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0
mirror of https://github.com/pcvolkmer/etl-processor.git synced 2025-07-01 22:22:53 +00:00

34 Commits

Author SHA1 Message Date
a31d2b4bcc build: bump version 2024-02-05 07:47:17 +01:00
67d5fb4c67 docs: mention quality report page access restriction 2024-02-05 07:29:47 +01:00
329be65d1a feat: forbid access to report if not logged in 2024-02-05 07:18:31 +01:00
91fe3d1c23 docs: add example login image 2024-02-01 18:30:02 +01:00
f4b86ce2ea docs: add OIDC configuration options to README.md 2024-02-01 18:28:33 +01:00
19d0daa442 docs: move README.md to bindings folder 2024-02-01 17:00:16 +01:00
cc9811d11d docs: move README.md to bindings folder 2024-02-01 16:59:23 +01:00
8ce5b06823 fix: make security config optional for login controller 2024-02-01 16:54:41 +01:00
3cc34fb30b feat: usage of CA certificate files within image/container 2024-02-01 16:45:22 +01:00
17e04a3f89 feat: add basic support for OIDC login 2024-01-31 15:57:16 +01:00
f71a775e12 chore: update spring boot to version 3.2.2 2024-01-23 01:04:35 +01:00
45c83e943b docs: Add information about other reference IDs anonymization 2024-01-22 10:33:27 +01:00
6dcbfde62e test: add tests for TokenService 2024-01-21 14:13:09 +01:00
4cdc419478 test: add test to ensure redirect of not logged in 2024-01-20 19:35:40 +01:00
90b529adb4 refactor: move test class to related package 2024-01-20 19:16:52 +01:00
a3bc60986b test: add security related tests for MtbFileRestController 2024-01-19 14:11:03 +01:00
f5df0b5d22 test: add tests to ensure TokenService is present if required 2024-01-19 13:10:36 +01:00
972ac745e9 fix: add missing token screenshot 2024-01-18 14:44:44 +01:00
358373cf70 Merge pull request #30 from CCC-MF/issue_29
Issue #29: Unterstützung für Endpoint-Tokens
2024-01-18 14:29:52 +01:00
27a62321fa docs: add documentation about token usage 2024-01-18 14:26:09 +01:00
30cf0fd22e feat #29: add initial support for mtbfile api tokens 2024-01-18 14:13:15 +01:00
531a8589db feat: push connection available state to client 2024-01-17 14:32:42 +01:00
fa89a64ddd Merge pull request #28 from CCC-MF/issue_24
feat #24: use htmx to refresh connection status every 20s
2024-01-17 12:35:35 +01:00
45ad5e8827 feat #24: use htmx to refresh connection status every 20s 2024-01-17 12:27:44 +01:00
c4eb4d0fe2 feat #25: add link to requests related to patient pseudonyme (#27) 2024-01-15 10:26:56 +01:00
4bc69a353c Merge pull request #26 from CCC-MF/issue_23
feat #23: add reload button to display on new request
2024-01-15 10:15:36 +01:00
9d30f750f7 feat #23: add reload button to display on new request 2024-01-15 09:17:38 +01:00
a1a252d5a9 build: use webjars for JS dependencies for now 2024-01-15 07:18:14 +01:00
568942bfe5 fix: typo in README.md 2024-01-14 17:31:30 +01:00
15f0432553 test: ensure configured generator bean is created 2024-01-12 21:27:55 +01:00
113bf2dd2e test: add pseudonymize generator property and default to tests 2024-01-12 19:59:01 +01:00
7ac151202a refactor: Use config new pseudonym generator config param
This deprecates the old param:
* `APP_PSEUDONYMIZER`: deprecated
* `APP_PSEUDONYM_GENERATOR`: has precedence
2024-01-12 16:55:18 +01:00
5d9d47c2df fix: append css class, not css style 2024-01-12 13:49:54 +01:00
585468314c feat: add admin credentials to deploy folder 2024-01-11 16:34:03 +01:00
40 changed files with 1153 additions and 106 deletions

2
.gitignore vendored
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@ -5,6 +5,8 @@ build/
!**/src/main/**/build/ !**/src/main/**/build/
!**/src/test/**/build/ !**/src/test/**/build/
bindings/ca-certificates/*.pem
### STS ### ### STS ###
.apt_generated .apt_generated
.classpath .classpath

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@ -36,6 +36,15 @@ Ist diese nicht gesetzt. wird intern eine Anonymisierung der Patienten-ID vorgen
* `APP_PSEUDONYMIZE_PREFIX`: Standortbezogenes Prefix - `UNKNOWN`, wenn nicht gesetzt * `APP_PSEUDONYMIZE_PREFIX`: Standortbezogenes Prefix - `UNKNOWN`, wenn nicht gesetzt
* `APP_PSEUDONYMIZE_GENERATOR`: `BUILDIN` oder `GPAS` - `BUILDIN`, wenn nicht gesetzt * `APP_PSEUDONYMIZE_GENERATOR`: `BUILDIN` oder `GPAS` - `BUILDIN`, wenn nicht gesetzt
**Hinweise**:
* Der alte Konfigurationsparameter `APP_PSEUDONYMIZER` mit den Werten `GPAS` oder `BUILDIN` sollte nicht
mehr verwendet werden.
* Die Pseudonymisierung erfolgt im ETL-Prozessor nur für die Patienten-ID.
Andere Referenz-IDs werden nicht anonymisiert.
Dies erfolgt bei Nutzung von **[onkostar-plugin-dnpmexport](https://github.com/CCC-MF/onkostar-plugin-dnpmexport)**
bereits im Plugin selbst.
#### Eingebaute Anonymisierung #### Eingebaute Anonymisierung
Wurde keine oder die Verwendung der eingebauten Anonymisierung konfiguriert, so wird für die Patienten-ID der Wurde keine oder die Verwendung der eingebauten Anonymisierung konfiguriert, so wird für die Patienten-ID der
@ -71,13 +80,59 @@ Hier Beispiele für das Beispielpasswort `very-secret`:
Wird kein Administrator-Passwort angegeben, wird ein zufälliger Wert generiert und beim Start der Anwendung in den Logs Wird kein Administrator-Passwort angegeben, wird ein zufälliger Wert generiert und beim Start der Anwendung in den Logs
angezeigt. angezeigt.
#### Weitere (nicht administrative) Nutzer mit OpenID Connect
Die folgenden Konfigurationsparameter werden benötigt, um die Authentifizierung weiterer Benutzer an einen OIDC-Provider
zu delegieren.
Ein Admin-Benutzer muss dabei konfiguriert sein.
* `APP_SECURITY_ENABLE_OIDC`: Aktiviert die Nutzung von OpenID Connect. Damit sind weitere Parameter erforderlich
* `SPRING_SECURITY_OAUTH2_CLIENT_REGISTRATION_CUSTOM_CLIENT_NAME`: Name. Wird beim zusätzlichen Loginbutton angezeigt.
* `SPRING_SECURITY_OAUTH2_CLIENT_REGISTRATION_CUSTOM_CLIENT_ID`: Client-ID
* `SPRING_SECURITY_OAUTH2_CLIENT_REGISTRATION_CUSTOM_CLIENT_SECRET`: Client-Secret
* `SPRING_SECURITY_OAUTH2_CLIENT_REGISTRATION_CUSTOM_CLIENT_SCOPE[0]`: Hier sollte immer `openid` angegeben werden.
* `SPRING_SECURITY_OAUTH2_CLIENT_PROVIDER_CUSTOM_ISSUER_URI`: Die URI des Providers,
z.B. `https://auth.example.com/realm/example`
* `SPRING_SECURITY_OAUTH2_CLIENT_PROVIDER_CUSTOM_USER_NAME_ATTRIBUTE`: Name des Attributes, welches den Benutzernamen
enthält.
Oft verwendet: `preferred_username`
Ist die Nutzung von OpenID Connect konfiguriert, erscheint ein zusätzlicher Login-Button zur Nutzung mit OpenID Connect
und dem konfigurierten `CLIENT_NAME`.
![Login mit OpenID Connect](docs/login.png)
Weitere Informationen zur Konfiguration des OIDC-Providers
sind [hier](https://docs.spring.io/spring-security/reference/servlet/oauth2/index.html#oauth2-client)
zu finden.
#### Auswirkungen auf den dargestellten Inhalt #### Auswirkungen auf den dargestellten Inhalt
Nur Administratoren haben Zugriff auf den Konfigurationsbereich, nur angemeldete Benutzer können die anonymisierte oder Nur Administratoren haben Zugriff auf den Konfigurationsbereich, nur angemeldete Benutzer können die anonymisierte oder
pseudonymisierte Patienten-ID einsehen. pseudonymisierte Patienten-ID sowie den Qualitätsbericht des bwHC-Backends einsehen.
Wurde kein Administrator-Account konfiguriert, sind diese Inhalte generell nicht verfügbar. Wurde kein Administrator-Account konfiguriert, sind diese Inhalte generell nicht verfügbar.
### Tokenbasierte Authentifizierung für MTBFile-Endpunkt
Die Anwendung unterstützt das Erstellen und Nutzen einer tokenbasierten Authentifizierung für den MTB-File-Endpunkt.
Dies kann mit der Umgebungsvariable `APP_SECURITY_ENABLE_TOKENS` aktiviert (`true` oder `false`) werden
und ist als Standardeinstellung nicht aktiv.
Ist diese Einstellung aktiviert worden, ist es Administratoren möglich, Zugriffstokens für Onkostar zu erstellen, die
zur Nutzung des MTB-File-Endpunkts eine HTTP-Basic-Authentifizierung voraussetzen.
![Tokenverwaltung](docs/tokens.png)
In diesem Fall können den Endpunkt für das Onkostar-Plugin **[onkostar-plugin-dnpmexport](https://github.com/CCC-MF/onkostar-plugin-dnpmexport)** wie folgt konfigurieren:
```
https://testonkostar:MTg1NTL...NGU4@etl.example.com/mtbfile
```
Ist die Verwendung von Tokens aktiv, werden Anfragen ohne die Angabe der Token-Information abgelehnt.
### Transformation von Werten ### Transformation von Werten
In Onkostar kann es vorkommen, dass ein Wert eines Merkmalskatalogs an einem Standort angepasst wurde und dadurch nicht dem Wert entspricht, In Onkostar kann es vorkommen, dass ein Wert eines Merkmalskatalogs an einem Standort angepasst wurde und dadurch nicht dem Wert entspricht,
@ -170,8 +225,37 @@ Diese Anwendung ist auch als Docker-Image verfügbar: https://github.com/CCC-MF/
./gradlew bootBuildImage ./gradlew bootBuildImage
``` ```
### Integration eines eigenen Root CA Zertifikats
Wird eine eigene Root CA verwendet, die nicht offiziell signiert ist, wird es zu Problemen beim SSL-Handshake kommen, wenn z.B. gPAS zur Generierung von Pseudonymen verwendet wird.
Hier bietet es sich an, das Root CA Zertifikat in das Image zu integrieren.
#### Integration beim Bauen des Images
Hier muss die Zeile `"BP_EMBED_CERTS" to "true"` in der Datei `build.gradle.kts` verwendet werden und darf nicht als Kommentar verwendet werden.
Die PEM-Datei mit dem/den Root CA Zertifikat(en) muss dabei im vorbereiteten Verzeichnis [`bindings/ca-certificates`](bindings/ca-certificates) enthalten sein.
#### Integration zur Laufzeit
Hier muss die Umgebungsvariable `SERVICE_BINDING_ROOT` z.B. auf den Wert `/bindings` gesetzt sein.
Zudem muss ein Verzeichnis `bindings/ca-certificates` - analog zum Verzeichnis [`bindings/ca-certificates`](bindings/ca-certificates) mit einer PEM-Datei als Docker-Volume eingebunden werden.
Beispiel für Docker-Compose:
```
...
environment:
SERVICE_BINDING_ROOT: /bindings
...
volumes:
- "/path/to/bindings/ca-certificates/:/bindings/ca-certificates/:ro"
...
```
## Deployment ## Deployment
*Ausführen als Docker Conatiner:* *Ausführen als Docker Container:*
```bash ```bash
cd ./deploy cd ./deploy

5
bindings/README.md Normal file
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@ -0,0 +1,5 @@
# Hinweis für Root CA Zertifikate
PEM-Datei(en) in das Verzeichnis `ca-certificates` ablegen.
Die Datei `type` gibt dabei an, dass hier CA Zertifikate zu finden sind.

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@ -0,0 +1 @@
ca-certificates

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@ -4,20 +4,23 @@ import org.springframework.boot.gradle.tasks.bundling.BootBuildImage
plugins { plugins {
war war
id("org.springframework.boot") version "3.2.1" id("org.springframework.boot") version "3.2.2"
id("io.spring.dependency-management") version "1.1.4" id("io.spring.dependency-management") version "1.1.4"
kotlin("jvm") version "1.9.22" kotlin("jvm") version "1.9.22"
kotlin("plugin.spring") version "1.9.22" kotlin("plugin.spring") version "1.9.22"
} }
group = "de.ukw.ccc" group = "de.ukw.ccc"
version = "0.4.0" version = "0.7.0"
var versions = mapOf( var versions = mapOf(
"bwhc-dto-java" to "0.2.0", "bwhc-dto-java" to "0.2.0",
"hapi-fhir" to "6.10.2", "hapi-fhir" to "6.10.2",
"httpclient5" to "5.2.1", "httpclient5" to "5.2.1",
"mockito-kotlin" to "5.2.1" "mockito-kotlin" to "5.2.1",
// Webjars
"echarts" to "5.4.3",
"htmx.org" to "1.9.10"
) )
java { java {
@ -55,6 +58,7 @@ dependencies {
implementation("org.springframework.boot:spring-boot-starter-web") implementation("org.springframework.boot:spring-boot-starter-web")
implementation("org.springframework.boot:spring-boot-starter-data-jdbc") implementation("org.springframework.boot:spring-boot-starter-data-jdbc")
implementation("org.springframework.boot:spring-boot-starter-security") implementation("org.springframework.boot:spring-boot-starter-security")
implementation("org.springframework.boot:spring-boot-starter-oauth2-client")
implementation("org.thymeleaf.extras:thymeleaf-extras-springsecurity6") implementation("org.thymeleaf.extras:thymeleaf-extras-springsecurity6")
implementation("com.fasterxml.jackson.module:jackson-module-kotlin") implementation("com.fasterxml.jackson.module:jackson-module-kotlin")
implementation("org.springframework.kafka:spring-kafka") implementation("org.springframework.kafka:spring-kafka")
@ -66,6 +70,9 @@ dependencies {
implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${versions["hapi-fhir"]}") implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${versions["hapi-fhir"]}")
implementation("org.apache.httpcomponents.client5:httpclient5:${versions["httpclient5"]}") implementation("org.apache.httpcomponents.client5:httpclient5:${versions["httpclient5"]}")
implementation("com.jayway.jsonpath:json-path") implementation("com.jayway.jsonpath:json-path")
implementation("org.webjars:webjars-locator:0.50")
implementation("org.webjars.npm:echarts:${versions["echarts"]}")
implementation("org.webjars.npm:htmx.org:${versions["htmx.org"]}")
runtimeOnly("org.mariadb.jdbc:mariadb-java-client") runtimeOnly("org.mariadb.jdbc:mariadb-java-client")
runtimeOnly("org.postgresql:postgresql") runtimeOnly("org.postgresql:postgresql")
developmentOnly("org.springframework.boot:spring-boot-devtools") developmentOnly("org.springframework.boot:spring-boot-devtools")
@ -73,6 +80,7 @@ dependencies {
annotationProcessor("org.springframework.boot:spring-boot-configuration-processor") annotationProcessor("org.springframework.boot:spring-boot-configuration-processor")
providedRuntime("org.springframework.boot:spring-boot-starter-tomcat") providedRuntime("org.springframework.boot:spring-boot-starter-tomcat")
testImplementation("org.springframework.boot:spring-boot-starter-test") testImplementation("org.springframework.boot:spring-boot-starter-test")
testImplementation("org.springframework.security:spring-security-test")
testImplementation("io.projectreactor:reactor-test") testImplementation("io.projectreactor:reactor-test")
testImplementation("org.mockito.kotlin:mockito-kotlin:${versions["mockito-kotlin"]}") testImplementation("org.mockito.kotlin:mockito-kotlin:${versions["mockito-kotlin"]}")
integrationTestImplementation("org.testcontainers:junit-jupiter") integrationTestImplementation("org.testcontainers:junit-jupiter")
@ -105,7 +113,14 @@ task<Test>("integrationTest") {
tasks.named<BootBuildImage>("bootBuildImage") { tasks.named<BootBuildImage>("bootBuildImage") {
imageName.set("ghcr.io/ccc-mf/etl-processor") imageName.set("ghcr.io/ccc-mf/etl-processor")
// Binding for CA Certs
bindings.set(listOf(
"$rootDir/bindings/ca-certificates/:/platform/bindings/ca-certificates"
))
environment.set(environment.get() + mapOf( environment.set(environment.get() + mapOf(
// Enable this line to embed CA Certs into image on build time
//"BP_EMBED_CERTS" to "true",
"BP_OCI_SOURCE" to "https://github.com/CCC-MF/etl-processor", "BP_OCI_SOURCE" to "https://github.com/CCC-MF/etl-processor",
"BP_OCI_LICENSES" to "AGPLv3", "BP_OCI_LICENSES" to "AGPLv3",
"BP_OCI_DESCRIPTION" to "ETL Processor for bwHC MTB files" "BP_OCI_DESCRIPTION" to "ETL Processor for bwHC MTB files"

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@ -18,6 +18,8 @@ services:
APP_KAFKA_GROUP_ID: ${DNPM_KAFKA_GROUP_ID} APP_KAFKA_GROUP_ID: ${DNPM_KAFKA_GROUP_ID}
APP_KAFKA_RESPONSE_TOPIC: ${DNPM_KAFKA_RESPONSE_TOPIC} APP_KAFKA_RESPONSE_TOPIC: ${DNPM_KAFKA_RESPONSE_TOPIC}
APP_REST_URI: ${DNPM_BWHC_REST_URI} APP_REST_URI: ${DNPM_BWHC_REST_URI}
APP_SECURITY_ADMIN_USER: ${DNPM_ADMIN_USER}
APP_SECURITY_ADMIN_PASSWORD: ${DNPM_ADMIN_PASSWORD}
SPRING_DATASOURCE_URL: ${DNPM_DATASOURCE_URL} SPRING_DATASOURCE_URL: ${DNPM_DATASOURCE_URL}
SPRING_DATASOURCE_PASSWORD: ${DNPM_MARIADB_USER_PW} SPRING_DATASOURCE_PASSWORD: ${DNPM_MARIADB_USER_PW}
SPRING_DATASOURCE_USERNAME: ${DNPM_MARIADB_DB} SPRING_DATASOURCE_USERNAME: ${DNPM_MARIADB_DB}

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@ -2,6 +2,10 @@
DNPM_MONITORING_HTTP_PORT=8088 DNPM_MONITORING_HTTP_PORT=8088
DNPM_LOG_LEVEL=INFO DNPM_LOG_LEVEL=INFO
# ADMIN USER CREDENTIALS
DNPM_ADMIN_USER=admin
DNPM_ADMIN_PASSWORD=
# GPAS or BUILDIN # GPAS or BUILDIN
DNPM_PSEUDONYMIZE_GENERATOR=BUILDIN DNPM_PSEUDONYMIZE_GENERATOR=BUILDIN
DNPM_APP_PSEUDONYMIZE_PREFIX=ANONYM DNPM_APP_PSEUDONYMIZE_PREFIX=ANONYM

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@ -48,7 +48,8 @@ import org.testcontainers.junit.jupiter.Testcontainers
@MockBean(MtbFileSender::class) @MockBean(MtbFileSender::class)
@TestPropertySource( @TestPropertySource(
properties = [ properties = [
"app.rest.uri=http://example.com" "app.rest.uri=http://example.com",
"app.pseudonymize.generator=buildin"
] ]
) )
class EtlProcessorApplicationTests : AbstractTestcontainerTest() { class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
@ -64,6 +65,7 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
@AutoConfigureMockMvc @AutoConfigureMockMvc
@TestPropertySource( @TestPropertySource(
properties = [ properties = [
"app.pseudonymize.generator=buildin",
"app.transformations[0].path=diagnoses[*].icd10.version", "app.transformations[0].path=diagnoses[*].icd10.version",
"app.transformations[0].from=2013", "app.transformations[0].from=2013",
"app.transformations[0].to=2014", "app.transformations[0].to=2014",

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@ -1,7 +1,7 @@
/* /*
* This file is part of ETL-Processor * This file is part of ETL-Processor
* *
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors * Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* *
* This program is free software: you can redistribute it and/or modify * This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published * it under the terms of the GNU Affero General Public License as published
@ -23,6 +23,10 @@ import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.monitoring.RequestRepository import dev.dnpm.etl.processor.monitoring.RequestRepository
import dev.dnpm.etl.processor.output.KafkaMtbFileSender import dev.dnpm.etl.processor.output.KafkaMtbFileSender
import dev.dnpm.etl.processor.output.RestMtbFileSender import dev.dnpm.etl.processor.output.RestMtbFileSender
import dev.dnpm.etl.processor.pseudonym.AnonymizingGenerator
import dev.dnpm.etl.processor.pseudonym.GpasPseudonymGenerator
import dev.dnpm.etl.processor.services.TokenRepository
import dev.dnpm.etl.processor.services.TokenService
import org.assertj.core.api.Assertions.assertThat import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.Nested import org.junit.jupiter.api.Nested
import org.junit.jupiter.api.Test import org.junit.jupiter.api.Test
@ -31,13 +35,27 @@ import org.springframework.beans.factory.NoSuchBeanDefinitionException
import org.springframework.boot.autoconfigure.kafka.KafkaAutoConfiguration import org.springframework.boot.autoconfigure.kafka.KafkaAutoConfiguration
import org.springframework.boot.test.context.SpringBootTest import org.springframework.boot.test.context.SpringBootTest
import org.springframework.boot.test.mock.mockito.MockBean import org.springframework.boot.test.mock.mockito.MockBean
import org.springframework.boot.test.mock.mockito.MockBeans
import org.springframework.context.ApplicationContext import org.springframework.context.ApplicationContext
import org.springframework.security.crypto.password.PasswordEncoder
import org.springframework.security.provisioning.InMemoryUserDetailsManager
import org.springframework.test.context.ContextConfiguration import org.springframework.test.context.ContextConfiguration
import org.springframework.test.context.TestPropertySource import org.springframework.test.context.TestPropertySource
@SpringBootTest @SpringBootTest
@ContextConfiguration(classes = [AppConfiguration::class, KafkaAutoConfiguration::class, AppKafkaConfiguration::class, AppRestConfiguration::class]) @ContextConfiguration(classes = [
AppConfiguration::class,
AppSecurityConfiguration::class,
KafkaAutoConfiguration::class,
AppKafkaConfiguration::class,
AppRestConfiguration::class
])
@MockBean(ObjectMapper::class) @MockBean(ObjectMapper::class)
@TestPropertySource(
properties = [
"app.pseudonymize.generator=BUILDIN",
]
)
class AppConfigurationTest { class AppConfigurationTest {
@Nested @Nested
@ -116,4 +134,108 @@ class AppConfigurationTest {
} }
@Nested
inner class AppConfigurationPseudonymizeTest {
@Nested
@TestPropertySource(
properties = [
"app.pseudonymize.generator=",
"app.pseudonymizer=buildin",
]
)
inner class AppConfigurationPseudonymizerBuildinTest(private val context: ApplicationContext) {
@Test
fun shouldUseConfiguredGenerator() {
assertThat(context.getBean(AnonymizingGenerator::class.java)).isNotNull
}
}
@Nested
@TestPropertySource(
properties = [
"app.pseudonymize.generator=",
"app.pseudonymizer=gpas",
]
)
inner class AppConfigurationPseudonymizerGpasTest(private val context: ApplicationContext) {
@Test
fun shouldUseConfiguredGenerator() {
assertThat(context.getBean(GpasPseudonymGenerator::class.java)).isNotNull
}
}
@Nested
@TestPropertySource(
properties = [
"app.pseudonymize.generator=buildin",
"app.pseudonymizer=",
]
)
inner class AppConfigurationPseudonymizeGeneratorBuildinTest(private val context: ApplicationContext) {
@Test
fun shouldUseConfiguredGenerator() {
assertThat(context.getBean(AnonymizingGenerator::class.java)).isNotNull
}
}
@Nested
@TestPropertySource(
properties = [
"app.pseudonymize.generator=gpas",
"app.pseudonymizer=",
]
)
inner class AppConfigurationPseudonymizeGeneratorGpasTest(private val context: ApplicationContext) {
@Test
fun shouldUseConfiguredGenerator() {
assertThat(context.getBean(GpasPseudonymGenerator::class.java)).isNotNull
}
}
@Nested
@TestPropertySource(
properties = [
"app.security.enable-tokens=true"
]
)
@MockBeans(value = [
MockBean(InMemoryUserDetailsManager::class),
MockBean(PasswordEncoder::class),
MockBean(TokenRepository::class)
])
inner class AppConfigurationTokenEnabledTest(private val context: ApplicationContext) {
@Test
fun checkTokenService() {
assertThat(context.getBean(TokenService::class.java)).isNotNull
}
}
@Nested
@MockBeans(value = [
MockBean(InMemoryUserDetailsManager::class),
MockBean(PasswordEncoder::class),
MockBean(TokenRepository::class)
])
inner class AppConfigurationTokenDisabledTest(private val context: ApplicationContext) {
@Test
fun checkTokenService() {
assertThrows<NoSuchBeanDefinitionException> { context.getBean(TokenService::class.java) }
}
}
}
} }

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@ -46,6 +46,7 @@ import java.util.*
@MockBean(MtbFileSender::class) @MockBean(MtbFileSender::class)
@TestPropertySource( @TestPropertySource(
properties = [ properties = [
"app.pseudonymize.generator=buildin",
"app.rest.uri=http://example.com" "app.rest.uri=http://example.com"
] ]
) )

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@ -0,0 +1,110 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.web
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
import dev.dnpm.etl.processor.output.MtbFileSender
import dev.dnpm.etl.processor.pseudonym.Generator
import dev.dnpm.etl.processor.services.RequestProcessor
import dev.dnpm.etl.processor.services.TransformationService
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith
import org.mockito.junit.jupiter.MockitoExtension
import org.springframework.beans.factory.annotation.Autowired
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
import org.springframework.boot.test.mock.mockito.MockBean
import org.springframework.http.HttpHeaders
import org.springframework.http.MediaType
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.anonymous
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user
import org.springframework.test.context.ContextConfiguration
import org.springframework.test.context.TestPropertySource
import org.springframework.test.context.junit.jupiter.SpringExtension
import org.springframework.test.web.servlet.MockMvc
import org.springframework.test.web.servlet.get
import reactor.core.publisher.Sinks
abstract class MockSink : Sinks.Many<Boolean>
@WebMvcTest(controllers = [ConfigController::class])
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
@ContextConfiguration(
classes = [
ConfigController::class,
AppSecurityConfiguration::class
]
)
@TestPropertySource(
properties = [
"app.pseudonymize.generator=BUILDIN",
"app.security.admin-user=admin",
"app.security.admin-password={noop}very-secret",
"app.security.enable-tokens=true"
]
)
@MockBean(name = "configsUpdateProducer", classes = [MockSink::class])
@MockBean(
Generator::class,
MtbFileSender::class,
ConnectionCheckService::class,
RequestProcessor::class,
TransformationService::class
)
class ConfigControllerTest {
private lateinit var mockMvc: MockMvc
private lateinit var requestProcessor: RequestProcessor
@BeforeEach
fun setup(
@Autowired mockMvc: MockMvc,
@Autowired requestProcessor: RequestProcessor
) {
this.mockMvc = mockMvc
this.requestProcessor = requestProcessor
}
@Test
fun testShouldShowConfigPageIfLoggedIn() {
mockMvc.get("/configs") {
with(user("admin").roles("ADMIN"))
accept(MediaType.TEXT_HTML)
}.andExpect {
status { isOk() }
}
}
@Test
fun testShouldRedirectToLoginPageIfNotLoggedIn() {
mockMvc.get("/configs") {
with(anonymous())
accept(MediaType.TEXT_HTML)
}.andExpect {
status { isFound() }
header {
stringValues(HttpHeaders.LOCATION, "http://localhost/login")
}
}
}
}

View File

@ -0,0 +1,157 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.web
import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.*
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
import dev.dnpm.etl.processor.services.RequestProcessor
import dev.dnpm.etl.processor.services.TokenRepository
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith
import org.mockito.ArgumentMatchers.anyString
import org.mockito.junit.jupiter.MockitoExtension
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.boot.test.mock.mockito.MockBean
import org.springframework.http.MediaType
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.anonymous
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user
import org.springframework.test.context.ContextConfiguration
import org.springframework.test.context.TestPropertySource
import org.springframework.test.context.junit.jupiter.SpringExtension
import org.springframework.test.web.servlet.MockMvc
import org.springframework.test.web.servlet.delete
import org.springframework.test.web.servlet.post
@WebMvcTest(controllers = [MtbFileRestController::class])
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
@ContextConfiguration(
classes = [
MtbFileRestController::class,
AppSecurityConfiguration::class
]
)
@MockBean(TokenRepository::class, RequestProcessor::class)
@TestPropertySource(
properties = [
"app.pseudonymize.generator=BUILDIN",
"app.security.admin-user=admin",
"app.security.admin-password={noop}very-secret",
"app.security.enable-tokens=true"
]
)
class MtbFileRestControllerTest {
private lateinit var mockMvc: MockMvc
private lateinit var requestProcessor: RequestProcessor
@BeforeEach
fun setup(
@Autowired mockMvc: MockMvc,
@Autowired requestProcessor: RequestProcessor
) {
this.mockMvc = mockMvc
this.requestProcessor = requestProcessor
}
@Test
fun testShouldGrantPermissionToSendMtbFile() {
mockMvc.post("/mtbfile") {
with(user("onkostarserver").roles("MTBFILE"))
contentType = MediaType.APPLICATION_JSON
content = ObjectMapper().writeValueAsString(mtbFile)
}.andExpect {
status { isAccepted() }
}
verify(requestProcessor, times(1)).processMtbFile(any())
}
@Test
fun testShouldDenyPermissionToSendMtbFile() {
mockMvc.post("/mtbfile") {
with(anonymous())
contentType = MediaType.APPLICATION_JSON
content = ObjectMapper().writeValueAsString(mtbFile)
}.andExpect {
status { isUnauthorized() }
}
verify(requestProcessor, never()).processMtbFile(any())
}
@Test
fun testShouldGrantPermissionToDeletePatientData() {
mockMvc.delete("/mtbfile/12345678") {
with(user("onkostarserver").roles("MTBFILE"))
}.andExpect {
status { isAccepted() }
}
verify(requestProcessor, times(1)).processDeletion(anyString())
}
@Test
fun testShouldDenyPermissionToDeletePatientData() {
mockMvc.delete("/mtbfile/12345678") {
with(anonymous())
}.andExpect {
status { isUnauthorized() }
}
verify(requestProcessor, never()).processDeletion(anyString())
}
companion object {
val mtbFile: MtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.withId("PID")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.withConsent(
Consent.builder()
.withId("1")
.withStatus(Consent.Status.ACTIVE)
.withPatient("PID")
.build()
)
.withEpisode(
Episode.builder()
.withId("1")
.withPatient("PID")
.withPeriod(PeriodStart("2023-08-08"))
.build()
)
.build()
}
}

View File

@ -20,11 +20,16 @@
package dev.dnpm.etl.processor.config package dev.dnpm.etl.processor.config
import org.springframework.boot.context.properties.ConfigurationProperties import org.springframework.boot.context.properties.ConfigurationProperties
import org.springframework.boot.context.properties.DeprecatedConfigurationProperty
@ConfigurationProperties(AppConfigProperties.NAME) @ConfigurationProperties(AppConfigProperties.NAME)
data class AppConfigProperties( data class AppConfigProperties(
var bwhcUri: String?, var bwhcUri: String?,
var generator: PseudonymGenerator = PseudonymGenerator.BUILDIN, @get:DeprecatedConfigurationProperty(
reason = "Deprecated in favor of 'app.pseudonymize.generator'",
replacement = "app.pseudonymize.generator"
)
var pseudonymizer: PseudonymGenerator = PseudonymGenerator.BUILDIN,
var transformations: List<TransformationProperties> = listOf() var transformations: List<TransformationProperties> = listOf()
) { ) {
companion object { companion object {
@ -34,6 +39,7 @@ data class AppConfigProperties(
@ConfigurationProperties(PseudonymizeConfigProperties.NAME) @ConfigurationProperties(PseudonymizeConfigProperties.NAME)
data class PseudonymizeConfigProperties( data class PseudonymizeConfigProperties(
var generator: PseudonymGenerator = PseudonymGenerator.BUILDIN,
val prefix: String = "UNKNOWN", val prefix: String = "UNKNOWN",
) { ) {
companion object { companion object {
@ -80,6 +86,8 @@ data class KafkaTargetProperties(
data class SecurityConfigProperties( data class SecurityConfigProperties(
val adminUser: String?, val adminUser: String?,
val adminPassword: String?, val adminPassword: String?,
val enableTokens: Boolean = false,
val enableOidc: Boolean = false
) { ) {
companion object { companion object {
const val NAME = "app.security" const val NAME = "app.security"

View File

@ -25,9 +25,12 @@ import dev.dnpm.etl.processor.pseudonym.AnonymizingGenerator
import dev.dnpm.etl.processor.pseudonym.Generator import dev.dnpm.etl.processor.pseudonym.Generator
import dev.dnpm.etl.processor.pseudonym.GpasPseudonymGenerator import dev.dnpm.etl.processor.pseudonym.GpasPseudonymGenerator
import dev.dnpm.etl.processor.pseudonym.PseudonymizeService import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
import dev.dnpm.etl.processor.services.TokenRepository
import dev.dnpm.etl.processor.services.TokenService
import dev.dnpm.etl.processor.services.Transformation import dev.dnpm.etl.processor.services.Transformation
import dev.dnpm.etl.processor.services.TransformationService import dev.dnpm.etl.processor.services.TransformationService
import org.slf4j.LoggerFactory import org.slf4j.LoggerFactory
import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty
import org.springframework.boot.context.properties.EnableConfigurationProperties import org.springframework.boot.context.properties.EnableConfigurationProperties
import org.springframework.context.annotation.Bean import org.springframework.context.annotation.Bean
@ -36,6 +39,9 @@ import org.springframework.retry.policy.SimpleRetryPolicy
import org.springframework.retry.support.RetryTemplate import org.springframework.retry.support.RetryTemplate
import org.springframework.retry.support.RetryTemplateBuilder import org.springframework.retry.support.RetryTemplateBuilder
import org.springframework.scheduling.annotation.EnableScheduling import org.springframework.scheduling.annotation.EnableScheduling
import org.springframework.security.crypto.password.PasswordEncoder
import org.springframework.security.provisioning.InMemoryUserDetailsManager
import org.springframework.security.provisioning.UserDetailsManager
import reactor.core.publisher.Sinks import reactor.core.publisher.Sinks
import kotlin.time.Duration.Companion.seconds import kotlin.time.Duration.Companion.seconds
import kotlin.time.toJavaDuration import kotlin.time.toJavaDuration
@ -54,18 +60,32 @@ class AppConfiguration {
private val logger = LoggerFactory.getLogger(AppConfiguration::class.java) private val logger = LoggerFactory.getLogger(AppConfiguration::class.java)
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS") @ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "GPAS")
@Bean @Bean
fun gpasPseudonymGenerator(configProperties: GPasConfigProperties): Generator { fun gpasPseudonymGenerator(configProperties: GPasConfigProperties): Generator {
return GpasPseudonymGenerator(configProperties) return GpasPseudonymGenerator(configProperties)
} }
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "BUILDIN", matchIfMissing = true) @ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "BUILDIN", matchIfMissing = true)
@Bean @Bean
fun buildinPseudonymGenerator(): Generator { fun buildinPseudonymGenerator(): Generator {
return AnonymizingGenerator() return AnonymizingGenerator()
} }
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS")
@ConditionalOnMissingBean
@Bean
fun gpasPseudonymGeneratorOnDeprecatedProperty(configProperties: GPasConfigProperties): Generator {
return GpasPseudonymGenerator(configProperties)
}
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "BUILDIN")
@ConditionalOnMissingBean
@Bean
fun buildinPseudonymGeneratorOnDeprecatedProperty(): Generator {
return AnonymizingGenerator()
}
@Bean @Bean
fun pseudonymizeService( fun pseudonymizeService(
generator: Generator, generator: Generator,
@ -79,11 +99,6 @@ class AppConfiguration {
return ReportService(objectMapper) return ReportService(objectMapper)
} }
@Bean
fun statisticsUpdateProducer(): Sinks.Many<Any> {
return Sinks.many().multicast().directBestEffort()
}
@Bean @Bean
fun transformationService( fun transformationService(
objectMapper: ObjectMapper, objectMapper: ObjectMapper,
@ -104,5 +119,21 @@ class AppConfiguration {
.build() .build()
} }
@ConditionalOnProperty(value = ["app.security.enable-tokens"], havingValue = "true")
@Bean
fun tokenService(userDetailsManager: InMemoryUserDetailsManager, passwordEncoder: PasswordEncoder, tokenRepository: TokenRepository): TokenService {
return TokenService(userDetailsManager, passwordEncoder, tokenRepository)
}
@Bean
fun statisticsUpdateProducer(): Sinks.Many<Any> {
return Sinks.many().multicast().directBestEffort()
}
@Bean
fun configsUpdateProducer(): Sinks.Many<Boolean> {
return Sinks.many().multicast().directBestEffort()
}
} }

View File

@ -38,6 +38,7 @@ import org.springframework.kafka.core.KafkaTemplate
import org.springframework.kafka.listener.ContainerProperties import org.springframework.kafka.listener.ContainerProperties
import org.springframework.kafka.listener.KafkaMessageListenerContainer import org.springframework.kafka.listener.KafkaMessageListenerContainer
import org.springframework.retry.support.RetryTemplate import org.springframework.retry.support.RetryTemplate
import reactor.core.publisher.Sinks
@Configuration @Configuration
@EnableConfigurationProperties( @EnableConfigurationProperties(
@ -81,8 +82,8 @@ class AppKafkaConfiguration {
} }
@Bean @Bean
fun connectionCheckService(consumerFactory: ConsumerFactory<String, String>): ConnectionCheckService { fun connectionCheckService(consumerFactory: ConsumerFactory<String, String>, configsUpdateProducer: Sinks.Many<Boolean>): ConnectionCheckService {
return KafkaConnectionCheckService(consumerFactory.createConsumer()) return KafkaConnectionCheckService(consumerFactory.createConsumer(), configsUpdateProducer)
} }
} }

View File

@ -32,6 +32,7 @@ import org.springframework.context.annotation.Configuration
import org.springframework.core.annotation.Order import org.springframework.core.annotation.Order
import org.springframework.retry.support.RetryTemplate import org.springframework.retry.support.RetryTemplate
import org.springframework.web.client.RestTemplate import org.springframework.web.client.RestTemplate
import reactor.core.publisher.Sinks
@Configuration @Configuration
@EnableConfigurationProperties( @EnableConfigurationProperties(
@ -64,9 +65,10 @@ class AppRestConfiguration {
@Bean @Bean
fun connectionCheckService( fun connectionCheckService(
restTemplate: RestTemplate, restTemplate: RestTemplate,
restTargetProperties: RestTargetProperties restTargetProperties: RestTargetProperties,
configsUpdateProducer: Sinks.Many<Boolean>
): ConnectionCheckService { ): ConnectionCheckService {
return RestConnectionCheckService(restTemplate, restTargetProperties) return RestConnectionCheckService(restTemplate, restTargetProperties, configsUpdateProducer)
} }
} }

View File

@ -76,12 +76,42 @@ class AppSecurityConfiguration(
} }
@Bean @Bean
fun filterChain(http: HttpSecurity): SecurityFilterChain { @ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "true")
fun filterChainOidc(http: HttpSecurity, passwordEncoder: PasswordEncoder): SecurityFilterChain {
http { http {
authorizeRequests { authorizeRequests {
authorize("/configs/**", hasRole("ADMIN")) authorize("/configs/**", hasRole("ADMIN"))
authorize("/mtbfile/**", hasAnyRole("MTBFILE"))
authorize("/report/**", fullyAuthenticated)
authorize(anyRequest, permitAll) authorize(anyRequest, permitAll)
} }
httpBasic {
realmName = "ETL-Processor"
}
formLogin {
loginPage = "/login"
}
oauth2Login {
loginPage = "/login"
}
csrf { disable() }
}
return http.build()
}
@Bean
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "false", matchIfMissing = true)
fun filterChain(http: HttpSecurity, passwordEncoder: PasswordEncoder): SecurityFilterChain {
http {
authorizeRequests {
authorize("/configs/**", hasRole("ADMIN"))
authorize("/mtbfile/**", hasAnyRole("MTBFILE"))
authorize("/report/**", hasRole("ADMIN"))
authorize(anyRequest, permitAll)
}
httpBasic {
realmName = "ETL-Processor"
}
formLogin { formLogin {
loginPage = "/login" loginPage = "/login"
} }

View File

@ -24,9 +24,11 @@ import dev.dnpm.etl.processor.config.RestTargetProperties
import jakarta.annotation.PostConstruct import jakarta.annotation.PostConstruct
import org.apache.kafka.clients.consumer.Consumer import org.apache.kafka.clients.consumer.Consumer
import org.apache.kafka.common.errors.TimeoutException import org.apache.kafka.common.errors.TimeoutException
import org.springframework.beans.factory.annotation.Qualifier
import org.springframework.http.HttpStatus import org.springframework.http.HttpStatus
import org.springframework.scheduling.annotation.Scheduled import org.springframework.scheduling.annotation.Scheduled
import org.springframework.web.client.RestTemplate import org.springframework.web.client.RestTemplate
import reactor.core.publisher.Sinks
import kotlin.time.Duration.Companion.seconds import kotlin.time.Duration.Companion.seconds
import kotlin.time.toJavaDuration import kotlin.time.toJavaDuration
@ -37,7 +39,9 @@ interface ConnectionCheckService {
} }
class KafkaConnectionCheckService( class KafkaConnectionCheckService(
private val consumer: Consumer<String, String> private val consumer: Consumer<String, String>,
@Qualifier("configsUpdateProducer")
private val configsUpdateProducer: Sinks.Many<Boolean>
) : ConnectionCheckService { ) : ConnectionCheckService {
private var connectionAvailable: Boolean = false private var connectionAvailable: Boolean = false
@ -51,6 +55,7 @@ class KafkaConnectionCheckService(
} catch (e: TimeoutException) { } catch (e: TimeoutException) {
false false
} }
configsUpdateProducer.emitNext(connectionAvailable, Sinks.EmitFailureHandler.FAIL_FAST)
} }
override fun connectionAvailable(): Boolean { override fun connectionAvailable(): Boolean {
@ -61,7 +66,9 @@ class KafkaConnectionCheckService(
class RestConnectionCheckService( class RestConnectionCheckService(
private val restTemplate: RestTemplate, private val restTemplate: RestTemplate,
private val restTargetProperties: RestTargetProperties private val restTargetProperties: RestTargetProperties,
@Qualifier("configsUpdateProducer")
private val configsUpdateProducer: Sinks.Many<Boolean>
) : ConnectionCheckService { ) : ConnectionCheckService {
private var connectionAvailable: Boolean = false private var connectionAvailable: Boolean = false
@ -77,6 +84,7 @@ class RestConnectionCheckService(
} catch (e: Exception) { } catch (e: Exception) {
false false
} }
configsUpdateProducer.emitNext(connectionAvailable, Sinks.EmitFailureHandler.FAIL_FAST)
} }
override fun connectionAvailable(): Boolean { override fun connectionAvailable(): Boolean {

View File

@ -20,6 +20,8 @@
package dev.dnpm.etl.processor.monitoring package dev.dnpm.etl.processor.monitoring
import org.springframework.data.annotation.Id import org.springframework.data.annotation.Id
import org.springframework.data.domain.Page
import org.springframework.data.domain.Pageable
import org.springframework.data.jdbc.repository.query.Query import org.springframework.data.jdbc.repository.query.Query
import org.springframework.data.relational.core.mapping.Embedded import org.springframework.data.relational.core.mapping.Embedded
import org.springframework.data.relational.core.mapping.Table import org.springframework.data.relational.core.mapping.Table
@ -59,6 +61,8 @@ interface RequestRepository : CrudRepository<Request, Long>, PagingAndSortingRep
fun findByUuidEquals(uuid: String): Optional<Request> fun findByUuidEquals(uuid: String): Optional<Request>
fun findRequestByPatientId(patientId: String, pageable: Pageable): Page<Request>
@Query("SELECT count(*) AS count, status FROM request WHERE type = 'MTB_FILE' GROUP BY status ORDER BY status, count DESC;") @Query("SELECT count(*) AS count, status FROM request WHERE type = 'MTB_FILE' GROUP BY status ORDER BY status, count DESC;")
fun countStates(): List<CountedState> fun countStates(): List<CountedState>

View File

@ -0,0 +1,92 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.services
import jakarta.annotation.PostConstruct
import org.springframework.data.annotation.Id
import org.springframework.data.relational.core.mapping.Table
import org.springframework.data.repository.CrudRepository
import org.springframework.data.repository.findByIdOrNull
import org.springframework.security.core.userdetails.User
import org.springframework.security.crypto.password.PasswordEncoder
import org.springframework.security.provisioning.InMemoryUserDetailsManager
import java.time.Instant
import java.util.*
class TokenService(
private val userDetailsManager: InMemoryUserDetailsManager,
private val passwordEncoder: PasswordEncoder,
private val tokenRepository: TokenRepository
) {
@PostConstruct
fun setup() {
tokenRepository.findAll().forEach {
userDetailsManager.createUser(
User.withUsername(it.username)
.password(it.password)
.roles("MTBFILE")
.build()
)
}
}
fun addToken(name: String): Result<String> {
val username = name.lowercase().replace("""[^a-z0-9]""".toRegex(), "")
if (userDetailsManager.userExists(username)) {
return Result.failure(RuntimeException("Cannot use token name"))
}
val password = Base64.getEncoder().encodeToString(UUID.randomUUID().toString().encodeToByteArray())
val encodedPassword = passwordEncoder.encode(password).toString()
userDetailsManager.createUser(
User.withUsername(username)
.password(encodedPassword)
.roles("MTBFILE")
.build()
)
tokenRepository.save(Token(name = name, username = username, password = encodedPassword))
return Result.success("$username:$password")
}
fun deleteToken(id: Long) {
val token = tokenRepository.findByIdOrNull(id) ?: return
userDetailsManager.deleteUser(token.username)
tokenRepository.delete(token)
}
fun findAll(): List<Token> {
return tokenRepository.findAll().toList()
}
}
@Table("token")
data class Token(
@Id val id: Long? = null,
val name: String,
val username: String,
val password: String,
val createdAt: Instant = Instant.now()
)
interface TokenRepository : CrudRepository<Token, Long>

View File

@ -22,20 +22,28 @@ package dev.dnpm.etl.processor.web
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
import dev.dnpm.etl.processor.output.MtbFileSender import dev.dnpm.etl.processor.output.MtbFileSender
import dev.dnpm.etl.processor.pseudonym.Generator import dev.dnpm.etl.processor.pseudonym.Generator
import dev.dnpm.etl.processor.services.Token
import dev.dnpm.etl.processor.services.TokenService
import dev.dnpm.etl.processor.services.TransformationService import dev.dnpm.etl.processor.services.TransformationService
import org.springframework.beans.factory.annotation.Qualifier
import org.springframework.http.MediaType
import org.springframework.http.codec.ServerSentEvent
import org.springframework.stereotype.Controller import org.springframework.stereotype.Controller
import org.springframework.ui.Model import org.springframework.ui.Model
import org.springframework.web.bind.annotation.GetMapping import org.springframework.web.bind.annotation.*
import org.springframework.web.bind.annotation.RequestMapping import reactor.core.publisher.Flux
import reactor.core.publisher.Sinks
@Controller @Controller
@RequestMapping(path = ["configs"]) @RequestMapping(path = ["configs"])
class ConfigController( class ConfigController(
@Qualifier("configsUpdateProducer")
private val configsUpdateProducer: Sinks.Many<Boolean>,
private val transformationService: TransformationService, private val transformationService: TransformationService,
private val pseudonymGenerator: Generator, private val pseudonymGenerator: Generator,
private val mtbFileSender: MtbFileSender, private val mtbFileSender: MtbFileSender,
private val connectionCheckService: ConnectionCheckService private val connectionCheckService: ConnectionCheckService,
private val tokenService: TokenService?
) { ) {
@GetMapping @GetMapping
@ -44,9 +52,73 @@ class ConfigController(
model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName) model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName)
model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint()) model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint())
model.addAttribute("connectionAvailable", connectionCheckService.connectionAvailable()) model.addAttribute("connectionAvailable", connectionCheckService.connectionAvailable())
model.addAttribute("tokensEnabled", tokenService != null)
if (tokenService != null) {
model.addAttribute("tokens", tokenService.findAll())
} else {
model.addAttribute("tokens", listOf<Token>())
}
model.addAttribute("transformations", transformationService.getTransformations()) model.addAttribute("transformations", transformationService.getTransformations())
return "configs" return "configs"
} }
@GetMapping(params = ["connectionAvailable"])
fun connectionAvailable(model: Model): String {
model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName)
model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint())
model.addAttribute("connectionAvailable", connectionCheckService.connectionAvailable())
if (tokenService != null) {
model.addAttribute("tokensEnabled", true)
model.addAttribute("tokens", tokenService.findAll())
} else {
model.addAttribute("tokens", listOf<Token>())
}
return "configs/connectionAvailable"
}
@PostMapping(path = ["tokens"])
fun addToken(@ModelAttribute("name") name: String, model: Model): String {
if (tokenService == null) {
model.addAttribute("tokensEnabled", false)
model.addAttribute("success", false)
} else {
model.addAttribute("tokensEnabled", true)
val result = tokenService.addToken(name)
if (result.isSuccess) {
model.addAttribute("newTokenValue", result.getOrDefault(""))
model.addAttribute("success", true)
} else {
model.addAttribute("success", false)
}
model.addAttribute("tokens", tokenService.findAll())
}
return "configs/tokens"
}
@DeleteMapping(path = ["tokens/{id}"])
fun deleteToken(@PathVariable id: Long, model: Model): String {
if (tokenService != null) {
tokenService.deleteToken(id)
model.addAttribute("tokensEnabled", true)
model.addAttribute("tokens", tokenService.findAll())
} else {
model.addAttribute("tokensEnabled", false)
model.addAttribute("tokens", listOf<Token>())
}
return "configs/tokens"
}
@GetMapping(path = ["events"], produces = [MediaType.TEXT_EVENT_STREAM_VALUE])
fun events(): Flux<ServerSentEvent<Any>> {
return configsUpdateProducer.asFlux().map {
ServerSentEvent.builder<Any>()
.event("connection-available").id("none").data("")
.build()
}
}
} }

View File

@ -40,13 +40,29 @@ class HomeController(
) { ) {
@GetMapping @GetMapping
fun index(@PageableDefault(page = 0, size = 20, sort = ["processedAt"], direction = Sort.Direction.DESC) pageable: Pageable, model: Model): String { fun index(
@PageableDefault(page = 0, size = 20, sort = ["processedAt"], direction = Sort.Direction.DESC) pageable: Pageable,
model: Model
): String {
val requests = requestRepository.findAll(pageable) val requests = requestRepository.findAll(pageable)
model.addAttribute("requests", requests) model.addAttribute("requests", requests)
return "index" return "index"
} }
@GetMapping(path = ["patient/{patientId}"])
fun byPatient(
@PathVariable patientId: String,
@PageableDefault(page = 0, size = 20, sort = ["processedAt"], direction = Sort.Direction.DESC) pageable: Pageable,
model: Model
): String {
val requests = requestRepository.findRequestByPatientId(patientId, pageable)
model.addAttribute("patientId", patientId)
model.addAttribute("requests", requests)
return "index"
}
@GetMapping(path = ["/report/{id}"]) @GetMapping(path = ["/report/{id}"])
fun report(@PathVariable id: RequestId, model: Model): String { fun report(@PathVariable id: RequestId, model: Model): String {
val request = requestRepository.findByUuidEquals(id.toString()).orElse(null) ?: throw NotFoundException() val request = requestRepository.findByUuidEquals(id.toString()).orElse(null) ?: throw NotFoundException()

View File

@ -19,14 +19,28 @@
package dev.dnpm.etl.processor.web package dev.dnpm.etl.processor.web
import dev.dnpm.etl.processor.config.SecurityConfigProperties
import org.springframework.boot.autoconfigure.security.oauth2.client.OAuth2ClientProperties
import org.springframework.stereotype.Controller import org.springframework.stereotype.Controller
import org.springframework.ui.Model
import org.springframework.web.bind.annotation.GetMapping import org.springframework.web.bind.annotation.GetMapping
@Controller @Controller
class LoginController { class LoginController(
private val securityConfigProperties: SecurityConfigProperties?,
private val oAuth2ClientProperties: OAuth2ClientProperties?
) {
@GetMapping(path = ["/login"]) @GetMapping(path = ["/login"])
fun login(): String { fun login(model: Model): String {
if (securityConfigProperties?.enableOidc == true) {
model.addAttribute(
"oidcLogins",
oAuth2ClientProperties?.registration?.map { (key, value) -> Pair(key, value.clientName) }.orEmpty()
)
} else {
model.addAttribute("oidcLogins", emptyList<Pair<String, String>>())
}
return "login" return "login"
} }

View File

@ -27,13 +27,19 @@ import org.springframework.http.ResponseEntity
import org.springframework.web.bind.annotation.* import org.springframework.web.bind.annotation.*
@RestController @RestController
@RequestMapping(path = ["mtbfile"])
class MtbFileRestController( class MtbFileRestController(
private val requestProcessor: RequestProcessor, private val requestProcessor: RequestProcessor,
) { ) {
private val logger = LoggerFactory.getLogger(MtbFileRestController::class.java) private val logger = LoggerFactory.getLogger(MtbFileRestController::class.java)
@PostMapping(path = ["/mtbfile"]) @GetMapping
fun info(): ResponseEntity<String> {
return ResponseEntity.ok("Test")
}
@PostMapping
fun mtbFile(@RequestBody mtbFile: MtbFile): ResponseEntity<Void> { fun mtbFile(@RequestBody mtbFile: MtbFile): ResponseEntity<Void> {
if (mtbFile.consent.status == Consent.Status.ACTIVE) { if (mtbFile.consent.status == Consent.Status.ACTIVE) {
logger.debug("Accepted MTB File for processing") logger.debug("Accepted MTB File for processing")
@ -45,7 +51,7 @@ class MtbFileRestController(
return ResponseEntity.accepted().build() return ResponseEntity.accepted().build()
} }
@DeleteMapping(path = ["/mtbfile/{patientId}"]) @DeleteMapping(path = ["{patientId}"])
fun deleteData(@PathVariable patientId: String): ResponseEntity<Void> { fun deleteData(@PathVariable patientId: String): ResponseEntity<Void> {
logger.debug("Accepted patient ID to process deletion") logger.debug("Accepted patient ID to process deletion")
requestProcessor.processDeletion(patientId) requestProcessor.processDeletion(patientId)

View File

@ -22,6 +22,7 @@ package dev.dnpm.etl.processor.web
import dev.dnpm.etl.processor.monitoring.RequestRepository import dev.dnpm.etl.processor.monitoring.RequestRepository
import dev.dnpm.etl.processor.monitoring.RequestStatus import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.monitoring.RequestType import dev.dnpm.etl.processor.monitoring.RequestType
import org.springframework.beans.factory.annotation.Qualifier
import org.springframework.http.MediaType import org.springframework.http.MediaType
import org.springframework.http.codec.ServerSentEvent import org.springframework.http.codec.ServerSentEvent
import org.springframework.web.bind.annotation.GetMapping import org.springframework.web.bind.annotation.GetMapping
@ -38,6 +39,7 @@ import java.time.temporal.ChronoUnit
@RestController @RestController
@RequestMapping(path = ["/statistics"]) @RequestMapping(path = ["/statistics"])
class StatisticsRestController( class StatisticsRestController(
@Qualifier("statisticsUpdateProducer")
private val statisticsUpdateProducer: Sinks.Many<Any>, private val statisticsUpdateProducer: Sinks.Many<Any>,
private val requestRepository: RequestRepository private val requestRepository: RequestRepository
) { ) {
@ -132,6 +134,7 @@ class StatisticsRestController(
@GetMapping(path = ["events"], produces = [MediaType.TEXT_EVENT_STREAM_VALUE]) @GetMapping(path = ["events"], produces = [MediaType.TEXT_EVENT_STREAM_VALUE])
fun updater(): Flux<ServerSentEvent<Any>> { fun updater(): Flux<ServerSentEvent<Any>> {
return statisticsUpdateProducer.asFlux().flatMap { return statisticsUpdateProducer.asFlux().flatMap {
println(it)
Flux.fromIterable( Flux.fromIterable(
listOf( listOf(
ServerSentEvent.builder<Any>() ServerSentEvent.builder<Any>()
@ -152,6 +155,10 @@ class StatisticsRestController(
.build(), .build(),
ServerSentEvent.builder<Any>() ServerSentEvent.builder<Any>()
.event("deleterequestpatientstates").id("none").data(this.requestPatientStates(true)) .event("deleterequestpatientstates").id("none").data(this.requestPatientStates(true))
.build(),
ServerSentEvent.builder<Any>()
.event("newrequest").id("none").data("newrequest")
.build() .build()
) )
) )

View File

@ -0,0 +1,8 @@
CREATE TABLE IF NOT EXISTS token
(
id int auto_increment primary key,
name varchar(255) not null,
username varchar(255) not null unique,
password varchar(255) not null,
created_at datetime default utc_timestamp() not null
);

View File

@ -0,0 +1,9 @@
CREATE TABLE IF NOT EXISTS token
(
id serial,
name varchar(255) not null,
username varchar(255) not null unique,
password varchar(255) not null,
created_at timestamp with time zone default now() not null,
PRIMARY KEY (id)
);

File diff suppressed because one or more lines are too long

View File

@ -4,14 +4,17 @@ const dateFormat = new Intl.DateTimeFormat('de-DE', dateFormatOptions);
const dateTimeFormatOptions = { year: 'numeric', month: '2-digit', day: '2-digit', hour: '2-digit', minute: 'numeric', second: 'numeric' }; const dateTimeFormatOptions = { year: 'numeric', month: '2-digit', day: '2-digit', hour: '2-digit', minute: 'numeric', second: 'numeric' };
const dateTimeFormat = new Intl.DateTimeFormat('de-DE', dateTimeFormatOptions); const dateTimeFormat = new Intl.DateTimeFormat('de-DE', dateTimeFormatOptions);
window.addEventListener('load', () => { const formatTimeElements = () => {
Array.from(document.getElementsByTagName('time')).forEach((timeTag) => { Array.from(document.getElementsByTagName('time')).forEach((timeTag) => {
let date = Date.parse(timeTag.getAttribute('datetime')); let date = Date.parse(timeTag.getAttribute('datetime'));
if (! isNaN(date)) { if (! isNaN(date)) {
timeTag.innerText = dateTimeFormat.format(date); timeTag.innerText = dateTimeFormat.format(date);
} }
}); });
}); };
window.addEventListener('load', formatTimeElements);
window.addEventListener('htmx:afterRequest', formatTimeElements);
function drawPieChart(url, elemId, title, data) { function drawPieChart(url, elemId, title, data) {
if (data) { if (data) {

View File

@ -202,13 +202,22 @@ form.samplecode-input input:focus-visible {
background: none; background: none;
} }
.login-form form * { .login-form form *,
.token-form form * {
padding: 0.5em; padding: 0.5em;
border: 1px solid var(--table-border); border: 1px solid var(--table-border);
border-radius: 3px; border-radius: 3px;
} }
.login-form button { .login-form form hr,
.token-form form hr {
padding: 0;
width: 100%;
}
.login-form button,
.login-form a.btn,
.token-form button {
margin: 1em 0; margin: 1em 0;
background: var(--bg-blue); background: var(--bg-blue);
color: white; color: white;
@ -521,3 +530,36 @@ input.inline:focus-visible {
.notification.error { .notification.error {
color: var(--bg-red); color: var(--bg-red);
} }
a.reload {
display: none;
position: absolute;
height: 1.2em;
width: 1.2em;
background: var(--bg-red);
border-radius: 50%;
color: white;
text-decoration: none;
font-size: .6em;
align-content: center;
justify-content: center;
}
.new-token {
padding: 1em;
background: var(--bg-green-op);
}
.new-token > pre {
margin: 0;
border: 1px solid var(--bg-green);
padding: .5em;
width: max-content;
display: inline-block;
}
.no-token {
padding: 1em;
background: var(--bg-red-op);
}

View File

@ -37,22 +37,11 @@
</table> </table>
</section> </section>
<section> <section th:insert="~{configs/tokens.html}">
<h2><span th:if="${connectionAvailable}"></span><span th:if="${not(connectionAvailable)}"></span> Verbindung zum bwHC-Backend</h2> </section>
<div>
Verbindung über <code>[[ ${mtbFileSender} ]]</code>. Die Verbindung ist aktuell <section hx-ext="sse" th:sse-connect="@{/configs/events}">
<strong th:if="${connectionAvailable}" style="color: green">verfügbar.</strong> <div th:insert="~{configs/connectionAvailable.html}" th:hx-get="@{/configs?connectionAvailable}" hx-trigger="sse:connection-available">
<strong th:if="${not(connectionAvailable)}" style="color: red">nicht verfügbar.</strong>
</div>
<div class="connection-display border">
<img th:src="@{/server.png}" alt="ETL-Processor" />
<span class="connection" th:styleappend="${connectionAvailable ? 'available' : ''}"></span>
<img th:if="${mtbFileSender.startsWith('Rest')}" th:src="@{/server.png}" alt="bwHC-Backend" />
<img th:if="${mtbFileSender.startsWith('Kafka')}" th:src="@{/kafka.png}" alt="Kafka-Broker" />
<span>ETL-Processor</span>
<span></span>
<span th:if="${mtbFileSender.startsWith('Rest')}">bwHC-Backend</span>
<span th:if="${mtbFileSender.startsWith('Kafka')}">Kafka-Broker</span>
</div> </div>
</section> </section>
@ -100,5 +89,8 @@
</th:block> </th:block>
</section> </section>
</main> </main>
<script th:src="@{/scripts.js}"></script>
<script th:src="@{/webjars/htmx.org/dist/htmx.min.js}"></script>
<script th:src="@{/webjars/htmx.org/dist/ext/sse.js}"></script>
</body> </body>
</html> </html>

View File

@ -0,0 +1,16 @@
<h2><span th:if="${connectionAvailable}"></span><span th:if="${not(connectionAvailable)}"></span> Verbindung zum bwHC-Backend</h2>
<div>
Verbindung über <code>[[ ${mtbFileSender} ]]</code>. Die Verbindung ist aktuell
<strong th:if="${connectionAvailable}" style="color: green">verfügbar.</strong>
<strong th:if="${not(connectionAvailable)}" style="color: red">nicht verfügbar.</strong>
</div>
<div class="connection-display border">
<img th:src="@{/server.png}" alt="ETL-Processor" />
<span class="connection" th:classappend="${connectionAvailable ? 'available' : ''}"></span>
<img th:if="${mtbFileSender.startsWith('Rest')}" th:src="@{/server.png}" alt="bwHC-Backend" />
<img th:if="${mtbFileSender.startsWith('Kafka')}" th:src="@{/kafka.png}" alt="Kafka-Broker" />
<span>ETL-Processor</span>
<span></span>
<span th:if="${mtbFileSender.startsWith('Rest')}">bwHC-Backend</span>
<span th:if="${mtbFileSender.startsWith('Kafka')}">Kafka-Broker</span>
</div>

View File

@ -0,0 +1,39 @@
<div th:if="${not tokensEnabled}">
<h2><span></span> Tokens</h2>
<p>Die Verwendung von Tokens ist nicht aktiviert.</p>
</div>
<div id="tokens" th:if="${tokensEnabled}">
<h2><span></span> Tokens</h2>
<div class="border">
<div th:if="${tokens.isEmpty()}">Noch keine Tokens vorhanden.</div>
<table th:if="${not tokens.isEmpty()}">
<thead>
<tr>
<th>Name</th>
<th>Erstellt</th>
<th></th>
</tr>
</thead>
<tbody>
<tr th:each="token : ${tokens}">
<td>[[ ${token.name} ]]</td>
<td><time th:datetime="${token.createdAt}">[[ ${token.createdAt} ]]</time></td>
<td><button class="btn btn-red" th:hx-delete="@{/configs/tokens/{id}(id=${token.id})}" hx-target="#tokens">Löschen</button></td>
</tr>
</tbody>
</table>
<div th:if="${newTokenValue != null and success}" class="new-token">
Verwendung über HTTP-Basic. Bitte notieren, wird nicht erneut angezeigt: <pre>[[ ${newTokenValue} ]]</pre>
</div>
<div th:if="${success != null and not success}" class="no-token">
Das Token konnte nicht erzeugt werden. Versuchen Sie einen anderen Namen.
</div>
<div class="token-form">
<form th:hx-post="@{/configs/tokens}" hx-target="#tokens">
<input placeholder="Token-Name" name="name" required />
<button>Token Erstellen</button>
</form>
</div>
</div>
</div>

View File

@ -21,6 +21,11 @@
<a th:href="@{/login}">Login</a> <a th:href="@{/login}">Login</a>
</li> </li>
<li class="login" sec:authorize="isAuthenticated()"> <li class="login" sec:authorize="isAuthenticated()">
<span>
<span>👤</span>
<span sec:authentication="name">?</span>
</span>
&nbsp;
<a th:href="@{/logout}">Abmelden</a> <a th:href="@{/logout}">Abmelden</a>
</li> </li>
</ul> </ul>

View File

@ -9,16 +9,30 @@
<div th:replace="~{fragments.html :: nav}"></div> <div th:replace="~{fragments.html :: nav}"></div>
<main> <main>
<h1>Letzte Anfragen</h1> <h1>Alle Anfragen<a id="reload-notify" class="reload" title="Neue Anfragen" th:href="@{/}"></a></h1>
<div>
<h2 th:if="${patientId != null}">
Betreffend Patienten-Pseudonym <span class="monospace" th:text="${patientId}">***</span>
<a class="btn btn-blue" th:if="${patientId != null}" th:href="@{/}">Alle anzeigen</a>
</h2>
</div>
<div class="border"> <div class="border">
<div class="page-control"> <div th:if="${patientId == null}" class="page-control">
<a id="first-page-link" th:href="@{/(page=${0})}" title="Zum Anfang: Taste W" th:if="${not requests.isFirst()}">&larrb;</a><a th:if="${requests.isFirst()}">&larrb;</a> <a id="first-page-link" th:href="@{/(page=${0})}" title="Zum Anfang: Taste W" th:if="${not requests.isFirst()}">&larrb;</a><a th:if="${requests.isFirst()}">&larrb;</a>
<a id="prev-page-link" th:href="@{/(page=${requests.getNumber() - 1})}" title="Seite zurück: Taste A" th:if="${not requests.isFirst()}">&larr;</a><a th:if="${requests.isFirst()}">&larr;</a> <a id="prev-page-link" th:href="@{/(page=${requests.getNumber() - 1})}" title="Seite zurück: Taste A" th:if="${not requests.isFirst()}">&larr;</a><a th:if="${requests.isFirst()}">&larr;</a>
<span>Seite [[ ${requests.getNumber() + 1} ]] von [[ ${requests.getTotalPages()} ]]</span> <span>Seite [[ ${requests.getNumber() + 1} ]] von [[ ${requests.getTotalPages()} ]]</span>
<a id="next-page-link" th:href="@{/(page=${requests.getNumber() + 1})}" title="Seite vor: Taste D" th:if="${not requests.isLast()}">&rarr;</a><a th:if="${requests.isLast()}">&rarr;</a> <a id="next-page-link" th:href="@{/(page=${requests.getNumber() + 1})}" title="Seite vor: Taste D" th:if="${not requests.isLast()}">&rarr;</a><a th:if="${requests.isLast()}">&rarr;</a>
<a id="last-page-link" th:href="@{/(page=${requests.getTotalPages() - 1})}" title="Zum Ende: Taste S" th:if="${not requests.isLast()}">&rarrb;</a><a th:if="${requests.isLast()}">&rarrb;</a> <a id="last-page-link" th:href="@{/(page=${requests.getTotalPages() - 1})}" title="Zum Ende: Taste S" th:if="${not requests.isLast()}">&rarrb;</a><a th:if="${requests.isLast()}">&rarrb;</a>
</div> </div>
<div th:if="${patientId != null}" class="page-control">
<a id="first-page-link" th:href="@{/patient/{patientId}(patientId=${patientId},page=${0})}" title="Zum Anfang: Taste W" th:if="${not requests.isFirst()}">&larrb;</a><a th:if="${requests.isFirst()}">&larrb;</a>
<a id="prev-page-link" th:href="@{/patient/{patientId}(patientId=${patientId},page=${requests.getNumber() - 1})}" title="Seite zurück: Taste A" th:if="${not requests.isFirst()}">&larr;</a><a th:if="${requests.isFirst()}">&larr;</a>
<span>Seite [[ ${requests.getNumber() + 1} ]] von [[ ${requests.getTotalPages()} ]]</span>
<a id="next-page-link" th:href="@{/patient/{patientId}(patientId=${patientId},page=${requests.getNumber() + 1})}" title="Seite vor: Taste D" th:if="${not requests.isLast()}">&rarr;</a><a th:if="${requests.isLast()}">&rarr;</a>
<a id="last-page-link" th:href="@{/patient/{patientId}(patientId=${patientId},page=${requests.getTotalPages() - 1})}" title="Zum Ende: Taste S" th:if="${not requests.isLast()}">&rarrb;</a><a th:if="${requests.isLast()}">&rarrb;</a>
</div>
<table class="paged"> <table class="paged">
<thead> <thead>
<tr> <tr>
@ -39,10 +53,16 @@
<td th:style="${request.type.value == 'delete'} ? 'color: red;'"><small>[[ ${request.type} ]]</small></td> <td th:style="${request.type.value == 'delete'} ? 'color: red;'"><small>[[ ${request.type} ]]</small></td>
<td th:if="not ${request.report}">[[ ${request.uuid} ]]</td> <td th:if="not ${request.report}">[[ ${request.uuid} ]]</td>
<td th:if="${request.report}"> <td th:if="${request.report}">
<a th:href="@{/report/{id}(id=${request.uuid})}">[[ ${request.uuid} ]]</a> <th:block sec:authorize="not authenticated">[[ ${request.uuid} ]]</th:block>
<a th:href="@{/report/{id}(id=${request.uuid})}" sec:authorize="authenticated">[[ ${request.uuid} ]]</a>
</td> </td>
<td><time th:datetime="${request.processedAt}">[[ ${request.processedAt} ]]</time></td> <td><time th:datetime="${request.processedAt}">[[ ${request.processedAt} ]]</time></td>
<td class="patient-id" sec:authorize="authenticated">[[ ${request.patientId} ]]</td> <td class="patient-id" th:if="${patientId != null}" sec:authorize="authenticated">
[[ ${request.patientId} ]]
</td>
<td class="patient-id" th:if="${patientId == null}" sec:authorize="authenticated">
<a th:href="@{/patient/{pid}(pid=${request.patientId})}">[[ ${request.patientId} ]]</a>
</td>
<td class="patient-id" sec:authorize="not authenticated">***</td> <td class="patient-id" sec:authorize="not authenticated">***</td>
</tr> </tr>
</tbody> </tbody>
@ -68,6 +88,12 @@
} }
}; };
}); });
const eventSource = new EventSource('statistics/events');
eventSource.addEventListener('newrequest', event => {
console.log(event);
document.getElementById('reload-notify').style.display = 'inline-flex';
});
</script> </script>
</body> </body>
</html> </html>

View File

@ -13,9 +13,11 @@
<div class="centered notification error" th:if="${param.error}">Anmeldung nicht erfolgreich</div> <div class="centered notification error" th:if="${param.error}">Anmeldung nicht erfolgreich</div>
<div class="centered notification success" th:if="${param.logout}">Sie haben sich abgemeldet</div> <div class="centered notification success" th:if="${param.logout}">Sie haben sich abgemeldet</div>
<form method="post" th:action="@{/login}"> <form method="post" th:action="@{/login}">
<input type="text" id="username" name="username" class="form-control" placeholder="Username" required="" autofocus=""> <input type="text" id="username" name="username" class="form-control" placeholder="Username" required="" autofocus="" />
<input type="password" id="password" name="password" class="form-control" placeholder="Password" required=""> <input type="password" id="password" name="password" class="form-control" placeholder="Password" required="" />
<button class="" type="submit">Anmelden</button> <button type="submit">Anmelden</button>
<hr th:if="${not oidcLogins.isEmpty()}" />
<a th:each="oidcLogin : ${oidcLogins}" class="btn" th:href="@{/oauth2/authorization/{provider}(provider=${oidcLogin.component1()})}">OIDC Login - [[ ${oidcLogin.component2()} ]]</a>
</form> </form>
</div> </div>
</main> </main>

View File

@ -38,7 +38,7 @@
</section> </section>
</main> </main>
<script th:src="@{/echarts.min.js}"></script> <script th:src="@{/webjars/echarts/dist/echarts.min.js}"></script>
<script th:src="@{/scripts.js}"></script> <script th:src="@{/scripts.js}"></script>
<script> <script>
window.onload = () => { window.onload = () => {

View File

@ -0,0 +1,154 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.services
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith
import org.mockito.ArgumentCaptor
import org.mockito.ArgumentMatchers.anyLong
import org.mockito.ArgumentMatchers.anyString
import org.mockito.Mock
import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.*
import org.springframework.security.crypto.password.PasswordEncoder
import org.springframework.security.provisioning.InMemoryUserDetailsManager
import java.util.*
import java.util.function.Consumer
@ExtendWith(MockitoExtension::class)
class TokenServiceTest {
private lateinit var userDetailsManager: InMemoryUserDetailsManager
private lateinit var passwordEncoder: PasswordEncoder
private lateinit var tokenRepository: TokenRepository
private lateinit var tokenService: TokenService
@BeforeEach
fun setup(
@Mock userDetailsManager: InMemoryUserDetailsManager,
@Mock passwordEncoder: PasswordEncoder,
@Mock tokenRepository: TokenRepository
) {
this.userDetailsManager = userDetailsManager
this.passwordEncoder = passwordEncoder
this.tokenRepository = tokenRepository
this.tokenService = TokenService(userDetailsManager, passwordEncoder, tokenRepository)
}
@Test
fun shouldEncodePasswordForNewToken() {
doAnswer { "{test}verysecret" }.whenever(passwordEncoder).encode(anyString())
val actual = this.tokenService.addToken("Test Token")
assertThat(actual).satisfies(
Consumer { assertThat(it.isSuccess).isTrue() },
Consumer { assertThat(it.getOrNull()).matches("testtoken:[A-Za-z0-9]{48}$") }
)
}
@Test
fun shouldContainAlphanumTokenUserPart() {
doAnswer { "{test}verysecret" }.whenever(passwordEncoder).encode(anyString())
val actual = this.tokenService.addToken("Test Token")
assertThat(actual).satisfies(
Consumer { assertThat(it.isSuccess).isTrue() },
Consumer { assertThat(it.getOrDefault("")).startsWith("testtoken:") }
)
}
@Test
fun shouldNotAllowSameTokenUserPartTwice() {
doReturn(true).whenever(userDetailsManager).userExists(anyString())
val actual = this.tokenService.addToken("Test Token")
assertThat(actual).satisfies(Consumer { assertThat(it.isFailure).isTrue() })
verify(tokenRepository, never()).save(any())
}
@Test
fun shouldSaveNewToken() {
doAnswer { "{test}verysecret" }.whenever(passwordEncoder).encode(anyString())
val actual = this.tokenService.addToken("Test Token")
val captor = ArgumentCaptor.forClass(Token::class.java)
verify(tokenRepository, times(1)).save(captor.capture())
assertThat(actual).satisfies(Consumer { assertThat(it.isSuccess).isTrue() })
assertThat(captor.value).satisfies(
Consumer { assertThat(it.name).isEqualTo("Test Token") },
Consumer { assertThat(it.username).isEqualTo("testtoken") },
Consumer { assertThat(it.password).isEqualTo("{test}verysecret") }
)
}
@Test
fun shouldDeleteExistingToken() {
doAnswer {
val id = it.arguments[0] as Long
Optional.of(Token(id, "Test Token", "testtoken", "{test}hsdajfgadskjhfgsdkfjg"))
}.whenever(tokenRepository).findById(anyLong())
this.tokenService.deleteToken(42)
val stringCaptor = ArgumentCaptor.forClass(String::class.java)
verify(userDetailsManager, times(1)).deleteUser(stringCaptor.capture())
assertThat(stringCaptor.value).isEqualTo("testtoken")
val tokenCaptor = ArgumentCaptor.forClass(Token::class.java)
verify(tokenRepository, times(1)).delete(tokenCaptor.capture())
assertThat(tokenCaptor.value.id).isEqualTo(42)
}
@Test
fun shouldReturnAllTokensFromRepository() {
val expected = listOf(
Token(1, "Test Token 1", "testtoken1", "{test}hsdajfgadskjhfgsdkfjg"),
Token(2, "Test Token 2", "testtoken2", "{test}asdasdasdasdasdasdasd")
)
doReturn(expected).whenever(tokenRepository).findAll()
assertThat(tokenService.findAll()).isEqualTo(expected)
}
@Test
fun shouldAddAllTokensFromRepositoryToUserDataManager() {
val expected = listOf(
Token(1, "Test Token 1", "testtoken1", "{test}hsdajfgadskjhfgsdkfjg"),
Token(2, "Test Token 2", "testtoken2", "{test}asdasdasdasdasdasdasd")
)
doReturn(expected).whenever(tokenRepository).findAll()
tokenService.setup()
verify(userDetailsManager, times(expected.size)).createUser(any())
}
}