Um die voll Betriebsbereitschaft herzustellen, muss eine erfolgreiche Übertragung mit dem
|
||||
Submission-Typ *Test* erfolgt sein. Über die Umgebungsvariable wird dieser Übertragungsmodus
|
||||
aktiviert. Alle Datensätze mit erteilter Teilnahme am Modelvorhaben werden mit der Test-Kennung
|
||||
übertragen.
|
||||
Zusätzlich zur Patienten Identifier Pseudonymisierung müssen Vorgangsummern generiert werden, die
|
||||
jede Übertragung eindeutig identifizieren aber gleichzeitig dem Patienten zugeordnet werden können.
|
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Dies lässt sich durch weitere Pseudonyme abbilden, allerdings werden pro Originalwert mehrere
|
||||
Pseudonyme benötigt.
|
||||
Zu diesem Zweck muss in gPas eine **Multi-Pseudonym-Domäne** konfiguriert werden (siehe auch
|
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*APP_PSEUDONYMIZE_GPAS_CCDN*).
|
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|
||||
`APP_GENOM_DE_TEST_SUBMISSION` -> `true` | `false` (falls fehlt wird `true` angenommen)
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**WICHTIG:** Deaktivierte Pseudonymisierung ist nur für Tests nutzbar. Vorgangsummern sind zufällig
|
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und werden anschließend verworfen.
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|
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### Datenübermittlung über HTTP/REST
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|
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@ -109,61 +112,11 @@ Wurde die Verwendung von gPAS konfiguriert, so sind weitere Angaben zu konfiguri
|
||||
|
||||
* `APP_PSEUDONYMIZE_GPAS_URI`: URI der gPAS-Instanz inklusive Endpoint (z.B.
|
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`http://localhost:8080/ttp-fhir/fhir/gpas/$$pseudonymizeAllowCreate`)
|
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* `APP_PSEUDONYMIZE_GPAS_TARGET`: gPas Domänenname
|
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* `APP_PSEUDONYMIZE_GPAS_TARGET`: gPas Domänenname für Patienten ID
|
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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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### Einwilligung gICS
|
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|
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Ab gIcs Version 2.13.0 kann
|
||||
per [REST-Schnittstelle](https://simplifier.net/guide/ttp-fhir-gateway-ig/ImplementationGuide-markdown-Einwilligungsmanagement-Operations-isConsented?version=current)
|
||||
der Einwilligungsstatus abgefragt werden.
|
||||
Vor der MTB-Übertragung kann der zum Sendezeitpunkt verfügbarer Einwilligungsstatus über Endpunkt
|
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*isConsented* abgefragt werden.
|
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|
||||
Falls Anbindung an gICS aktiviert wurde, wird der Einwilligungsstatus der MTB Datei ignoriert.
|
||||
Stattdessen werden vorhandene Einwilligungen abgefragt und in die MTB Datei eingebettet.
|
||||
|
||||
Es werden zwei Einwilligungsdomänen unterstützt, eine für Broad Consent und als zweites GenomDE
|
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Modelvorhaben §64e.
|
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|
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#### Hinweise
|
||||
|
||||
1. Die aktuelle Impl. nimmt an, dass die hinterlegten Domänen der Einwilligungen ausschließlich für
|
||||
die genannten Art von Einwilligungen genutzt werden. Es finde keine weitere Filterung statt. Wir
|
||||
fragen pro Domäne die Schnittstelle `CurrentPolicyStatesForPerson` - siehe
|
||||
auch [IG TTP-FHIR Gateway
|
||||
](https://www.ths-greifswald.de/wp-content/uploads/tools/fhirgw/ig/2024-3-0/ImplementationGuide-markdown-Einwilligungsmanagement-Operations-currentPolicyStatesForPerson.html)
|
||||
ab.
|
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2. Die Einwilligung wird für den Patienten-Identifier der MTB abgerufen und anschließend durch das
|
||||
DNPM Pseudonym ersetzt.
|
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3. Abfragen von Einwilligungen über gesonderte Pseudonyme anstatt des MTB-Identifiers fehlt in der
|
||||
ersten Implementierung.
|
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4. Bei Verarbeitung von MTB Version 1.x Inhalten ist eine positive Einwilligung für die
|
||||
Weiterverarbeitung notwendig. Das Fehlen einer Einwilligung löst die Löschung des Patienten im
|
||||
Brückenkopf aus.
|
||||
|
||||
#### Konfiguration
|
||||
|
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* `APP_CONSENT_GICS_ENABLED`: Aktiviert oder deaktiviert `true` oder `false`, `false` wenn nicht
|
||||
gesetzt.
|
||||
* `APP_CONSENT_GICS_CHECKGNOMEDE`: Aktiviert oder deaktiviert `true` oder `false`, `false` wenn
|
||||
nicht gesetzt. Versuche Einwilligungsdaten zu GENOM DE Modelvorhaben über gIcs abzurufen.
|
||||
* `APP_CONSENT_GICS_CHECKBROADCONSENT`: Aktiviert oder deaktiviert `true` oder `false`, `false` wenn
|
||||
nicht gesetzt. Versuche Einwilligungsdaten zu Broad Consent über gIcs abzurufen.
|
||||
* `APP_CONSENT_GICS_URI`: URI der gICS-Instanz (z.B. `http://localhost:8090/ttp-fhir/fhir/gics`)
|
||||
* `APP_CONSENT_GICS_USERNAME`: gIcs Basic-Auth Benutzername
|
||||
* `APP_CONSENT_GICS_PASSWORD`: gIcs Basic-Auth Passwort
|
||||
* `APP_CONSENT_GICS_PERSONIDENTIFIERSYSTEM`: Derzeit wird nur die PID unterstützt. wenn leer wird
|
||||
`https://ths-greifswald.de/fhir/gics/identifiers/Patienten-ID` angenommen
|
||||
* `APP_CONSENT_GICS_BROADCONSENTDOMAINNAME`: Domäne in der gIcs Broad Consent Einwilligungen
|
||||
verwaltet. Falls Wert leer, wird `MII` angenommen.
|
||||
* `APP_CONSENT_GICS_GNOMDECONSENTDOMAINNAME`: Domäne in der gIcs GenomDE Modelvorhaben §64e
|
||||
Einwilligungen verwaltet. Falls Wert leer, wird `GenomDE_MV` angenommen.
|
||||
* `APP_CONSENT_GICS_POLICYCODE`: Die entscheidende Objekt-ID der zu prüfenden Einwilligung-Regel.
|
||||
Falls leer wird `2.16.840.1.113883.3.1937.777.24.5.3.6` angenommen.
|
||||
* `APP_CONSENT_GICS_POLICYSYSTEM`: Das System der Einwilligung-Regel der Objekt-IDs. Falls leer wird
|
||||
`urn:oid:2.16.840.1.113883.3.1937.777.24.5.3` angenommen.
|
||||
* `APP_PSEUDONYMIZE_GPAS_GENOM_DE_DOMAIN`: gPas Multi-Pseudonym-Domäne für genomDE Vorgangsnummern (
|
||||
Clinical data node)
|
||||
|
||||
### Anmeldung mit einem Passwort
|
||||
|
||||
@ -541,4 +494,4 @@ Beim Ausführen der Integrationstests wird eine Testdatenbank in einem Docker-Co
|
||||
Siehe hier auch die Klasse `AbstractTestcontainerTest` unter `src/integrationTest`.
|
||||
|
||||
Ein einfaches Entwickler-Setup inklusive DNPM:DIP ist mit Hilfe
|
||||
von https://github.com/pcvolkmer/dnpmdip-devenv realisierbar.
|
||||
von https://github.com/pcvolkmer/dnpmdip-devenv realisierbar.
|
@ -90,6 +90,7 @@ dependencies {
|
||||
implementation("org.webjars:webjars-locator:${versions["webjars-locator"]}")
|
||||
implementation("org.webjars.npm:echarts:${versions["echarts"]}")
|
||||
implementation("org.webjars.npm:htmx.org:${versions["htmx.org"]}")
|
||||
implementation ("org.apache.commons:commons-math3:3.6.1")
|
||||
|
||||
runtimeOnly("org.mariadb.jdbc:mariadb-java-client")
|
||||
runtimeOnly("org.postgresql:postgresql")
|
||||
|
@ -16,11 +16,6 @@ services:
|
||||
KAFKA_CFG_AUTO_CREATE_TOPICS_ENABLE: true
|
||||
KAFKA_CFG_CONTROLLER_QUORUM_VOTERS: 0@kafka:9093
|
||||
KAFKA_CFG_CONTROLLER_LISTENER_NAMES: CONTROLLER
|
||||
healthcheck:
|
||||
test: kafka-topics --bootstrap-server kafka:9092 --list
|
||||
interval: 30s
|
||||
timeout: 10s
|
||||
retries: 3
|
||||
|
||||
## Use AKHQ as Kafka web frontend
|
||||
akhq:
|
||||
@ -58,4 +53,4 @@ services:
|
||||
# environment:
|
||||
# POSTGRES_DB: dev
|
||||
# POSTGRES_USER: dev
|
||||
# POSTGRES_PASSWORD: dev
|
||||
# POSTGRES_PASSWORD: dev
|
@ -2,55 +2,31 @@ version: '3.7'
|
||||
|
||||
services:
|
||||
|
||||
zoo:
|
||||
image: zookeeper:3.9.2
|
||||
restart: unless-stopped
|
||||
zoo1:
|
||||
image: zookeeper:3.8.0
|
||||
hostname: zoo1
|
||||
ports:
|
||||
- "2181:2181"
|
||||
environment:
|
||||
ZOO_MY_ID: 1
|
||||
ZOO_PORT: 2181
|
||||
ZOO_SERVERS: server.1=zoo:2888:3888;2181
|
||||
ZOO_SERVERS: server.1=zoo1:2888:3888;2181
|
||||
|
||||
kafka:
|
||||
image: confluentinc/cp-kafka:7.6.1
|
||||
kafka1:
|
||||
image: confluentinc/cp-kafka:7.2.1
|
||||
hostname: kafka1
|
||||
ports:
|
||||
- "9092:9092"
|
||||
environment:
|
||||
KAFKA_ADVERTISED_LISTENERS: LISTENER_DOCKER_INTERNAL://kafka:19092,LISTENER_DOCKER_EXTERNAL://172.17.0.1:9093,LISTENER_EXTERNAL://127.0.0.1:9092
|
||||
KAFKA_LISTENER_SECURITY_PROTOCOL_MAP: LISTENER_DOCKER_INTERNAL:PLAINTEXT,LISTENER_DOCKER_EXTERNAL:PLAINTEXT,LISTENER_EXTERNAL:PLAINTEXT
|
||||
KAFKA_ADVERTISED_LISTENERS: LISTENER_DOCKER_INTERNAL://kafka1:19092,LISTENER_DOCKER_EXTERNAL://${DOCKER_HOST_IP:-127.0.0.1}:9092
|
||||
KAFKA_LISTENER_SECURITY_PROTOCOL_MAP: LISTENER_DOCKER_INTERNAL:PLAINTEXT,LISTENER_DOCKER_EXTERNAL:PLAINTEXT
|
||||
KAFKA_INTER_BROKER_LISTENER_NAME: LISTENER_DOCKER_INTERNAL
|
||||
KAFKA_ZOOKEEPER_CONNECT: zoo:2181
|
||||
KAFKA_ZOOKEEPER_CONNECT: "zoo1:2181"
|
||||
KAFKA_BROKER_ID: 1
|
||||
KAFKA_LOG4J_LOGGERS: kafka.controller=INFO,kafka.producer.async.DefaultEventHandler=INFO,state.change.logger=INFO
|
||||
KAFKA_LOG4J_LOGGERS: "kafka.controller=INFO,kafka.producer.async.DefaultEventHandler=INFO,state.change.logger=INFO"
|
||||
KAFKA_OFFSETS_TOPIC_REPLICATION_FACTOR: 1
|
||||
KAFKA_MESSAGE_MAX_BYTES: 5242880
|
||||
KAFKA_REPLICA_FETCH_MAX_BYTES: 5242880
|
||||
KAFKA_COMPRESSION_TYPE: gzip
|
||||
depends_on:
|
||||
- zoo
|
||||
healthcheck:
|
||||
test: kafka-topics --bootstrap-server kafka:9092 --list
|
||||
interval: 30s
|
||||
timeout: 10s
|
||||
retries: 3
|
||||
|
||||
akhq:
|
||||
image: tchiotludo/akhq:0.25.0
|
||||
environment:
|
||||
AKHQ_CONFIGURATION: |
|
||||
akhq:
|
||||
ui-options:
|
||||
topic.show-all-consumer-groups: true
|
||||
topic-data.sort: NEWEST
|
||||
connections:
|
||||
docker-kafka-server:
|
||||
properties:
|
||||
bootstrap.servers: "kafka:19092"
|
||||
ports:
|
||||
- "9000:8080"
|
||||
depends_on:
|
||||
- kafka
|
||||
- zoo1
|
||||
|
||||
kafka-rest-proxy:
|
||||
image: confluentinc/cp-kafka-rest:7.2.1
|
||||
@ -64,8 +40,8 @@ services:
|
||||
KAFKA_REST_HOST_NAME: kafka-rest-proxy
|
||||
KAFKA_REST_BOOTSTRAP_SERVERS: PLAINTEXT://kafka1:19092
|
||||
depends_on:
|
||||
- zoo
|
||||
- kafka
|
||||
- zoo1
|
||||
- kafka1
|
||||
|
||||
kafka-connect:
|
||||
image: confluentinc/cp-kafka-connect:7.2.1
|
||||
@ -91,6 +67,24 @@ services:
|
||||
#volumes:
|
||||
# - ./connectors:/etc/kafka-connect/jars/
|
||||
depends_on:
|
||||
- zoo
|
||||
- kafka
|
||||
- zoo1
|
||||
- kafka1
|
||||
- kafka-rest-proxy
|
||||
|
||||
akhq:
|
||||
image: tchiotludo/akhq:0.21.0
|
||||
environment:
|
||||
AKHQ_CONFIGURATION: |
|
||||
akhq:
|
||||
connections:
|
||||
docker-kafka-server:
|
||||
properties:
|
||||
bootstrap.servers: "kafka1:19092"
|
||||
connect:
|
||||
- name: "kafka-connect"
|
||||
url: "http://kafka-connect:8083"
|
||||
ports:
|
||||
- "8084:8080"
|
||||
depends_on:
|
||||
- kafka1
|
||||
- kafka-connect
|
||||
|
@ -23,9 +23,6 @@ import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import de.ukw.ccc.bwhc.dto.*
|
||||
import dev.dnpm.etl.processor.anyValueClass
|
||||
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||
import dev.dnpm.etl.processor.consent.ConsentByMtbFile
|
||||
import dev.dnpm.etl.processor.consent.TtpConsentStatus
|
||||
import dev.dnpm.etl.processor.consent.IGetConsent
|
||||
import dev.dnpm.etl.processor.security.TokenRepository
|
||||
import dev.dnpm.etl.processor.security.UserRoleRepository
|
||||
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||
@ -34,7 +31,10 @@ import org.junit.jupiter.api.Nested
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.mockito.kotlin.*
|
||||
import org.mockito.kotlin.any
|
||||
import org.mockito.kotlin.never
|
||||
import org.mockito.kotlin.times
|
||||
import org.mockito.kotlin.verify
|
||||
import org.springframework.beans.factory.annotation.Autowired
|
||||
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
||||
import org.springframework.http.MediaType
|
||||
@ -54,8 +54,7 @@ import org.springframework.test.web.servlet.post
|
||||
@ContextConfiguration(
|
||||
classes = [
|
||||
MtbFileRestController::class,
|
||||
AppSecurityConfiguration::class,
|
||||
ConsentByMtbFile::class, IGetConsent::class
|
||||
AppSecurityConfiguration::class
|
||||
]
|
||||
)
|
||||
@MockitoBean(types = [TokenRepository::class, RequestProcessor::class])
|
||||
@ -64,8 +63,7 @@ import org.springframework.test.web.servlet.post
|
||||
"app.pseudonymize.generator=BUILDIN",
|
||||
"app.security.admin-user=admin",
|
||||
"app.security.admin-password={noop}very-secret",
|
||||
"app.security.enable-tokens=true",
|
||||
"app.consent.gics.enabled=false"
|
||||
"app.security.enable-tokens=true"
|
||||
]
|
||||
)
|
||||
class MtbFileRestControllerTest {
|
||||
@ -143,7 +141,7 @@ class MtbFileRestControllerTest {
|
||||
status { isAccepted() }
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processDeletion(anyValueClass(), eq(TtpConsentStatus.UNKNOWN_CHECK_FILE))
|
||||
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
|
||||
}
|
||||
|
||||
@Test
|
||||
@ -154,7 +152,7 @@ class MtbFileRestControllerTest {
|
||||
status { isUnauthorized() }
|
||||
}
|
||||
|
||||
verify(requestProcessor, never()).processDeletion(anyValueClass(), any())
|
||||
verify(requestProcessor, never()).processDeletion(anyValueClass())
|
||||
}
|
||||
|
||||
@Nested
|
||||
@ -165,8 +163,7 @@ class MtbFileRestControllerTest {
|
||||
"app.security.admin-user=admin",
|
||||
"app.security.admin-password={noop}very-secret",
|
||||
"app.security.enable-tokens=true",
|
||||
"app.security.enable-oidc=true",
|
||||
"app.consent.gics.enabled=false"
|
||||
"app.security.enable-oidc=true"
|
||||
]
|
||||
)
|
||||
inner class WithOidcEnabled {
|
||||
|
@ -19,7 +19,6 @@
|
||||
|
||||
package dev.dnpm.etl.processor.pseudonym
|
||||
|
||||
import dev.dnpm.etl.processor.config.AppFhirConfig
|
||||
import dev.dnpm.etl.processor.config.GPasConfigProperties
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
@ -43,22 +42,20 @@ class GpasPseudonymGeneratorTest {
|
||||
private lateinit var mockRestServiceServer: MockRestServiceServer
|
||||
private lateinit var generator: GpasPseudonymGenerator
|
||||
private lateinit var restTemplate: RestTemplate
|
||||
private var appFhirConfig: AppFhirConfig = AppFhirConfig()
|
||||
|
||||
@BeforeEach
|
||||
fun setup() {
|
||||
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
|
||||
val gPasConfigProperties = GPasConfigProperties(
|
||||
"https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate",
|
||||
"test",
|
||||
"test", "test2",
|
||||
null,
|
||||
null
|
||||
)
|
||||
|
||||
this.restTemplate = RestTemplate()
|
||||
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
|
||||
this.generator =
|
||||
GpasPseudonymGenerator(gPasConfigProperties, retryTemplate, restTemplate, appFhirConfig)
|
||||
this.generator = GpasPseudonymGenerator(gPasConfigProperties, retryTemplate, restTemplate)
|
||||
}
|
||||
|
||||
@Test
|
||||
|
@ -22,7 +22,6 @@ package dev.dnpm.etl.processor.web
|
||||
import dev.dnpm.etl.processor.config.AppConfiguration
|
||||
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
|
||||
import dev.dnpm.etl.processor.monitoring.GIcsConnectionCheckService
|
||||
import dev.dnpm.etl.processor.monitoring.GPasConnectionCheckService
|
||||
import dev.dnpm.etl.processor.monitoring.RestConnectionCheckService
|
||||
import dev.dnpm.etl.processor.output.MtbFileSender
|
||||
@ -90,8 +89,7 @@ abstract class MockSink : Sinks.Many<Boolean>
|
||||
RequestProcessor::class,
|
||||
TransformationService::class,
|
||||
GPasConnectionCheckService::class,
|
||||
RestConnectionCheckService::class,
|
||||
GIcsConnectionCheckService::class
|
||||
RestConnectionCheckService::class
|
||||
]
|
||||
)
|
||||
class ConfigControllerTest {
|
||||
@ -184,13 +182,7 @@ class ConfigControllerTest {
|
||||
|
||||
@Test
|
||||
fun testShouldNotSaveTokenWithExstingName() {
|
||||
whenever(tokenService.addToken(anyString())).thenReturn(
|
||||
Result.failure(
|
||||
RuntimeException(
|
||||
"Testfailure"
|
||||
)
|
||||
)
|
||||
)
|
||||
whenever(tokenService.addToken(anyString())).thenReturn(Result.failure(RuntimeException("Testfailure")))
|
||||
|
||||
mockMvc.post("/configs/tokens") {
|
||||
with(user("admin").roles("ADMIN"))
|
||||
@ -311,10 +303,7 @@ class ConfigControllerTest {
|
||||
|
||||
val idCaptor = argumentCaptor<Long>()
|
||||
val roleCaptor = argumentCaptor<Role>()
|
||||
verify(userRoleService, times(1)).updateUserRole(
|
||||
idCaptor.capture(),
|
||||
roleCaptor.capture()
|
||||
)
|
||||
verify(userRoleService, times(1)).updateUserRole(idCaptor.capture(), roleCaptor.capture())
|
||||
|
||||
assertThat(idCaptor.firstValue).isEqualTo(42)
|
||||
assertThat(roleCaptor.firstValue).isEqualTo(Role.ADMIN)
|
||||
@ -352,26 +341,23 @@ class ConfigControllerTest {
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
applicationContext: WebApplicationContext
|
||||
applicationContext: WebApplicationContext,
|
||||
) {
|
||||
this.webClient = MockMvcWebTestClient
|
||||
.bindToApplicationContext(applicationContext).build()
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldRequestGPasSSE() {
|
||||
val expectedEvent =
|
||||
ConnectionCheckResult.GPasConnectionCheckResult(true, Instant.now(), Instant.now())
|
||||
fun testShouldRequestSSE() {
|
||||
val expectedEvent = ConnectionCheckResult.GPasConnectionCheckResult(true, Instant.now(), Instant.now())
|
||||
|
||||
connectionCheckUpdateProducer.tryEmitNext(expectedEvent)
|
||||
connectionCheckUpdateProducer.emitComplete { _, _ -> true }
|
||||
|
||||
val result =
|
||||
webClient.get().uri("http://localhost/configs/events").accept(TEXT_EVENT_STREAM)
|
||||
.exchange()
|
||||
.expectStatus().isOk()
|
||||
.expectHeader().contentType(TEXT_EVENT_STREAM)
|
||||
.returnResult(ConnectionCheckResult.GPasConnectionCheckResult::class.java)
|
||||
val result = webClient.get().uri("http://localhost/configs/events").accept(TEXT_EVENT_STREAM).exchange()
|
||||
.expectStatus().isOk()
|
||||
.expectHeader().contentType(TEXT_EVENT_STREAM)
|
||||
.returnResult(ConnectionCheckResult.GPasConnectionCheckResult::class.java)
|
||||
|
||||
StepVerifier.create(result.responseBody)
|
||||
.expectNext(expectedEvent)
|
||||
|
@ -1,36 +0,0 @@
|
||||
package dev.dnpm.etl.processor.consent;
|
||||
|
||||
import java.util.Date;
|
||||
import org.hl7.fhir.r4.model.Bundle;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
public class ConsentByMtbFile implements IGetConsent {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(ConsentByMtbFile.class);
|
||||
|
||||
public ConsentByMtbFile() {
|
||||
log.info("ConsentCheckFileBased initialized...");
|
||||
}
|
||||
|
||||
@Override
|
||||
public TtpConsentStatus getTtpBroadConsentStatus(String personIdentifierValue) {
|
||||
return TtpConsentStatus.UNKNOWN_CHECK_FILE;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Bundle getBroadConsent(String personIdentifierValue, Date requestDate) {
|
||||
return IGetConsent.super.getBroadConsent(personIdentifierValue, requestDate);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Bundle getGenomDeConsent(String personIdentifierValue, Date requestDate) {
|
||||
return IGetConsent.super.getGenomDeConsent(personIdentifierValue, requestDate);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Bundle currentConsentForPersonAndTemplate(String personIdentifierValue,
|
||||
ConsentDomain targetConsentDomain, Date requestDate) {
|
||||
return new Bundle();
|
||||
}
|
||||
}
|
@ -1,13 +0,0 @@
|
||||
package dev.dnpm.etl.processor.consent;
|
||||
|
||||
public enum ConsentDomain {
|
||||
/**
|
||||
* MII Broad consent
|
||||
*/
|
||||
BroadConsent,
|
||||
|
||||
/**
|
||||
* GenomDe Modelvohaben §64e
|
||||
*/
|
||||
Modelvorhaben64e
|
||||
}
|
@ -1,266 +0,0 @@
|
||||
package dev.dnpm.etl.processor.consent;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.parser.DataFormatException;
|
||||
import dev.dnpm.etl.processor.config.AppFhirConfig;
|
||||
import dev.dnpm.etl.processor.config.GIcsConfigProperties;
|
||||
import java.util.Date;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.hl7.fhir.r4.model.BooleanType;
|
||||
import org.hl7.fhir.r4.model.Bundle;
|
||||
import org.hl7.fhir.r4.model.Coding;
|
||||
import org.hl7.fhir.r4.model.DateType;
|
||||
import org.hl7.fhir.r4.model.Identifier;
|
||||
import org.hl7.fhir.r4.model.OperationOutcome;
|
||||
import org.hl7.fhir.r4.model.Parameters;
|
||||
import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
|
||||
import org.hl7.fhir.r4.model.StringType;
|
||||
import org.jetbrains.annotations.NotNull;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.springframework.http.HttpEntity;
|
||||
import org.springframework.http.HttpHeaders;
|
||||
import org.springframework.http.HttpMethod;
|
||||
import org.springframework.http.MediaType;
|
||||
import org.springframework.http.ResponseEntity;
|
||||
import org.springframework.retry.TerminatedRetryException;
|
||||
import org.springframework.retry.support.RetryTemplate;
|
||||
import org.springframework.web.client.RestClientException;
|
||||
import org.springframework.web.client.RestTemplate;
|
||||
import org.springframework.web.util.UriComponentsBuilder;
|
||||
|
||||
|
||||
public class GicsConsentService implements IGetConsent {
|
||||
|
||||
private final Logger log = LoggerFactory.getLogger(GicsConsentService.class);
|
||||
|
||||
public static final String IS_CONSENTED_ENDPOINT = "/$isConsented";
|
||||
public static final String IS_POLICY_STATES_FOR_PERSON_ENDPOINT = "/$currentPolicyStatesForPerson";
|
||||
private final RetryTemplate retryTemplate;
|
||||
private final RestTemplate restTemplate;
|
||||
private final FhirContext fhirContext;
|
||||
private final HttpHeaders httpHeader;
|
||||
private final GIcsConfigProperties gIcsConfigProperties;
|
||||
private String url;
|
||||
|
||||
public GicsConsentService(GIcsConfigProperties gIcsConfigProperties,
|
||||
RetryTemplate retryTemplate, RestTemplate restTemplate, AppFhirConfig appFhirConfig) {
|
||||
|
||||
this.retryTemplate = retryTemplate;
|
||||
this.restTemplate = restTemplate;
|
||||
this.fhirContext = appFhirConfig.fhirContext();
|
||||
httpHeader = buildHeader(gIcsConfigProperties.getUsername(),
|
||||
gIcsConfigProperties.getPassword());
|
||||
this.gIcsConfigProperties = gIcsConfigProperties;
|
||||
log.info("GicsConsentService initialized...");
|
||||
}
|
||||
|
||||
public String getGicsUri(String endpoint) {
|
||||
if (url == null) {
|
||||
final String gIcsBaseUri = gIcsConfigProperties.getUri();
|
||||
if (StringUtils.isBlank(gIcsBaseUri)) {
|
||||
throw new IllegalArgumentException(
|
||||
"gICS base URL is empty - should call gICS with false configuration.");
|
||||
}
|
||||
url = UriComponentsBuilder.fromUriString(gIcsBaseUri).path(endpoint)
|
||||
.toUriString();
|
||||
}
|
||||
return url;
|
||||
}
|
||||
|
||||
@NotNull
|
||||
private static HttpHeaders buildHeader(String gPasUserName, String gPasPassword) {
|
||||
var headers = new HttpHeaders();
|
||||
headers.setContentType(MediaType.APPLICATION_XML);
|
||||
|
||||
if (StringUtils.isBlank(gPasUserName) || StringUtils.isBlank(gPasPassword)) {
|
||||
return headers;
|
||||
}
|
||||
|
||||
headers.setBasicAuth(gPasUserName, gPasPassword);
|
||||
return headers;
|
||||
}
|
||||
|
||||
protected static Parameters getIsConsentedRequestParam(GIcsConfigProperties configProperties,
|
||||
String personIdentifierValue) {
|
||||
var result = new Parameters();
|
||||
result.addParameter(new ParametersParameterComponent().setName("personIdentifier").setValue(
|
||||
new Identifier().setValue(personIdentifierValue)
|
||||
.setSystem(configProperties.getPersonIdentifierSystem())));
|
||||
result.addParameter(new ParametersParameterComponent().setName("domain")
|
||||
.setValue(new StringType().setValue(configProperties.getBroadConsentDomainName())));
|
||||
result.addParameter(new ParametersParameterComponent().setName("policy").setValue(
|
||||
new Coding().setCode(configProperties.getBroadConsentPolicyCode())
|
||||
.setSystem(configProperties.getBroadConsentPolicySystem())));
|
||||
|
||||
/*
|
||||
* is mandatory parameter, but we ignore it via additional configuration parameter
|
||||
* 'ignoreVersionNumber'.
|
||||
*/
|
||||
result.addParameter(new ParametersParameterComponent().setName("version")
|
||||
.setValue(new StringType().setValue("1.1")));
|
||||
|
||||
/* add config parameter with:
|
||||
* ignoreVersionNumber -> true ->> Reason is we cannot know which policy version each patient
|
||||
* has possibly signed or not, therefore we are happy with any version found.
|
||||
* unknownStateIsConsideredAsDecline -> true
|
||||
*/
|
||||
var config = new ParametersParameterComponent().setName("config").addPart(
|
||||
new ParametersParameterComponent().setName("ignoreVersionNumber")
|
||||
.setValue(new BooleanType().setValue(true))).addPart(
|
||||
new ParametersParameterComponent().setName("unknownStateIsConsideredAsDecline")
|
||||
.setValue(new BooleanType().setValue(false)));
|
||||
result.addParameter(config);
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
protected String callGicsApi(Parameters parameter, String endpoint) {
|
||||
var parameterAsXml = fhirContext.newXmlParser().encodeResourceToString(parameter);
|
||||
|
||||
HttpEntity<String> requestEntity = new HttpEntity<>(parameterAsXml, this.httpHeader);
|
||||
ResponseEntity<String> responseEntity;
|
||||
try {
|
||||
var url = getGicsUri(endpoint);
|
||||
|
||||
responseEntity = retryTemplate.execute(
|
||||
ctx -> restTemplate.exchange(url, HttpMethod.POST, requestEntity, String.class));
|
||||
} catch (RestClientException e) {
|
||||
var msg = String.format("Get consents status request failed reason: '%s",
|
||||
e.getMessage());
|
||||
log.error(msg);
|
||||
return null;
|
||||
|
||||
} catch (TerminatedRetryException terminatedRetryException) {
|
||||
var msg = String.format(
|
||||
"Get consents status process has been terminated. termination reason: '%s",
|
||||
terminatedRetryException.getMessage());
|
||||
log.error(msg);
|
||||
return null;
|
||||
|
||||
}
|
||||
if (responseEntity.getStatusCode().is2xxSuccessful()) {
|
||||
return responseEntity.getBody();
|
||||
} else {
|
||||
var msg = String.format(
|
||||
"Trusted party system reached but request failed! code: '%s' response: '%s'",
|
||||
responseEntity.getStatusCode(), responseEntity.getBody());
|
||||
log.error(msg);
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public TtpConsentStatus getTtpBroadConsentStatus(String personIdentifierValue) {
|
||||
var parameter = GicsConsentService.getIsConsentedRequestParam(gIcsConfigProperties,
|
||||
personIdentifierValue);
|
||||
|
||||
var consentStatusResponse = callGicsApi(parameter,
|
||||
GicsConsentService.IS_CONSENTED_ENDPOINT);
|
||||
return evaluateConsentResponse(consentStatusResponse);
|
||||
}
|
||||
|
||||
public Bundle currentConsentForPersonAndTemplate(String personIdentifierValue,
|
||||
ConsentDomain targetConsentDomain, Date requestDate) {
|
||||
|
||||
String consentDomain = getConsentDomain(targetConsentDomain);
|
||||
|
||||
var requestParameter = GicsConsentService.buildRequestParameterCurrentPolicyStatesForPerson(
|
||||
gIcsConfigProperties, personIdentifierValue, requestDate, consentDomain);
|
||||
|
||||
var consentDataSerialized = callGicsApi(requestParameter,
|
||||
GicsConsentService.IS_POLICY_STATES_FOR_PERSON_ENDPOINT);
|
||||
|
||||
if (consentDataSerialized == null) {
|
||||
// error occurred - should not process further!
|
||||
throw new IllegalStateException(
|
||||
"consent data request failed - stopping processing! - try again or fix other problems first.");
|
||||
}
|
||||
var iBaseResource = fhirContext.newJsonParser()
|
||||
.parseResource(consentDataSerialized);
|
||||
if (iBaseResource instanceof OperationOutcome) {
|
||||
// log error - very likely a configuration error
|
||||
String errorMessage =
|
||||
"Consent request failed! Check outcome:\n " + consentDataSerialized;
|
||||
log.error(errorMessage);
|
||||
throw new IllegalStateException(errorMessage);
|
||||
} else if (iBaseResource instanceof Bundle) {
|
||||
return (Bundle) iBaseResource;
|
||||
} else {
|
||||
String errorMessage = "Consent request failed! Unexpected response received! -> "
|
||||
+ consentDataSerialized;
|
||||
log.error(errorMessage);
|
||||
throw new IllegalStateException(errorMessage);
|
||||
}
|
||||
}
|
||||
|
||||
@NotNull
|
||||
private String getConsentDomain(ConsentDomain targetConsentDomain) {
|
||||
String consentDomain;
|
||||
switch (targetConsentDomain) {
|
||||
case BroadConsent -> consentDomain = gIcsConfigProperties.getBroadConsentDomainName();
|
||||
case Modelvorhaben64e ->
|
||||
consentDomain = gIcsConfigProperties.getGenomDeConsentDomainName();
|
||||
default -> throw new IllegalArgumentException(
|
||||
"target ConsentDomain is missing but must be provided!");
|
||||
}
|
||||
return consentDomain;
|
||||
}
|
||||
|
||||
protected static Parameters buildRequestParameterCurrentPolicyStatesForPerson(
|
||||
GIcsConfigProperties gIcsConfigProperties, String personIdentifierValue, Date requestDate,
|
||||
String targetDomain) {
|
||||
var requestParameter = new Parameters();
|
||||
requestParameter.addParameter(new ParametersParameterComponent().setName("personIdentifier")
|
||||
.setValue(new Identifier().setValue(personIdentifierValue)
|
||||
.setSystem(gIcsConfigProperties.getPersonIdentifierSystem())));
|
||||
|
||||
requestParameter.addParameter(new ParametersParameterComponent().setName("domain")
|
||||
.setValue(new StringType().setValue(targetDomain)));
|
||||
|
||||
Parameters nestedConfigParameters = new Parameters();
|
||||
nestedConfigParameters.addParameter(
|
||||
new ParametersParameterComponent().setName("idMatchingType").setValue(
|
||||
new Coding().setSystem(
|
||||
"https://ths-greifswald.de/fhir/CodeSystem/gics/IdMatchingType")
|
||||
.setCode("AT_LEAST_ONE"))).addParameter("ignoreVersionNumber", false)
|
||||
.addParameter("unknownStateIsConsideredAsDecline", false)
|
||||
.addParameter("requestDate", new DateType().setValue(requestDate));
|
||||
|
||||
requestParameter.addParameter(new ParametersParameterComponent().setName("config").addPart()
|
||||
.setResource(nestedConfigParameters));
|
||||
|
||||
return requestParameter;
|
||||
}
|
||||
|
||||
private TtpConsentStatus evaluateConsentResponse(String consentStatusResponse) {
|
||||
if (consentStatusResponse == null) {
|
||||
return TtpConsentStatus.FAILED_TO_ASK;
|
||||
}
|
||||
try {
|
||||
var response = fhirContext.newJsonParser().parseResource(consentStatusResponse);
|
||||
|
||||
if (response instanceof Parameters responseParameters) {
|
||||
|
||||
var responseValue = responseParameters.getParameter("consented").getValue();
|
||||
var isConsented = responseValue.castToBoolean(responseValue);
|
||||
if (!isConsented.hasValue()) {
|
||||
return TtpConsentStatus.FAILED_TO_ASK;
|
||||
}
|
||||
if (isConsented.booleanValue()) {
|
||||
return TtpConsentStatus.BROAD_CONSENT_GIVEN;
|
||||
} else {
|
||||
return TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED;
|
||||
}
|
||||
} else if (response instanceof OperationOutcome outcome) {
|
||||
log.error("failed to get consent status from ttp. probably configuration error. "
|
||||
+ "outcome: '{}'", fhirContext.newJsonParser().encodeToString(outcome));
|
||||
|
||||
}
|
||||
} catch (DataFormatException dfe) {
|
||||
log.error("failed to parse response to FHIR R4 resource.", dfe);
|
||||
}
|
||||
return TtpConsentStatus.FAILED_TO_ASK;
|
||||
}
|
||||
|
||||
}
|
@ -1,52 +0,0 @@
|
||||
package dev.dnpm.etl.processor.consent;
|
||||
|
||||
import java.util.Date;
|
||||
import org.hl7.fhir.r4.model.Bundle;
|
||||
|
||||
public interface IGetConsent {
|
||||
|
||||
/**
|
||||
* Get broad consent status for a patient identifier
|
||||
*
|
||||
* @param personIdentifierValue patient identifier used for consent data
|
||||
* @return status of broad consent
|
||||
* @apiNote cannot not differ between not asked and rejected
|
||||
*/
|
||||
TtpConsentStatus getTtpBroadConsentStatus(String personIdentifierValue);
|
||||
|
||||
/**
|
||||
* Get broad consent policies with respect to a request date
|
||||
*
|
||||
* @param personIdentifierValue patient identifier used for consent data
|
||||
* @param requestDate target date until consent data should be considered
|
||||
* @return consent policies as bundle; <p>if empty patient has not been asked, yet.</p>
|
||||
*/
|
||||
default Bundle getBroadConsent(String personIdentifierValue, Date requestDate) {
|
||||
return currentConsentForPersonAndTemplate(personIdentifierValue, ConsentDomain.BroadConsent,
|
||||
requestDate);
|
||||
}
|
||||
|
||||
/**
|
||||
* Get 'GenomDe Modelvorhaben §64e' consent policies with respect to a request date
|
||||
*
|
||||
* @param personIdentifierValue patient identifier used for consent data
|
||||
* @param requestDate target date until consent data should be considered
|
||||
* @return consent policies as bundle; <p>if empty patient has not been asked, yet.</p>
|
||||
*/
|
||||
default Bundle getGenomDeConsent(String personIdentifierValue, Date requestDate) {
|
||||
return currentConsentForPersonAndTemplate(personIdentifierValue,
|
||||
ConsentDomain.Modelvorhaben64e, requestDate);
|
||||
}
|
||||
|
||||
/**
|
||||
* Get consent policies with respect to a request date
|
||||
*
|
||||
* @param personIdentifierValue patient identifier used for consent data
|
||||
* @param targetConsentDomain domain which should be used to request consent
|
||||
* @param requestDate target date until consent data should be considered
|
||||
* @return consent policies as bundle; <p>if empty patient has not been asked, yet.</p>
|
||||
*/
|
||||
Bundle currentConsentForPersonAndTemplate(String personIdentifierValue,
|
||||
ConsentDomain targetConsentDomain, Date requestDate);
|
||||
|
||||
}
|
@ -1,38 +0,0 @@
|
||||
package dev.dnpm.etl.processor.consent;
|
||||
|
||||
public enum TtpConsentStatus {
|
||||
/**
|
||||
* Valid consent found
|
||||
*/
|
||||
BROAD_CONSENT_GIVEN,
|
||||
/**
|
||||
* Missing or rejected...actually unknown
|
||||
*/
|
||||
BROAD_CONSENT_MISSING_OR_REJECTED,
|
||||
/**
|
||||
* No Broad consent policy found
|
||||
*/
|
||||
BROAD_CONSENT_MISSING,
|
||||
/**
|
||||
* Research policy has been rejected
|
||||
*/
|
||||
BROAD_CONSENT_REJECTED,
|
||||
|
||||
GENOM_DE_CONSENT_SEQUENCING_PERMIT,
|
||||
/**
|
||||
* No GenomDE consent policy found
|
||||
*/
|
||||
GENOM_DE_CONSENT_MISSING,
|
||||
/**
|
||||
* GenomDE consent policy found, but has been rejected
|
||||
*/
|
||||
GENOM_DE_SEQUENCING_REJECTED,
|
||||
/**
|
||||
* Consent status is validate via file property 'consent.status'
|
||||
*/
|
||||
UNKNOWN_CHECK_FILE,
|
||||
/**
|
||||
* Due technical problems consent status is unknown
|
||||
*/
|
||||
FAILED_TO_ASK
|
||||
}
|
@ -23,4 +23,6 @@ public interface Generator {
|
||||
|
||||
String generate(String id);
|
||||
|
||||
String generateGenomDeTan(String id);
|
||||
|
||||
}
|
||||
|
@ -21,7 +21,6 @@ package dev.dnpm.etl.processor.pseudonym;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.parser.IParser;
|
||||
import dev.dnpm.etl.processor.config.AppFhirConfig;
|
||||
import dev.dnpm.etl.processor.config.GPasConfigProperties;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.hl7.fhir.r4.model.Identifier;
|
||||
@ -33,38 +32,44 @@ import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.springframework.http.*;
|
||||
import org.springframework.retry.support.RetryTemplate;
|
||||
import org.springframework.web.client.HttpClientErrorException.BadRequest;
|
||||
import org.springframework.web.client.HttpClientErrorException.Unauthorized;
|
||||
import org.springframework.web.client.RestClientException;
|
||||
import org.springframework.web.client.RestTemplate;
|
||||
|
||||
public class GpasPseudonymGenerator implements Generator {
|
||||
|
||||
private final FhirContext r4Context;
|
||||
private final static FhirContext r4Context = FhirContext.forR4();
|
||||
private final String gPasUrl;
|
||||
private final String psnTargetDomain;
|
||||
private final HttpHeaders httpHeader;
|
||||
private final RetryTemplate retryTemplate;
|
||||
private final Logger log = LoggerFactory.getLogger(GpasPseudonymGenerator.class);
|
||||
|
||||
private final RestTemplate restTemplate;
|
||||
private final @NotNull String genomDeDomain;
|
||||
private final @NotNull String psnTargetDomain;
|
||||
|
||||
public GpasPseudonymGenerator(GPasConfigProperties gpasCfg, RetryTemplate retryTemplate,
|
||||
RestTemplate restTemplate, AppFhirConfig appFhirConfig) {
|
||||
RestTemplate restTemplate) {
|
||||
this.retryTemplate = retryTemplate;
|
||||
this.restTemplate = restTemplate;
|
||||
this.gPasUrl = gpasCfg.getUri();
|
||||
this.psnTargetDomain = gpasCfg.getTarget();
|
||||
this.r4Context = appFhirConfig.fhirContext();
|
||||
this.genomDeDomain = gpasCfg.getGenomDeDomain();
|
||||
httpHeader = getHttpHeaders(gpasCfg.getUsername(), gpasCfg.getPassword());
|
||||
|
||||
log.debug(String.format("%s has been initialized", this.getClass().getName()));
|
||||
log.debug("{} has been initialized", this.getClass().getName());
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public String generate(String id) {
|
||||
var gPasRequestBody = getGpasRequestBody(id);
|
||||
return generate(id, psnTargetDomain);
|
||||
}
|
||||
|
||||
@Override
|
||||
public String generateGenomDeTan(String id) {
|
||||
return generate(id, genomDeDomain);
|
||||
}
|
||||
|
||||
protected String generate(String id, String targetDomain) {
|
||||
var gPasRequestBody = getGpasRequestBody(id, targetDomain);
|
||||
var responseEntity = getGpasPseudonym(gPasRequestBody);
|
||||
var gPasPseudonymResult = (Parameters) r4Context.newJsonParser()
|
||||
.parseResource(responseEntity.getBody());
|
||||
@ -103,46 +108,36 @@ public class GpasPseudonymGenerator implements Generator {
|
||||
return psnValue.replaceAll(forbiddenCharsRegex, "_");
|
||||
}
|
||||
|
||||
|
||||
@NotNull
|
||||
protected ResponseEntity<String> getGpasPseudonym(String gPasRequestBody) {
|
||||
|
||||
HttpEntity<String> requestEntity = new HttpEntity<>(gPasRequestBody, this.httpHeader);
|
||||
ResponseEntity<String> responseEntity;
|
||||
|
||||
try {
|
||||
ResponseEntity<String> responseEntity = retryTemplate.execute(
|
||||
responseEntity = retryTemplate.execute(
|
||||
ctx -> restTemplate.exchange(gPasUrl, HttpMethod.POST, requestEntity,
|
||||
String.class));
|
||||
|
||||
if (responseEntity.getStatusCode().is2xxSuccessful()) {
|
||||
log.debug("API request succeeded. Response: {}", responseEntity.getStatusCode());
|
||||
return responseEntity;
|
||||
}
|
||||
} catch (RestClientException rce) {
|
||||
if (rce instanceof BadRequest) {
|
||||
String msg = "gPas or request configuration is incorrect. Please check both."
|
||||
+ rce.getMessage();
|
||||
log.debug(
|
||||
msg);
|
||||
throw new PseudonymRequestFailed(msg, rce);
|
||||
}
|
||||
if (rce instanceof Unauthorized) {
|
||||
var msg = "gPas access credentials are invalid check your configuration. msg: '%s".formatted(
|
||||
rce.getMessage());
|
||||
log.error(msg);
|
||||
throw new PseudonymRequestFailed(msg, rce);
|
||||
} else {
|
||||
log.warn("API request unsuccessful. Response: {}", requestEntity.getBody());
|
||||
throw new PseudonymRequestFailed("API request unsuccessful gPas unsuccessful.");
|
||||
}
|
||||
|
||||
return responseEntity;
|
||||
} catch (Exception unexpected) {
|
||||
throw new PseudonymRequestFailed(
|
||||
"API request due unexpected error unsuccessful gPas unsuccessful.", unexpected);
|
||||
}
|
||||
throw new PseudonymRequestFailed(
|
||||
"API request due unexpected error unsuccessful gPas unsuccessful.");
|
||||
|
||||
}
|
||||
|
||||
protected String getGpasRequestBody(String id) {
|
||||
protected String getGpasRequestBody(String id, String targetDomain) {
|
||||
var requestParameters = new Parameters();
|
||||
requestParameters.addParameter().setName("target")
|
||||
.setValue(new StringType().setValue(psnTargetDomain));
|
||||
.setValue(new StringType().setValue(targetDomain));
|
||||
requestParameters.addParameter().setName("original")
|
||||
.setValue(new StringType().setValue(id));
|
||||
final IParser iParser = r4Context.newJsonParser();
|
||||
|
@ -27,8 +27,7 @@ data class AppConfigProperties(
|
||||
var bwhcUri: String?,
|
||||
var transformations: List<TransformationProperties> = listOf(),
|
||||
var maxRetryAttempts: Int = 3,
|
||||
var duplicationDetection: Boolean = true,
|
||||
var genomDeTestSubmission: Boolean = true
|
||||
var duplicationDetection: Boolean = true
|
||||
) {
|
||||
companion object {
|
||||
const val NAME = "app"
|
||||
@ -49,6 +48,7 @@ data class PseudonymizeConfigProperties(
|
||||
data class GPasConfigProperties(
|
||||
val uri: String?,
|
||||
val target: String = "etl-processor",
|
||||
val genomDeDomain: String = "ccdn",
|
||||
val username: String?,
|
||||
val password: String?,
|
||||
) {
|
||||
@ -57,70 +57,6 @@ data class GPasConfigProperties(
|
||||
}
|
||||
}
|
||||
|
||||
@ConfigurationProperties(GIcsConfigProperties.NAME)
|
||||
data class GIcsConfigProperties(
|
||||
/**
|
||||
* Base URL to gICS System
|
||||
*
|
||||
*/
|
||||
val uri: String?,
|
||||
val username: String?,
|
||||
val password: String?,
|
||||
|
||||
/**
|
||||
* If value is 'true' valid consent at processing time is mandatory for transmission of DNPM
|
||||
* files otherwise they will be flagged and skipped.
|
||||
* If value 'false' or missing consent status is assumed to be valid.
|
||||
*/
|
||||
val enabled: Boolean?,
|
||||
|
||||
/**
|
||||
* gICS specific system
|
||||
* **/
|
||||
val personIdentifierSystem: String =
|
||||
"https://ths-greifswald.de/fhir/gics/identifiers/Patienten-ID",
|
||||
|
||||
/**
|
||||
* Domain of broad consent resources
|
||||
**/
|
||||
val broadConsentDomainName: String = "MII",
|
||||
|
||||
/**
|
||||
* Domain of Modelvorhaben 64e consent resources
|
||||
**/
|
||||
val genomDeConsentDomainName: String = "GenomDE_MV",
|
||||
|
||||
/**
|
||||
* Value to expect in case of positiv consent
|
||||
*/
|
||||
val broadConsentPolicyCode: String = "2.16.840.1.113883.3.1937.777.24.5.3.6",
|
||||
|
||||
/**
|
||||
* Consent Policy which should be used for consent check
|
||||
*/
|
||||
val broadConsentPolicySystem: String = "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3",
|
||||
|
||||
/**
|
||||
* Value to expect in case of positiv consent
|
||||
*/
|
||||
val genomeDePolicyCode: String = "sequencing",
|
||||
|
||||
/**
|
||||
* Consent Policy which should be used for consent check
|
||||
*/
|
||||
val genomeDePolicySystem: String = "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
|
||||
/**
|
||||
* Consent version (fixed version)
|
||||
*
|
||||
*/
|
||||
val genomeDeConsentVersion: String = "2.0"
|
||||
) {
|
||||
companion object {
|
||||
const val NAME = "app.consent.gics"
|
||||
}
|
||||
}
|
||||
|
||||
@ConfigurationProperties(RestTargetProperties.NAME)
|
||||
data class RestTargetProperties(
|
||||
val uri: String?,
|
||||
|
@ -20,17 +20,16 @@
|
||||
package dev.dnpm.etl.processor.config
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import dev.dnpm.etl.processor.consent.ConsentByMtbFile
|
||||
import dev.dnpm.etl.processor.consent.IGetConsent
|
||||
import dev.dnpm.etl.processor.consent.GicsConsentService
|
||||
import dev.dnpm.etl.processor.monitoring.*
|
||||
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
|
||||
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
|
||||
import dev.dnpm.etl.processor.monitoring.GPasConnectionCheckService
|
||||
import dev.dnpm.etl.processor.monitoring.ReportService
|
||||
import dev.dnpm.etl.processor.pseudonym.AnonymizingGenerator
|
||||
import dev.dnpm.etl.processor.pseudonym.Generator
|
||||
import dev.dnpm.etl.processor.pseudonym.GpasPseudonymGenerator
|
||||
import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
|
||||
import dev.dnpm.etl.processor.security.TokenRepository
|
||||
import dev.dnpm.etl.processor.security.TokenService
|
||||
import dev.dnpm.etl.processor.services.ConsentProcessor
|
||||
import dev.dnpm.etl.processor.services.Transformation
|
||||
import dev.dnpm.etl.processor.services.TransformationService
|
||||
import org.slf4j.LoggerFactory
|
||||
@ -61,8 +60,7 @@ import kotlin.time.toJavaDuration
|
||||
value = [
|
||||
AppConfigProperties::class,
|
||||
PseudonymizeConfigProperties::class,
|
||||
GPasConfigProperties::class,
|
||||
GIcsConfigProperties::class
|
||||
GPasConfigProperties::class
|
||||
]
|
||||
)
|
||||
@EnableScheduling
|
||||
@ -75,27 +73,13 @@ class AppConfiguration {
|
||||
return RestTemplate()
|
||||
}
|
||||
|
||||
@Bean
|
||||
fun appFhirConfig(): AppFhirConfig {
|
||||
return AppFhirConfig()
|
||||
}
|
||||
|
||||
@ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "GPAS")
|
||||
@Bean
|
||||
fun gpasPseudonymGenerator(
|
||||
configProperties: GPasConfigProperties,
|
||||
retryTemplate: RetryTemplate,
|
||||
restTemplate: RestTemplate,
|
||||
appFhirConfig: AppFhirConfig
|
||||
): Generator {
|
||||
return GpasPseudonymGenerator(configProperties, retryTemplate, restTemplate, appFhirConfig)
|
||||
fun gpasPseudonymGenerator(configProperties: GPasConfigProperties, retryTemplate: RetryTemplate, restTemplate: RestTemplate): Generator {
|
||||
return GpasPseudonymGenerator(configProperties, retryTemplate, restTemplate)
|
||||
}
|
||||
|
||||
@ConditionalOnProperty(
|
||||
value = ["app.pseudonymize.generator"],
|
||||
havingValue = "BUILDIN",
|
||||
matchIfMissing = true
|
||||
)
|
||||
@ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "BUILDIN", matchIfMissing = true)
|
||||
@Bean
|
||||
fun buildinPseudonymGenerator(): Generator {
|
||||
return AnonymizingGenerator()
|
||||
@ -110,21 +94,17 @@ class AppConfiguration {
|
||||
}
|
||||
|
||||
@Bean
|
||||
fun reportService(): ReportService {
|
||||
return ReportService(getObjectMapper())
|
||||
}
|
||||
|
||||
@Bean
|
||||
fun getObjectMapper(): ObjectMapper {
|
||||
return JacksonConfig().objectMapper()
|
||||
fun reportService(objectMapper: ObjectMapper): ReportService {
|
||||
return ReportService(objectMapper)
|
||||
}
|
||||
|
||||
@Bean
|
||||
fun transformationService(
|
||||
objectMapper: ObjectMapper,
|
||||
configProperties: AppConfigProperties
|
||||
): TransformationService {
|
||||
logger.info("Apply ${configProperties.transformations.size} transformation rules")
|
||||
return TransformationService(getObjectMapper(), configProperties.transformations.map {
|
||||
return TransformationService(objectMapper, configProperties.transformations.map {
|
||||
Transformation.of(it.path) from it.from to it.to
|
||||
})
|
||||
}
|
||||
@ -143,11 +123,7 @@ class AppConfiguration {
|
||||
callback: RetryCallback<T, E>,
|
||||
throwable: Throwable
|
||||
) {
|
||||
logger.warn(
|
||||
"Error occured: {}. Retrying {}",
|
||||
throwable.message,
|
||||
context.retryCount
|
||||
)
|
||||
logger.warn("Error occured: {}. Retrying {}", throwable.message, context.retryCount)
|
||||
}
|
||||
})
|
||||
.build()
|
||||
@ -155,11 +131,7 @@ class AppConfiguration {
|
||||
|
||||
@ConditionalOnProperty(value = ["app.security.enable-tokens"], havingValue = "true")
|
||||
@Bean
|
||||
fun tokenService(
|
||||
userDetailsManager: InMemoryUserDetailsManager,
|
||||
passwordEncoder: PasswordEncoder,
|
||||
tokenRepository: TokenRepository
|
||||
): TokenService {
|
||||
fun tokenService(userDetailsManager: InMemoryUserDetailsManager, passwordEncoder: PasswordEncoder, tokenRepository: TokenRepository): TokenService {
|
||||
return TokenService(userDetailsManager, passwordEncoder, tokenRepository)
|
||||
}
|
||||
|
||||
@ -180,11 +152,7 @@ class AppConfiguration {
|
||||
gPasConfigProperties: GPasConfigProperties,
|
||||
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||
): ConnectionCheckService {
|
||||
return GPasConnectionCheckService(
|
||||
restTemplate,
|
||||
gPasConfigProperties,
|
||||
connectionCheckUpdateProducer
|
||||
)
|
||||
return GPasConnectionCheckService(restTemplate, gPasConfigProperties, connectionCheckUpdateProducer)
|
||||
}
|
||||
|
||||
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS")
|
||||
@ -195,68 +163,12 @@ class AppConfiguration {
|
||||
gPasConfigProperties: GPasConfigProperties,
|
||||
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||
): ConnectionCheckService {
|
||||
return GPasConnectionCheckService(
|
||||
restTemplate,
|
||||
gPasConfigProperties,
|
||||
connectionCheckUpdateProducer
|
||||
)
|
||||
return GPasConnectionCheckService(restTemplate, gPasConfigProperties, connectionCheckUpdateProducer)
|
||||
}
|
||||
|
||||
@Bean
|
||||
fun jdbcConfiguration(): AbstractJdbcConfiguration {
|
||||
return AppJdbcConfiguration()
|
||||
}
|
||||
|
||||
@Bean
|
||||
@ConditionalOnProperty(name = ["app.consent.gics.enabled"], havingValue = "true")
|
||||
fun gicsConsentService(
|
||||
gIcsConfigProperties: GIcsConfigProperties,
|
||||
retryTemplate: RetryTemplate, restTemplate: RestTemplate, appFhirConfig: AppFhirConfig
|
||||
): IGetConsent {
|
||||
return GicsConsentService(
|
||||
gIcsConfigProperties,
|
||||
retryTemplate,
|
||||
restTemplate,
|
||||
appFhirConfig
|
||||
)
|
||||
}
|
||||
|
||||
@Bean
|
||||
@ConditionalOnProperty(name = ["app.consent.gics.enabled"], havingValue = "true")
|
||||
fun gicsConsentProcessor(
|
||||
configProperties: AppConfigProperties,
|
||||
gIcsConfigProperties: GIcsConfigProperties,
|
||||
getObjectMapper: ObjectMapper,
|
||||
appFhirConfig: AppFhirConfig,
|
||||
gicsConsentService: IGetConsent
|
||||
): ConsentProcessor {
|
||||
return ConsentProcessor(
|
||||
configProperties,
|
||||
gIcsConfigProperties,
|
||||
getObjectMapper,
|
||||
appFhirConfig.fhirContext(),
|
||||
gicsConsentService
|
||||
)
|
||||
}
|
||||
|
||||
@ConditionalOnProperty(name = ["app.consent.gics.enabled"], havingValue = "true")
|
||||
@Bean
|
||||
fun gIcsConnectionCheckService(
|
||||
restTemplate: RestTemplate,
|
||||
gIcsConfigProperties: GIcsConfigProperties,
|
||||
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||
): ConnectionCheckService {
|
||||
return GIcsConnectionCheckService(
|
||||
restTemplate,
|
||||
gIcsConfigProperties,
|
||||
connectionCheckUpdateProducer
|
||||
)
|
||||
}
|
||||
|
||||
@Bean
|
||||
@ConditionalOnMissingBean
|
||||
fun iGetConsentService(): IGetConsent {
|
||||
return ConsentByMtbFile()
|
||||
}
|
||||
}
|
||||
|
||||
|
@ -1,16 +0,0 @@
|
||||
package dev.dnpm.etl.processor.config
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext
|
||||
import org.springframework.context.annotation.Bean
|
||||
import org.springframework.context.annotation.Configuration
|
||||
|
||||
|
||||
@Configuration
|
||||
class AppFhirConfig {
|
||||
private val fhirCtx: FhirContext = FhirContext.forR4()
|
||||
|
||||
@Bean
|
||||
fun fhirContext(): FhirContext {
|
||||
return fhirCtx
|
||||
}
|
||||
}
|
@ -1,18 +0,0 @@
|
||||
package dev.dnpm.etl.processor.config
|
||||
|
||||
import com.fasterxml.jackson.core.JsonParser
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationContext
|
||||
import com.fasterxml.jackson.databind.JsonDeserializer
|
||||
import com.fasterxml.jackson.databind.JsonNode
|
||||
import org.hl7.fhir.r4.model.Consent
|
||||
|
||||
class ConsentResourceDeserializer : JsonDeserializer<Consent>() {
|
||||
override fun deserialize(p: JsonParser?, ctxt: DeserializationContext?): Consent {
|
||||
|
||||
val jsonNode = p?.readValueAsTree<JsonNode>()
|
||||
val json = jsonNode?.toString()
|
||||
|
||||
return JacksonConfig.fhirContext().newJsonParser().parseResource(json) as Consent
|
||||
}
|
||||
}
|
@ -1,15 +0,0 @@
|
||||
package dev.dnpm.etl.processor.config
|
||||
|
||||
import com.fasterxml.jackson.core.JsonGenerator
|
||||
import com.fasterxml.jackson.databind.JsonSerializer
|
||||
import com.fasterxml.jackson.databind.SerializerProvider
|
||||
import org.hl7.fhir.r4.model.Consent
|
||||
|
||||
class ConsentResourceSerializer : JsonSerializer<Consent>() {
|
||||
override fun serialize(
|
||||
value: Consent, gen: JsonGenerator, serializers: SerializerProvider
|
||||
) {
|
||||
val json = JacksonConfig.fhirContext().newJsonParser().encodeResourceToString(value)
|
||||
gen.writeRawValue(json)
|
||||
}
|
||||
}
|
@ -1,12 +0,0 @@
|
||||
package dev.dnpm.etl.processor.config
|
||||
|
||||
|
||||
import com.fasterxml.jackson.databind.module.SimpleModule
|
||||
import org.hl7.fhir.r4.model.Consent
|
||||
|
||||
class FhirResourceModule : SimpleModule() {
|
||||
init {
|
||||
addSerializer(Consent::class.java, ConsentResourceSerializer())
|
||||
addDeserializer(Consent::class.java, ConsentResourceDeserializer())
|
||||
}
|
||||
}
|
@ -1,27 +0,0 @@
|
||||
package dev.dnpm.etl.processor.config
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext
|
||||
import org.springframework.context.annotation.Bean
|
||||
import org.springframework.context.annotation.Configuration
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import com.fasterxml.jackson.databind.SerializationFeature
|
||||
import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule
|
||||
|
||||
@Configuration
|
||||
class JacksonConfig {
|
||||
|
||||
companion object {
|
||||
var fhirContext: FhirContext = FhirContext.forR4()
|
||||
|
||||
@JvmStatic
|
||||
fun fhirContext(): FhirContext {
|
||||
return fhirContext
|
||||
}
|
||||
}
|
||||
|
||||
@Bean
|
||||
fun objectMapper(): ObjectMapper = ObjectMapper().registerModule(FhirResourceModule())
|
||||
.disable(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS).registerModule(
|
||||
JavaTimeModule()
|
||||
)
|
||||
}
|
@ -25,7 +25,6 @@ import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import dev.dnpm.etl.processor.CustomMediaType
|
||||
import dev.dnpm.etl.processor.PatientId
|
||||
import dev.dnpm.etl.processor.RequestId
|
||||
import dev.dnpm.etl.processor.consent.TtpConsentStatus
|
||||
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||
import org.apache.kafka.clients.consumer.ConsumerRecord
|
||||
import org.slf4j.LoggerFactory
|
||||
@ -77,13 +76,9 @@ class KafkaInputListener(
|
||||
} else {
|
||||
logger.debug("Accepted MTB File and process deletion")
|
||||
if (requestId.isBlank()) {
|
||||
requestProcessor.processDeletion(patientId, TtpConsentStatus.UNKNOWN_CHECK_FILE)
|
||||
requestProcessor.processDeletion(patientId)
|
||||
} else {
|
||||
requestProcessor.processDeletion(
|
||||
patientId,
|
||||
requestId,
|
||||
TtpConsentStatus.UNKNOWN_CHECK_FILE
|
||||
)
|
||||
requestProcessor.processDeletion(patientId, requestId)
|
||||
}
|
||||
}
|
||||
}
|
||||
|
@ -23,8 +23,6 @@ import de.ukw.ccc.bwhc.dto.Consent
|
||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import dev.dnpm.etl.processor.CustomMediaType
|
||||
import dev.dnpm.etl.processor.PatientId
|
||||
import dev.dnpm.etl.processor.consent.IGetConsent
|
||||
import dev.dnpm.etl.processor.consent.TtpConsentStatus
|
||||
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||
import org.slf4j.LoggerFactory
|
||||
@ -35,7 +33,7 @@ import org.springframework.web.bind.annotation.*
|
||||
@RestController
|
||||
@RequestMapping(path = ["mtbfile", "mtb"])
|
||||
class MtbFileRestController(
|
||||
private val requestProcessor: RequestProcessor, private val iGetConsent: IGetConsent
|
||||
private val requestProcessor: RequestProcessor,
|
||||
) {
|
||||
|
||||
private val logger = LoggerFactory.getLogger(MtbFileRestController::class.java)
|
||||
@ -45,39 +43,20 @@ class MtbFileRestController(
|
||||
return ResponseEntity.ok("Test")
|
||||
}
|
||||
|
||||
@PostMapping(consumes = [MediaType.APPLICATION_JSON_VALUE])
|
||||
@PostMapping( consumes = [ MediaType.APPLICATION_JSON_VALUE ] )
|
||||
fun mtbFile(@RequestBody mtbFile: MtbFile): ResponseEntity<Unit> {
|
||||
val consentStatusBooleanPair = checkConsentStatus(mtbFile)
|
||||
val ttpConsentStatus = consentStatusBooleanPair.first
|
||||
val isConsentOK = consentStatusBooleanPair.second
|
||||
if (isConsentOK) {
|
||||
if (mtbFile.consent.status == Consent.Status.ACTIVE) {
|
||||
logger.debug("Accepted MTB File (bwHC V1) for processing")
|
||||
requestProcessor.processMtbFile(mtbFile)
|
||||
} else {
|
||||
|
||||
logger.debug("Accepted MTB File (bwHC V1) and process deletion")
|
||||
val patientId = PatientId(mtbFile.patient.id)
|
||||
requestProcessor.processDeletion(patientId, ttpConsentStatus)
|
||||
requestProcessor.processDeletion(patientId)
|
||||
}
|
||||
return ResponseEntity.accepted().build()
|
||||
}
|
||||
|
||||
private fun checkConsentStatus(mtbFile: MtbFile): Pair<TtpConsentStatus, Boolean> {
|
||||
var ttpConsentStatus = iGetConsent.getTtpBroadConsentStatus(mtbFile.patient.id)
|
||||
|
||||
val isConsentOK =
|
||||
(ttpConsentStatus.equals(TtpConsentStatus.UNKNOWN_CHECK_FILE) && mtbFile.consent.status == Consent.Status.ACTIVE) ||
|
||||
ttpConsentStatus.equals(
|
||||
TtpConsentStatus.BROAD_CONSENT_GIVEN
|
||||
)
|
||||
if (ttpConsentStatus.equals(TtpConsentStatus.UNKNOWN_CHECK_FILE) && mtbFile.consent.status == Consent.Status.REJECTED) {
|
||||
// in case ttp check is disabled - we propagate rejected status anyway
|
||||
ttpConsentStatus = TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED
|
||||
}
|
||||
return Pair(ttpConsentStatus, isConsentOK)
|
||||
}
|
||||
|
||||
@PostMapping(consumes = [CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE])
|
||||
@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)
|
||||
@ -87,7 +66,7 @@ class MtbFileRestController(
|
||||
@DeleteMapping(path = ["{patientId}"])
|
||||
fun deleteData(@PathVariable patientId: String): ResponseEntity<Unit> {
|
||||
logger.debug("Accepted patient ID to process deletion")
|
||||
requestProcessor.processDeletion(PatientId(patientId), TtpConsentStatus.UNKNOWN_CHECK_FILE)
|
||||
requestProcessor.processDeletion(PatientId(patientId))
|
||||
return ResponseEntity.accepted().build()
|
||||
}
|
||||
|
||||
|
@ -20,7 +20,6 @@
|
||||
|
||||
package dev.dnpm.etl.processor.monitoring
|
||||
|
||||
import dev.dnpm.etl.processor.config.GIcsConfigProperties
|
||||
import dev.dnpm.etl.processor.config.GPasConfigProperties
|
||||
import dev.dnpm.etl.processor.config.RestTargetProperties
|
||||
import jakarta.annotation.PostConstruct
|
||||
@ -69,12 +68,6 @@ sealed class ConnectionCheckResult {
|
||||
override val timestamp: Instant,
|
||||
override val lastChange: Instant
|
||||
) : ConnectionCheckResult()
|
||||
|
||||
data class GIcsConnectionCheckResult(
|
||||
override val available: Boolean,
|
||||
override val timestamp: Instant,
|
||||
override val lastChange: Instant
|
||||
) : ConnectionCheckResult()
|
||||
}
|
||||
|
||||
class KafkaConnectionCheckService(
|
||||
@ -214,57 +207,4 @@ class GPasConnectionCheckService(
|
||||
override fun connectionAvailable(): ConnectionCheckResult.GPasConnectionCheckResult {
|
||||
return this.result
|
||||
}
|
||||
}
|
||||
|
||||
class GIcsConnectionCheckService(
|
||||
private val restTemplate: RestTemplate,
|
||||
private val gIcsConfigProperties: GIcsConfigProperties,
|
||||
@Qualifier("connectionCheckUpdateProducer")
|
||||
private val connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||
) : ConnectionCheckService {
|
||||
|
||||
private var result = ConnectionCheckResult.GIcsConnectionCheckResult(false, Instant.now(), Instant.now())
|
||||
|
||||
@PostConstruct
|
||||
@Scheduled(cron = "0 * * * * *")
|
||||
fun check() {
|
||||
result = try {
|
||||
|
||||
val uri = UriComponentsBuilder.fromUriString(
|
||||
gIcsConfigProperties.uri.toString()).path("/metadata").build().toUri()
|
||||
|
||||
val headers = HttpHeaders()
|
||||
headers.contentType = MediaType.APPLICATION_JSON
|
||||
if (!gIcsConfigProperties.username.isNullOrBlank() && !gIcsConfigProperties.password.isNullOrBlank()) {
|
||||
headers.setBasicAuth(gIcsConfigProperties.username, gIcsConfigProperties.password)
|
||||
}
|
||||
|
||||
val available = restTemplate.exchange(
|
||||
uri,
|
||||
HttpMethod.GET,
|
||||
HttpEntity<Void>(headers),
|
||||
Void::class.java
|
||||
).statusCode == HttpStatus.OK
|
||||
|
||||
ConnectionCheckResult.GIcsConnectionCheckResult(
|
||||
available,
|
||||
Instant.now(),
|
||||
if (result.available == available) { result.lastChange } else { Instant.now() }
|
||||
)
|
||||
} catch (_: Exception) {
|
||||
ConnectionCheckResult.GIcsConnectionCheckResult(
|
||||
false,
|
||||
Instant.now(),
|
||||
if (!result.available) { result.lastChange } else { Instant.now() }
|
||||
)
|
||||
}
|
||||
connectionCheckUpdateProducer.emitNext(
|
||||
result,
|
||||
Sinks.EmitFailureHandler.FAIL_FAST
|
||||
)
|
||||
}
|
||||
|
||||
override fun connectionAvailable(): ConnectionCheckResult.GIcsConnectionCheckResult {
|
||||
return this.result
|
||||
}
|
||||
}
|
@ -24,6 +24,5 @@ enum class RequestStatus(val value: String) {
|
||||
WARNING("warning"),
|
||||
ERROR("error"),
|
||||
UNKNOWN("unknown"),
|
||||
DUPLICATION("duplication"),
|
||||
NO_CONSENT("no-consent")
|
||||
DUPLICATION("duplication")
|
||||
}
|
@ -21,6 +21,7 @@ package dev.dnpm.etl.processor.pseudonym
|
||||
|
||||
import org.apache.commons.codec.binary.Base32
|
||||
import org.apache.commons.codec.digest.DigestUtils
|
||||
import org.apache.commons.math3.random.RandomDataGenerator
|
||||
|
||||
|
||||
class AnonymizingGenerator : Generator {
|
||||
@ -31,4 +32,9 @@ class AnonymizingGenerator : Generator {
|
||||
.lowercase()
|
||||
}
|
||||
|
||||
override fun generateGenomDeTan(id: String?): String? {
|
||||
val randomDataGenerator = RandomDataGenerator()
|
||||
return randomDataGenerator.nextSecureHexString(64).lowercase()
|
||||
}
|
||||
|
||||
}
|
@ -35,6 +35,10 @@ class PseudonymizeService(
|
||||
}
|
||||
}
|
||||
|
||||
fun genomDeTan(patientId: PatientId): String {
|
||||
return generator.generateGenomDeTan(patientId.value)
|
||||
}
|
||||
|
||||
fun prefix(): String {
|
||||
return configProperties.prefix
|
||||
}
|
||||
|
@ -21,9 +21,7 @@ package dev.dnpm.etl.processor.pseudonym
|
||||
|
||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import dev.dnpm.etl.processor.PatientId
|
||||
import dev.pcvolkmer.mv64e.mtb.ModelProjectConsent
|
||||
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||
import dev.pcvolkmer.mv64e.mtb.MvhMetadata
|
||||
import org.apache.commons.codec.digest.DigestUtils
|
||||
|
||||
/** Replaces patient ID with generated patient pseudonym
|
||||
@ -291,16 +289,6 @@ infix fun Mtb.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
|
||||
this.followUps?.forEach {
|
||||
it.patient.id = patientPseudonym
|
||||
}
|
||||
|
||||
this.metadata?.researchConsents?.forEach { it ->
|
||||
val entry = it ?: return@forEach
|
||||
if (entry.contains("patient")) {
|
||||
// here we expect only a patient reference any other data like display
|
||||
// need to be removed, since may contain unsecure data
|
||||
entry.remove("patient")
|
||||
entry["patient"] = mapOf("reference" to "Patient/$patientPseudonym")
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
@ -330,22 +318,7 @@ infix fun Mtb.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
|
||||
// TODO all other properties
|
||||
}
|
||||
|
||||
fun Mtb.ensureMetaDataIsInitialized() {
|
||||
// init metadata if necessary
|
||||
if (this.metadata == null) {
|
||||
val mvhMetadata = MvhMetadata.builder().build()
|
||||
this.metadata = mvhMetadata
|
||||
}
|
||||
if (this.metadata.researchConsents == null) {
|
||||
this.metadata.researchConsents = mutableListOf()
|
||||
}
|
||||
if (this.metadata.modelProjectConsent == null) {
|
||||
this.metadata.modelProjectConsent = ModelProjectConsent()
|
||||
this.metadata.modelProjectConsent.provisions = mutableListOf()
|
||||
} else
|
||||
if (this.metadata.modelProjectConsent.provisions != null) {
|
||||
// make sure list can be changed
|
||||
this.metadata.modelProjectConsent.provisions =
|
||||
this.metadata.modelProjectConsent.provisions.toMutableList()
|
||||
}
|
||||
}
|
||||
infix fun Mtb.addGenomDeTan(pseudonymizeService: PseudonymizeService)
|
||||
{
|
||||
this.metadata.transferTan = pseudonymizeService.genomDeTan(PatientId(this.patient.id))
|
||||
}
|
@ -1,276 +0,0 @@
|
||||
package dev.dnpm.etl.processor.services
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext
|
||||
import com.fasterxml.jackson.core.JsonProcessingException
|
||||
import com.fasterxml.jackson.core.type.TypeReference
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import dev.dnpm.etl.processor.config.AppConfigProperties
|
||||
import dev.dnpm.etl.processor.config.GIcsConfigProperties
|
||||
import dev.dnpm.etl.processor.consent.ConsentDomain
|
||||
import dev.dnpm.etl.processor.consent.IGetConsent
|
||||
import dev.dnpm.etl.processor.pseudonym.ensureMetaDataIsInitialized
|
||||
import dev.pcvolkmer.mv64e.mtb.*
|
||||
import org.apache.commons.lang3.NotImplementedException
|
||||
import org.hl7.fhir.r4.model.*
|
||||
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent
|
||||
import org.hl7.fhir.r4.model.Coding
|
||||
import org.hl7.fhir.r4.model.Consent.ConsentState
|
||||
import org.hl7.fhir.r4.model.Consent.ProvisionComponent
|
||||
import org.slf4j.Logger
|
||||
import org.slf4j.LoggerFactory
|
||||
import org.springframework.stereotype.Service
|
||||
import java.io.IOException
|
||||
import java.time.Clock
|
||||
import java.time.Instant
|
||||
import java.util.*
|
||||
|
||||
@Service
|
||||
class ConsentProcessor(
|
||||
private val appConfigProperties: AppConfigProperties,
|
||||
private val gIcsConfigProperties: GIcsConfigProperties,
|
||||
private val objectMapper: ObjectMapper,
|
||||
private val fhirContext: FhirContext,
|
||||
private val consentService: IGetConsent?
|
||||
) {
|
||||
private var logger: Logger = LoggerFactory.getLogger("ConsentProcessor")
|
||||
|
||||
/**
|
||||
* In case an instance of {@link ICheckConsent} is active, consent will be embedded and checked.
|
||||
*
|
||||
* Logik:
|
||||
* * <c>true</c> IF consent check is disabled.
|
||||
* * <c>true</c> IF broad consent (BC) has been given.
|
||||
* * <c>true</c> BC has been asked AND declined but genomDe consent has been consented.
|
||||
* * ELSE <c>false</c> is returned.
|
||||
*
|
||||
* @param mtbFile File v2 (will be enriched with consent data)
|
||||
* @return true if consent is given
|
||||
*
|
||||
*/
|
||||
fun consentGatedCheckAndTryEmbedding(mtbFile: Mtb): Boolean {
|
||||
if (consentService == null) {
|
||||
// consent check seems to be disabled
|
||||
return true
|
||||
}
|
||||
|
||||
mtbFile.ensureMetaDataIsInitialized()
|
||||
|
||||
val personIdentifierValue = mtbFile.patient.id
|
||||
val requestDate = Date.from(Instant.now(Clock.systemUTC()))
|
||||
|
||||
// 1. Broad consent Entry exists?
|
||||
// 1.1. -> yes and research consent is given -> send mtb file
|
||||
// 1.2. -> no -> return status error - consent has not been asked
|
||||
// 2. -> Broad consent found but rejected -> is GenomDe consent provision 'sequencing' given?
|
||||
// 2.1 -> yes -> send mtb file
|
||||
// 2.2 -> no -> warn/info no consent given
|
||||
|
||||
/*
|
||||
* broad consent
|
||||
*/
|
||||
val broadConsent = consentService.getBroadConsent(personIdentifierValue, requestDate)
|
||||
val broadConsentHasBeenAsked = !broadConsent.entry.isEmpty()
|
||||
|
||||
// fast exit - if patient has not been asked, we can skip and exit
|
||||
if (!broadConsentHasBeenAsked) return false
|
||||
|
||||
val genomeDeConsent = consentService.getGenomDeConsent(
|
||||
personIdentifierValue, requestDate
|
||||
)
|
||||
|
||||
addGenomeDbProvisions(mtbFile, genomeDeConsent)
|
||||
|
||||
|
||||
if (!genomeDeConsent.entry.isEmpty()) setGenomDeSubmissionType(mtbFile)
|
||||
|
||||
embedBroadConsentResources(mtbFile, broadConsent)
|
||||
|
||||
val broadConsentStatus = getProvisionTypeByPolicyCode(
|
||||
broadConsent, requestDate, ConsentDomain.BroadConsent
|
||||
)
|
||||
|
||||
val genomDeSequencingStatus = getProvisionTypeByPolicyCode(
|
||||
genomeDeConsent, requestDate, ConsentDomain.Modelvorhaben64e
|
||||
)
|
||||
|
||||
if (Consent.ConsentProvisionType.NULL == broadConsentStatus) {
|
||||
// bc not asked
|
||||
return false
|
||||
}
|
||||
if (Consent.ConsentProvisionType.PERMIT == broadConsentStatus || Consent.ConsentProvisionType.PERMIT == genomDeSequencingStatus) return true
|
||||
|
||||
return false
|
||||
}
|
||||
|
||||
fun embedBroadConsentResources(mtbFile: Mtb, broadConsent: Bundle) {
|
||||
for (entry in broadConsent.getEntry()) {
|
||||
val resource = entry.getResource()
|
||||
if (resource is Consent) {
|
||||
// since jackson convertValue does not work here,
|
||||
// we need another step to back to string, before we convert to object map
|
||||
val asJsonString = fhirContext.newJsonParser().encodeResourceToString(resource)
|
||||
try {
|
||||
val mapOfJson: HashMap<String?, Any?>? =
|
||||
objectMapper.readValue<HashMap<String?, Any?>?>(
|
||||
asJsonString, object : TypeReference<HashMap<String?, Any?>?>() {})
|
||||
mtbFile.metadata.researchConsents.add(mapOfJson)
|
||||
} catch (e: JsonProcessingException) {
|
||||
throw RuntimeException(e)
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
fun addGenomeDbProvisions(mtbFile: Mtb, consentGnomeDe: Bundle) {
|
||||
for (entry in consentGnomeDe.getEntry()) {
|
||||
val resource = entry.getResource()
|
||||
if (resource !is Consent) {
|
||||
continue
|
||||
}
|
||||
|
||||
// We expect only one provision in collection, therefore get first or none
|
||||
val provisions = resource.getProvision().getProvision()
|
||||
if (provisions.isEmpty()) {
|
||||
continue
|
||||
}
|
||||
|
||||
val provisionComponent: ProvisionComponent = provisions.first()
|
||||
|
||||
var provisionCode: String? = null
|
||||
if (provisionComponent.getCode() != null && !provisionComponent.getCode().isEmpty()) {
|
||||
val codableConcept: CodeableConcept = provisionComponent.getCode().first()
|
||||
if (codableConcept.getCoding() != null && !codableConcept.getCoding().isEmpty()) {
|
||||
provisionCode = codableConcept.getCoding().first().getCode()
|
||||
}
|
||||
}
|
||||
|
||||
if (provisionCode != null) {
|
||||
try {
|
||||
val modelProjectConsentPurpose =
|
||||
ModelProjectConsentPurpose.forValue(provisionCode)
|
||||
|
||||
if (ModelProjectConsentPurpose.SEQUENCING == modelProjectConsentPurpose) {
|
||||
// CONVENTION: wrapping date is date of SEQUENCING consent
|
||||
mtbFile.metadata.modelProjectConsent.date = resource.getDateTime()
|
||||
}
|
||||
|
||||
val provision = Provision.builder()
|
||||
.type(ConsentProvision.valueOf(provisionComponent.getType().name))
|
||||
.date(provisionComponent.getPeriod().getStart())
|
||||
.purpose(modelProjectConsentPurpose).build()
|
||||
|
||||
mtbFile.metadata.modelProjectConsent.provisions.add(provision)
|
||||
} catch (ioe: IOException) {
|
||||
logger.error(
|
||||
"Provision code '$provisionCode' is unknown and cannot be mapped.",
|
||||
ioe.toString()
|
||||
)
|
||||
}
|
||||
}
|
||||
|
||||
if (!mtbFile.metadata.modelProjectConsent.provisions.isEmpty()) {
|
||||
mtbFile.metadata.modelProjectConsent.version =
|
||||
gIcsConfigProperties.genomeDeConsentVersion
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* fixme: currently we do not have information about submission type
|
||||
*/
|
||||
private fun setGenomDeSubmissionType(mtbFile: Mtb) {
|
||||
if (appConfigProperties.genomDeTestSubmission) {
|
||||
// fixme: uncomment when data model is updated
|
||||
// mtbFile.metadata.type = MvhSubmissionType.Test
|
||||
logger.info("genomeDe submission mit TEST")
|
||||
} else {
|
||||
mtbFile.metadata.type = MvhSubmissionType.INITIAL
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* @param consentBundle consent resource
|
||||
* @param requestDate date which must be within validation period of provision
|
||||
* @return type of provision, will be [org.hl7.fhir.r4.model.Consent.ConsentProvisionType.NULL] if none is found.
|
||||
*/
|
||||
fun getProvisionTypeByPolicyCode(
|
||||
consentBundle: Bundle, requestDate: Date?, consentDomain: ConsentDomain
|
||||
): Consent.ConsentProvisionType {
|
||||
val code: String?
|
||||
val system: String?
|
||||
if (ConsentDomain.BroadConsent == consentDomain) {
|
||||
code = gIcsConfigProperties.broadConsentPolicyCode
|
||||
system = gIcsConfigProperties.broadConsentPolicySystem
|
||||
} else if (ConsentDomain.Modelvorhaben64e == consentDomain) {
|
||||
code = gIcsConfigProperties.genomeDePolicyCode
|
||||
system = gIcsConfigProperties.genomeDePolicySystem
|
||||
} else {
|
||||
throw NotImplementedException("unknown consent domain " + consentDomain.name)
|
||||
}
|
||||
|
||||
val provisionTypeByPolicyCode = getProvisionTypeByPolicyCode(
|
||||
consentBundle, code, system, requestDate
|
||||
)
|
||||
return provisionTypeByPolicyCode
|
||||
}
|
||||
|
||||
/**
|
||||
* @param consentBundle consent resource
|
||||
* @param policyAndProvisionCode policyRule and provision code value
|
||||
* @param policyAndProvisionSystem policyRule and provision system value
|
||||
* @param requestDate date which must be within validation period of provision
|
||||
* @return type of provision, will be [org.hl7.fhir.r4.model.Consent.ConsentProvisionType.NULL] if none is found.
|
||||
*/
|
||||
fun getProvisionTypeByPolicyCode(
|
||||
consentBundle: Bundle,
|
||||
policyAndProvisionCode: String?,
|
||||
policyAndProvisionSystem: String?,
|
||||
requestDate: Date?
|
||||
): Consent.ConsentProvisionType {
|
||||
val entriesOfInterest = consentBundle.entry.filter { entry ->
|
||||
entry.resource.isResource && entry.resource.resourceType == ResourceType.Consent && (entry.resource as Consent).status == ConsentState.ACTIVE && checkCoding(
|
||||
policyAndProvisionCode,
|
||||
policyAndProvisionSystem,
|
||||
(entry.resource as Consent).policyRule.codingFirstRep
|
||||
) && isIsRequestDateInRange(
|
||||
requestDate, (entry.resource as Consent).provision.period
|
||||
)
|
||||
}.map { consentWithTargetPolicy: BundleEntryComponent ->
|
||||
val provision = (consentWithTargetPolicy.getResource() as Consent).getProvision()
|
||||
val provisionComponentByCode =
|
||||
provision.getProvision().stream().filter { prov: ProvisionComponent? ->
|
||||
checkCoding(
|
||||
policyAndProvisionCode,
|
||||
policyAndProvisionSystem,
|
||||
prov!!.getCodeFirstRep().getCodingFirstRep()
|
||||
) && isIsRequestDateInRange(
|
||||
requestDate, prov.getPeriod()
|
||||
)
|
||||
}.findFirst()
|
||||
if (provisionComponentByCode.isPresent) {
|
||||
// actual provision we search for
|
||||
return@map provisionComponentByCode.get().getType()
|
||||
} else {
|
||||
if (provision.type != null) return provision.type
|
||||
|
||||
}
|
||||
return Consent.ConsentProvisionType.NULL
|
||||
}.firstOrNull()
|
||||
|
||||
if (entriesOfInterest == null) return Consent.ConsentProvisionType.NULL
|
||||
return entriesOfInterest
|
||||
}
|
||||
|
||||
fun checkCoding(
|
||||
researchAllowedPolicyOid: String?, researchAllowedPolicySystem: String?, coding: Coding
|
||||
): Boolean {
|
||||
return coding.getSystem() == researchAllowedPolicySystem && (coding.getCode() == researchAllowedPolicyOid)
|
||||
}
|
||||
|
||||
fun isIsRequestDateInRange(requestdate: Date?, provPeriod: Period): Boolean {
|
||||
val isRequestDateAfterOrEqualStart = provPeriod.getStart().compareTo(requestdate)
|
||||
val isRequestDateBeforeOrEqualEnd = provPeriod.getEnd().compareTo(requestdate)
|
||||
return isRequestDateAfterOrEqualStart <= 0 && isRequestDateBeforeOrEqualEnd >= 0
|
||||
}
|
||||
|
||||
}
|
@ -23,23 +23,22 @@ import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import dev.dnpm.etl.processor.*
|
||||
import dev.dnpm.etl.processor.config.AppConfigProperties
|
||||
import dev.dnpm.etl.processor.consent.TtpConsentStatus
|
||||
import dev.dnpm.etl.processor.monitoring.Report
|
||||
import dev.dnpm.etl.processor.monitoring.Request
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import dev.dnpm.etl.processor.monitoring.RequestType
|
||||
import dev.dnpm.etl.processor.output.*
|
||||
import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
|
||||
import dev.dnpm.etl.processor.pseudonym.addGenomDeTan
|
||||
import dev.dnpm.etl.processor.pseudonym.anonymizeContentWith
|
||||
import dev.dnpm.etl.processor.pseudonym.pseudonymizeWith
|
||||
import dev.pcvolkmer.mv64e.mtb.ConsentProvision
|
||||
import dev.pcvolkmer.mv64e.mtb.ModelProjectConsentPurpose
|
||||
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||
import org.apache.commons.codec.binary.Base32
|
||||
import org.apache.commons.codec.digest.DigestUtils
|
||||
import org.slf4j.Logger
|
||||
import org.slf4j.LoggerFactory
|
||||
import org.springframework.context.ApplicationEventPublisher
|
||||
import org.springframework.stereotype.Service
|
||||
import java.lang.RuntimeException
|
||||
import java.time.Instant
|
||||
import java.util.*
|
||||
|
||||
@ -51,11 +50,9 @@ class RequestProcessor(
|
||||
private val requestService: RequestService,
|
||||
private val objectMapper: ObjectMapper,
|
||||
private val applicationEventPublisher: ApplicationEventPublisher,
|
||||
private val appConfigProperties: AppConfigProperties,
|
||||
private val consentProcessor: ConsentProcessor?
|
||||
private val appConfigProperties: AppConfigProperties
|
||||
) {
|
||||
|
||||
private var logger: Logger = LoggerFactory.getLogger("RequestProcessor")
|
||||
fun processMtbFile(mtbFile: MtbFile) {
|
||||
processMtbFile(mtbFile, randomRequestId())
|
||||
}
|
||||
@ -72,25 +69,19 @@ class RequestProcessor(
|
||||
processMtbFile(mtbFile, randomRequestId())
|
||||
}
|
||||
|
||||
|
||||
fun processMtbFile(mtbFile: Mtb, requestId: RequestId) {
|
||||
val pid = PatientId(extractPatientIdentifier(mtbFile))
|
||||
|
||||
val isConsentOk = consentProcessor != null &&
|
||||
consentProcessor.consentGatedCheckAndTryEmbedding(mtbFile) || consentProcessor == null
|
||||
if (isConsentOk) {
|
||||
mtbFile pseudonymizeWith pseudonymizeService
|
||||
mtbFile anonymizeContentWith pseudonymizeService
|
||||
val request = DnpmV2MtbFileRequest(requestId, transformationService.transform(mtbFile))
|
||||
saveAndSend(request, pid)
|
||||
} else {
|
||||
logger.warn("consent check failed file will not be processed further!")
|
||||
applicationEventPublisher.publishEvent(
|
||||
ResponseEvent(
|
||||
requestId, Instant.now(), RequestStatus.NO_CONSENT
|
||||
)
|
||||
)
|
||||
val pid = PatientId(mtbFile.patient.id)
|
||||
val isModelProjectConsented = mtbFile.metadata?.modelProjectConsent?.provisions?.any { p ->
|
||||
p.purpose == ModelProjectConsentPurpose.SEQUENCING
|
||||
&& p.type == ConsentProvision.PERMIT
|
||||
} == true
|
||||
if (isModelProjectConsented) {
|
||||
mtbFile addGenomDeTan pseudonymizeService
|
||||
}
|
||||
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) {
|
||||
@ -108,7 +99,9 @@ class RequestProcessor(
|
||||
if (appConfigProperties.duplicationDetection && isDuplication(request)) {
|
||||
applicationEventPublisher.publishEvent(
|
||||
ResponseEvent(
|
||||
request.requestId, Instant.now(), RequestStatus.DUPLICATION
|
||||
request.requestId,
|
||||
Instant.now(),
|
||||
RequestStatus.DUPLICATION
|
||||
)
|
||||
)
|
||||
return
|
||||
@ -140,28 +133,21 @@ class RequestProcessor(
|
||||
val isLastRequestDeletion =
|
||||
requestService.isLastRequestWithKnownStatusDeletion(patientPseudonym)
|
||||
|
||||
return null != lastMtbFileRequestForPatient && !isLastRequestDeletion && lastMtbFileRequestForPatient.fingerprint == fingerprint(
|
||||
return null != lastMtbFileRequestForPatient
|
||||
&& !isLastRequestDeletion
|
||||
&& lastMtbFileRequestForPatient.fingerprint == fingerprint(
|
||||
pseudonymizedMtbFileRequest
|
||||
)
|
||||
}
|
||||
|
||||
fun processDeletion(patientId: PatientId, isConsented: TtpConsentStatus) {
|
||||
processDeletion(patientId, randomRequestId(), isConsented)
|
||||
fun processDeletion(patientId: PatientId) {
|
||||
processDeletion(patientId, randomRequestId())
|
||||
}
|
||||
|
||||
fun processDeletion(patientId: PatientId, requestId: RequestId, isConsented: TtpConsentStatus) {
|
||||
fun processDeletion(patientId: PatientId, requestId: RequestId) {
|
||||
try {
|
||||
val patientPseudonym = pseudonymizeService.patientPseudonym(patientId)
|
||||
|
||||
val requestStatus: RequestStatus = when (isConsented) {
|
||||
TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED, TtpConsentStatus.BROAD_CONSENT_MISSING, TtpConsentStatus.BROAD_CONSENT_REJECTED -> RequestStatus.NO_CONSENT
|
||||
TtpConsentStatus.FAILED_TO_ASK -> RequestStatus.ERROR
|
||||
TtpConsentStatus.BROAD_CONSENT_GIVEN, TtpConsentStatus.UNKNOWN_CHECK_FILE -> RequestStatus.UNKNOWN
|
||||
TtpConsentStatus.GENOM_DE_CONSENT_SEQUENCING_PERMIT, TtpConsentStatus.GENOM_DE_CONSENT_MISSING, TtpConsentStatus.GENOM_DE_SEQUENCING_REJECTED -> {
|
||||
throw RuntimeException("processDelete should never deal with '" + isConsented.name + "' consent status. This is a bug and need to be fixed!")
|
||||
}
|
||||
}
|
||||
|
||||
requestService.save(
|
||||
Request(
|
||||
requestId,
|
||||
@ -169,7 +155,7 @@ class RequestProcessor(
|
||||
patientId,
|
||||
fingerprint(patientPseudonym.value),
|
||||
RequestType.DELETE,
|
||||
requestStatus
|
||||
RequestStatus.UNKNOWN
|
||||
)
|
||||
)
|
||||
|
||||
@ -177,14 +163,17 @@ class RequestProcessor(
|
||||
|
||||
applicationEventPublisher.publishEvent(
|
||||
ResponseEvent(
|
||||
requestId, Instant.now(), responseStatus.status, when (responseStatus.status) {
|
||||
requestId,
|
||||
Instant.now(),
|
||||
responseStatus.status,
|
||||
when (responseStatus.status) {
|
||||
RequestStatus.WARNING, RequestStatus.ERROR -> Optional.of(responseStatus.body)
|
||||
else -> Optional.empty()
|
||||
}
|
||||
)
|
||||
)
|
||||
|
||||
} catch (_: Exception) {
|
||||
} catch (e: Exception) {
|
||||
requestService.save(
|
||||
Request(
|
||||
uuid = requestId,
|
||||
@ -208,10 +197,10 @@ class RequestProcessor(
|
||||
|
||||
private fun fingerprint(s: String): Fingerprint {
|
||||
return Fingerprint(
|
||||
Base32().encodeAsString(DigestUtils.sha256(s)).replace("=", "").lowercase()
|
||||
Base32().encodeAsString(DigestUtils.sha256(s))
|
||||
.replace("=", "")
|
||||
.lowercase()
|
||||
)
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private fun extractPatientIdentifier(mtbFile: Mtb): String = mtbFile.patient.id
|
||||
|
@ -70,12 +70,6 @@ class ResponseProcessor(
|
||||
)
|
||||
}
|
||||
|
||||
RequestStatus.NO_CONSENT -> {
|
||||
it.report = Report(
|
||||
"Einwilligung Status fehlt, widerrufen oder ungeklärt."
|
||||
)
|
||||
}
|
||||
|
||||
else -> {
|
||||
logger.error("Cannot process response: Unknown response!")
|
||||
return@ifPresentOrElse
|
||||
|
@ -19,7 +19,10 @@
|
||||
|
||||
package dev.dnpm.etl.processor.web
|
||||
|
||||
import dev.dnpm.etl.processor.monitoring.*
|
||||
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
|
||||
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
|
||||
import dev.dnpm.etl.processor.monitoring.GPasConnectionCheckService
|
||||
import dev.dnpm.etl.processor.monitoring.OutputConnectionCheckService
|
||||
import dev.dnpm.etl.processor.output.MtbFileSender
|
||||
import dev.dnpm.etl.processor.pseudonym.Generator
|
||||
import dev.dnpm.etl.processor.security.Role
|
||||
@ -58,15 +61,11 @@ class ConfigController(
|
||||
val gPasConnectionAvailable =
|
||||
connectionCheckServices.filterIsInstance<GPasConnectionCheckService>().firstOrNull()?.connectionAvailable()
|
||||
|
||||
val gIcsConnectionAvailable =
|
||||
connectionCheckServices.filterIsInstance<GIcsConnectionCheckService>().firstOrNull()?.connectionAvailable()
|
||||
|
||||
model.addAttribute("pseudonymGenerator", pseudonymGenerator.javaClass.simpleName)
|
||||
model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName)
|
||||
model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint())
|
||||
model.addAttribute("outputConnectionAvailable", outputConnectionAvailable)
|
||||
model.addAttribute("gPasConnectionAvailable", gPasConnectionAvailable)
|
||||
model.addAttribute("gIcsConnectionAvailable", gIcsConnectionAvailable)
|
||||
model.addAttribute("tokensEnabled", tokenService != null)
|
||||
if (tokenService != null) {
|
||||
model.addAttribute("tokens", tokenService.findAll())
|
||||
@ -120,24 +119,6 @@ class ConfigController(
|
||||
return "configs/gPasConnectionAvailable"
|
||||
}
|
||||
|
||||
@GetMapping(params = ["gIcsConnectionAvailable"])
|
||||
fun gIcsConnectionAvailable(model: Model): String {
|
||||
val gIcsConnectionAvailable =
|
||||
connectionCheckServices.filterIsInstance<GIcsConnectionCheckService>().firstOrNull()?.connectionAvailable()
|
||||
|
||||
model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName)
|
||||
model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint())
|
||||
model.addAttribute("gIcsConnectionAvailable", gIcsConnectionAvailable)
|
||||
if (tokenService != null) {
|
||||
model.addAttribute("tokensEnabled", true)
|
||||
model.addAttribute("tokens", tokenService.findAll())
|
||||
} else {
|
||||
model.addAttribute("tokens", listOf<Token>())
|
||||
}
|
||||
|
||||
return "configs/gIcsConnectionAvailable"
|
||||
}
|
||||
|
||||
@PostMapping(path = ["tokens"])
|
||||
fun addToken(@ModelAttribute("name") name: String, model: Model): String {
|
||||
if (tokenService == null) {
|
||||
@ -209,7 +190,6 @@ class ConfigController(
|
||||
is ConnectionCheckResult.KafkaConnectionCheckResult -> "output-connection-check"
|
||||
is ConnectionCheckResult.RestConnectionCheckResult -> "output-connection-check"
|
||||
is ConnectionCheckResult.GPasConnectionCheckResult -> "gpas-connection-check"
|
||||
is ConnectionCheckResult.GIcsConnectionCheckResult -> "gics-connection-check"
|
||||
}
|
||||
|
||||
ServerSentEvent.builder<Any>()
|
||||
|
@ -16,7 +16,6 @@ spring:
|
||||
content:
|
||||
enabled: true
|
||||
paths: /**/*.js,/**/*.css,/**/*.svg,/**/*.jpeg
|
||||
app:
|
||||
isGenomDeTestSubmission: true
|
||||
|
||||
server:
|
||||
forward-headers-strategy: framework
|
@ -49,11 +49,6 @@
|
||||
</div>
|
||||
</section>
|
||||
|
||||
<section hx-ext="sse" th:sse-connect="@{/configs/events}">
|
||||
<div th:insert="~{configs/gIcsConnectionAvailable.html}" th:hx-get="@{/configs?gIcsConnectionAvailable}" hx-trigger="sse:gics-connection-check">
|
||||
</div>
|
||||
</section>
|
||||
|
||||
<section hx-ext="sse" th:sse-connect="@{/configs/events}">
|
||||
<div th:insert="~{configs/outputConnectionAvailable.html}" th:hx-get="@{/configs?outputConnectionAvailable}" hx-trigger="sse:output-connection-check">
|
||||
</div>
|
||||
|
@ -1,24 +0,0 @@
|
||||
<th:block th:if="${gIcsConnectionAvailable == null}">
|
||||
<h2><span>🟦</span> gICS nicht konfiguriert - Einwilligung wird über Dateiinhalt geprüft</h2>
|
||||
</th:block>
|
||||
<th:block th:if="${gIcsConnectionAvailable != null}">
|
||||
<h2><span th:if="${gIcsConnectionAvailable.available}">✅</span><span th:if="${not(gIcsConnectionAvailable.available)}">⚡</span> Verbindung zu gICS</h2>
|
||||
<div>
|
||||
Stand: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(gIcsConnectionAvailable.timestamp)}" th:text="${#temporals.formatISO(gIcsConnectionAvailable.timestamp)}"></time>
|
||||
|
|
||||
Letzte Änderung: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(gIcsConnectionAvailable.lastChange)}" th:text="${#temporals.formatISO(gIcsConnectionAvailable.lastChange)}"></time>
|
||||
</div>
|
||||
<div>
|
||||
<span>Die Verbindung ist aktuell</span>
|
||||
<strong th:if="${gIcsConnectionAvailable.available}" style="color: green">verfügbar.</strong>
|
||||
<strong th:if="${not(gIcsConnectionAvailable.available)}" style="color: red">nicht verfügbar.</strong>
|
||||
</div>
|
||||
<div class="connection-display border">
|
||||
<img th:src="@{/server.png}" alt="ETL-Processor" />
|
||||
<span class="connection" th:classappend="${gIcsConnectionAvailable.available ? 'available' : ''}"></span>
|
||||
<img th:src="@{/server.png}" alt="gICS" />
|
||||
<span>ETL-Processor</span>
|
||||
<span></span>
|
||||
<span>gICS</span>
|
||||
</div>
|
||||
</th:block>
|
@ -1,123 +0,0 @@
|
||||
package dev.dnpm.etl.processor.consent;
|
||||
|
||||
import static org.assertj.core.api.Assertions.assertThat;
|
||||
import static org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo;
|
||||
import static org.springframework.test.web.client.response.MockRestResponseCreators.withSuccess;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import dev.dnpm.etl.processor.config.AppConfiguration;
|
||||
import dev.dnpm.etl.processor.config.AppFhirConfig;
|
||||
import dev.dnpm.etl.processor.config.GIcsConfigProperties;
|
||||
import java.time.Instant;
|
||||
import java.util.Date;
|
||||
import org.hl7.fhir.r4.model.BooleanType;
|
||||
import org.hl7.fhir.r4.model.Identifier;
|
||||
import org.hl7.fhir.r4.model.OperationOutcome;
|
||||
import org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity;
|
||||
import org.hl7.fhir.r4.model.OperationOutcome.IssueType;
|
||||
import org.hl7.fhir.r4.model.OperationOutcome.OperationOutcomeIssueComponent;
|
||||
import org.hl7.fhir.r4.model.Parameters;
|
||||
import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
|
||||
import org.hl7.fhir.r4.model.StringType;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.boot.test.autoconfigure.web.client.RestClientTest;
|
||||
import org.springframework.http.MediaType;
|
||||
import org.springframework.test.context.ContextConfiguration;
|
||||
import org.springframework.test.context.TestPropertySource;
|
||||
import org.springframework.test.web.client.MockRestServiceServer;
|
||||
|
||||
@ContextConfiguration(classes = {AppConfiguration.class, ObjectMapper.class})
|
||||
@TestPropertySource(properties = {"app.consent.gics.enabled=true",
|
||||
"app.consent.gics.uri=http://localhost:8090/ttp-fhir/fhir/gics"})
|
||||
@RestClientTest
|
||||
public class GicsConsentServiceTest {
|
||||
|
||||
public static final String GICS_BASE_URI = "http://localhost:8090/ttp-fhir/fhir/gics";
|
||||
@Autowired
|
||||
MockRestServiceServer mockRestServiceServer;
|
||||
|
||||
@Autowired
|
||||
GicsConsentService gicsConsentService;
|
||||
|
||||
@Autowired
|
||||
AppConfiguration appConfiguration;
|
||||
|
||||
@Autowired
|
||||
AppFhirConfig appFhirConfig;
|
||||
|
||||
@Autowired
|
||||
GIcsConfigProperties gIcsConfigProperties;
|
||||
|
||||
@BeforeEach
|
||||
public void setUp() {
|
||||
mockRestServiceServer = MockRestServiceServer.createServer(appConfiguration.restTemplate());
|
||||
}
|
||||
|
||||
@Test
|
||||
void getTtpBroadConsentStatus() {
|
||||
final Parameters responseConsented = new Parameters().addParameter(
|
||||
new ParametersParameterComponent().setName("consented")
|
||||
.setValue(new BooleanType().setValue(true)));
|
||||
|
||||
mockRestServiceServer.expect(requestTo(
|
||||
"http://localhost:8090/ttp-fhir/fhir/gics" + GicsConsentService.IS_CONSENTED_ENDPOINT))
|
||||
.andRespond(withSuccess(appFhirConfig.fhirContext().newJsonParser()
|
||||
.encodeResourceToString(responseConsented), MediaType.APPLICATION_JSON));
|
||||
|
||||
var consentStatus = gicsConsentService.getTtpBroadConsentStatus("123456");
|
||||
assertThat(consentStatus).isEqualTo(TtpConsentStatus.BROAD_CONSENT_GIVEN);
|
||||
}
|
||||
|
||||
@Test
|
||||
void consentRevoced() {
|
||||
final Parameters responseRevoced = new Parameters().addParameter(
|
||||
new ParametersParameterComponent().setName("consented")
|
||||
.setValue(new BooleanType().setValue(false)));
|
||||
|
||||
mockRestServiceServer.expect(requestTo(
|
||||
"http://localhost:8090/ttp-fhir/fhir/gics" + GicsConsentService.IS_CONSENTED_ENDPOINT))
|
||||
.andRespond(withSuccess(
|
||||
appFhirConfig.fhirContext().newJsonParser().encodeResourceToString(responseRevoced),
|
||||
MediaType.APPLICATION_JSON));
|
||||
|
||||
var consentStatus = gicsConsentService.getTtpBroadConsentStatus("123456");
|
||||
assertThat(consentStatus).isEqualTo(TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED);
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
void gicsParameterInvalid() {
|
||||
final OperationOutcome responseErrorOutcome = new OperationOutcome().addIssue(
|
||||
new OperationOutcomeIssueComponent().setSeverity(IssueSeverity.ERROR)
|
||||
.setCode(IssueType.PROCESSING).setDiagnostics("Invalid policy parameter..."));
|
||||
|
||||
mockRestServiceServer.expect(
|
||||
requestTo(GICS_BASE_URI + GicsConsentService.IS_CONSENTED_ENDPOINT)).andRespond(
|
||||
withSuccess(appFhirConfig.fhirContext().newJsonParser()
|
||||
.encodeResourceToString(responseErrorOutcome), MediaType.APPLICATION_JSON));
|
||||
|
||||
var consentStatus = gicsConsentService.getTtpBroadConsentStatus("123456");
|
||||
assertThat(consentStatus).isEqualTo(TtpConsentStatus.FAILED_TO_ASK);
|
||||
}
|
||||
|
||||
@Test
|
||||
void buildRequestParameterCurrentPolicyStatesForPersonTest() {
|
||||
|
||||
String pid = "12345678";
|
||||
var result = GicsConsentService.buildRequestParameterCurrentPolicyStatesForPerson(
|
||||
gIcsConfigProperties, pid, Date.from(Instant.now()),
|
||||
gIcsConfigProperties.getGenomDeConsentDomainName());
|
||||
|
||||
assertThat(result.getParameter().size()).as("should contain 3 parameter resources")
|
||||
.isEqualTo(3);
|
||||
|
||||
assertThat(((StringType) result.getParameter("domain").getValue()).getValue()).isEqualTo(
|
||||
gIcsConfigProperties.getGenomDeConsentDomainName());
|
||||
assertThat(
|
||||
((Identifier) result.getParameter("personIdentifier").getValue()).getValue()).isEqualTo(
|
||||
pid);
|
||||
}
|
||||
|
||||
|
||||
}
|
@ -23,7 +23,6 @@ import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import de.ukw.ccc.bwhc.dto.Consent
|
||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import de.ukw.ccc.bwhc.dto.Patient
|
||||
import dev.dnpm.etl.processor.consent.TtpConsentStatus
|
||||
import dev.dnpm.etl.processor.CustomMediaType
|
||||
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||
import org.apache.kafka.clients.consumer.ConsumerRecord
|
||||
@ -35,7 +34,10 @@ import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.mockito.Mock
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.mockito.kotlin.*
|
||||
import org.mockito.kotlin.any
|
||||
import org.mockito.kotlin.anyValueClass
|
||||
import org.mockito.kotlin.times
|
||||
import org.mockito.kotlin.verify
|
||||
import java.util.*
|
||||
|
||||
@ExtendWith(MockitoExtension::class)
|
||||
@ -47,7 +49,7 @@ class KafkaInputListenerTest {
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Mock requestProcessor: RequestProcessor,
|
||||
@Mock requestProcessor: RequestProcessor
|
||||
) {
|
||||
this.requestProcessor = requestProcessor
|
||||
this.objectMapper = ObjectMapper()
|
||||
@ -92,10 +94,7 @@ class KafkaInputListenerTest {
|
||||
)
|
||||
)
|
||||
|
||||
verify(requestProcessor, times(1)).processDeletion(
|
||||
anyValueClass(),
|
||||
eq(TtpConsentStatus.UNKNOWN_CHECK_FILE)
|
||||
)
|
||||
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
|
||||
}
|
||||
|
||||
@Test
|
||||
@ -148,8 +147,7 @@ class KafkaInputListenerTest {
|
||||
Optional.empty()
|
||||
)
|
||||
)
|
||||
verify(requestProcessor, times(1)).processDeletion(anyValueClass(), anyValueClass(), eq(
|
||||
TtpConsentStatus.UNKNOWN_CHECK_FILE))
|
||||
verify(requestProcessor, times(1)).processDeletion(anyValueClass(), anyValueClass())
|
||||
}
|
||||
|
||||
@Test
|
||||
@ -180,8 +178,7 @@ class KafkaInputListenerTest {
|
||||
Optional.empty()
|
||||
)
|
||||
)
|
||||
verify(requestProcessor, times(0)).processDeletion(anyValueClass(), anyValueClass(), eq(
|
||||
TtpConsentStatus.UNKNOWN_CHECK_FILE))
|
||||
verify(requestProcessor, times(0)).processDeletion(anyValueClass(), anyValueClass())
|
||||
}
|
||||
|
||||
}
|
||||
|
@ -21,29 +21,21 @@ package dev.dnpm.etl.processor.input
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import de.ukw.ccc.bwhc.dto.*
|
||||
import de.ukw.ccc.bwhc.dto.Consent.Status
|
||||
import dev.dnpm.etl.processor.CustomMediaType
|
||||
import dev.dnpm.etl.processor.consent.ConsentByMtbFile
|
||||
import dev.dnpm.etl.processor.consent.GicsConsentService
|
||||
import dev.dnpm.etl.processor.consent.TtpConsentStatus
|
||||
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Nested
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.junit.jupiter.params.ParameterizedTest
|
||||
import org.junit.jupiter.params.provider.ValueSource
|
||||
import org.mockito.Mock
|
||||
import org.mockito.Mockito.times
|
||||
import org.mockito.Mockito.verify
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.mockito.kotlin.any
|
||||
import org.mockito.kotlin.anyValueClass
|
||||
import org.mockito.kotlin.whenever
|
||||
import org.springframework.core.io.ClassPathResource
|
||||
import org.springframework.http.MediaType
|
||||
import org.springframework.test.context.TestPropertySource
|
||||
import org.springframework.test.web.servlet.MockMvc
|
||||
import org.springframework.test.web.servlet.delete
|
||||
import org.springframework.test.web.servlet.post
|
||||
@ -61,22 +53,19 @@ class MtbFileRestControllerTest {
|
||||
|
||||
private lateinit var requestProcessor: RequestProcessor
|
||||
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Mock requestProcessor: RequestProcessor
|
||||
) {
|
||||
this.requestProcessor = requestProcessor
|
||||
val controller = MtbFileRestController(requestProcessor,
|
||||
ConsentByMtbFile()
|
||||
)
|
||||
val controller = MtbFileRestController(requestProcessor)
|
||||
this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build()
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldProcessPostRequest() {
|
||||
mockMvc.post("/mtbfile") {
|
||||
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Status.ACTIVE))
|
||||
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Consent.Status.ACTIVE))
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
}.andExpect {
|
||||
status {
|
||||
@ -90,8 +79,7 @@ class MtbFileRestControllerTest {
|
||||
@Test
|
||||
fun shouldProcessPostRequestWithRejectedConsent() {
|
||||
mockMvc.post("/mtbfile") {
|
||||
content =
|
||||
objectMapper.writeValueAsString(bwhcMtbFileContent(Status.REJECTED))
|
||||
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Consent.Status.REJECTED))
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
}.andExpect {
|
||||
status {
|
||||
@ -99,10 +87,7 @@ class MtbFileRestControllerTest {
|
||||
}
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processDeletion(
|
||||
anyValueClass(),
|
||||
org.mockito.kotlin.eq(TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED)
|
||||
)
|
||||
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
|
||||
}
|
||||
|
||||
@Test
|
||||
@ -113,100 +98,10 @@ class MtbFileRestControllerTest {
|
||||
}
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processDeletion(
|
||||
anyValueClass(),
|
||||
org.mockito.kotlin.eq(TtpConsentStatus.UNKNOWN_CHECK_FILE)
|
||||
)
|
||||
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
|
||||
}
|
||||
}
|
||||
|
||||
@TestPropertySource(
|
||||
properties = ["app.consent.gics.enabled=true",
|
||||
"app.consent.gics.gIcsBaseUri=http://localhost:8090/ttp-fhir/fhir/gics"]
|
||||
)
|
||||
@Nested
|
||||
inner class BwhcRequestsCheckConsentViaTtp {
|
||||
|
||||
private lateinit var mockMvc: MockMvc
|
||||
|
||||
private lateinit var requestProcessor: RequestProcessor
|
||||
|
||||
private lateinit var gicsConsentService: GicsConsentService
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Mock requestProcessor: RequestProcessor,
|
||||
@Mock gicsConsentService: GicsConsentService
|
||||
) {
|
||||
this.requestProcessor = requestProcessor
|
||||
val controller = MtbFileRestController(requestProcessor, gicsConsentService)
|
||||
this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build()
|
||||
this.gicsConsentService = gicsConsentService
|
||||
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@ValueSource(strings = ["ACTIVE", "REJECTED"])
|
||||
fun shouldProcessPostRequest(status: String) {
|
||||
|
||||
whenever(gicsConsentService.getTtpBroadConsentStatus(any())).thenReturn(TtpConsentStatus.BROAD_CONSENT_GIVEN)
|
||||
|
||||
mockMvc.post("/mtbfile") {
|
||||
content =
|
||||
objectMapper.writeValueAsString(bwhcMtbFileContent(Status.valueOf(status)))
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
}.andExpect {
|
||||
status {
|
||||
isAccepted()
|
||||
}
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
|
||||
}
|
||||
|
||||
|
||||
@ParameterizedTest
|
||||
@ValueSource(strings = ["ACTIVE", "REJECTED"])
|
||||
fun shouldProcessPostRequestWithRejectedConsent(status: String) {
|
||||
|
||||
whenever(gicsConsentService.getTtpBroadConsentStatus(any())).thenReturn(TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED)
|
||||
|
||||
mockMvc.post("/mtbfile") {
|
||||
content =
|
||||
objectMapper.writeValueAsString(bwhcMtbFileContent(Status.valueOf(status)))
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
}.andExpect {
|
||||
status {
|
||||
isAccepted()
|
||||
}
|
||||
}
|
||||
|
||||
// consent status from ttp should override file consent value
|
||||
verify(requestProcessor, times(1)).processDeletion(
|
||||
anyValueClass(),
|
||||
org.mockito.kotlin.eq(TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED)
|
||||
)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldProcessDeleteRequest() {
|
||||
|
||||
mockMvc.delete("/mtbfile/TEST_12345678").andExpect {
|
||||
status {
|
||||
isAccepted()
|
||||
}
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processDeletion(
|
||||
anyValueClass(),
|
||||
org.mockito.kotlin.eq(TtpConsentStatus.UNKNOWN_CHECK_FILE)
|
||||
)
|
||||
verify(gicsConsentService, times(0)).getTtpBroadConsentStatus(any())
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@Nested
|
||||
inner class BwhcRequestsWithAlias {
|
||||
|
||||
@ -219,16 +114,14 @@ class MtbFileRestControllerTest {
|
||||
@Mock requestProcessor: RequestProcessor
|
||||
) {
|
||||
this.requestProcessor = requestProcessor
|
||||
val controller = MtbFileRestController(requestProcessor,
|
||||
ConsentByMtbFile()
|
||||
)
|
||||
val controller = MtbFileRestController(requestProcessor)
|
||||
this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build()
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldProcessPostRequest() {
|
||||
mockMvc.post("/mtb") {
|
||||
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Status.ACTIVE))
|
||||
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Consent.Status.ACTIVE))
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
}.andExpect {
|
||||
status {
|
||||
@ -242,8 +135,7 @@ class MtbFileRestControllerTest {
|
||||
@Test
|
||||
fun shouldProcessPostRequestWithRejectedConsent() {
|
||||
mockMvc.post("/mtb") {
|
||||
content =
|
||||
objectMapper.writeValueAsString(bwhcMtbFileContent(Status.REJECTED))
|
||||
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Consent.Status.REJECTED))
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
}.andExpect {
|
||||
status {
|
||||
@ -251,11 +143,7 @@ class MtbFileRestControllerTest {
|
||||
}
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processDeletion(
|
||||
anyValueClass(), org.mockito.kotlin.eq(
|
||||
TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED
|
||||
)
|
||||
)
|
||||
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
|
||||
}
|
||||
|
||||
@Test
|
||||
@ -266,11 +154,7 @@ class MtbFileRestControllerTest {
|
||||
}
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processDeletion(
|
||||
anyValueClass(), org.mockito.kotlin.eq(
|
||||
TtpConsentStatus.UNKNOWN_CHECK_FILE
|
||||
)
|
||||
)
|
||||
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
|
||||
}
|
||||
}
|
||||
|
||||
@ -283,21 +167,16 @@ class MtbFileRestControllerTest {
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Mock requestProcessor: RequestProcessor,
|
||||
@Mock gicsConsentService: GicsConsentService
|
||||
@Mock requestProcessor: RequestProcessor
|
||||
) {
|
||||
this.requestProcessor = requestProcessor
|
||||
val controller = MtbFileRestController(requestProcessor,
|
||||
gicsConsentService
|
||||
)
|
||||
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)
|
||||
val mtbFileContent = ClassPathResource("mv64e-mtb-fake-patient.json").inputStream.readAllBytes().toString(Charsets.UTF_8)
|
||||
|
||||
mockMvc.post("/mtb") {
|
||||
content = mtbFileContent
|
||||
@ -314,7 +193,7 @@ class MtbFileRestControllerTest {
|
||||
}
|
||||
|
||||
companion object {
|
||||
fun bwhcMtbFileContent(consentStatus: Status) = MtbFile.builder()
|
||||
fun bwhcMtbFileContent(consentStatus: Consent.Status) = MtbFile.builder()
|
||||
.withPatient(
|
||||
Patient.builder()
|
||||
.withId("TEST_12345678")
|
||||
|
@ -19,18 +19,11 @@
|
||||
|
||||
package dev.dnpm.etl.processor.pseudonym
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import de.ukw.ccc.bwhc.dto.*
|
||||
import de.ukw.ccc.bwhc.dto.Patient
|
||||
import dev.dnpm.etl.processor.config.AppConfigProperties
|
||||
import dev.dnpm.etl.processor.config.GIcsConfigProperties
|
||||
import dev.dnpm.etl.processor.config.JacksonConfig
|
||||
import dev.dnpm.etl.processor.services.ConsentProcessor
|
||||
import dev.dnpm.etl.processor.services.ConsentProcessorTest
|
||||
import dev.pcvolkmer.mv64e.mtb.*
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.hl7.fhir.r4.model.Bundle
|
||||
import org.junit.jupiter.api.Nested
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.assertThrows
|
||||
@ -46,9 +39,6 @@ import java.util.*
|
||||
|
||||
@ExtendWith(MockitoExtension::class)
|
||||
class ExtensionsTest {
|
||||
fun getObjectMapper(): ObjectMapper {
|
||||
return JacksonConfig().objectMapper()
|
||||
}
|
||||
|
||||
@Nested
|
||||
inner class UsingBwhcDatamodel {
|
||||
@ -56,14 +46,13 @@ class ExtensionsTest {
|
||||
val FAKE_MTB_FILE_PATH = "fake_MTBFile.json"
|
||||
val CLEAN_PATIENT_ID = "5dad2f0b-49c6-47d8-a952-7b9e9e0f7549"
|
||||
|
||||
|
||||
private fun fakeMtbFile(): MtbFile {
|
||||
val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
|
||||
return getObjectMapper().readValue(mtbFile, MtbFile::class.java)
|
||||
return ObjectMapper().readValue(mtbFile, MtbFile::class.java)
|
||||
}
|
||||
|
||||
private fun MtbFile.serialized(): String {
|
||||
return getObjectMapper().writeValueAsString(this)
|
||||
return ObjectMapper().writeValueAsString(this)
|
||||
}
|
||||
|
||||
@Test
|
||||
@ -97,9 +86,7 @@ class ExtensionsTest {
|
||||
mtbFile.pseudonymizeWith(pseudonymizeService)
|
||||
mtbFile.anonymizeContentWith(pseudonymizeService)
|
||||
|
||||
val pattern =
|
||||
"\"[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}\"".toRegex()
|
||||
.toPattern()
|
||||
val pattern = "\"[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}\"".toRegex().toPattern()
|
||||
val matcher = pattern.matcher(mtbFile.serialized())
|
||||
|
||||
assertThrows<IllegalStateException> {
|
||||
@ -224,11 +211,11 @@ class ExtensionsTest {
|
||||
|
||||
private fun fakeMtbFile(): Mtb {
|
||||
val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
|
||||
return getObjectMapper().readValue(mtbFile, Mtb::class.java)
|
||||
return ObjectMapper().readValue(mtbFile, Mtb::class.java)
|
||||
}
|
||||
|
||||
private fun Mtb.serialized(): String {
|
||||
return getObjectMapper().writeValueAsString(this)
|
||||
return ObjectMapper().writeValueAsString(this)
|
||||
}
|
||||
|
||||
@Test
|
||||
@ -239,8 +226,6 @@ class ExtensionsTest {
|
||||
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||
|
||||
val mtbFile = fakeMtbFile()
|
||||
mtbFile.ensureMetaDataIsInitialized()
|
||||
addConsentData(mtbFile)
|
||||
|
||||
mtbFile.pseudonymizeWith(pseudonymizeService)
|
||||
|
||||
@ -248,25 +233,6 @@ class ExtensionsTest {
|
||||
assertThat(mtbFile.serialized()).doesNotContain(CLEAN_PATIENT_ID)
|
||||
}
|
||||
|
||||
private fun addConsentData(mtbFile: Mtb) {
|
||||
val gIcsConfigProperties = GIcsConfigProperties("", "", "", true)
|
||||
val appConfigProperties = AppConfigProperties(null, emptyList())
|
||||
|
||||
val bundle = Bundle()
|
||||
val dummyConsent = ConsentProcessorTest.getDummyGenomDeConsent()
|
||||
dummyConsent.patient.reference = "Patient/$CLEAN_PATIENT_ID"
|
||||
bundle.addEntry().resource = dummyConsent
|
||||
|
||||
ConsentProcessor(
|
||||
appConfigProperties,
|
||||
gIcsConfigProperties,
|
||||
JacksonConfig().objectMapper(),
|
||||
FhirContext.forR4(),
|
||||
null
|
||||
).embedBroadConsentResources(mtbFile, bundle)
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldNotThrowExceptionOnNullValues(@Mock pseudonymizeService: PseudonymizeService) {
|
||||
doAnswer {
|
||||
|
@ -72,7 +72,7 @@ class PseudonymizeServiceTest {
|
||||
|
||||
@Test
|
||||
fun sanitizeFileName(@Mock generator: GpasPseudonymGenerator) {
|
||||
val result= GpasPseudonymGenerator.sanitizeValue("l://a\\bs;1*2?3>")
|
||||
val result = GpasPseudonymGenerator.sanitizeValue("l://a\\bs;1*2?3>")
|
||||
|
||||
assertThat(result).isEqualTo("l___a_bs_1_2_3_")
|
||||
}
|
||||
@ -90,4 +90,10 @@ class PseudonymizeServiceTest {
|
||||
assertThat(mtbFile.patient.id).isEqualTo("UNKNOWN_123")
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldReturnDifferentValues() {
|
||||
val ag = AnonymizingGenerator()
|
||||
val tan = ag.generateGenomDeTan("12345")
|
||||
assertThat(tan).hasSize(64)
|
||||
}
|
||||
}
|
@ -1,168 +0,0 @@
|
||||
package dev.dnpm.etl.processor.services
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import dev.dnpm.etl.processor.config.AppConfigProperties
|
||||
import dev.dnpm.etl.processor.config.GIcsConfigProperties
|
||||
import dev.dnpm.etl.processor.config.JacksonConfig
|
||||
import dev.dnpm.etl.processor.consent.GicsConsentService
|
||||
import dev.pcvolkmer.mv64e.mtb.*
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.hl7.fhir.r4.model.Bundle
|
||||
import org.hl7.fhir.r4.model.CodeableConcept
|
||||
import org.hl7.fhir.r4.model.Coding
|
||||
import org.hl7.fhir.r4.model.Consent
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.junit.jupiter.params.ParameterizedTest
|
||||
import org.junit.jupiter.params.provider.CsvSource
|
||||
import org.mockito.Mock
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.mockito.kotlin.any
|
||||
import org.mockito.kotlin.doAnswer
|
||||
import org.mockito.kotlin.whenever
|
||||
import org.springframework.core.io.ClassPathResource
|
||||
import java.io.IOException
|
||||
import java.io.InputStream
|
||||
import java.time.Instant
|
||||
import java.time.OffsetDateTime
|
||||
import java.util.*
|
||||
|
||||
@ExtendWith(MockitoExtension::class)
|
||||
class ConsentProcessorTest {
|
||||
|
||||
private lateinit var appConfigProperties: AppConfigProperties
|
||||
private lateinit var gicsConsentService: GicsConsentService
|
||||
private lateinit var objectMapper: ObjectMapper
|
||||
private lateinit var gIcsConfigProperties: GIcsConfigProperties
|
||||
private lateinit var fhirContext: FhirContext
|
||||
private lateinit var consentProcessor: ConsentProcessor
|
||||
|
||||
@BeforeEach
|
||||
fun setups(
|
||||
@Mock gicsConsentService: GicsConsentService,
|
||||
) {
|
||||
|
||||
this.gIcsConfigProperties = GIcsConfigProperties(null, null, null, true)
|
||||
val jacksonConfig = JacksonConfig()
|
||||
this.objectMapper = jacksonConfig.objectMapper()
|
||||
this.fhirContext = JacksonConfig.fhirContext()
|
||||
this.gicsConsentService = gicsConsentService
|
||||
this.appConfigProperties = AppConfigProperties(null, emptyList())
|
||||
this.consentProcessor =
|
||||
ConsentProcessor(
|
||||
appConfigProperties,
|
||||
gIcsConfigProperties,
|
||||
objectMapper,
|
||||
fhirContext,
|
||||
gicsConsentService
|
||||
)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun consentOk() {
|
||||
assertThat(consentProcessor.toString()).isNotNull
|
||||
// prep gICS response
|
||||
doAnswer { getDummyBroadConsentBundle() }.whenever(gicsConsentService)
|
||||
.getBroadConsent(any(), any())
|
||||
doAnswer { Bundle() }.whenever(gicsConsentService)
|
||||
.getGenomDeConsent(any(), any())
|
||||
|
||||
val inputMtb = Mtb.builder()
|
||||
.patient(Patient.builder().id("d611d429-5003-11f0-a144-661e92ac9503").build()).build()
|
||||
val checkResult = consentProcessor.consentGatedCheckAndTryEmbedding(inputMtb)
|
||||
|
||||
assertThat(checkResult).isTrue
|
||||
assertThat(inputMtb.metadata.researchConsents).hasSize(13)
|
||||
}
|
||||
|
||||
companion object {
|
||||
fun getDummyGenomDeConsent(): Consent {
|
||||
val consent = Consent()
|
||||
consent.id = "consent 1 id"
|
||||
consent.patient.reference = "Patient/1234-pat1"
|
||||
|
||||
consent.provision.setType(
|
||||
Consent.ConsentProvisionType.fromCode(
|
||||
"deny"
|
||||
)
|
||||
)
|
||||
consent.provision.period.start =
|
||||
Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
|
||||
consent.provision.period.end =
|
||||
Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
|
||||
|
||||
val addProvision1 = consent.provision.addProvision()
|
||||
addProvision1.setType(Consent.ConsentProvisionType.fromCode("permit"))
|
||||
addProvision1.period.start = Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
|
||||
addProvision1.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
|
||||
addProvision1.code.addLast(
|
||||
CodeableConcept(
|
||||
Coding(
|
||||
"https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"Teilnahme",
|
||||
"Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
|
||||
)
|
||||
)
|
||||
)
|
||||
|
||||
val addProvision2 = consent.provision.addProvision()
|
||||
addProvision2.setType(Consent.ConsentProvisionType.fromCode("deny"))
|
||||
addProvision2.period.start = Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
|
||||
addProvision2.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
|
||||
addProvision2.code.addLast(
|
||||
CodeableConcept(
|
||||
Coding(
|
||||
"https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"Rekontaktierung",
|
||||
"Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
|
||||
)
|
||||
)
|
||||
)
|
||||
return consent
|
||||
}
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@CsvSource(
|
||||
"2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2025-07-23T00:00:00+02:00,PERMIT,expect permit",
|
||||
"2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2025-06-23T00:00:00+02:00,PERMIT,expect permit date is exactly on start",
|
||||
"2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2055-06-23T00:00:00+02:00,PERMIT,expect permit date is exactly on end",
|
||||
"2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2021-06-23T00:00:00+02:00,NULL,date is before start",
|
||||
"2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2060-06-23T00:00:00+02:00,NULL,date is after end",
|
||||
"2.16.840.1.113883.3.1937.777.24.5.3.8,XXXX,2025-07-23T00:00:00+02:00,NULL,system not found - therefore expect NULL",
|
||||
"2.16.840.1.113883.3.1937.777.24.5.3.27,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2025-07-23T00:00:00+02:00,DENY,provision is denied"
|
||||
)
|
||||
fun getProvisionTypeByPolicyCode(
|
||||
code: String?, system: String?, timeStamp: String, expected: String?,
|
||||
desc: String?
|
||||
) {
|
||||
val testData = getDummyBroadConsentBundle()
|
||||
|
||||
val requestDate = Date.from(OffsetDateTime.parse(timeStamp).toInstant())
|
||||
|
||||
val result: Consent.ConsentProvisionType =
|
||||
consentProcessor.getProvisionTypeByPolicyCode(testData, code, system, requestDate)
|
||||
assertThat(result).isNotNull()
|
||||
|
||||
|
||||
assertThat(result).`as`(desc)
|
||||
.isEqualTo(Consent.ConsentProvisionType.valueOf(expected!!))
|
||||
}
|
||||
|
||||
fun getDummyBroadConsentBundle(): Bundle {
|
||||
val bundle: InputStream?
|
||||
try {
|
||||
bundle = ClassPathResource(
|
||||
"fake_broadConsent_gics_response_permit.json"
|
||||
).getInputStream()
|
||||
} catch (e: IOException) {
|
||||
throw RuntimeException(e)
|
||||
}
|
||||
|
||||
return FhirContext.forR4().newJsonParser()
|
||||
.parseResource<Bundle>(Bundle::class.java, bundle)
|
||||
}
|
||||
|
||||
}
|
@ -25,8 +25,6 @@ import dev.dnpm.etl.processor.Fingerprint
|
||||
import dev.dnpm.etl.processor.PatientId
|
||||
import dev.dnpm.etl.processor.PatientPseudonym
|
||||
import dev.dnpm.etl.processor.config.AppConfigProperties
|
||||
import dev.dnpm.etl.processor.consent.GicsConsentService
|
||||
import dev.dnpm.etl.processor.consent.TtpConsentStatus
|
||||
import dev.dnpm.etl.processor.monitoring.Request
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import dev.dnpm.etl.processor.monitoring.RequestType
|
||||
@ -60,7 +58,7 @@ class RequestProcessorTest {
|
||||
private lateinit var requestService: RequestService
|
||||
private lateinit var applicationEventPublisher: ApplicationEventPublisher
|
||||
private lateinit var appConfigProperties: AppConfigProperties
|
||||
private lateinit var consentProcessor: ConsentProcessor
|
||||
|
||||
private lateinit var requestProcessor: RequestProcessor
|
||||
|
||||
@BeforeEach
|
||||
@ -69,8 +67,7 @@ class RequestProcessorTest {
|
||||
@Mock transformationService: TransformationService,
|
||||
@Mock sender: RestMtbFileSender,
|
||||
@Mock requestService: RequestService,
|
||||
@Mock applicationEventPublisher: ApplicationEventPublisher,
|
||||
@Mock consentProcessor: ConsentProcessor
|
||||
@Mock applicationEventPublisher: ApplicationEventPublisher
|
||||
) {
|
||||
this.pseudonymizeService = pseudonymizeService
|
||||
this.transformationService = transformationService
|
||||
@ -78,7 +75,6 @@ class RequestProcessorTest {
|
||||
this.requestService = requestService
|
||||
this.applicationEventPublisher = applicationEventPublisher
|
||||
this.appConfigProperties = AppConfigProperties(null)
|
||||
this.consentProcessor = consentProcessor
|
||||
|
||||
val objectMapper = ObjectMapper()
|
||||
|
||||
@ -89,8 +85,7 @@ class RequestProcessorTest {
|
||||
requestService,
|
||||
objectMapper,
|
||||
applicationEventPublisher,
|
||||
appConfigProperties,
|
||||
consentProcessor
|
||||
appConfigProperties
|
||||
)
|
||||
}
|
||||
|
||||
@ -348,10 +343,7 @@ class RequestProcessorTest {
|
||||
MtbFileSender.Response(status = RequestStatus.UNKNOWN)
|
||||
}.whenever(sender).send(any<DeleteRequest>())
|
||||
|
||||
this.requestProcessor.processDeletion(
|
||||
TEST_PATIENT_ID,
|
||||
isConsented = TtpConsentStatus.UNKNOWN_CHECK_FILE
|
||||
)
|
||||
this.requestProcessor.processDeletion(TEST_PATIENT_ID)
|
||||
|
||||
val requestCaptor = argumentCaptor<Request>()
|
||||
verify(requestService, times(1)).save(requestCaptor.capture())
|
||||
@ -369,10 +361,7 @@ class RequestProcessorTest {
|
||||
MtbFileSender.Response(status = RequestStatus.SUCCESS)
|
||||
}.whenever(sender).send(any<DeleteRequest>())
|
||||
|
||||
this.requestProcessor.processDeletion(
|
||||
TEST_PATIENT_ID,
|
||||
isConsented = TtpConsentStatus.UNKNOWN_CHECK_FILE
|
||||
)
|
||||
this.requestProcessor.processDeletion(TEST_PATIENT_ID)
|
||||
|
||||
val eventCaptor = argumentCaptor<ResponseEvent>()
|
||||
verify(applicationEventPublisher, times(1)).publishEvent(eventCaptor.capture())
|
||||
@ -390,10 +379,7 @@ class RequestProcessorTest {
|
||||
MtbFileSender.Response(status = RequestStatus.ERROR)
|
||||
}.whenever(sender).send(any<DeleteRequest>())
|
||||
|
||||
this.requestProcessor.processDeletion(
|
||||
TEST_PATIENT_ID,
|
||||
isConsented = TtpConsentStatus.UNKNOWN_CHECK_FILE
|
||||
)
|
||||
this.requestProcessor.processDeletion(TEST_PATIENT_ID)
|
||||
|
||||
val eventCaptor = argumentCaptor<ResponseEvent>()
|
||||
verify(applicationEventPublisher, times(1)).publishEvent(eventCaptor.capture())
|
||||
@ -405,10 +391,7 @@ class RequestProcessorTest {
|
||||
fun testShouldSendDeleteRequestWithPseudonymErrorAndSaveErrorRequestStatus() {
|
||||
doThrow(RuntimeException()).whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||
|
||||
this.requestProcessor.processDeletion(
|
||||
TEST_PATIENT_ID,
|
||||
isConsented = TtpConsentStatus.UNKNOWN_CHECK_FILE
|
||||
)
|
||||
this.requestProcessor.processDeletion(TEST_PATIENT_ID)
|
||||
|
||||
val requestCaptor = argumentCaptor<Request>()
|
||||
verify(requestService, times(1)).save(requestCaptor.capture())
|
||||
|
@ -19,23 +19,14 @@
|
||||
|
||||
package dev.dnpm.etl.processor.services
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import de.ukw.ccc.bwhc.dto.Consent
|
||||
import de.ukw.ccc.bwhc.dto.Diagnosis
|
||||
import de.ukw.ccc.bwhc.dto.Icd10
|
||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import dev.dnpm.etl.processor.config.JacksonConfig
|
||||
import dev.pcvolkmer.mv64e.mtb.ConsentProvision
|
||||
import dev.pcvolkmer.mv64e.mtb.ModelProjectConsent
|
||||
import dev.pcvolkmer.mv64e.mtb.ModelProjectConsentPurpose
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Test
|
||||
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||
import dev.pcvolkmer.mv64e.mtb.MvhMetadata
|
||||
import dev.pcvolkmer.mv64e.mtb.Provision
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource
|
||||
import java.time.Instant
|
||||
import java.util.Date
|
||||
|
||||
class TransformationServiceTest {
|
||||
|
||||
@ -44,7 +35,7 @@ class TransformationServiceTest {
|
||||
@BeforeEach
|
||||
fun setup() {
|
||||
this.service = TransformationService(
|
||||
JacksonConfig().objectMapper(), listOf(
|
||||
ObjectMapper(), listOf(
|
||||
Transformation.of("consent.status") from Consent.Status.ACTIVE to Consent.Status.REJECTED,
|
||||
Transformation.of("diagnoses[*].icd10.version") from "2013" to "2014",
|
||||
)
|
||||
@ -101,59 +92,4 @@ class TransformationServiceTest {
|
||||
assertThat(actual.consent.status).isEqualTo(Consent.Status.REJECTED)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldTransformConsentValues() {
|
||||
val mtbFile = MtbFile.builder().withDiagnoses(
|
||||
listOf(
|
||||
Diagnosis.builder().withId("1234").withIcd10(Icd10("F79.9").also {
|
||||
it.version = "2013"
|
||||
}).build(),
|
||||
Diagnosis.builder().withId("5678").withIcd10(Icd10("F79.8").also {
|
||||
it.version = "2019"
|
||||
}).build()
|
||||
)
|
||||
).build()
|
||||
|
||||
val actual = this.service.transform(mtbFile)
|
||||
|
||||
assertThat(actual).isNotNull
|
||||
assertThat(actual.diagnoses[0].icd10.code).isEqualTo("F79.9")
|
||||
assertThat(actual.diagnoses[0].icd10.version).isEqualTo("2014")
|
||||
assertThat(actual.diagnoses[1].icd10.code).isEqualTo("F79.8")
|
||||
assertThat(actual.diagnoses[1].icd10.version).isEqualTo("2019")
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldTransformConsent() {
|
||||
val mvhMetadata = MvhMetadata.builder().transferTan("transfertan12345").build()
|
||||
|
||||
assertThat(mvhMetadata).isNotNull
|
||||
mvhMetadata.modelProjectConsent =
|
||||
ModelProjectConsent.builder().date(Date.from(Instant.parse("2025-06-23T00:00:00.00Z")))
|
||||
.version("1").provisions(
|
||||
listOf(
|
||||
Provision.builder().type(ConsentProvision.PERMIT)
|
||||
.purpose(ModelProjectConsentPurpose.SEQUENCING)
|
||||
.date(Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))).build(),
|
||||
Provision.builder().type(ConsentProvision.PERMIT)
|
||||
.purpose(ModelProjectConsentPurpose.REIDENTIFICATION)
|
||||
.date(Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))).build(),
|
||||
Provision.builder().type(ConsentProvision.DENY)
|
||||
.purpose(ModelProjectConsentPurpose.CASE_IDENTIFICATION)
|
||||
.date(Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))).build()
|
||||
)
|
||||
).build()
|
||||
val consent = ConsentProcessorTest.getDummyGenomDeConsent()
|
||||
|
||||
mvhMetadata.researchConsents = mutableListOf()
|
||||
mvhMetadata.researchConsents.add(mapOf(consent.id to consent as IBaseResource))
|
||||
|
||||
val mtbFile = Mtb.builder().metadata(mvhMetadata).build()
|
||||
|
||||
val transformed = service.transform(mtbFile)
|
||||
assertThat(transformed.metadata.modelProjectConsent.date).isNotNull
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,333 +0,0 @@
|
||||
{
|
||||
"resourceType": "Bundle",
|
||||
"type": "collection",
|
||||
"entry": [
|
||||
{
|
||||
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/24673204-50e1-11f0-a144-661e92ac9503",
|
||||
"resource": {
|
||||
"resourceType": "Consent",
|
||||
"id": "24673204-50e1-11f0-a144-661e92ac9503",
|
||||
"meta": {
|
||||
"lastUpdated": "2025-06-24T11:58:27.178+02:00",
|
||||
"profile": [
|
||||
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
|
||||
]
|
||||
},
|
||||
"extension": [
|
||||
{
|
||||
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
|
||||
"extension": [
|
||||
{
|
||||
"url": "domain",
|
||||
"valueReference": {
|
||||
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
|
||||
}
|
||||
},
|
||||
{
|
||||
"url": "status",
|
||||
"valueCoding": {
|
||||
"system": "http://hl7.org/fhir/publication-status",
|
||||
"code": "active"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"status": "active",
|
||||
"scope": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
|
||||
"code": "research"
|
||||
}
|
||||
]
|
||||
},
|
||||
"category": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://loinc.org",
|
||||
"code": "59284-0"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
|
||||
"code": "policy"
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"patient": {
|
||||
"reference": "Patient/2466d49b-50e1-11f0-a144-661e92ac9503",
|
||||
"display": "Patienten-ID 999999"
|
||||
},
|
||||
"dateTime": "2025-06-24T00:00:00+02:00",
|
||||
"organization": [
|
||||
{
|
||||
"display": "GenomDE_MV"
|
||||
}
|
||||
],
|
||||
"sourceReference": {
|
||||
"reference": "QuestionnaireResponse/24670c77-50e1-11f0-a144-661e92ac9503"
|
||||
},
|
||||
"policyRule": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Teilnahme",
|
||||
"display": "Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
|
||||
}
|
||||
]
|
||||
},
|
||||
"provision": {
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"provision": [
|
||||
{
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"code": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Teilnahme",
|
||||
"display": "Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
},
|
||||
{
|
||||
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/24673913-50e1-11f0-a144-661e92ac9503",
|
||||
"resource": {
|
||||
"resourceType": "Consent",
|
||||
"id": "24673913-50e1-11f0-a144-661e92ac9503",
|
||||
"meta": {
|
||||
"lastUpdated": "2025-06-24T11:58:27.194+02:00",
|
||||
"profile": [
|
||||
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
|
||||
]
|
||||
},
|
||||
"extension": [
|
||||
{
|
||||
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
|
||||
"extension": [
|
||||
{
|
||||
"url": "domain",
|
||||
"valueReference": {
|
||||
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
|
||||
}
|
||||
},
|
||||
{
|
||||
"url": "status",
|
||||
"valueCoding": {
|
||||
"system": "http://hl7.org/fhir/publication-status",
|
||||
"code": "active"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"status": "active",
|
||||
"scope": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
|
||||
"code": "research"
|
||||
}
|
||||
]
|
||||
},
|
||||
"category": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://loinc.org",
|
||||
"code": "59284-0"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
|
||||
"code": "policy"
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"patient": {
|
||||
"reference": "Patient/2466d49b-50e1-11f0-a144-661e92ac9503",
|
||||
"display": "Patienten-ID 999999"
|
||||
},
|
||||
"dateTime": "2025-06-24T00:00:00+02:00",
|
||||
"organization": [
|
||||
{
|
||||
"display": "GenomDE_MV"
|
||||
}
|
||||
],
|
||||
"sourceReference": {
|
||||
"reference": "QuestionnaireResponse/24670c77-50e1-11f0-a144-661e92ac9503"
|
||||
},
|
||||
"policyRule": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Fallidentifizierung",
|
||||
"display": "Fallidentifizierung zum fachlichen Austausch unter Behandelnden"
|
||||
}
|
||||
]
|
||||
},
|
||||
"provision": {
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"provision": [
|
||||
{
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"code": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Fallidentifizierung",
|
||||
"display": "Fallidentifizierung zum fachlichen Austausch unter Behandelnden"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
},
|
||||
{
|
||||
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/24673da9-50e1-11f0-a144-661e92ac9503",
|
||||
"resource": {
|
||||
"resourceType": "Consent",
|
||||
"id": "24673da9-50e1-11f0-a144-661e92ac9503",
|
||||
"meta": {
|
||||
"lastUpdated": "2025-06-24T11:58:27.211+02:00",
|
||||
"profile": [
|
||||
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
|
||||
]
|
||||
},
|
||||
"extension": [
|
||||
{
|
||||
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
|
||||
"extension": [
|
||||
{
|
||||
"url": "domain",
|
||||
"valueReference": {
|
||||
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
|
||||
}
|
||||
},
|
||||
{
|
||||
"url": "status",
|
||||
"valueCoding": {
|
||||
"system": "http://hl7.org/fhir/publication-status",
|
||||
"code": "active"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"status": "active",
|
||||
"scope": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
|
||||
"code": "research"
|
||||
}
|
||||
]
|
||||
},
|
||||
"category": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://loinc.org",
|
||||
"code": "59284-0"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
|
||||
"code": "policy"
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"patient": {
|
||||
"reference": "Patient/2466d49b-50e1-11f0-a144-661e92ac9503",
|
||||
"display": "Patienten-ID 999999"
|
||||
},
|
||||
"dateTime": "2025-06-24T00:00:00+02:00",
|
||||
"organization": [
|
||||
{
|
||||
"display": "GenomDE_MV"
|
||||
}
|
||||
],
|
||||
"sourceReference": {
|
||||
"reference": "QuestionnaireResponse/24670c77-50e1-11f0-a144-661e92ac9503"
|
||||
},
|
||||
"policyRule": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Rekontaktierung",
|
||||
"display": "Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
|
||||
}
|
||||
]
|
||||
},
|
||||
"provision": {
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"provision": [
|
||||
{
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"code": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Rekontaktierung",
|
||||
"display": "Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
@ -1,333 +0,0 @@
|
||||
{
|
||||
"resourceType": "Bundle",
|
||||
"type": "collection",
|
||||
"entry": [
|
||||
{
|
||||
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/121a8368-50e1-11f0-a144-661e92ac9503",
|
||||
"resource": {
|
||||
"resourceType": "Consent",
|
||||
"id": "121a8368-50e1-11f0-a144-661e92ac9503",
|
||||
"meta": {
|
||||
"lastUpdated": "2025-06-24T11:55:42.079+02:00",
|
||||
"profile": [
|
||||
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
|
||||
]
|
||||
},
|
||||
"extension": [
|
||||
{
|
||||
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
|
||||
"extension": [
|
||||
{
|
||||
"url": "domain",
|
||||
"valueReference": {
|
||||
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
|
||||
}
|
||||
},
|
||||
{
|
||||
"url": "status",
|
||||
"valueCoding": {
|
||||
"system": "http://hl7.org/fhir/publication-status",
|
||||
"code": "active"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"status": "active",
|
||||
"scope": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
|
||||
"code": "research"
|
||||
}
|
||||
]
|
||||
},
|
||||
"category": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://loinc.org",
|
||||
"code": "59284-0"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
|
||||
"code": "policy"
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"patient": {
|
||||
"reference": "Patient/12194791-50e1-11f0-a144-661e92ac9503",
|
||||
"display": "Patienten-ID 12345678"
|
||||
},
|
||||
"dateTime": "2025-06-24T00:00:00+02:00",
|
||||
"organization": [
|
||||
{
|
||||
"display": "GenomDE_MV"
|
||||
}
|
||||
],
|
||||
"sourceReference": {
|
||||
"reference": "QuestionnaireResponse/1219ca42-50e1-11f0-a144-661e92ac9503"
|
||||
},
|
||||
"policyRule": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Teilnahme",
|
||||
"display": "Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
|
||||
}
|
||||
]
|
||||
},
|
||||
"provision": {
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"provision": [
|
||||
{
|
||||
"type": "permit",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"code": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Teilnahme",
|
||||
"display": "Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
},
|
||||
{
|
||||
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/121aad40-50e1-11f0-a144-661e92ac9503",
|
||||
"resource": {
|
||||
"resourceType": "Consent",
|
||||
"id": "121aad40-50e1-11f0-a144-661e92ac9503",
|
||||
"meta": {
|
||||
"lastUpdated": "2025-06-24T11:55:42.096+02:00",
|
||||
"profile": [
|
||||
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
|
||||
]
|
||||
},
|
||||
"extension": [
|
||||
{
|
||||
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
|
||||
"extension": [
|
||||
{
|
||||
"url": "domain",
|
||||
"valueReference": {
|
||||
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
|
||||
}
|
||||
},
|
||||
{
|
||||
"url": "status",
|
||||
"valueCoding": {
|
||||
"system": "http://hl7.org/fhir/publication-status",
|
||||
"code": "active"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"status": "active",
|
||||
"scope": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
|
||||
"code": "research"
|
||||
}
|
||||
]
|
||||
},
|
||||
"category": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://loinc.org",
|
||||
"code": "59284-0"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
|
||||
"code": "policy"
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"patient": {
|
||||
"reference": "Patient/12194791-50e1-11f0-a144-661e92ac9503",
|
||||
"display": "Patienten-ID 12345678"
|
||||
},
|
||||
"dateTime": "2025-06-24T00:00:00+02:00",
|
||||
"organization": [
|
||||
{
|
||||
"display": "GenomDE_MV"
|
||||
}
|
||||
],
|
||||
"sourceReference": {
|
||||
"reference": "QuestionnaireResponse/1219ca42-50e1-11f0-a144-661e92ac9503"
|
||||
},
|
||||
"policyRule": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Fallidentifizierung",
|
||||
"display": "Fallidentifizierung zum fachlichen Austausch unter Behandelnden"
|
||||
}
|
||||
]
|
||||
},
|
||||
"provision": {
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"provision": [
|
||||
{
|
||||
"type": "permit",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"code": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Fallidentifizierung",
|
||||
"display": "Fallidentifizierung zum fachlichen Austausch unter Behandelnden"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
},
|
||||
{
|
||||
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/121ac5f8-50e1-11f0-a144-661e92ac9503",
|
||||
"resource": {
|
||||
"resourceType": "Consent",
|
||||
"id": "121ac5f8-50e1-11f0-a144-661e92ac9503",
|
||||
"meta": {
|
||||
"lastUpdated": "2025-06-24T11:55:42.110+02:00",
|
||||
"profile": [
|
||||
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
|
||||
]
|
||||
},
|
||||
"extension": [
|
||||
{
|
||||
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
|
||||
"extension": [
|
||||
{
|
||||
"url": "domain",
|
||||
"valueReference": {
|
||||
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
|
||||
}
|
||||
},
|
||||
{
|
||||
"url": "status",
|
||||
"valueCoding": {
|
||||
"system": "http://hl7.org/fhir/publication-status",
|
||||
"code": "active"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"status": "active",
|
||||
"scope": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
|
||||
"code": "research"
|
||||
}
|
||||
]
|
||||
},
|
||||
"category": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://loinc.org",
|
||||
"code": "59284-0"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
|
||||
"code": "policy"
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"patient": {
|
||||
"reference": "Patient/12194791-50e1-11f0-a144-661e92ac9503",
|
||||
"display": "Patienten-ID 12345678"
|
||||
},
|
||||
"dateTime": "2025-06-24T00:00:00+02:00",
|
||||
"organization": [
|
||||
{
|
||||
"display": "GenomDE_MV"
|
||||
}
|
||||
],
|
||||
"sourceReference": {
|
||||
"reference": "QuestionnaireResponse/1219ca42-50e1-11f0-a144-661e92ac9503"
|
||||
},
|
||||
"policyRule": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Rekontaktierung",
|
||||
"display": "Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
|
||||
}
|
||||
]
|
||||
},
|
||||
"provision": {
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"provision": [
|
||||
{
|
||||
"type": "permit",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"code": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Rekontaktierung",
|
||||
"display": "Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
Reference in New Issue
Block a user