1
0
mirror of https://github.com/pcvolkmer/etl-processor.git synced 2025-07-01 14:12:55 +00:00

88 Commits

Author SHA1 Message Date
6806c4fd69 build: bump version 2024-03-04 13:21:07 +01:00
b2016df852 style: fix some style issued 2024-03-04 13:17:57 +01:00
b332f3c5ff Merge pull request #50 from CCC-MF/issue_49
Administrative Rechte für OIDC-Benutzer
2024-03-04 12:54:31 +01:00
9eb65788e1 style: change login/logout style 2024-03-04 12:50:07 +01:00
9392bcadc9 feat: add admin role assignment 2024-03-04 10:12:12 +01:00
a008641192 fix: remove maxSessionsPreventsLogin 2024-03-01 15:07:23 +01:00
5928d52237 Merge pull request #48 from CCC-MF/issue_36
Freigabe und Berechtigung für OIDC-Benutzer
2024-03-01 14:09:06 +01:00
1eb40b40c9 docs: add documentation for user roles 2024-03-01 14:02:50 +01:00
feb9f2430c feat: add config page for user role assignment 2024-03-01 13:51:06 +01:00
200c5338ea feat: add default new user role config option 2024-03-01 09:34:51 +01:00
5c15ad4518 feat: add user role database table and role-based permissions 2024-03-01 09:30:07 +01:00
0b6decf88d Merge pull request #47 from CCC-MF/issue_43
feat: add config option to deactivate duplication check
2024-03-01 07:33:16 +01:00
cfdf41d550 feat: add config option to deactivate duplication check 2024-03-01 07:27:58 +01:00
45c65d53ce docs: add information about Kafka input topics 2024-02-29 13:55:14 +01:00
4568f491f5 Merge pull request #46 from CCC-MF/issue_42_kafka
Dateneingang über Apache-Kafka als Alternative zu HTTP-Request
2024-02-29 13:15:57 +01:00
952ad8c0cf test: add test for incoming kafka message processing 2024-02-29 12:49:06 +01:00
3e45bf8494 feat: implement KafkaInputListener 2024-02-29 09:19:32 +01:00
46ddaf10f7 Merge pull request #45 from CCC-MF/issue_34
Verwendung einer applikationsweiten Retry-Konfiguration
2024-02-29 08:57:00 +01:00
408b121f26 test: add test for max retry attempts 2024-02-29 08:47:17 +01:00
61e5273158 feat: add max-retry-attempts config option 2024-02-29 08:29:26 +01:00
50b8f7bbd4 feat: use global RetryTemplate 2024-02-29 08:26:54 +01:00
25f286f73b chore: update spring boot to version 3.2.3 2024-02-25 12:28:34 +01:00
50a6d66718 feat: new kafka config due to kafka input 2024-02-19 17:06:02 +01:00
f5c80f6d81 Merge pull request #41 from CCC-MF/issue_39
feat: add cache-control headers for static resources
2024-02-19 09:08:19 +01:00
7659939d3c Merge pull request #40 from CCC-MF/issue_37
build: use JDK 21 and update gradle version
2024-02-19 09:02:40 +01:00
f58d4a76cf build: use JDK 21 within workflows 2024-02-19 08:59:42 +01:00
c2dd450579 feat: add cache-control headers for static resources 2024-02-19 08:54:38 +01:00
a1b62ad754 build: use JDK 21 and update gradle version 2024-02-19 08:53:21 +01:00
59d8744c84 refactor: move mtb file controller into package input 2024-02-17 14:58:24 +01:00
d2a6ec17ea docs: add ports to example docker compose file 2024-02-16 13:00:22 +01:00
550403cc9f build: bump snapshot version 2024-02-15 13:41:11 +01:00
d3a4500568 Merge pull request #35 from CCC-MF/issue_33
Deprecate usage of ...SSL_CA_LOCATION config param
2024-02-09 08:19:07 +01:00
2e4fee97a8 feat: Deprecate usage of ...SSL_CA_LOCATION config param 2024-02-09 08:15:01 +01:00
5355eee05c docs: mark gPAS ssl config param as deprecated 2024-02-08 10:05:06 +01:00
3e22000541 Merge pull request #32 from CCC-MF/issue_31
build: update used actions
2024-02-05 08:18:26 +01:00
8c319197d0 build: update used actions 2024-02-05 08:12:28 +01:00
a31d2b4bcc build: bump version 2024-02-05 07:47:17 +01:00
67d5fb4c67 docs: mention quality report page access restriction 2024-02-05 07:29:47 +01:00
329be65d1a feat: forbid access to report if not logged in 2024-02-05 07:18:31 +01:00
91fe3d1c23 docs: add example login image 2024-02-01 18:30:02 +01:00
f4b86ce2ea docs: add OIDC configuration options to README.md 2024-02-01 18:28:33 +01:00
19d0daa442 docs: move README.md to bindings folder 2024-02-01 17:00:16 +01:00
cc9811d11d docs: move README.md to bindings folder 2024-02-01 16:59:23 +01:00
8ce5b06823 fix: make security config optional for login controller 2024-02-01 16:54:41 +01:00
3cc34fb30b feat: usage of CA certificate files within image/container 2024-02-01 16:45:22 +01:00
17e04a3f89 feat: add basic support for OIDC login 2024-01-31 15:57:16 +01:00
f71a775e12 chore: update spring boot to version 3.2.2 2024-01-23 01:04:35 +01:00
45c83e943b docs: Add information about other reference IDs anonymization 2024-01-22 10:33:27 +01:00
6dcbfde62e test: add tests for TokenService 2024-01-21 14:13:09 +01:00
4cdc419478 test: add test to ensure redirect of not logged in 2024-01-20 19:35:40 +01:00
90b529adb4 refactor: move test class to related package 2024-01-20 19:16:52 +01:00
a3bc60986b test: add security related tests for MtbFileRestController 2024-01-19 14:11:03 +01:00
f5df0b5d22 test: add tests to ensure TokenService is present if required 2024-01-19 13:10:36 +01:00
972ac745e9 fix: add missing token screenshot 2024-01-18 14:44:44 +01:00
358373cf70 Merge pull request #30 from CCC-MF/issue_29
Issue #29: Unterstützung für Endpoint-Tokens
2024-01-18 14:29:52 +01:00
27a62321fa docs: add documentation about token usage 2024-01-18 14:26:09 +01:00
30cf0fd22e feat #29: add initial support for mtbfile api tokens 2024-01-18 14:13:15 +01:00
531a8589db feat: push connection available state to client 2024-01-17 14:32:42 +01:00
fa89a64ddd Merge pull request #28 from CCC-MF/issue_24
feat #24: use htmx to refresh connection status every 20s
2024-01-17 12:35:35 +01:00
45ad5e8827 feat #24: use htmx to refresh connection status every 20s 2024-01-17 12:27:44 +01:00
c4eb4d0fe2 feat #25: add link to requests related to patient pseudonyme (#27) 2024-01-15 10:26:56 +01:00
4bc69a353c Merge pull request #26 from CCC-MF/issue_23
feat #23: add reload button to display on new request
2024-01-15 10:15:36 +01:00
9d30f750f7 feat #23: add reload button to display on new request 2024-01-15 09:17:38 +01:00
a1a252d5a9 build: use webjars for JS dependencies for now 2024-01-15 07:18:14 +01:00
568942bfe5 fix: typo in README.md 2024-01-14 17:31:30 +01:00
15f0432553 test: ensure configured generator bean is created 2024-01-12 21:27:55 +01:00
113bf2dd2e test: add pseudonymize generator property and default to tests 2024-01-12 19:59:01 +01:00
7ac151202a refactor: Use config new pseudonym generator config param
This deprecates the old param:
* `APP_PSEUDONYMIZER`: deprecated
* `APP_PSEUDONYM_GENERATOR`: has precedence
2024-01-12 16:55:18 +01:00
5d9d47c2df fix: append css class, not css style 2024-01-12 13:49:54 +01:00
585468314c feat: add admin credentials to deploy folder 2024-01-11 16:34:03 +01:00
441bff3783 feat: use password with encoding prefix 2024-01-11 15:00:26 +01:00
21959c1698 Merge pull request #21 from CCC-MF/feat_18
feat #18: initial support for authentication
2024-01-11 13:32:37 +01:00
8a11e6e85b feat #18: initial support for authentication 2024-01-11 13:29:33 +01:00
5579ad1453 docs: update documentation 2024-01-11 12:11:38 +01:00
c2026bdd07 feat: show configured endpoints 2024-01-11 08:51:30 +01:00
de6faecb02 refactor: rename css style 2024-01-11 08:50:51 +01:00
3be8bc53ff feat: add graphic to show connection state 2024-01-10 11:16:34 +01:00
fad2f33fd6 refactor: use event listener to listen for page load event 2024-01-10 09:22:51 +01:00
d88e2973da feat: add paginator to request page 2024-01-10 09:12:02 +01:00
af767e4ea6 chore: update images 2024-01-10 07:44:10 +01:00
f98c970348 chore: layout and style changes 2024-01-09 18:09:44 +01:00
75872a149f docs: add some more information within README.doc 2024-01-05 11:53:51 +01:00
e24ba430a5 feat #20: add server forward headers config
closes #20
2024-01-05 11:43:58 +01:00
08914a6f86 docs: link simple docker-compose.yml example within README.md 2024-01-04 13:29:49 +01:00
104f50afcb docs: add docker-compose.yml example 2024-01-04 13:14:10 +01:00
0083e75940 Merge pull request #19 from CCC-MF/feat_17
feat #17: add request retry
2024-01-04 11:56:40 +01:00
c892ff2461 test #17: add tests for retry 2024-01-04 11:50:39 +01:00
4a9cffbaa5 feat #17: initial support for request retry 2024-01-04 07:33:03 +01:00
70 changed files with 2870 additions and 442 deletions

View File

@ -1,4 +1,4 @@
name: "Run build and deploy"
name: 'Run build and deploy'
on:
release:
@ -8,17 +8,17 @@ jobs:
docker:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/setup-java@v3
- uses: actions/checkout@v4
- uses: actions/setup-java@v4
with:
java-version: '17'
java-version: '21'
distribution: 'temurin'
- name: Setup Gradle
uses: gradle/gradle-build-action@v2.4.2
uses: gradle/actions/setup-gradle@v3
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Login to Docker Hub
uses: docker/login-action@v2

View File

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

2
.gitignore vendored
View File

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

228
README.md
View File

@ -2,29 +2,38 @@
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 HTTP/REST-Anfragen aus dem Onkostar-Plugin **[onkostar-plugin-dnpmexport](https://github.com/CCC-MF/onkostar-plugin-dnpmexport)**.
Diese Anwendung erlaubt das Entgegennehmen von HTTP/REST-Anfragen aus dem Onkostar-Plugin **[onkostar-plugin-dnpmexport](https://github.com/CCC-MF/onkostar-plugin-dnpmexport)**.
Der Inhalt einer Anfrage, wenn ein bwHC-MTBFile, wird pseudonymisiert und auf Duplikate geprüft.
Duplikate werden verworfen, Änderungen werden weitergeleitet.
Löschanfragen werden immer als Löschanfrage an das bwHC-backend weitergeleitet.
Zudem ist eine minimalistische Weboberfläche integriert, die einen Einblick in den aktuellen Zustand der Anwendung gewährt.
![Modell DNPM-ETL-Strecke](docs/etl.png)
#### HTTP/REST-Konfiguration
### Duplikaterkennung
Die Erkennung von Duplikaten ist normalerweise immer aktiv, kann jedoch über den Konfigurationsparameter
`APP_DUPLICATION_DETECTION=false` deaktiviert werden.
### Datenübermittlung über HTTP/REST
Anfragen werden, wenn nicht als Duplikat behandelt, nach der Pseudonymisierung direkt an das bwHC-Backend gesendet.
#### Konfiguration für Apache Kafka
### Datenübermittlung mit 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
## Pseudonymisierung der Patienten-ID
## Konfiguration
### 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.
@ -32,24 +41,124 @@ Ist diese nicht gesetzt. wird intern eine Anonymisierung der Patienten-ID vorgen
* `APP_PSEUDONYMIZE_PREFIX`: Standortbezogenes Prefix - `UNKNOWN`, wenn nicht gesetzt
* `APP_PSEUDONYMIZE_GENERATOR`: `BUILDIN` oder `GPAS` - `BUILDIN`, wenn nicht gesetzt
### Eingebaute Pseudonymisierung
**Hinweise**:
Wurde keine oder die Verwendung der eingebauten Pseudonymisierung konfiguriert, so wird für die Patienten-ID der
* Der alte Konfigurationsparameter `APP_PSEUDONYMIZER` mit den Werten `GPAS` oder `BUILDIN` sollte nicht
mehr verwendet werden.
* Die Pseudonymisierung erfolgt im ETL-Prozessor nur für die Patienten-ID.
Andere Referenz-IDs werden nicht anonymisiert.
Dies erfolgt bei Nutzung von **[onkostar-plugin-dnpmexport](https://github.com/CCC-MF/onkostar-plugin-dnpmexport)**
bereits im Plugin selbst.
#### Eingebaute Anonymisierung
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 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.
* ~~`APP_PSEUDONYMIZE_GPAS_SSLCALOCATION`~~: **Veraltet** - Root Zertifikat für gPas, falls es dediziert hinzugefügt werden muss.
## Transformation von Werten
Der Konfigurationsparameter `APP_PSEUDONYMIZE_GPAS_SSLCALOCATION` sollte nicht mehr verwendet werden und wird in einer kommenden Version entfernt.
Stattdessen sollte das Root Zertifikat wie unter [_Integration eines eigenen Root CA Zertifikats_](#integration-eines-eigenen-root-ca-zertifikats) beschrieben eingebunden werden.
### 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-Prefixes 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 des bwHC-Backends 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 können den Endpunkt für das Onkostar-Plugin **[onkostar-plugin-dnpmexport](https://github.com/CCC-MF/onkostar-plugin-dnpmexport)** wie folgt konfigurieren:
```
https://testonkostar:MTg1NTL...NGU4@etl.example.com/mtbfile
```
Ist die Verwendung von Tokens aktiv, werden Anfragen ohne die Angabe der Token-Information abgelehnt.
### Transformation von Werten
In Onkostar kann es vorkommen, dass ein Wert eines Merkmalskatalogs an einem Standort angepasst wurde und dadurch nicht dem Wert entspricht,
der vom bwHC-Backend akzeptiert wird.
@ -57,31 +166,33 @@ 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
### Mögliche Endpunkte zur Datenübermittlung
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 das bwHC-Backend gesendet wird:
* `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_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_OUTPUT_TOPIC`: Zu verwendendes Topic zum Versenden von Anfragen.
Ersetzt in einer kommenden Version `APP_KAFKA_TOPIC`.
* `APP_KAFKA_OUTPUT_RESPONSE_TOPIC`: Topic mit Antworten über den Erfolg des Versendens. Standardwert: `APP_KAFKA_TOPIC` mit Anhang "_response".
Ersetzt in einer kommenden Version `APP_KAFKA_RESPONSE_TOPIC`.
* `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
@ -92,7 +203,9 @@ Weitere Einstellungen können über die Parameter von Spring Kafka konfiguriert
Lässt sich keine Verbindung zu dem bwHC-Backend aufbauen, wird eine Rückantwort mit Status-Code `900` erwartet, welchen es
für HTTP nicht gibt.
#### Retention Time
Wird die Umgebungsvariable `APP_KAFKA_INPUT_TOPIC` gesetzt, kann eine Nachricht auch über dieses Kafka-Topic an den ETL-Prozessor übermittelt werden.
##### 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.
@ -105,7 +218,7 @@ 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.
@ -141,8 +254,37 @@ Diese Anwendung ist auch als Docker-Image verfügbar: https://github.com/CCC-MF/
./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 Conatiner:*
*Ausführen als Docker Container:*
```bash
cd ./deploy
@ -154,6 +296,50 @@ 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-Prefix
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.

5
bindings/README.md Normal file
View File

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

View File

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

View File

@ -4,24 +4,27 @@ import org.springframework.boot.gradle.tasks.bundling.BootBuildImage
plugins {
war
id("org.springframework.boot") version "3.2.1"
id("org.springframework.boot") version "3.2.3"
id("io.spring.dependency-management") version "1.1.4"
kotlin("jvm") version "1.9.22"
kotlin("plugin.spring") version "1.9.22"
}
group = "de.ukw.ccc"
version = "0.4.0"
version = "0.8.0"
var versions = mapOf(
"bwhc-dto-java" to "0.2.0",
"hapi-fhir" to "6.10.2",
"httpclient5" to "5.2.1",
"mockito-kotlin" to "5.2.1"
"mockito-kotlin" to "5.2.1",
// Webjars
"echarts" to "5.4.3",
"htmx.org" to "1.9.10"
)
java {
sourceCompatibility = JavaVersion.VERSION_17
sourceCompatibility = JavaVersion.VERSION_21
}
sourceSets {
@ -54,6 +57,9 @@ 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-mysql")
@ -64,6 +70,9 @@ dependencies {
implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${versions["hapi-fhir"]}")
implementation("org.apache.httpcomponents.client5:httpclient5:${versions["httpclient5"]}")
implementation("com.jayway.jsonpath:json-path")
implementation("org.webjars:webjars-locator:0.50")
implementation("org.webjars.npm:echarts:${versions["echarts"]}")
implementation("org.webjars.npm:htmx.org:${versions["htmx.org"]}")
runtimeOnly("org.mariadb.jdbc:mariadb-java-client")
runtimeOnly("org.postgresql:postgresql")
developmentOnly("org.springframework.boot:spring-boot-devtools")
@ -71,6 +80,7 @@ dependencies {
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:${versions["mockito-kotlin"]}")
integrationTestImplementation("org.testcontainers:junit-jupiter")
@ -80,7 +90,7 @@ dependencies {
tasks.withType<KotlinCompile> {
kotlinOptions {
freeCompilerArgs += "-Xjsr305=strict"
jvmTarget = "17"
jvmTarget = "21"
}
}
@ -103,7 +113,14 @@ task<Test>("integrationTest") {
tasks.named<BootBuildImage>("bootBuildImage") {
imageName.set("ghcr.io/ccc-mf/etl-processor")
// Binding for CA Certs
bindings.set(listOf(
"$rootDir/bindings/ca-certificates/:/platform/bindings/ca-certificates"
))
environment.set(environment.get() + mapOf(
// Enable this line to embed CA Certs into image on build time
//"BP_EMBED_CERTS" to "true",
"BP_OCI_SOURCE" to "https://github.com/CCC-MF/etl-processor",
"BP_OCI_LICENSES" to "AGPLv3",
"BP_OCI_DESCRIPTION" to "ETL Processor for bwHC MTB files"

View File

@ -18,6 +18,8 @@ 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_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}

View File

@ -2,6 +2,10 @@
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
docs/docker-compose.yml Normal file
View File

@ -0,0 +1,28 @@
### 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

BIN
docs/login.png Normal file

Binary file not shown.

After

Width:  |  Height:  |  Size: 9.2 KiB

BIN
docs/tokens.png Normal file

Binary file not shown.

After

Width:  |  Height:  |  Size: 30 KiB

BIN
docs/userroles.png Normal file

Binary file not shown.

After

Width:  |  Height:  |  Size: 16 KiB

View File

@ -1,6 +1,6 @@
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
distributionUrl=https\://services.gradle.org/distributions/gradle-8.1.1-bin.zip
distributionUrl=https\://services.gradle.org/distributions/gradle-8.6-bin.zip
networkTimeout=10000
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists

View File

@ -48,7 +48,8 @@ import org.testcontainers.junit.jupiter.Testcontainers
@MockBean(MtbFileSender::class)
@TestPropertySource(
properties = [
"app.rest.uri=http://example.com"
"app.rest.uri=http://example.com",
"app.pseudonymize.generator=buildin"
]
)
class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
@ -64,6 +65,7 @@ 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",

View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
@ -20,9 +20,15 @@
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.services.RequestProcessor
import dev.dnpm.etl.processor.services.TokenRepository
import dev.dnpm.etl.processor.services.TokenService
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.Nested
import org.junit.jupiter.api.Test
@ -31,13 +37,28 @@ 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.boot.test.mock.mockito.MockBeans
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
@SpringBootTest
@ContextConfiguration(classes = [AppConfiguration::class, KafkaAutoConfiguration::class, AppKafkaConfiguration::class, AppRestConfiguration::class])
@ContextConfiguration(classes = [
AppConfiguration::class,
AppSecurityConfiguration::class,
KafkaAutoConfiguration::class,
AppKafkaConfiguration::class,
AppRestConfiguration::class
])
@MockBean(ObjectMapper::class)
@TestPropertySource(
properties = [
"app.pseudonymize.generator=BUILDIN",
]
)
class AppConfigurationTest {
@Nested
@ -60,8 +81,8 @@ class AppConfigurationTest {
@TestPropertySource(
properties = [
"app.kafka.servers=localhost:9092",
"app.kafka.topic=test",
"app.kafka.response-topic=test-response",
"app.kafka.output-topic=test",
"app.kafka.output-response-topic=test-response",
"app.kafka.group-id=test"
]
)
@ -81,8 +102,8 @@ class AppConfigurationTest {
properties = [
"app.rest.uri=http://localhost:9000",
"app.kafka.servers=localhost:9092",
"app.kafka.topic=test",
"app.kafka.response-topic=test-response",
"app.kafka.output-topic=test",
"app.kafka.output-response-topic=test-response",
"app.kafka.group-id=test"
]
)
@ -96,6 +117,44 @@ 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"
]
)
@MockBean(RequestProcessor::class)
inner class AppConfigurationUsingKafkaInputTest(private val context: ApplicationContext) {
@Test
fun shouldUseKafkaInputListener() {
assertThat(context.getBean(KafkaInputListener::class.java)).isNotNull
}
}
@Nested
@TestPropertySource(
properties = [
@ -116,4 +175,134 @@ class AppConfigurationTest {
}
@Nested
inner class AppConfigurationPseudonymizeTest {
@Nested
@TestPropertySource(
properties = [
"app.pseudonymize.generator=",
"app.pseudonymizer=buildin",
]
)
inner class AppConfigurationPseudonymizerBuildinTest(private val context: ApplicationContext) {
@Test
fun shouldUseConfiguredGenerator() {
assertThat(context.getBean(AnonymizingGenerator::class.java)).isNotNull
}
}
@Nested
@TestPropertySource(
properties = [
"app.pseudonymize.generator=",
"app.pseudonymizer=gpas",
]
)
inner class AppConfigurationPseudonymizerGpasTest(private val context: ApplicationContext) {
@Test
fun shouldUseConfiguredGenerator() {
assertThat(context.getBean(GpasPseudonymGenerator::class.java)).isNotNull
}
}
@Nested
@TestPropertySource(
properties = [
"app.pseudonymize.generator=buildin",
"app.pseudonymizer=",
]
)
inner class AppConfigurationPseudonymizeGeneratorBuildinTest(private val context: ApplicationContext) {
@Test
fun shouldUseConfiguredGenerator() {
assertThat(context.getBean(AnonymizingGenerator::class.java)).isNotNull
}
}
@Nested
@TestPropertySource(
properties = [
"app.pseudonymize.generator=gpas",
"app.pseudonymizer=",
]
)
inner class AppConfigurationPseudonymizeGeneratorGpasTest(private val context: ApplicationContext) {
@Test
fun shouldUseConfiguredGenerator() {
assertThat(context.getBean(GpasPseudonymGenerator::class.java)).isNotNull
}
}
@Nested
@TestPropertySource(
properties = [
"app.security.enable-tokens=true"
]
)
@MockBeans(value = [
MockBean(InMemoryUserDetailsManager::class),
MockBean(PasswordEncoder::class),
MockBean(TokenRepository::class)
])
inner class AppConfigurationTokenEnabledTest(private val context: ApplicationContext) {
@Test
fun checkTokenService() {
assertThat(context.getBean(TokenService::class.java)).isNotNull
}
}
@Nested
@MockBeans(value = [
MockBean(InMemoryUserDetailsManager::class),
MockBean(PasswordEncoder::class),
MockBean(TokenRepository::class)
])
inner class AppConfigurationTokenDisabledTest(private val context: ApplicationContext) {
@Test
fun checkTokenService() {
assertThrows<NoSuchBeanDefinitionException> { context.getBean(TokenService::class.java) }
}
}
}
@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()
}
}
}
}
}

View File

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

View File

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

View File

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

View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
@ -22,21 +22,6 @@ package dev.dnpm.etl.processor.pseudonym;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.IParser;
import dev.dnpm.etl.processor.config.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;
@ -54,35 +39,39 @@ import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.http.HttpEntity;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpMethod;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.http.*;
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;
import javax.net.ssl.SSLContext;
import javax.net.ssl.TrustManagerFactory;
import java.io.BufferedInputStream;
import java.io.FileInputStream;
import java.io.IOException;
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;
public class GpasPseudonymGenerator implements Generator {
private final static FhirContext r4Context = FhirContext.forR4();
private final String gPasUrl;
private final String psnTargetDomain;
private final HttpHeaders httpHeader;
private final RetryTemplate retryTemplate = defaultTemplate();
private final RetryTemplate retryTemplate;
private final Logger log = LoggerFactory.getLogger(GpasPseudonymGenerator.class);
private SSLContext customSslContext;
private RestTemplate restTemplate;
public GpasPseudonymGenerator(GPasConfigProperties gpasCfg) {
public GpasPseudonymGenerator(GPasConfigProperties gpasCfg, RetryTemplate retryTemplate) {
this.retryTemplate = retryTemplate;
this.gPasUrl = gpasCfg.getUri();
this.psnTargetDomain = gpasCfg.getTarget();
@ -91,7 +80,7 @@ public class GpasPseudonymGenerator implements Generator {
try {
if (StringUtils.isNotBlank(gpasCfg.getSslCaLocation())) {
customSslContext = getSslContext(gpasCfg.getSslCaLocation());
log.debug(String.format("%s has been initialized with SSL certificate %s",
log.warn(String.format("%s has been initialized with SSL certificate %s. This is deprecated in favor of including Root CA.",
this.getClass().getName(), gpasCfg.getSslCaLocation()));
}
} catch (IOException | KeyManagementException | KeyStoreException | CertificateException |
@ -202,31 +191,6 @@ public class GpasPseudonymGenerator implements Generator {
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
*

View File

@ -20,9 +20,10 @@
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
@SpringBootApplication(exclude = [SecurityAutoConfiguration::class])
class EtlProcessorApplication
fun main(args: Array<String>) {

View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
@ -19,13 +19,21 @@
package dev.dnpm.etl.processor.config
import dev.dnpm.etl.processor.security.Role
import org.springframework.boot.context.properties.ConfigurationProperties
import org.springframework.boot.context.properties.DeprecatedConfigurationProperty
@ConfigurationProperties(AppConfigProperties.NAME)
data class AppConfigProperties(
var bwhcUri: String?,
var generator: PseudonymGenerator = PseudonymGenerator.BUILDIN,
var transformations: List<TransformationProperties> = listOf()
@get:DeprecatedConfigurationProperty(
reason = "Deprecated in favor of 'app.pseudonymize.generator'",
replacement = "app.pseudonymize.generator"
)
var pseudonymizer: PseudonymGenerator = PseudonymGenerator.BUILDIN,
var transformations: List<TransformationProperties> = listOf(),
var maxRetryAttempts: Int = 3,
var duplicationDetection: Boolean = true
) {
companion object {
const val NAME = "app"
@ -34,6 +42,7 @@ data class AppConfigProperties(
@ConfigurationProperties(PseudonymizeConfigProperties.NAME)
data class PseudonymizeConfigProperties(
var generator: PseudonymGenerator = PseudonymGenerator.BUILDIN,
val prefix: String = "UNKNOWN",
) {
companion object {
@ -47,9 +56,11 @@ data class GPasConfigProperties(
val target: String = "etl-processor",
val username: String?,
val password: String?,
val sslCaLocation: String?,
) {
@get:DeprecatedConfigurationProperty(
reason = "Deprecated in favor of including Root CA"
)
val sslCaLocation: String?
) {
companion object {
const val NAME = "app.pseudonymize.gpas"
}
@ -64,10 +75,21 @@ data class RestTargetProperties(
}
}
@ConfigurationProperties(KafkaTargetProperties.NAME)
data class KafkaTargetProperties(
val topic: String = "etl-processor",
val responseTopic: String = "${topic}_response",
@ConfigurationProperties(KafkaProperties.NAME)
data class KafkaProperties(
val inputTopic: String?,
val outputTopic: String = "etl-processor",
@get:DeprecatedConfigurationProperty(
reason = "Deprecated",
replacement = "outputTopic"
)
val topic: String = outputTopic,
val outputResponseTopic: String = "${outputTopic}_response",
@get:DeprecatedConfigurationProperty(
reason = "Deprecated",
replacement = "outputResponseTopic"
)
val responseTopic: String = outputResponseTopic,
val groupId: String = "${topic}_group",
val servers: String = ""
) {
@ -76,6 +98,19 @@ data class KafkaTargetProperties(
}
}
@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

View File

@ -25,15 +25,29 @@ 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.services.TokenRepository
import dev.dnpm.etl.processor.services.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.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 reactor.core.publisher.Sinks
import kotlin.time.Duration.Companion.seconds
import kotlin.time.toJavaDuration
@Configuration
@EnableConfigurationProperties(
@ -48,18 +62,32 @@ class AppConfiguration {
private val logger = LoggerFactory.getLogger(AppConfiguration::class.java)
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS")
@ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "GPAS")
@Bean
fun gpasPseudonymGenerator(configProperties: GPasConfigProperties): Generator {
return GpasPseudonymGenerator(configProperties)
fun gpasPseudonymGenerator(configProperties: GPasConfigProperties, retryTemplate: RetryTemplate): Generator {
return GpasPseudonymGenerator(configProperties, retryTemplate)
}
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "BUILDIN", matchIfMissing = true)
@ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "BUILDIN", matchIfMissing = true)
@Bean
fun buildinPseudonymGenerator(): Generator {
return AnonymizingGenerator()
}
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS")
@ConditionalOnMissingBean
@Bean
fun gpasPseudonymGeneratorOnDeprecatedProperty(configProperties: GPasConfigProperties, retryTemplate: RetryTemplate): Generator {
return GpasPseudonymGenerator(configProperties, retryTemplate)
}
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "BUILDIN")
@ConditionalOnMissingBean
@Bean
fun buildinPseudonymGeneratorOnDeprecatedProperty(): Generator {
return AnonymizingGenerator()
}
@Bean
fun pseudonymizeService(
generator: Generator,
@ -73,11 +101,6 @@ class AppConfiguration {
return ReportService(objectMapper)
}
@Bean
fun statisticsUpdateProducer(): Sinks.Many<Any> {
return Sinks.many().multicast().directBestEffort()
}
@Bean
fun transformationService(
objectMapper: ObjectMapper,
@ -89,5 +112,39 @@ class AppConfiguration {
})
}
@Bean
fun retryTemplate(configProperties: AppConfigProperties): RetryTemplate {
return RetryTemplateBuilder()
.notRetryOn(IllegalArgumentException::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 configsUpdateProducer(): Sinks.Many<Boolean> {
return Sinks.many().multicast().directBestEffort()
}
}

View File

@ -20,10 +20,12 @@
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.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
@ -37,12 +39,14 @@ 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 = [KafkaTargetProperties::class]
value = [KafkaProperties::class]
)
@ConditionalOnProperty(value = ["app.kafka.topic", "app.kafka.servers"])
@ConditionalOnProperty(value = ["app.kafka.servers"])
@ConditionalOnMissingBean(MtbFileSender::class)
@Order(-5)
class AppKafkaConfiguration {
@ -52,20 +56,21 @@ class AppKafkaConfiguration {
@Bean
fun kafkaMtbFileSender(
kafkaTemplate: KafkaTemplate<String, String>,
kafkaTargetProperties: KafkaTargetProperties,
kafkaProperties: KafkaProperties,
retryTemplate: RetryTemplate,
objectMapper: ObjectMapper
): MtbFileSender {
logger.info("Selected 'KafkaMtbFileSender'")
return KafkaMtbFileSender(kafkaTemplate, kafkaTargetProperties, objectMapper)
return KafkaMtbFileSender(kafkaTemplate, kafkaProperties, retryTemplate, objectMapper)
}
@Bean
fun kafkaListenerContainer(
fun kafkaResponseListenerContainer(
consumerFactory: ConsumerFactory<String, String>,
kafkaTargetProperties: KafkaTargetProperties,
kafkaProperties: KafkaProperties,
kafkaResponseProcessor: KafkaResponseProcessor
): KafkaMessageListenerContainer<String, String> {
val containerProperties = ContainerProperties(kafkaTargetProperties.responseTopic)
val containerProperties = ContainerProperties(kafkaProperties.responseTopic)
containerProperties.messageListener = kafkaResponseProcessor
return KafkaMessageListenerContainer(consumerFactory, containerProperties)
}
@ -79,8 +84,29 @@ class AppKafkaConfiguration {
}
@Bean
fun connectionCheckService(consumerFactory: ConsumerFactory<String, String>): ConnectionCheckService {
return KafkaConnectionCheckService(consumerFactory.createConsumer())
@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 connectionCheckService(consumerFactory: ConsumerFactory<String, String>, configsUpdateProducer: Sinks.Many<Boolean>): ConnectionCheckService {
return KafkaConnectionCheckService(consumerFactory.createConsumer(), configsUpdateProducer)
}
}

View File

@ -30,7 +30,9 @@ 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(
@ -51,17 +53,22 @@ class AppRestConfiguration {
}
@Bean
fun restMtbFileSender(restTemplate: RestTemplate, restTargetProperties: RestTargetProperties): MtbFileSender {
fun restMtbFileSender(
restTemplate: RestTemplate,
restTargetProperties: RestTargetProperties,
retryTemplate: RetryTemplate
): MtbFileSender {
logger.info("Selected 'RestMtbFileSender'")
return RestMtbFileSender(restTemplate, restTargetProperties)
return RestMtbFileSender(restTemplate, restTargetProperties, retryTemplate)
}
@Bean
fun connectionCheckService(
restTemplate: RestTemplate,
restTargetProperties: RestTargetProperties
restTargetProperties: RestTargetProperties,
configsUpdateProducer: Sinks.Many<Boolean>
): ConnectionCheckService {
return RestConnectionCheckService(restTemplate, restTargetProperties)
return RestConnectionCheckService(restTemplate, restTargetProperties, configsUpdateProducer)
}
}

View File

@ -0,0 +1,180 @@
/*
* 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.config
import dev.dnpm.etl.processor.security.UserRole
import dev.dnpm.etl.processor.security.UserRoleRepository
import dev.dnpm.etl.processor.services.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.*
@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 {
authorizeRequests {
authorize("/configs/**", hasRole("ADMIN"))
authorize("/mtbfile/**", hasAnyRole("MTBFILE"))
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"
}
oauth2Login {
loginPage = "/login"
}
sessionManagement {
sessionConcurrency {
maximumSessions = 1
expiredUrl = "/login?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 {
authorizeRequests {
authorize("/configs/**", hasRole("ADMIN"))
authorize("/mtbfile/**", hasAnyRole("MTBFILE"))
authorize("/report/**", hasRole("ADMIN"))
authorize(anyRequest, permitAll)
}
httpBasic {
realmName = "ETL-Processor"
}
formLogin {
loginPage = "/login"
}
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)
}
}

View File

@ -0,0 +1,46 @@
/*
* 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.Consent
import de.ukw.ccc.bwhc.dto.MtbFile
import dev.dnpm.etl.processor.services.RequestProcessor
import org.apache.kafka.clients.consumer.ConsumerRecord
import org.slf4j.LoggerFactory
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(data: ConsumerRecord<String, String>) {
val mtbFile = objectMapper.readValue(data.value(), MtbFile::class.java)
if (mtbFile.consent.status == Consent.Status.ACTIVE) {
logger.debug("Accepted MTB File for processing")
requestProcessor.processMtbFile(mtbFile)
} else {
logger.debug("Accepted MTB File and process deletion")
requestProcessor.processDeletion(mtbFile.patient.id)
}
}
}

View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
@ -17,7 +17,7 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.web
package dev.dnpm.etl.processor.input
import de.ukw.ccc.bwhc.dto.Consent
import de.ukw.ccc.bwhc.dto.MtbFile
@ -27,13 +27,19 @@ import org.springframework.http.ResponseEntity
import org.springframework.web.bind.annotation.*
@RestController
@RequestMapping(path = ["mtbfile"])
class MtbFileRestController(
private val requestProcessor: RequestProcessor,
) {
private val logger = LoggerFactory.getLogger(MtbFileRestController::class.java)
@PostMapping(path = ["/mtbfile"])
@GetMapping
fun info(): ResponseEntity<String> {
return ResponseEntity.ok("Test")
}
@PostMapping
fun mtbFile(@RequestBody mtbFile: MtbFile): ResponseEntity<Void> {
if (mtbFile.consent.status == Consent.Status.ACTIVE) {
logger.debug("Accepted MTB File for processing")
@ -45,7 +51,7 @@ class MtbFileRestController(
return ResponseEntity.accepted().build()
}
@DeleteMapping(path = ["/mtbfile/{patientId}"])
@DeleteMapping(path = ["{patientId}"])
fun deleteData(@PathVariable patientId: String): ResponseEntity<Void> {
logger.debug("Accepted patient ID to process deletion")
requestProcessor.processDeletion(patientId)

View File

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

View File

@ -20,10 +20,13 @@
package dev.dnpm.etl.processor.monitoring
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.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.*
@ -52,12 +55,14 @@ data class CountedState(
val status: RequestStatus,
)
interface RequestRepository : CrudRepository<Request, Long> {
interface RequestRepository : CrudRepository<Request, Long>, PagingAndSortingRepository<Request, Long> {
fun findAllByPatientIdOrderByProcessedAtDesc(patientId: String): List<Request>
fun findByUuidEquals(uuid: String): Optional<Request>
fun findRequestByPatientId(patientId: String, pageable: Pageable): Page<Request>
@Query("SELECT count(*) AS count, status FROM request WHERE type = 'MTB_FILE' GROUP BY status ORDER BY status, count DESC;")
fun countStates(): List<CountedState>

View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
@ -22,14 +22,16 @@ 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.config.KafkaTargetProperties
import dev.dnpm.etl.processor.config.KafkaProperties
import dev.dnpm.etl.processor.monitoring.RequestStatus
import org.slf4j.LoggerFactory
import org.springframework.kafka.core.KafkaTemplate
import org.springframework.retry.support.RetryTemplate
class KafkaMtbFileSender(
private val kafkaTemplate: KafkaTemplate<String, String>,
private val kafkaTargetProperties: KafkaTargetProperties,
private val kafkaProperties: KafkaProperties,
private val retryTemplate: RetryTemplate,
private val objectMapper: ObjectMapper
) : MtbFileSender {
@ -37,16 +39,18 @@ class KafkaMtbFileSender(
override fun send(request: MtbFileSender.MtbFileRequest): MtbFileSender.Response {
return try {
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)
return retryTemplate.execute<MtbFileSender.Response, Exception> {
val result = kafkaTemplate.send(
kafkaProperties.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)
@ -65,17 +69,19 @@ class KafkaMtbFileSender(
.build()
return try {
val result = kafkaTemplate.send(
kafkaTargetProperties.topic,
key(request),
objectMapper.writeValueAsString(Data(request.requestId, dummyMtbFile))
)
return retryTemplate.execute<MtbFileSender.Response, Exception> {
val result = kafkaTemplate.send(
kafkaProperties.topic,
key(request),
objectMapper.writeValueAsString(Data(request.requestId, dummyMtbFile))
)
if (result.get() != null) {
logger.debug("Sent deletion request via KafkaMtbFileSender")
MtbFileSender.Response(RequestStatus.UNKNOWN)
} else {
MtbFileSender.Response(RequestStatus.ERROR)
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)
@ -83,6 +89,10 @@ class KafkaMtbFileSender(
}
}
override fun endpoint(): String {
return "${this.kafkaProperties.servers} (${this.kafkaProperties.topic}/${this.kafkaProperties.responseTopic})"
}
private fun key(request: MtbFileSender.MtbFileRequest): String {
return "{\"pid\": \"${request.mtbFile.patient.id}\", " +
"\"eid\": \"${request.mtbFile.episode.id}\"}"

View File

@ -28,6 +28,8 @@ interface MtbFileSender {
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)

View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
@ -25,32 +25,39 @@ 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.RestTemplate
class RestMtbFileSender(
private val restTemplate: RestTemplate,
private val restTargetProperties: RestTargetProperties
private val restTargetProperties: RestTargetProperties,
private val retryTemplate: RetryTemplate
) : MtbFileSender {
private val logger = LoggerFactory.getLogger(RestMtbFileSender::class.java)
override fun send(request: MtbFileSender.MtbFileRequest): MtbFileSender.Response {
try {
val headers = HttpHeaders()
headers.contentType = MediaType.APPLICATION_JSON
val entityReq = HttpEntity(request.mtbFile, headers)
val response = restTemplate.postForEntity(
"${restTargetProperties.uri}/MTBFile",
entityReq,
String::class.java
)
if (!response.statusCode.is2xxSuccessful) {
logger.warn("Error sending to remote system: {}", response.body)
return MtbFileSender.Response(response.statusCode.asRequestStatus(), "Status-Code: ${response.statusCode.value()}")
return retryTemplate.execute<MtbFileSender.Response, Exception> {
val headers = HttpHeaders()
headers.contentType = MediaType.APPLICATION_JSON
val entityReq = HttpEntity(request.mtbFile, headers)
val response = restTemplate.postForEntity(
"${restTargetProperties.uri}/MTBFile",
entityReq,
String::class.java
)
if (!response.statusCode.is2xxSuccessful) {
logger.warn("Error sending to remote system: {}", response.body)
return@execute MtbFileSender.Response(
response.statusCode.asRequestStatus(),
"Status-Code: ${response.statusCode.value()}"
)
}
logger.debug("Sent file via RestMtbFileSender")
return@execute MtbFileSender.Response(response.statusCode.asRequestStatus(), response.body.orEmpty())
}
logger.debug("Sent file via RestMtbFileSender")
return MtbFileSender.Response(response.statusCode.asRequestStatus(), response.body.orEmpty())
} catch (e: IllegalArgumentException) {
logger.error("Not a valid URI to export to: '{}'", restTargetProperties.uri!!)
} catch (e: RestClientException) {
@ -62,16 +69,18 @@ class RestMtbFileSender(
override fun send(request: MtbFileSender.DeleteRequest): MtbFileSender.Response {
try {
val headers = HttpHeaders()
headers.contentType = MediaType.APPLICATION_JSON
val entityReq = HttpEntity(null, headers)
restTemplate.delete(
"${restTargetProperties.uri}/Patient/${request.patientId}",
entityReq,
String::class.java
)
logger.debug("Sent file via RestMtbFileSender")
return MtbFileSender.Response(RequestStatus.SUCCESS)
return retryTemplate.execute<MtbFileSender.Response, Exception> {
val headers = HttpHeaders()
headers.contentType = MediaType.APPLICATION_JSON
val entityReq = HttpEntity(null, headers)
restTemplate.delete(
"${restTargetProperties.uri}/Patient/${request.patientId}",
entityReq,
String::class.java
)
logger.debug("Sent file via RestMtbFileSender")
return@execute MtbFileSender.Response(RequestStatus.SUCCESS)
}
} catch (e: IllegalArgumentException) {
logger.error("Not a valid URI to export to: '{}'", restTargetProperties.uri!!)
} catch (e: RestClientException) {
@ -81,4 +90,8 @@ class RestMtbFileSender(
return MtbFileSender.Response(RequestStatus.ERROR, "Sonstiger Fehler bei der Übertragung")
}
override fun endpoint(): String {
return this.restTargetProperties.uri.orEmpty()
}
}

View File

@ -0,0 +1,45 @@
/*
* 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>
}

View File

@ -21,6 +21,7 @@ package dev.dnpm.etl.processor.services
import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.MtbFile
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
@ -42,7 +43,8 @@ class RequestProcessor(
private val sender: MtbFileSender,
private val requestService: RequestService,
private val objectMapper: ObjectMapper,
private val applicationEventPublisher: ApplicationEventPublisher
private val applicationEventPublisher: ApplicationEventPublisher,
private val appConfigProperties: AppConfigProperties
) {
fun processMtbFile(mtbFile: MtbFile) {
@ -64,7 +66,7 @@ class RequestProcessor(
)
)
if (isDuplication(mtbFile)) {
if (appConfigProperties.duplicationDetection && isDuplication(mtbFile)) {
applicationEventPublisher.publishEvent(
ResponseEvent(
requestId,

View File

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

View File

@ -0,0 +1,61 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.services
import dev.dnpm.etl.processor.security.Role
import dev.dnpm.etl.processor.security.UserRole
import dev.dnpm.etl.processor.security.UserRoleRepository
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()
}
}
}

View File

@ -22,30 +22,141 @@ package dev.dnpm.etl.processor.web
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
import dev.dnpm.etl.processor.output.MtbFileSender
import dev.dnpm.etl.processor.pseudonym.Generator
import dev.dnpm.etl.processor.security.Role
import dev.dnpm.etl.processor.security.UserRole
import dev.dnpm.etl.processor.services.Token
import dev.dnpm.etl.processor.services.TokenService
import dev.dnpm.etl.processor.services.TransformationService
import dev.dnpm.etl.processor.services.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.GetMapping
import org.springframework.web.bind.annotation.RequestMapping
import org.springframework.web.bind.annotation.*
import reactor.core.publisher.Flux
import reactor.core.publisher.Sinks
@Controller
@RequestMapping(path = ["configs"])
class ConfigController(
@Qualifier("configsUpdateProducer")
private val configsUpdateProducer: Sinks.Many<Boolean>,
private val transformationService: TransformationService,
private val pseudonymGenerator: Generator,
private val mtbFileSender: MtbFileSender,
private val connectionCheckService: ConnectionCheckService
private val connectionCheckService: ConnectionCheckService,
private val tokenService: TokenService?,
private val userRoleService: UserRoleService?
) {
@GetMapping
fun index(model: Model): String {
model.addAttribute("pseudonymGenerator", pseudonymGenerator.javaClass.simpleName)
model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName)
model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint())
model.addAttribute("connectionAvailable", connectionCheckService.connectionAvailable())
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 = ["connectionAvailable"])
fun connectionAvailable(model: Model): String {
model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName)
model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint())
model.addAttribute("connectionAvailable", connectionCheckService.connectionAvailable())
if (tokenService != null) {
model.addAttribute("tokensEnabled", true)
model.addAttribute("tokens", tokenService.findAll())
} else {
model.addAttribute("tokens", listOf<Token>())
}
return "configs/connectionAvailable"
}
@PostMapping(path = ["tokens"])
fun addToken(@ModelAttribute("name") name: String, model: Model): String {
if (tokenService == null) {
model.addAttribute("tokensEnabled", false)
model.addAttribute("success", false)
} else {
model.addAttribute("tokensEnabled", true)
val result = tokenService.addToken(name)
if (result.isSuccess) {
model.addAttribute("newTokenValue", result.getOrDefault(""))
model.addAttribute("success", true)
} else {
model.addAttribute("success", false)
}
model.addAttribute("tokens", tokenService.findAll())
}
return "configs/tokens"
}
@DeleteMapping(path = ["tokens/{id}"])
fun deleteToken(@PathVariable id: Long, model: Model): String {
if (tokenService != null) {
tokenService.deleteToken(id)
model.addAttribute("tokensEnabled", true)
model.addAttribute("tokens", tokenService.findAll())
} else {
model.addAttribute("tokensEnabled", false)
model.addAttribute("tokens", listOf<Token>())
}
return "configs/tokens"
}
@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])
fun events(): Flux<ServerSentEvent<Any>> {
return configsUpdateProducer.asFlux().map {
ServerSentEvent.builder<Any>()
.event("connection-available").id("none").data("")
.build()
}
}
}

View File

@ -23,6 +23,9 @@ import dev.dnpm.etl.processor.NotFoundException
import dev.dnpm.etl.processor.monitoring.ReportService
import dev.dnpm.etl.processor.monitoring.RequestId
import dev.dnpm.etl.processor.monitoring.RequestRepository
import org.springframework.data.domain.Pageable
import org.springframework.data.domain.Sort
import org.springframework.data.web.PageableDefault
import org.springframework.stereotype.Controller
import org.springframework.ui.Model
import org.springframework.web.bind.annotation.GetMapping
@ -37,8 +40,24 @@ class HomeController(
) {
@GetMapping
fun index(model: Model): String {
val requests = requestRepository.findAll().sortedByDescending { it.processedAt }.take(25)
fun index(
@PageableDefault(page = 0, size = 20, sort = ["processedAt"], direction = Sort.Direction.DESC) pageable: Pageable,
model: Model
): String {
val requests = requestRepository.findAll(pageable)
model.addAttribute("requests", requests)
return "index"
}
@GetMapping(path = ["patient/{patientId}"])
fun byPatient(
@PathVariable patientId: String,
@PageableDefault(page = 0, size = 20, sort = ["processedAt"], direction = Sort.Direction.DESC) pageable: Pageable,
model: Model
): String {
val requests = requestRepository.findRequestByPatientId(patientId, pageable)
model.addAttribute("patientId", patientId)
model.addAttribute("requests", requests)
return "index"

View File

@ -0,0 +1,47 @@
/*
* 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.SecurityConfigProperties
import org.springframework.boot.autoconfigure.security.oauth2.client.OAuth2ClientProperties
import org.springframework.stereotype.Controller
import org.springframework.ui.Model
import org.springframework.web.bind.annotation.GetMapping
@Controller
class LoginController(
private val securityConfigProperties: SecurityConfigProperties?,
private val oAuth2ClientProperties: OAuth2ClientProperties?
) {
@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"
}
}

View File

@ -22,6 +22,7 @@ package dev.dnpm.etl.processor.web
import dev.dnpm.etl.processor.monitoring.RequestRepository
import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.monitoring.RequestType
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
@ -38,6 +39,7 @@ import java.time.temporal.ChronoUnit
@RestController
@RequestMapping(path = ["/statistics"])
class StatisticsRestController(
@Qualifier("statisticsUpdateProducer")
private val statisticsUpdateProducer: Sinks.Many<Any>,
private val requestRepository: RequestRepository
) {
@ -132,6 +134,7 @@ class StatisticsRestController(
@GetMapping(path = ["events"], produces = [MediaType.TEXT_EVENT_STREAM_VALUE])
fun updater(): Flux<ServerSentEvent<Any>> {
return statisticsUpdateProducer.asFlux().flatMap {
println(it)
Flux.fromIterable(
listOf(
ServerSentEvent.builder<Any>()
@ -152,6 +155,10 @@ 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()
)
)

View File

@ -10,6 +10,9 @@ app:
topic: test
response-topic: test_response
servers: localhost:9094
#security:
# admin-user: admin
# admin-password: "{noop}very-secret"
server:
port: 8000

View File

@ -4,4 +4,18 @@ spring:
consumer:
group-id: ${app.kafka.group-id}
flyway:
locations: "classpath:db/migration/{vendor}"
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

View File

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

View File

@ -0,0 +1,7 @@
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
);

View File

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

View File

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

Binary file not shown.

After

Width:  |  Height:  |  Size: 3.0 KiB

File diff suppressed because one or more lines are too long

View File

@ -0,0 +1,41 @@
<?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>

After

Width:  |  Height:  |  Size: 1.6 KiB

Binary file not shown.

After

Width:  |  Height:  |  Size: 1.6 KiB

View File

@ -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);
window.onload = () => {
const formatTimeElements = () => {
Array.from(document.getElementsByTagName('time')).forEach((timeTag) => {
let date = Date.parse(timeTag.getAttribute('datetime'));
if (! isNaN(date)) {
@ -13,6 +13,9 @@ window.onload = () => {
});
};
window.addEventListener('load', formatTimeElements);
window.addEventListener('htmx:afterRequest', formatTimeElements);
function drawPieChart(url, elemId, title, data) {
if (data) {
update(elemId, data);

Binary file not shown.

After

Width:  |  Height:  |  Size: 1.4 KiB

View File

@ -1,5 +1,8 @@
:root {
--table-border: rgba(96, 96, 96, 1);
--text: #333;
--table-border: rgba(16, 24, 40, .1);
--dark: brightness(.90);
--bg-blue: rgb(0, 74, 157);
--bg-blue-op: rgba(0, 74, 157, .35);
@ -19,47 +22,132 @@
--bg-gray-op: rgba(112, 128, 144, .35);
}
html {
background: linear-gradient(-5deg, var(--bg-blue-op), transparent 10em);
min-height: 100vh;
overflow-y: scroll;
}
body {
margin: 0;
margin: 0 0 5em 0;
font-family: sans-serif;
font-size: .8rem;
color: #333;
color: var(--text);
min-height: 100vh;
background: url(bg.jpeg) no-repeat;
background-size: contain;
}
nav {
margin: 0 auto;
background: #d5dad5;
height: 3rem;
padding: 1em 0;
line-height: 1.5rem;
max-width: 1140px;
border-bottom: 1px solid var(--table-border);
}
nav a {
color: #004a8f;
text-transform: uppercase;
nav a.nav-home {
float: left;
color: var(--text);
line-height: 1.5em;
text-decoration: none;
line-height: 2rem;
font-weight: 700;
font-size: 2em;
font-weight: bold;
}
nav a:hover {
text-decoration: underline;
nav a.nav-home > img {
width: 1.5em;
vertical-align: middle;
}
nav > ul {
margin: 0 3rem;
margin: 0 0 0 auto;
padding: 0;
width: max-content;
}
nav > ul > li {
background: #fbfbfb;
display: block;
float: left;
padding: 2px 1rem;
border-left: 1px solid #d5dad5;
display: inline-block;
padding: 0 1rem;
}
nav > ul > li:first-of-type {
border-left: none;
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);
text-transform: uppercase;
text-decoration: none;
font-weight: 700;
}
nav li a:hover {
text-decoration: underline;
}
a {
color: var(--bg-blue);
}
.breadcrumps {
@ -85,7 +173,7 @@ nav > ul > li:first-of-type {
}
.breadcrumps ul li a {
color: #333333;
color: var(--text);
text-decoration: none;
}
@ -98,6 +186,10 @@ main {
max-width: 1140px;
}
section {
margin: 3em 0;
}
form {
margin: 1rem 0;
padding: 1rem;
@ -139,16 +231,126 @@ form.samplecode-input input:focus-visible {
background: lightgreen;
}
table {
border-top: 1px solid var(--table-border);
border-left: 1px solid var(--table-border);
border-spacing: 0;
border-radius: 3px;
.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 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 {
min-width: 100%;
font-family: sans-serif;
}
.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;
@ -165,64 +367,78 @@ table.samples {
display: block;
}
th {
background: #eee;
}
td, th {
th, td {
padding: 0.4rem .2rem;
border-right: 1px solid var(--table-border);
border-bottom: 1px solid var(--table-border);
line-height: 2em;
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);
}
td.bg-blue, th.bg-blue {
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 {
background: var(--bg-blue);
color: white;
border-radius: 0.4em;
}
tr:has(td.bg-blue) {
background: var(--bg-blue-op);
}
td.bg-green, th.bg-green {
td.bg-green > small, th.bg-green > small {
background: var(--bg-green);
color: white;
border-radius: 0.4em;
}
tr:has(td.bg-green) {
background: var(--bg-green-op);
}
td.bg-yellow, th.bg-yellow {
td.bg-yellow > small, th.bg-yellow > small {
background: var(--bg-yellow);
color: white;
border-radius: 0.4em;
}
tr:has(td.bg-yellow) {
background: var(--bg-yellow-op);
}
td.bg-red, th.bg-red {
td.bg-red > small, th.bg-red > small {
background: var(--bg-red);
color: white;
border-radius: 0.4em;
}
tr:has(td.bg-red) {
background: var(--bg-red-op);
}
td.bg-gray, th.bg-gray {
td.bg-gray > small, th.bg-gray > small {
background: var(--bg-gray);
color: white;
border-radius: 0.4em;
}
.bg-path {
@ -261,7 +477,6 @@ td.clipboard.clipped {
padding: 4px 8px;
line-height: 1.2rem;
vertical-align: middle;
border: 0 solid transparent;
border-radius: 3px;
@ -273,38 +488,38 @@ td.clipboard.clipped {
cursor: pointer;
}
.btn:active,
.btn:hover {
filter: drop-shadow(1px 2px 2px gray);
filter: drop-shadow(1px 1px 1px gray) var(--dark);
}
.btn:active {
filter: drop-shadow(1px 1px 2px gray);
translate: 0 1px;
}
.btn.btn-red {
background: red;
background: var(--bg-red);
color: white;
}
.btn.btn-red:hover, .btn.btn-red:active {
background: darkred !important;
}
.btn.btn-blue {
background: slategray;
background: var(--bg-blue);
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;
@ -341,12 +556,6 @@ input.inline:focus-visible {
}
.chart {
padding: 1rem;
margin: .2rem;
border: 1px solid var(--table-border);
border-radius: 3px;
width: calc(100% - 2.4rem - 4px);
height: 320px;
@ -355,4 +564,80 @@ input.inline:focus-visible {
.chart-50pc {
width: calc(50% - 2.4rem - 4px);
}
.connection-display {
display: grid;
grid-template-columns: 10em 16em 10em;
place-items: center;
width: fit-content;
margin: 1em 0;
}
.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-radius: 3px;
text-align: center;
}
.notification.success {
color: var(--bg-green);
}
.notification.notice {
color: var(--bg-yellow);
}
.notification.error {
color: var(--bg-red);
}
a.reload {
display: none;
position: absolute;
height: 1.2em;
width: 1.2em;
background: var(--bg-red);
border-radius: 50%;
color: white;
text-decoration: none;
font-size: .6em;
align-content: center;
justify-content: center;
}
.new-token {
padding: 1em;
background: var(--bg-green-op);
}
.new-token > pre {
margin: 0;
border: 1px solid var(--bg-green);
padding: .5em;
width: max-content;
display: inline-block;
}
.no-token {
padding: 1em;
background: var(--bg-red-op);
}

View File

@ -0,0 +1,11 @@
<?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>

After

Width:  |  Height:  |  Size: 588 B

View File

@ -10,67 +10,90 @@
<main>
<h1>Konfiguration</h1>
<h2>Allgemeine Konfiguration</h2>
<table>
<thead>
<tr>
<th>Name</th>
<th>Wert</th>
</tr>
</thead>
<tbody>
<section>
<h2>🔧 Allgemeine Konfiguration</h2>
<table>
<thead>
<tr>
<td>Pseudonym erzeugt über</td>
<td>[[ ${pseudonymGenerator} ]]</td>
<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>[[ ${mtbFileEndpoint} ]]</td>
</tr>
</tbody>
</table>
</section>
<section th:insert="~{configs/tokens.html}">
</section>
<section th:insert="~{configs/userroles.html}">
</section>
<section hx-ext="sse" th:sse-connect="@{/configs/events}">
<div th:insert="~{configs/connectionAvailable.html}" th:hx-get="@{/configs?connectionAvailable}" hx-trigger="sse:connection-available">
</div>
</section>
<section>
<h2><span th:if="${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>
<thead>
<tr>
<td>MTBFile-Sender</td>
<td>[[ ${mtbFileSender} ]]</td>
<th>JSON-Path</th>
<th>Transformation von &rArr; nach</th>
</tr>
</tbody>
</table>
<h2><span th:if="${connectionAvailable}"></span><span th:if="${not(connectionAvailable)}"></span> Verbindung zum bwHC-Backend</h2>
<p>
Verbindung über <code>[[ ${mtbFileSender} ]]</code>. Die Verbindung ist aktuell
<strong th:if="${connectionAvailable}" style="color: green">verfügbar.</strong>
<strong th:if="${not(connectionAvailable)}" style="color: red">nicht verfügbar!</strong>
</p>
<h2>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>
<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>
</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>
</main>
<script th:src="@{/scripts.js}"></script>
<script th:src="@{/webjars/htmx.org/dist/htmx.min.js}"></script>
<script th:src="@{/webjars/htmx.org/dist/ext/sse.js}"></script>
</body>
</html>

View File

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

View File

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

View File

@ -0,0 +1,40 @@
<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()}">
<thead>
<tr>
<th>Benutzername</th>
<th>Rolle</th>
<th></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="${#authorization.authentication.getName() == userRole.username}">Übernehmen</button>
</form>
</div>
</td>
<td>
<button class="btn btn-red" th:hx-delete="@{/configs/userroles/{id}(id=${userRole.id})}" hx-target="#userroles" th:disabled="${#authorization.authentication.getName() == userRole.username}">Löschen</button>
</td>
</tr>
</tbody>
</table>
</div>
</div>

View File

@ -1,5 +1,5 @@
<!DOCTYPE html>
<html xmlns:th="http://www.thymeleaf.org">
<html xmlns:th="http://www.thymeleaf.org" xmlns:sec="http://www.thymeleaf.org">
<head>
<meta charset="UTF-8">
<link rel="stylesheet" th:href="@{/style.css}" />
@ -7,10 +7,33 @@
<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><a th:href="@{/configs}">Konfiguration</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>
</ul>
</nav>
</div>

View File

@ -1,5 +1,5 @@
<!DOCTYPE html>
<html lang="de" xmlns:th="http://www.thymeleaf.org">
<html lang="de" xmlns:th="http://www.thymeleaf.org" xmlns:sec="http://www.thymeleaf.org">
<head>
<meta charset="UTF-8">
<title>ETL-Prozessor</title>
@ -9,37 +9,91 @@
<div th:replace="~{fragments.html :: nav}"></div>
<main>
<h1>Letzte Anfragen</h1>
<h1>Alle Anfragen<a id="reload-notify" class="reload" title="Neue Anfragen" th:href="@{/}"></a></h1>
<table>
<thead>
<tr>
<th>Status</th>
<th>Typ</th>
<th>ID</th>
<th>Datum</th>
<th>Patienten-ID</th>
</tr>
</thead>
<tbody>
<tr th:each="request : ${requests}">
<td th:if="${request.status.value.contains('success')}" class="bg-green"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value.contains('warning')}" class="bg-yellow"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value.contains('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 th:if="not ${request.report}">[[ ${request.uuid} ]]</td>
<td th:if="${request.report}">
<a th:href="@{/report/{id}(id=${request.uuid})}">[[ ${request.uuid} ]]</a>
</td>
<td><time th:datetime="${request.processedAt}">[[ ${request.processedAt} ]]</time></td>
<td>[[ ${request.patientId} ]]</td>
</tr>
</tbody>
</table>
<div>
<h2 th:if="${patientId != null}">
Betreffend Patienten-Pseudonym <span class="monospace" th:text="${patientId}">***</span>
<a class="btn btn-blue" th:if="${patientId != null}" th:href="@{/}">Alle anzeigen</a>
</h2>
</div>
<div class="border">
<div th:if="${patientId == null}" class="page-control">
<a id="first-page-link" th:href="@{/(page=${0})}" title="Zum Anfang: Taste W" th:if="${not requests.isFirst()}">&larrb;</a><a th:if="${requests.isFirst()}">&larrb;</a>
<a id="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="${requests.isLast()}">&rarrb;</a>
</div>
<div th:if="${patientId != null}" class="page-control">
<a id="first-page-link" th:href="@{/patient/{patientId}(patientId=${patientId},page=${0})}" title="Zum Anfang: Taste W" th:if="${not requests.isFirst()}">&larrb;</a><a th:if="${requests.isFirst()}">&larrb;</a>
<a id="prev-page-link" th:href="@{/patient/{patientId}(patientId=${patientId},page=${requests.getNumber() - 1})}" title="Seite zurück: Taste A" th:if="${not requests.isFirst()}">&larr;</a><a th:if="${requests.isFirst()}">&larr;</a>
<span>Seite [[ ${requests.getNumber() + 1} ]] von [[ ${requests.getTotalPages()} ]]</span>
<a id="next-page-link" th:href="@{/patient/{patientId}(patientId=${patientId},page=${requests.getNumber() + 1})}" title="Seite vor: Taste D" th:if="${not requests.isLast()}">&rarr;</a><a th:if="${requests.isLast()}">&rarr;</a>
<a id="last-page-link" th:href="@{/patient/{patientId}(patientId=${patientId},page=${requests.getTotalPages() - 1})}" title="Zum Ende: Taste S" th:if="${not requests.isLast()}">&rarrb;</a><a th:if="${requests.isLast()}">&rarrb;</a>
</div>
<table class="paged">
<thead>
<tr>
<th>Status</th>
<th>Typ</th>
<th>ID</th>
<th>Datum</th>
<th>Patienten-ID</th>
</tr>
</thead>
<tbody>
<tr th:each="request : ${requests}">
<td th:if="${request.status.value.contains('success')}" class="bg-green"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value.contains('warning')}" class="bg-yellow"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value.contains('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 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'))">[[ ${request.uuid} ]]</th:block>
</td>
<td><time th:datetime="${request.processedAt}">[[ ${request.processedAt} ]]</time></td>
<td class="patient-id" th:if="${patientId != null}" sec:authorize="hasRole('USER') or hasRole('ADMIN')">
[[ ${request.patientId} ]]
</td>
<td class="patient-id" th:if="${patientId == null}" sec:authorize="hasRole('USER') or hasRole('ADMIN')">
<a th:href="@{/patient/{pid}(pid=${request.patientId})}">[[ ${request.patientId} ]]</a>
</td>
<td class="patient-id" sec:authorize="not (hasRole('USER') or hasRole('ADMIN'))">***</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>

View File

@ -0,0 +1,27 @@
<!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>

View File

@ -1,5 +1,5 @@
<!DOCTYPE html>
<html lang="de" xmlns:th="http://www.thymeleaf.org">
<html lang="de" xmlns:th="http://www.thymeleaf.org" xmlns:sec="http://www.thymeleaf.org">
<head>
<meta charset="UTF-8">
<title>ETL-Prozessor</title>
@ -15,6 +15,7 @@
<thead>
<tr>
<th>Status</th>
<th>Typ</th>
<th>ID</th>
<th>Datum</th>
<th>Patienten-ID</th>
@ -27,21 +28,27 @@
<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>[[ ${request.patientId} ]]</td>
<td class="patient-id" sec:authorize="authenticated">[[ ${request.patientId} ]]</td>
<td class="patient-id" sec:authorize="not authenticated">***</td>
</tr>
</tbody>
</table>
<h2 th:text="${request.report.description}"></h2>
<table th:if="not ${issues.isEmpty()}">
<p th:if="${issues.isEmpty()}">
Keine weiteren Angaben.
</p>
<table th:if="${not issues.isEmpty()}">
<thead>
<tr>
<th>Schweregrad</th>
<th>Beschreibung</th>
</tr>
<tr>
<th>Schweregrad</th>
<th>Beschreibung</th>
</tr>
</thead>
<tbody>
<tr th:each="issue : ${issues}">

View File

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

View File

@ -0,0 +1,79 @@
/*
* 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.Consent
import de.ukw.ccc.bwhc.dto.MtbFile
import de.ukw.ccc.bwhc.dto.Patient
import dev.dnpm.etl.processor.services.RequestProcessor
import org.apache.kafka.clients.consumer.ConsumerRecord
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith
import org.mockito.ArgumentMatchers.anyString
import org.mockito.Mock
import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.any
import org.mockito.kotlin.times
import org.mockito.kotlin.verify
@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())
}
@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(anyString())
}
}

View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
@ -17,7 +17,7 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.web
package dev.dnpm.etl.processor.input
import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.*

View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
@ -21,7 +21,7 @@ package dev.dnpm.etl.processor.output
import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.*
import dev.dnpm.etl.processor.config.KafkaTargetProperties
import dev.dnpm.etl.processor.config.KafkaProperties
import dev.dnpm.etl.processor.monitoring.RequestStatus
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach
@ -35,6 +35,8 @@ import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.*
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
@ -51,11 +53,13 @@ class KafkaMtbFileSenderTest {
fun setup(
@Mock kafkaTemplate: KafkaTemplate<String, String>
) {
val kafkaTargetProperties = KafkaTargetProperties("testtopic")
val kafkaProperties = KafkaProperties("testtopic")
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
this.objectMapper = ObjectMapper()
this.kafkaTemplate = kafkaTemplate
this.kafkaMtbFileSender = KafkaMtbFileSender(kafkaTemplate, kafkaTargetProperties, objectMapper)
this.kafkaMtbFileSender = KafkaMtbFileSender(kafkaTemplate, kafkaProperties, retryTemplate, objectMapper)
}
@ParameterizedTest
@ -118,6 +122,58 @@ class KafkaMtbFileSenderTest {
assertThat(captor.secondValue).isEqualTo(objectMapper.writeValueAsString(kafkaRecordData("TestID", Consent.Status.REJECTED)))
}
@ParameterizedTest
@MethodSource("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(anyString(), anyString(), anyString())
kafkaMtbFileSender.send(MtbFileSender.MtbFileRequest("TestID", mtbFile(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(anyString(), anyString(), anyString())
}
@ParameterizedTest
@MethodSource("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(anyString(), anyString(), anyString())
kafkaMtbFileSender.send(MtbFileSender.DeleteRequest("TestID", "PID"))
val expectedCount = when (testData.exception) {
// OK - No Retry
null -> times(1)
// Request failed - Retry max 3 times
else -> times(3)
}
verify(kafkaTemplate, expectedCount).send(anyString(), anyString(), anyString())
}
companion object {
fun mtbFile(consentStatus: Consent.Status): MtbFile {
return if (consentStatus == Consent.Status.ACTIVE) {

View File

@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
@ -28,6 +28,9 @@ 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.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.method
import org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo
@ -44,10 +47,11 @@ class RestMtbFileSenderTest {
fun setup() {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile")
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.restMtbFileSender = RestMtbFileSender(restTemplate, restTargetProperties)
this.restMtbFileSender = RestMtbFileSender(restTemplate, restTargetProperties, retryTemplate)
}
@ParameterizedTest
@ -80,6 +84,64 @@ class RestMtbFileSenderTest {
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
@ParameterizedTest
@MethodSource("mtbFileRequestWithResponseSource")
fun shouldRetryOnMtbFileHttpRequestError(requestWithResponse: RequestWithResponse) {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile")
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.restMtbFileSender = RestMtbFileSender(restTemplate, restTargetProperties, retryTemplate)
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)
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)
}
@ParameterizedTest
@MethodSource("deleteRequestWithResponseSource")
fun shouldRetryOnDeleteHttpRequestError(requestWithResponse: RequestWithResponse) {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile")
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.restMtbFileSender = RestMtbFileSender(restTemplate, restTargetProperties, retryTemplate)
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)
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)
}
companion object {
data class RequestWithResponse(
val httpStatus: HttpStatus,

View File

@ -21,6 +21,7 @@ package dev.dnpm.etl.processor.services
import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.*
import dev.dnpm.etl.processor.config.AppConfigProperties
import dev.dnpm.etl.processor.monitoring.Request
import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.monitoring.RequestType
@ -51,6 +52,7 @@ class RequestProcessorTest {
private lateinit var sender: MtbFileSender
private lateinit var requestService: RequestService
private lateinit var applicationEventPublisher: ApplicationEventPublisher
private lateinit var appConfigProperties: AppConfigProperties
private lateinit var requestProcessor: RequestProcessor
@ -67,6 +69,7 @@ class RequestProcessorTest {
this.sender = sender
this.requestService = requestService
this.applicationEventPublisher = applicationEventPublisher
this.appConfigProperties = AppConfigProperties(null)
val objectMapper = ObjectMapper()
@ -76,7 +79,8 @@ class RequestProcessorTest {
sender,
requestService,
objectMapper,
applicationEventPublisher
applicationEventPublisher,
appConfigProperties
)
}
@ -390,4 +394,52 @@ class RequestProcessorTest {
assertThat(requestCaptor.firstValue.status).isEqualTo(RequestStatus.ERROR)
}
@Test
fun testShouldNotDetectMtbFileDuplicationIfDuplicationNotConfigured() {
this.appConfigProperties.duplicationDetection = false
doAnswer {
it.arguments[0] as String
}.`when`(pseudonymizeService).patientPseudonym(any())
doAnswer {
it.arguments[0]
}.whenever(transformationService).transform(any())
doAnswer {
MtbFileSender.Response(status = RequestStatus.SUCCESS)
}.`when`(sender).send(any<MtbFileSender.MtbFileRequest>())
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()
this.requestProcessor.processMtbFile(mtbFile)
val eventCaptor = argumentCaptor<ResponseEvent>()
verify(applicationEventPublisher, times(1)).publishEvent(eventCaptor.capture())
assertThat(eventCaptor.firstValue).isNotNull
assertThat(eventCaptor.firstValue.status).isEqualTo(RequestStatus.SUCCESS)
}
}

View File

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