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20
.github/workflows/deploy.yml vendored
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@ -1,4 +1,4 @@
name: 'Run build and deploy'
name: "Run build and deploy"
on:
release:
@ -8,20 +8,20 @@ jobs:
docker:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/setup-java@v4
- uses: actions/checkout@v3
- uses: actions/setup-java@v3
with:
java-version: '21'
java-version: '17'
distribution: 'temurin'
- name: Setup Gradle
uses: gradle/actions/setup-gradle@v3
uses: gradle/gradle-build-action@v2.4.2
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
uses: docker/setup-buildx-action@v2
- name: Login to Docker Hub
uses: docker/login-action@v3
uses: docker/login-action@v2
with:
registry: ghcr.io
username: ${{ github.actor }}
@ -30,6 +30,6 @@ jobs:
- name: Execute image build and push
run: |
./gradlew bootBuildImage
docker tag ghcr.io/${{ github.repository }} ghcr.io/${{ github.repository }}:${{ github.ref_name }}
docker push ghcr.io/${{ github.repository }}
docker push ghcr.io/${{ github.repository }}:${{ github.ref_name }}
docker tag ghcr.io/ccc-mf/etl-processor ghcr.io/ccc-mf/etl-processor:${{ github.ref_name }}
docker push ghcr.io/ccc-mf/etl-processor
docker push ghcr.io/ccc-mf/etl-processor:${{ github.ref_name }}

16
.github/workflows/test.yml vendored
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@ -11,14 +11,14 @@ jobs:
tests:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/setup-java@v4
- uses: actions/checkout@v3
- uses: actions/setup-java@v3
with:
java-version: '21'
java-version: '17'
distribution: 'temurin'
- name: Setup Gradle
uses: gradle/actions/setup-gradle@v3
uses: gradle/gradle-build-action@v2.4.2
- name: Execute tests
run: ./gradlew test
@ -26,14 +26,14 @@ jobs:
integrationTests:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/setup-java@v4
- uses: actions/checkout@v3
- uses: actions/setup-java@v3
with:
java-version: '21'
java-version: '17'
distribution: 'temurin'
- name: Setup Gradle
uses: gradle/actions/setup-gradle@v3
uses: gradle/gradle-build-action@v2.4.2
- name: Execute integration tests
run: ./gradlew integrationTest

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

306
README.md
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@ -1,221 +1,87 @@
# ETL-Processor for DNPM:DIP [![Run Tests](https://github.com/pcvolkmer/etl-processor/actions/workflows/test.yml/badge.svg)](https://github.com/pcvolkmer/etl-processor/actions/workflows/test.yml)
# ETL-Processor for bwHC data [![Run Tests](https://github.com/CCC-MF/etl-processor/actions/workflows/test.yml/badge.svg)](https://github.com/CCC-MF/etl-processor/actions/workflows/test.yml)
Diese Anwendung versendet ein bwHC-MTB-File im bwHC-Datenmodell 1.0 an DNPM:DIP und pseudonymisiert die Patienten-ID.
Diese Anwendung versendet ein bwHC-MTB-File an das bwHC-Backend und pseudonymisiert die Patienten-ID.
## Einordnung innerhalb einer DNPM-ETL-Strecke
### Einordnung innerhalb einer DNPM-ETL-Strecke
Diese Anwendung erlaubt das Entgegennehmen von HTTP/REST-Anfragen aus dem Onkostar-Plugin **[onkostar-plugin-dnpmexport](https://github.com/CCC-MF/onkostar-plugin-dnpmexport)**.
Diese Anwendung erlaubt das Entgegennehmen HTTP/REST-Anfragen aus dem Onkostar-Plugin **[onkostar-plugin-dnpmexport](https://github.com/CCC-MF/onkostar-plugin-dnpmexport)**.
Der Inhalt einer Anfrage, wenn ein bwHC-MTBFile, wird pseudonymisiert und auf Duplikate geprüft.
Duplikate werden verworfen, Änderungen werden weitergeleitet.
Löschanfragen werden immer als Löschanfrage an DNPM:DIP weitergeleitet.
Zudem ist eine minimalistische Weboberfläche integriert, die einen Einblick in den aktuellen Zustand der Anwendung gewährt.
Löschanfragen werden immer als Löschanfrage an das bwHC-backend weitergeleitet.
![Modell DNPM-ETL-Strecke](docs/etl.png)
### Duplikaterkennung
#### HTTP/REST-Konfiguration
Die Erkennung von Duplikaten ist normalerweise immer aktiv, kann jedoch über den Konfigurationsparameter
`APP_DUPLICATION_DETECTION=false` deaktiviert werden.
Anfragen werden, wenn nicht als Duplikat behandelt, nach der Pseudonymisierung direkt an das bwHC-Backend gesendet.
### Datenübermittlung über HTTP/REST
Anfragen werden, wenn nicht als Duplikat behandelt, nach der Pseudonymisierung direkt an DNPM:DIP gesendet.
Ein HTTP Request kann, angenommen die Installation erfolgte auf dem Host `dnpm.example.com` an nachfolgende URLs gesendet werden:
| HTTP-Request | URL | Consent-Status im Datensatz | Bemerkung |
|--------------|-----------------------------------------|-----------------------------|---------------------------------------------------------------------------------|
| `POST` | `https://dnpm.example.com/mtb` | `ACTIVE` | Die Anwendung verarbeitet den eingehenden Datensatz |
| `POST` | `https://dnpm.example.com/mtb` | `REJECT` | Die Anwendung sendet einen Lösch-Request für die im Datensatz angegebene Pat-ID |
| `DELETE` | `https://dnpm.example.com/mtb/12345678` | - | Die Anwendung sendet einen Lösch-Request für Pat-ID `12345678` |
Anstelle des Pfads `/mtb` kann auch, wie in Version 0.9 und älter üblich, `/mtbfile` verwendet werden.
### Datenübermittlung mit Apache Kafka
#### Konfiguration für Apache Kafka
Anfragen werden, wenn nicht als Duplikat behandelt, nach der Pseudonymisierung an Apache Kafka übergeben.
Eine Antwort wird dabei ebenfalls mithilfe von Apache Kafka übermittelt und nach der Entgegennahme verarbeitet.
Siehe hierzu auch: https://github.com/CCC-MF/kafka-to-bwhc
## Konfiguration
### 🔥 Wichtige Änderungen in Version 0.10
Ab Version 0.10 wird [DNPM:DIP](https://github.com/dnpm-dip) unterstützt und als Standardendpunkt verwendet.
Soll noch das alte bwHC-Backend verwendet werden, so ist die Umgebungsvariable `APP_REST_IS_BWHC` auf `true` zu setzen.
### 🔥 Breaking Changes nach Version 0.10
In Versionen des ETL-Processors **nach Version 0.10** werden die folgenden Konfigurationsoptionen entfernt:
* `APP_KAFKA_TOPIC`: Nutzen Sie nun die Konfigurationsoption `APP_KAFKA_OUTPUT_TOPIC`
* `APP_KAFKA_RESPONSE_TOPIC`: Nutzen Sie nun die Konfigurationsoption `APP_KAFKA_OUTPUT_RESPONSE_TOPIC`
Der Pfad zum Versenden von MTB-Daten ist nun offiziell `/mtb`.
In Versionen **nach Version 0.10** wird die Unterstützung des Pfads `/mtbfile` entfernt.
### Pseudonymisierung der Patienten-ID
## Pseudonymisierung der Patienten-ID
Wenn eine URI zu einer gPAS-Instanz (Version >= 2023.1.0) angegeben ist, wird diese verwendet.
Ist diese nicht gesetzt. wird intern eine Anonymisierung der Patienten-ID vorgenommen.
* `APP_PSEUDONYMIZE_PREFIX`: Standortbezogenes Präfix - `UNKNOWN`, wenn nicht gesetzt
* `APP_PSEUDONYMIZE_PREFIX`: Standortbezogenes Prefix - `UNKNOWN`, wenn nicht gesetzt
* `APP_PSEUDONYMIZE_GENERATOR`: `BUILDIN` oder `GPAS` - `BUILDIN`, wenn nicht gesetzt
**Hinweis**
### Eingebaute Pseudonymisierung
Die Pseudonymisierung erfolgt im ETL-Prozessor nur für die Patienten-ID.
Andere IDs werden mithilfe des standortbezogenen Präfixes (erneut) anonymisiert, um für den aktuellen Kontext nicht
vergleichbare IDs bereitzustellen.
#### Eingebaute Anonymisierung
Wurde keine oder die Verwendung der eingebauten Anonymisierung konfiguriert, so wird für die Patienten-ID der
entsprechende SHA-256-Hash gebildet und Base64-codiert - hier ohne endende "=" - zuzüglich des konfigurierten Präfixes
Wurde keine oder die Verwendung der eingebauten Pseudonymisierung konfiguriert, so wird für die Patienten-ID der
entsprechende SHA-256-Hash gebildet und Base64-codiert - hier ohne endende "=" - zuzüglich des konfigurierten Prefixes
als Patienten-Pseudonym verwendet.
#### Pseudonymisierung mit gPAS
### Pseudonymisierung mit gPAS
Wurde die Verwendung von gPAS konfiguriert, so sind weitere Angaben zu konfigurieren.
* `APP_PSEUDONYMIZE_GPAS_URI`: URI der gPAS-Instanz inklusive Endpoint (z.B. `http://localhost:8080/ttp-fhir/fhir/gpas/$$pseudonymizeAllowCreate`)
* `APP_PSEUDONYMIZE_GPAS_URI`: URI der gPAS-Instanz inklusive Endpoint (
z.B. `http://localhost:8080/ttp-fhir/fhir/gpas/$$pseudonymizeAllowCreate`)
* `APP_PSEUDONYMIZE_GPAS_TARGET`: gPas Domänenname
* `APP_PSEUDONYMIZE_GPAS_USERNAME`: gPas Basic-Auth Benutzername
* `APP_PSEUDONYMIZE_GPAS_PASSWORD`: gPas Basic-Auth Passwort
* `APP_PSEUDONYMIZE_GPAS_SSLCALOCATION`: Root Zertifikat für gPas, falls es dediziert hinzugefügt werden muss.
### Anmeldung mit einem Passwort
Ein initialer Administrator-Account kann optional konfiguriert werden und sorgt dafür, dass bestimmte Bereiche nur nach
einem erfolgreichen Login erreichbar sind.
* `APP_SECURITY_ADMIN_USER`: Muss angegeben werden zur Aktivierung der Zugriffsbeschränkung.
* `APP_SECURITY_ADMIN_PASSWORD`: Das Passwort für den Administrator (Empfohlen).
Ein Administrator-Passwort muss inklusive des Encoding-Präfixes vorliegen.
Hier Beispiele für das Beispielpasswort `very-secret`:
* `{noop}very-secret` (Das Passwort liegt im Klartext vor - nicht empfohlen!)
* `{bcrypt}$2y$05$CCkfsMr/wbTleMyjVIK8g.Aa3RCvrvoLXVAsL.f6KeouS88vXD9b6`
* `{sha256}9a34717f0646b5e9cfcba70055de62edb026ff4f68671ba3db96aa29297d2df5f1a037d58c745657`
Wird kein Administrator-Passwort angegeben, wird ein zufälliger Wert generiert und beim Start der Anwendung in den Logs
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.
#### Rollenbasierte Berechtigungen
Wird OpenID Connect verwendet, gibt es eine rollenbasierte Berechtigungszuweisung.
Die Standardrolle für neue OIDC-Benutzer kann mit der Option `APP_SECURITY_DEFAULT_USER_ROLE` festgelegt werden.
Mögliche Werte sind `user` oder `guest`. Standardwert ist `user`.
Benutzer mit der Rolle "Gast" sehen nur die Inhalte, die auch nicht angemeldete Benutzer sehen.
Hierdurch ist es möglich, einzelne Benutzer einzuschränken oder durch Änderung der Standardrolle auf `guest` nur
einzelne Benutzer als vollwertige Nutzer zuzulassen.
![Rollenverwaltung](docs/userroles.png)
Benutzer werden nach dem Entfernen oder der Änderung der vergebenen Rolle automatisch abgemeldet und müssen sich neu anmelden.
Sie bekommen dabei wieder die Standardrolle zugewiesen.
#### Auswirkungen auf den dargestellten Inhalt
Nur Administratoren haben Zugriff auf den Konfigurationsbereich, nur angemeldete Benutzer können die anonymisierte oder
pseudonymisierte Patienten-ID sowie den Qualitätsbericht von DNPM:DIP einsehen.
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 kann der Endpunkt für das Onkostar-Plugin **[onkostar-plugin-dnpmexport](https://github.com/CCC-MF/onkostar-plugin-dnpmexport)** wie folgt konfiguriert werden:
```
https://testonkostar:MTg1NTL...NGU4@etl.example.com/mtbfile
```
Ist die Verwendung von Tokens aktiv, werden Anfragen ohne die Angabe der Token-Information abgelehnt.
Alternativ kann eine Authentifizierung über Benutzername/Passwort oder OIDC erfolgen.
### 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,
der von DNPM:DIP akzeptiert wird.
der vom bwHC-Backend akzeptiert wird.
Diese Anwendung bietet daher die Möglichkeit, eine Transformation vorzunehmen. Hierzu muss der "Pfad" innerhalb des JSON-MTB-Files angegeben werden und
welcher Wert wie ersetzt werden soll.
Hier ein Beispiel für die erste (Index 0 - weitere dann mit 1,2, ...) Transformationsregel:
Hier ein Beispiel für die erste (Index 0 - weitere dann mit 1,2,...) Transformationsregel:
* `APP_TRANSFORMATIONS_0_PATH`: Pfad zum Wert in der JSON-MTB-Datei. Beispiel: `diagnoses[*].icd10.version` für **alle** Diagnosen
* `APP_TRANSFORMATIONS_0_FROM`: Angabe des Werts, der ersetzt werden soll. Andere Werte bleiben dabei unverändert.
* `APP_TRANSFORMATIONS_0_TO`: Angabe des neuen Werts.
### Mögliche Endpunkte zur Datenübermittlung
## Mögliche Endpunkte
Für REST-Requests als auch zur Nutzung von Kafka-Topics können Endpunkte konfiguriert werden.
Es ist dabei nur die Konfiguration eines Endpunkts zulässig.
Werden sowohl REST als auch Kafka-Endpunkt konfiguriert, wird nur der REST-Endpunkt verwendet.
#### REST
### REST
Folgende Umgebungsvariablen müssen gesetzt sein, damit ein bwHC-MTB-File an DNPM:DIP gesendet wird:
Folgende Umgebungsvariablen müssen gesetzt sein, damit ein bwHC-MTB-File an das bwHC-Backend gesendet wird:
* `APP_REST_URI`: URI der zu benutzenden API der Backend-Instanz. Zum Beispiel:
* `http://localhost:9000/bwhc/etl/api` für **bwHC Backend**
* `http://localhost:9000/api` für **dnpm:dip**
* `APP_REST_USERNAME`: Basic-Auth-Benutzername für den REST-Endpunkt
* `APP_REST_PASSWORD`: Basic-Auth-Passwort für den REST-Endpunkt
* `APP_REST_IS_BWHC`: `true` für **bwHC Backend**, weglassen oder `false` für **dnpm:dip**
* `APP_REST_URI`: URI der zu benutzenden API der bwHC-Backend-Instanz. z.B.: `http://localhost:9000/bwhc/etl/api`
#### Kafka-Topics
### Kafka-Topics
Folgende Umgebungsvariablen müssen gesetzt sein, damit ein bwHC-MTB-File an ein Kafka-Topic übermittelt wird:
* `APP_KAFKA_OUTPUT_TOPIC`: Zu verwendendes Topic zum Versenden von Anfragen.
* `APP_KAFKA_OUTPUT_RESPONSE_TOPIC`: Topic mit Antworten über den Erfolg des Versendens. Standardwert: `APP_KAFKA_TOPIC` mit Anhang "_response".
* `APP_KAFKA_TOPIC`: Zu verwendendes Topic zum Versenden von Anfragen
* `APP_KAFKA_RESPONSE_TOPIC`: Topic mit Antworten über den Erfolg des Versendens. Standardwert: `APP_KAFKA_TOPIC` mit Anhang "_response".
* `APP_KAFKA_GROUP_ID`: Kafka GroupID des Consumers. Standardwert: `APP_KAFKA_TOPIC` mit Anhang "_group".
* `APP_KAFKA_SERVERS`: Zu verwendende Kafka-Bootstrap-Server als kommagetrennte Liste
@ -223,12 +89,10 @@ Wird keine Rückantwort über Apache Kafka empfangen und es gibt keine weitere M
Weitere Einstellungen können über die Parameter von Spring Kafka konfiguriert werden.
Lässt sich keine Verbindung zu dem Backend aufbauen, wird eine Rückantwort mit Status-Code `900` erwartet, welchen es
Lässt sich keine Verbindung zu dem bwHC-Backend aufbauen, wird eine Rückantwort mit Status-Code `900` erwartet, welchen es
für HTTP nicht gibt.
Wird die Umgebungsvariable `APP_KAFKA_INPUT_TOPIC` gesetzt, kann eine Nachricht auch über dieses Kafka-Topic an den ETL-Prozessor übermittelt werden.
##### Retention Time
#### Retention Time
Generell werden in Apache Kafka alle Records entsprechend der Konfiguration vorgehalten.
So wird ohne spezielle Konfiguration ein Record für 7 Tage in Apache Kafka gespeichert.
@ -241,7 +105,7 @@ Beispiel - auszuführen innerhalb des Kafka-Containers: Löschen alter Records n
kafka-configs.sh --bootstrap-server localhost:9092 --alter --topic test --add-config retention.ms=86400000
```
##### Key based Retention
#### Key based Retention
Möchten Sie hingegen immer nur die letzte Meldung für einen Patienten und eine Erkrankung in Apache Kafka vorhalten,
so ist die nachfolgend genannte Konfiguration der Kafka-Topics hilfreich.
@ -257,42 +121,19 @@ kafka-configs.sh --bootstrap-server localhost:9092 --alter --topic test --add-co
kafka-configs.sh --bootstrap-server localhost:9092 --alter --topic test --add-config cleanup.policy=[delete,compact]
```
Da als Key eines Records die (pseudonymisierte) Patienten-ID verwendet wird, stehen mit obiger Konfiguration
der Kafka-Topics nach 10 Sekunden nur noch der jeweils letzte Eintrag für den entsprechenden Key zur Verfügung.
Da als Key eines Records die (pseudonymisierte) Patienten-ID und die (anonymisierte) Erkrankungs-ID verwendet wird,
stehen mit obiger Konfiguration der Kafka-Topics nach 10 Sekunden nur noch der jeweils letzte Eintrag für den entsprechenden
Key zur Verfügung.
Da der Key sowohl für die Records in Richtung DNPM:DIP, als auch für die Rückantwort identisch aufgebaut ist, lassen sich so
Da der Key sowohl für die Records in Richtung bwHC-Backend für die Rückantwort identisch aufgebaut ist, lassen sich so
auch im Falle eines Consent-Widerspruchs die enthaltenen Daten als auch die Offenlegung durch Verifikationsdaten in der
Antwort effektiv verhindern, da diese nach 10 Sekunden gelöscht werden.
Es steht dann nur noch die jeweils letzten Information zur Verfügung, dass für einen Patienten/eine Erkrankung
ein Consent-Widerspruch erfolgte.
Dieses Vorgehen empfiehlt sich, wenn Sie gespeicherte Records nachgelagert für andere Auswertungen verwenden möchten.
### Antworten und Statusauswertung
Anfragen an das bwHC-Backend aus Versionen bis 0.9.x wurden wie folgt behandelt:
| HTTP-Response | Status |
|----------------|-----------|
| `HTTP 200` | `SUCCESS` |
| `HTTP 201` | `WARNING` |
| `HTTP 400-...` | `ERROR` |
Dies konnte dazu führen, dass zwar mit einem `HTTP 201` geantwortet wurde, aber dennoch in der Issue-Liste die
Severity `error` aufgetaucht ist.
Ab Version 0.10 wird die Issue-Liste der Antwort verwendet und die darion enthaltene höchste Severity-Stufe als Ergebnis verwendet.
| Höchste Severity | Status |
|------------------|-----------|
| `info` | `SUCCESS` |
| `warning` | `WARNING` |
| `error`, `fatal` | `ERROR` |
## Docker-Images
Diese Anwendung ist auch als Docker-Image verfügbar: https://github.com/pcvolkmer/etl-processor/pkgs/container/etl-processor
Diese Anwendung ist auch als Docker-Image verfügbar: https://github.com/CCC-MF/etl-processor/pkgs/container/etl-processor
### Images lokal bauen
@ -300,37 +141,8 @@ Diese Anwendung ist auch als Docker-Image verfügbar: https://github.com/pcvolkm
./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
*Ausführen als Docker Container:*
*Ausführen als Docker Conatiner:*
```bash
cd ./deploy
@ -342,50 +154,6 @@ Wenn gewünscht, Änderungen in der `.env` vornehmen.
docker compose up -d
```
### Einfaches Beispiel für ein eigenes Docker-Compose-File
Die Datei [`docs/docker-compose.yml`](docs/docker-compose.yml) zeigt eine einfache Konfiguration für REST-Requests basierend
auf Docker-Compose mit der gestartet werden kann.
### Betrieb hinter einem Reverse-Proxy
Die Anwendung verarbeitet `X-Forwarded`-HTTP-Header und kann daher auch hinter einem Reverse-Proxy betrieben werden.
Dabei werden, je nachdem welche Header durch den Reverse-Proxy gesendet werden auch Protokoll, Host oder auch Path-Präfix
automatisch erkannt und verwendet werden. Dadurch ist z.B. eine abweichende Angabe des Pfads problemlos möglich.
#### Beispiel *Traefik* (mit Docker-Labels):
Das folgende Beispiel zeigt die Konfiguration in einer Docker-Compose-Datei mit Service-Labels.
```
...
deploy:
labels:
- "traefik.http.routers.etl.rule=PathPrefix(`/etl-processor`)"
- "traefik.http.routers.etl.middlewares=etl-path-strip"
- "traefik.http.middlewares.etl-path-strip.stripprefix.prefixes=/etl-processor"
...
```
#### Beispiel *nginx*
Das folgende Beispiel zeigt die Konfiguration einer _location_ in einer nginx-Konfigurationsdatei.
```
...
location /etl-processor {
set $upstream http://<beispiel:8080>/;
proxy_set_header Host $host;
proxy_set_header X-Forwarded-Scheme $scheme;
proxy_set_header X-Forwarded-Proto $scheme;
proxy_set_header X-Forwarded-For $remote_addr;
proxy_set_header X-Real-IP $remote_addr;
proxy_pass $upstream;
}
...
```
## Entwicklungssetup
Zum Starten einer lokalen Entwicklungs- und Testumgebung kann die beiliegende Datei `dev-compose.yml` verwendet werden.
@ -405,5 +173,3 @@ Die Datei `application-dev.yml` enthält hierzu die Konfiguration für das Profi
Beim Ausführen der Integrationstests wird eine Testdatenbank in einem Docker-Container gestartet.
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.

5
bindings/README.md
View File

@ -1,5 +0,0 @@
# 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.

1
bindings/ca-certificates/type
View File

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

102
build.gradle.kts
View File

@ -1,36 +1,31 @@
import org.gradle.api.tasks.testing.logging.TestLogEvent
import org.jetbrains.kotlin.gradle.dsl.JvmTarget
import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
import org.springframework.boot.gradle.tasks.bundling.BootBuildImage
plugins {
war
id("org.springframework.boot") version "3.4.4"
id("io.spring.dependency-management") version "1.1.7"
kotlin("jvm") version "1.9.25"
kotlin("plugin.spring") version "1.9.25"
jacoco
id("org.springframework.boot") version "3.2.0"
id("io.spring.dependency-management") version "1.1.4"
kotlin("jvm") version "1.9.21"
kotlin("plugin.spring") version "1.9.21"
}
group = "dev.dnpm"
version = "0.11.0-SNAPSHOT"
group = "de.ukw.ccc"
version = "0.3.0"
var versions = mapOf(
"bwhc-dto-java" to "0.4.0",
"mtb-dto" to "0.1.0-SNAPSHOT",
"hapi-fhir" to "7.6.0",
"mockito-kotlin" to "5.4.0",
"archunit" to "1.3.0",
// Webjars
"webjars-locator" to "0.52",
"echarts" to "5.4.3",
"htmx.org" to "1.9.12"
"bwhc-dto-java" to "0.2.0",
"hapi-fhir" to "6.6.2",
"httpclient5" to "5.2.1",
"mockito-kotlin" to "5.1.0"
)
// Override Apache Kafka to be used
// Fixes: CVE-2023-34455, CVE-2023-34454, CVE-2023-34453 and CVE-2023-43642
extra["kafka.version"] = "3.6.0"
java {
toolchain {
languageVersion = JavaLanguageVersion.of(21)
}
sourceCompatibility = JavaVersion.VERSION_17
}
sourceSets {
@ -49,18 +44,9 @@ configurations {
compileOnly {
extendsFrom(configurations.annotationProcessor.get())
}
all {
resolutionStrategy {
cacheChangingModulesFor(5, "minutes")
}
}
}
repositories {
maven {
url = uri("https://git.dnpm.dev/api/packages/public-snapshots/maven")
}
maven {
url = uri("https://git.dnpm.dev/api/packages/public/maven")
}
@ -72,51 +58,35 @@ dependencies {
implementation("org.springframework.boot:spring-boot-starter-thymeleaf")
implementation("org.springframework.boot:spring-boot-starter-web")
implementation("org.springframework.boot:spring-boot-starter-data-jdbc")
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("com.fasterxml.jackson.module:jackson-module-kotlin")
implementation("org.springframework.kafka:spring-kafka")
implementation("org.flywaydb:flyway-database-postgresql")
// fix CVE-2022-1471
implementation("org.yaml:snakeyaml:2.1")
implementation("org.flywaydb:flyway-mysql")
implementation("commons-codec:commons-codec")
implementation("io.projectreactor.kotlin:reactor-kotlin-extensions")
implementation("de.ukw.ccc:bwhc-dto-java:${versions["bwhc-dto-java"]}")
implementation("dev.pcvolkmer.mv64e:mtb-dto:${versions["mtb-dto"]}") { isChanging = true }
implementation("ca.uhn.hapi.fhir:hapi-fhir-base:${versions["hapi-fhir"]}")
implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${versions["hapi-fhir"]}")
implementation("org.apache.httpcomponents.client5:httpclient5")
implementation("org.apache.httpcomponents.client5:httpclient5:${versions["httpclient5"]}")
implementation("com.jayway.jsonpath:json-path")
implementation("org.webjars:webjars-locator:${versions["webjars-locator"]}")
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.postgresql:postgresql")
developmentOnly("org.springframework.boot:spring-boot-devtools")
developmentOnly("org.springframework.boot:spring-boot-docker-compose")
annotationProcessor("org.springframework.boot:spring-boot-configuration-processor")
providedRuntime("org.springframework.boot:spring-boot-starter-tomcat")
testImplementation("org.springframework.boot:spring-boot-starter-test")
testImplementation("org.springframework.security:spring-security-test")
testImplementation("io.projectreactor:reactor-test")
testImplementation("org.mockito.kotlin:mockito-kotlin:${versions["mockito-kotlin"]}")
integrationTestImplementation("org.testcontainers:junit-jupiter")
integrationTestImplementation("org.testcontainers:postgresql")
integrationTestImplementation("com.tngtech.archunit:archunit:${versions["archunit"]}")
integrationTestImplementation("org.htmlunit:htmlunit")
integrationTestImplementation("org.springframework:spring-webflux")
}
tasks.withType<KotlinCompile> {
compilerOptions {
freeCompilerArgs.add("-Xjsr305=strict")
jvmTarget.set(JvmTarget.JVM_21)
kotlinOptions {
freeCompilerArgs += "-Xjsr305=strict"
jvmTarget = "17"
}
}
@ -127,9 +97,8 @@ tasks.withType<Test> {
}
}
tasks.register<Test>("integrationTest") {
task<Test>("integrationTest") {
description = "Runs integration tests"
group = "verification"
testClassesDirs = sourceSets["integrationTest"].output.classesDirs
classpath = sourceSets["integrationTest"].runtimeClasspath
@ -137,34 +106,11 @@ tasks.register<Test>("integrationTest") {
shouldRunAfter("test")
}
tasks.register("allTests") {
description = "Run all tests"
group = JavaBasePlugin.VERIFICATION_GROUP
dependsOn(tasks.withType<Test>())
}
tasks.jacocoTestReport {
dependsOn("allTests")
executionData(fileTree(project.rootDir.absolutePath).include("**/build/jacoco/*.exec"))
reports {
xml.required = true
}
}
tasks.named<BootBuildImage>("bootBuildImage") {
imageName.set("ghcr.io/pcvolkmer/etl-processor")
// Binding for CA Certs
bindings.set(listOf(
"$rootDir/bindings/ca-certificates/:/platform/bindings/ca-certificates"
))
imageName.set("ghcr.io/ccc-mf/etl-processor")
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/pcvolkmer/etl-processor",
"BP_OCI_SOURCE" to "https://github.com/CCC-MF/etl-processor",
"BP_OCI_LICENSES" to "AGPLv3",
"BP_OCI_DESCRIPTION" to "ETL Processor for bwHC MTB files"
))

5
deploy/docker-compose.yaml
View File

@ -18,11 +18,6 @@ services:
APP_KAFKA_GROUP_ID: ${DNPM_KAFKA_GROUP_ID}
APP_KAFKA_RESPONSE_TOPIC: ${DNPM_KAFKA_RESPONSE_TOPIC}
APP_REST_URI: ${DNPM_BWHC_REST_URI}
APP_REST_USERNAME: ${DNPM_BWHC_REST_USERNAME}
APP_REST_PASSWORD: ${DNPM_BWHC_REST_PASSWORD}
APP_REST_IS_BWHC: ${DNPM_BWHC_REST_IS_BWHC}
APP_SECURITY_ADMIN_USER: ${DNPM_ADMIN_USER}
APP_SECURITY_ADMIN_PASSWORD: ${DNPM_ADMIN_PASSWORD}
SPRING_DATASOURCE_URL: ${DNPM_DATASOURCE_URL}
SPRING_DATASOURCE_PASSWORD: ${DNPM_MARIADB_USER_PW}
SPRING_DATASOURCE_USERNAME: ${DNPM_MARIADB_DB}

7
deploy/env-sample.env
View File

@ -2,10 +2,6 @@
DNPM_MONITORING_HTTP_PORT=8088
DNPM_LOG_LEVEL=INFO
# ADMIN USER CREDENTIALS
DNPM_ADMIN_USER=admin
DNPM_ADMIN_PASSWORD=
# GPAS or BUILDIN
DNPM_PSEUDONYMIZE_GENERATOR=BUILDIN
DNPM_APP_PSEUDONYMIZE_PREFIX=ANONYM
@ -28,9 +24,6 @@ DNPM_DATASOURCE_URL=jdbc:mariadb://dnpm-monitor-db:3306/$DNPM_MARIADB_DB
## TARGET SYSTEMS CONFIG
# in case of direct access to bwhc enter endpoint url here
DNPM_BWHC_REST_URI=
DNPM_BWHC_REST_USERNAME=
DNPM_BWHC_REST_PASSWORD=
DNPM_BWHC_REST_IS_BWHC=false
# produce mtb files to this topic - values 'false' disabling kafka processing
DNPM_KAFKA_TOPIC=false

6
dev-compose.yml
View File

@ -17,9 +17,8 @@ services:
KAFKA_CFG_CONTROLLER_QUORUM_VOTERS: 0@kafka:9093
KAFKA_CFG_CONTROLLER_LISTENER_NAMES: CONTROLLER
## Use AKHQ as Kafka web frontend
akhq:
image: tchiotludo/akhq:0.25.0
image: tchiotludo/akhq:0.21.0
environment:
AKHQ_CONFIGURATION: |
akhq:
@ -33,8 +32,6 @@ services:
ports:
- "8084:8080"
## For use with MariaDB
mariadb:
image: mariadb:10
ports:
@ -45,7 +42,6 @@ services:
MARIADB_PASSWORD: dev
MARIADB_ROOT_PASSWORD: dev
## For use with Postgres
# postgres:
# image: postgres:alpine
# ports:

28
docs/docker-compose.yml
View File

@ -1,28 +0,0 @@
### Example for docker-compose
version: '3.7'
volumes:
data:
services:
### ETL-Processor
etl-processor:
image: ghcr.io/ccc-mf/etl-processor:latest
ports:
- 8080:8080
environment:
APP_REST_URI: http://bwhc-backend/bwhc/etl/api
SPRING_DATASOURCE_URL: jdbc:postgresql://postgres/etl
SPRING_DATASOURCE_USERNAME: etl
SPRING_DATASOURCE_PASSWORD: etl-password
### Database
postgres:
image: postgres:alpine
environment:
POSTGRES_DB: etl
POSTGRES_USER: etl
POSTGRES_PASSWORD: etl-password
volumes:
- data:/var/lib/postgresql/data

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2
gradle/wrapper/gradle-wrapper.properties vendored
View File

@ -1,6 +1,6 @@
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
distributionUrl=https\://services.gradle.org/distributions/gradle-8.13-bin.zip
distributionUrl=https\://services.gradle.org/distributions/gradle-8.1.1-bin.zip
networkTimeout=10000
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists

20
src/integrationTest/kotlin/dev/dnpm/etl/processor/EtlProcessorApplicationTests.kt
View File

@ -23,7 +23,6 @@ import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.*
import dev.dnpm.etl.processor.monitoring.RequestRepository
import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.output.BwhcV1MtbFileRequest
import dev.dnpm.etl.processor.output.MtbFileSender
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach
@ -34,10 +33,10 @@ import org.mockito.kotlin.*
import org.springframework.beans.factory.annotation.Autowired
import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc
import org.springframework.boot.test.context.SpringBootTest
import org.springframework.boot.test.mock.mockito.MockBean
import org.springframework.context.ApplicationContext
import org.springframework.http.MediaType
import org.springframework.test.context.TestPropertySource
import org.springframework.test.context.bean.override.mockito.MockitoBean
import org.springframework.test.context.junit.jupiter.SpringExtension
import org.springframework.test.web.servlet.MockMvc
import org.springframework.test.web.servlet.post
@ -46,13 +45,7 @@ import org.testcontainers.junit.jupiter.Testcontainers
@Testcontainers
@ExtendWith(SpringExtension::class)
@SpringBootTest
@MockitoBean(types = [MtbFileSender::class])
@TestPropertySource(
properties = [
"app.rest.uri=http://example.com",
"app.pseudonymize.generator=buildin"
]
)
@MockBean(MtbFileSender::class)
class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
@Test
@ -66,7 +59,6 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
@AutoConfigureMockMvc
@TestPropertySource(
properties = [
"app.pseudonymize.generator=buildin",
"app.transformations[0].path=diagnoses[*].icd10.version",
"app.transformations[0].from=2013",
"app.transformations[0].to=2014",
@ -74,7 +66,7 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
)
inner class TransformationTest {
@MockitoBean
@MockBean
private lateinit var mtbFileSender: MtbFileSender
@Autowired
@ -92,7 +84,7 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
fun mtbFileIsTransformed() {
doAnswer {
MtbFileSender.Response(RequestStatus.SUCCESS)
}.whenever(mtbFileSender).send(any<BwhcV1MtbFileRequest>())
}.whenever(mtbFileSender).send(any<MtbFileSender.MtbFileRequest>())
val mtbFile = MtbFile.builder()
.withPatient(
@ -135,9 +127,9 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
}
}
val captor = argumentCaptor<BwhcV1MtbFileRequest>()
val captor = argumentCaptor<MtbFileSender.MtbFileRequest>()
verify(mtbFileSender).send(captor.capture())
assertThat(captor.firstValue.content.diagnoses).hasSize(1).allMatch { diagnosis ->
assertThat(captor.firstValue.mtbFile.diagnoses).hasSize(1).allMatch { diagnosis ->
diagnosis.icd10.version == "2014"
}
}

73
src/integrationTest/kotlin/dev/dnpm/etl/processor/EtlProcessorArchTest.kt
View File

@ -1,73 +0,0 @@
package dev.dnpm.etl.processor
import com.tngtech.archunit.core.domain.JavaClasses
import com.tngtech.archunit.core.importer.ClassFileImporter
import com.tngtech.archunit.lang.syntax.ArchRuleDefinition.classes
import com.tngtech.archunit.lang.syntax.ArchRuleDefinition.noClasses
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Test
import org.springframework.data.repository.Repository
class EtlProcessorArchTest {
private lateinit var noTestClasses: JavaClasses
@BeforeEach
fun setUp() {
this.noTestClasses = ClassFileImporter()
.withImportOption { !(it.contains("/test/") || it.contains("/integrationTest/")) }
.importPackages("dev.dnpm.etl.processor")
}
@Test
fun noClassesInInputPackageShouldDependOnMonitoringPackage() {
val rule = noClasses()
.that()
.resideInAPackage("..input")
.should().dependOnClassesThat()
.resideInAnyPackage("..monitoring")
rule.check(noTestClasses)
}
@Test
fun noClassesInInputPackageShouldDependOnRepositories() {
val rule = noClasses()
.that()
.resideInAPackage("..input")
.should().dependOnClassesThat().haveSimpleNameEndingWith("Repository")
rule.check(noTestClasses)
}
@Test
fun noClassesInOutputPackageShouldDependOnRepositories() {
val rule = noClasses()
.that()
.resideInAPackage("..output")
.should().dependOnClassesThat().haveSimpleNameEndingWith("Repository")
rule.check(noTestClasses)
}
@Test
fun noClassesInWebPackageShouldDependOnRepositories() {
val rule = noClasses()
.that()
.resideInAPackage("..web")
.should().dependOnClassesThat().haveSimpleNameEndingWith("Repository")
rule.check(noTestClasses)
}
@Test
fun repositoryClassNamesShouldEndWithRepository() {
val rule = classes()
.that()
.areInterfaces().and().areAssignableTo(Repository::class.java)
.should().haveSimpleNameEndingWith("Repository")
rule.check(noTestClasses)
}
}

178
src/integrationTest/kotlin/dev/dnpm/etl/processor/config/AppConfigurationTest.kt
View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2023 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
@ -20,15 +20,9 @@
package dev.dnpm.etl.processor.config
import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.input.KafkaInputListener
import dev.dnpm.etl.processor.monitoring.RequestRepository
import dev.dnpm.etl.processor.output.KafkaMtbFileSender
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.security.TokenRepository
import dev.dnpm.etl.processor.security.TokenService
import dev.dnpm.etl.processor.services.RequestProcessor
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.Nested
import org.junit.jupiter.api.Test
@ -36,30 +30,14 @@ import org.junit.jupiter.api.assertThrows
import org.springframework.beans.factory.NoSuchBeanDefinitionException
import org.springframework.boot.autoconfigure.kafka.KafkaAutoConfiguration
import org.springframework.boot.test.context.SpringBootTest
import org.springframework.boot.test.mock.mockito.MockBean
import org.springframework.context.ApplicationContext
import org.springframework.retry.support.RetryTemplate
import org.springframework.security.crypto.password.PasswordEncoder
import org.springframework.security.provisioning.InMemoryUserDetailsManager
import org.springframework.test.context.ContextConfiguration
import org.springframework.test.context.TestPropertySource
import org.springframework.test.context.bean.override.mockito.MockitoBean
@SpringBootTest
@ContextConfiguration(
classes = [
AppConfiguration::class,
AppSecurityConfiguration::class,
KafkaAutoConfiguration::class,
AppKafkaConfiguration::class,
AppRestConfiguration::class
]
)
@MockitoBean(types = [ObjectMapper::class])
@TestPropertySource(
properties = [
"app.pseudonymize.generator=BUILDIN",
]
)
@ContextConfiguration(classes = [AppConfiguration::class, KafkaAutoConfiguration::class, AppKafkaConfiguration::class, AppRestConfiguration::class])
@MockBean(ObjectMapper::class)
class AppConfigurationTest {
@Nested
@ -82,12 +60,12 @@ class AppConfigurationTest {
@TestPropertySource(
properties = [
"app.kafka.servers=localhost:9092",
"app.kafka.output-topic=test",
"app.kafka.output-response-topic=test-response",
"app.kafka.topic=test",
"app.kafka.response-topic=test-response",
"app.kafka.group-id=test"
]
)
@MockitoBean(types = [RequestRepository::class])
@MockBean(RequestRepository::class)
inner class AppConfigurationKafkaTest(private val context: ApplicationContext) {
@Test
@ -103,8 +81,8 @@ class AppConfigurationTest {
properties = [
"app.rest.uri=http://localhost:9000",
"app.kafka.servers=localhost:9092",
"app.kafka.output-topic=test",
"app.kafka.output-response-topic=test-response",
"app.kafka.topic=test",
"app.kafka.response-topic=test-response",
"app.kafka.group-id=test"
]
)
@ -118,44 +96,6 @@ class AppConfigurationTest {
}
@Nested
@TestPropertySource(
properties = [
"app.kafka.servers=localhost:9092",
"app.kafka.output-topic=test",
"app.kafka.output-response-topic=test-response",
"app.kafka.group-id=test"
]
)
inner class AppConfigurationWithoutKafkaInputTest(private val context: ApplicationContext) {
@Test
fun shouldNotUseKafkaInputListener() {
assertThrows<NoSuchBeanDefinitionException> { context.getBean(KafkaInputListener::class.java) }
}
}
@Nested
@TestPropertySource(
properties = [
"app.kafka.servers=localhost:9092",
"app.kafka.input-topic=test_input",
"app.kafka.output-topic=test",
"app.kafka.output-response-topic=test-response",
"app.kafka.group-id=test"
]
)
@MockitoBean(types = [RequestProcessor::class])
inner class AppConfigurationUsingKafkaInputTest(private val context: ApplicationContext) {
@Test
fun shouldUseKafkaInputListener() {
assertThat(context.getBean(KafkaInputListener::class.java)).isNotNull
}
}
@Nested
@TestPropertySource(
properties = [
@ -176,104 +116,4 @@ class AppConfigurationTest {
}
@Nested
inner class AppConfigurationPseudonymizeTest {
@Nested
@TestPropertySource(
properties = [
"app.pseudonymize.generator=buildin"
]
)
inner class AppConfigurationPseudonymizeGeneratorBuildinTest(private val context: ApplicationContext) {
@Test
fun shouldUseConfiguredGenerator() {
assertThat(context.getBean(AnonymizingGenerator::class.java)).isNotNull
}
}
@Nested
@TestPropertySource(
properties = [
"app.pseudonymize.generator=gpas"
]
)
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"
]
)
@MockitoBean(
types = [
InMemoryUserDetailsManager::class,
PasswordEncoder::class,
TokenRepository::class
]
)
inner class AppConfigurationTokenEnabledTest(private val context: ApplicationContext) {
@Test
fun checkTokenService() {
assertThat(context.getBean(TokenService::class.java)).isNotNull
}
}
@Nested
@MockitoBean(
types = [
InMemoryUserDetailsManager::class,
PasswordEncoder::class,
TokenRepository::class
]
)
inner class AppConfigurationTokenDisabledTest(private val context: ApplicationContext) {
@Test
fun checkTokenService() {
assertThrows<NoSuchBeanDefinitionException> { context.getBean(TokenService::class.java) }
}
}
}
@Nested
@TestPropertySource(
properties = [
"app.rest.uri=http://localhost:9000",
"app.max-retry-attempts=5"
]
)
inner class AppConfigurationRetryTest(private val context: ApplicationContext) {
private val maxRetryAttempts = 5
@Test
fun shouldUseRetryTemplateWithConfiguredMaxAttempts() {
val retryTemplate = context.getBean(RetryTemplate::class.java)
assertThat(retryTemplate).isNotNull
assertThrows<RuntimeException> {
retryTemplate.execute<Void, RuntimeException> {
assertThat(it.retryCount).isLessThan(maxRetryAttempts)
throw RuntimeException()
}
}
}
}
}

30
src/integrationTest/kotlin/dev/dnpm/etl/processor/helpers.kt
View File

@ -1,30 +0,0 @@
/*
* 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
import org.mockito.ArgumentMatchers
@Suppress("UNCHECKED_CAST")
inline fun <reified T> anyValueClass(): T {
val unboxedClass = T::class.java.declaredFields.first().type
return ArgumentMatchers.any(unboxedClass as Class<T>)
?: T::class.java.getDeclaredMethod("box-impl", unboxedClass)
.invoke(null, null) as T
}

225
src/integrationTest/kotlin/dev/dnpm/etl/processor/input/MtbFileRestControllerTest.kt
View File

@ -1,225 +0,0 @@
/*
* 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.input
import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.*
import dev.dnpm.etl.processor.anyValueClass
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
import dev.dnpm.etl.processor.security.TokenRepository
import dev.dnpm.etl.processor.security.UserRoleRepository
import dev.dnpm.etl.processor.services.RequestProcessor
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.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.http.MediaType
import org.springframework.security.oauth2.client.registration.ClientRegistrationRepository
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.anonymous
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user
import org.springframework.test.context.ContextConfiguration
import org.springframework.test.context.TestPropertySource
import org.springframework.test.context.bean.override.mockito.MockitoBean
import org.springframework.test.context.junit.jupiter.SpringExtension
import org.springframework.test.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
]
)
@MockitoBean(types = [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<MtbFile>())
}
@Test
fun testShouldGrantPermissionToSendMtbFileToAdminUser() {
mockMvc.post("/mtbfile") {
with(user("onkostarserver").roles("ADMIN"))
contentType = MediaType.APPLICATION_JSON
content = ObjectMapper().writeValueAsString(mtbFile)
}.andExpect {
status { isAccepted() }
}
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
}
@Test
fun testShouldDenyPermissionToSendMtbFile() {
mockMvc.post("/mtbfile") {
with(anonymous())
contentType = MediaType.APPLICATION_JSON
content = ObjectMapper().writeValueAsString(mtbFile)
}.andExpect {
status { isUnauthorized() }
}
verify(requestProcessor, never()).processMtbFile(any<MtbFile>())
}
@Test
fun testShouldDenyPermissionToSendMtbFileForUser() {
mockMvc.post("/mtbfile") {
with(user("fakeuser").roles("USER"))
contentType = MediaType.APPLICATION_JSON
content = ObjectMapper().writeValueAsString(mtbFile)
}.andExpect {
status { isForbidden() }
}
verify(requestProcessor, never()).processMtbFile(any<MtbFile>())
}
@Test
fun testShouldGrantPermissionToDeletePatientData() {
mockMvc.delete("/mtbfile/12345678") {
with(user("onkostarserver").roles("MTBFILE"))
}.andExpect {
status { isAccepted() }
}
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
}
@Test
fun testShouldDenyPermissionToDeletePatientData() {
mockMvc.delete("/mtbfile/12345678") {
with(anonymous())
}.andExpect {
status { isUnauthorized() }
}
verify(requestProcessor, never()).processDeletion(anyValueClass())
}
@Nested
@MockitoBean(types = [UserRoleRepository::class, ClientRegistrationRepository::class])
@TestPropertySource(
properties = [
"app.pseudonymize.generator=BUILDIN",
"app.security.admin-user=admin",
"app.security.admin-password={noop}very-secret",
"app.security.enable-tokens=true",
"app.security.enable-oidc=true"
]
)
inner class WithOidcEnabled {
@Test
fun testShouldGrantPermissionToSendMtbFileToAdminUser() {
mockMvc.post("/mtbfile") {
with(user("onkostarserver").roles("ADMIN"))
contentType = MediaType.APPLICATION_JSON
content = ObjectMapper().writeValueAsString(mtbFile)
}.andExpect {
status { isAccepted() }
}
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
}
@Test
fun testShouldGrantPermissionToSendMtbFileToUser() {
mockMvc.post("/mtbfile") {
with(user("onkostarserver").roles("USER"))
contentType = MediaType.APPLICATION_JSON
content = ObjectMapper().writeValueAsString(mtbFile)
}.andExpect {
status { isAccepted() }
}
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
}
}
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()
}
}

75
src/integrationTest/kotlin/dev/dnpm/etl/processor/monitoring/RequestRepositoryTest.kt
View File

@ -1,75 +0,0 @@
/*
* 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.monitoring
import dev.dnpm.etl.processor.*
import dev.dnpm.etl.processor.output.MtbFileSender
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith
import org.springframework.beans.factory.annotation.Autowired
import org.springframework.boot.test.autoconfigure.data.jdbc.DataJdbcTest
import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase
import org.springframework.test.context.TestPropertySource
import org.springframework.test.context.bean.override.mockito.MockitoBean
import org.springframework.test.context.junit.jupiter.SpringExtension
import org.springframework.transaction.annotation.Transactional
import org.testcontainers.junit.jupiter.Testcontainers
import java.time.Instant
@Testcontainers
@ExtendWith(SpringExtension::class)
@DataJdbcTest
@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE)
@Transactional
@MockitoBean(types = [MtbFileSender::class])
@TestPropertySource(
properties = [
"app.pseudonymize.generator=buildin",
"app.rest.uri=http://example.com"
]
)
class RequestRepositoryTest : AbstractTestcontainerTest() {
private lateinit var requestRepository: RequestRepository
@BeforeEach
fun setUp(
@Autowired requestRepository: RequestRepository
) {
this.requestRepository = requestRepository
}
@Test
fun shouldSaveRequest() {
val request = Request(
randomRequestId(),
PatientPseudonym("TEST_12345678901"),
PatientId("P1"),
Fingerprint("0123456789abcdef1"),
RequestType.MTB_FILE,
RequestStatus.WARNING,
Instant.parse("2023-07-07T00:00:00Z")
)
requestRepository.save(request)
}
}

135
src/integrationTest/kotlin/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGeneratorTest.kt
View File

@ -1,135 +0,0 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.pseudonym
import dev.dnpm.etl.processor.config.GPasConfigProperties
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Test
import org.junit.jupiter.api.assertThrows
import org.springframework.http.HttpHeaders
import org.springframework.http.HttpMethod
import org.springframework.http.HttpStatus
import org.springframework.retry.policy.SimpleRetryPolicy
import org.springframework.retry.support.RetryTemplateBuilder
import org.springframework.test.web.client.MockRestServiceServer
import org.springframework.test.web.client.match.MockRestRequestMatchers.method
import org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo
import org.springframework.test.web.client.response.MockRestResponseCreators.withException
import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus
import org.springframework.web.client.RestTemplate
import java.io.IOException
class GpasPseudonymGeneratorTest {
private lateinit var mockRestServiceServer: MockRestServiceServer
private lateinit var generator: GpasPseudonymGenerator
private lateinit var restTemplate: RestTemplate
@BeforeEach
fun setup() {
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
val gPasConfigProperties = GPasConfigProperties(
"https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate",
"test",
null,
null
)
this.restTemplate = RestTemplate()
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.generator = GpasPseudonymGenerator(gPasConfigProperties, retryTemplate, restTemplate)
}
@Test
fun shouldReturnExpectedPseudonym() {
this.mockRestServiceServer.expect {
method(HttpMethod.POST)
requestTo("https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
}.andRespond {
withStatus(HttpStatus.OK).body(getDummyResponseBody("1234", "test", "test1234ABCDEF567890"))
.createResponse(it)
}
assertThat(this.generator.generate("ID1234")).isEqualTo("test1234ABCDEF567890")
}
@Test
fun shouldThrowExceptionIfGpasNotAvailable() {
this.mockRestServiceServer.expect {
method(HttpMethod.POST)
requestTo("https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
}.andRespond {
withException(IOException("Simulated IO error")).createResponse(it)
}
assertThrows<PseudonymRequestFailed> { this.generator.generate("ID1234") }
}
@Test
fun shouldThrowExceptionIfGpasDoesNotReturn2xxResponse() {
this.mockRestServiceServer.expect {
method(HttpMethod.POST)
requestTo("https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
}.andRespond {
withStatus(HttpStatus.FOUND)
.header(HttpHeaders.LOCATION, "https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
.createResponse(it)
}
assertThrows<PseudonymRequestFailed> { this.generator.generate("ID1234") }
}
companion object {
fun getDummyResponseBody(original: String, target: String, pseudonym: String) = """{
"resourceType": "Parameters",
"parameter": [
{
"name": "pseudonym",
"part": [
{
"name": "original",
"valueIdentifier": {
"system": "https://ths-greifswald.de/gpas",
"value": "$original"
}
},
{
"name": "target",
"valueIdentifier": {
"system": "https://ths-greifswald.de/gpas",
"value": "$target"
}
},
{
"name": "pseudonym",
"valueIdentifier": {
"system": "https://ths-greifswald.de/gpas",
"value": "$pseudonym"
}
}
]
}
]
}""".trimIndent()
}
}

74
src/integrationTest/kotlin/dev/dnpm/etl/processor/services/RequestServiceIntegrationTest.kt
View File

@ -19,7 +19,7 @@
package dev.dnpm.etl.processor.services
import dev.dnpm.etl.processor.*
import dev.dnpm.etl.processor.AbstractTestcontainerTest
import dev.dnpm.etl.processor.monitoring.Request
import dev.dnpm.etl.processor.monitoring.RequestRepository
import dev.dnpm.etl.processor.monitoring.RequestStatus
@ -31,24 +31,18 @@ import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith
import org.springframework.beans.factory.annotation.Autowired
import org.springframework.boot.test.context.SpringBootTest
import org.springframework.test.context.TestPropertySource
import org.springframework.test.context.bean.override.mockito.MockitoBean
import org.springframework.boot.test.mock.mockito.MockBean
import org.springframework.test.context.junit.jupiter.SpringExtension
import org.springframework.transaction.annotation.Transactional
import org.testcontainers.junit.jupiter.Testcontainers
import java.time.Instant
import java.util.*
@Testcontainers
@ExtendWith(SpringExtension::class)
@SpringBootTest
@Transactional
@MockitoBean(types = [MtbFileSender::class])
@TestPropertySource(
properties = [
"app.pseudonymize.generator=buildin",
"app.rest.uri=http://example.com"
]
)
@MockBean(MtbFileSender::class)
class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
private lateinit var requestRepository: RequestRepository
@ -65,7 +59,7 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
@Test
fun shouldResultInEmptyRequestList() {
val actual = requestService.allRequestsByPatientPseudonym(TEST_PATIENT_PSEUDONYM)
val actual = requestService.allRequestsByPatientPseudonym("TEST_12345678901")
assertThat(actual).isEmpty()
}
@ -75,33 +69,33 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
this.requestRepository.saveAll(
listOf(
Request(
randomRequestId(),
PatientPseudonym("TEST_12345678901"),
PatientId("P1"),
Fingerprint("0123456789abcdef1"),
RequestType.MTB_FILE,
RequestStatus.SUCCESS,
Instant.parse("2023-07-07T02:00:00Z")
uuid = UUID.randomUUID().toString(),
patientId = "TEST_12345678901",
pid = "P1",
fingerprint = "0123456789abcdef1",
type = RequestType.MTB_FILE,
status = RequestStatus.SUCCESS,
processedAt = Instant.parse("2023-07-07T02:00:00Z")
),
// Should be ignored - wrong patient ID -->
Request(
randomRequestId(),
PatientPseudonym("TEST_12345678902"),
PatientId("P2"),
Fingerprint("0123456789abcdef2"),
RequestType.MTB_FILE,
RequestStatus.WARNING,
Instant.parse("2023-08-08T00:00:00Z")
uuid = UUID.randomUUID().toString(),
patientId = "TEST_12345678902",
pid = "P2",
fingerprint = "0123456789abcdef2",
type = RequestType.MTB_FILE,
status = RequestStatus.WARNING,
processedAt = Instant.parse("2023-08-08T00:00:00Z")
),
// <--
Request(
randomRequestId(),
PatientPseudonym("TEST_12345678901"),
PatientId("P2"),
Fingerprint("0123456789abcdee1"),
RequestType.DELETE,
RequestStatus.SUCCESS,
Instant.parse("2023-08-08T02:00:00Z")
uuid = UUID.randomUUID().toString(),
patientId = "TEST_12345678901",
pid = "P2",
fingerprint = "0123456789abcdee1",
type = RequestType.DELETE,
status = RequestStatus.SUCCESS,
processedAt = Instant.parse("2023-08-08T02:00:00Z")
)
)
)
@ -111,18 +105,18 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
fun shouldResultInSortedRequestList() {
setupTestData()
val actual = requestService.allRequestsByPatientPseudonym(TEST_PATIENT_PSEUDONYM)
val actual = requestService.allRequestsByPatientPseudonym("TEST_12345678901")
assertThat(actual).hasSize(2)
assertThat(actual[0].fingerprint).isEqualTo(Fingerprint("0123456789abcdee1"))
assertThat(actual[1].fingerprint).isEqualTo(Fingerprint("0123456789abcdef1"))
assertThat(actual[0].fingerprint).isEqualTo("0123456789abcdee1")
assertThat(actual[1].fingerprint).isEqualTo("0123456789abcdef1")
}
@Test
fun shouldReturnDeleteRequestAsLastRequest() {
setupTestData()
val actual = requestService.isLastRequestWithKnownStatusDeletion(TEST_PATIENT_PSEUDONYM)
val actual = requestService.isLastRequestWithKnownStatusDeletion("TEST_12345678901")
assertThat(actual).isTrue()
}
@ -131,14 +125,10 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
fun shouldReturnLastMtbFileRequest() {
setupTestData()
val actual = requestService.lastMtbFileRequestForPatientPseudonym(TEST_PATIENT_PSEUDONYM)
val actual = requestService.lastMtbFileRequestForPatientPseudonym("TEST_12345678901")
assertThat(actual).isNotNull
assertThat(actual?.fingerprint).isEqualTo(Fingerprint("0123456789abcdef1"))
}
companion object {
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("TEST_12345678901")
assertThat(actual?.fingerprint).isEqualTo("0123456789abcdef1")
}
}

369
src/integrationTest/kotlin/dev/dnpm/etl/processor/web/ConfigControllerTest.kt
View File

@ -1,369 +0,0 @@
/*
* 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.AppConfiguration
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
import dev.dnpm.etl.processor.monitoring.GPasConnectionCheckService
import dev.dnpm.etl.processor.monitoring.RestConnectionCheckService
import dev.dnpm.etl.processor.output.MtbFileSender
import dev.dnpm.etl.processor.pseudonym.Generator
import dev.dnpm.etl.processor.security.Role
import dev.dnpm.etl.processor.security.TokenService
import dev.dnpm.etl.processor.security.UserRoleService
import dev.dnpm.etl.processor.services.RequestProcessor
import dev.dnpm.etl.processor.services.TransformationService
import org.assertj.core.api.Assertions.assertThat
import org.htmlunit.WebClient
import org.htmlunit.html.HtmlPage
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.mockito.ArgumentMatchers.anyString
import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.argumentCaptor
import org.mockito.kotlin.times
import org.mockito.kotlin.verify
import org.mockito.kotlin.whenever
import org.springframework.beans.factory.annotation.Autowired
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
import org.springframework.http.HttpHeaders
import org.springframework.http.MediaType
import org.springframework.http.MediaType.TEXT_EVENT_STREAM
import org.springframework.security.test.context.support.WithMockUser
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.bean.override.mockito.MockitoBean
import org.springframework.test.context.junit.jupiter.SpringExtension
import org.springframework.test.web.reactive.server.WebTestClient
import org.springframework.test.web.servlet.*
import org.springframework.test.web.servlet.client.MockMvcWebTestClient
import org.springframework.test.web.servlet.htmlunit.MockMvcWebClientBuilder
import org.springframework.web.context.WebApplicationContext
import reactor.core.publisher.Sinks
import reactor.test.StepVerifier
import java.time.Instant
abstract class MockSink : Sinks.Many<Boolean>
@WebMvcTest(controllers = [ConfigController::class])
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
@ContextConfiguration(
classes = [
ConfigController::class,
AppConfiguration::class,
AppSecurityConfiguration::class
]
)
@TestPropertySource(
properties = [
"app.pseudonymize.generator=BUILDIN"
]
)
@MockitoBean(name = "configsUpdateProducer", types = [MockSink::class])
@MockitoBean(
types = [
Generator::class,
MtbFileSender::class,
RequestProcessor::class,
TransformationService::class,
GPasConnectionCheckService::class,
RestConnectionCheckService::class
]
)
class ConfigControllerTest {
private lateinit var mockMvc: MockMvc
private lateinit var webClient: WebClient
private lateinit var requestProcessor: RequestProcessor
private lateinit var connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
@BeforeEach
fun setup(
@Autowired mockMvc: MockMvc,
@Autowired requestProcessor: RequestProcessor,
@Autowired connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
) {
this.mockMvc = mockMvc
this.webClient = MockMvcWebClientBuilder.mockMvcSetup(mockMvc).build()
this.requestProcessor = requestProcessor
this.connectionCheckUpdateProducer = connectionCheckUpdateProducer
webClient.options.isThrowExceptionOnScriptError = false
}
@Test
fun testShouldRequestConfigPageIfLoggedIn() {
mockMvc.get("/configs") {
with(user("admin").roles("ADMIN"))
accept(MediaType.TEXT_HTML)
}.andExpect {
status { isOk() }
view { name("configs") }
}
}
@Test
fun testShouldRedirectToLoginPageIfNotLoggedIn() {
mockMvc.get("/configs") {
with(anonymous())
accept(MediaType.TEXT_HTML)
}.andExpect {
status { isFound() }
header {
stringValues(HttpHeaders.LOCATION, "http://localhost/login")
}
}
}
@Nested
@TestPropertySource(
properties = [
"app.security.enable-tokens=true",
"app.security.admin-user=admin"
]
)
@MockitoBean(
types = [
TokenService::class
]
)
inner class WithTokensEnabled {
private lateinit var tokenService: TokenService
@BeforeEach
fun setup(
@Autowired tokenService: TokenService
) {
webClient.options.isThrowExceptionOnScriptError = false
this.tokenService = tokenService
}
@Test
fun testShouldSaveNewToken() {
mockMvc.post("/configs/tokens") {
with(user("admin").roles("ADMIN"))
accept(MediaType.TEXT_HTML)
contentType = MediaType.APPLICATION_FORM_URLENCODED
content = "name=Testtoken"
}.andExpect {
status { is2xxSuccessful() }
view { name("configs/tokens") }
}
val captor = argumentCaptor<String>()
verify(tokenService, times(1)).addToken(captor.capture())
assertThat(captor.firstValue).isEqualTo("Testtoken")
}
@Test
fun testShouldNotSaveTokenWithExstingName() {
whenever(tokenService.addToken(anyString())).thenReturn(Result.failure(RuntimeException("Testfailure")))
mockMvc.post("/configs/tokens") {
with(user("admin").roles("ADMIN"))
accept(MediaType.TEXT_HTML)
contentType = MediaType.APPLICATION_FORM_URLENCODED
content = "name=Testtoken"
}.andExpect {
status { is2xxSuccessful() }
view { name("configs/tokens") }
}
val captor = argumentCaptor<String>()
verify(tokenService, times(1)).addToken(captor.capture())
assertThat(captor.firstValue).isEqualTo("Testtoken")
}
@Test
fun testShouldDeleteToken() {
mockMvc.delete("/configs/tokens/42") {
with(user("admin").roles("ADMIN"))
accept(MediaType.TEXT_HTML)
}.andExpect {
status { is2xxSuccessful() }
view { name("configs/tokens") }
}
val captor = argumentCaptor<Long>()
verify(tokenService, times(1)).deleteToken(captor.capture())
assertThat(captor.firstValue).isEqualTo(42)
}
@Test
@WithMockUser(username = "admin", roles = ["ADMIN"])
fun testShouldRenderConfigPageWithTokens() {
val page = webClient.getPage<HtmlPage>("http://localhost/configs")
assertThat(
page.getElementById("tokens")
).isNotNull
}
}
@Nested
@TestPropertySource(
properties = [
"app.security.enable-tokens=false"
]
)
inner class WithTokensDisabled {
@BeforeEach
fun setup() {
webClient.options.isThrowExceptionOnScriptError = false
}
@Test
@WithMockUser(username = "admin", roles = ["ADMIN"])
fun testShouldRenderConfigPageWithoutTokens() {
val page = webClient.getPage<HtmlPage>("http://localhost/configs")
assertThat(
page.getElementById("tokens")
).isNull()
}
}
@Nested
@TestPropertySource(
properties = [
"app.security.enable-tokens=false",
"app.security.admin-user=admin",
"app.security.admin-password={noop}very-secret"
]
)
@MockitoBean(
types = [
UserRoleService::class
]
)
inner class WithUserRolesEnabled {
private lateinit var userRoleService: UserRoleService
@BeforeEach
fun setup(
@Autowired userRoleService: UserRoleService
) {
webClient.options.isThrowExceptionOnScriptError = false
this.userRoleService = userRoleService
}
@Test
fun testShouldDeleteUserRole() {
mockMvc.delete("/configs/userroles/42") {
with(user("admin").roles("ADMIN"))
accept(MediaType.TEXT_HTML)
}.andExpect {
status { is2xxSuccessful() }
view { name("configs/userroles") }
}
val captor = argumentCaptor<Long>()
verify(userRoleService, times(1)).deleteUserRole(captor.capture())
assertThat(captor.firstValue).isEqualTo(42)
}
@Test
fun testShouldUpdateUserRole() {
mockMvc.put("/configs/userroles/42") {
with(user("admin").roles("ADMIN"))
accept(MediaType.TEXT_HTML)
contentType = MediaType.APPLICATION_FORM_URLENCODED
content = "role=ADMIN"
}.andExpect {
status { is2xxSuccessful() }
view { name("configs/userroles") }
}
val idCaptor = argumentCaptor<Long>()
val roleCaptor = argumentCaptor<Role>()
verify(userRoleService, times(1)).updateUserRole(idCaptor.capture(), roleCaptor.capture())
assertThat(idCaptor.firstValue).isEqualTo(42)
assertThat(roleCaptor.firstValue).isEqualTo(Role.ADMIN)
}
@Test
@WithMockUser(username = "admin", roles = ["ADMIN"])
fun testShouldRenderConfigPageWithUserRoles() {
val page = webClient.getPage<HtmlPage>("http://localhost/configs")
assertThat(
page.getElementById("userroles")
).isNotNull
}
}
@Nested
inner class WithUserRolesDisabled {
@BeforeEach
fun setup() {
webClient.options.isThrowExceptionOnScriptError = false
}
@Test
fun testShouldRenderConfigPageWithoutUserRoles() {
val page = webClient.getPage<HtmlPage>("http://localhost/configs")
assertThat(
page.getElementById("userroles")
).isNull()
}
}
@Nested
inner class SseTest {
private lateinit var webClient: WebTestClient
@BeforeEach
fun setup(
applicationContext: WebApplicationContext,
) {
this.webClient = MockMvcWebTestClient
.bindToApplicationContext(applicationContext).build()
}
@Test
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)
StepVerifier.create(result.responseBody)
.expectNext(expectedEvent)
.expectComplete()
.verify()
}
}
}

287
src/integrationTest/kotlin/dev/dnpm/etl/processor/web/HomeControllerTest.kt
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@ -1,287 +0,0 @@
/*
* 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.*
import dev.dnpm.etl.processor.config.AppConfiguration
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
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.services.RequestService
import org.assertj.core.api.Assertions.assertThat
import org.htmlunit.WebClient
import org.htmlunit.html.HtmlPage
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Nested
import org.junit.jupiter.api.Test
import org.junit.jupiter.api.assertThrows
import org.junit.jupiter.api.extension.ExtendWith
import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.any
import org.mockito.kotlin.whenever
import org.springframework.beans.factory.annotation.Autowired
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
import org.springframework.data.domain.Page
import org.springframework.data.domain.PageImpl
import org.springframework.data.domain.Pageable
import org.springframework.security.test.context.support.WithMockUser
import org.springframework.test.context.ContextConfiguration
import org.springframework.test.context.TestPropertySource
import org.springframework.test.context.bean.override.mockito.MockitoBean
import org.springframework.test.context.junit.jupiter.SpringExtension
import org.springframework.test.web.servlet.MockMvc
import org.springframework.test.web.servlet.get
import org.springframework.test.web.servlet.htmlunit.MockMvcWebClientBuilder
import java.io.IOException
import java.time.Instant
import java.util.*
@WebMvcTest(controllers = [HomeController::class])
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
@ContextConfiguration(
classes = [
HomeController::class,
AppConfiguration::class,
AppSecurityConfiguration::class
]
)
@TestPropertySource(
properties = [
"app.pseudonymize.generator=BUILDIN",
"app.security.admin-user=admin",
"app.security.admin-password={noop}very-secret"
]
)
@MockitoBean(
types = [RequestService::class]
)
class HomeControllerTest {
private lateinit var mockMvc: MockMvc
private lateinit var webClient: WebClient
@BeforeEach
fun setup(
@Autowired mockMvc: MockMvc,
@Autowired requestService: RequestService
) {
this.mockMvc = mockMvc
this.webClient = MockMvcWebClientBuilder.mockMvcSetup(mockMvc).build()
whenever(requestService.findAll(any<Pageable>())).thenReturn(Page.empty())
}
@Test
fun testShouldRequestHomePage() {
mockMvc.get("/").andExpect {
status { isOk() }
view { name("index") }
}
}
@Nested
inner class WithRequests {
private lateinit var requestService: RequestService
@BeforeEach
fun setup(
@Autowired requestService: RequestService
) {
this.requestService = requestService
}
@Test
fun testShouldShowHomePage() {
whenever(requestService.findAll(any<Pageable>())).thenReturn(
PageImpl(
listOf(
Request(
2L,
randomRequestId(),
PatientPseudonym("PSEUDO1"),
PatientId("PATIENT1"),
Fingerprint("ashdkasdh"),
RequestType.MTB_FILE,
RequestStatus.SUCCESS
),
Request(
1L,
randomRequestId(),
PatientPseudonym("PSEUDO1"),
PatientId("PATIENT1"),
Fingerprint("asdasdasd"),
RequestType.MTB_FILE,
RequestStatus.ERROR
)
)
)
)
val page = webClient.getPage<HtmlPage>("http://localhost/")
assertThat(page.querySelectorAll("tbody tr")).hasSize(2)
assertThat(page.querySelectorAll("div.notification.info")).isEmpty()
}
@Test
@WithMockUser(username = "admin", roles = ["ADMIN"])
fun testShouldShowRequestDetails() {
val requestId = randomRequestId()
whenever(requestService.findByUuid(anyValueClass())).thenReturn(
Optional.of(
Request(
2L,
requestId,
PatientPseudonym("PSEUDO1"),
PatientId("PATIENT1"),
Fingerprint("ashdkasdh"),
RequestType.MTB_FILE,
RequestStatus.SUCCESS,
Instant.now(),
Report("Test")
)
)
)
val page = webClient.getPage<HtmlPage>("http://localhost/report/${requestId.value}")
assertThat(page.querySelectorAll("tbody tr")).hasSize(1)
assertThat(page.querySelectorAll("div.notification.info")).isEmpty()
}
@Test
@WithMockUser(username = "admin", roles = ["ADMIN"])
fun testShouldShowPatientDetails() {
whenever(requestService.findRequestByPatientId(anyValueClass(), any<Pageable>())).thenReturn(
PageImpl(
listOf(
Request(
2L,
randomRequestId(),
PatientPseudonym("PSEUDO1"),
PatientId("PATIENT1"),
Fingerprint("ashdkasdh"),
RequestType.MTB_FILE,
RequestStatus.SUCCESS
),
Request(
1L,
randomRequestId(),
PatientPseudonym("PSEUDO1"),
PatientId("PATIENT1"),
Fingerprint("asdasdasd"),
RequestType.MTB_FILE,
RequestStatus.ERROR
)
)
)
)
val page = webClient.getPage<HtmlPage>("http://localhost/patient/PSEUDO1")
assertThat(page.querySelectorAll("tbody tr")).hasSize(2)
assertThat(page.querySelectorAll("div.notification.info")).isEmpty()
}
@Test
@WithMockUser(username = "admin", roles = ["ADMIN"])
fun testShouldShowPatientPseudonym() {
whenever(requestService.findRequestByPatientId(anyValueClass(), any<Pageable>())).thenReturn(
PageImpl(
listOf(
Request(
2L,
randomRequestId(),
PatientPseudonym("PSEUDO1"),
PatientId("PATIENT1"),
Fingerprint("ashdkasdh"),
RequestType.MTB_FILE,
RequestStatus.SUCCESS
),
Request(
1L,
randomRequestId(),
PatientPseudonym("PSEUDO1"),
PatientId("PATIENT1"),
Fingerprint("asdasdasd"),
RequestType.MTB_FILE,
RequestStatus.ERROR
)
)
)
)
val page = webClient.getPage<HtmlPage>("http://localhost/patient/PSEUDO1")
assertThat(page.querySelectorAll("h2 > span")).hasSize(1)
assertThat(page.querySelectorAll("h2 > span").first().textContent).isEqualTo("PSEUDO1")
}
}
@Nested
inner class WithoutRequests {
private lateinit var requestService: RequestService
@BeforeEach
fun setup(
@Autowired requestService: RequestService
) {
this.requestService = requestService
whenever(requestService.findAll(any<Pageable>())).thenReturn(Page.empty())
}
@Test
fun testShouldShowHomePage() {
val page = webClient.getPage<HtmlPage>("http://localhost/")
assertThat(page.querySelectorAll("tbody tr")).isEmpty()
assertThat(page.querySelectorAll("div.notification.info")).hasSize(1)
}
@Test
@WithMockUser(username = "admin", roles = ["ADMIN"])
fun testShouldThrowNotFoundExceptionForUnknownReport() {
val requestId = randomRequestId()
whenever(requestService.findByUuid(anyValueClass())).thenReturn(
Optional.empty()
)
assertThrows<IOException> {
webClient.getPage<HtmlPage>("http://localhost/report/${requestId.value}")
}.also {
assertThat(it).hasRootCauseInstanceOf(NotFoundException::class.java)
}
}
@Test
@WithMockUser(username = "admin", roles = ["ADMIN"])
fun testShouldShowEmptyPatientDetails() {
whenever(requestService.findRequestByPatientId(anyValueClass(), any<Pageable>())).thenReturn(Page.empty())
val page = webClient.getPage<HtmlPage>("http://localhost/patient/PSEUDO1")
assertThat(page.querySelectorAll("tbody tr")).isEmpty()
assertThat(page.querySelectorAll("div.notification.info")).hasSize(1)
}
}
}

88
src/integrationTest/kotlin/dev/dnpm/etl/processor/web/LoginControllerTest.kt
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@ -1,88 +0,0 @@
/*
* 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.AppConfiguration
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
import dev.dnpm.etl.processor.security.TokenService
import org.assertj.core.api.Assertions.assertThat
import org.htmlunit.WebClient
import org.htmlunit.html.HtmlPage
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.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.test.context.ContextConfiguration
import org.springframework.test.context.TestPropertySource
import org.springframework.test.context.bean.override.mockito.MockitoBean
import org.springframework.test.context.junit.jupiter.SpringExtension
import org.springframework.test.web.servlet.MockMvc
import org.springframework.test.web.servlet.get
import org.springframework.test.web.servlet.htmlunit.MockMvcWebClientBuilder
@WebMvcTest(controllers = [LoginController::class])
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
@ContextConfiguration(
classes = [
LoginController::class,
AppConfiguration::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"
]
)
@MockitoBean(
types = [TokenService::class]
)
class LoginControllerTest {
private lateinit var mockMvc: MockMvc
private lateinit var webClient: WebClient
@BeforeEach
fun setup(@Autowired mockMvc: MockMvc) {
this.mockMvc = mockMvc
this.webClient = MockMvcWebClientBuilder.mockMvcSetup(mockMvc).build()
}
@Test
fun testShouldRequestLoginPage() {
mockMvc.get("/login").andExpect {
status { isOk() }
view { name("login") }
}
}
@Test
fun testShouldShowLoginForm() {
val page = webClient.getPage<HtmlPage>("http://localhost/login")
assertThat(
page.getElementsByTagName("main").first().firstElementChild.getAttribute("class")
).isEqualTo("login-form")
}
}

73
src/integrationTest/kotlin/dev/dnpm/etl/processor/web/StatisticsControllerTest.kt
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@ -1,73 +0,0 @@
/*
* 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.AppConfiguration
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
import org.htmlunit.WebClient
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.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 org.springframework.test.web.servlet.htmlunit.MockMvcWebClientBuilder
@WebMvcTest(controllers = [StatisticsController::class])
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
@ContextConfiguration(
classes = [
StatisticsController::class,
AppConfiguration::class,
AppSecurityConfiguration::class
]
)
@TestPropertySource(
properties = [
"app.pseudonymize.generator=BUILDIN",
"app.security.admin-user=admin",
"app.security.admin-password={noop}very-secret"
]
)
class StatisticsControllerTest {
private lateinit var mockMvc: MockMvc
private lateinit var webClient: WebClient
@BeforeEach
fun setup(@Autowired mockMvc: MockMvc) {
this.mockMvc = mockMvc
this.webClient = MockMvcWebClientBuilder.mockMvcSetup(mockMvc).build()
}
@Test
fun testShouldRequestLoginPage() {
mockMvc.get("/statistics").andExpect {
status { isOk() }
view { name("statistics") }
}
}
}

314
src/integrationTest/kotlin/dev/dnpm/etl/processor/web/StatisticsRestControllerTest.kt
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@ -1,314 +0,0 @@
/*
* 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.Fingerprint
import dev.dnpm.etl.processor.PatientId
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.config.AppConfiguration
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
import dev.dnpm.etl.processor.monitoring.CountedState
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.randomRequestId
import dev.dnpm.etl.processor.services.RequestService
import org.hamcrest.Matchers.equalTo
import org.hamcrest.Matchers.hasSize
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.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.doAnswer
import org.mockito.kotlin.whenever
import org.springframework.beans.factory.annotation.Autowired
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
import org.springframework.http.MediaType.TEXT_EVENT_STREAM
import org.springframework.test.context.ContextConfiguration
import org.springframework.test.context.TestPropertySource
import org.springframework.test.context.bean.override.mockito.MockitoBean
import org.springframework.test.context.junit.jupiter.SpringExtension
import org.springframework.test.web.reactive.server.WebTestClient
import org.springframework.test.web.servlet.MockMvc
import org.springframework.test.web.servlet.client.MockMvcWebTestClient
import org.springframework.test.web.servlet.get
import org.springframework.web.context.WebApplicationContext
import reactor.core.publisher.Sinks
import reactor.test.StepVerifier
import java.time.Instant
import java.time.ZoneId
import java.time.temporal.ChronoUnit
@WebMvcTest(controllers = [StatisticsRestController::class])
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
@ContextConfiguration(
classes = [
StatisticsRestController::class,
AppConfiguration::class,
AppSecurityConfiguration::class
]
)
@TestPropertySource(
properties = [
"app.pseudonymize.generator=BUILDIN",
"app.security.admin-user=admin",
"app.security.admin-password={noop}very-secret"
]
)
@MockitoBean(
types = [RequestService::class]
)
class StatisticsRestControllerTest {
private lateinit var mockMvc: MockMvc
private lateinit var statisticsUpdateProducer: Sinks.Many<Any>
private lateinit var requestService: RequestService
@BeforeEach
fun setup(
@Autowired mockMvc: MockMvc,
@Autowired statisticsUpdateProducer: Sinks.Many<Any>,
@Autowired requestService: RequestService
) {
this.mockMvc = mockMvc
this.statisticsUpdateProducer = statisticsUpdateProducer
this.requestService = requestService
}
@Nested
inner class RequestStatesTest {
@Test
fun testShouldRequestStatesForMtbFiles() {
doAnswer { _ ->
listOf(
CountedState(42, RequestStatus.WARNING),
CountedState(1, RequestStatus.UNKNOWN)
)
}.whenever(requestService).countStates()
mockMvc.get("/statistics/requeststates").andExpect {
status { isOk() }.also {
jsonPath("$", hasSize<Int>(2))
jsonPath("$[0].name", equalTo(RequestStatus.WARNING.name))
jsonPath("$[0].value", equalTo(42))
jsonPath("$[1].name", equalTo(RequestStatus.UNKNOWN.name))
jsonPath("$[1].value", equalTo(1))
}
}
}
@Test
fun testShouldRequestStatesForDeletes() {
doAnswer { _ ->
listOf(
CountedState(42, RequestStatus.SUCCESS),
CountedState(1, RequestStatus.ERROR)
)
}.whenever(requestService).countDeleteStates()
mockMvc.get("/statistics/requeststates?delete=true").andExpect {
status { isOk() }.also {
jsonPath("$", hasSize<Int>(2))
jsonPath("$[0].name", equalTo(RequestStatus.SUCCESS.name))
jsonPath("$[0].value", equalTo(42))
jsonPath("$[1].name", equalTo(RequestStatus.ERROR.name))
jsonPath("$[1].value", equalTo(1))
}
}
}
}
@Nested
inner class PatientRequestStatesTest {
@Test
fun testShouldRequestPatientStatesForMtbFiles() {
doAnswer { _ ->
listOf(
CountedState(42, RequestStatus.WARNING),
CountedState(1, RequestStatus.UNKNOWN)
)
}.whenever(requestService).findPatientUniqueStates()
mockMvc.get("/statistics/requestpatientstates").andExpect {
status { isOk() }.also {
jsonPath("$", hasSize<Int>(2))
jsonPath("$[0].name", equalTo(RequestStatus.WARNING.name))
jsonPath("$[0].value", equalTo(42))
jsonPath("$[1].name", equalTo(RequestStatus.UNKNOWN.name))
jsonPath("$[1].value", equalTo(1))
}
}
}
@Test
fun testShouldRequestPatientStatesForDeletes() {
doAnswer { _ ->
listOf(
CountedState(42, RequestStatus.SUCCESS),
CountedState(1, RequestStatus.ERROR)
)
}.whenever(requestService).findPatientUniqueDeleteStates()
mockMvc.get("/statistics/requestpatientstates?delete=true").andExpect {
status { isOk() }.also {
jsonPath("$", hasSize<Int>(2))
jsonPath("$[0].name", equalTo(RequestStatus.SUCCESS.name))
jsonPath("$[0].value", equalTo(42))
jsonPath("$[1].name", equalTo(RequestStatus.ERROR.name))
jsonPath("$[1].value", equalTo(1))
}
}
}
}
@Nested
inner class LastMonthStatesTest {
@BeforeEach
fun setup() {
val zoneId = ZoneId.of("Europe/Berlin")
doAnswer { _ ->
listOf(
Request(
1,
randomRequestId(),
PatientPseudonym("TEST_12345678901"),
PatientId("P1"),
Fingerprint("0123456789abcdef1"),
RequestType.MTB_FILE,
RequestStatus.SUCCESS,
Instant.now().atZone(zoneId).truncatedTo(ChronoUnit.DAYS).minus(2, ChronoUnit.DAYS).toInstant()
),
Request(
2,
randomRequestId(),
PatientPseudonym("TEST_12345678902"),
PatientId("P2"),
Fingerprint("0123456789abcdef2"),
RequestType.MTB_FILE,
RequestStatus.WARNING,
Instant.now().atZone(zoneId).truncatedTo(ChronoUnit.DAYS).minus(2, ChronoUnit.DAYS).toInstant()
),
Request(
3,
randomRequestId(),
PatientPseudonym("TEST_12345678901"),
PatientId("P2"),
Fingerprint("0123456789abcdee1"),
RequestType.DELETE,
RequestStatus.ERROR,
Instant.now().atZone(zoneId).truncatedTo(ChronoUnit.DAYS).minus(1, ChronoUnit.DAYS).toInstant()
),
Request(
4,
randomRequestId(),
PatientPseudonym("TEST_12345678902"),
PatientId("P2"),
Fingerprint("0123456789abcdef2"),
RequestType.MTB_FILE,
RequestStatus.DUPLICATION,
Instant.now().atZone(zoneId).truncatedTo(ChronoUnit.DAYS).minus(1, ChronoUnit.DAYS).toInstant()
),
Request(
5,
randomRequestId(),
PatientPseudonym("TEST_12345678902"),
PatientId("P2"),
Fingerprint("0123456789abcdef2"),
RequestType.DELETE,
RequestStatus.UNKNOWN,
Instant.now().atZone(zoneId).truncatedTo(ChronoUnit.DAYS).toInstant()
),
)
}.whenever(requestService).findAll()
}
@Test
fun testShouldRequestLastMonthForMtbFiles() {
mockMvc.get("/statistics/requestslastmonth").andExpect {
status { isOk() }.also {
jsonPath("$", hasSize<Int>(31))
}.also {
jsonPath("$[28].nameValues.error", equalTo(0))
jsonPath("$[28].nameValues.warning", equalTo(1))
jsonPath("$[28].nameValues.success", equalTo(1))
jsonPath("$[28].nameValues.duplication", equalTo(0))
jsonPath("$[28].nameValues.unknown", equalTo(0))
jsonPath("$[29].nameValues.error", equalTo(0))
jsonPath("$[29].nameValues.warning", equalTo(0))
jsonPath("$[29].nameValues.success", equalTo(0))
jsonPath("$[29].nameValues.duplication", equalTo(1))
jsonPath("$[29].nameValues.unknown", equalTo(0))
}
}
}
@Test
fun testShouldRequestLastMonthForDeletes() {
mockMvc.get("/statistics/requestslastmonth?delete=true").andExpect {
status { isOk() }.also {
jsonPath("$", hasSize<Int>(31))
}.also {
jsonPath("$[29].nameValues.error", equalTo(1))
jsonPath("$[29].nameValues.warning", equalTo(0))
jsonPath("$[29].nameValues.success", equalTo(0))
jsonPath("$[29].nameValues.duplication", equalTo(0))
jsonPath("$[29].nameValues.unknown", equalTo(0))
jsonPath("$[30].nameValues.error", equalTo(0))
jsonPath("$[30].nameValues.warning", equalTo(0))
jsonPath("$[30].nameValues.success", equalTo(0))
jsonPath("$[30].nameValues.duplication", equalTo(0))
jsonPath("$[30].nameValues.unknown", equalTo(1))
}
}
}
}
@Nested
inner class SseTest {
private lateinit var webClient: WebTestClient
@BeforeEach
fun setup(
applicationContext: WebApplicationContext,
) {
this.webClient = MockMvcWebTestClient
.bindToApplicationContext(applicationContext).build()
}
@Test
fun testShouldRequestSSE() {
statisticsUpdateProducer.emitComplete { _, _ -> true }
val result = webClient.get().uri("http://localhost/statistics/events").accept(TEXT_EVENT_STREAM).exchange()
.expectStatus().isOk()
.expectHeader().contentType(TEXT_EVENT_STREAM)
.returnResult(String::class.java)
StepVerifier.create(result.responseBody)
.expectComplete()
.verify()
}
}
}

156
src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java
View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2023 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
@ -22,16 +22,52 @@ package dev.dnpm.etl.processor.pseudonym;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.IParser;
import dev.dnpm.etl.processor.config.GPasConfigProperties;
import java.io.BufferedInputStream;
import java.io.FileInputStream;
import java.io.IOException;
import java.net.ConnectException;
import java.security.KeyManagementException;
import java.security.KeyStore;
import java.security.KeyStoreException;
import java.security.NoSuchAlgorithmException;
import java.security.cert.CertificateException;
import java.security.cert.CertificateFactory;
import java.security.cert.X509Certificate;
import java.util.Base64;
import java.util.HashMap;
import javax.net.ssl.SSLContext;
import javax.net.ssl.TrustManagerFactory;
import org.apache.commons.lang3.StringUtils;
import org.apache.hc.client5.http.impl.classic.CloseableHttpClient;
import org.apache.hc.client5.http.impl.classic.HttpClients;
import org.apache.hc.client5.http.impl.io.BasicHttpClientConnectionManager;
import org.apache.hc.client5.http.socket.ConnectionSocketFactory;
import org.apache.hc.client5.http.socket.PlainConnectionSocketFactory;
import org.apache.hc.client5.http.ssl.SSLConnectionSocketFactory;
import org.apache.hc.core5.http.config.Registry;
import org.apache.hc.core5.http.config.RegistryBuilder;
import org.hl7.fhir.r4.model.Identifier;
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.jetbrains.annotations.Nullable;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.http.*;
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.http.client.HttpComponentsClientHttpRequestFactory;
import org.springframework.retry.RetryCallback;
import org.springframework.retry.RetryContext;
import org.springframework.retry.RetryListener;
import org.springframework.retry.RetryPolicy;
import org.springframework.retry.backoff.ExponentialBackOffPolicy;
import org.springframework.retry.policy.SimpleRetryPolicy;
import org.springframework.retry.support.RetryTemplate;
import org.springframework.web.client.RestClientException;
import org.springframework.web.client.RestTemplate;
public class GpasPseudonymGenerator implements Generator {
@ -40,18 +76,29 @@ public class GpasPseudonymGenerator implements Generator {
private final String gPasUrl;
private final String psnTargetDomain;
private final HttpHeaders httpHeader;
private final RetryTemplate retryTemplate;
private final RetryTemplate retryTemplate = defaultTemplate();
private final Logger log = LoggerFactory.getLogger(GpasPseudonymGenerator.class);
private final RestTemplate restTemplate;
private SSLContext customSslContext;
private RestTemplate restTemplate;
public GpasPseudonymGenerator(GPasConfigProperties gpasCfg) {
public GpasPseudonymGenerator(GPasConfigProperties gpasCfg, RetryTemplate retryTemplate, RestTemplate restTemplate) {
this.retryTemplate = retryTemplate;
this.restTemplate = restTemplate;
this.gPasUrl = gpasCfg.getUri();
this.psnTargetDomain = gpasCfg.getTarget();
httpHeader = getHttpHeaders(gpasCfg.getUsername(), gpasCfg.getPassword());
try {
if (StringUtils.isNotBlank(gpasCfg.getSslCaLocation())) {
customSslContext = getSslContext(gpasCfg.getSslCaLocation());
log.debug(String.format("%s has been initialized with SSL certificate %s",
this.getClass().getName(), gpasCfg.getSslCaLocation()));
}
} catch (IOException | KeyManagementException | KeyStoreException | CertificateException |
NoSuchAlgorithmException e) {
throw new RuntimeException(e);
}
log.debug(String.format("%s has been initialized", this.getClass().getName()));
}
@ -103,6 +150,7 @@ public class GpasPseudonymGenerator implements Generator {
HttpEntity<String> requestEntity = new HttpEntity<>(gPasRequestBody, this.httpHeader);
ResponseEntity<String> responseEntity;
var restTemplate = getRestTemplete();
try {
responseEntity = retryTemplate.execute(
@ -142,7 +190,99 @@ public class GpasPseudonymGenerator implements Generator {
return headers;
}
headers.setBasicAuth(gPasUserName, gPasPassword);
String authHeader = gPasUserName + ":" + gPasPassword;
byte[] authHeaderBytes = authHeader.getBytes();
byte[] encodedAuthHeaderBytes = Base64.getEncoder().encode(authHeaderBytes);
String encodedAuthHeader = new String(encodedAuthHeaderBytes);
if (StringUtils.isNotBlank(gPasUserName) && StringUtils.isNotBlank(gPasPassword)) {
headers.set("Authorization", "Basic " + encodedAuthHeader);
}
return headers;
}
protected RetryTemplate defaultTemplate() {
RetryTemplate retryTemplate = new RetryTemplate();
ExponentialBackOffPolicy backOffPolicy = new ExponentialBackOffPolicy();
backOffPolicy.setInitialInterval(1000);
backOffPolicy.setMultiplier(1.25);
retryTemplate.setBackOffPolicy(backOffPolicy);
HashMap<Class<? extends Throwable>, Boolean> retryableExceptions = new HashMap<>();
retryableExceptions.put(RestClientException.class, true);
retryableExceptions.put(ConnectException.class, true);
RetryPolicy retryPolicy = new SimpleRetryPolicy(3, retryableExceptions);
retryTemplate.setRetryPolicy(retryPolicy);
retryTemplate.registerListener(new RetryListener() {
@Override
public <T, E extends Throwable> void onError(RetryContext context,
RetryCallback<T, E> callback, Throwable throwable) {
log.warn("HTTP Error occurred: {}. Retrying {}", throwable.getMessage(),
context.getRetryCount());
RetryListener.super.onError(context, callback, throwable);
}
});
return retryTemplate;
}
/**
* Read SSL root certificate and return SSLContext
*
* @param certificateLocation file location to root certificate (PEM)
* @return initialized SSLContext
* @throws IOException file cannot be read
* @throws CertificateException in case we have an invalid certificate of type X.509
* @throws KeyStoreException keystore cannot be initialized
* @throws NoSuchAlgorithmException missing trust manager algorithmus
* @throws KeyManagementException key management failed at init SSLContext
*/
@Nullable
protected SSLContext getSslContext(String certificateLocation)
throws IOException, CertificateException, KeyStoreException, KeyManagementException, NoSuchAlgorithmException {
KeyStore ks = KeyStore.getInstance(KeyStore.getDefaultType());
FileInputStream fis = new FileInputStream(certificateLocation);
X509Certificate ca = (X509Certificate) CertificateFactory.getInstance("X.509")
.generateCertificate(new BufferedInputStream(fis));
ks.load(null, null);
ks.setCertificateEntry(Integer.toString(1), ca);
TrustManagerFactory tmf = TrustManagerFactory.getInstance(
TrustManagerFactory.getDefaultAlgorithm());
tmf.init(ks);
SSLContext sslContext = SSLContext.getInstance("TLS");
sslContext.init(null, tmf.getTrustManagers(), null);
return sslContext;
}
protected RestTemplate getRestTemplete() {
if (restTemplate != null) {
return restTemplate;
}
if (customSslContext == null) {
restTemplate = new RestTemplate();
return restTemplate;
}
final var sslsf = new SSLConnectionSocketFactory(customSslContext);
final Registry<ConnectionSocketFactory> socketFactoryRegistry = RegistryBuilder.<ConnectionSocketFactory>create()
.register("https", sslsf).register("http", new PlainConnectionSocketFactory()).build();
final BasicHttpClientConnectionManager connectionManager = new BasicHttpClientConnectionManager(
socketFactoryRegistry);
final CloseableHttpClient httpClient = HttpClients.custom()
.setConnectionManager(connectionManager).build();
final HttpComponentsClientHttpRequestFactory requestFactory = new HttpComponentsClientHttpRequestFactory(
httpClient);
restTemplate = new RestTemplate(requestFactory);
return restTemplate;
}
}

3
src/main/kotlin/dev/dnpm/etl/processor/EtlProcessorApplication.kt
View File

@ -20,10 +20,9 @@
package dev.dnpm.etl.processor
import org.springframework.boot.autoconfigure.SpringBootApplication
import org.springframework.boot.autoconfigure.security.servlet.SecurityAutoConfiguration
import org.springframework.boot.runApplication
@SpringBootApplication(exclude = [SecurityAutoConfiguration::class])
@SpringBootApplication
class EtlProcessorApplication
fun main(args: Array<String>) {

40
src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt
View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2023 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
@ -19,15 +19,13 @@
package dev.dnpm.etl.processor.config
import dev.dnpm.etl.processor.security.Role
import org.springframework.boot.context.properties.ConfigurationProperties
@ConfigurationProperties(AppConfigProperties.NAME)
data class AppConfigProperties(
var bwhcUri: String?,
var transformations: List<TransformationProperties> = listOf(),
var maxRetryAttempts: Int = 3,
var duplicationDetection: Boolean = true
var generator: PseudonymGenerator = PseudonymGenerator.BUILDIN,
var transformations: List<TransformationProperties> = listOf()
) {
companion object {
const val NAME = "app"
@ -36,7 +34,6 @@ data class AppConfigProperties(
@ConfigurationProperties(PseudonymizeConfigProperties.NAME)
data class PseudonymizeConfigProperties(
var generator: PseudonymGenerator = PseudonymGenerator.BUILDIN,
val prefix: String = "UNKNOWN",
) {
companion object {
@ -50,7 +47,9 @@ data class GPasConfigProperties(
val target: String = "etl-processor",
val username: String?,
val password: String?,
) {
val sslCaLocation: String?,
) {
companion object {
const val NAME = "app.pseudonymize.gpas"
}
@ -59,21 +58,17 @@ data class GPasConfigProperties(
@ConfigurationProperties(RestTargetProperties.NAME)
data class RestTargetProperties(
val uri: String?,
val username: String?,
val password: String?,
val isBwhc: Boolean = false,
) {
companion object {
const val NAME = "app.rest"
}
}
@ConfigurationProperties(KafkaProperties.NAME)
data class KafkaProperties(
val inputTopic: String?,
val outputTopic: String = "etl-processor",
val outputResponseTopic: String = "${outputTopic}_response",
val groupId: String = "${outputTopic}_group",
@ConfigurationProperties(KafkaTargetProperties.NAME)
data class KafkaTargetProperties(
val topic: String = "etl-processor",
val responseTopic: String = "${topic}_response",
val groupId: String = "${topic}_group",
val servers: String = ""
) {
companion object {
@ -81,19 +76,6 @@ data class KafkaProperties(
}
}
@ConfigurationProperties(SecurityConfigProperties.NAME)
data class SecurityConfigProperties(
val adminUser: String?,
val adminPassword: String?,
val enableTokens: Boolean = false,
val enableOidc: Boolean = false,
val defaultNewUserRole: Role = Role.USER
) {
companion object {
const val NAME = "app.security"
}
}
enum class PseudonymGenerator {
BUILDIN,
GPAS

103
src/main/kotlin/dev/dnpm/etl/processor/config/AppConfiguration.kt
View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2023 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
@ -20,40 +20,19 @@
package dev.dnpm.etl.processor.config
import com.fasterxml.jackson.databind.ObjectMapper
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.Transformation
import dev.dnpm.etl.processor.services.TransformationService
import org.slf4j.LoggerFactory
import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty
import org.springframework.boot.context.properties.EnableConfigurationProperties
import org.springframework.context.annotation.Bean
import org.springframework.context.annotation.Configuration
import org.springframework.data.jdbc.repository.config.AbstractJdbcConfiguration
import org.springframework.retry.RetryCallback
import org.springframework.retry.RetryContext
import org.springframework.retry.RetryListener
import org.springframework.retry.policy.SimpleRetryPolicy
import org.springframework.retry.support.RetryTemplate
import org.springframework.retry.support.RetryTemplateBuilder
import org.springframework.scheduling.annotation.EnableScheduling
import org.springframework.security.crypto.password.PasswordEncoder
import org.springframework.security.provisioning.InMemoryUserDetailsManager
import org.springframework.web.client.HttpClientErrorException
import org.springframework.web.client.RestTemplate
import reactor.core.publisher.Sinks
import kotlin.time.Duration.Companion.seconds
import kotlin.time.toJavaDuration
@Configuration
@EnableConfigurationProperties(
@ -63,23 +42,17 @@ import kotlin.time.toJavaDuration
GPasConfigProperties::class
]
)
@EnableScheduling
class AppConfiguration {
private val logger = LoggerFactory.getLogger(AppConfiguration::class.java)
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS")
@Bean
fun restTemplate(): RestTemplate {
return RestTemplate()
fun gpasPseudonymGenerator(configProperties: GPasConfigProperties): Generator {
return GpasPseudonymGenerator(configProperties)
}
@ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "GPAS")
@Bean
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.pseudonymizer"], havingValue = "BUILDIN", matchIfMissing = true)
@Bean
fun buildinPseudonymGenerator(): Generator {
return AnonymizingGenerator()
@ -98,6 +71,11 @@ class AppConfiguration {
return ReportService(objectMapper)
}
@Bean
fun statisticsUpdateProducer(): Sinks.Many<Any> {
return Sinks.many().multicast().directBestEffort()
}
@Bean
fun transformationService(
objectMapper: ObjectMapper,
@ -109,66 +87,5 @@ class AppConfiguration {
})
}
@Bean
fun retryTemplate(configProperties: AppConfigProperties): RetryTemplate {
return RetryTemplateBuilder()
.notRetryOn(IllegalArgumentException::class.java)
.notRetryOn(HttpClientErrorException.BadRequest::class.java)
.notRetryOn(HttpClientErrorException.UnprocessableEntity::class.java)
.exponentialBackoff(2.seconds.toJavaDuration(), 1.25, 5.seconds.toJavaDuration())
.customPolicy(SimpleRetryPolicy(configProperties.maxRetryAttempts))
.withListener(object : RetryListener {
override fun <T : Any, E : Throwable> onError(
context: RetryContext,
callback: RetryCallback<T, E>,
throwable: Throwable
) {
logger.warn("Error occured: {}. Retrying {}", throwable.message, context.retryCount)
}
})
.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 connectionCheckUpdateProducer(): Sinks.Many<ConnectionCheckResult> {
return Sinks.many().multicast().onBackpressureBuffer()
}
@ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "GPAS")
@Bean
fun gPasConnectionCheckService(
restTemplate: RestTemplate,
gPasConfigProperties: GPasConfigProperties,
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
): ConnectionCheckService {
return GPasConnectionCheckService(restTemplate, gPasConfigProperties, connectionCheckUpdateProducer)
}
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS")
@ConditionalOnMissingBean
@Bean
fun gPasConnectionCheckServiceOnDeprecatedProperty(
restTemplate: RestTemplate,
gPasConfigProperties: GPasConfigProperties,
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
): ConnectionCheckService {
return GPasConnectionCheckService(restTemplate, gPasConfigProperties, connectionCheckUpdateProducer)
}
@Bean
fun jdbcConfiguration(): AbstractJdbcConfiguration {
return AppJdbcConfiguration()
}
}

25
src/main/kotlin/dev/dnpm/etl/processor/config/AppJdbcConfiguration.kt
View File

@ -1,25 +0,0 @@
package dev.dnpm.etl.processor.config
import dev.dnpm.etl.processor.Fingerprint
import org.springframework.context.annotation.Configuration
import org.springframework.core.convert.converter.Converter
import org.springframework.data.jdbc.repository.config.AbstractJdbcConfiguration
@Configuration
class AppJdbcConfiguration : AbstractJdbcConfiguration() {
override fun userConverters(): MutableList<*> {
return mutableListOf(StringToFingerprintConverter(), FingerprintToStringConverter())
}
}
class StringToFingerprintConverter : Converter<String, Fingerprint> {
override fun convert(source: String): Fingerprint {
return Fingerprint(source)
}
}
class FingerprintToStringConverter : Converter<Fingerprint, String> {
override fun convert(source: Fingerprint): String {
return source.value
}
}

53
src/main/kotlin/dev/dnpm/etl/processor/config/AppKafkaConfiguration.kt
View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2023 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
@ -20,13 +20,8 @@
package dev.dnpm.etl.processor.config
import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.input.KafkaInputListener
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
import dev.dnpm.etl.processor.monitoring.KafkaConnectionCheckService
import dev.dnpm.etl.processor.output.KafkaMtbFileSender
import dev.dnpm.etl.processor.output.MtbFileSender
import dev.dnpm.etl.processor.services.RequestProcessor
import dev.dnpm.etl.processor.services.kafka.KafkaResponseProcessor
import org.slf4j.LoggerFactory
import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean
@ -40,14 +35,12 @@ import org.springframework.kafka.core.ConsumerFactory
import org.springframework.kafka.core.KafkaTemplate
import org.springframework.kafka.listener.ContainerProperties
import org.springframework.kafka.listener.KafkaMessageListenerContainer
import org.springframework.retry.support.RetryTemplate
import reactor.core.publisher.Sinks
@Configuration
@EnableConfigurationProperties(
value = [KafkaProperties::class]
value = [KafkaTargetProperties::class]
)
@ConditionalOnProperty(value = ["app.kafka.servers"])
@ConditionalOnProperty(value = ["app.kafka.topic", "app.kafka.servers"])
@ConditionalOnMissingBean(MtbFileSender::class)
@Order(-5)
class AppKafkaConfiguration {
@ -57,21 +50,20 @@ class AppKafkaConfiguration {
@Bean
fun kafkaMtbFileSender(
kafkaTemplate: KafkaTemplate<String, String>,
kafkaProperties: KafkaProperties,
retryTemplate: RetryTemplate,
kafkaTargetProperties: KafkaTargetProperties,
objectMapper: ObjectMapper
): MtbFileSender {
logger.info("Selected 'KafkaMtbFileSender'")
return KafkaMtbFileSender(kafkaTemplate, kafkaProperties, retryTemplate, objectMapper)
return KafkaMtbFileSender(kafkaTemplate, kafkaTargetProperties, objectMapper)
}
@Bean
fun kafkaResponseListenerContainer(
fun kafkaListenerContainer(
consumerFactory: ConsumerFactory<String, String>,
kafkaProperties: KafkaProperties,
kafkaTargetProperties: KafkaTargetProperties,
kafkaResponseProcessor: KafkaResponseProcessor
): KafkaMessageListenerContainer<String, String> {
val containerProperties = ContainerProperties(kafkaProperties.outputResponseTopic)
val containerProperties = ContainerProperties(kafkaTargetProperties.responseTopic)
containerProperties.messageListener = kafkaResponseProcessor
return KafkaMessageListenerContainer(consumerFactory, containerProperties)
}
@ -84,33 +76,4 @@ class AppKafkaConfiguration {
return KafkaResponseProcessor(applicationEventPublisher, objectMapper)
}
@Bean
@ConditionalOnProperty(value = ["app.kafka.input-topic"])
fun kafkaInputListenerContainer(
consumerFactory: ConsumerFactory<String, String>,
kafkaProperties: KafkaProperties,
kafkaInputListener: KafkaInputListener
): KafkaMessageListenerContainer<String, String> {
val containerProperties = ContainerProperties(kafkaProperties.inputTopic)
containerProperties.messageListener = kafkaInputListener
return KafkaMessageListenerContainer(consumerFactory, containerProperties)
}
@Bean
@ConditionalOnProperty(value = ["app.kafka.input-topic"])
fun kafkaInputListener(
requestProcessor: RequestProcessor,
objectMapper: ObjectMapper
): KafkaInputListener {
return KafkaInputListener(requestProcessor, objectMapper)
}
@Bean
fun kafkaConnectionCheckService(
consumerFactory: ConsumerFactory<String, String>,
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
): ConnectionCheckService {
return KafkaConnectionCheckService(consumerFactory.createConsumer(), connectionCheckUpdateProducer)
}
}

35
src/main/kotlin/dev/dnpm/etl/processor/config/AppRestConfiguration.kt
View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2023 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
@ -19,13 +19,8 @@
package dev.dnpm.etl.processor.config
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
import dev.dnpm.etl.processor.monitoring.ReportService
import dev.dnpm.etl.processor.monitoring.RestConnectionCheckService
import dev.dnpm.etl.processor.output.MtbFileSender
import dev.dnpm.etl.processor.output.RestBwhcMtbFileSender
import dev.dnpm.etl.processor.output.RestDipMtbFileSender
import dev.dnpm.etl.processor.output.RestMtbFileSender
import org.slf4j.LoggerFactory
import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty
@ -33,9 +28,7 @@ import org.springframework.boot.context.properties.EnableConfigurationProperties
import org.springframework.context.annotation.Bean
import org.springframework.context.annotation.Configuration
import org.springframework.core.annotation.Order
import org.springframework.retry.support.RetryTemplate
import org.springframework.web.client.RestTemplate
import reactor.core.publisher.Sinks
@Configuration
@EnableConfigurationProperties(
@ -51,28 +44,14 @@ class AppRestConfiguration {
private val logger = LoggerFactory.getLogger(AppRestConfiguration::class.java)
@Bean
fun restMtbFileSender(
restTemplate: RestTemplate,
restTargetProperties: RestTargetProperties,
retryTemplate: RetryTemplate,
reportService: ReportService,
): MtbFileSender {
if (restTargetProperties.isBwhc) {
logger.info("Selected 'RestBwhcMtbFileSender'")
return RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
}
logger.info("Selected 'RestDipMtbFileSender'")
return RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
fun restTemplate(): RestTemplate {
return RestTemplate()
}
@Bean
fun restConnectionCheckService(
restTemplate: RestTemplate,
restTargetProperties: RestTargetProperties,
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
): ConnectionCheckService {
return RestConnectionCheckService(restTemplate, restTargetProperties, connectionCheckUpdateProducer)
fun restMtbFileSender(restTemplate: RestTemplate, restTargetProperties: RestTargetProperties): MtbFileSender {
logger.info("Selected 'RestMtbFileSender'")
return RestMtbFileSender(restTemplate, restTargetProperties)
}
}

196
src/main/kotlin/dev/dnpm/etl/processor/config/AppSecurityConfiguration.kt
View File

@ -1,196 +0,0 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.config
import dev.dnpm.etl.processor.security.UserRole
import dev.dnpm.etl.processor.security.UserRoleRepository
import dev.dnpm.etl.processor.security.UserRoleService
import org.slf4j.LoggerFactory
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty
import org.springframework.boot.context.properties.EnableConfigurationProperties
import org.springframework.context.annotation.Bean
import org.springframework.context.annotation.Configuration
import org.springframework.security.config.annotation.web.builders.HttpSecurity
import org.springframework.security.config.annotation.web.configuration.EnableWebSecurity
import org.springframework.security.config.annotation.web.invoke
import org.springframework.security.core.authority.SimpleGrantedAuthority
import org.springframework.security.core.authority.mapping.GrantedAuthoritiesMapper
import org.springframework.security.core.session.SessionRegistry
import org.springframework.security.core.session.SessionRegistryImpl
import org.springframework.security.core.userdetails.User
import org.springframework.security.core.userdetails.UserDetails
import org.springframework.security.crypto.factory.PasswordEncoderFactories
import org.springframework.security.crypto.password.PasswordEncoder
import org.springframework.security.oauth2.core.oidc.user.OidcUserAuthority
import org.springframework.security.provisioning.InMemoryUserDetailsManager
import org.springframework.security.web.SecurityFilterChain
import java.util.*
private const val LOGIN_PATH = "/login"
@Configuration
@EnableConfigurationProperties(
value = [
SecurityConfigProperties::class
]
)
@ConditionalOnProperty(value = ["app.security.admin-user"])
@EnableWebSecurity
class AppSecurityConfiguration(
private val securityConfigProperties: SecurityConfigProperties
) {
private val logger = LoggerFactory.getLogger(AppSecurityConfiguration::class.java)
@Bean
fun userDetailsService(passwordEncoder: PasswordEncoder): InMemoryUserDetailsManager {
val adminUser = if (securityConfigProperties.adminUser.isNullOrBlank()) {
logger.warn("Using random Admin User: admin")
"admin"
} else {
securityConfigProperties.adminUser
}
val adminPassword = if (securityConfigProperties.adminPassword.isNullOrBlank()) {
val random = UUID.randomUUID().toString()
logger.warn("Using random Admin Passwort: {}", random)
passwordEncoder.encode(random)
} else {
securityConfigProperties.adminPassword
}
val user: UserDetails = User.withUsername(adminUser)
.password(adminPassword)
.roles("ADMIN")
.build()
return InMemoryUserDetailsManager(user)
}
@Bean
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "true")
fun filterChainOidc(
http: HttpSecurity,
passwordEncoder: PasswordEncoder,
userRoleRepository: UserRoleRepository,
sessionRegistry: SessionRegistry
): SecurityFilterChain {
http {
authorizeHttpRequests {
authorize("/configs/**", hasRole("ADMIN"))
authorize("/mtbfile/**", hasAnyRole("MTBFILE", "ADMIN", "USER"))
authorize("/report/**", hasAnyRole("ADMIN", "USER"))
authorize("*.css", permitAll)
authorize("*.ico", permitAll)
authorize("*.jpeg", permitAll)
authorize("*.js", permitAll)
authorize("*.svg", permitAll)
authorize("*.css", permitAll)
authorize("/login/**", permitAll)
authorize(anyRequest, permitAll)
}
httpBasic {
realmName = "ETL-Processor"
}
formLogin {
loginPage = LOGIN_PATH
}
oauth2Login {
loginPage = LOGIN_PATH
}
sessionManagement {
sessionConcurrency {
maximumSessions = 1
expiredUrl = "$LOGIN_PATH?expired"
}
sessionFixation {
newSession()
}
}
csrf { disable() }
}
return http.build()
}
@Bean
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "true")
fun grantedAuthoritiesMapper(
userRoleRepository: UserRoleRepository,
appSecurityConfigProperties: SecurityConfigProperties
): GrantedAuthoritiesMapper {
return GrantedAuthoritiesMapper { grantedAuthority ->
grantedAuthority.filterIsInstance<OidcUserAuthority>()
.onEach {
val userRole = userRoleRepository.findByUsername(it.userInfo.preferredUsername)
if (userRole.isEmpty) {
userRoleRepository.save(
UserRole(
null,
it.userInfo.preferredUsername,
appSecurityConfigProperties.defaultNewUserRole
)
)
}
}
.map {
val userRole = userRoleRepository.findByUsername(it.userInfo.preferredUsername)
SimpleGrantedAuthority("ROLE_${userRole.get().role.toString().uppercase()}")
}
}
}
@Bean
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "false", matchIfMissing = true)
fun filterChain(http: HttpSecurity, passwordEncoder: PasswordEncoder): SecurityFilterChain {
http {
authorizeHttpRequests {
authorize("/configs/**", hasRole("ADMIN"))
authorize("/mtbfile/**", hasAnyRole("MTBFILE", "ADMIN"))
authorize("/report/**", hasRole("ADMIN"))
authorize(anyRequest, permitAll)
}
httpBasic {
realmName = "ETL-Processor"
}
formLogin {
loginPage = LOGIN_PATH
}
csrf { disable() }
}
return http.build()
}
@Bean
fun sessionRegistry(): SessionRegistry {
return SessionRegistryImpl()
}
@Bean
fun passwordEncoder(): PasswordEncoder {
return PasswordEncoderFactories.createDelegatingPasswordEncoder()
}
@Bean
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "true")
fun userRoleService(userRoleRepository: UserRoleRepository, sessionRegistry: SessionRegistry): UserRoleService {
return UserRoleService(userRoleRepository, sessionRegistry)
}
}

91
src/main/kotlin/dev/dnpm/etl/processor/input/KafkaInputListener.kt
View File

@ -1,91 +0,0 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.input
import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.Consent
import de.ukw.ccc.bwhc.dto.MtbFile
import dev.dnpm.etl.processor.CustomMediaType
import dev.dnpm.etl.processor.PatientId
import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.services.RequestProcessor
import org.apache.kafka.clients.consumer.ConsumerRecord
import org.slf4j.LoggerFactory
import org.springframework.http.MediaType
import org.springframework.kafka.listener.MessageListener
class KafkaInputListener(
private val requestProcessor: RequestProcessor,
private val objectMapper: ObjectMapper
) : MessageListener<String, String> {
private val logger = LoggerFactory.getLogger(KafkaInputListener::class.java)
override fun onMessage(record: ConsumerRecord<String, String>) {
when (guessMimeType(record)) {
MediaType.APPLICATION_JSON_VALUE -> handleBwhcMessage(record)
CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE -> handleDnpmV2Message(record)
else -> {
/* ignore other messages */
}
}
}
private fun guessMimeType(record: ConsumerRecord<String, String>): String {
if (record.headers().headers("contentType").toList().isEmpty()) {
// Fallback if no contentType set (old behavior)
return MediaType.APPLICATION_JSON_VALUE
}
return record.headers().headers("contentType")?.firstOrNull()?.value().contentToString()
}
private fun handleBwhcMessage(record: ConsumerRecord<String, String>) {
val mtbFile = objectMapper.readValue(record.value(), MtbFile::class.java)
val patientId = PatientId(mtbFile.patient.id)
val firstRequestIdHeader = record.headers().headers("requestId")?.firstOrNull()
val requestId = if (null != firstRequestIdHeader) {
RequestId(String(firstRequestIdHeader.value()))
} else {
RequestId("")
}
if (mtbFile.consent.status == Consent.Status.ACTIVE) {
logger.debug("Accepted MTB File for processing")
if (requestId.isBlank()) {
requestProcessor.processMtbFile(mtbFile)
} else {
requestProcessor.processMtbFile(mtbFile, requestId)
}
} else {
logger.debug("Accepted MTB File and process deletion")
if (requestId.isBlank()) {
requestProcessor.processDeletion(patientId)
} else {
requestProcessor.processDeletion(patientId, requestId)
}
}
}
private fun handleDnpmV2Message(record: ConsumerRecord<String, String>) {
// Do not handle DNPM-V2 for now
logger.warn("Ignoring MTB File in DNPM V2 format: Not implemented yet")
}
}

210
src/main/kotlin/dev/dnpm/etl/processor/monitoring/ConnectionCheckService.kt
View File

@ -1,210 +0,0 @@
/*
* 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.monitoring
import dev.dnpm.etl.processor.config.GPasConfigProperties
import dev.dnpm.etl.processor.config.RestTargetProperties
import jakarta.annotation.PostConstruct
import org.apache.kafka.clients.consumer.Consumer
import org.apache.kafka.common.errors.TimeoutException
import org.springframework.beans.factory.annotation.Qualifier
import org.springframework.http.*
import org.springframework.scheduling.annotation.Scheduled
import org.springframework.web.client.RestTemplate
import org.springframework.web.util.UriComponentsBuilder
import reactor.core.publisher.Sinks
import java.time.Instant
import kotlin.time.Duration.Companion.seconds
import kotlin.time.toJavaDuration
fun interface ConnectionCheckService {
fun connectionAvailable(): ConnectionCheckResult
}
interface OutputConnectionCheckService : ConnectionCheckService
sealed class ConnectionCheckResult {
abstract val available: Boolean
abstract val timestamp: Instant
abstract val lastChange: Instant
data class KafkaConnectionCheckResult(
override val available: Boolean,
override val timestamp: Instant,
override val lastChange: Instant
) : ConnectionCheckResult()
data class RestConnectionCheckResult(
override val available: Boolean,
override val timestamp: Instant,
override val lastChange: Instant
) : ConnectionCheckResult()
data class GPasConnectionCheckResult(
override val available: Boolean,
override val timestamp: Instant,
override val lastChange: Instant
) : ConnectionCheckResult()
}
class KafkaConnectionCheckService(
private val consumer: Consumer<String, String>,
@Qualifier("connectionCheckUpdateProducer")
private val connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
) : OutputConnectionCheckService {
private var result = ConnectionCheckResult.KafkaConnectionCheckResult(false, Instant.now(), Instant.now())
@PostConstruct
@Scheduled(cron = "0 * * * * *")
fun check() {
result = try {
val available = null != consumer.listTopics(5.seconds.toJavaDuration())
ConnectionCheckResult.KafkaConnectionCheckResult(
available,
Instant.now(),
if (result.available == available) { result.lastChange } else { Instant.now() }
)
} catch (_: TimeoutException) {
ConnectionCheckResult.KafkaConnectionCheckResult(
false,
Instant.now(),
if (!result.available) { result.lastChange } else { Instant.now() }
)
}
connectionCheckUpdateProducer.emitNext(
result,
Sinks.EmitFailureHandler.FAIL_FAST
)
}
override fun connectionAvailable(): ConnectionCheckResult.KafkaConnectionCheckResult {
return this.result
}
}
class RestConnectionCheckService(
private val restTemplate: RestTemplate,
private val restTargetProperties: RestTargetProperties,
@Qualifier("connectionCheckUpdateProducer")
private val connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
) : OutputConnectionCheckService {
private var result = ConnectionCheckResult.RestConnectionCheckResult(false, Instant.now(), Instant.now())
@PostConstruct
@Scheduled(cron = "0 * * * * *")
fun check() {
result = try {
val available = restTemplate.getForEntity(
if (restTargetProperties.isBwhc) {
UriComponentsBuilder.fromUriString(restTargetProperties.uri.toString()).path("").toUriString()
} else {
UriComponentsBuilder.fromUriString(restTargetProperties.uri.toString())
.pathSegment("mtb")
.pathSegment("kaplan-meier")
.pathSegment("config")
.toUriString()
},
String::class.java
).statusCode == HttpStatus.OK
ConnectionCheckResult.RestConnectionCheckResult(
available,
Instant.now(),
if (result.available == available) { result.lastChange } else { Instant.now() }
)
} catch (_: Exception) {
ConnectionCheckResult.RestConnectionCheckResult(
false,
Instant.now(),
if (!result.available) { result.lastChange } else { Instant.now() }
)
}
connectionCheckUpdateProducer.emitNext(
result,
Sinks.EmitFailureHandler.FAIL_FAST
)
}
override fun connectionAvailable(): ConnectionCheckResult.RestConnectionCheckResult {
return this.result
}
}
class GPasConnectionCheckService(
private val restTemplate: RestTemplate,
private val gPasConfigProperties: GPasConfigProperties,
@Qualifier("connectionCheckUpdateProducer")
private val connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
) : ConnectionCheckService {
private var result = ConnectionCheckResult.GPasConnectionCheckResult(false, Instant.now(), Instant.now())
@PostConstruct
@Scheduled(cron = "0 * * * * *")
fun check() {
result = try {
val uri = UriComponentsBuilder.fromUriString(
gPasConfigProperties.uri?.replace("/\$pseudonymizeAllowCreate", "/metadata").toString()
).build().toUri()
val headers = HttpHeaders()
headers.contentType = MediaType.APPLICATION_JSON
if (!gPasConfigProperties.username.isNullOrBlank() && !gPasConfigProperties.password.isNullOrBlank()) {
headers.setBasicAuth(gPasConfigProperties.username, gPasConfigProperties.password)
}
val available = restTemplate.exchange(
uri,
HttpMethod.GET,
HttpEntity<Void>(headers),
Void::class.java
).statusCode == HttpStatus.OK
ConnectionCheckResult.GPasConnectionCheckResult(
available,
Instant.now(),
if (result.available == available) { result.lastChange } else { Instant.now() }
)
} catch (_: Exception) {
ConnectionCheckResult.GPasConnectionCheckResult(
false,
Instant.now(),
if (!result.available) { result.lastChange } else { Instant.now() }
)
}
connectionCheckUpdateProducer.emitNext(
result,
Sinks.EmitFailureHandler.FAIL_FAST
)
}
override fun connectionAvailable(): ConnectionCheckResult.GPasConnectionCheckResult {
return this.result
}
}

20
src/main/kotlin/dev/dnpm/etl/processor/monitoring/ReportService.kt
View File

@ -19,15 +19,11 @@
package dev.dnpm.etl.processor.monitoring
import com.fasterxml.jackson.annotation.JsonAlias
import com.fasterxml.jackson.annotation.JsonIgnoreProperties
import com.fasterxml.jackson.annotation.JsonValue
import com.fasterxml.jackson.core.JsonParseException
import com.fasterxml.jackson.databind.JsonMappingException
import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.monitoring.ReportService.Issue
import dev.dnpm.etl.processor.monitoring.ReportService.Severity
import java.util.Optional
class ReportService(
private val objectMapper: ObjectMapper
@ -58,25 +54,11 @@ class ReportService(
private data class DataQualityReport(val issues: List<Issue>)
@JsonIgnoreProperties(ignoreUnknown = true)
data class Issue(
val severity: Severity,
@JsonAlias("details") val message: String,
val path: Optional<String> = Optional.empty()
)
data class Issue(val severity: Severity, val message: String)
enum class Severity(@JsonValue val value: String) {
FATAL("fatal"),
ERROR("error"),
WARNING("warning"),
INFO("info")
}
}
fun List<Issue>.asRequestStatus(): RequestStatus {
val severity = this.minOfOrNull { it.severity }
return when (severity) {
Severity.FATAL, Severity.ERROR -> RequestStatus.ERROR
Severity.WARNING -> RequestStatus.WARNING
else -> RequestStatus.SUCCESS
}
}

53
src/main/kotlin/dev/dnpm/etl/processor/monitoring/Request.kt
View File

@ -19,79 +19,50 @@
package dev.dnpm.etl.processor.monitoring
import dev.dnpm.etl.processor.*
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.relational.core.mapping.Column
import org.springframework.data.relational.core.mapping.Embedded
import org.springframework.data.relational.core.mapping.Table
import org.springframework.data.repository.CrudRepository
import org.springframework.data.repository.PagingAndSortingRepository
import java.time.Instant
import java.util.*
typealias RequestId = UUID
@Table("request")
data class Request(
@Id val id: Long? = null,
val uuid: RequestId = randomRequestId(),
val patientPseudonym: PatientPseudonym,
val pid: PatientId,
@Column("fingerprint")
val fingerprint: Fingerprint,
val uuid: String = RequestId.randomUUID().toString(),
val patientId: String,
val pid: String,
val fingerprint: String,
val type: RequestType,
var status: RequestStatus,
var processedAt: Instant = Instant.now(),
@Embedded.Nullable var report: Report? = null
) {
constructor(
uuid: RequestId,
patientPseudonym: PatientPseudonym,
pid: PatientId,
fingerprint: Fingerprint,
type: RequestType,
status: RequestStatus
) :
this(null, uuid, patientPseudonym, pid, fingerprint, type, status, Instant.now())
)
constructor(
uuid: RequestId,
patientPseudonym: PatientPseudonym,
pid: PatientId,
fingerprint: Fingerprint,
type: RequestType,
status: RequestStatus,
processedAt: Instant
) :
this(null, uuid, patientPseudonym, pid, fingerprint, type, status, processedAt)
}
@JvmRecord
data class Report(
val description: String,
val dataQualityReport: String = ""
)
@JvmRecord
data class CountedState(
val count: Int,
val status: RequestStatus,
)
interface RequestRepository : CrudRepository<Request, Long>, PagingAndSortingRepository<Request, Long> {
interface RequestRepository : CrudRepository<Request, Long> {
fun findAllByPatientPseudonymOrderByProcessedAtDesc(patientId: PatientPseudonym): List<Request>
fun findAllByPatientIdOrderByProcessedAtDesc(patientId: String): List<Request>
fun findByUuidEquals(uuid: RequestId): Optional<Request>
fun findRequestByPatientPseudonym(patientPseudonym: PatientPseudonym, pageable: Pageable): Page<Request>
fun findByUuidEquals(uuid: String): Optional<Request>
@Query("SELECT count(*) AS count, status FROM request WHERE type = 'MTB_FILE' GROUP BY status ORDER BY status, count DESC;")
fun countStates(): List<CountedState>
@Query("SELECT count(*) AS count, status FROM (" +
"SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " +
"SELECT status, rank() OVER (PARTITION BY patient_id ORDER BY processed_at DESC) AS rank FROM request " +
"WHERE type = 'MTB_FILE' AND status NOT IN ('DUPLICATION') " +
") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;")
fun findPatientUniqueStates(): List<CountedState>
@ -100,7 +71,7 @@ interface RequestRepository : CrudRepository<Request, Long>, PagingAndSortingRep
fun countDeleteStates(): List<CountedState>
@Query("SELECT count(*) AS count, status FROM (" +
"SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " +
"SELECT status, rank() OVER (PARTITION BY patient_id ORDER BY processed_at DESC) AS rank FROM request " +
"WHERE type = 'DELETE'" +
") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;")
fun findPatientUniqueDeleteStates(): List<CountedState>

62
src/main/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSender.kt
View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2023 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
@ -22,95 +22,75 @@ package dev.dnpm.etl.processor.output
import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.Consent
import de.ukw.ccc.bwhc.dto.MtbFile
import dev.dnpm.etl.processor.CustomMediaType
import dev.dnpm.etl.processor.config.KafkaProperties
import dev.dnpm.etl.processor.config.KafkaTargetProperties
import dev.dnpm.etl.processor.monitoring.RequestStatus
import org.apache.kafka.clients.producer.ProducerRecord
import org.slf4j.LoggerFactory
import org.springframework.http.MediaType
import org.springframework.kafka.core.KafkaTemplate
import org.springframework.retry.support.RetryTemplate
class KafkaMtbFileSender(
private val kafkaTemplate: KafkaTemplate<String, String>,
private val kafkaProperties: KafkaProperties,
private val retryTemplate: RetryTemplate,
private val kafkaTargetProperties: KafkaTargetProperties,
private val objectMapper: ObjectMapper
) : MtbFileSender {
private val logger = LoggerFactory.getLogger(KafkaMtbFileSender::class.java)
override fun <T> send(request: MtbFileRequest<T>): MtbFileSender.Response {
override fun send(request: MtbFileSender.MtbFileRequest): MtbFileSender.Response {
return try {
return retryTemplate.execute<MtbFileSender.Response, Exception> {
val record =
ProducerRecord(kafkaProperties.outputTopic, key(request), objectMapper.writeValueAsString(request))
when (request) {
is BwhcV1MtbFileRequest -> record.headers()
.add("contentType", MediaType.APPLICATION_JSON_VALUE.toByteArray())
is DnpmV2MtbFileRequest -> record.headers()
.add("contentType", CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE.toByteArray())
}
val result = kafkaTemplate.send(record)
val result = kafkaTemplate.send(
kafkaTargetProperties.topic,
key(request),
objectMapper.writeValueAsString(Data(request.requestId, request.mtbFile))
)
if (result.get() != null) {
logger.debug("Sent file via KafkaMtbFileSender")
MtbFileSender.Response(RequestStatus.UNKNOWN)
} else {
MtbFileSender.Response(RequestStatus.ERROR)
}
}
} catch (e: Exception) {
logger.error("An error occurred sending to kafka", e)
MtbFileSender.Response(RequestStatus.ERROR)
}
}
override fun send(request: DeleteRequest): MtbFileSender.Response {
override fun send(request: MtbFileSender.DeleteRequest): MtbFileSender.Response {
val dummyMtbFile = MtbFile.builder()
.withConsent(
Consent.builder()
.withPatient(request.patientId.value)
.withPatient(request.patientId)
.withStatus(Consent.Status.REJECTED)
.build()
)
.build()
return try {
return retryTemplate.execute<MtbFileSender.Response, Exception> {
val record =
ProducerRecord(
kafkaProperties.outputTopic,
val result = kafkaTemplate.send(
kafkaTargetProperties.topic,
key(request),
// Always use old BwhcV1FileRequest with Consent REJECT
objectMapper.writeValueAsString(BwhcV1MtbFileRequest(request.requestId, dummyMtbFile))
objectMapper.writeValueAsString(Data(request.requestId, dummyMtbFile))
)
val result = kafkaTemplate.send(record)
if (result.get() != null) {
logger.debug("Sent deletion request via KafkaMtbFileSender")
MtbFileSender.Response(RequestStatus.UNKNOWN)
} else {
MtbFileSender.Response(RequestStatus.ERROR)
}
}
} catch (e: Exception) {
logger.error("An error occurred sending to kafka", e)
MtbFileSender.Response(RequestStatus.ERROR)
}
}
override fun endpoint(): String {
return "${this.kafkaProperties.servers} (${this.kafkaProperties.outputTopic}/${this.kafkaProperties.outputResponseTopic})"
private fun key(request: MtbFileSender.MtbFileRequest): String {
return "{\"pid\": \"${request.mtbFile.patient.id}\", " +
"\"eid\": \"${request.mtbFile.episode.id}\"}"
}
private fun key(request: MtbRequest): String {
return when (request) {
is BwhcV1MtbFileRequest -> "{\"pid\": \"${request.content.patient.id}\"}"
is DnpmV2MtbFileRequest -> "{\"pid\": \"${request.content.patient.id}\"}"
is DeleteRequest -> "{\"pid\": \"${request.patientId.value}\"}"
else -> throw IllegalArgumentException("Unsupported request type: ${request::class.simpleName}")
}
private fun key(request: MtbFileSender.DeleteRequest): String {
return "{\"pid\": \"${request.patientId}\"}"
}
data class Data(val requestId: String, val content: MtbFile)
}

10
src/main/kotlin/dev/dnpm/etl/processor/output/MtbFileSender.kt
View File

@ -19,17 +19,21 @@
package dev.dnpm.etl.processor.output
import de.ukw.ccc.bwhc.dto.MtbFile
import dev.dnpm.etl.processor.monitoring.RequestStatus
import org.springframework.http.HttpStatusCode
interface MtbFileSender {
fun <T> send(request: MtbFileRequest<T>): Response
fun send(request: MtbFileRequest): Response
fun send(request: DeleteRequest): Response
fun endpoint(): String
data class Response(val status: RequestStatus, val body: String = "")
data class MtbFileRequest(val requestId: String, val mtbFile: MtbFile)
data class DeleteRequest(val requestId: String, val patientId: String)
}
fun Int.asRequestStatus(): RequestStatus {

59
src/main/kotlin/dev/dnpm/etl/processor/output/MtbRequest.kt
View File

@ -1,59 +0,0 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.output
import de.ukw.ccc.bwhc.dto.MtbFile
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.RequestId
import dev.pcvolkmer.mv64e.mtb.Mtb
interface MtbRequest {
val requestId: RequestId
}
sealed interface MtbFileRequest<out T> : MtbRequest {
override val requestId: RequestId
val content: T
fun patientPseudonym(): PatientPseudonym
}
data class BwhcV1MtbFileRequest(
override val requestId: RequestId,
override val content: MtbFile
) : MtbFileRequest<MtbFile> {
override fun patientPseudonym(): PatientPseudonym {
return PatientPseudonym(content.patient.id)
}
}
data class DnpmV2MtbFileRequest(
override val requestId: RequestId,
override val content: Mtb
) : MtbFileRequest<Mtb> {
override fun patientPseudonym(): PatientPseudonym {
return PatientPseudonym(content.patient.id)
}
}
data class DeleteRequest(
override val requestId: RequestId,
val patientId: PatientPseudonym
) : MtbRequest

51
src/main/kotlin/dev/dnpm/etl/processor/output/RestBwhcMtbFileSender.kt
View File

@ -1,51 +0,0 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.output
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.config.RestTargetProperties
import dev.dnpm.etl.processor.monitoring.ReportService
import org.springframework.retry.support.RetryTemplate
import org.springframework.web.client.RestTemplate
import org.springframework.web.util.UriComponentsBuilder
class RestBwhcMtbFileSender(
restTemplate: RestTemplate,
private val restTargetProperties: RestTargetProperties,
retryTemplate: RetryTemplate,
reportService: ReportService,
) : RestMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService) {
override fun sendUrl(): String {
return UriComponentsBuilder
.fromUriString(restTargetProperties.uri.toString())
.pathSegment("MTBFile")
.toUriString()
}
override fun deleteUrl(patientId: PatientPseudonym): String {
return UriComponentsBuilder
.fromUriString(restTargetProperties.uri.toString())
.pathSegment("Patient")
.pathSegment(patientId.value)
.toUriString()
}
}

55
src/main/kotlin/dev/dnpm/etl/processor/output/RestDipMtbFileSender.kt
View File

@ -1,55 +0,0 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.output
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.config.RestTargetProperties
import dev.dnpm.etl.processor.monitoring.ReportService
import org.springframework.retry.support.RetryTemplate
import org.springframework.web.client.RestTemplate
import org.springframework.web.util.UriComponentsBuilder
class RestDipMtbFileSender(
restTemplate: RestTemplate,
private val restTargetProperties: RestTargetProperties,
retryTemplate: RetryTemplate,
reportService: ReportService
) : RestMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService) {
override fun sendUrl(): String {
return UriComponentsBuilder
.fromUriString(restTargetProperties.uri.toString())
.pathSegment("mtb")
.pathSegment("etl")
.pathSegment("patient-record")
.toUriString()
}
override fun deleteUrl(patientId: PatientPseudonym): String {
return UriComponentsBuilder
.fromUriString(restTargetProperties.uri.toString())
.pathSegment("mtb")
.pathSegment("etl")
.pathSegment("patient")
.pathSegment(patientId.value)
.toUriString()
}
}

94
src/main/kotlin/dev/dnpm/etl/processor/output/RestMtbFileSender.kt
View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2023 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
@ -19,77 +19,38 @@
package dev.dnpm.etl.processor.output
import dev.dnpm.etl.processor.CustomMediaType
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.config.RestTargetProperties
import dev.dnpm.etl.processor.monitoring.ReportService
import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.monitoring.asRequestStatus
import org.slf4j.LoggerFactory
import org.springframework.http.HttpEntity
import org.springframework.http.HttpHeaders
import org.springframework.http.MediaType
import org.springframework.retry.support.RetryTemplate
import org.springframework.web.client.RestClientException
import org.springframework.web.client.RestClientResponseException
import org.springframework.web.client.RestTemplate
abstract class RestMtbFileSender(
class RestMtbFileSender(
private val restTemplate: RestTemplate,
private val restTargetProperties: RestTargetProperties,
private val retryTemplate: RetryTemplate,
private val reportService: ReportService
private val restTargetProperties: RestTargetProperties
) : MtbFileSender {
private val logger = LoggerFactory.getLogger(RestMtbFileSender::class.java)
abstract fun sendUrl(): String
abstract fun deleteUrl(patientId: PatientPseudonym): String
override fun <T> send(request: MtbFileRequest<T>): MtbFileSender.Response {
override fun send(request: MtbFileSender.MtbFileRequest): MtbFileSender.Response {
try {
return retryTemplate.execute<MtbFileSender.Response, Exception> {
val headers = getHttpHeaders(request)
val entityReq = HttpEntity(request.content, headers)
val headers = HttpHeaders()
headers.contentType = MediaType.APPLICATION_JSON
val entityReq = HttpEntity(request.mtbFile, headers)
val response = restTemplate.postForEntity(
sendUrl(),
"${restTargetProperties.uri}/MTBFile",
entityReq,
String::class.java
)
if (!response.statusCode.is2xxSuccessful) {
logger.warn("Error sending to remote system: {}", response.body)
return@execute MtbFileSender.Response(
reportService.deserialize(response.body).asRequestStatus(),
"Status-Code: ${response.statusCode.value()}"
)
return MtbFileSender.Response(response.statusCode.asRequestStatus(), "Status-Code: ${response.statusCode.value()}")
}
logger.debug("Sent file via RestMtbFileSender")
return@execute MtbFileSender.Response(reportService.deserialize(response.body).asRequestStatus(), response.body.orEmpty())
}
} catch (e: IllegalArgumentException) {
logger.error("Not a valid URI to export to: '{}'", restTargetProperties.uri!!)
} catch (e: RestClientResponseException) {
logger.info(restTargetProperties.uri!!.toString())
logger.error("Request data not accepted by remote system", e)
return MtbFileSender.Response(reportService.deserialize(e.responseBodyAsString).asRequestStatus(), e.responseBodyAsString)
}
return MtbFileSender.Response(RequestStatus.ERROR, "Sonstiger Fehler bei der Übertragung")
}
override fun send(request: DeleteRequest): MtbFileSender.Response {
try {
return retryTemplate.execute<MtbFileSender.Response, Exception> {
val headers = getHttpHeaders(request)
val entityReq = HttpEntity(null, headers)
restTemplate.delete(
deleteUrl(request.patientId),
entityReq,
String::class.java
)
logger.debug("Sent file via RestMtbFileSender")
return@execute MtbFileSender.Response(RequestStatus.SUCCESS)
}
return MtbFileSender.Response(response.statusCode.asRequestStatus(), response.body.orEmpty())
} catch (e: IllegalArgumentException) {
logger.error("Not a valid URI to export to: '{}'", restTargetProperties.uri!!)
} catch (e: RestClientException) {
@ -99,26 +60,25 @@ abstract class RestMtbFileSender(
return MtbFileSender.Response(RequestStatus.ERROR, "Sonstiger Fehler bei der Übertragung")
}
override fun endpoint(): String {
return this.restTargetProperties.uri.orEmpty()
}
private fun getHttpHeaders(request: MtbRequest): HttpHeaders {
val username = restTargetProperties.username
val password = restTargetProperties.password
override fun send(request: MtbFileSender.DeleteRequest): MtbFileSender.Response {
try {
val headers = HttpHeaders()
headers.contentType = when (request) {
is BwhcV1MtbFileRequest -> MediaType.APPLICATION_JSON
is DnpmV2MtbFileRequest -> CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON
else -> MediaType.APPLICATION_JSON
headers.contentType = MediaType.APPLICATION_JSON
val entityReq = HttpEntity(null, headers)
restTemplate.delete(
"${restTargetProperties.uri}/Patient/${request.patientId}",
entityReq,
String::class.java
)
logger.debug("Sent file via RestMtbFileSender")
return MtbFileSender.Response(RequestStatus.SUCCESS)
} catch (e: IllegalArgumentException) {
logger.error("Not a valid URI to export to: '{}'", restTargetProperties.uri!!)
} catch (e: RestClientException) {
logger.info(restTargetProperties.uri!!.toString())
logger.error("Cannot send data to remote system", e)
}
if (username.isNullOrBlank() || password.isNullOrBlank()) {
return headers
}
headers.setBasicAuth(username, password)
return headers
return MtbFileSender.Response(RequestStatus.ERROR, "Sonstiger Fehler bei der Übertragung")
}
}

12
src/main/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeService.kt
View File

@ -19,8 +19,6 @@
package dev.dnpm.etl.processor.pseudonym
import dev.dnpm.etl.processor.PatientId
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.config.PseudonymizeConfigProperties
class PseudonymizeService(
@ -28,15 +26,11 @@ class PseudonymizeService(
private val configProperties: PseudonymizeConfigProperties
) {
fun patientPseudonym(patientId: PatientId): PatientPseudonym {
fun patientPseudonym(patientId: String): String {
return when (generator) {
is GpasPseudonymGenerator -> PatientPseudonym(generator.generate(patientId.value))
else -> PatientPseudonym("${configProperties.prefix}_${generator.generate(patientId.value)}")
is GpasPseudonymGenerator -> generator.generate(patientId)
else -> "${configProperties.prefix}_${generator.generate(patientId)}"
}
}
fun prefix(): String {
return configProperties.prefix
}
}

312
src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2023 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
@ -20,296 +20,34 @@
package dev.dnpm.etl.processor.pseudonym
import de.ukw.ccc.bwhc.dto.MtbFile
import dev.dnpm.etl.processor.PatientId
import dev.pcvolkmer.mv64e.mtb.Mtb
import org.apache.commons.codec.digest.DigestUtils
/** Replaces patient ID with generated patient pseudonym
*
* @param pseudonymizeService The pseudonymizeService to be used
* @return The MTB file containing patient pseudonymes
*/
infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
val patientPseudonym = pseudonymizeService.patientPseudonym(PatientId(this.patient.id)).value
val patientPseudonym = pseudonymizeService.patientPseudonym(this.patient.id)
this.episode?.patient = patientPseudonym
this.carePlans?.forEach { it.patient = patientPseudonym }
this.episode.patient = patientPseudonym
this.carePlans.forEach { it.patient = patientPseudonym }
this.patient.id = patientPseudonym
this.claims?.forEach { it.patient = patientPseudonym }
this.consent?.patient = patientPseudonym
this.claimResponses?.forEach { it.patient = patientPseudonym }
this.diagnoses?.forEach { it.patient = patientPseudonym }
this.ecogStatus?.forEach { it.patient = patientPseudonym }
this.familyMemberDiagnoses?.forEach { it.patient = patientPseudonym }
this.geneticCounsellingRequests?.forEach { it.patient = patientPseudonym }
this.histologyReevaluationRequests?.forEach { it.patient = patientPseudonym }
this.histologyReports?.forEach {
this.claims.forEach { it.patient = patientPseudonym }
this.consent.patient = patientPseudonym
this.claimResponses.forEach { it.patient = patientPseudonym }
this.diagnoses.forEach { it.patient = patientPseudonym }
this.ecogStatus.forEach { it.patient = patientPseudonym }
this.familyMemberDiagnoses.forEach { it.patient = patientPseudonym }
this.geneticCounsellingRequests.forEach { it.patient = patientPseudonym }
this.histologyReevaluationRequests.forEach { it.patient = patientPseudonym }
this.histologyReports.forEach {
it.patient = patientPseudonym
it.tumorMorphology?.patient = patientPseudonym
it.tumorMorphology.patient = patientPseudonym
}
this.lastGuidelineTherapies?.forEach { it.patient = patientPseudonym }
this.molecularPathologyFindings?.forEach { it.patient = patientPseudonym }
this.molecularTherapies?.forEach { molecularTherapy ->
molecularTherapy.history.forEach {
it.patient = patientPseudonym
}
}
this.ngsReports?.forEach { it.patient = patientPseudonym }
this.previousGuidelineTherapies?.forEach { it.patient = patientPseudonym }
this.rebiopsyRequests?.forEach { it.patient = patientPseudonym }
this.recommendations?.forEach { it.patient = patientPseudonym }
this.responses?.forEach { it.patient = patientPseudonym }
this.studyInclusionRequests?.forEach { it.patient = patientPseudonym }
this.specimens?.forEach { it.patient = patientPseudonym }
}
/**
* Creates new hash of content IDs with given prefix except for patient IDs
*
* @param pseudonymizeService The pseudonymizeService to be used
* @return The MTB file containing rehashed content IDs
*/
infix fun MtbFile.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
val prefix = pseudonymizeService.prefix()
fun anonymize(id: String): String {
val hash = DigestUtils.sha256Hex("$prefix-$id").substring(0, 41).lowercase()
return "$prefix$hash"
}
this.episode?.apply {
id = id?.let {
anonymize(it)
}
}
this.carePlans?.onEach { carePlan ->
carePlan?.apply {
id = id?.let { anonymize(it) }
diagnosis = diagnosis?.let { anonymize(it) }
geneticCounsellingRequest = geneticCounsellingRequest?.let { anonymize(it) }
rebiopsyRequests = rebiopsyRequests.map { it?.let { anonymize(it) } }
recommendations = recommendations.map { it?.let { anonymize(it) } }
studyInclusionRequests = studyInclusionRequests.map { it?.let { anonymize(it) } }
}
}
this.claims?.onEach { claim ->
claim?.apply {
id = id?.let { anonymize(it) }
therapy = therapy?.let { anonymize(it) }
}
}
this.claimResponses?.onEach { claimResponse ->
claimResponse?.apply {
id = id?.let { anonymize(it) }
claim = claim?.let { anonymize(it) }
}
}
this.consent?.apply {
id = id?.let { anonymize(it) }
}
this.diagnoses?.onEach { diagnosis ->
diagnosis?.apply {
id = id?.let { anonymize(it) }
histologyResults = histologyResults?.map { it?.let { anonymize(it) } }
}
}
this.ecogStatus?.onEach { ecogStatus ->
ecogStatus?.apply {
id = id?.let { anonymize(it) }
}
}
this.familyMemberDiagnoses?.onEach { familyMemberDiagnosis ->
familyMemberDiagnosis?.apply {
id = id?.let { anonymize(it) }
}
}
this.geneticCounsellingRequests?.onEach { geneticCounsellingRequest ->
geneticCounsellingRequest?.apply {
id = id?.let { anonymize(it) }
}
}
this.histologyReevaluationRequests?.onEach { histologyReevaluationRequest ->
histologyReevaluationRequest?.apply {
id = id?.let { anonymize(it) }
specimen = specimen?.let { anonymize(it) }
}
}
this.histologyReports?.onEach { histologyReport ->
histologyReport?.apply {
id = id?.let { anonymize(it) }
specimen = specimen?.let { anonymize(it) }
tumorMorphology?.apply {
id = id?.let { anonymize(it) }
specimen = specimen?.let { anonymize(it) }
}
tumorCellContent?.apply {
id = id?.let { anonymize(it) }
specimen = specimen?.let { anonymize(it) }
}
}
}
this.lastGuidelineTherapies?.onEach { lastGuidelineTherapy ->
lastGuidelineTherapy?.apply {
id = id?.let { anonymize(it) }
diagnosis = diagnosis?.let { anonymize(it) }
}
}
this.molecularPathologyFindings?.onEach { molecularPathologyFinding ->
molecularPathologyFinding?.apply {
id = id?.let { anonymize(it) }
specimen = specimen?.let { anonymize(it) }
}
}
this.molecularTherapies?.onEach { molecularTherapy ->
molecularTherapy?.apply {
history?.onEach { history ->
history?.apply {
id = id?.let { anonymize(it) }
basedOn = basedOn?.let { anonymize(it) }
}
}
}
}
this.ngsReports?.onEach { ngsReport ->
ngsReport?.apply {
id = id?.let { anonymize(it) }
specimen = specimen?.let { anonymize(it) }
tumorCellContent?.apply {
id = id?.let { anonymize(it) }
specimen = specimen?.let { anonymize(it) }
}
simpleVariants?.onEach { simpleVariant ->
simpleVariant?.apply {
id = id?.let { anonymize(it) }
}
}
}
}
this.previousGuidelineTherapies?.onEach { previousGuidelineTherapy ->
previousGuidelineTherapy?.apply {
id = id?.let { anonymize(it) }
diagnosis = diagnosis?.let { anonymize(it) }
medication.forEach { medication ->
medication?.apply {
id = id?.let { anonymize(it) }
}
}
}
}
this.rebiopsyRequests?.onEach { rebiopsyRequest ->
rebiopsyRequest?.apply {
id = id?.let { anonymize(it) }
specimen = specimen?.let { anonymize(it) }
}
}
this.recommendations?.onEach { recommendation ->
recommendation?.apply {
id = id?.let { anonymize(it) }
diagnosis = diagnosis?.let { anonymize(it) }
ngsReport = ngsReport?.let { anonymize(it) }
}
}
this.responses?.onEach { response ->
response?.apply {
id = id?.let { anonymize(it) }
therapy = therapy?.let { anonymize(it) }
}
}
this.studyInclusionRequests?.onEach { studyInclusionRequest ->
studyInclusionRequest?.apply {
id = id?.let { anonymize(it) }
reason = reason?.let { anonymize(it) }
}
}
this.specimens?.onEach { specimen ->
specimen?.apply {
id = id?.let { anonymize(it) }
}
}
}
/** Replaces patient ID with generated patient pseudonym
*
* @since 0.11.0
*
* @param pseudonymizeService The pseudonymizeService to be used
* @return The MTB file containing patient pseudonymes
*/
infix fun Mtb.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
val patientPseudonym = pseudonymizeService.patientPseudonym(PatientId(this.patient.id)).value
this.episodesOfCare?.forEach { it.patient.id = patientPseudonym }
this.carePlans?.forEach {
it.patient.id = patientPseudonym
it.rebiopsyRequests?.forEach { it.patient.id = patientPseudonym }
it.histologyReevaluationRequests?.forEach { it.patient.id = patientPseudonym }
it.medicationRecommendations.forEach { it.patient.id = patientPseudonym }
it.studyEnrollmentRecommendations?.forEach { it.patient.id = patientPseudonym }
it.procedureRecommendations?.forEach { it.patient.id = patientPseudonym }
it.geneticCounselingRecommendation.patient.id = patientPseudonym
}
this.diagnoses?.forEach { it.patient.id = patientPseudonym }
this.guidelineTherapies?.forEach { it.patient.id = patientPseudonym }
this.guidelineProcedures?.forEach { it.patient.id = patientPseudonym }
this.patient.id = patientPseudonym
this.claims?.forEach { it.patient.id = patientPseudonym }
this.claimResponses?.forEach { it.patient.id = patientPseudonym }
this.diagnoses?.forEach { it.patient.id = patientPseudonym }
this.histologyReports?.forEach {
it.patient.id = patientPseudonym
it.results.tumorMorphology?.patient?.id = patientPseudonym
it.results.tumorCellContent?.patient?.id = patientPseudonym
}
this.ngsReports?.forEach {
it.patient.id = patientPseudonym
it.results.simpleVariants?.forEach { it.patient.id = patientPseudonym }
it.results.copyNumberVariants?.forEach { it.patient.id = patientPseudonym }
it.results.dnaFusions?.forEach { it.patient.id = patientPseudonym }
it.results.rnaFusions?.forEach { it.patient.id = patientPseudonym }
it.results.tumorCellContent?.patient?.id = patientPseudonym
it.results.brcaness?.patient?.id = patientPseudonym
it.results.tmb?.patient?.id = patientPseudonym
it.results.hrdScore?.patient?.id = patientPseudonym
}
this.ihcReports?.forEach {
it.patient.id = patientPseudonym
it.results.msiMmr?.forEach { it.patient.id = patientPseudonym }
it.results.proteinExpression?.forEach { it.patient.id = patientPseudonym }
}
this.responses?.forEach { it.patient.id = patientPseudonym }
this.specimens?.forEach { it.patient.id = patientPseudonym }
this.priorDiagnosticReports?.forEach { it.patient.id = patientPseudonym }
this.performanceStatus.forEach { it.patient.id = patientPseudonym }
this.systemicTherapies.forEach {
it.history?.forEach {
it.patient.id = patientPseudonym
}
}
}
/**
* Creates new hash of content IDs with given prefix except for patient IDs
*
* @since 0.11.0
*
* @param pseudonymizeService The pseudonymizeService to be used
* @return The MTB file containing rehashed content IDs
*/
infix fun Mtb.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
val prefix = pseudonymizeService.prefix()
fun anonymize(id: String): String {
val hash = DigestUtils.sha256Hex("$prefix-$id").substring(0, 41).lowercase()
return "$prefix$hash"
}
this.episodesOfCare?.forEach {
it?.apply {
id = id?.let {
anonymize(it)
}
}
}
// TODO all other properties
this.lastGuidelineTherapies.forEach { it.patient = patientPseudonym }
this.molecularPathologyFindings.forEach { it.patient = patientPseudonym }
this.molecularTherapies.forEach { molecularTherapy -> molecularTherapy.history.forEach { it.patient = patientPseudonym } }
this.ngsReports.forEach { it.patient = patientPseudonym }
this.previousGuidelineTherapies.forEach { it.patient = patientPseudonym }
this.rebiopsyRequests.forEach { it.patient = patientPseudonym }
this.recommendations.forEach { it.patient = patientPseudonym }
this.recommendations.forEach { it.patient = patientPseudonym }
this.responses.forEach { it.patient = patientPseudonym }
this.studyInclusionRequests.forEach { it.patient = patientPseudonym }
this.specimens.forEach { it.patient = patientPseudonym }
}

92
src/main/kotlin/dev/dnpm/etl/processor/security/TokenService.kt
View File

@ -1,92 +0,0 @@
/*
* 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.security
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>

45
src/main/kotlin/dev/dnpm/etl/processor/security/UserRole.kt
View File

@ -1,45 +0,0 @@
/*
* 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.security
import org.springframework.data.annotation.Id
import org.springframework.data.relational.core.mapping.Table
import org.springframework.data.repository.CrudRepository
import java.util.*
@Table("user_role")
data class UserRole(
@Id val id: Long? = null,
val username: String,
var role: Role = Role.GUEST
)
enum class Role(val value: String) {
GUEST("guest"),
USER("user"),
ADMIN("admin")
}
interface UserRoleRepository : CrudRepository<UserRole, Long> {
fun findByUsername(username: String): Optional<UserRole>
}

58
src/main/kotlin/dev/dnpm/etl/processor/security/UserRoleService.kt
View File

@ -1,58 +0,0 @@
/*
* 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.security
import org.springframework.data.repository.findByIdOrNull
import org.springframework.security.core.session.SessionRegistry
import org.springframework.security.oauth2.core.oidc.user.OidcUser
class UserRoleService(
private val userRoleRepository: UserRoleRepository,
private val sessionRegistry: SessionRegistry
) {
fun updateUserRole(id: Long, role: Role) {
val userRole = userRoleRepository.findByIdOrNull(id) ?: return
userRole.role = role
userRoleRepository.save(userRole)
expireSessionFor(userRole.username)
}
fun deleteUserRole(id: Long) {
val userRole = userRoleRepository.findByIdOrNull(id) ?: return
userRoleRepository.delete(userRole)
expireSessionFor(userRole.username)
}
fun findAll(): List<UserRole> {
return userRoleRepository.findAll().toList()
}
private fun expireSessionFor(username: String) {
sessionRegistry.allPrincipals
.filterIsInstance<OidcUser>()
.filter { it.preferredUsername == username }
.flatMap {
sessionRegistry.getAllSessions(it, true)
}
.onEach {
it.expireNow()
}
}
}

104
src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2023 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
@ -21,17 +21,13 @@ package dev.dnpm.etl.processor.services
import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.MtbFile
import dev.dnpm.etl.processor.*
import dev.dnpm.etl.processor.config.AppConfigProperties
import dev.dnpm.etl.processor.monitoring.Report
import dev.dnpm.etl.processor.monitoring.Request
import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.monitoring.RequestType
import dev.dnpm.etl.processor.output.*
import dev.dnpm.etl.processor.output.MtbFileSender
import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
import dev.dnpm.etl.processor.pseudonym.anonymizeContentWith
import dev.dnpm.etl.processor.pseudonym.pseudonymizeWith
import dev.pcvolkmer.mv64e.mtb.Mtb
import org.apache.commons.codec.binary.Base32
import org.apache.commons.codec.digest.DigestUtils
import org.springframework.context.ApplicationEventPublisher
@ -46,50 +42,32 @@ class RequestProcessor(
private val sender: MtbFileSender,
private val requestService: RequestService,
private val objectMapper: ObjectMapper,
private val applicationEventPublisher: ApplicationEventPublisher,
private val appConfigProperties: AppConfigProperties
private val applicationEventPublisher: ApplicationEventPublisher
) {
fun processMtbFile(mtbFile: MtbFile) {
processMtbFile(mtbFile, randomRequestId())
}
val requestId = UUID.randomUUID().toString()
val pid = mtbFile.patient.id
fun processMtbFile(mtbFile: MtbFile, requestId: RequestId) {
val pid = PatientId(mtbFile.patient.id)
mtbFile pseudonymizeWith pseudonymizeService
mtbFile anonymizeContentWith pseudonymizeService
val request = BwhcV1MtbFileRequest(requestId, transformationService.transform(mtbFile))
saveAndSend(request, pid)
}
fun processMtbFile(mtbFile: Mtb) {
processMtbFile(mtbFile, randomRequestId())
}
val request = MtbFileSender.MtbFileRequest(requestId, transformationService.transform(mtbFile))
fun processMtbFile(mtbFile: Mtb, requestId: RequestId) {
val pid = PatientId(mtbFile.patient.id)
mtbFile pseudonymizeWith pseudonymizeService
mtbFile anonymizeContentWith pseudonymizeService
val request = DnpmV2MtbFileRequest(requestId, transformationService.transform(mtbFile))
saveAndSend(request, pid)
}
private fun <T> saveAndSend(request: MtbFileRequest<T>, pid: PatientId) {
requestService.save(
Request(
request.requestId,
request.patientPseudonym(),
pid,
fingerprint(request),
RequestType.MTB_FILE,
RequestStatus.UNKNOWN
uuid = requestId,
patientId = request.mtbFile.patient.id,
pid = pid,
fingerprint = fingerprint(request.mtbFile),
status = RequestStatus.UNKNOWN,
type = RequestType.MTB_FILE
)
)
if (appConfigProperties.duplicationDetection && isDuplication(request)) {
if (isDuplication(mtbFile)) {
applicationEventPublisher.publishEvent(
ResponseEvent(
request.requestId,
requestId,
Instant.now(),
RequestStatus.DUPLICATION
)
@ -101,52 +79,45 @@ class RequestProcessor(
applicationEventPublisher.publishEvent(
ResponseEvent(
request.requestId,
requestId,
Instant.now(),
responseStatus.status,
when (responseStatus.status) {
RequestStatus.ERROR, RequestStatus.WARNING -> Optional.of(responseStatus.body)
RequestStatus.WARNING -> Optional.of(responseStatus.body)
else -> Optional.empty()
}
)
)
}
private fun <T> isDuplication(pseudonymizedMtbFileRequest: MtbFileRequest<T>): Boolean {
val patientPseudonym = when (pseudonymizedMtbFileRequest) {
is BwhcV1MtbFileRequest -> PatientPseudonym(pseudonymizedMtbFileRequest.content.patient.id)
is DnpmV2MtbFileRequest -> PatientPseudonym(pseudonymizedMtbFileRequest.content.patient.id)
}
private fun isDuplication(pseudonymizedMtbFile: MtbFile): Boolean {
val lastMtbFileRequestForPatient =
requestService.lastMtbFileRequestForPatientPseudonym(patientPseudonym)
val isLastRequestDeletion = requestService.isLastRequestWithKnownStatusDeletion(patientPseudonym)
requestService.lastMtbFileRequestForPatientPseudonym(pseudonymizedMtbFile.patient.id)
val isLastRequestDeletion = requestService.isLastRequestWithKnownStatusDeletion(pseudonymizedMtbFile.patient.id)
return null != lastMtbFileRequestForPatient
&& !isLastRequestDeletion
&& lastMtbFileRequestForPatient.fingerprint == fingerprint(pseudonymizedMtbFileRequest)
&& lastMtbFileRequestForPatient.fingerprint == fingerprint(pseudonymizedMtbFile)
}
fun processDeletion(patientId: PatientId) {
processDeletion(patientId, randomRequestId())
}
fun processDeletion(patientId: String) {
val requestId = UUID.randomUUID().toString()
fun processDeletion(patientId: PatientId, requestId: RequestId) {
try {
val patientPseudonym = pseudonymizeService.patientPseudonym(patientId)
requestService.save(
Request(
requestId,
patientPseudonym,
patientId,
fingerprint(patientPseudonym.value),
RequestType.DELETE,
RequestStatus.UNKNOWN
uuid = requestId,
patientId = patientPseudonym,
pid = patientId,
fingerprint = fingerprint(patientPseudonym),
status = RequestStatus.UNKNOWN,
type = RequestType.DELETE
)
)
val responseStatus = sender.send(DeleteRequest(requestId, patientPseudonym))
val responseStatus = sender.send(MtbFileSender.DeleteRequest(requestId, patientPseudonym))
applicationEventPublisher.publishEvent(
ResponseEvent(
@ -164,9 +135,9 @@ class RequestProcessor(
requestService.save(
Request(
uuid = requestId,
patientPseudonym = emptyPatientPseudonym(),
patientId = "???",
pid = patientId,
fingerprint = Fingerprint.empty(),
fingerprint = "",
status = RequestStatus.ERROR,
type = RequestType.DELETE,
report = Report("Fehler bei der Pseudonymisierung")
@ -175,19 +146,14 @@ class RequestProcessor(
}
}
private fun <T> fingerprint(request: MtbFileRequest<T>): Fingerprint {
return when (request) {
is BwhcV1MtbFileRequest -> fingerprint(objectMapper.writeValueAsString(request.content))
is DnpmV2MtbFileRequest -> fingerprint(objectMapper.writeValueAsString(request.content))
}
private fun fingerprint(mtbFile: MtbFile): String {
return fingerprint(objectMapper.writeValueAsString(mtbFile))
}
private fun fingerprint(s: String): Fingerprint {
return Fingerprint(
Base32().encodeAsString(DigestUtils.sha256(s))
private fun fingerprint(s: String): String {
return Base32().encodeAsString(DigestUtils.sha256(s))
.replace("=", "")
.lowercase()
)
}
}

35
src/main/kotlin/dev/dnpm/etl/processor/services/RequestService.kt
View File

@ -19,13 +19,11 @@
package dev.dnpm.etl.processor.services
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.monitoring.*
import org.springframework.data.domain.Page
import org.springframework.data.domain.Pageable
import dev.dnpm.etl.processor.monitoring.Request
import dev.dnpm.etl.processor.monitoring.RequestRepository
import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.monitoring.RequestType
import org.springframework.stereotype.Service
import java.util.*
@Service
class RequestService(
@ -34,32 +32,15 @@ class RequestService(
fun save(request: Request) = requestRepository.save(request)
fun findAll(): Iterable<Request> = requestRepository.findAll()
fun allRequestsByPatientPseudonym(patientPseudonym: String) = requestRepository
.findAllByPatientIdOrderByProcessedAtDesc(patientPseudonym)
fun findAll(pageable: Pageable): Page<Request> = requestRepository.findAll(pageable)
fun findByUuid(uuid: RequestId): Optional<Request> =
requestRepository.findByUuidEquals(uuid)
fun findRequestByPatientId(patientPseudonym: PatientPseudonym, pageable: Pageable): Page<Request> = requestRepository.findRequestByPatientPseudonym(patientPseudonym, pageable)
fun allRequestsByPatientPseudonym(patientPseudonym: PatientPseudonym) = requestRepository
.findAllByPatientPseudonymOrderByProcessedAtDesc(patientPseudonym)
fun lastMtbFileRequestForPatientPseudonym(patientPseudonym: PatientPseudonym) =
fun lastMtbFileRequestForPatientPseudonym(patientPseudonym: String) =
Companion.lastMtbFileRequestForPatientPseudonym(allRequestsByPatientPseudonym(patientPseudonym))
fun isLastRequestWithKnownStatusDeletion(patientPseudonym: PatientPseudonym) =
fun isLastRequestWithKnownStatusDeletion(patientPseudonym: String) =
Companion.isLastRequestWithKnownStatusDeletion(allRequestsByPatientPseudonym(patientPseudonym))
fun countStates(): Iterable<CountedState> = requestRepository.countStates()
fun countDeleteStates(): Iterable<CountedState> = requestRepository.countDeleteStates()
fun findPatientUniqueStates(): List<CountedState> = requestRepository.findPatientUniqueStates()
fun findPatientUniqueDeleteStates(): List<CountedState> = requestRepository.findPatientUniqueDeleteStates()
companion object {
fun lastMtbFileRequestForPatientPseudonym(allRequests: List<Request>) = allRequests

10
src/main/kotlin/dev/dnpm/etl/processor/services/ResponseProcessor.kt
View File

@ -19,8 +19,8 @@
package dev.dnpm.etl.processor.services
import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.monitoring.Report
import dev.dnpm.etl.processor.monitoring.RequestRepository
import dev.dnpm.etl.processor.monitoring.RequestStatus
import org.slf4j.LoggerFactory
import org.springframework.context.event.EventListener
@ -31,7 +31,7 @@ import java.util.*
@Service
class ResponseProcessor(
private val requestService: RequestService,
private val requestRepository: RequestRepository,
private val statisticsUpdateProducer: Sinks.Many<Any>
) {
@ -39,7 +39,7 @@ class ResponseProcessor(
@EventListener(classes = [ResponseEvent::class])
fun handleResponseEvent(event: ResponseEvent) {
requestService.findByUuid(event.requestUuid).ifPresentOrElse({
requestRepository.findByUuidEquals(event.requestUuid).ifPresentOrElse({
it.processedAt = event.timestamp
it.status = event.status
@ -76,7 +76,7 @@ class ResponseProcessor(
}
}
requestService.save(it)
requestRepository.save(it)
statisticsUpdateProducer.emitNext("", Sinks.EmitFailureHandler.FAIL_FAST)
}, {
@ -87,7 +87,7 @@ class ResponseProcessor(
}
data class ResponseEvent(
val requestUuid: RequestId,
val requestUuid: String,
val timestamp: Instant,
val status: RequestStatus,
val body: Optional<String> = Optional.empty()

15
src/main/kotlin/dev/dnpm/etl/processor/services/TransformationService.kt
View File

@ -23,21 +23,10 @@ import com.fasterxml.jackson.databind.ObjectMapper
import com.jayway.jsonpath.JsonPath
import com.jayway.jsonpath.PathNotFoundException
import de.ukw.ccc.bwhc.dto.MtbFile
import dev.pcvolkmer.mv64e.mtb.Mtb
class TransformationService(private val objectMapper: ObjectMapper, private val transformations: List<Transformation>) {
fun transform(mtbFile: MtbFile): MtbFile {
val json = transform(objectMapper.writeValueAsString(mtbFile))
return objectMapper.readValue(json, MtbFile::class.java)
}
fun transform(mtbFile: Mtb): Mtb {
val json = transform(objectMapper.writeValueAsString(mtbFile))
return objectMapper.readValue(json, Mtb::class.java)
}
private fun transform(content: String): String {
var json = content
var json = objectMapper.writeValueAsString(mtbFile)
transformations.forEach { transformation ->
val jsonPath = JsonPath.parse(json)
@ -59,7 +48,7 @@ class TransformationService(private val objectMapper: ObjectMapper, private val
json = jsonPath.jsonString()
}
return json
return objectMapper.readValue(json, MtbFile::class.java)
}
fun getTransformations(): List<Transformation> {

3
src/main/kotlin/dev/dnpm/etl/processor/services/kafka/KafkaResponseProcessor.kt
View File

@ -22,7 +22,6 @@ package dev.dnpm.etl.processor.services.kafka
import com.fasterxml.jackson.annotation.JsonAlias
import com.fasterxml.jackson.annotation.JsonProperty
import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.output.asRequestStatus
import dev.dnpm.etl.processor.services.ResponseEvent
@ -48,7 +47,7 @@ class KafkaResponseProcessor(
Optional.empty()
}.ifPresentOrElse({ responseBody ->
val event = ResponseEvent(
RequestId(responseBody.requestId),
responseBody.requestId,
Instant.ofEpochMilli(data.timestamp()),
responseBody.statusCode.asRequestStatus(),
when (responseBody.statusCode.asRequestStatus()) {

63
src/main/kotlin/dev/dnpm/etl/processor/types.kt
View File

@ -1,63 +0,0 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor
import org.springframework.http.MediaType
import java.util.*
class Fingerprint(val value: String) {
override fun hashCode() = value.hashCode()
override fun equals(other: Any?) = other is Fingerprint && other.value == value
companion object {
fun empty() = Fingerprint("")
}
}
@JvmInline
value class RequestId(val value: String) {
fun isBlank() = value.isBlank()
}
fun randomRequestId() = RequestId(UUID.randomUUID().toString())
@JvmInline
value class PatientId(val value: String)
@JvmInline
value class PatientPseudonym(val value: String)
fun emptyPatientPseudonym() = PatientPseudonym("")
/**
* Custom MediaTypes
*
* @since 0.11.0
*/
object CustomMediaType {
val APPLICATION_VND_DNPM_V2_MTB_JSON = MediaType("application", "vnd.dnpm.v2.mtb+json")
const val APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE = "application/vnd.dnpm.v2.mtb+json"
val APPLICATION_VND_DNPM_V2_RD_JSON = MediaType("application", "vnd.dnpm.v2.rd+json")
const val APPLICATION_VND_DNPM_V2_RD_JSON_VALUE = "application/vnd.dnpm.v2.rd+json"
}

201
src/main/kotlin/dev/dnpm/etl/processor/web/ConfigController.kt
View File

@ -1,201 +0,0 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2023 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.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
import dev.dnpm.etl.processor.security.UserRole
import dev.dnpm.etl.processor.security.Token
import dev.dnpm.etl.processor.security.TokenService
import dev.dnpm.etl.processor.services.TransformationService
import dev.dnpm.etl.processor.security.UserRoleService
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.ui.Model
import org.springframework.web.bind.annotation.*
import reactor.core.publisher.Flux
import reactor.core.publisher.Sinks
@Controller
@RequestMapping(path = ["configs"])
class ConfigController(
@Qualifier("connectionCheckUpdateProducer")
private val connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>,
private val transformationService: TransformationService,
private val pseudonymGenerator: Generator,
private val mtbFileSender: MtbFileSender,
private val connectionCheckServices: List<ConnectionCheckService>,
private val tokenService: TokenService?,
private val userRoleService: UserRoleService?
) {
@GetMapping
fun index(model: Model): String {
val outputConnectionAvailable =
connectionCheckServices.filterIsInstance<OutputConnectionCheckService>().firstOrNull()?.connectionAvailable()
val gPasConnectionAvailable =
connectionCheckServices.filterIsInstance<GPasConnectionCheckService>().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("tokensEnabled", tokenService != null)
if (tokenService != null) {
model.addAttribute("tokens", tokenService.findAll())
} else {
model.addAttribute("tokens", emptyList<Token>())
}
model.addAttribute("transformations", transformationService.getTransformations())
if (userRoleService != null) {
model.addAttribute("userRolesEnabled", true)
model.addAttribute("userRoles", userRoleService.findAll())
} else {
model.addAttribute("userRolesEnabled", false)
model.addAttribute("userRoles", emptyList<UserRole>())
}
return "configs"
}
@GetMapping(params = ["outputConnectionAvailable"])
fun outputConnectionAvailable(model: Model): String {
val outputConnectionAvailable =
connectionCheckServices.filterIsInstance<OutputConnectionCheckService>().first().connectionAvailable()
model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName)
model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint())
model.addAttribute("outputConnectionAvailable", outputConnectionAvailable)
if (tokenService != null) {
model.addAttribute("tokensEnabled", true)
model.addAttribute("tokens", tokenService.findAll())
} else {
model.addAttribute("tokens", listOf<Token>())
}
return "configs/outputConnectionAvailable"
}
@GetMapping(params = ["gPasConnectionAvailable"])
fun gPasConnectionAvailable(model: Model): String {
val gPasConnectionAvailable =
connectionCheckServices.filterIsInstance<GPasConnectionCheckService>().firstOrNull()?.connectionAvailable()
model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName)
model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint())
model.addAttribute("gPasConnectionAvailable", gPasConnectionAvailable)
if (tokenService != null) {
model.addAttribute("tokensEnabled", true)
model.addAttribute("tokens", tokenService.findAll())
} else {
model.addAttribute("tokens", listOf<Token>())
}
return "configs/gPasConnectionAvailable"
}
@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)
result.onSuccess {
model.addAttribute("newTokenValue", it)
model.addAttribute("success", true)
}
result.onFailure {
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"
}
@DeleteMapping(path = ["userroles/{id}"])
fun deleteUserRole(@PathVariable id: Long, model: Model): String {
if (userRoleService != null) {
userRoleService.deleteUserRole(id)
model.addAttribute("userRolesEnabled", true)
model.addAttribute("userRoles", userRoleService.findAll())
} else {
model.addAttribute("userRolesEnabled", false)
model.addAttribute("userRoles", emptyList<UserRole>())
}
return "configs/userroles"
}
@PutMapping(path = ["userroles/{id}"])
fun updateUserRole(@PathVariable id: Long, @ModelAttribute("role") role: Role, model: Model): String {
if (userRoleService != null) {
userRoleService.updateUserRole(id, role)
model.addAttribute("userRolesEnabled", true)
model.addAttribute("userRoles", userRoleService.findAll())
} else {
model.addAttribute("userRolesEnabled", false)
model.addAttribute("userRoles", emptyList<UserRole>())
}
return "configs/userroles"
}
@GetMapping(path = ["events"], produces = [MediaType.TEXT_EVENT_STREAM_VALUE])
@ResponseBody
fun events(): Flux<ServerSentEvent<Any>> {
return connectionCheckUpdateProducer.asFlux().map {
val event = when (it) {
is ConnectionCheckResult.KafkaConnectionCheckResult -> "output-connection-check"
is ConnectionCheckResult.RestConnectionCheckResult -> "output-connection-check"
is ConnectionCheckResult.GPasConnectionCheckResult -> "gpas-connection-check"
}
ServerSentEvent.builder<Any>()
.event(event).id("none").data(it)
.build()
}
}
}

32
src/main/kotlin/dev/dnpm/etl/processor/web/HomeController.kt
View File

@ -20,13 +20,9 @@
package dev.dnpm.etl.processor.web
import dev.dnpm.etl.processor.NotFoundException
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.monitoring.ReportService
import dev.dnpm.etl.processor.services.RequestService
import org.springframework.data.domain.Pageable
import org.springframework.data.domain.Sort
import org.springframework.data.web.PageableDefault
import dev.dnpm.etl.processor.monitoring.RequestId
import dev.dnpm.etl.processor.monitoring.RequestRepository
import org.springframework.stereotype.Controller
import org.springframework.ui.Model
import org.springframework.web.bind.annotation.GetMapping
@ -36,29 +32,13 @@ import org.springframework.web.bind.annotation.RequestMapping
@Controller
@RequestMapping(path = ["/"])
class HomeController(
private val requestService: RequestService,
private val requestRepository: RequestRepository,
private val reportService: ReportService
) {
@GetMapping
fun index(
@PageableDefault(page = 0, size = 20, sort = ["processedAt"], direction = Sort.Direction.DESC) pageable: Pageable,
model: Model
): String {
val requests = requestService.findAll(pageable)
model.addAttribute("requests", requests)
return "index"
}
@GetMapping(path = ["patient/{patientPseudonym}"])
fun byPatient(
@PathVariable patientPseudonym: PatientPseudonym,
@PageableDefault(page = 0, size = 20, sort = ["processedAt"], direction = Sort.Direction.DESC) pageable: Pageable,
model: Model
): String {
val requests = requestService.findRequestByPatientId(patientPseudonym, pageable)
model.addAttribute("patientPseudonym", patientPseudonym.value)
fun index(model: Model): String {
val requests = requestRepository.findAll().sortedByDescending { it.processedAt }.take(25)
model.addAttribute("requests", requests)
return "index"
@ -66,7 +46,7 @@ class HomeController(
@GetMapping(path = ["/report/{id}"])
fun report(@PathVariable id: RequestId, model: Model): String {
val request = requestService.findByUuid(id).orElse(null) ?: throw NotFoundException()
val request = requestRepository.findByUuidEquals(id.toString()).orElse(null) ?: throw NotFoundException()
model.addAttribute("request", request)
model.addAttribute("issues", reportService.deserialize(request.report?.dataQualityReport))

38
src/main/kotlin/dev/dnpm/etl/processor/input/MtbFileRestController.kt → src/main/kotlin/dev/dnpm/etl/processor/web/MtbFileRestController.kt
View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2023 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
@ -17,56 +17,38 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.input
package dev.dnpm.etl.processor.web
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.services.RequestProcessor
import dev.pcvolkmer.mv64e.mtb.Mtb
import org.slf4j.LoggerFactory
import org.springframework.http.MediaType
import org.springframework.http.ResponseEntity
import org.springframework.web.bind.annotation.*
@RestController
@RequestMapping(path = ["mtbfile", "mtb"])
class MtbFileRestController(
private val requestProcessor: RequestProcessor,
) {
private val logger = LoggerFactory.getLogger(MtbFileRestController::class.java)
@GetMapping
fun info(): ResponseEntity<String> {
return ResponseEntity.ok("Test")
}
@PostMapping( consumes = [ MediaType.APPLICATION_JSON_VALUE ] )
fun mtbFile(@RequestBody mtbFile: MtbFile): ResponseEntity<Unit> {
@PostMapping(path = ["/mtbfile"])
fun mtbFile(@RequestBody mtbFile: MtbFile): ResponseEntity<Void> {
if (mtbFile.consent.status == Consent.Status.ACTIVE) {
logger.debug("Accepted MTB File (bwHC V1) for processing")
logger.debug("Accepted MTB File 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)
logger.debug("Accepted MTB File and process deletion")
requestProcessor.processDeletion(mtbFile.patient.id)
}
return ResponseEntity.accepted().build()
}
@PostMapping( consumes = [ CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE] )
fun mtbFile(@RequestBody mtbFile: Mtb): ResponseEntity<Unit> {
logger.debug("Accepted MTB File (DNPM V2) for processing")
requestProcessor.processMtbFile(mtbFile)
return ResponseEntity.accepted().build()
}
@DeleteMapping(path = ["{patientId}"])
fun deleteData(@PathVariable patientId: String): ResponseEntity<Unit> {
@DeleteMapping(path = ["/mtbfile/{patientId}"])
fun deleteData(@PathVariable patientId: String): ResponseEntity<Void> {
logger.debug("Accepted patient ID to process deletion")
requestProcessor.processDeletion(PatientId(patientId))
requestProcessor.processDeletion(patientId)
return ResponseEntity.accepted().build()
}

20
src/main/kotlin/dev/dnpm/etl/processor/web/StatisticsRestController.kt
View File

@ -19,10 +19,9 @@
package dev.dnpm.etl.processor.web
import dev.dnpm.etl.processor.monitoring.RequestRepository
import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.monitoring.RequestType
import dev.dnpm.etl.processor.services.RequestService
import org.springframework.beans.factory.annotation.Qualifier
import org.springframework.http.MediaType
import org.springframework.http.codec.ServerSentEvent
import org.springframework.web.bind.annotation.GetMapping
@ -39,17 +38,16 @@ import java.time.temporal.ChronoUnit
@RestController
@RequestMapping(path = ["/statistics"])
class StatisticsRestController(
@Qualifier("statisticsUpdateProducer")
private val statisticsUpdateProducer: Sinks.Many<Any>,
private val requestService: RequestService
private val requestRepository: RequestRepository
) {
@GetMapping(path = ["requeststates"])
fun requestStates(@RequestParam(required = false, defaultValue = "false") delete: Boolean): List<NameValue> {
val states = if (delete) {
requestService.countDeleteStates()
requestRepository.countDeleteStates()
} else {
requestService.countStates()
requestRepository.countStates()
}
return states
@ -79,7 +77,7 @@ class StatisticsRestController(
}
val formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd").withZone(ZoneId.of("Europe/Berlin"))
val data = requestService.findAll()
val data = requestRepository.findAll()
.filter { it.type == requestType }
.filter { it.processedAt.isAfter(Instant.now().minus(30, ChronoUnit.DAYS)) }
.groupBy { formatter.format(it.processedAt) }
@ -115,9 +113,9 @@ class StatisticsRestController(
@GetMapping(path = ["requestpatientstates"])
fun requestPatientStates(@RequestParam(required = false, defaultValue = "false") delete: Boolean): List<NameValue> {
val states = if (delete) {
requestService.findPatientUniqueDeleteStates()
requestRepository.findPatientUniqueDeleteStates()
} else {
requestService.findPatientUniqueStates()
requestRepository.findPatientUniqueStates()
}
return states.map {
@ -154,10 +152,6 @@ class StatisticsRestController(
.build(),
ServerSentEvent.builder<Any>()
.event("deleterequestpatientstates").id("none").data(this.requestPatientStates(true))
.build(),
ServerSentEvent.builder<Any>()
.event("newrequest").id("none").data("newrequest")
.build()
)
)

28
src/main/kotlin/dev/dnpm/etl/processor/web/LoginController.kt → src/main/kotlin/dev/dnpm/etl/processor/web/TransformationController.kt
View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2023 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
@ -19,29 +19,23 @@
package dev.dnpm.etl.processor.web
import dev.dnpm.etl.processor.config.SecurityConfigProperties
import org.springframework.boot.autoconfigure.security.oauth2.client.OAuth2ClientProperties
import dev.dnpm.etl.processor.services.TransformationService
import org.springframework.stereotype.Controller
import org.springframework.ui.Model
import org.springframework.web.bind.annotation.GetMapping
import org.springframework.web.bind.annotation.RequestMapping
@Controller
class LoginController(
private val securityConfigProperties: SecurityConfigProperties?,
private val oAuth2ClientProperties: OAuth2ClientProperties?
@RequestMapping(path = ["transformations"])
class TransformationController(
private val transformationService: TransformationService
) {
@GetMapping(path = ["/login"])
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"
@GetMapping
fun index(model: Model): String {
model.addAttribute("transformations", transformationService.getTransformations())
return "transformations"
}
}

32
src/main/resources/application-dev.yml
View File

@ -3,34 +3,14 @@ spring:
compose:
file: ./dev-compose.yml
security:
oauth2:
client:
registration:
custom:
client-name: App-Dev
client-id: app-dev
client-secret: very-secret-ae3f7a-5a9f-1190
scope:
- openid
provider:
custom:
issuer-uri: https://dnpm.dev/auth/realms/intern
user-name-attribute: name
app:
rest:
uri: http://localhost:9000/bwhc/etl/api
#kafka:
# topic: test
# response-topic: test_response
# servers: localhost:9094
security:
admin-user: admin
admin-password: "{noop}very-secret"
enable-oidc: "true"
#rest:
# uri: http://localhost:9000/bwhc/etl/api
kafka:
topic: test
response-topic: test_response
servers: localhost:9094
server:
port: 8000

14
src/main/resources/application.yml
View File

@ -5,17 +5,3 @@ spring:
group-id: ${app.kafka.group-id}
flyway:
locations: "classpath:db/migration/{vendor}"
web:
resources:
cache:
cachecontrol:
max-age: 1d
chain:
strategy:
content:
enabled: true
paths: /**/*.js,/**/*.css,/**/*.svg,/**/*.jpeg
server:
forward-headers-strategy: framework

8
src/main/resources/db/migration/mariadb/V0_2_0__Tokens.sql
View File

@ -1,8 +0,0 @@
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
);

7
src/main/resources/db/migration/mariadb/V0_3_0__UserRoles.sql
View File

@ -1,7 +0,0 @@
CREATE TABLE IF NOT EXISTS user_role
(
id int auto_increment primary key,
username varchar(255) not null unique,
role varchar(255) not null,
created_at datetime default utc_timestamp() not null
);

1
src/main/resources/db/migration/mariadb/V0_4_0__RenamePatientPseudonym.sql
View File

@ -1 +0,0 @@
ALTER TABLE request RENAME COLUMN patient_id TO patient_pseudonym;

9
src/main/resources/db/migration/postgresql/V0_2_0__Tokens.sql
View File

@ -1,9 +0,0 @@
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)
);

8
src/main/resources/db/migration/postgresql/V0_3_0__UserRoles.sql
View File

@ -1,8 +0,0 @@
CREATE TABLE IF NOT EXISTS user_role
(
id serial,
username varchar(255) not null unique,
role varchar(255) not null,
created_at timestamp with time zone default now() not null,
PRIMARY KEY (id)
);

1
src/main/resources/db/migration/postgresql/V0_4_0__RenamePatientPseudonym.sql
View File

@ -1 +0,0 @@
ALTER TABLE request RENAME COLUMN patient_id TO patient_pseudonym;

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45
src/main/resources/static/echarts.min.js vendored Normal file
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41
src/main/resources/static/icon.svg
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@ -1,41 +0,0 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Created with Inkscape (http://www.inkscape.org/) -->
<svg
width="256"
height="256"
viewBox="0 0 67.733332 67.733335"
version="1.1"
id="svg5"
xmlns="http://www.w3.org/2000/svg"
xmlns:svg="http://www.w3.org/2000/svg">
<defs
id="defs2" />
<g
id="layer1">
<g
id="g26002"
transform="matrix(1.5,0,0,1.5,-16.933333,-1.8487648)">
<path
id="path12437"
transform="matrix(0.21771408,0,0,0.21771408,73.025692,24.874779)"
style="fill:#f59e00;fill-opacity:1"
d="m -110.41995,43.223174 -55.55561,-2e-6 -27.7778,-48.1125685 27.77781,-48.1125655 55.5556,3e-6 27.777803,48.1125679 z" />
<path
id="path13446"
transform="matrix(0.21771408,0,0,0.21771408,54.882836,14.399994)"
style="fill:#004d6e;fill-opacity:1"
d="m -110.41995,43.223174 -55.55561,-2e-6 -27.7778,-48.1125685 27.77781,-48.1125655 55.5556,3e-6 27.777803,48.1125679 z" />
<path
id="path13448"
transform="matrix(0.21771408,0,0,0.21771408,54.882835,35.349561)"
style="fill:#706f6f;fill-opacity:1"
d="m -110.41995,43.223174 -55.55561,-2e-6 -27.7778,-48.1125685 27.77781,-48.1125655 55.5556,3e-6 27.777803,48.1125679 z" />
<path
id="path25844"
transform="matrix(0.21771408,0,0,0.21771408,60.930454,24.874778)"
style="fill:#ffffff;fill-opacity:1"
d="m -110.41995,43.223174 -55.55561,-2e-6 -27.7778,-48.1125685 27.77781,-48.1125655 55.5556,3e-6 27.777803,48.1125679 z" />
</g>
</g>
</svg>
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5
src/main/resources/static/scripts.js
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@ -4,7 +4,7 @@ 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 dateTimeFormat = new Intl.DateTimeFormat('de-DE', dateTimeFormatOptions);
const formatTimeElements = () => {
window.onload = () => {
Array.from(document.getElementsByTagName('time')).forEach((timeTag) => {
let date = Date.parse(timeTag.getAttribute('datetime'));
if (! isNaN(date)) {
@ -13,9 +13,6 @@ const formatTimeElements = () => {
});
};
window.addEventListener('load', formatTimeElements);
window.addEventListener('htmx:afterRequest', formatTimeElements);
function drawPieChart(url, elemId, title, data) {
if (data) {
update(elemId, data);

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src/main/resources/static/style.css
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@ -1,8 +1,5 @@
:root {
--text: #333;
--table-border: rgba(16, 24, 40, .1);
--dark: brightness(.90);
--table-border: rgba(96, 96, 96, 1);
--bg-blue: rgb(0, 74, 157);
--bg-blue-op: rgba(0, 74, 157, .35);
@ -22,135 +19,47 @@
--bg-gray-op: rgba(112, 128, 144, .35);
}
* {
font-family: sans-serif;
}
html {
background: linear-gradient(-5deg, var(--bg-blue-op), transparent 10em);
min-height: 100vh;
overflow-y: scroll;
}
body {
margin: 0 0 5em 0;
margin: 0;
font-family: sans-serif;
font-size: .8rem;
color: var(--text);
min-height: 100vh;
background: url(bg.jpeg) no-repeat;
background-size: contain;
color: #333;
}
nav {
margin: 0 auto;
padding: 1em 0;
line-height: 1.5rem;
background: #d5dad5;
height: 3rem;
max-width: 1140px;
border-bottom: 1px solid var(--table-border);
}
nav a.nav-home {
float: left;
color: var(--text);
line-height: 1.5em;
text-decoration: none;
font-size: 2em;
font-weight: bold;
}
nav a.nav-home > img {
width: 1.5em;
vertical-align: middle;
}
nav > ul {
margin: 0 0 0 auto;
padding: 0;
width: max-content;
}
nav > ul > li {
display: inline-block;
padding: 0 1rem;
}
nav > ul > li.login {
margin: 0 0 0 1em;
padding: 0 0 0 2em;
border-left: 1px solid var(--table-border);
line-height: 3.5em;
}
nav > ul > li.login a {
text-decoration: none;
text-transform: none;
padding: 1em;
}
nav .login .user-name {
font-weight: bold;
}
nav > ul > li.login > span {
display: inline-block;
margin: 0 .5em;
}
nav > ul > li.login .user-icon {
flex-direction: column;
display: inline flex;
vertical-align: middle;
inline-size: 4em;
}
nav > ul > li.login .user-icon img {
margin: 0 0 -1em 0;
width: 80%;
align-self: center;
}
nav > ul > li.login .user-icon span {
padding: 0 .6em;
color: white;
font-size: .8em;
font-weight: bold;
border-radius: 4px;
line-height: normal;
text-align: center;
}
nav > ul > li.login .user-icon span.guest {
background: darkslategray;
}
nav > ul > li.login .user-icon span.user {
background: darkgreen;
}
nav > ul > li.login .user-icon span.admin {
background: darkred;
}
nav li a {
color: var(--bg-blue);
nav a {
color: #004a8f;
text-transform: uppercase;
text-decoration: none;
line-height: 2rem;
font-weight: 700;
}
nav li a:hover {
nav a:hover {
text-decoration: underline;
}
a {
color: var(--bg-blue);
nav > ul {
margin: 0 3rem;
padding: 0;
}
nav > ul > li {
background: #fbfbfb;
display: block;
float: left;
padding: 2px 1rem;
border-left: 1px solid #d5dad5;
}
nav > ul > li:first-of-type {
border-left: none;
}
.breadcrumps {
@ -176,7 +85,7 @@ a {
}
.breadcrumps ul li a {
color: var(--text);
color: #333333;
text-decoration: none;
}
@ -189,10 +98,6 @@ main {
max-width: 1140px;
}
section {
margin: 3em 0;
}
form {
margin: 1rem 0;
padding: 1rem;
@ -234,139 +139,16 @@ form.samplecode-input input:focus-visible {
background: lightgreen;
}
.login-form {
width: fit-content;
margin: 3em auto;
padding: 2em 5em;
border: 1px solid var(--table-border);
border-radius: .5em;
background: white;
}
.login-form form {
width: 20em;
margin: 0 auto;
display: grid;
grid-gap: .5em;
border: none;
background: none;
}
.login-form img {
margin: 0 auto;
width: 4em;
display: block;
}
.userrole-form {
display: inline-block;
}
.userrole-form form {
margin: 0;
padding: 0;
border: none;
border-radius: 0;
background: none;
text-align: inherit;
}
.login-form form *,
.token-form form * {
padding: 0.5em;
border: 1px solid var(--table-border);
border-radius: 3px;
}
.login-form form hr,
.token-form form hr,
.userrole-form form hr {
padding: 0;
width: 100%;
}
.login-form button,
.login-form a.btn,
.token-form button {
margin: 1em 0;
background: var(--bg-blue);
color: white;
border: none;
}
.userrole-form form select {
padding: 0.5em;
border: none;
border-radius: 3px;
line-height: 1.2rem;
font-size: 0.8rem;
}
.border {
padding: 1.5em;
border: 1px solid var(--table-border);
border-radius: .5em;
background: white;
}
table, .chart {
border: 1px solid var(--table-border);
padding: 1.5em;
border-spacing: 0;
border-radius: .5em;
background: white;
}
table {
border-top: 1px solid var(--table-border);
border-left: 1px solid var(--table-border);
border-spacing: 0;
border-radius: 3px;
min-width: 100%;
font-family: sans-serif;
}
table.config-table td:first-child {
width: 24em;
min-width: fit-content;
}
table.config-table td > button:last-of-type {
float: right;
}
.border > table {
padding: 0;
border: none;
background: transparent;
}
.page-control {
border-radius: .5em;
padding: 1em 2em;
text-align: center;
line-height: 1.75em;
}
.page-control a {
padding: 0 .25em;
font-size: 1.75em;
color: var(--bg-gray);
text-decoration: none;
}
.page-control a[href] {
color: var(--bg-blue);
}
.page-control span {
padding: 0 .5em;
vertical-align: text-bottom;
}
#samples-table.max {
width: 100vw;
position: fixed;
@ -383,78 +165,64 @@ table.samples {
display: block;
}
th, td {
th {
background: #eee;
}
td, th {
padding: 0.4rem .2rem;
line-height: 2em;
border-right: 1px solid var(--table-border);
border-bottom: 1px solid var(--table-border);
text-align: left;
white-space: nowrap;
vertical-align: top;
}
th {
border-bottom: 1px solid var(--bg-gray);
}
td {
font-family: monospace;
border-bottom: 1px solid var(--bg-gray-op);
}
tr:last-of-type > td {
border-bottom: none;
}
td > small {
display: block;
text-align: center;
}
td.patient-id {
width: 32em;
text-overflow: ellipsis;
overflow: hidden;
display: block;
}
td.bg-blue, th.bg-blue,
td.bg-green, th.bg-green,
td.bg-yellow, th.bg-yellow,
td.bg-red, th.bg-red,
td.bg-gray, th.bg-gray
{
width: 8em;
}
td.bg-blue > small, th.bg-blue > small {
td.bg-blue, th.bg-blue {
background: var(--bg-blue);
color: white;
border-radius: 0.4em;
}
td.bg-green > small, th.bg-green > small {
tr:has(td.bg-blue) {
background: var(--bg-blue-op);
}
td.bg-green, th.bg-green {
background: var(--bg-green);
color: white;
border-radius: 0.4em;
}
td.bg-yellow > small, th.bg-yellow > small {
tr:has(td.bg-green) {
background: var(--bg-green-op);
}
td.bg-yellow, th.bg-yellow {
background: var(--bg-yellow);
color: white;
border-radius: 0.4em;
}
td.bg-red > small, th.bg-red > small {
tr:has(td.bg-yellow) {
background: var(--bg-yellow-op);
}
td.bg-red, th.bg-red {
background: var(--bg-red);
color: white;
border-radius: 0.4em;
}
td.bg-gray > small, th.bg-gray > small {
tr:has(td.bg-red) {
background: var(--bg-red-op);
}
td.bg-gray, th.bg-gray {
background: var(--bg-gray);
color: white;
border-radius: 0.4em;
}
.bg-path {
@ -493,6 +261,7 @@ td.clipboard.clipped {
padding: 4px 8px;
line-height: 1.2rem;
vertical-align: middle;
border: 0 solid transparent;
border-radius: 3px;
@ -504,38 +273,38 @@ td.clipboard.clipped {
cursor: pointer;
}
.btn:active,
.btn:hover {
filter: drop-shadow(0px 1px 1px var(--bg-gray)) var(--dark);
filter: drop-shadow(1px 2px 2px gray);
}
.btn:active {
filter: drop-shadow(1px 1px 2px gray);
translate: 0 1px;
}
.btn.btn-red {
background: var(--bg-red);
background: red;
color: white;
}
.btn.btn-red:hover, .btn.btn-red:active {
background: darkred !important;
}
.btn.btn-blue {
background: var(--bg-blue);
background: slategray;
color: white;
}
.btn.btn-blue:hover, .btn.btn-blue:active {
background: darkslategray !important;
}
.btn.btn-delete:before {
content: '\1F5D1';
padding: .2rem;
}
button:disabled,
.btn:disabled {
background: slategray !important;
color: lightgray;
filter: none;
cursor: default;
}
input.inline {
border: none;
font-size: 1.1rem;
@ -571,140 +340,19 @@ input.inline:focus-visible {
font-weight: bold;
}
.charts {
display: grid;
grid-gap: 1em;
grid-template:
"a b" 28em
"c c" 28em / 1fr 1fr;
}
.chart {
padding: 1rem;
margin: .2rem;
.charts > .grid-left {
grid-area: a;
}
.charts > .grid-right {
grid-area: b;
}
.charts > .grid-full {
grid-area: c;
}
.connection-display {
display: grid;
grid-template-columns: 10em 16em 10em;
place-items: center;
width: fit-content;
margin: 1em auto;
}
.connection-display > * {
text-align: center;
margin: auto 0;
}
.connection-display .connection {
display: block;
width: 100%;
height: 4px;
background: repeating-linear-gradient(to left, white, white 2px, transparent 2px, transparent 8px, white 8px) var(--bg-red);
}
.connection-display .connection.available {
background: var(--bg-green);
}
.notification {
margin: 1em;
padding: .5em;
border: 1px solid var(--table-border);
border-radius: 3px;
text-align: center;
}
.notification.info {
color: var(--bg-blue);
}
width: calc(100% - 2.4rem - 4px);
height: 320px;
.notification.success {
color: var(--bg-green);
}
.notification.notice {
color: var(--bg-yellow);
}
.notification.error {
color: var(--bg-red);
}
.tab {
padding: 1em;
border: none;
border-radius: 3px 3px 0 0;
cursor: pointer;
transition: all 0.2s;
font-weight: bold;
}
.tab:hover,
.tab.active {
background: var(--bg-gray);
color: white;
}
.tabcontent {
border: 2px solid var(--bg-gray);
border-radius: 0 .5em .5em .5em;
display: none;
padding: 1em;
background: white;
}
.tabcontent.active {
display: block;
}
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);
}
.issue-message {
font-family: monospace;
font-weight: bolder;
}
.issue-path {
font-family: monospace;
line-height: 1rem;
.chart-50pc {
width: calc(50% - 2.4rem - 4px);
}

11
src/main/resources/static/user.svg
View File

@ -1,11 +0,0 @@
<?xml version="1.0" encoding="UTF-8"?>
<!-- Created with Inkscape (http://www.inkscape.org/) -->
<svg width="24" height="24" version="1.1" viewBox="0 0 6.35 6.35" xmlns="http://www.w3.org/2000/svg">
<g transform="matrix(1.2 0 0 1.2 -108.01 -85.977)">
<rect x="90.01" y="71.647" width="5.2917" height="5.2917" rx=".96212" fill="#b3b3b3"/>
<g transform="matrix(1.6667 0 0 1.6667 -60.888 -47.952)" fill="#fff">
<circle cx="92.126" cy="72.802" r=".70556"/>
<path d="m91.068 74.598a1.0583 1.0583 0 0 1 1.0583-1.0583 1.0583 1.0583 0 0 1 1.0583 1.0583h-1.0583z"/>
</g>
</g>
</svg>
Side by Side

Before

Width:  |  Height:  |  Size: 588 B

125
src/main/resources/templates/configs.html
View File

@ -1,125 +0,0 @@
<!DOCTYPE html>
<html lang="de" xmlns:th="http://www.thymeleaf.org">
<head>
<meta charset="UTF-8">
<title>ETL-Prozessor</title>
<link rel="stylesheet" th:href="@{/style.css}" />
</head>
<body>
<div th:replace="~{fragments.html :: nav}"></div>
<main>
<h1>Konfiguration</h1>
<div class="tabs">
<button class="tab active" onclick="selectTab(this, 'common');">Allgemeine Informationen</button>
<button class="tab" onclick="selectTab(this, 'security');">Sicherheit</button>
<button class="tab" onclick="selectTab(this, 'transformation');">Transformationen</button>
</div>
<div id="common" class="tabcontent active">
<section>
<h2>🔧 Allgemeine Konfiguration</h2>
<table class="config-table">
<thead>
<tr>
<th>Name</th>
<th>Wert</th>
</tr>
</thead>
<tbody>
<tr>
<td>Pseudonym erzeugt über</td>
<td>[[ ${pseudonymGenerator} ]]</td>
</tr>
<tr>
<td>MTBFile-Sender</td>
<td>[[ ${mtbFileSender} ]]</td>
</tr>
<tr>
<td th:if="${mtbFileSender.startsWith('Rest')}">REST-Endpunkt</td>
<td th:if="${mtbFileSender.startsWith('Kafka')}">Kafka-Broker und Topics</td>
<td>[[ ${mtbFileEndpoint} ]]</td>
</tr>
</tbody>
</table>
</section>
<section hx-ext="sse" th:sse-connect="@{/configs/events}">
<div th:insert="~{configs/gPasConnectionAvailable.html}" th:hx-get="@{/configs?gPasConnectionAvailable}" hx-trigger="sse:gpas-connection-check">
</div>
</section>
<section hx-ext="sse" th:sse-connect="@{/configs/events}">
<div th:insert="~{configs/outputConnectionAvailable.html}" th:hx-get="@{/configs?outputConnectionAvailable}" hx-trigger="sse:output-connection-check">
</div>
</section>
</div>
<div id="security" class="tabcontent">
<section th:insert="~{configs/tokens.html}">
</section>
<section th:insert="~{configs/userroles.html}">
</section>
</div>
<div id="transformation" class="tabcontent">
<section>
<h2><span th:if="${not transformations.isEmpty()}">✅</span><span th:if="${transformations.isEmpty()}">⛔</span> Transformationen</h2>
<h3>Syntax</h3>
Hier einige Beispiele zum Syntax des JSON-Path
<ul>
<li style="padding: 0.6rem 0;"><span class="bg-path">diagnoses[*].icdO3T.version</span>: Ersetze die ICD-O3T-Version in allen Diagnosen, z.B. zur Version der deutschen Übersetzung</li>
<li style="padding: 0.6rem 0;"><span class="bg-path">patient.gender</span>: Ersetze das Geschlecht des Patienten, z.B. in das von bwHC verlangte Format</li>
</ul>
<h3>Konfigurierte Transformationen</h3>
<th:block th:if="${transformations.isEmpty()}">
<p>
Keine konfigurierten Transformationen.
</p>
</th:block>
<th:block th:if="${not transformations.isEmpty()}">
<p>
Hier sehen Sie eine Übersicht der konfigurierten Transformationen.
</p>
<table class="config-table">
<thead>
<tr>
<th>JSON-Path</th>
<th>Transformation von &rArr; nach</th>
</tr>
</thead>
<tbody>
<tr th:each="transformation : ${transformations}">
<td>
<span class="bg-path" title="Ersetze Wert(e) an dieser Stelle im MTB-File">[[ ${transformation.path} ]]</span>
</td>
<td>
<span class="bg-from" title="Ersetze immer dann, wenn dieser Wert enthalten ist">[[ ${transformation.existingValue} ]]</span>
<strong>&rArr;</strong>
<span class="bg-to" title="Ersetze durch diesen Wert">[[ ${transformation.newValue} ]]</span>
</td>
</tr>
</tbody>
</table>
</th:block>
</section>
</div>
</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>
<script>
function selectTab(self, elem) {
Array.from(document.getElementsByClassName('tab')).forEach(e => e.className = 'tab');
self.className = 'tab active';
Array.from(document.getElementsByClassName('tabcontent')).forEach(e => e.className = 'tabcontent');
document.getElementById(elem).className = 'tabcontent active';
}
</script>
</body>
</html>

24
src/main/resources/templates/configs/gPasConnectionAvailable.html
View File

@ -1,24 +0,0 @@
<th:block th:if="${gPasConnectionAvailable == null}">
<h2><span>🟦</span> gPAS nicht konfiguriert - Patienten-IDs werden intern anonymisiert</h2>
</th:block>
<th:block th:if="${gPasConnectionAvailable != null}">
<h2><span th:if="${gPasConnectionAvailable.available}">✅</span><span th:if="${not(gPasConnectionAvailable.available)}">⚡</span> Verbindung zu gPAS</h2>
<div>
Stand: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(gPasConnectionAvailable.timestamp)}" th:text="${#temporals.formatISO(gPasConnectionAvailable.timestamp)}"></time>
&nbsp;|&nbsp;
Letzte Änderung: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(gPasConnectionAvailable.lastChange)}" th:text="${#temporals.formatISO(gPasConnectionAvailable.lastChange)}"></time>
</div>
<div>
<span>Die Verbindung ist aktuell</span>
<strong th:if="${gPasConnectionAvailable.available}" style="color: green">verfügbar.</strong>
<strong th:if="${not(gPasConnectionAvailable.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="${gPasConnectionAvailable.available ? 'available' : ''}"></span>
<img th:src="@{/server.png}" alt="gPAS" />
<span>ETL-Processor</span>
<span></span>
<span>gPAS</span>
</div>
</th:block>

27
src/main/resources/templates/configs/outputConnectionAvailable.html
View File

@ -1,27 +0,0 @@
<th:block th:if="${outputConnectionAvailable == null}">
<h2><span>🟦</span> Keine Ausgabenkonfiguration</h2>
</th:block>
<th:block th:if="${outputConnectionAvailable != null}">
<h2><span th:if="${outputConnectionAvailable.available}">✅</span><span th:if="${not(outputConnectionAvailable.available)}">⚡</span> MTB-File Verbindung</h2>
<div>
Stand: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(outputConnectionAvailable.timestamp)}" th:text="${#temporals.formatISO(outputConnectionAvailable.timestamp)}"></time>
&nbsp;|&nbsp;
Letzte Änderung: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(outputConnectionAvailable.lastChange)}" th:text="${#temporals.formatISO(outputConnectionAvailable.lastChange)}"></time>
</div>
<div>
Verbindung über <code>[[ ${mtbFileSender} ]]</code>. Die Verbindung ist aktuell
<strong th:if="${outputConnectionAvailable.available}" style="color: green">verfügbar.</strong>
<strong th:if="${not(outputConnectionAvailable.available)}" style="color: red">nicht verfügbar.</strong>
</div>
<div class="connection-display border">
<img th:src="@{/server.png}" alt="ETL-Processor" />
<span class="connection" th:classappend="${outputConnectionAvailable.available ? '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="${mtbFileSender.startsWith('RestBwhc')}">bwHC-Backend</span>
<span th:if="${mtbFileSender.startsWith('RestDip')}">DNPM:DIP-Backend</span>
<span th:if="${mtbFileSender.startsWith('Kafka')}">Kafka-Broker</span>
</div>
</th:block>

40
src/main/resources/templates/configs/tokens.html
View File

@ -1,40 +0,0 @@
<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()}" class="config-table">
<thead>
<tr>
<th>Name</th>
<th>Erstellt</th>
</tr>
</thead>
<tbody>
<tr th:each="token : ${tokens}">
<td>[[ ${token.name} ]]</td>
<td>
<time th:datetime="${token.createdAt}">[[ ${token.createdAt} ]]</time>
<button class="btn btn-red" th:hx-delete="@{/configs/tokens/{id}(id=${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 class="btn">Token Erstellen</button>
</form>
</div>
</div>
</div>

37
src/main/resources/templates/configs/userroles.html
View File

@ -1,37 +0,0 @@
<div th:if="${not userRolesEnabled}">
<h2><span>⛔</span> Benutzerberechtigungen</h2>
<p>Die Verwendung von rollenbasierten Benutzerberechtigungen ist nicht aktiviert.</p>
</div>
<div id="userroles" th:if="${userRolesEnabled}">
<h2><span>✅</span> Benutzerberechtigungen</h2>
<div class="border">
<div th:if="${userRoles.isEmpty()}">Noch keine Benutzerberechtigungen vorhanden.</div>
<table th:if="${not userRoles.isEmpty()}" class="config-table">
<thead>
<tr>
<th>Benutzername</th>
<th>Rolle</th>
</tr>
</thead>
<tbody>
<tr th:each="userRole : ${userRoles}">
<td>[[ ${userRole.username} ]]</td>
<td>
<div class="userrole-form">
<form th:hx-put="@{/configs/userroles/{id}(id=${userRole.id})}" hx-target="#userroles">
<select name="role" th:disabled="${#authorization.authentication.getName() == userRole.username}">
<option th:selected="${userRole.role.value == 'guest'}" value="GUEST">Gast</option>
<option th:selected="${userRole.role.value == 'user'}" value="USER">Benutzer</option>
<option th:selected="${userRole.role.value == 'admin'}" value="ADMIN">Administrator</option>
</select>
<button class="btn btn-blue" th:disabled="${#authorization.authentication.getName() == userRole.username}">Übernehmen</button>
</form>
</div>
<button class="btn btn-red" th:hx-delete="@{/configs/userroles/{id}(id=${userRole.id})}" hx-target="#userroles" th:disabled="${#authorization.authentication.getName() == userRole.username}">Löschen</button>
</td>
</tr>
</tbody>
</table>
</div>
</div>

27
src/main/resources/templates/fragments.html
View File

@ -1,5 +1,5 @@
<!DOCTYPE html>
<html xmlns:th="http://www.thymeleaf.org" xmlns:sec="http://www.thymeleaf.org">
<html xmlns:th="http://www.thymeleaf.org">
<head>
<meta charset="UTF-8">
<link rel="stylesheet" th:href="@{/style.css}" />
@ -7,33 +7,10 @@
<body>
<div th:fragment="nav">
<nav>
<span>
<a class="nav-home" th:href="@{/}">
<img th:src="@{/icon.svg}" alt="Icon" />
<span>ETL-Processor</span>
</a>
</span>
<ul>
<li><a th:href="@{/}">Übersicht</a></li>
<li><a th:href="@{/statistics}">Statistiken</a></li>
<li sec:authorize="hasRole('ADMIN')">
<a th:href="@{/configs}">Konfiguration</a>
</li>
<li class="login" sec:authorize="not isAuthenticated()">
<a class="btn btn-blue" th:href="@{/login}">Login</a>
</li>
<li class="login" sec:authorize="isAuthenticated()">
<span>
<div class="user-icon">
<img th:src="@{/user.svg}" alt="User-Image">
<span sec:authorize="hasRole('ADMIN')" class="user-role admin">Admin</span>
<span sec:authorize="hasRole('USER')" class="user-role user">User</span>
<span sec:authorize="hasRole('GUEST')" class="user-role guest">Guest</span>
</div>
<span class="user-name" sec:authentication="name">?</span>
</span>
<a class="btn btn-red" th:href="@{/logout}">Abmelden</a>
</li>
<li><a th:href="@{/transformations}">Transformationen</a></li>
</ul>
</nav>
</div>

68
src/main/resources/templates/index.html
View File

@ -1,5 +1,5 @@
<!DOCTYPE html>
<html lang="de" xmlns:th="http://www.thymeleaf.org" xmlns:sec="http://www.thymeleaf.org">
<html lang="de" xmlns:th="http://www.thymeleaf.org">
<head>
<meta charset="UTF-8">
<title>ETL-Prozessor</title>
@ -9,35 +9,9 @@
<div th:replace="~{fragments.html :: nav}"></div>
<main>
<h1>Alle Anfragen<a id="reload-notify" class="reload" title="Neue Anfragen" th:href="@{/}">⟳</a></h1>
<h1>Letzte Anfragen</h1>
<div>
<h2 th:if="${patientPseudonym != null}">
Betreffend Patienten-Pseudonym <span class="monospace" th:text="${patientPseudonym}">***</span>
<a class="btn btn-blue" th:if="${patientPseudonym != null}" th:href="@{/}">Alle anzeigen</a>
</h2>
</div>
<div class="border" th:if="${requests.totalElements == 0}">
<div class="notification info">Noch keine Anfragen eingegangen</div>
</div>
<div class="border" th:if="${requests.totalElements > 0}">
<div th:if="${patientPseudonym == 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="${requests.isFirst()}">&larrb;</a>
<a id="prev-page-link" th:href="@{/(page=${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 [[ ${requests.getTotalPages()} ]]</span>
<a id="next-page-link" th:href="@{/(page=${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="${requests.isLast()}">&rarrb;</a>
</div>
<div th:if="${patientPseudonym != null}" class="page-control">
<a id="first-page-link" th:href="@{/patient/{patientPseudonym}(patientPseudonym=${patientPseudonym},page=${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/{patientPseudonym}(patientPseudonym=${patientPseudonym},page=${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 [[ ${requests.getTotalPages()} ]]</span>
<a id="next-page-link" th:href="@{/patient/{patientPseudonym}(patientPseudonym=${patientPseudonym},page=${requests.getNumber() + 1})}" title="Seite vor: Taste D" th:if="${not requests.isLast()}">&rarr;</a><a th:if="${requests.isLast()}">&rarr;</a>
<a id="last-page-link" th:href="@{/patient/{patientPseudonym}(patientPseudonym=${patientPseudonym},page=${requests.getTotalPages() - 1})}" title="Zum Ende: Taste S" th:if="${not requests.isLast()}">&rarrb;</a><a th:if="${requests.isLast()}">&rarrb;</a>
</div>
<table class="paged">
<table>
<thead>
<tr>
<th>Status</th>
@ -57,47 +31,15 @@
<td th:style="${request.type.value == 'delete'} ? 'color: red;'"><small>[[ ${request.type} ]]</small></td>
<td th:if="not ${request.report}">[[ ${request.uuid} ]]</td>
<td th:if="${request.report}">
<a th:href="@{/report/{id}(id=${request.uuid})}" sec:authorize="hasRole('USER') or hasRole('ADMIN')">[[ ${request.uuid} ]]</a>
<th:block sec:authorize="not (hasRole('USER') or hasRole('ADMIN'))">[[ ${request.uuid} ]]</th:block>
<a th:href="@{/report/{id}(id=${request.uuid})}">[[ ${request.uuid} ]]</a>
</td>
<td><time th:datetime="${request.processedAt}">[[ ${request.processedAt} ]]</time></td>
<td class="patient-id" th:if="${patientPseudonym != null}" sec:authorize="hasRole('USER') or hasRole('ADMIN')">
[[ ${request.patientPseudonym} ]]
</td>
<td class="patient-id" th:if="${patientPseudonym == null}" sec:authorize="hasRole('USER') or hasRole('ADMIN')">
<a th:href="@{/patient/{pid}(pid=${request.patientPseudonym})}">[[ ${request.patientPseudonym} ]]</a>
</td>
<td class="patient-id" sec:authorize="not (hasRole('USER') or hasRole('ADMIN'))">***</td>
<td>[[ ${request.patientId} ]]</td>
</tr>
</tbody>
</table>
</div>
</main>
<script th:src="@{/scripts.js}"></script>
<script>
window.addEventListener('load', () => {
let keyBindings = {
'w': 'first-page-link',
'a': 'prev-page-link',
'd': 'next-page-link',
's': 'last-page-link'
};
window.onkeydown = (event) => {
for (const [key, elemId] of Object.entries(keyBindings)) {
if (event.key === key && document.getElementById(elemId)) {
document.getElementById(elemId).style.background = 'yellow';
document.getElementById(elemId).click();
}
}
};
});
const eventSource = new EventSource('statistics/events');
eventSource.addEventListener('newrequest', event => {
console.log(event);
document.getElementById('reload-notify').style.display = 'inline-flex';
});
</script>
</body>
</html>

27
src/main/resources/templates/login.html
View File

@ -1,27 +0,0 @@
<!DOCTYPE html>
<html lang="de" xmlns:th="http://www.thymeleaf.org">
<head>
<meta charset="UTF-8">
<title>ETL-Prozessor</title>
<link rel="stylesheet" th:href="@{/style.css}" />
</head>
<body>
<div th:replace="~{fragments.html :: nav}"></div>
<main>
<div class="login-form">
<img th:src="@{/user.svg}" alt="user-logo" />
<h2 class="centered">Anmelden</h2>
<div class="centered notification error" th:if="${param.error}">Anmeldung nicht erfolgreich</div>
<div class="centered notification notice" th:if="${param.expired}">Sitzung abgelaufen oder von einem Administrator beendet.</div>
<div class="centered notification success" th:if="${param.logout}">Sie haben sich abgemeldet</div>
<form method="post" th:action="@{/login}">
<input type="text" id="username" name="username" class="form-control" placeholder="Username" required="" autofocus="" />
<input type="password" id="password" name="password" class="form-control" placeholder="Password" required="" />
<button class="btn" type="submit">Anmelden</button>
<hr th:if="${not oidcLogins.isEmpty()}" />
<a th:each="oidcLogin : ${oidcLogins}" class="btn" th:href="@{/oauth2/authorization/{provider}(provider=${oidcLogin.component1()})}">OIDC Login - [[ ${oidcLogin.component2()} ]]</a>
</form>
</div>
</main>
</body>
</html>

22
src/main/resources/templates/report.html
View File

@ -1,5 +1,5 @@
<!DOCTYPE html>
<html lang="de" xmlns:th="http://www.thymeleaf.org" xmlns:sec="http://www.thymeleaf.org">
<html lang="de" xmlns:th="http://www.thymeleaf.org">
<head>
<meta charset="UTF-8">
<title>ETL-Prozessor</title>
@ -15,7 +15,6 @@
<thead>
<tr>
<th>Status</th>
<th>Typ</th>
<th>ID</th>
<th>Datum</th>
<th>Patienten-ID</th>
@ -28,26 +27,20 @@
<td th:if="${request.status.value == 'error'}" class="bg-red"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value == 'unknown'}" class="bg-gray"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value == 'duplication'}" class="bg-gray"><small>[[ ${request.status} ]]</small></td>
<td th:style="${request.type.value == 'delete'} ? 'color: red;'"><small>[[ ${request.type} ]]</small></td>
<td>[[ ${request.uuid} ]]</td>
<td><time th:datetime="${request.processedAt}">[[ ${request.processedAt} ]]</time></td>
<td class="patient-id" sec:authorize="authenticated">[[ ${request.patientPseudonym} ]]</td>
<td class="patient-id" sec:authorize="not authenticated">***</td>
<td>[[ ${request.patientId} ]]</td>
</tr>
</tbody>
</table>
<h2 th:text="${request.report.description}"></h2>
<p th:if="${issues.isEmpty()}">
Keine weiteren Angaben.
</p>
<table th:if="${not issues.isEmpty()}">
<table th:if="not ${issues.isEmpty()}">
<thead>
<tr>
<th>Schweregrad</th>
<th>Beschreibung und Pfad</th>
<th>Beschreibung</th>
</tr>
</thead>
<tbody>
@ -55,12 +48,7 @@
<td th:if="${issue.severity.value == 'info'}" class="bg-blue"><small>[[ ${issue.severity} ]]</small></td>
<td th:if="${issue.severity.value == 'warning'}" class="bg-yellow"><small>[[ ${issue.severity} ]]</small></td>
<td th:if="${issue.severity.value == 'error'}" class="bg-red"><small>[[ ${issue.severity} ]]</small></td>
<td th:if="${issue.severity.value == 'fatal'}" class="bg-red"><small>[[ ${issue.severity} ]]</small></td>
<td>
<div class="issue-message">[[ ${issue.message} ]]</div>
<div class="issue-path" th:if="${issue.path.isPresent()}">[[ ${issue.path.get()} ]]</div>
<div class="issue-path" th:if="${issue.path.isEmpty()}"><i>Keine Angabe</i></div>
</td>
<td>[[ ${issue.message} ]]</td>
</tr>
</tbody>
</table>

22
src/main/resources/templates/statistics.html
View File

@ -13,32 +13,28 @@
Hier sehen Sie eine Übersicht über eingegangene Anfragen.
</p>
<section>
<h2>MTB-File-Anfragen</h2>
<p>
Anfragen zur Aktualisierung von Patientendaten durch Übermittlung eines MTB-Files.
</p>
<div class="charts">
<div id="piechart1" class="chart grid-left"></div>
<div id="piechart2" class="chart grid-right"></div>
<div id="barchart" class="chart grid-full"></div>
<div>
<div id="piechart1" class="chart chart-50pc"></div>
<div id="piechart2" class="chart chart-50pc"></div>
</div>
</section>
<div id="barchart" class="chart"></div>
<section>
<h2>Löschanfragen</h2>
<p>
Anfragen zur Löschung von Patientendaten, wenn kein Consent vorliegt.
</p>
<div class="charts">
<div id="piechartdel1" class="chart grid-left"></div>
<div id="piechartdel2" class="chart grid-right"></div>
<div id="barchartdel" class="chart grid-full"></div>
<div>
<div id="piechartdel1" class="chart chart-50pc"></div>
<div id="piechartdel2" class="chart chart-50pc"></div>
</div>
</section>
<div id="barchartdel" class="chart"></div>
</main>
<script th:src="@{/webjars/echarts/dist/echarts.min.js}"></script>
<script th:src="@{/echarts.min.js}"></script>
<script th:src="@{/scripts.js}"></script>
<script>
window.onload = () => {

47
src/main/resources/templates/transformations.html Normal file
View File

@ -0,0 +1,47 @@
<!DOCTYPE html>
<html lang="de" xmlns:th="http://www.thymeleaf.org">
<head>
<meta charset="UTF-8">
<title>ETL-Prozessor</title>
<link rel="stylesheet" th:href="@{/style.css}" />
</head>
<body>
<div th:replace="~{fragments.html :: nav}"></div>
<main>
<h1>Transformationen</h1>
<h2>Syntax</h2>
Hier einige Beispiele zum Syntax des JSON-Path
<ul>
<li style="padding: 0.6rem 0;"><span class="bg-path">diagnoses[*].icdO3T.version</span>: Ersetze die ICD-O3T-Version in allen Diagnosen, z.B. zur Version der deutschen Übersetzung</li>
<li style="padding: 0.6rem 0;"><span class="bg-path">patient.gender</span>: Ersetze das Geschlecht des Patienten, z.B. in das von bwHC verlangte Format</li>
</ul>
<h2>Konfigurierte Transformationen</h2>
<p>
Hier sehen Sie eine Übersicht der konfigurierten Transformationen.
</p>
<table>
<thead>
<tr>
<th>JSON-Path</th>
<th>Transformation von &rArr; nach</th>
</tr>
</thead>
<tbody>
<tr th:each="transformation : ${transformations}">
<td>
<span class="bg-path" title="Ersetze Wert(e) an dieser Stelle im MTB-File">[[ ${transformation.path} ]]</span>
</td>
<td>
<span class="bg-from" title="Ersetze immer dann, wenn dieser Wert enthalten ist">[[ ${transformation.existingValue} ]]</span>
<strong>&rArr;</strong>
<span class="bg-to" title="Ersetze durch diesen Wert">[[ ${transformation.newValue} ]]</span>
</td>
</tr>
</tbody>
</table>
</main>
</body>
</html>

20
src/test/kotlin/dev/dnpm/etl/processor/helpers.kt
View File

@ -1,20 +0,0 @@
/*
* 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

184
src/test/kotlin/dev/dnpm/etl/processor/input/KafkaInputListenerTest.kt
View File

@ -1,184 +0,0 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.input
import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.Consent
import de.ukw.ccc.bwhc.dto.MtbFile
import de.ukw.ccc.bwhc.dto.Patient
import dev.dnpm.etl.processor.CustomMediaType
import dev.dnpm.etl.processor.services.RequestProcessor
import org.apache.kafka.clients.consumer.ConsumerRecord
import org.apache.kafka.common.header.internals.RecordHeader
import org.apache.kafka.common.header.internals.RecordHeaders
import org.apache.kafka.common.record.TimestampType
import org.junit.jupiter.api.BeforeEach
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.any
import org.mockito.kotlin.anyValueClass
import org.mockito.kotlin.times
import org.mockito.kotlin.verify
import java.util.*
@ExtendWith(MockitoExtension::class)
class KafkaInputListenerTest {
private lateinit var requestProcessor: RequestProcessor
private lateinit var objectMapper: ObjectMapper
private lateinit var kafkaInputListener: KafkaInputListener
@BeforeEach
fun setup(
@Mock requestProcessor: RequestProcessor
) {
this.requestProcessor = requestProcessor
this.objectMapper = ObjectMapper()
this.kafkaInputListener = KafkaInputListener(requestProcessor, objectMapper)
}
@Test
fun shouldProcessMtbFileRequest() {
val mtbFile = MtbFile.builder()
.withPatient(Patient.builder().withId("DUMMY_12345678").build())
.withConsent(Consent.builder().withStatus(Consent.Status.ACTIVE).build())
.build()
kafkaInputListener.onMessage(
ConsumerRecord(
"testtopic",
0,
0,
"",
this.objectMapper.writeValueAsString(mtbFile)
)
)
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
}
@Test
fun shouldProcessDeleteRequest() {
val mtbFile = MtbFile.builder()
.withPatient(Patient.builder().withId("DUMMY_12345678").build())
.withConsent(Consent.builder().withStatus(Consent.Status.REJECTED).build())
.build()
kafkaInputListener.onMessage(
ConsumerRecord(
"testtopic",
0,
0,
"",
this.objectMapper.writeValueAsString(mtbFile)
)
)
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
}
@Test
fun shouldProcessMtbFileRequestWithExistingRequestId() {
val mtbFile = MtbFile.builder()
.withPatient(Patient.builder().withId("DUMMY_12345678").build())
.withConsent(Consent.builder().withStatus(Consent.Status.ACTIVE).build())
.build()
val headers = RecordHeaders(listOf(RecordHeader("requestId", UUID.randomUUID().toString().toByteArray())))
kafkaInputListener.onMessage(
ConsumerRecord(
"testtopic",
0,
0,
-1L,
TimestampType.NO_TIMESTAMP_TYPE,
-1,
-1,
"",
this.objectMapper.writeValueAsString(mtbFile),
headers,
Optional.empty()
)
)
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>(), anyValueClass())
}
@Test
fun shouldProcessDeleteRequestWithExistingRequestId() {
val mtbFile = MtbFile.builder()
.withPatient(Patient.builder().withId("DUMMY_12345678").build())
.withConsent(Consent.builder().withStatus(Consent.Status.REJECTED).build())
.build()
val headers = RecordHeaders(listOf(RecordHeader("requestId", UUID.randomUUID().toString().toByteArray())))
kafkaInputListener.onMessage(
ConsumerRecord(
"testtopic",
0,
0,
-1L,
TimestampType.NO_TIMESTAMP_TYPE,
-1,
-1,
"",
this.objectMapper.writeValueAsString(mtbFile),
headers,
Optional.empty()
)
)
verify(requestProcessor, times(1)).processDeletion(anyValueClass(), anyValueClass())
}
@Test
fun shouldNotProcessDnpmV2Request() {
val mtbFile = MtbFile.builder()
.withPatient(Patient.builder().withId("DUMMY_12345678").build())
.withConsent(Consent.builder().withStatus(Consent.Status.REJECTED).build())
.build()
val headers = RecordHeaders(
listOf(
RecordHeader("requestId", UUID.randomUUID().toString().toByteArray()),
RecordHeader("contentType", CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE.toByteArray())
)
)
kafkaInputListener.onMessage(
ConsumerRecord(
"testtopic",
0,
0,
-1L,
TimestampType.NO_TIMESTAMP_TYPE,
-1,
-1,
"",
this.objectMapper.writeValueAsString(mtbFile),
headers,
Optional.empty()
)
)
verify(requestProcessor, times(0)).processDeletion(anyValueClass(), anyValueClass())
}
}

220
src/test/kotlin/dev/dnpm/etl/processor/input/MtbFileRestControllerTest.kt
View File

@ -1,220 +0,0 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.input
import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.*
import dev.dnpm.etl.processor.CustomMediaType
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.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.springframework.core.io.ClassPathResource
import org.springframework.http.MediaType
import org.springframework.test.web.servlet.MockMvc
import org.springframework.test.web.servlet.delete
import org.springframework.test.web.servlet.post
import org.springframework.test.web.servlet.setup.MockMvcBuilders
@ExtendWith(MockitoExtension::class)
class MtbFileRestControllerTest {
private val objectMapper = ObjectMapper()
@Nested
inner class BwhcRequests {
private lateinit var mockMvc: MockMvc
private lateinit var requestProcessor: RequestProcessor
@BeforeEach
fun setup(
@Mock requestProcessor: RequestProcessor
) {
this.requestProcessor = requestProcessor
val controller = MtbFileRestController(requestProcessor)
this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build()
}
@Test
fun shouldProcessPostRequest() {
mockMvc.post("/mtbfile") {
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Consent.Status.ACTIVE))
contentType = MediaType.APPLICATION_JSON
}.andExpect {
status {
isAccepted()
}
}
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
}
@Test
fun shouldProcessPostRequestWithRejectedConsent() {
mockMvc.post("/mtbfile") {
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Consent.Status.REJECTED))
contentType = MediaType.APPLICATION_JSON
}.andExpect {
status {
isAccepted()
}
}
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
}
@Test
fun shouldProcessDeleteRequest() {
mockMvc.delete("/mtbfile/TEST_12345678").andExpect {
status {
isAccepted()
}
}
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
}
}
@Nested
inner class BwhcRequestsWithAlias {
private lateinit var mockMvc: MockMvc
private lateinit var requestProcessor: RequestProcessor
@BeforeEach
fun setup(
@Mock requestProcessor: RequestProcessor
) {
this.requestProcessor = requestProcessor
val controller = MtbFileRestController(requestProcessor)
this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build()
}
@Test
fun shouldProcessPostRequest() {
mockMvc.post("/mtb") {
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Consent.Status.ACTIVE))
contentType = MediaType.APPLICATION_JSON
}.andExpect {
status {
isAccepted()
}
}
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
}
@Test
fun shouldProcessPostRequestWithRejectedConsent() {
mockMvc.post("/mtb") {
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Consent.Status.REJECTED))
contentType = MediaType.APPLICATION_JSON
}.andExpect {
status {
isAccepted()
}
}
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
}
@Test
fun shouldProcessDeleteRequest() {
mockMvc.delete("/mtb/TEST_12345678").andExpect {
status {
isAccepted()
}
}
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
}
}
@Nested
inner class RequestsForDnpmDataModel21 {
private lateinit var mockMvc: MockMvc
private lateinit var requestProcessor: RequestProcessor
@BeforeEach
fun setup(
@Mock requestProcessor: RequestProcessor
) {
this.requestProcessor = requestProcessor
val controller = MtbFileRestController(requestProcessor)
this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build()
}
@Test
fun shouldRespondPostRequest() {
val mtbFileContent = ClassPathResource("mv64e-mtb-fake-patient.json").inputStream.readAllBytes().toString(Charsets.UTF_8)
mockMvc.post("/mtb") {
content = mtbFileContent
contentType = CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON
}.andExpect {
status {
isAccepted()
}
}
verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
}
}
companion object {
fun bwhcMtbFileContent(consentStatus: Consent.Status) = MtbFile.builder()
.withPatient(
Patient.builder()
.withId("TEST_12345678")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.withConsent(
Consent.builder()
.withId("1")
.withStatus(consentStatus)
.withPatient("TEST_12345678")
.build()
)
.withEpisode(
Episode.builder()
.withId("1")
.withPatient("TEST_12345678")
.withPeriod(PeriodStart("2023-08-08"))
.build()
)
.build()
}
}

240
src/test/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSenderTest.kt
View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2023 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
@ -21,38 +21,26 @@ package dev.dnpm.etl.processor.output
import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.*
import de.ukw.ccc.bwhc.dto.Patient
import dev.dnpm.etl.processor.CustomMediaType
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.config.KafkaProperties
import dev.dnpm.etl.processor.config.KafkaTargetProperties
import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.pcvolkmer.mv64e.mtb.*
import org.apache.kafka.clients.producer.ProducerRecord
import org.assertj.core.api.Assertions.assertThat
import org.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.MethodSource
import org.mockito.ArgumentMatchers.anyString
import org.mockito.Mock
import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.*
import org.springframework.http.MediaType
import org.springframework.kafka.core.KafkaTemplate
import org.springframework.kafka.support.SendResult
import org.springframework.retry.policy.SimpleRetryPolicy
import org.springframework.retry.support.RetryTemplateBuilder
import java.util.concurrent.CompletableFuture.completedFuture
import java.util.concurrent.ExecutionException
@ExtendWith(MockitoExtension::class)
class KafkaMtbFileSenderTest {
@Nested
inner class BwhcV1Record {
private lateinit var kafkaTemplate: KafkaTemplate<String, String>
private lateinit var kafkaMtbFileSender: KafkaMtbFileSender
@ -63,218 +51,75 @@ class KafkaMtbFileSenderTest {
fun setup(
@Mock kafkaTemplate: KafkaTemplate<String, String>
) {
val kafkaProperties = KafkaProperties("testtopic")
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
val kafkaTargetProperties = KafkaTargetProperties("testtopic")
this.objectMapper = ObjectMapper()
this.kafkaTemplate = kafkaTemplate
this.kafkaMtbFileSender = KafkaMtbFileSender(kafkaTemplate, kafkaProperties, retryTemplate, objectMapper)
this.kafkaMtbFileSender = KafkaMtbFileSender(kafkaTemplate, kafkaTargetProperties, objectMapper)
}
@ParameterizedTest
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
@MethodSource("requestWithResponseSource")
fun shouldSendMtbFileRequestAndReturnExpectedState(testData: TestData) {
doAnswer {
if (null != testData.exception) {
throw testData.exception
}
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
val response = kafkaMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1MtbFile(Consent.Status.ACTIVE)))
val response = kafkaMtbFileSender.send(MtbFileSender.MtbFileRequest("TestID", mtbFile(Consent.Status.ACTIVE)))
assertThat(response.status).isEqualTo(testData.requestStatus)
}
@ParameterizedTest
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
@MethodSource("requestWithResponseSource")
fun shouldSendDeleteRequestAndReturnExpectedState(testData: TestData) {
doAnswer {
if (null != testData.exception) {
throw testData.exception
}
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
val response = kafkaMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
val response = kafkaMtbFileSender.send(MtbFileSender.DeleteRequest("TestID", "PID"))
assertThat(response.status).isEqualTo(testData.requestStatus)
}
@Test
fun shouldSendMtbFileRequestWithCorrectKeyAndHeaderAndBody() {
fun shouldSendMtbFileRequestWithCorrectKeyAndBody() {
doAnswer {
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
kafkaMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1MtbFile(Consent.Status.ACTIVE)))
kafkaMtbFileSender.send(MtbFileSender.MtbFileRequest("TestID", mtbFile(Consent.Status.ACTIVE)))
val captor = argumentCaptor<ProducerRecord<String, String>>()
verify(kafkaTemplate, times(1)).send(captor.capture())
assertThat(captor.firstValue.key()).isNotNull
assertThat(captor.firstValue.key()).isEqualTo("{\"pid\": \"PID\"}")
assertThat(captor.firstValue.headers().headers("contentType")).isNotNull
assertThat(captor.firstValue.headers().headers("contentType")?.firstOrNull()?.value()).isEqualTo(MediaType.APPLICATION_JSON_VALUE.toByteArray())
assertThat(captor.firstValue.value()).isNotNull
assertThat(captor.firstValue.value()).isEqualTo(objectMapper.writeValueAsString(bwhcV1kafkaRecordData(TEST_REQUEST_ID, Consent.Status.ACTIVE)))
val captor = argumentCaptor<String>()
verify(kafkaTemplate, times(1)).send(anyString(), captor.capture(), captor.capture())
assertThat(captor.firstValue).isNotNull
assertThat(captor.firstValue).isEqualTo("{\"pid\": \"PID\", \"eid\": \"1\"}")
assertThat(captor.secondValue).isNotNull
assertThat(captor.secondValue).isEqualTo(objectMapper.writeValueAsString(kafkaRecordData("TestID", Consent.Status.ACTIVE)))
}
@Test
fun shouldSendDeleteRequestWithCorrectKeyAndBody() {
doAnswer {
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
kafkaMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
val captor = argumentCaptor<ProducerRecord<String, String>>()
verify(kafkaTemplate, times(1)).send(captor.capture())
assertThat(captor.firstValue.key()).isNotNull
assertThat(captor.firstValue.key()).isEqualTo("{\"pid\": \"PID\"}")
assertThat(captor.firstValue.value()).isNotNull
assertThat(captor.firstValue.value()).isEqualTo(objectMapper.writeValueAsString(bwhcV1kafkaRecordData(TEST_REQUEST_ID, Consent.Status.REJECTED)))
}
@ParameterizedTest
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
fun shouldRetryOnMtbFileKafkaSendError(testData: TestData) {
val kafkaProperties = KafkaProperties("testtopic")
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
this.kafkaMtbFileSender = KafkaMtbFileSender(this.kafkaTemplate, kafkaProperties, retryTemplate, this.objectMapper)
doAnswer {
if (null != testData.exception) {
throw testData.exception
}
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
kafkaMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1MtbFile(Consent.Status.ACTIVE)))
val expectedCount = when (testData.exception) {
// OK - No Retry
null -> times(1)
// Request failed - Retry max 3 times
else -> times(3)
}
verify(kafkaTemplate, expectedCount).send(any<ProducerRecord<String, String>>())
}
@ParameterizedTest
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
fun shouldRetryOnDeleteKafkaSendError(testData: TestData) {
val kafkaProperties = KafkaProperties("testtopic")
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
this.kafkaMtbFileSender = KafkaMtbFileSender(this.kafkaTemplate, kafkaProperties, retryTemplate, this.objectMapper)
doAnswer {
if (null != testData.exception) {
throw testData.exception
}
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
kafkaMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
val expectedCount = when (testData.exception) {
// OK - No Retry
null -> times(1)
// Request failed - Retry max 3 times
else -> times(3)
}
verify(kafkaTemplate, expectedCount).send(any<ProducerRecord<String, String>>())
}
}
@Nested
inner class DnpmV2Record {
private lateinit var kafkaTemplate: KafkaTemplate<String, String>
private lateinit var kafkaMtbFileSender: KafkaMtbFileSender
private lateinit var objectMapper: ObjectMapper
@BeforeEach
fun setup(
@Mock kafkaTemplate: KafkaTemplate<String, String>
) {
val kafkaProperties = KafkaProperties("testtopic")
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
this.objectMapper = ObjectMapper()
this.kafkaTemplate = kafkaTemplate
this.kafkaMtbFileSender = KafkaMtbFileSender(kafkaTemplate, kafkaProperties, retryTemplate, objectMapper)
}
@ParameterizedTest
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
fun shouldSendMtbFileRequestAndReturnExpectedState(testData: TestData) {
doAnswer {
if (null != testData.exception) {
throw testData.exception
}
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
val response = kafkaMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile()))
assertThat(response.status).isEqualTo(testData.requestStatus)
}
@Test
fun shouldSendMtbFileRequestWithCorrectKeyAndHeaderAndBody() {
doAnswer {
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
kafkaMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile()))
val captor = argumentCaptor<ProducerRecord<String, String>>()
verify(kafkaTemplate, times(1)).send(captor.capture())
assertThat(captor.firstValue.key()).isNotNull
assertThat(captor.firstValue.key()).isEqualTo("{\"pid\": \"PID\"}")
assertThat(captor.firstValue.headers().headers("contentType")).isNotNull
assertThat(captor.firstValue.headers().headers("contentType")?.firstOrNull()?.value()).isEqualTo(CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE.toByteArray())
assertThat(captor.firstValue.value()).isNotNull
assertThat(captor.firstValue.value()).isEqualTo(objectMapper.writeValueAsString(dnmpV2kafkaRecordData(TEST_REQUEST_ID)))
}
@ParameterizedTest
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
fun shouldRetryOnMtbFileKafkaSendError(testData: TestData) {
val kafkaProperties = KafkaProperties("testtopic")
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
this.kafkaMtbFileSender = KafkaMtbFileSender(this.kafkaTemplate, kafkaProperties, retryTemplate, this.objectMapper)
doAnswer {
if (null != testData.exception) {
throw testData.exception
}
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
kafkaMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile()))
val expectedCount = when (testData.exception) {
// OK - No Retry
null -> times(1)
// Request failed - Retry max 3 times
else -> times(3)
}
verify(kafkaTemplate, expectedCount).send(any<ProducerRecord<String, String>>())
}
kafkaMtbFileSender.send(MtbFileSender.DeleteRequest("TestID", "PID"))
val captor = argumentCaptor<String>()
verify(kafkaTemplate, times(1)).send(anyString(), captor.capture(), captor.capture())
assertThat(captor.firstValue).isNotNull
assertThat(captor.firstValue).isEqualTo("{\"pid\": \"PID\"}")
assertThat(captor.secondValue).isNotNull
assertThat(captor.secondValue).isEqualTo(objectMapper.writeValueAsString(kafkaRecordData("TestID", Consent.Status.REJECTED)))
}
companion object {
val TEST_REQUEST_ID = RequestId("TestId")
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID")
fun bwhcV1MtbFile(consentStatus: Consent.Status): MtbFile {
fun mtbFile(consentStatus: Consent.Status): MtbFile {
return if (consentStatus == Consent.Status.ACTIVE) {
MtbFile.builder()
.withPatient(
@ -309,31 +154,8 @@ class KafkaMtbFileSenderTest {
}.build()
}
fun dnpmV2MtbFile(): Mtb = Mtb.builder()
.withPatient(
dev.pcvolkmer.mv64e.mtb.Patient.builder()
.withId("PID")
.withBirthDate("2000-08-08")
.withGender(CodingGender.builder().withCode(CodingGender.Code.MALE).build())
.build()
)
.withEpisodesOfCare(
listOf(
MTBEpisodeOfCare.builder()
.withId("1")
.withPatient(Reference("PID"))
.withPeriod(PeriodDate.builder().withStart("2023-08-08").build())
.build()
)
)
.build()
fun bwhcV1kafkaRecordData(requestId: RequestId, consentStatus: Consent.Status): MtbRequest {
return BwhcV1MtbFileRequest(requestId, bwhcV1MtbFile(consentStatus))
}
fun dnmpV2kafkaRecordData(requestId: RequestId): MtbRequest {
return DnpmV2MtbFileRequest(requestId, dnpmV2MtbFile())
fun kafkaRecordData(requestId: String, consentStatus: Consent.Status): KafkaMtbFileSender.Data {
return KafkaMtbFileSender.Data(requestId, mtbFile(consentStatus))
}
data class TestData(val requestStatus: RequestStatus, val exception: Throwable? = null)

313
src/test/kotlin/dev/dnpm/etl/processor/output/RestBwhcMtbFileSenderTest.kt
View File

@ -1,313 +0,0 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.output
import com.fasterxml.jackson.databind.ObjectMapper
import com.fasterxml.jackson.module.kotlin.KotlinModule
import de.ukw.ccc.bwhc.dto.*
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.config.RestTargetProperties
import dev.dnpm.etl.processor.monitoring.ReportService
import dev.dnpm.etl.processor.monitoring.RequestStatus
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.params.ParameterizedTest
import org.junit.jupiter.params.provider.MethodSource
import org.springframework.http.HttpHeaders
import org.springframework.http.HttpMethod
import org.springframework.http.HttpStatus
import org.springframework.http.MediaType
import org.springframework.retry.policy.SimpleRetryPolicy
import org.springframework.retry.support.RetryTemplateBuilder
import org.springframework.test.web.client.ExpectedCount
import org.springframework.test.web.client.MockRestServiceServer
import org.springframework.test.web.client.match.MockRestRequestMatchers.*
import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus
import org.springframework.web.client.RestTemplate
class RestBwhcMtbFileSenderTest {
private lateinit var mockRestServiceServer: MockRestServiceServer
private lateinit var restMtbFileSender: RestMtbFileSender
private var reportService = ReportService(ObjectMapper().registerModule(KotlinModule.Builder().build()))
@BeforeEach
fun setup() {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile", null, null)
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.restMtbFileSender =
RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
}
@ParameterizedTest
@MethodSource("deleteRequestWithResponseSource")
fun shouldReturnExpectedResponseForDelete(requestWithResponse: RequestWithResponse) {
this.mockRestServiceServer
.expect(method(HttpMethod.DELETE))
.andExpect(requestTo("http://localhost:9000/mtbfile/Patient/${TEST_PATIENT_PSEUDONYM.value}"))
.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
@ParameterizedTest
@MethodSource("mtbFileRequestWithResponseSource")
fun shouldReturnExpectedResponseForMtbFilePost(requestWithResponse: RequestWithResponse) {
this.mockRestServiceServer
.expect(method(HttpMethod.POST))
.andExpect(requestTo("http://localhost:9000/mtbfile/MTBFile"))
.andExpect(header(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE))
.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, mtbFile))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
@ParameterizedTest
@MethodSource("mtbFileRequestWithResponseSource")
fun shouldRetryOnMtbFileHttpRequestError(requestWithResponse: RequestWithResponse) {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile", null, null)
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.restMtbFileSender =
RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
val expectedCount = when (requestWithResponse.httpStatus) {
// OK - No Retry
HttpStatus.OK, HttpStatus.CREATED -> ExpectedCount.max(1)
// Request failed - Retry max 3 times
else -> ExpectedCount.max(3)
}
this.mockRestServiceServer
.expect(expectedCount, method(HttpMethod.POST))
.andExpect(requestTo("http://localhost:9000/mtbfile/MTBFile"))
.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, mtbFile))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
@ParameterizedTest
@MethodSource("deleteRequestWithResponseSource")
fun shouldRetryOnDeleteHttpRequestError(requestWithResponse: RequestWithResponse) {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile", null, null)
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.restMtbFileSender =
RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
val expectedCount = when (requestWithResponse.httpStatus) {
// OK - No Retry
HttpStatus.OK, HttpStatus.CREATED -> ExpectedCount.max(1)
// Request failed - Retry max 3 times
else -> ExpectedCount.max(3)
}
this.mockRestServiceServer
.expect(expectedCount, method(HttpMethod.DELETE))
.andExpect(requestTo("http://localhost:9000/mtbfile/Patient/${TEST_PATIENT_PSEUDONYM.value}"))
.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
companion object {
data class RequestWithResponse(
val httpStatus: HttpStatus,
val body: String,
val response: MtbFileSender.Response
)
val TEST_REQUEST_ID = RequestId("TestId")
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID")
val mtbFile: MtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.withId("PID")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.withConsent(
Consent.builder()
.withId("1")
.withStatus(Consent.Status.ACTIVE)
.withPatient("PID")
.build()
)
.withEpisode(
Episode.builder()
.withId("1")
.withPatient("PID")
.withPeriod(PeriodStart("2023-08-08"))
.build()
)
.build()
private const val ERROR_RESPONSE_BODY = "Sonstiger Fehler bei der Übertragung"
/**
* Synthetic http responses with related request status
* Also see: https://ibmi-intra.cs.uni-tuebingen.de/display/ZPM/bwHC+REST+API
*/
@JvmStatic
fun mtbFileRequestWithResponseSource(): Set<RequestWithResponse> {
return setOf(
RequestWithResponse(
HttpStatus.OK,
responseBodyWithMaxSeverity(ReportService.Severity.INFO),
MtbFileSender.Response(
RequestStatus.SUCCESS,
responseBodyWithMaxSeverity(ReportService.Severity.INFO)
)
),
RequestWithResponse(
HttpStatus.CREATED,
responseBodyWithMaxSeverity(ReportService.Severity.WARNING),
MtbFileSender.Response(
RequestStatus.WARNING,
responseBodyWithMaxSeverity(ReportService.Severity.WARNING)
)
),
RequestWithResponse(
HttpStatus.BAD_REQUEST,
responseBodyWithMaxSeverity(ReportService.Severity.ERROR),
MtbFileSender.Response(RequestStatus.ERROR, responseBodyWithMaxSeverity(ReportService.Severity.ERROR))
),
RequestWithResponse(
HttpStatus.UNPROCESSABLE_ENTITY,
responseBodyWithMaxSeverity(ReportService.Severity.FATAL),
MtbFileSender.Response(
RequestStatus.ERROR,
responseBodyWithMaxSeverity(ReportService.Severity.FATAL)
)
),
// Some more errors not mentioned in documentation
RequestWithResponse(
HttpStatus.NOT_FOUND,
ERROR_RESPONSE_BODY,
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
),
RequestWithResponse(
HttpStatus.INTERNAL_SERVER_ERROR,
ERROR_RESPONSE_BODY,
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
)
)
}
/**
* Synthetic http responses with related request status
* Also see: https://ibmi-intra.cs.uni-tuebingen.de/display/ZPM/bwHC+REST+API
*/
@JvmStatic
fun deleteRequestWithResponseSource(): Set<RequestWithResponse> {
return setOf(
RequestWithResponse(HttpStatus.OK, "", MtbFileSender.Response(RequestStatus.SUCCESS)),
// Some more errors not mentioned in documentation
RequestWithResponse(
HttpStatus.NOT_FOUND,
"what????",
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
),
RequestWithResponse(
HttpStatus.INTERNAL_SERVER_ERROR,
"what????",
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
)
)
}
fun responseBodyWithMaxSeverity(severity: ReportService.Severity): String {
return when (severity) {
ReportService.Severity.INFO -> """
{
"patient": "PID",
"issues": [
{ "severity": "info", "message": "Info Message" }
]
}
"""
ReportService.Severity.WARNING -> """
{
"patient": "PID",
"issues": [
{ "severity": "info", "message": "Info Message" },
{ "severity": "warning", "message": "Warning Message" }
]
}
"""
ReportService.Severity.ERROR -> """
{
"patient": "PID",
"issues": [
{ "severity": "info", "message": "Info Message" },
{ "severity": "warning", "message": "Warning Message" },
{ "severity": "error", "message": "Error Message" }
]
}
"""
ReportService.Severity.FATAL -> """
{
"patient": "PID",
"issues": [
{ "severity": "info", "message": "Info Message" },
{ "severity": "warning", "message": "Warning Message" },
{ "severity": "error", "message": "Error Message" },
{ "severity": "fatal", "message": "Fatal Message" }
]
}
"""
}
}
}
}

405
src/test/kotlin/dev/dnpm/etl/processor/output/RestDipMtbFileSenderTest.kt
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@ -1,405 +0,0 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.output
import com.fasterxml.jackson.databind.ObjectMapper
import com.fasterxml.jackson.module.kotlin.KotlinModule
import de.ukw.ccc.bwhc.dto.*
import de.ukw.ccc.bwhc.dto.Patient
import dev.dnpm.etl.processor.CustomMediaType
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.config.AppConfigProperties
import dev.dnpm.etl.processor.config.AppConfiguration
import dev.dnpm.etl.processor.config.RestTargetProperties
import dev.dnpm.etl.processor.monitoring.ReportService
import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.pcvolkmer.mv64e.mtb.*
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Nested
import org.junit.jupiter.params.ParameterizedTest
import org.junit.jupiter.params.provider.MethodSource
import org.springframework.http.HttpHeaders
import org.springframework.http.HttpMethod
import org.springframework.http.HttpStatus
import org.springframework.http.MediaType
import org.springframework.retry.backoff.NoBackOffPolicy
import org.springframework.retry.policy.SimpleRetryPolicy
import org.springframework.retry.support.RetryTemplateBuilder
import org.springframework.test.web.client.ExpectedCount
import org.springframework.test.web.client.MockRestServiceServer
import org.springframework.test.web.client.match.MockRestRequestMatchers.*
import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus
import org.springframework.web.client.RestTemplate
class RestDipMtbFileSenderTest {
@Nested
inner class BwhcV1ContentRequest {
private lateinit var mockRestServiceServer: MockRestServiceServer
private lateinit var restMtbFileSender: RestMtbFileSender
private var reportService = ReportService(ObjectMapper().registerModule(KotlinModule.Builder().build()))
@BeforeEach
fun setup() {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false)
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.restMtbFileSender =
RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
}
@ParameterizedTest
@MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#mtbFileRequestWithResponseSource")
fun shouldReturnExpectedResponseForMtbFilePost(requestWithResponse: RequestWithResponse) {
this.mockRestServiceServer
.expect(method(HttpMethod.POST))
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient-record"))
.andExpect(header(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE))
.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1mtbFile))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
@ParameterizedTest
@MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#mtbFileRequestWithResponseSource")
fun shouldRetryOnMtbFileHttpRequestError(requestWithResponse: RequestWithResponse) {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false)
val retryTemplate = AppConfiguration().retryTemplate(AppConfigProperties("http://localhost:9000"))
retryTemplate.setBackOffPolicy(NoBackOffPolicy())
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.restMtbFileSender =
RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
val expectedCount = when (requestWithResponse.httpStatus) {
// OK - No Retry
HttpStatus.OK, HttpStatus.CREATED, HttpStatus.UNPROCESSABLE_ENTITY, HttpStatus.BAD_REQUEST -> ExpectedCount.max(
1
)
// Request failed - Retry max 3 times
else -> ExpectedCount.max(3)
}
this.mockRestServiceServer
.expect(expectedCount, method(HttpMethod.POST))
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient-record"))
.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1mtbFile))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
}
@Nested
inner class DnpmV2ContentRequest {
private lateinit var mockRestServiceServer: MockRestServiceServer
private lateinit var restMtbFileSender: RestMtbFileSender
private var reportService = ReportService(ObjectMapper().registerModule(KotlinModule.Builder().build()))
@BeforeEach
fun setup() {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false)
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.restMtbFileSender = RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
}
@ParameterizedTest
@MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#mtbFileRequestWithResponseSource")
fun shouldReturnExpectedResponseForDnpmV2MtbFilePost(requestWithResponse: RequestWithResponse) {
this.mockRestServiceServer
.expect(method(HttpMethod.POST))
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient-record"))
.andExpect(header(HttpHeaders.CONTENT_TYPE, CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE))
.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
}
@Nested
inner class DeleteRequest {
private lateinit var mockRestServiceServer: MockRestServiceServer
private lateinit var restMtbFileSender: RestMtbFileSender
private var reportService = ReportService(ObjectMapper().registerModule(KotlinModule.Builder().build()))
@BeforeEach
fun setup() {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false)
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.restMtbFileSender =
RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
}
@ParameterizedTest
@MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#deleteRequestWithResponseSource")
fun shouldReturnExpectedResponseForDelete(requestWithResponse: RequestWithResponse) {
this.mockRestServiceServer
.expect(method(HttpMethod.DELETE))
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient/${TEST_PATIENT_PSEUDONYM.value}"))
.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
@ParameterizedTest
@MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#deleteRequestWithResponseSource")
fun shouldRetryOnDeleteHttpRequestError(requestWithResponse: RequestWithResponse) {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false)
val retryTemplate = AppConfiguration().retryTemplate(AppConfigProperties("http://localhost:9000"))
retryTemplate.setBackOffPolicy(NoBackOffPolicy())
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.restMtbFileSender =
RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
val expectedCount = when (requestWithResponse.httpStatus) {
// OK - No Retry
HttpStatus.OK, HttpStatus.CREATED, HttpStatus.UNPROCESSABLE_ENTITY, HttpStatus.BAD_REQUEST -> ExpectedCount.max(
1
)
// Request failed - Retry max 3 times
else -> ExpectedCount.max(3)
}
this.mockRestServiceServer
.expect(expectedCount, method(HttpMethod.DELETE))
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient/${TEST_PATIENT_PSEUDONYM.value}"))
.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
}
companion object {
data class RequestWithResponse(
val httpStatus: HttpStatus,
val body: String,
val response: MtbFileSender.Response
)
val TEST_REQUEST_ID = RequestId("TestId")
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID")
val bwhcV1mtbFile: MtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.withId("PID")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.withConsent(
Consent.builder()
.withId("1")
.withStatus(Consent.Status.ACTIVE)
.withPatient("PID")
.build()
)
.withEpisode(
Episode.builder()
.withId("1")
.withPatient("PID")
.withPeriod(PeriodStart("2023-08-08"))
.build()
)
.build()
val dnpmV2MtbFile: Mtb = Mtb.builder()
.withPatient(
dev.pcvolkmer.mv64e.mtb.Patient.builder()
.withId("PID")
.withBirthDate("2000-08-08")
.withGender(CodingGender.builder().withCode(CodingGender.Code.MALE).build())
.build()
)
.withEpisodesOfCare(
listOf(
MTBEpisodeOfCare.builder()
.withId("1")
.withPatient(Reference("PID"))
.withPeriod(PeriodDate.builder().withStart("2023-08-08").build())
.build()
)
)
.build()
private const val ERROR_RESPONSE_BODY = "Sonstiger Fehler bei der Übertragung"
/**
* Synthetic http responses with related request status
* Also see: https://ibmi-intra.cs.uni-tuebingen.de/display/ZPM/bwHC+REST+API
*/
@JvmStatic
fun mtbFileRequestWithResponseSource(): Set<RequestWithResponse> {
return setOf(
RequestWithResponse(
HttpStatus.OK,
responseBodyWithMaxSeverity(ReportService.Severity.INFO),
MtbFileSender.Response(
RequestStatus.SUCCESS,
responseBodyWithMaxSeverity(ReportService.Severity.INFO)
)
),
RequestWithResponse(
HttpStatus.CREATED,
responseBodyWithMaxSeverity(ReportService.Severity.WARNING),
MtbFileSender.Response(RequestStatus.WARNING, responseBodyWithMaxSeverity(ReportService.Severity.WARNING))
),
RequestWithResponse(
HttpStatus.BAD_REQUEST,
responseBodyWithMaxSeverity(ReportService.Severity.ERROR),
MtbFileSender.Response(RequestStatus.ERROR, responseBodyWithMaxSeverity(ReportService.Severity.ERROR))
),
RequestWithResponse(
HttpStatus.UNPROCESSABLE_ENTITY,
responseBodyWithMaxSeverity(ReportService.Severity.ERROR),
MtbFileSender.Response(RequestStatus.ERROR, responseBodyWithMaxSeverity(ReportService.Severity.ERROR))
),
// Some more errors not mentioned in documentation
RequestWithResponse(
HttpStatus.NOT_FOUND,
ERROR_RESPONSE_BODY,
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
),
RequestWithResponse(
HttpStatus.INTERNAL_SERVER_ERROR,
ERROR_RESPONSE_BODY,
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
)
)
}
/**
* Synthetic http responses with related request status
* Also see: https://ibmi-intra.cs.uni-tuebingen.de/display/ZPM/bwHC+REST+API
*/
@JvmStatic
fun deleteRequestWithResponseSource(): Set<RequestWithResponse> {
return setOf(
RequestWithResponse(HttpStatus.OK, "", MtbFileSender.Response(RequestStatus.SUCCESS)),
// Some more errors not mentioned in documentation
RequestWithResponse(
HttpStatus.NOT_FOUND,
"what????",
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
),
RequestWithResponse(
HttpStatus.INTERNAL_SERVER_ERROR,
"what????",
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
)
)
}
fun responseBodyWithMaxSeverity(severity: ReportService.Severity): String {
return when (severity) {
ReportService.Severity.INFO -> """
{
"patient": "PID",
"issues": [
{ "severity": "info", "message": "Info Message" }
]
}
"""
ReportService.Severity.WARNING -> """
{
"patient": "PID",
"issues": [
{ "severity": "info", "message": "Info Message" },
{ "severity": "warning", "message": "Warning Message" }
]
}
"""
ReportService.Severity.ERROR -> """
{
"patient": "PID",
"issues": [
{ "severity": "info", "message": "Info Message" },
{ "severity": "warning", "message": "Warning Message" },
{ "severity": "error", "message": "Error Message" }
]
}
"""
ReportService.Severity.FATAL -> """
{
"patient": "PID",
"issues": [
{ "severity": "info", "message": "Info Message" },
{ "severity": "warning", "message": "Warning Message" },
{ "severity": "error", "message": "Error Message" },
{ "severity": "fatal", "message": "Fatal Message" }
]
}
"""
}
}
}
}

195
src/test/kotlin/dev/dnpm/etl/processor/output/RestMtbFileSenderTest.kt Normal file
View File

@ -0,0 +1,195 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.output
import de.ukw.ccc.bwhc.dto.*
import dev.dnpm.etl.processor.config.RestTargetProperties
import dev.dnpm.etl.processor.monitoring.RequestStatus
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.params.ParameterizedTest
import org.junit.jupiter.params.provider.MethodSource
import org.springframework.http.HttpMethod
import org.springframework.http.HttpStatus
import org.springframework.test.web.client.MockRestServiceServer
import org.springframework.test.web.client.match.MockRestRequestMatchers.method
import org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo
import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus
import org.springframework.web.client.RestTemplate
class RestMtbFileSenderTest {
private lateinit var mockRestServiceServer: MockRestServiceServer
private lateinit var restMtbFileSender: RestMtbFileSender
@BeforeEach
fun setup() {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile")
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.restMtbFileSender = RestMtbFileSender(restTemplate, restTargetProperties)
}
@ParameterizedTest
@MethodSource("deleteRequestWithResponseSource")
fun shouldReturnExpectedResponseForDelete(requestWithResponse: RequestWithResponse) {
this.mockRestServiceServer.expect {
method(HttpMethod.DELETE)
requestTo("/mtbfile")
}.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(MtbFileSender.DeleteRequest("TestID", "PID"))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
@ParameterizedTest
@MethodSource("mtbFileRequestWithResponseSource")
fun shouldReturnExpectedResponseForMtbFilePost(requestWithResponse: RequestWithResponse) {
this.mockRestServiceServer.expect {
method(HttpMethod.POST)
requestTo("/mtbfile")
}.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(MtbFileSender.MtbFileRequest("TestID", mtbFile))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
companion object {
data class RequestWithResponse(
val httpStatus: HttpStatus,
val body: String,
val response: MtbFileSender.Response
)
private val warningBody = """
{
"patient_id": "PID",
"issues": [
{ "severity": "warning", "message": "Something is not right" }
]
}
""".trimIndent()
private val errorBody = """
{
"patient_id": "PID",
"issues": [
{ "severity": "error", "message": "Something is very bad" }
]
}
""".trimIndent()
val mtbFile: MtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.withId("PID")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.withConsent(
Consent.builder()
.withId("1")
.withStatus(Consent.Status.ACTIVE)
.withPatient("PID")
.build()
)
.withEpisode(
Episode.builder()
.withId("1")
.withPatient("PID")
.withPeriod(PeriodStart("2023-08-08"))
.build()
)
.build()
private const val ERROR_RESPONSE_BODY = "Sonstiger Fehler bei der Übertragung"
/**
* Synthetic http responses with related request status
* Also see: https://ibmi-intra.cs.uni-tuebingen.de/display/ZPM/bwHC+REST+API
*/
@JvmStatic
fun mtbFileRequestWithResponseSource(): Set<RequestWithResponse> {
return setOf(
RequestWithResponse(HttpStatus.OK, "{}", MtbFileSender.Response(RequestStatus.SUCCESS, "{}")),
RequestWithResponse(
HttpStatus.CREATED,
warningBody,
MtbFileSender.Response(RequestStatus.WARNING, warningBody)
),
RequestWithResponse(
HttpStatus.BAD_REQUEST,
"??",
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
),
RequestWithResponse(
HttpStatus.UNPROCESSABLE_ENTITY,
errorBody,
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
),
// Some more errors not mentioned in documentation
RequestWithResponse(
HttpStatus.NOT_FOUND,
"what????",
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
),
RequestWithResponse(
HttpStatus.INTERNAL_SERVER_ERROR,
"what????",
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
)
)
}
/**
* Synthetic http responses with related request status
* Also see: https://ibmi-intra.cs.uni-tuebingen.de/display/ZPM/bwHC+REST+API
*/
@JvmStatic
fun deleteRequestWithResponseSource(): Set<RequestWithResponse> {
return setOf(
RequestWithResponse(HttpStatus.OK, "", MtbFileSender.Response(RequestStatus.SUCCESS)),
// Some more errors not mentioned in documentation
RequestWithResponse(
HttpStatus.NOT_FOUND,
"what????",
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
),
RequestWithResponse(
HttpStatus.INTERNAL_SERVER_ERROR,
"what????",
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
)
)
}
}
}

231
src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt
View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2023 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
@ -20,32 +20,23 @@
package dev.dnpm.etl.processor.pseudonym
import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.*
import dev.pcvolkmer.mv64e.mtb.MTBEpisodeOfCare
import dev.pcvolkmer.mv64e.mtb.Mtb
import dev.pcvolkmer.mv64e.mtb.PeriodDate
import dev.pcvolkmer.mv64e.mtb.Reference
import de.ukw.ccc.bwhc.dto.MtbFile
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.Nested
import org.junit.jupiter.api.Test
import org.junit.jupiter.api.assertThrows
import org.junit.jupiter.api.extension.ExtendWith
import org.mockito.ArgumentMatchers
import org.mockito.Mock
import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.anyValueClass
import org.mockito.kotlin.doAnswer
import org.mockito.kotlin.whenever
import org.springframework.core.io.ClassPathResource
const val FAKE_MTB_FILE_PATH = "fake_MTBFile.json"
const val CLEAN_PATIENT_ID = "5dad2f0b-49c6-47d8-a952-7b9e9e0f7549"
@ExtendWith(MockitoExtension::class)
class ExtensionsTest {
@Nested
inner class UsingBwhcDatamodel {
val FAKE_MTB_FILE_PATH = "fake_MTBFile.json"
val CLEAN_PATIENT_ID = "5dad2f0b-49c6-47d8-a952-7b9e9e0f7549"
private fun fakeMtbFile(): MtbFile {
val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
return ObjectMapper().readValue(mtbFile, MtbFile::class.java)
@ -60,7 +51,7 @@ class ExtensionsTest {
doAnswer {
it.arguments[0]
"PSEUDO-ID"
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
}.whenever(pseudonymizeService).patientPseudonym(ArgumentMatchers.anyString())
val mtbFile = fakeMtbFile()
@ -70,212 +61,4 @@ class ExtensionsTest {
assertThat(mtbFile.serialized()).doesNotContain(CLEAN_PATIENT_ID)
}
@Test
fun shouldNotContainAnyUuidAfterRehashingOfIds(@Mock pseudonymizeService: PseudonymizeService) {
doAnswer {
it.arguments[0]
"PSEUDO-ID"
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
doAnswer {
"TESTDOMAIN"
}.whenever(pseudonymizeService).prefix()
val mtbFile = fakeMtbFile()
mtbFile.pseudonymizeWith(pseudonymizeService)
mtbFile.anonymizeContentWith(pseudonymizeService)
val pattern = "\"[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}\"".toRegex().toPattern()
val matcher = pattern.matcher(mtbFile.serialized())
assertThrows<IllegalStateException> {
matcher.find()
matcher.group()
}.also {
assertThat(it.message).isEqualTo("No match found")
}
}
@Test
fun shouldRehashIdsWithPrefix(@Mock pseudonymizeService: PseudonymizeService) {
doAnswer {
it.arguments[0]
"PSEUDO-ID"
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
doAnswer {
"TESTDOMAIN"
}.whenever(pseudonymizeService).prefix()
val mtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.withId("1")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.withConsent(
Consent.builder()
.withId("1")
.withStatus(Consent.Status.ACTIVE)
.withPatient("123")
.build()
)
.withEpisode(
Episode.builder()
.withId("1")
.withPatient("1")
.withPeriod(PeriodStart("2023-08-08"))
.build()
)
.build()
mtbFile.pseudonymizeWith(pseudonymizeService)
mtbFile.anonymizeContentWith(pseudonymizeService)
assertThat(mtbFile.episode.id)
// TESTDOMAIN<sha256(TESTDOMAIN-1)[0-41]>
.isEqualTo("TESTDOMAIN44e20a53bbbf9f3ae39626d05df7014dcd77d6098")
}
@Test
fun shouldNotThrowExceptionOnNullValues(@Mock pseudonymizeService: PseudonymizeService) {
doAnswer {
it.arguments[0]
"PSEUDO-ID"
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
doAnswer {
"TESTDOMAIN"
}.whenever(pseudonymizeService).prefix()
val mtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.withId("1")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.withConsent(
Consent.builder()
.withId("1")
.withStatus(Consent.Status.ACTIVE)
.withPatient("123")
.build()
)
.withEpisode(
Episode.builder()
.withId("1")
.withPatient("1")
.withPeriod(PeriodStart("2023-08-08"))
.build()
)
.withClaims(null)
.withDiagnoses(null)
.withCarePlans(null)
.withClaimResponses(null)
.withEcogStatus(null)
.withFamilyMemberDiagnoses(null)
.withGeneticCounsellingRequests(null)
.withHistologyReevaluationRequests(null)
.withHistologyReports(null)
.withLastGuidelineTherapies(null)
.withMolecularPathologyFindings(null)
.withMolecularTherapies(null)
.withNgsReports(null)
.withPreviousGuidelineTherapies(null)
.withRebiopsyRequests(null)
.withRecommendations(null)
.withResponses(null)
.withStudyInclusionRequests(null)
.withSpecimens(null)
.build()
mtbFile.pseudonymizeWith(pseudonymizeService)
mtbFile.anonymizeContentWith(pseudonymizeService)
assertThat(mtbFile.episode.id).isNotNull()
}
}
@Nested
inner class UsingDnpmV2Datamodel {
val FAKE_MTB_FILE_PATH = "mv64e-mtb-fake-patient.json"
val CLEAN_PATIENT_ID = "63f8fd7b-8127-4f3c-8843-aa9199e21c29"
private fun fakeMtbFile(): Mtb {
val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
return ObjectMapper().readValue(mtbFile, Mtb::class.java)
}
private fun Mtb.serialized(): String {
return ObjectMapper().writeValueAsString(this)
}
@Test
fun shouldNotContainCleanPatientId(@Mock pseudonymizeService: PseudonymizeService) {
doAnswer {
it.arguments[0]
"PSEUDO-ID"
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
val mtbFile = fakeMtbFile()
mtbFile.pseudonymizeWith(pseudonymizeService)
assertThat(mtbFile.patient.id).isEqualTo("PSEUDO-ID")
assertThat(mtbFile.serialized()).doesNotContain(CLEAN_PATIENT_ID)
}
@Test
fun shouldNotThrowExceptionOnNullValues(@Mock pseudonymizeService: PseudonymizeService) {
doAnswer {
it.arguments[0]
"PSEUDO-ID"
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
doAnswer {
"TESTDOMAIN"
}.whenever(pseudonymizeService).prefix()
val mtbFile = Mtb.builder()
.withPatient(
dev.pcvolkmer.mv64e.mtb.Patient.builder()
.withId("1")
.withBirthDate("2000-08-08")
.withGender(null)
.build()
)
.withEpisodesOfCare(
listOf(
MTBEpisodeOfCare.builder()
.withId("1")
.withPatient(Reference("1"))
.withPeriod(PeriodDate.builder().withStart("2023-08-08").build())
.build()
)
)
.withClaims(null)
.withDiagnoses(null)
.withCarePlans(null)
.withClaimResponses(null)
.withHistologyReports(null)
.withNgsReports(null)
.withResponses(null)
.withSpecimens(null)
.build()
mtbFile.pseudonymizeWith(pseudonymizeService)
mtbFile.anonymizeContentWith(pseudonymizeService)
assertThat(mtbFile.episodesOfCare).hasSize(1)
assertThat(mtbFile.episodesOfCare.map { it.id }).isNotNull
}
}
}

153
src/test/kotlin/dev/dnpm/etl/processor/security/TokenServiceTest.kt
View File

@ -1,153 +0,0 @@
/*
* 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.security
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.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<Token>()
verify(tokenRepository, times(1)).save(captor.capture())
assertThat(actual).satisfies(Consumer { assertThat(it.isSuccess).isTrue() })
assertThat(captor.firstValue).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<String>()
verify(userDetailsManager, times(1)).deleteUser(stringCaptor.capture())
assertThat(stringCaptor.firstValue).isEqualTo("testtoken")
val tokenCaptor = argumentCaptor<Token>()
verify(tokenRepository, times(1)).delete(tokenCaptor.capture())
assertThat(tokenCaptor.firstValue.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())
}
}

202
src/test/kotlin/dev/dnpm/etl/processor/security/UserRoleServiceTest.kt
View File

@ -1,202 +0,0 @@
/*
* 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.security
import org.assertj.core.api.Assertions.assertThat
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.mockito.Mock
import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.*
import org.springframework.security.core.session.SessionInformation
import org.springframework.security.core.session.SessionRegistry
import org.springframework.security.oauth2.core.oidc.OidcIdToken
import org.springframework.security.oauth2.core.oidc.user.DefaultOidcUser
import org.springframework.security.oauth2.core.oidc.user.OidcUser
import java.time.Instant
import java.util.*
@ExtendWith(MockitoExtension::class)
class UserRoleServiceTest {
private lateinit var userRoleRepository: UserRoleRepository
private lateinit var sessionRegistry: SessionRegistry
private lateinit var userRoleService: UserRoleService
@BeforeEach
fun setup(
@Mock userRoleRepository: UserRoleRepository,
@Mock sessionRegistry: SessionRegistry
) {
this.userRoleRepository = userRoleRepository
this.sessionRegistry = sessionRegistry
this.userRoleService = UserRoleService(userRoleRepository, sessionRegistry)
}
@Test
fun shouldDelegateFindAllToRepository() {
userRoleService.findAll()
verify(userRoleRepository, times(1)).findAll()
}
@Nested
inner class WithExistingUserRole {
@BeforeEach
fun setup() {
doAnswer { invocation ->
Optional.of(
UserRole(invocation.getArgument(0), "patrick.tester", Role.USER)
)
}.whenever(userRoleRepository).findById(any<Long>())
doAnswer { _ ->
listOf(
dummyPrincipal()
)
}.whenever(sessionRegistry).allPrincipals
}
@Test
fun shouldUpdateUserRole() {
userRoleService.updateUserRole(1, Role.ADMIN)
val userRoleCaptor = argumentCaptor<UserRole>()
verify(userRoleRepository, times(1)).save(userRoleCaptor.capture())
assertThat(userRoleCaptor.firstValue.id).isEqualTo(1L)
assertThat(userRoleCaptor.firstValue.role).isEqualTo(Role.ADMIN)
}
@Test
fun shouldExpireSessionOnUpdate() {
val dummySessions = dummySessions()
whenever(sessionRegistry.getAllSessions(any(), any<Boolean>())).thenReturn(
dummySessions
)
assertThat(dummySessions.filter { it.isExpired }).hasSize(0)
userRoleService.updateUserRole(1, Role.ADMIN)
verify(sessionRegistry, times(1)).getAllSessions(any<OidcUser>(), any<Boolean>())
assertThat(dummySessions.filter { it.isExpired }).hasSize(2)
}
@Test
fun shouldDeleteUserRole() {
userRoleService.deleteUserRole(1)
val userRoleCaptor = argumentCaptor<UserRole>()
verify(userRoleRepository, times(1)).delete(userRoleCaptor.capture())
assertThat(userRoleCaptor.firstValue.id).isEqualTo(1L)
assertThat(userRoleCaptor.firstValue.role).isEqualTo(Role.USER)
}
@Test
fun shouldExpireSessionOnDelete() {
val dummySessions = dummySessions()
whenever(sessionRegistry.getAllSessions(any(), any<Boolean>())).thenReturn(
dummySessions
)
assertThat(dummySessions.filter { it.isExpired }).hasSize(0)
userRoleService.deleteUserRole(1)
verify(sessionRegistry, times(1)).getAllSessions(any<OidcUser>(), any<Boolean>())
assertThat(dummySessions.filter { it.isExpired }).hasSize(2)
}
}
@Nested
inner class WithoutExistingUserRole {
@BeforeEach
fun setup() {
doAnswer { _ ->
Optional.empty<UserRole>()
}.whenever(userRoleRepository).findById(any<Long>())
}
@Test
fun shouldNotUpdateUserRole() {
userRoleService.updateUserRole(1, Role.ADMIN)
verify(userRoleRepository, never()).save(any<UserRole>())
}
@Test
fun shouldNotExpireSessionOnUpdate() {
userRoleService.updateUserRole(1, Role.ADMIN)
verify(sessionRegistry, never()).getAllSessions(any<OidcUser>(), any<Boolean>())
}
@Test
fun shouldNotDeleteUserRole() {
userRoleService.deleteUserRole(1)
verify(userRoleRepository, never()).delete(any<UserRole>())
}
@Test
fun shouldNotExpireSessionOnDelete() {
userRoleService.deleteUserRole(1)
verify(sessionRegistry, never()).getAllSessions(any<OidcUser>(), any<Boolean>())
}
}
companion object {
private fun dummyPrincipal() = DefaultOidcUser(
listOf(),
OidcIdToken(
"anytokenvalue",
Instant.now(),
Instant.now().plusSeconds(10),
mapOf("sub" to "testsub", "preferred_username" to "patrick.tester")
)
)
private fun dummySessions() = listOf(
SessionInformation(
dummyPrincipal(),
"SESSIONID1",
Date.from(Instant.now()),
),
SessionInformation(
dummyPrincipal(),
"SESSIONID2",
Date.from(Instant.now()),
)
)
}
}

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