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8
.github/workflows/deploy.yml
vendored
8
.github/workflows/deploy.yml
vendored
@ -21,7 +21,7 @@ jobs:
|
||||
uses: docker/setup-buildx-action@v3
|
||||
|
||||
- name: Login to Docker Hub
|
||||
uses: docker/login-action@v2
|
||||
uses: docker/login-action@v3
|
||||
with:
|
||||
registry: ghcr.io
|
||||
username: ${{ github.actor }}
|
||||
@ -30,6 +30,6 @@ jobs:
|
||||
- name: Execute image build and push
|
||||
run: |
|
||||
./gradlew bootBuildImage
|
||||
docker tag ghcr.io/ccc-mf/etl-processor ghcr.io/ccc-mf/etl-processor:${{ github.ref_name }}
|
||||
docker push ghcr.io/ccc-mf/etl-processor
|
||||
docker push ghcr.io/ccc-mf/etl-processor:${{ github.ref_name }}
|
||||
docker tag ghcr.io/${{ github.repository }} ghcr.io/${{ github.repository }}:${{ github.ref_name }}
|
||||
docker push ghcr.io/${{ github.repository }}
|
||||
docker push ghcr.io/${{ github.repository }}:${{ github.ref_name }}
|
4
.github/workflows/test.yml
vendored
4
.github/workflows/test.yml
vendored
@ -12,7 +12,7 @@ jobs:
|
||||
runs-on: ubuntu-latest
|
||||
steps:
|
||||
- uses: actions/checkout@v4
|
||||
- uses: actions/setup-java@v3
|
||||
- uses: actions/setup-java@v4
|
||||
with:
|
||||
java-version: '21'
|
||||
distribution: 'temurin'
|
||||
@ -27,7 +27,7 @@ jobs:
|
||||
runs-on: ubuntu-latest
|
||||
steps:
|
||||
- uses: actions/checkout@v4
|
||||
- uses: actions/setup-java@v3
|
||||
- uses: actions/setup-java@v4
|
||||
with:
|
||||
java-version: '21'
|
||||
distribution: 'temurin'
|
||||
|
2
.gitignore
vendored
2
.gitignore
vendored
@ -39,3 +39,5 @@ out/
|
||||
.vscode/
|
||||
/dev/gpas*
|
||||
/deploy/.env
|
||||
/dev/gICS*
|
||||
/dev/gPAS*
|
||||
|
140
README.md
140
README.md
@ -1,6 +1,6 @@
|
||||
# ETL-Processor for bwHC data [](https://github.com/CCC-MF/etl-processor/actions/workflows/test.yml)
|
||||
# ETL-Processor for DNPM:DIP [](https://github.com/pcvolkmer/etl-processor/actions/workflows/test.yml)
|
||||
|
||||
Diese Anwendung versendet ein bwHC-MTB-File an das bwHC-Backend und pseudonymisiert die Patienten-ID.
|
||||
Diese Anwendung versendet ein bwHC-MTB-File im bwHC-Datenmodell 1.0 an DNPM:DIP und pseudonymisiert die Patienten-ID.
|
||||
|
||||
## Einordnung innerhalb einer DNPM-ETL-Strecke
|
||||
|
||||
@ -9,7 +9,7 @@ Diese Anwendung erlaubt das Entgegennehmen von HTTP/REST-Anfragen aus dem Onkost
|
||||
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.
|
||||
Löschanfragen werden immer als Löschanfrage an DNPM:DIP weitergeleitet.
|
||||
|
||||
Zudem ist eine minimalistische Weboberfläche integriert, die einen Einblick in den aktuellen Zustand der Anwendung gewährt.
|
||||
|
||||
@ -22,7 +22,17 @@ Die Erkennung von Duplikaten ist normalerweise immer aktiv, kann jedoch über de
|
||||
|
||||
### Datenübermittlung über HTTP/REST
|
||||
|
||||
Anfragen werden, wenn nicht als Duplikat behandelt, nach der Pseudonymisierung direkt an das bwHC-Backend gesendet.
|
||||
Anfragen werden, wenn nicht als Duplikat behandelt, nach der Pseudonymisierung direkt an DNPM:DIP gesendet.
|
||||
|
||||
Ein HTTP Request kann, angenommen die Installation erfolgte auf dem Host `dnpm.example.com` an nachfolgende URLs gesendet werden:
|
||||
|
||||
| HTTP-Request | URL | Consent-Status im Datensatz | Bemerkung |
|
||||
|--------------|-----------------------------------------|-----------------------------|---------------------------------------------------------------------------------|
|
||||
| `POST` | `https://dnpm.example.com/mtb` | `ACTIVE` | Die Anwendung verarbeitet den eingehenden Datensatz |
|
||||
| `POST` | `https://dnpm.example.com/mtb` | `REJECT` | Die Anwendung sendet einen Lösch-Request für die im Datensatz angegebene Pat-ID |
|
||||
| `DELETE` | `https://dnpm.example.com/mtb/12345678` | - | Die Anwendung sendet einen Lösch-Request für Pat-ID `12345678` |
|
||||
|
||||
Anstelle des Pfads `/mtb` kann auch, wie in Version 0.9 und älter üblich, `/mtbfile` verwendet werden.
|
||||
|
||||
### Datenübermittlung mit Apache Kafka
|
||||
|
||||
@ -33,27 +43,39 @@ Siehe hierzu auch: https://github.com/CCC-MF/kafka-to-bwhc
|
||||
|
||||
## Konfiguration
|
||||
|
||||
### 🔥 Wichtige Änderungen in Version 0.10
|
||||
|
||||
Ab Version 0.10 wird [DNPM:DIP](https://github.com/dnpm-dip) unterstützt und als Standardendpunkt verwendet.
|
||||
Soll noch das alte bwHC-Backend verwendet werden, so ist die Umgebungsvariable `APP_REST_IS_BWHC` auf `true` zu setzen.
|
||||
|
||||
### 🔥 Breaking Changes nach Version 0.10
|
||||
|
||||
In Versionen des ETL-Processors **nach Version 0.10** werden die folgenden Konfigurationsoptionen entfernt:
|
||||
|
||||
* `APP_KAFKA_TOPIC`: Nutzen Sie nun die Konfigurationsoption `APP_KAFKA_OUTPUT_TOPIC`
|
||||
* `APP_KAFKA_RESPONSE_TOPIC`: Nutzen Sie nun die Konfigurationsoption `APP_KAFKA_OUTPUT_RESPONSE_TOPIC`
|
||||
|
||||
Der Pfad zum Versenden von MTB-Daten ist nun offiziell `/mtb`.
|
||||
In Versionen **nach Version 0.10** wird die Unterstützung des Pfads `/mtbfile` entfernt.
|
||||
|
||||
### Pseudonymisierung der Patienten-ID
|
||||
|
||||
Wenn eine URI zu einer gPAS-Instanz (Version >= 2023.1.0) angegeben ist, wird diese verwendet.
|
||||
Ist diese nicht gesetzt. wird intern eine Anonymisierung der Patienten-ID vorgenommen.
|
||||
|
||||
* `APP_PSEUDONYMIZE_PREFIX`: Standortbezogenes Prefix - `UNKNOWN`, wenn nicht gesetzt
|
||||
* `APP_PSEUDONYMIZE_PREFIX`: Standortbezogenes Präfix - `UNKNOWN`, wenn nicht gesetzt
|
||||
* `APP_PSEUDONYMIZE_GENERATOR`: `BUILDIN` oder `GPAS` - `BUILDIN`, wenn nicht gesetzt
|
||||
|
||||
**Hinweise**:
|
||||
**Hinweis**
|
||||
|
||||
* 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.
|
||||
Die Pseudonymisierung erfolgt im ETL-Prozessor nur für die Patienten-ID.
|
||||
Andere IDs werden mithilfe des standortbezogenen Präfixes (erneut) anonymisiert, um für den aktuellen Kontext nicht
|
||||
vergleichbare IDs bereitzustellen.
|
||||
|
||||
#### Eingebaute Anonymisierung
|
||||
|
||||
Wurde keine oder die Verwendung der eingebauten Anonymisierung konfiguriert, so wird für die Patienten-ID der
|
||||
entsprechende SHA-256-Hash gebildet und Base64-codiert - hier ohne endende "=" - zuzüglich des konfigurierten Prefixes
|
||||
entsprechende SHA-256-Hash gebildet und Base64-codiert - hier ohne endende "=" - zuzüglich des konfigurierten Präfixes
|
||||
als Patienten-Pseudonym verwendet.
|
||||
|
||||
#### Pseudonymisierung mit gPAS
|
||||
@ -64,10 +86,36 @@ Wurde die Verwendung von gPAS konfiguriert, so sind weitere Angaben zu konfiguri
|
||||
* `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`~~: **Veraltet** - Root Zertifikat für gPas, falls es dediziert hinzugefügt werden muss.
|
||||
|
||||
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.
|
||||
### Einwilligung gICS
|
||||
Ab gIcs Version 2.13.0 kann per [REST-Schnittstelle](https://simplifier.net/guide/ttp-fhir-gateway-ig/ImplementationGuide-markdown-Einwilligungsmanagement-Operations-isConsented?version=current) der Einwilligungsstatus abgefragt werden.
|
||||
Vor der MTB-Übertragung kann der zum Sendezeitpunkt verfügbarer Einwilligungsstatus über Endpunkt *isConsented* abgefragt werden.
|
||||
|
||||
Falls Anbindung an gICS aktiviert wurde, wird der Einwilligungsstatus der MTB Datei ignoriert.
|
||||
Stattdessen werden vorhandene Einwilligungen abgefragt und in die MTB Datei eingebettet.
|
||||
|
||||
Es werden zwei Einwilligungsdomänen unterstützt, eine für Broad Consent und als zweites GenomDE Modelvorhaben §64e.
|
||||
|
||||
#### Hinweise
|
||||
1. Die aktuelle Impl. nimmt an, dass die hinterlegten Domänen der Einwilligungen ausschließlich für die genannten Art von Einwilligungen genutzt werden. Es finde keine weitere Filterung statt. Wir fragen pro Domäne die Schnittstelle `CurrentPolicyStatesForPerson` - siehe auch [IG TTP-FHIR Gateway
|
||||
](https://www.ths-greifswald.de/wp-content/uploads/tools/fhirgw/ig/2024-3-0/ImplementationGuide-markdown-Einwilligungsmanagement-Operations-currentPolicyStatesForPerson.html) ab.
|
||||
2. Die Einwilligung wird für den Patienten-Identifier der MTB abgerufen und anschließend durch das DNPM Pseudonym ersetzt.
|
||||
3. Abfragen von Einwilligungen über gesonderte Pseudonyme anstatt des MTB-Identifiers fehlt in der ersten Implementierung.
|
||||
4. Bei Verarbeitung von MTB Version 1.x Inhalten ist eine positive Einwilligung für die
|
||||
Weiterverarbeitung notwendig. Das Fehlen einer Einwilligung löst die Löschung des Patienten im Brückenkopf aus.
|
||||
|
||||
#### Konfiguration
|
||||
* `APP_CONSENT_GICS_ENABLED`: Aktiviert oder deaktiviert `true` oder `false`, `false` wenn nicht gesetzt.
|
||||
* `APP_CONSENT_GICS_CHECKGNOMEDE`: Aktiviert oder deaktiviert `true` oder `false`, `false` wenn nicht gesetzt. Versuche Einwilligungsdaten zu GENOM DE Modelvorhaben über gIcs abzurufen.
|
||||
* `APP_CONSENT_GICS_CHECKBROADCONSENT`: Aktiviert oder deaktiviert `true` oder `false`, `false` wenn nicht gesetzt. Versuche Einwilligungsdaten zu Broad Consent über gIcs abzurufen.
|
||||
* `APP_CONSENT_GICS_URI`: URI der gICS-Instanz (z.B. `http://localhost:8090/ttp-fhir/fhir/gics`)
|
||||
* `APP_CONSENT_GICS_USERNAME`: gIcs Basic-Auth Benutzername
|
||||
* `APP_CONSENT_GICS_PASSWORD`: gIcs Basic-Auth Passwort
|
||||
* `APP_CONSENT_GICS_PERSONIDENTIFIERSYSTEM`: Derzeit wird nur die PID unterstützt. wenn leer wird `https://ths-greifswald.de/fhir/gics/identifiers/Patienten-ID` angenommen
|
||||
* `APP_CONSENT_GICS_BROADCONSENTDOMAINNAME`: Domäne in der gIcs Broad Consent Einwilligungen verwaltet. Falls Wert leer, wird `MII` angenommen.
|
||||
* `APP_CONSENT_GICS_GNOMDECONSENTDOMAINNAME`: Domäne in der gIcs GenomDE Modelvorhaben §64e Einwilligungen verwaltet. Falls Wert leer, wird `GenomDE_MV` angenommen.
|
||||
* `APP_CONSENT_GICS_POLICYCODE`: Die entscheidende Objekt-ID der zu prüfenden Einwilligung-Regel. Falls leer wird `2.16.840.1.113883.3.1937.777.24.5.3.6` angenommen.
|
||||
* `APP_CONSENT_GICS_POLICYSYSTEM`: Das System der Einwilligung-Regel der Objekt-IDs. Falls leer wird `urn:oid:2.16.840.1.113883.3.1937.777.24.5.3` angenommen.
|
||||
|
||||
### Anmeldung mit einem Passwort
|
||||
|
||||
@ -77,7 +125,7 @@ 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.
|
||||
Ein Administrator-Passwort muss inklusive des Encoding-Präfixes vorliegen.
|
||||
|
||||
Hier Beispiele für das Beispielpasswort `very-secret`:
|
||||
|
||||
@ -134,7 +182,7 @@ 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.
|
||||
pseudonymisierte Patienten-ID sowie den Qualitätsbericht von DNPM:DIP einsehen.
|
||||
|
||||
Wurde kein Administrator-Account konfiguriert, sind diese Inhalte generell nicht verfügbar.
|
||||
|
||||
@ -150,7 +198,7 @@ zur Nutzung des MTB-File-Endpunkts eine HTTP-Basic-Authentifizierung voraussetze
|
||||
|
||||

|
||||
|
||||
In diesem Fall können den Endpunkt für das Onkostar-Plugin **[onkostar-plugin-dnpmexport](https://github.com/CCC-MF/onkostar-plugin-dnpmexport)** wie folgt konfigurieren:
|
||||
In diesem Fall kann der Endpunkt für das Onkostar-Plugin **[onkostar-plugin-dnpmexport](https://github.com/CCC-MF/onkostar-plugin-dnpmexport)** wie folgt konfiguriert werden:
|
||||
|
||||
```
|
||||
https://testonkostar:MTg1NTL...NGU4@etl.example.com/mtbfile
|
||||
@ -158,10 +206,12 @@ https://testonkostar:MTg1NTL...NGU4@etl.example.com/mtbfile
|
||||
|
||||
Ist die Verwendung von Tokens aktiv, werden Anfragen ohne die Angabe der Token-Information abgelehnt.
|
||||
|
||||
Alternativ kann eine Authentifizierung über Benutzername/Passwort oder OIDC erfolgen.
|
||||
|
||||
### Transformation von Werten
|
||||
|
||||
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.
|
||||
der von DNPM:DIP 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.
|
||||
@ -181,18 +231,21 @@ Werden sowohl REST als auch Kafka-Endpunkt konfiguriert, wird nur der REST-Endpu
|
||||
|
||||
#### REST
|
||||
|
||||
Folgende Umgebungsvariablen müssen gesetzt sein, damit ein bwHC-MTB-File an das bwHC-Backend gesendet wird:
|
||||
Folgende Umgebungsvariablen müssen gesetzt sein, damit ein bwHC-MTB-File an DNPM:DIP gesendet wird:
|
||||
|
||||
* `APP_REST_URI`: URI der zu benutzenden API der bwHC-Backend-Instanz. z.B.: `http://localhost:9000/bwhc/etl/api`
|
||||
* `APP_REST_URI`: URI der zu benutzenden API der Backend-Instanz. Zum Beispiel:
|
||||
* `http://localhost:9000/bwhc/etl/api` für **bwHC Backend**
|
||||
* `http://localhost:9000/api` für **dnpm:dip**
|
||||
* `APP_REST_USERNAME`: Basic-Auth-Benutzername für den REST-Endpunkt
|
||||
* `APP_REST_PASSWORD`: Basic-Auth-Passwort für den REST-Endpunkt
|
||||
* `APP_REST_IS_BWHC`: `true` für **bwHC Backend**, weglassen oder `false` für **dnpm:dip**
|
||||
|
||||
#### Kafka-Topics
|
||||
|
||||
Folgende Umgebungsvariablen müssen gesetzt sein, damit ein bwHC-MTB-File an ein Kafka-Topic übermittelt wird:
|
||||
|
||||
* `APP_KAFKA_OUTPUT_TOPIC`: Zu verwendendes Topic zum Versenden von Anfragen.
|
||||
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
|
||||
|
||||
@ -200,7 +253,7 @@ Wird keine Rückantwort über Apache Kafka empfangen und es gibt keine weitere M
|
||||
|
||||
Weitere Einstellungen können über die Parameter von Spring Kafka konfiguriert werden.
|
||||
|
||||
Lässt sich keine Verbindung zu dem bwHC-Backend aufbauen, wird eine Rückantwort mit Status-Code `900` erwartet, welchen es
|
||||
Lässt sich keine Verbindung zu dem Backend aufbauen, wird eine Rückantwort mit Status-Code `900` erwartet, welchen es
|
||||
für HTTP nicht gibt.
|
||||
|
||||
Wird die Umgebungsvariable `APP_KAFKA_INPUT_TOPIC` gesetzt, kann eine Nachricht auch über dieses Kafka-Topic an den ETL-Prozessor übermittelt werden.
|
||||
@ -234,19 +287,42 @@ kafka-configs.sh --bootstrap-server localhost:9092 --alter --topic test --add-co
|
||||
kafka-configs.sh --bootstrap-server localhost:9092 --alter --topic test --add-config cleanup.policy=[delete,compact]
|
||||
```
|
||||
|
||||
Da als Key eines Records die (pseudonymisierte) Patienten-ID und die (anonymisierte) Erkrankungs-ID verwendet wird,
|
||||
stehen mit obiger Konfiguration der Kafka-Topics nach 10 Sekunden nur noch der jeweils letzte Eintrag für den entsprechenden
|
||||
Key zur Verfügung.
|
||||
Da als Key eines Records die (pseudonymisierte) Patienten-ID verwendet wird, stehen mit obiger Konfiguration
|
||||
der Kafka-Topics nach 10 Sekunden nur noch der jeweils letzte Eintrag für den entsprechenden Key zur Verfügung.
|
||||
|
||||
Da der Key sowohl für die Records in Richtung bwHC-Backend für die Rückantwort identisch aufgebaut ist, lassen sich so
|
||||
Da der Key sowohl für die Records in Richtung DNPM:DIP, als auch für die Rückantwort identisch aufgebaut ist, lassen sich so
|
||||
auch im Falle eines Consent-Widerspruchs die enthaltenen Daten als auch die Offenlegung durch Verifikationsdaten in der
|
||||
Antwort effektiv verhindern, da diese nach 10 Sekunden gelöscht werden.
|
||||
|
||||
Es steht dann nur noch die jeweils letzten Information zur Verfügung, dass für einen Patienten/eine Erkrankung
|
||||
ein Consent-Widerspruch erfolgte.
|
||||
|
||||
Dieses Vorgehen empfiehlt sich, wenn Sie gespeicherte Records nachgelagert für andere Auswertungen verwenden möchten.
|
||||
|
||||
### Antworten und Statusauswertung
|
||||
|
||||
Anfragen an das bwHC-Backend aus Versionen bis 0.9.x wurden wie folgt behandelt:
|
||||
|
||||
| HTTP-Response | Status |
|
||||
|----------------|-----------|
|
||||
| `HTTP 200` | `SUCCESS` |
|
||||
| `HTTP 201` | `WARNING` |
|
||||
| `HTTP 400-...` | `ERROR` |
|
||||
|
||||
Dies konnte dazu führen, dass zwar mit einem `HTTP 201` geantwortet wurde, aber dennoch in der Issue-Liste die
|
||||
Severity `error` aufgetaucht ist.
|
||||
|
||||
Ab Version 0.10 wird die Issue-Liste der Antwort verwendet und die darion enthaltene höchste Severity-Stufe als Ergebnis verwendet.
|
||||
|
||||
| Höchste Severity | Status |
|
||||
|------------------|-----------|
|
||||
| `info` | `SUCCESS` |
|
||||
| `warning` | `WARNING` |
|
||||
| `error`, `fatal` | `ERROR` |
|
||||
|
||||
## Docker-Images
|
||||
|
||||
Diese Anwendung ist auch als Docker-Image verfügbar: https://github.com/CCC-MF/etl-processor/pkgs/container/etl-processor
|
||||
Diese Anwendung ist auch als Docker-Image verfügbar: https://github.com/pcvolkmer/etl-processor/pkgs/container/etl-processor
|
||||
|
||||
### Images lokal bauen
|
||||
|
||||
@ -305,7 +381,7 @@ auf Docker-Compose mit der gestartet werden kann.
|
||||
|
||||
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
|
||||
Dabei werden, je nachdem welche Header durch den Reverse-Proxy gesendet werden auch Protokoll, Host oder auch Path-Präfix
|
||||
automatisch erkannt und verwendet werden. Dadurch ist z.B. eine abweichende Angabe des Pfads problemlos möglich.
|
||||
|
||||
#### Beispiel *Traefik* (mit Docker-Labels):
|
||||
@ -359,3 +435,5 @@ Die Datei `application-dev.yml` enthält hierzu die Konfiguration für das Profi
|
||||
|
||||
Beim Ausführen der Integrationstests wird eine Testdatenbank in einem Docker-Container gestartet.
|
||||
Siehe hier auch die Klasse `AbstractTestcontainerTest` unter `src/integrationTest`.
|
||||
|
||||
Ein einfaches Entwickler-Setup inklusive DNPM:DIP ist mit Hilfe von https://github.com/pcvolkmer/dnpmdip-devenv realisierbar.
|
||||
|
@ -1,30 +1,36 @@
|
||||
import org.gradle.api.tasks.testing.logging.TestLogEvent
|
||||
import org.jetbrains.kotlin.gradle.dsl.JvmTarget
|
||||
import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
|
||||
import org.springframework.boot.gradle.tasks.bundling.BootBuildImage
|
||||
|
||||
plugins {
|
||||
war
|
||||
id("org.springframework.boot") version "3.2.3"
|
||||
id("io.spring.dependency-management") version "1.1.4"
|
||||
kotlin("jvm") version "1.9.22"
|
||||
kotlin("plugin.spring") version "1.9.22"
|
||||
id("org.springframework.boot") version "3.5.0"
|
||||
id("io.spring.dependency-management") version "1.1.7"
|
||||
kotlin("jvm") version "1.9.25"
|
||||
kotlin("plugin.spring") version "1.9.25"
|
||||
jacoco
|
||||
}
|
||||
|
||||
group = "de.ukw.ccc"
|
||||
version = "0.8.0"
|
||||
group = "dev.dnpm"
|
||||
version = "0.11.0-SNAPSHOT"
|
||||
|
||||
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",
|
||||
"bwhc-dto-java" to "0.4.0",
|
||||
"mtb-dto" to "0.1.0-SNAPSHOT",
|
||||
"hapi-fhir" to "7.6.0",
|
||||
"mockito-kotlin" to "5.4.0",
|
||||
"archunit" to "1.3.0",
|
||||
// Webjars
|
||||
"webjars-locator" to "0.52",
|
||||
"echarts" to "5.4.3",
|
||||
"htmx.org" to "1.9.10"
|
||||
"htmx.org" to "1.9.12"
|
||||
)
|
||||
|
||||
java {
|
||||
sourceCompatibility = JavaVersion.VERSION_21
|
||||
toolchain {
|
||||
languageVersion = JavaLanguageVersion.of(21)
|
||||
}
|
||||
}
|
||||
|
||||
sourceSets {
|
||||
@ -43,9 +49,18 @@ configurations {
|
||||
compileOnly {
|
||||
extendsFrom(configurations.annotationProcessor.get())
|
||||
}
|
||||
|
||||
all {
|
||||
resolutionStrategy {
|
||||
cacheChangingModulesFor(5, "minutes")
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
repositories {
|
||||
maven {
|
||||
url = uri("https://git.dnpm.dev/api/packages/public-snapshots/maven")
|
||||
}
|
||||
maven {
|
||||
url = uri("https://git.dnpm.dev/api/packages/public/maven")
|
||||
}
|
||||
@ -62,35 +77,46 @@ dependencies {
|
||||
implementation("org.thymeleaf.extras:thymeleaf-extras-springsecurity6")
|
||||
implementation("com.fasterxml.jackson.module:jackson-module-kotlin")
|
||||
implementation("org.springframework.kafka:spring-kafka")
|
||||
implementation("org.flywaydb:flyway-database-postgresql")
|
||||
implementation("org.flywaydb:flyway-mysql")
|
||||
implementation("commons-codec:commons-codec")
|
||||
implementation("io.projectreactor.kotlin:reactor-kotlin-extensions")
|
||||
implementation("de.ukw.ccc:bwhc-dto-java:${versions["bwhc-dto-java"]}")
|
||||
implementation("dev.pcvolkmer.mv64e:mtb-dto:${versions["mtb-dto"]}") { isChanging = true }
|
||||
implementation("ca.uhn.hapi.fhir:hapi-fhir-base:${versions["hapi-fhir"]}")
|
||||
implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${versions["hapi-fhir"]}")
|
||||
implementation("org.apache.httpcomponents.client5:httpclient5:${versions["httpclient5"]}")
|
||||
implementation("org.apache.httpcomponents.client5:httpclient5")
|
||||
implementation("com.jayway.jsonpath:json-path")
|
||||
implementation("org.webjars:webjars-locator:0.50")
|
||||
implementation("org.webjars:webjars-locator:${versions["webjars-locator"]}")
|
||||
implementation("org.webjars.npm:echarts:${versions["echarts"]}")
|
||||
implementation("org.webjars.npm:htmx.org:${versions["htmx.org"]}")
|
||||
|
||||
runtimeOnly("org.mariadb.jdbc:mariadb-java-client")
|
||||
runtimeOnly("org.postgresql:postgresql")
|
||||
|
||||
developmentOnly("org.springframework.boot:spring-boot-devtools")
|
||||
developmentOnly("org.springframework.boot:spring-boot-docker-compose")
|
||||
|
||||
annotationProcessor("org.springframework.boot:spring-boot-configuration-processor")
|
||||
|
||||
providedRuntime("org.springframework.boot:spring-boot-starter-tomcat")
|
||||
|
||||
testImplementation("org.springframework.boot:spring-boot-starter-test")
|
||||
testImplementation("org.springframework.security:spring-security-test")
|
||||
testImplementation("io.projectreactor:reactor-test")
|
||||
testImplementation("org.mockito.kotlin:mockito-kotlin:${versions["mockito-kotlin"]}")
|
||||
|
||||
integrationTestImplementation("org.testcontainers:junit-jupiter")
|
||||
integrationTestImplementation("org.testcontainers:postgresql")
|
||||
integrationTestImplementation("com.tngtech.archunit:archunit:${versions["archunit"]}")
|
||||
integrationTestImplementation("org.htmlunit:htmlunit")
|
||||
integrationTestImplementation("org.springframework:spring-webflux")
|
||||
}
|
||||
|
||||
tasks.withType<KotlinCompile> {
|
||||
kotlinOptions {
|
||||
freeCompilerArgs += "-Xjsr305=strict"
|
||||
jvmTarget = "21"
|
||||
compilerOptions {
|
||||
freeCompilerArgs.add("-Xjsr305=strict")
|
||||
jvmTarget.set(JvmTarget.JVM_21)
|
||||
}
|
||||
}
|
||||
|
||||
@ -101,8 +127,9 @@ tasks.withType<Test> {
|
||||
}
|
||||
}
|
||||
|
||||
task<Test>("integrationTest") {
|
||||
tasks.register<Test>("integrationTest") {
|
||||
description = "Runs integration tests"
|
||||
group = "verification"
|
||||
|
||||
testClassesDirs = sourceSets["integrationTest"].output.classesDirs
|
||||
classpath = sourceSets["integrationTest"].runtimeClasspath
|
||||
@ -110,8 +137,24 @@ task<Test>("integrationTest") {
|
||||
shouldRunAfter("test")
|
||||
}
|
||||
|
||||
tasks.register("allTests") {
|
||||
description = "Run all tests"
|
||||
group = JavaBasePlugin.VERIFICATION_GROUP
|
||||
dependsOn(tasks.withType<Test>())
|
||||
}
|
||||
|
||||
tasks.jacocoTestReport {
|
||||
dependsOn("allTests")
|
||||
|
||||
executionData(fileTree(project.rootDir.absolutePath).include("**/build/jacoco/*.exec"))
|
||||
|
||||
reports {
|
||||
xml.required = true
|
||||
}
|
||||
}
|
||||
|
||||
tasks.named<BootBuildImage>("bootBuildImage") {
|
||||
imageName.set("ghcr.io/ccc-mf/etl-processor")
|
||||
imageName.set("ghcr.io/pcvolkmer/etl-processor")
|
||||
|
||||
// Binding for CA Certs
|
||||
bindings.set(listOf(
|
||||
@ -121,7 +164,7 @@ tasks.named<BootBuildImage>("bootBuildImage") {
|
||||
environment.set(environment.get() + mapOf(
|
||||
// Enable this line to embed CA Certs into image on build time
|
||||
//"BP_EMBED_CERTS" to "true",
|
||||
"BP_OCI_SOURCE" to "https://github.com/CCC-MF/etl-processor",
|
||||
"BP_OCI_SOURCE" to "https://github.com/pcvolkmer/etl-processor",
|
||||
"BP_OCI_LICENSES" to "AGPLv3",
|
||||
"BP_OCI_DESCRIPTION" to "ETL Processor for bwHC MTB files"
|
||||
))
|
||||
|
@ -18,6 +18,9 @@ services:
|
||||
APP_KAFKA_GROUP_ID: ${DNPM_KAFKA_GROUP_ID}
|
||||
APP_KAFKA_RESPONSE_TOPIC: ${DNPM_KAFKA_RESPONSE_TOPIC}
|
||||
APP_REST_URI: ${DNPM_BWHC_REST_URI}
|
||||
APP_REST_USERNAME: ${DNPM_BWHC_REST_USERNAME}
|
||||
APP_REST_PASSWORD: ${DNPM_BWHC_REST_PASSWORD}
|
||||
APP_REST_IS_BWHC: ${DNPM_BWHC_REST_IS_BWHC}
|
||||
APP_SECURITY_ADMIN_USER: ${DNPM_ADMIN_USER}
|
||||
APP_SECURITY_ADMIN_PASSWORD: ${DNPM_ADMIN_PASSWORD}
|
||||
SPRING_DATASOURCE_URL: ${DNPM_DATASOURCE_URL}
|
||||
|
@ -28,6 +28,9 @@ DNPM_DATASOURCE_URL=jdbc:mariadb://dnpm-monitor-db:3306/$DNPM_MARIADB_DB
|
||||
## TARGET SYSTEMS CONFIG
|
||||
# in case of direct access to bwhc enter endpoint url here
|
||||
DNPM_BWHC_REST_URI=
|
||||
DNPM_BWHC_REST_USERNAME=
|
||||
DNPM_BWHC_REST_PASSWORD=
|
||||
DNPM_BWHC_REST_IS_BWHC=false
|
||||
|
||||
# produce mtb files to this topic - values 'false' disabling kafka processing
|
||||
DNPM_KAFKA_TOPIC=false
|
||||
|
@ -16,9 +16,15 @@ services:
|
||||
KAFKA_CFG_AUTO_CREATE_TOPICS_ENABLE: true
|
||||
KAFKA_CFG_CONTROLLER_QUORUM_VOTERS: 0@kafka:9093
|
||||
KAFKA_CFG_CONTROLLER_LISTENER_NAMES: CONTROLLER
|
||||
healthcheck:
|
||||
test: kafka-topics --bootstrap-server kafka:9092 --list
|
||||
interval: 30s
|
||||
timeout: 10s
|
||||
retries: 3
|
||||
|
||||
## Use AKHQ as Kafka web frontend
|
||||
akhq:
|
||||
image: tchiotludo/akhq:0.21.0
|
||||
image: tchiotludo/akhq:0.25.0
|
||||
environment:
|
||||
AKHQ_CONFIGURATION: |
|
||||
akhq:
|
||||
@ -32,6 +38,8 @@ services:
|
||||
ports:
|
||||
- "8084:8080"
|
||||
|
||||
|
||||
## For use with MariaDB
|
||||
mariadb:
|
||||
image: mariadb:10
|
||||
ports:
|
||||
@ -42,6 +50,7 @@ services:
|
||||
MARIADB_PASSWORD: dev
|
||||
MARIADB_ROOT_PASSWORD: dev
|
||||
|
||||
## For use with Postgres
|
||||
# postgres:
|
||||
# image: postgres:alpine
|
||||
# ports:
|
||||
|
@ -2,31 +2,55 @@ version: '3.7'
|
||||
|
||||
services:
|
||||
|
||||
zoo1:
|
||||
image: zookeeper:3.8.0
|
||||
hostname: zoo1
|
||||
zoo:
|
||||
image: zookeeper:3.9.2
|
||||
restart: unless-stopped
|
||||
ports:
|
||||
- "2181:2181"
|
||||
environment:
|
||||
ZOO_MY_ID: 1
|
||||
ZOO_PORT: 2181
|
||||
ZOO_SERVERS: server.1=zoo1:2888:3888;2181
|
||||
ZOO_SERVERS: server.1=zoo:2888:3888;2181
|
||||
|
||||
kafka1:
|
||||
image: confluentinc/cp-kafka:7.2.1
|
||||
hostname: kafka1
|
||||
kafka:
|
||||
image: confluentinc/cp-kafka:7.6.1
|
||||
ports:
|
||||
- "9092:9092"
|
||||
environment:
|
||||
KAFKA_ADVERTISED_LISTENERS: LISTENER_DOCKER_INTERNAL://kafka1:19092,LISTENER_DOCKER_EXTERNAL://${DOCKER_HOST_IP:-127.0.0.1}:9092
|
||||
KAFKA_LISTENER_SECURITY_PROTOCOL_MAP: LISTENER_DOCKER_INTERNAL:PLAINTEXT,LISTENER_DOCKER_EXTERNAL:PLAINTEXT
|
||||
KAFKA_ADVERTISED_LISTENERS: LISTENER_DOCKER_INTERNAL://kafka:19092,LISTENER_DOCKER_EXTERNAL://172.17.0.1:9093,LISTENER_EXTERNAL://127.0.0.1:9092
|
||||
KAFKA_LISTENER_SECURITY_PROTOCOL_MAP: LISTENER_DOCKER_INTERNAL:PLAINTEXT,LISTENER_DOCKER_EXTERNAL:PLAINTEXT,LISTENER_EXTERNAL:PLAINTEXT
|
||||
KAFKA_INTER_BROKER_LISTENER_NAME: LISTENER_DOCKER_INTERNAL
|
||||
KAFKA_ZOOKEEPER_CONNECT: "zoo1:2181"
|
||||
KAFKA_ZOOKEEPER_CONNECT: zoo:2181
|
||||
KAFKA_BROKER_ID: 1
|
||||
KAFKA_LOG4J_LOGGERS: "kafka.controller=INFO,kafka.producer.async.DefaultEventHandler=INFO,state.change.logger=INFO"
|
||||
KAFKA_LOG4J_LOGGERS: kafka.controller=INFO,kafka.producer.async.DefaultEventHandler=INFO,state.change.logger=INFO
|
||||
KAFKA_OFFSETS_TOPIC_REPLICATION_FACTOR: 1
|
||||
KAFKA_MESSAGE_MAX_BYTES: 5242880
|
||||
KAFKA_REPLICA_FETCH_MAX_BYTES: 5242880
|
||||
KAFKA_COMPRESSION_TYPE: gzip
|
||||
depends_on:
|
||||
- zoo1
|
||||
- zoo
|
||||
healthcheck:
|
||||
test: kafka-topics --bootstrap-server kafka:9092 --list
|
||||
interval: 30s
|
||||
timeout: 10s
|
||||
retries: 3
|
||||
|
||||
akhq:
|
||||
image: tchiotludo/akhq:0.25.0
|
||||
environment:
|
||||
AKHQ_CONFIGURATION: |
|
||||
akhq:
|
||||
ui-options:
|
||||
topic.show-all-consumer-groups: true
|
||||
topic-data.sort: NEWEST
|
||||
connections:
|
||||
docker-kafka-server:
|
||||
properties:
|
||||
bootstrap.servers: "kafka:19092"
|
||||
ports:
|
||||
- "9000:8080"
|
||||
depends_on:
|
||||
- kafka
|
||||
|
||||
kafka-rest-proxy:
|
||||
image: confluentinc/cp-kafka-rest:7.2.1
|
||||
@ -40,8 +64,8 @@ services:
|
||||
KAFKA_REST_HOST_NAME: kafka-rest-proxy
|
||||
KAFKA_REST_BOOTSTRAP_SERVERS: PLAINTEXT://kafka1:19092
|
||||
depends_on:
|
||||
- zoo1
|
||||
- kafka1
|
||||
- zoo
|
||||
- kafka
|
||||
|
||||
kafka-connect:
|
||||
image: confluentinc/cp-kafka-connect:7.2.1
|
||||
@ -67,24 +91,6 @@ services:
|
||||
#volumes:
|
||||
# - ./connectors:/etc/kafka-connect/jars/
|
||||
depends_on:
|
||||
- zoo1
|
||||
- kafka1
|
||||
- zoo
|
||||
- kafka
|
||||
- kafka-rest-proxy
|
||||
|
||||
akhq:
|
||||
image: tchiotludo/akhq:0.21.0
|
||||
environment:
|
||||
AKHQ_CONFIGURATION: |
|
||||
akhq:
|
||||
connections:
|
||||
docker-kafka-server:
|
||||
properties:
|
||||
bootstrap.servers: "kafka1:19092"
|
||||
connect:
|
||||
- name: "kafka-connect"
|
||||
url: "http://kafka-connect:8083"
|
||||
ports:
|
||||
- "8084:8080"
|
||||
depends_on:
|
||||
- kafka1
|
||||
- kafka-connect
|
||||
|
BIN
docs/etl.png
BIN
docs/etl.png
Binary file not shown.
Before Width: | Height: | Size: 75 KiB After Width: | Height: | Size: 115 KiB |
2
gradle/wrapper/gradle-wrapper.properties
vendored
2
gradle/wrapper/gradle-wrapper.properties
vendored
@ -1,6 +1,6 @@
|
||||
distributionBase=GRADLE_USER_HOME
|
||||
distributionPath=wrapper/dists
|
||||
distributionUrl=https\://services.gradle.org/distributions/gradle-8.6-bin.zip
|
||||
distributionUrl=https\://services.gradle.org/distributions/gradle-8.13-bin.zip
|
||||
networkTimeout=10000
|
||||
zipStoreBase=GRADLE_USER_HOME
|
||||
zipStorePath=wrapper/dists
|
||||
|
@ -23,6 +23,7 @@ import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import de.ukw.ccc.bwhc.dto.*
|
||||
import dev.dnpm.etl.processor.monitoring.RequestRepository
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import dev.dnpm.etl.processor.output.BwhcV1MtbFileRequest
|
||||
import dev.dnpm.etl.processor.output.MtbFileSender
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
@ -33,10 +34,10 @@ import org.mockito.kotlin.*
|
||||
import org.springframework.beans.factory.annotation.Autowired
|
||||
import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc
|
||||
import org.springframework.boot.test.context.SpringBootTest
|
||||
import org.springframework.boot.test.mock.mockito.MockBean
|
||||
import org.springframework.context.ApplicationContext
|
||||
import org.springframework.http.MediaType
|
||||
import org.springframework.test.context.TestPropertySource
|
||||
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||
import org.springframework.test.web.servlet.MockMvc
|
||||
import org.springframework.test.web.servlet.post
|
||||
@ -45,7 +46,7 @@ import org.testcontainers.junit.jupiter.Testcontainers
|
||||
@Testcontainers
|
||||
@ExtendWith(SpringExtension::class)
|
||||
@SpringBootTest
|
||||
@MockBean(MtbFileSender::class)
|
||||
@MockitoBean(types = [MtbFileSender::class])
|
||||
@TestPropertySource(
|
||||
properties = [
|
||||
"app.rest.uri=http://example.com",
|
||||
@ -73,7 +74,7 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
|
||||
)
|
||||
inner class TransformationTest {
|
||||
|
||||
@MockBean
|
||||
@MockitoBean
|
||||
private lateinit var mtbFileSender: MtbFileSender
|
||||
|
||||
@Autowired
|
||||
@ -91,7 +92,7 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
|
||||
fun mtbFileIsTransformed() {
|
||||
doAnswer {
|
||||
MtbFileSender.Response(RequestStatus.SUCCESS)
|
||||
}.whenever(mtbFileSender).send(any<MtbFileSender.MtbFileRequest>())
|
||||
}.whenever(mtbFileSender).send(any<BwhcV1MtbFileRequest>())
|
||||
|
||||
val mtbFile = MtbFile.builder()
|
||||
.withPatient(
|
||||
@ -134,9 +135,9 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
|
||||
}
|
||||
}
|
||||
|
||||
val captor = argumentCaptor<MtbFileSender.MtbFileRequest>()
|
||||
val captor = argumentCaptor<BwhcV1MtbFileRequest>()
|
||||
verify(mtbFileSender).send(captor.capture())
|
||||
assertThat(captor.firstValue.mtbFile.diagnoses).hasSize(1).allMatch { diagnosis ->
|
||||
assertThat(captor.firstValue.content.diagnoses).hasSize(1).allMatch { diagnosis ->
|
||||
diagnosis.icd10.version == "2014"
|
||||
}
|
||||
}
|
||||
|
@ -0,0 +1,73 @@
|
||||
package dev.dnpm.etl.processor
|
||||
|
||||
import com.tngtech.archunit.core.domain.JavaClasses
|
||||
import com.tngtech.archunit.core.importer.ClassFileImporter
|
||||
import com.tngtech.archunit.lang.syntax.ArchRuleDefinition.classes
|
||||
import com.tngtech.archunit.lang.syntax.ArchRuleDefinition.noClasses
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.springframework.data.repository.Repository
|
||||
|
||||
class EtlProcessorArchTest {
|
||||
|
||||
private lateinit var noTestClasses: JavaClasses
|
||||
|
||||
@BeforeEach
|
||||
fun setUp() {
|
||||
this.noTestClasses = ClassFileImporter()
|
||||
.withImportOption { !(it.contains("/test/") || it.contains("/integrationTest/")) }
|
||||
.importPackages("dev.dnpm.etl.processor")
|
||||
}
|
||||
|
||||
@Test
|
||||
fun noClassesInInputPackageShouldDependOnMonitoringPackage() {
|
||||
val rule = noClasses()
|
||||
.that()
|
||||
.resideInAPackage("..input")
|
||||
.should().dependOnClassesThat()
|
||||
.resideInAnyPackage("..monitoring")
|
||||
|
||||
rule.check(noTestClasses)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun noClassesInInputPackageShouldDependOnRepositories() {
|
||||
val rule = noClasses()
|
||||
.that()
|
||||
.resideInAPackage("..input")
|
||||
.should().dependOnClassesThat().haveSimpleNameEndingWith("Repository")
|
||||
|
||||
rule.check(noTestClasses)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun noClassesInOutputPackageShouldDependOnRepositories() {
|
||||
val rule = noClasses()
|
||||
.that()
|
||||
.resideInAPackage("..output")
|
||||
.should().dependOnClassesThat().haveSimpleNameEndingWith("Repository")
|
||||
|
||||
rule.check(noTestClasses)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun noClassesInWebPackageShouldDependOnRepositories() {
|
||||
val rule = noClasses()
|
||||
.that()
|
||||
.resideInAPackage("..web")
|
||||
.should().dependOnClassesThat().haveSimpleNameEndingWith("Repository")
|
||||
|
||||
rule.check(noTestClasses)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun repositoryClassNamesShouldEndWithRepository() {
|
||||
val rule = classes()
|
||||
.that()
|
||||
.areInterfaces().and().areAssignableTo(Repository::class.java)
|
||||
.should().haveSimpleNameEndingWith("Repository")
|
||||
|
||||
rule.check(noTestClasses)
|
||||
}
|
||||
|
||||
}
|
@ -26,9 +26,9 @@ import dev.dnpm.etl.processor.output.KafkaMtbFileSender
|
||||
import dev.dnpm.etl.processor.output.RestMtbFileSender
|
||||
import dev.dnpm.etl.processor.pseudonym.AnonymizingGenerator
|
||||
import dev.dnpm.etl.processor.pseudonym.GpasPseudonymGenerator
|
||||
import dev.dnpm.etl.processor.security.TokenRepository
|
||||
import dev.dnpm.etl.processor.security.TokenService
|
||||
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||
import 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
|
||||
@ -36,24 +36,25 @@ import org.junit.jupiter.api.assertThrows
|
||||
import org.springframework.beans.factory.NoSuchBeanDefinitionException
|
||||
import org.springframework.boot.autoconfigure.kafka.KafkaAutoConfiguration
|
||||
import org.springframework.boot.test.context.SpringBootTest
|
||||
import org.springframework.boot.test.mock.mockito.MockBean
|
||||
import org.springframework.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
|
||||
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||
|
||||
@SpringBootTest
|
||||
@ContextConfiguration(classes = [
|
||||
AppConfiguration::class,
|
||||
AppSecurityConfiguration::class,
|
||||
KafkaAutoConfiguration::class,
|
||||
AppKafkaConfiguration::class,
|
||||
AppRestConfiguration::class
|
||||
])
|
||||
@MockBean(ObjectMapper::class)
|
||||
@ContextConfiguration(
|
||||
classes = [
|
||||
AppConfiguration::class,
|
||||
AppSecurityConfiguration::class,
|
||||
KafkaAutoConfiguration::class,
|
||||
AppKafkaConfiguration::class,
|
||||
AppRestConfiguration::class
|
||||
]
|
||||
)
|
||||
@MockitoBean(types = [ObjectMapper::class])
|
||||
@TestPropertySource(
|
||||
properties = [
|
||||
"app.pseudonymize.generator=BUILDIN",
|
||||
@ -86,7 +87,7 @@ class AppConfigurationTest {
|
||||
"app.kafka.group-id=test"
|
||||
]
|
||||
)
|
||||
@MockBean(RequestRepository::class)
|
||||
@MockitoBean(types = [RequestRepository::class])
|
||||
inner class AppConfigurationKafkaTest(private val context: ApplicationContext) {
|
||||
|
||||
@Test
|
||||
@ -145,7 +146,7 @@ class AppConfigurationTest {
|
||||
"app.kafka.group-id=test"
|
||||
]
|
||||
)
|
||||
@MockBean(RequestProcessor::class)
|
||||
@MockitoBean(types = [RequestProcessor::class])
|
||||
inner class AppConfigurationUsingKafkaInputTest(private val context: ApplicationContext) {
|
||||
|
||||
@Test
|
||||
@ -181,40 +182,7 @@ class AppConfigurationTest {
|
||||
@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=",
|
||||
"app.pseudonymize.generator=buildin"
|
||||
]
|
||||
)
|
||||
inner class AppConfigurationPseudonymizeGeneratorBuildinTest(private val context: ApplicationContext) {
|
||||
@ -229,8 +197,7 @@ class AppConfigurationTest {
|
||||
@Nested
|
||||
@TestPropertySource(
|
||||
properties = [
|
||||
"app.pseudonymize.generator=gpas",
|
||||
"app.pseudonymizer=",
|
||||
"app.pseudonymize.generator=gpas"
|
||||
]
|
||||
)
|
||||
inner class AppConfigurationPseudonymizeGeneratorGpasTest(private val context: ApplicationContext) {
|
||||
@ -248,11 +215,13 @@ class AppConfigurationTest {
|
||||
"app.security.enable-tokens=true"
|
||||
]
|
||||
)
|
||||
@MockBeans(value = [
|
||||
MockBean(InMemoryUserDetailsManager::class),
|
||||
MockBean(PasswordEncoder::class),
|
||||
MockBean(TokenRepository::class)
|
||||
])
|
||||
@MockitoBean(
|
||||
types = [
|
||||
InMemoryUserDetailsManager::class,
|
||||
PasswordEncoder::class,
|
||||
TokenRepository::class
|
||||
]
|
||||
)
|
||||
inner class AppConfigurationTokenEnabledTest(private val context: ApplicationContext) {
|
||||
|
||||
@Test
|
||||
@ -263,11 +232,13 @@ class AppConfigurationTest {
|
||||
}
|
||||
|
||||
@Nested
|
||||
@MockBeans(value = [
|
||||
MockBean(InMemoryUserDetailsManager::class),
|
||||
MockBean(PasswordEncoder::class),
|
||||
MockBean(TokenRepository::class)
|
||||
])
|
||||
@MockitoBean(
|
||||
types = [
|
||||
InMemoryUserDetailsManager::class,
|
||||
PasswordEncoder::class,
|
||||
TokenRepository::class
|
||||
]
|
||||
)
|
||||
inner class AppConfigurationTokenDisabledTest(private val context: ApplicationContext) {
|
||||
|
||||
@Test
|
||||
|
30
src/integrationTest/kotlin/dev/dnpm/etl/processor/helpers.kt
Normal file
30
src/integrationTest/kotlin/dev/dnpm/etl/processor/helpers.kt
Normal file
@ -0,0 +1,30 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
* by the Free Software Foundation, either version 3 of the License, or
|
||||
* (at your option) any later version.
|
||||
*
|
||||
* This program is distributed in the hope that it will be useful,
|
||||
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
* GNU Affero General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Affero General Public License
|
||||
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
*/
|
||||
|
||||
package dev.dnpm.etl.processor
|
||||
|
||||
import org.mockito.ArgumentMatchers
|
||||
|
||||
@Suppress("UNCHECKED_CAST")
|
||||
inline fun <reified T> anyValueClass(): T {
|
||||
val unboxedClass = T::class.java.declaredFields.first().type
|
||||
return ArgumentMatchers.any(unboxedClass as Class<T>)
|
||||
?: T::class.java.getDeclaredMethod("box-impl", unboxedClass)
|
||||
.invoke(null, null) as T
|
||||
}
|
@ -21,26 +21,29 @@ package dev.dnpm.etl.processor.input
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import de.ukw.ccc.bwhc.dto.*
|
||||
import dev.dnpm.etl.processor.anyValueClass
|
||||
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||
import dev.dnpm.etl.processor.consent.ConsentCheckFileBased
|
||||
import dev.dnpm.etl.processor.consent.TtpConsentStatus
|
||||
import dev.dnpm.etl.processor.consent.ICheckConsent
|
||||
import dev.dnpm.etl.processor.security.TokenRepository
|
||||
import dev.dnpm.etl.processor.security.UserRoleRepository
|
||||
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.Nested
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.mockito.ArgumentMatchers.anyString
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.mockito.kotlin.any
|
||||
import org.mockito.kotlin.never
|
||||
import org.mockito.kotlin.times
|
||||
import org.mockito.kotlin.verify
|
||||
import org.mockito.kotlin.*
|
||||
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.oauth2.client.registration.ClientRegistrationRepository
|
||||
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.anonymous
|
||||
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user
|
||||
import org.springframework.test.context.ContextConfiguration
|
||||
import org.springframework.test.context.TestPropertySource
|
||||
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||
import org.springframework.test.web.servlet.MockMvc
|
||||
import org.springframework.test.web.servlet.delete
|
||||
@ -51,16 +54,18 @@ import org.springframework.test.web.servlet.post
|
||||
@ContextConfiguration(
|
||||
classes = [
|
||||
MtbFileRestController::class,
|
||||
AppSecurityConfiguration::class
|
||||
AppSecurityConfiguration::class,
|
||||
ConsentCheckFileBased::class, ICheckConsent::class
|
||||
]
|
||||
)
|
||||
@MockBean(TokenRepository::class, RequestProcessor::class)
|
||||
@MockitoBean(types = [TokenRepository::class, RequestProcessor::class])
|
||||
@TestPropertySource(
|
||||
properties = [
|
||||
"app.pseudonymize.generator=BUILDIN",
|
||||
"app.security.admin-user=admin",
|
||||
"app.security.admin-password={noop}very-secret",
|
||||
"app.security.enable-tokens=true"
|
||||
"app.security.enable-tokens=true",
|
||||
"app.consent.gics.enabled=false"
|
||||
]
|
||||
)
|
||||
class MtbFileRestControllerTest {
|
||||
@ -88,7 +93,20 @@ class MtbFileRestControllerTest {
|
||||
status { isAccepted() }
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processMtbFile(any())
|
||||
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldGrantPermissionToSendMtbFileToAdminUser() {
|
||||
mockMvc.post("/mtbfile") {
|
||||
with(user("onkostarserver").roles("ADMIN"))
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
content = ObjectMapper().writeValueAsString(mtbFile)
|
||||
}.andExpect {
|
||||
status { isAccepted() }
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
|
||||
}
|
||||
|
||||
@Test
|
||||
@ -101,7 +119,20 @@ class MtbFileRestControllerTest {
|
||||
status { isUnauthorized() }
|
||||
}
|
||||
|
||||
verify(requestProcessor, never()).processMtbFile(any())
|
||||
verify(requestProcessor, never()).processMtbFile(any<MtbFile>())
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldDenyPermissionToSendMtbFileForUser() {
|
||||
mockMvc.post("/mtbfile") {
|
||||
with(user("fakeuser").roles("USER"))
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
content = ObjectMapper().writeValueAsString(mtbFile)
|
||||
}.andExpect {
|
||||
status { isForbidden() }
|
||||
}
|
||||
|
||||
verify(requestProcessor, never()).processMtbFile(any<MtbFile>())
|
||||
}
|
||||
|
||||
@Test
|
||||
@ -112,7 +143,7 @@ class MtbFileRestControllerTest {
|
||||
status { isAccepted() }
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processDeletion(anyString())
|
||||
verify(requestProcessor, times(1)).processDeletion(anyValueClass(), eq(TtpConsentStatus.UNKNOWN_CHECK_FILE))
|
||||
}
|
||||
|
||||
@Test
|
||||
@ -123,7 +154,47 @@ class MtbFileRestControllerTest {
|
||||
status { isUnauthorized() }
|
||||
}
|
||||
|
||||
verify(requestProcessor, never()).processDeletion(anyString())
|
||||
verify(requestProcessor, never()).processDeletion(anyValueClass(), any())
|
||||
}
|
||||
|
||||
@Nested
|
||||
@MockitoBean(types = [UserRoleRepository::class, ClientRegistrationRepository::class])
|
||||
@TestPropertySource(
|
||||
properties = [
|
||||
"app.pseudonymize.generator=BUILDIN",
|
||||
"app.security.admin-user=admin",
|
||||
"app.security.admin-password={noop}very-secret",
|
||||
"app.security.enable-tokens=true",
|
||||
"app.security.enable-oidc=true",
|
||||
"app.consent.gics.enabled=false"
|
||||
]
|
||||
)
|
||||
inner class WithOidcEnabled {
|
||||
@Test
|
||||
fun testShouldGrantPermissionToSendMtbFileToAdminUser() {
|
||||
mockMvc.post("/mtbfile") {
|
||||
with(user("onkostarserver").roles("ADMIN"))
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
content = ObjectMapper().writeValueAsString(mtbFile)
|
||||
}.andExpect {
|
||||
status { isAccepted() }
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldGrantPermissionToSendMtbFileToUser() {
|
||||
mockMvc.post("/mtbfile") {
|
||||
with(user("onkostarserver").roles("USER"))
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
content = ObjectMapper().writeValueAsString(mtbFile)
|
||||
}.andExpect {
|
||||
status { isAccepted() }
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
|
||||
}
|
||||
}
|
||||
|
||||
companion object {
|
||||
|
@ -0,0 +1,75 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
* by the Free Software Foundation, either version 3 of the License, or
|
||||
* (at your option) any later version.
|
||||
*
|
||||
* This program is distributed in the hope that it will be useful,
|
||||
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
* GNU Affero General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Affero General Public License
|
||||
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
*/
|
||||
|
||||
package dev.dnpm.etl.processor.monitoring
|
||||
|
||||
import dev.dnpm.etl.processor.*
|
||||
import dev.dnpm.etl.processor.output.MtbFileSender
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.springframework.beans.factory.annotation.Autowired
|
||||
import org.springframework.boot.test.autoconfigure.data.jdbc.DataJdbcTest
|
||||
import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase
|
||||
import org.springframework.test.context.TestPropertySource
|
||||
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||
import org.springframework.transaction.annotation.Transactional
|
||||
import org.testcontainers.junit.jupiter.Testcontainers
|
||||
import java.time.Instant
|
||||
|
||||
@Testcontainers
|
||||
@ExtendWith(SpringExtension::class)
|
||||
@DataJdbcTest
|
||||
@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE)
|
||||
@Transactional
|
||||
@MockitoBean(types = [MtbFileSender::class])
|
||||
@TestPropertySource(
|
||||
properties = [
|
||||
"app.pseudonymize.generator=buildin",
|
||||
"app.rest.uri=http://example.com"
|
||||
]
|
||||
)
|
||||
class RequestRepositoryTest : AbstractTestcontainerTest() {
|
||||
|
||||
private lateinit var requestRepository: RequestRepository
|
||||
|
||||
@BeforeEach
|
||||
fun setUp(
|
||||
@Autowired requestRepository: RequestRepository
|
||||
) {
|
||||
this.requestRepository = requestRepository
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldSaveRequest() {
|
||||
val request = Request(
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678901"),
|
||||
PatientId("P1"),
|
||||
Fingerprint("0123456789abcdef1"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.WARNING,
|
||||
Instant.parse("2023-07-07T00:00:00Z")
|
||||
)
|
||||
|
||||
requestRepository.save(request)
|
||||
}
|
||||
|
||||
}
|
@ -0,0 +1,147 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
* by the Free Software Foundation, either version 3 of the License, or
|
||||
* (at your option) any later version.
|
||||
*
|
||||
* This program is distributed in the hope that it will be useful,
|
||||
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
* GNU Affero General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Affero General Public License
|
||||
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
*/
|
||||
|
||||
package dev.dnpm.etl.processor.pseudonym
|
||||
|
||||
import dev.dnpm.etl.processor.config.AppFhirConfig
|
||||
import dev.dnpm.etl.processor.config.GPasConfigProperties
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.assertThrows
|
||||
import org.springframework.http.HttpHeaders
|
||||
import org.springframework.http.HttpMethod
|
||||
import org.springframework.http.HttpStatus
|
||||
import org.springframework.retry.policy.SimpleRetryPolicy
|
||||
import org.springframework.retry.support.RetryTemplateBuilder
|
||||
import org.springframework.test.web.client.MockRestServiceServer
|
||||
import org.springframework.test.web.client.match.MockRestRequestMatchers.method
|
||||
import org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo
|
||||
import org.springframework.test.web.client.response.MockRestResponseCreators.withException
|
||||
import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus
|
||||
import org.springframework.web.client.RestTemplate
|
||||
import java.io.IOException
|
||||
|
||||
class GpasPseudonymGeneratorTest {
|
||||
|
||||
private lateinit var mockRestServiceServer: MockRestServiceServer
|
||||
private lateinit var generator: GpasPseudonymGenerator
|
||||
private lateinit var restTemplate: RestTemplate
|
||||
private var appFhirConfig: AppFhirConfig = AppFhirConfig()
|
||||
|
||||
@BeforeEach
|
||||
fun setup() {
|
||||
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
|
||||
val gPasConfigProperties = GPasConfigProperties(
|
||||
"https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate",
|
||||
"test",
|
||||
null,
|
||||
null
|
||||
)
|
||||
|
||||
this.restTemplate = RestTemplate()
|
||||
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
|
||||
this.generator =
|
||||
GpasPseudonymGenerator(gPasConfigProperties, retryTemplate, restTemplate, appFhirConfig)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldReturnExpectedPseudonym() {
|
||||
this.mockRestServiceServer.expect {
|
||||
method(HttpMethod.POST)
|
||||
requestTo("https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
|
||||
}.andRespond {
|
||||
withStatus(HttpStatus.OK).body(
|
||||
getDummyResponseBody(
|
||||
"1234",
|
||||
"test",
|
||||
"test1234ABCDEF567890"
|
||||
)
|
||||
)
|
||||
.createResponse(it)
|
||||
}
|
||||
|
||||
assertThat(this.generator.generate("ID1234")).isEqualTo("test1234ABCDEF567890")
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldThrowExceptionIfGpasNotAvailable() {
|
||||
this.mockRestServiceServer.expect {
|
||||
method(HttpMethod.POST)
|
||||
requestTo("https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
|
||||
}.andRespond {
|
||||
withException(IOException("Simulated IO error")).createResponse(it)
|
||||
}
|
||||
|
||||
assertThrows<PseudonymRequestFailed> { this.generator.generate("ID1234") }
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldThrowExceptionIfGpasDoesNotReturn2xxResponse() {
|
||||
this.mockRestServiceServer.expect {
|
||||
method(HttpMethod.POST)
|
||||
requestTo("https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
|
||||
}.andRespond {
|
||||
withStatus(HttpStatus.FOUND)
|
||||
.header(
|
||||
HttpHeaders.LOCATION,
|
||||
"https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate"
|
||||
)
|
||||
.createResponse(it)
|
||||
}
|
||||
|
||||
assertThrows<PseudonymRequestFailed> { this.generator.generate("ID1234") }
|
||||
}
|
||||
|
||||
companion object {
|
||||
|
||||
fun getDummyResponseBody(original: String, target: String, pseudonym: String) = """{
|
||||
"resourceType": "Parameters",
|
||||
"parameter": [
|
||||
{
|
||||
"name": "pseudonym",
|
||||
"part": [
|
||||
{
|
||||
"name": "original",
|
||||
"valueIdentifier": {
|
||||
"system": "https://ths-greifswald.de/gpas",
|
||||
"value": "$original"
|
||||
}
|
||||
},
|
||||
{
|
||||
"name": "target",
|
||||
"valueIdentifier": {
|
||||
"system": "https://ths-greifswald.de/gpas",
|
||||
"value": "$target"
|
||||
}
|
||||
},
|
||||
{
|
||||
"name": "pseudonym",
|
||||
"valueIdentifier": {
|
||||
"system": "https://ths-greifswald.de/gpas",
|
||||
"value": "$pseudonym"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}""".trimIndent()
|
||||
|
||||
}
|
||||
}
|
@ -19,7 +19,7 @@
|
||||
|
||||
package dev.dnpm.etl.processor.services
|
||||
|
||||
import dev.dnpm.etl.processor.AbstractTestcontainerTest
|
||||
import dev.dnpm.etl.processor.*
|
||||
import dev.dnpm.etl.processor.monitoring.Request
|
||||
import dev.dnpm.etl.processor.monitoring.RequestRepository
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
@ -31,19 +31,18 @@ import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.springframework.beans.factory.annotation.Autowired
|
||||
import org.springframework.boot.test.context.SpringBootTest
|
||||
import org.springframework.boot.test.mock.mockito.MockBean
|
||||
import org.springframework.test.context.TestPropertySource
|
||||
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||
import org.springframework.transaction.annotation.Transactional
|
||||
import org.testcontainers.junit.jupiter.Testcontainers
|
||||
import java.time.Instant
|
||||
import java.util.*
|
||||
|
||||
@Testcontainers
|
||||
@ExtendWith(SpringExtension::class)
|
||||
@SpringBootTest
|
||||
@Transactional
|
||||
@MockBean(MtbFileSender::class)
|
||||
@MockitoBean(types = [MtbFileSender::class])
|
||||
@TestPropertySource(
|
||||
properties = [
|
||||
"app.pseudonymize.generator=buildin",
|
||||
@ -66,7 +65,7 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
|
||||
|
||||
@Test
|
||||
fun shouldResultInEmptyRequestList() {
|
||||
val actual = requestService.allRequestsByPatientPseudonym("TEST_12345678901")
|
||||
val actual = requestService.allRequestsByPatientPseudonym(TEST_PATIENT_PSEUDONYM)
|
||||
|
||||
assertThat(actual).isEmpty()
|
||||
}
|
||||
@ -76,33 +75,33 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
|
||||
this.requestRepository.saveAll(
|
||||
listOf(
|
||||
Request(
|
||||
uuid = UUID.randomUUID().toString(),
|
||||
patientId = "TEST_12345678901",
|
||||
pid = "P1",
|
||||
fingerprint = "0123456789abcdef1",
|
||||
type = RequestType.MTB_FILE,
|
||||
status = RequestStatus.SUCCESS,
|
||||
processedAt = Instant.parse("2023-07-07T02:00:00Z")
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678901"),
|
||||
PatientId("P1"),
|
||||
Fingerprint("0123456789abcdef1"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.SUCCESS,
|
||||
Instant.parse("2023-07-07T02:00:00Z")
|
||||
),
|
||||
// Should be ignored - wrong patient ID -->
|
||||
Request(
|
||||
uuid = UUID.randomUUID().toString(),
|
||||
patientId = "TEST_12345678902",
|
||||
pid = "P2",
|
||||
fingerprint = "0123456789abcdef2",
|
||||
type = RequestType.MTB_FILE,
|
||||
status = RequestStatus.WARNING,
|
||||
processedAt = Instant.parse("2023-08-08T00:00:00Z")
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678902"),
|
||||
PatientId("P2"),
|
||||
Fingerprint("0123456789abcdef2"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.WARNING,
|
||||
Instant.parse("2023-08-08T00:00:00Z")
|
||||
),
|
||||
// <--
|
||||
Request(
|
||||
uuid = UUID.randomUUID().toString(),
|
||||
patientId = "TEST_12345678901",
|
||||
pid = "P2",
|
||||
fingerprint = "0123456789abcdee1",
|
||||
type = RequestType.DELETE,
|
||||
status = RequestStatus.SUCCESS,
|
||||
processedAt = Instant.parse("2023-08-08T02:00:00Z")
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678901"),
|
||||
PatientId("P2"),
|
||||
Fingerprint("0123456789abcdee1"),
|
||||
RequestType.DELETE,
|
||||
RequestStatus.SUCCESS,
|
||||
Instant.parse("2023-08-08T02:00:00Z")
|
||||
)
|
||||
)
|
||||
)
|
||||
@ -112,18 +111,18 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
|
||||
fun shouldResultInSortedRequestList() {
|
||||
setupTestData()
|
||||
|
||||
val actual = requestService.allRequestsByPatientPseudonym("TEST_12345678901")
|
||||
val actual = requestService.allRequestsByPatientPseudonym(TEST_PATIENT_PSEUDONYM)
|
||||
|
||||
assertThat(actual).hasSize(2)
|
||||
assertThat(actual[0].fingerprint).isEqualTo("0123456789abcdee1")
|
||||
assertThat(actual[1].fingerprint).isEqualTo("0123456789abcdef1")
|
||||
assertThat(actual[0].fingerprint).isEqualTo(Fingerprint("0123456789abcdee1"))
|
||||
assertThat(actual[1].fingerprint).isEqualTo(Fingerprint("0123456789abcdef1"))
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldReturnDeleteRequestAsLastRequest() {
|
||||
setupTestData()
|
||||
|
||||
val actual = requestService.isLastRequestWithKnownStatusDeletion("TEST_12345678901")
|
||||
val actual = requestService.isLastRequestWithKnownStatusDeletion(TEST_PATIENT_PSEUDONYM)
|
||||
|
||||
assertThat(actual).isTrue()
|
||||
}
|
||||
@ -132,10 +131,14 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
|
||||
fun shouldReturnLastMtbFileRequest() {
|
||||
setupTestData()
|
||||
|
||||
val actual = requestService.lastMtbFileRequestForPatientPseudonym("TEST_12345678901")
|
||||
val actual = requestService.lastMtbFileRequestForPatientPseudonym(TEST_PATIENT_PSEUDONYM)
|
||||
|
||||
assertThat(actual).isNotNull
|
||||
assertThat(actual?.fingerprint).isEqualTo("0123456789abcdef1")
|
||||
assertThat(actual?.fingerprint).isEqualTo(Fingerprint("0123456789abcdef1"))
|
||||
}
|
||||
|
||||
companion object {
|
||||
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("TEST_12345678901")
|
||||
}
|
||||
|
||||
}
|
@ -19,29 +19,52 @@
|
||||
|
||||
package dev.dnpm.etl.processor.web
|
||||
|
||||
import dev.dnpm.etl.processor.config.AppConfiguration
|
||||
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
|
||||
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
|
||||
import dev.dnpm.etl.processor.monitoring.GIcsConnectionCheckService
|
||||
import dev.dnpm.etl.processor.monitoring.GPasConnectionCheckService
|
||||
import dev.dnpm.etl.processor.monitoring.RestConnectionCheckService
|
||||
import dev.dnpm.etl.processor.output.MtbFileSender
|
||||
import dev.dnpm.etl.processor.pseudonym.Generator
|
||||
import dev.dnpm.etl.processor.security.Role
|
||||
import dev.dnpm.etl.processor.security.TokenService
|
||||
import dev.dnpm.etl.processor.security.UserRoleService
|
||||
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||
import dev.dnpm.etl.processor.services.TransformationService
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.htmlunit.WebClient
|
||||
import org.htmlunit.html.HtmlPage
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Nested
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.mockito.ArgumentMatchers.anyString
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.mockito.kotlin.argumentCaptor
|
||||
import org.mockito.kotlin.times
|
||||
import org.mockito.kotlin.verify
|
||||
import org.mockito.kotlin.whenever
|
||||
import org.springframework.beans.factory.annotation.Autowired
|
||||
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
||||
import org.springframework.boot.test.mock.mockito.MockBean
|
||||
import org.springframework.http.HttpHeaders
|
||||
import org.springframework.http.MediaType
|
||||
import org.springframework.http.MediaType.TEXT_EVENT_STREAM
|
||||
import org.springframework.security.test.context.support.WithMockUser
|
||||
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.anonymous
|
||||
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user
|
||||
import org.springframework.test.context.ContextConfiguration
|
||||
import org.springframework.test.context.TestPropertySource
|
||||
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||
import org.springframework.test.web.servlet.MockMvc
|
||||
import org.springframework.test.web.servlet.get
|
||||
import org.springframework.test.web.reactive.server.WebTestClient
|
||||
import org.springframework.test.web.servlet.*
|
||||
import org.springframework.test.web.servlet.client.MockMvcWebTestClient
|
||||
import org.springframework.test.web.servlet.htmlunit.MockMvcWebClientBuilder
|
||||
import org.springframework.web.context.WebApplicationContext
|
||||
import reactor.core.publisher.Sinks
|
||||
import reactor.test.StepVerifier
|
||||
import java.time.Instant
|
||||
|
||||
abstract class MockSink : Sinks.Many<Boolean>
|
||||
|
||||
@ -50,47 +73,57 @@ abstract class MockSink : Sinks.Many<Boolean>
|
||||
@ContextConfiguration(
|
||||
classes = [
|
||||
ConfigController::class,
|
||||
AppConfiguration::class,
|
||||
AppSecurityConfiguration::class
|
||||
]
|
||||
)
|
||||
@TestPropertySource(
|
||||
properties = [
|
||||
"app.pseudonymize.generator=BUILDIN",
|
||||
"app.security.admin-user=admin",
|
||||
"app.security.admin-password={noop}very-secret",
|
||||
"app.security.enable-tokens=true"
|
||||
"app.pseudonymize.generator=BUILDIN"
|
||||
]
|
||||
)
|
||||
@MockBean(name = "configsUpdateProducer", classes = [MockSink::class])
|
||||
@MockBean(
|
||||
Generator::class,
|
||||
MtbFileSender::class,
|
||||
ConnectionCheckService::class,
|
||||
RequestProcessor::class,
|
||||
TransformationService::class
|
||||
@MockitoBean(name = "configsUpdateProducer", types = [MockSink::class])
|
||||
@MockitoBean(
|
||||
types = [
|
||||
Generator::class,
|
||||
MtbFileSender::class,
|
||||
RequestProcessor::class,
|
||||
TransformationService::class,
|
||||
GPasConnectionCheckService::class,
|
||||
RestConnectionCheckService::class,
|
||||
GIcsConnectionCheckService::class
|
||||
]
|
||||
)
|
||||
class ConfigControllerTest {
|
||||
|
||||
private lateinit var mockMvc: MockMvc
|
||||
private lateinit var webClient: WebClient
|
||||
|
||||
private lateinit var requestProcessor: RequestProcessor
|
||||
private lateinit var connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Autowired mockMvc: MockMvc,
|
||||
@Autowired requestProcessor: RequestProcessor
|
||||
@Autowired requestProcessor: RequestProcessor,
|
||||
@Autowired connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||
) {
|
||||
this.mockMvc = mockMvc
|
||||
this.webClient = MockMvcWebClientBuilder.mockMvcSetup(mockMvc).build()
|
||||
this.requestProcessor = requestProcessor
|
||||
this.connectionCheckUpdateProducer = connectionCheckUpdateProducer
|
||||
|
||||
webClient.options.isThrowExceptionOnScriptError = false
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldShowConfigPageIfLoggedIn() {
|
||||
fun testShouldRequestConfigPageIfLoggedIn() {
|
||||
mockMvc.get("/configs") {
|
||||
with(user("admin").roles("ADMIN"))
|
||||
accept(MediaType.TEXT_HTML)
|
||||
}.andExpect {
|
||||
status { isOk() }
|
||||
view { name("configs") }
|
||||
}
|
||||
}
|
||||
|
||||
@ -107,4 +140,244 @@ class ConfigControllerTest {
|
||||
}
|
||||
}
|
||||
|
||||
@Nested
|
||||
@TestPropertySource(
|
||||
properties = [
|
||||
"app.security.enable-tokens=true",
|
||||
"app.security.admin-user=admin"
|
||||
]
|
||||
)
|
||||
@MockitoBean(
|
||||
types = [
|
||||
TokenService::class
|
||||
]
|
||||
)
|
||||
inner class WithTokensEnabled {
|
||||
private lateinit var tokenService: TokenService
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Autowired tokenService: TokenService
|
||||
) {
|
||||
webClient.options.isThrowExceptionOnScriptError = false
|
||||
|
||||
this.tokenService = tokenService
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldSaveNewToken() {
|
||||
mockMvc.post("/configs/tokens") {
|
||||
with(user("admin").roles("ADMIN"))
|
||||
accept(MediaType.TEXT_HTML)
|
||||
contentType = MediaType.APPLICATION_FORM_URLENCODED
|
||||
content = "name=Testtoken"
|
||||
}.andExpect {
|
||||
status { is2xxSuccessful() }
|
||||
view { name("configs/tokens") }
|
||||
}
|
||||
|
||||
val captor = argumentCaptor<String>()
|
||||
verify(tokenService, times(1)).addToken(captor.capture())
|
||||
|
||||
assertThat(captor.firstValue).isEqualTo("Testtoken")
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldNotSaveTokenWithExstingName() {
|
||||
whenever(tokenService.addToken(anyString())).thenReturn(
|
||||
Result.failure(
|
||||
RuntimeException(
|
||||
"Testfailure"
|
||||
)
|
||||
)
|
||||
)
|
||||
|
||||
mockMvc.post("/configs/tokens") {
|
||||
with(user("admin").roles("ADMIN"))
|
||||
accept(MediaType.TEXT_HTML)
|
||||
contentType = MediaType.APPLICATION_FORM_URLENCODED
|
||||
content = "name=Testtoken"
|
||||
}.andExpect {
|
||||
status { is2xxSuccessful() }
|
||||
view { name("configs/tokens") }
|
||||
}
|
||||
|
||||
val captor = argumentCaptor<String>()
|
||||
verify(tokenService, times(1)).addToken(captor.capture())
|
||||
|
||||
assertThat(captor.firstValue).isEqualTo("Testtoken")
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldDeleteToken() {
|
||||
mockMvc.delete("/configs/tokens/42") {
|
||||
with(user("admin").roles("ADMIN"))
|
||||
accept(MediaType.TEXT_HTML)
|
||||
}.andExpect {
|
||||
status { is2xxSuccessful() }
|
||||
view { name("configs/tokens") }
|
||||
}
|
||||
|
||||
val captor = argumentCaptor<Long>()
|
||||
verify(tokenService, times(1)).deleteToken(captor.capture())
|
||||
|
||||
assertThat(captor.firstValue).isEqualTo(42)
|
||||
}
|
||||
|
||||
@Test
|
||||
@WithMockUser(username = "admin", roles = ["ADMIN"])
|
||||
fun testShouldRenderConfigPageWithTokens() {
|
||||
val page = webClient.getPage<HtmlPage>("http://localhost/configs")
|
||||
assertThat(
|
||||
page.getElementById("tokens")
|
||||
).isNotNull
|
||||
}
|
||||
}
|
||||
|
||||
@Nested
|
||||
@TestPropertySource(
|
||||
properties = [
|
||||
"app.security.enable-tokens=false"
|
||||
]
|
||||
)
|
||||
inner class WithTokensDisabled {
|
||||
@BeforeEach
|
||||
fun setup() {
|
||||
webClient.options.isThrowExceptionOnScriptError = false
|
||||
}
|
||||
|
||||
@Test
|
||||
@WithMockUser(username = "admin", roles = ["ADMIN"])
|
||||
fun testShouldRenderConfigPageWithoutTokens() {
|
||||
val page = webClient.getPage<HtmlPage>("http://localhost/configs")
|
||||
assertThat(
|
||||
page.getElementById("tokens")
|
||||
).isNull()
|
||||
}
|
||||
}
|
||||
|
||||
@Nested
|
||||
@TestPropertySource(
|
||||
properties = [
|
||||
"app.security.enable-tokens=false",
|
||||
"app.security.admin-user=admin",
|
||||
"app.security.admin-password={noop}very-secret"
|
||||
]
|
||||
)
|
||||
@MockitoBean(
|
||||
types = [
|
||||
UserRoleService::class
|
||||
]
|
||||
)
|
||||
inner class WithUserRolesEnabled {
|
||||
private lateinit var userRoleService: UserRoleService
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Autowired userRoleService: UserRoleService
|
||||
) {
|
||||
webClient.options.isThrowExceptionOnScriptError = false
|
||||
|
||||
this.userRoleService = userRoleService
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldDeleteUserRole() {
|
||||
mockMvc.delete("/configs/userroles/42") {
|
||||
with(user("admin").roles("ADMIN"))
|
||||
accept(MediaType.TEXT_HTML)
|
||||
}.andExpect {
|
||||
status { is2xxSuccessful() }
|
||||
view { name("configs/userroles") }
|
||||
}
|
||||
|
||||
val captor = argumentCaptor<Long>()
|
||||
verify(userRoleService, times(1)).deleteUserRole(captor.capture())
|
||||
|
||||
assertThat(captor.firstValue).isEqualTo(42)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldUpdateUserRole() {
|
||||
mockMvc.put("/configs/userroles/42") {
|
||||
with(user("admin").roles("ADMIN"))
|
||||
accept(MediaType.TEXT_HTML)
|
||||
contentType = MediaType.APPLICATION_FORM_URLENCODED
|
||||
content = "role=ADMIN"
|
||||
}.andExpect {
|
||||
status { is2xxSuccessful() }
|
||||
view { name("configs/userroles") }
|
||||
}
|
||||
|
||||
val idCaptor = argumentCaptor<Long>()
|
||||
val roleCaptor = argumentCaptor<Role>()
|
||||
verify(userRoleService, times(1)).updateUserRole(
|
||||
idCaptor.capture(),
|
||||
roleCaptor.capture()
|
||||
)
|
||||
|
||||
assertThat(idCaptor.firstValue).isEqualTo(42)
|
||||
assertThat(roleCaptor.firstValue).isEqualTo(Role.ADMIN)
|
||||
}
|
||||
|
||||
@Test
|
||||
@WithMockUser(username = "admin", roles = ["ADMIN"])
|
||||
fun testShouldRenderConfigPageWithUserRoles() {
|
||||
val page = webClient.getPage<HtmlPage>("http://localhost/configs")
|
||||
assertThat(
|
||||
page.getElementById("userroles")
|
||||
).isNotNull
|
||||
}
|
||||
}
|
||||
|
||||
@Nested
|
||||
inner class WithUserRolesDisabled {
|
||||
@BeforeEach
|
||||
fun setup() {
|
||||
webClient.options.isThrowExceptionOnScriptError = false
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldRenderConfigPageWithoutUserRoles() {
|
||||
val page = webClient.getPage<HtmlPage>("http://localhost/configs")
|
||||
assertThat(
|
||||
page.getElementById("userroles")
|
||||
).isNull()
|
||||
}
|
||||
}
|
||||
|
||||
@Nested
|
||||
inner class SseTest {
|
||||
private lateinit var webClient: WebTestClient
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
applicationContext: WebApplicationContext
|
||||
) {
|
||||
this.webClient = MockMvcWebTestClient
|
||||
.bindToApplicationContext(applicationContext).build()
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldRequestGPasSSE() {
|
||||
val expectedEvent =
|
||||
ConnectionCheckResult.GPasConnectionCheckResult(true, Instant.now(), Instant.now())
|
||||
|
||||
connectionCheckUpdateProducer.tryEmitNext(expectedEvent)
|
||||
connectionCheckUpdateProducer.emitComplete { _, _ -> true }
|
||||
|
||||
val result =
|
||||
webClient.get().uri("http://localhost/configs/events").accept(TEXT_EVENT_STREAM)
|
||||
.exchange()
|
||||
.expectStatus().isOk()
|
||||
.expectHeader().contentType(TEXT_EVENT_STREAM)
|
||||
.returnResult(ConnectionCheckResult.GPasConnectionCheckResult::class.java)
|
||||
|
||||
StepVerifier.create(result.responseBody)
|
||||
.expectNext(expectedEvent)
|
||||
.expectComplete()
|
||||
.verify()
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
@ -0,0 +1,287 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
* by the Free Software Foundation, either version 3 of the License, or
|
||||
* (at your option) any later version.
|
||||
*
|
||||
* This program is distributed in the hope that it will be useful,
|
||||
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
* GNU Affero General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Affero General Public License
|
||||
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
*/
|
||||
|
||||
package dev.dnpm.etl.processor.web
|
||||
|
||||
import dev.dnpm.etl.processor.*
|
||||
import dev.dnpm.etl.processor.config.AppConfiguration
|
||||
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||
import dev.dnpm.etl.processor.monitoring.Report
|
||||
import dev.dnpm.etl.processor.monitoring.Request
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import dev.dnpm.etl.processor.monitoring.RequestType
|
||||
import dev.dnpm.etl.processor.services.RequestService
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.htmlunit.WebClient
|
||||
import org.htmlunit.html.HtmlPage
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Nested
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.assertThrows
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.mockito.kotlin.any
|
||||
import org.mockito.kotlin.whenever
|
||||
import org.springframework.beans.factory.annotation.Autowired
|
||||
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
||||
import org.springframework.data.domain.Page
|
||||
import org.springframework.data.domain.PageImpl
|
||||
import org.springframework.data.domain.Pageable
|
||||
import org.springframework.security.test.context.support.WithMockUser
|
||||
import org.springframework.test.context.ContextConfiguration
|
||||
import org.springframework.test.context.TestPropertySource
|
||||
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||
import org.springframework.test.web.servlet.MockMvc
|
||||
import org.springframework.test.web.servlet.get
|
||||
import org.springframework.test.web.servlet.htmlunit.MockMvcWebClientBuilder
|
||||
import java.io.IOException
|
||||
import java.time.Instant
|
||||
import java.util.*
|
||||
|
||||
@WebMvcTest(controllers = [HomeController::class])
|
||||
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
|
||||
@ContextConfiguration(
|
||||
classes = [
|
||||
HomeController::class,
|
||||
AppConfiguration::class,
|
||||
AppSecurityConfiguration::class
|
||||
]
|
||||
)
|
||||
@TestPropertySource(
|
||||
properties = [
|
||||
"app.pseudonymize.generator=BUILDIN",
|
||||
"app.security.admin-user=admin",
|
||||
"app.security.admin-password={noop}very-secret"
|
||||
]
|
||||
)
|
||||
@MockitoBean(
|
||||
types = [RequestService::class]
|
||||
)
|
||||
class HomeControllerTest {
|
||||
|
||||
private lateinit var mockMvc: MockMvc
|
||||
private lateinit var webClient: WebClient
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Autowired mockMvc: MockMvc,
|
||||
@Autowired requestService: RequestService
|
||||
) {
|
||||
this.mockMvc = mockMvc
|
||||
this.webClient = MockMvcWebClientBuilder.mockMvcSetup(mockMvc).build()
|
||||
|
||||
whenever(requestService.findAll(any<Pageable>())).thenReturn(Page.empty())
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldRequestHomePage() {
|
||||
mockMvc.get("/").andExpect {
|
||||
status { isOk() }
|
||||
view { name("index") }
|
||||
}
|
||||
}
|
||||
|
||||
@Nested
|
||||
inner class WithRequests {
|
||||
|
||||
private lateinit var requestService: RequestService
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Autowired requestService: RequestService
|
||||
) {
|
||||
this.requestService = requestService
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldShowHomePage() {
|
||||
whenever(requestService.findAll(any<Pageable>())).thenReturn(
|
||||
PageImpl(
|
||||
listOf(
|
||||
Request(
|
||||
2L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("PSEUDO1"),
|
||||
PatientId("PATIENT1"),
|
||||
Fingerprint("ashdkasdh"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.SUCCESS
|
||||
),
|
||||
Request(
|
||||
1L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("PSEUDO1"),
|
||||
PatientId("PATIENT1"),
|
||||
Fingerprint("asdasdasd"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.ERROR
|
||||
)
|
||||
)
|
||||
)
|
||||
)
|
||||
|
||||
val page = webClient.getPage<HtmlPage>("http://localhost/")
|
||||
assertThat(page.querySelectorAll("tbody tr")).hasSize(2)
|
||||
assertThat(page.querySelectorAll("div.notification.info")).isEmpty()
|
||||
}
|
||||
|
||||
@Test
|
||||
@WithMockUser(username = "admin", roles = ["ADMIN"])
|
||||
fun testShouldShowRequestDetails() {
|
||||
val requestId = randomRequestId()
|
||||
|
||||
whenever(requestService.findByUuid(anyValueClass())).thenReturn(
|
||||
Optional.of(
|
||||
Request(
|
||||
2L,
|
||||
requestId,
|
||||
PatientPseudonym("PSEUDO1"),
|
||||
PatientId("PATIENT1"),
|
||||
Fingerprint("ashdkasdh"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.SUCCESS,
|
||||
Instant.now(),
|
||||
Report("Test")
|
||||
)
|
||||
)
|
||||
)
|
||||
|
||||
val page = webClient.getPage<HtmlPage>("http://localhost/report/${requestId.value}")
|
||||
assertThat(page.querySelectorAll("tbody tr")).hasSize(1)
|
||||
assertThat(page.querySelectorAll("div.notification.info")).isEmpty()
|
||||
}
|
||||
|
||||
@Test
|
||||
@WithMockUser(username = "admin", roles = ["ADMIN"])
|
||||
fun testShouldShowPatientDetails() {
|
||||
whenever(requestService.findRequestByPatientId(anyValueClass(), any<Pageable>())).thenReturn(
|
||||
PageImpl(
|
||||
listOf(
|
||||
Request(
|
||||
2L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("PSEUDO1"),
|
||||
PatientId("PATIENT1"),
|
||||
Fingerprint("ashdkasdh"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.SUCCESS
|
||||
),
|
||||
Request(
|
||||
1L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("PSEUDO1"),
|
||||
PatientId("PATIENT1"),
|
||||
Fingerprint("asdasdasd"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.ERROR
|
||||
)
|
||||
)
|
||||
)
|
||||
)
|
||||
|
||||
val page = webClient.getPage<HtmlPage>("http://localhost/patient/PSEUDO1")
|
||||
assertThat(page.querySelectorAll("tbody tr")).hasSize(2)
|
||||
assertThat(page.querySelectorAll("div.notification.info")).isEmpty()
|
||||
}
|
||||
|
||||
@Test
|
||||
@WithMockUser(username = "admin", roles = ["ADMIN"])
|
||||
fun testShouldShowPatientPseudonym() {
|
||||
whenever(requestService.findRequestByPatientId(anyValueClass(), any<Pageable>())).thenReturn(
|
||||
PageImpl(
|
||||
listOf(
|
||||
Request(
|
||||
2L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("PSEUDO1"),
|
||||
PatientId("PATIENT1"),
|
||||
Fingerprint("ashdkasdh"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.SUCCESS
|
||||
),
|
||||
Request(
|
||||
1L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("PSEUDO1"),
|
||||
PatientId("PATIENT1"),
|
||||
Fingerprint("asdasdasd"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.ERROR
|
||||
)
|
||||
)
|
||||
)
|
||||
)
|
||||
|
||||
val page = webClient.getPage<HtmlPage>("http://localhost/patient/PSEUDO1")
|
||||
assertThat(page.querySelectorAll("h2 > span")).hasSize(1)
|
||||
assertThat(page.querySelectorAll("h2 > span").first().textContent).isEqualTo("PSEUDO1")
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Nested
|
||||
inner class WithoutRequests {
|
||||
|
||||
private lateinit var requestService: RequestService
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Autowired requestService: RequestService
|
||||
) {
|
||||
this.requestService = requestService
|
||||
|
||||
whenever(requestService.findAll(any<Pageable>())).thenReturn(Page.empty())
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldShowHomePage() {
|
||||
val page = webClient.getPage<HtmlPage>("http://localhost/")
|
||||
assertThat(page.querySelectorAll("tbody tr")).isEmpty()
|
||||
assertThat(page.querySelectorAll("div.notification.info")).hasSize(1)
|
||||
}
|
||||
|
||||
@Test
|
||||
@WithMockUser(username = "admin", roles = ["ADMIN"])
|
||||
fun testShouldThrowNotFoundExceptionForUnknownReport() {
|
||||
val requestId = randomRequestId()
|
||||
|
||||
whenever(requestService.findByUuid(anyValueClass())).thenReturn(
|
||||
Optional.empty()
|
||||
)
|
||||
|
||||
assertThrows<IOException> {
|
||||
webClient.getPage<HtmlPage>("http://localhost/report/${requestId.value}")
|
||||
}.also {
|
||||
assertThat(it).hasRootCauseInstanceOf(NotFoundException::class.java)
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
@WithMockUser(username = "admin", roles = ["ADMIN"])
|
||||
fun testShouldShowEmptyPatientDetails() {
|
||||
whenever(requestService.findRequestByPatientId(anyValueClass(), any<Pageable>())).thenReturn(Page.empty())
|
||||
|
||||
val page = webClient.getPage<HtmlPage>("http://localhost/patient/PSEUDO1")
|
||||
assertThat(page.querySelectorAll("tbody tr")).isEmpty()
|
||||
assertThat(page.querySelectorAll("div.notification.info")).hasSize(1)
|
||||
}
|
||||
}
|
||||
|
||||
}
|
@ -0,0 +1,88 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
* by the Free Software Foundation, either version 3 of the License, or
|
||||
* (at your option) any later version.
|
||||
*
|
||||
* This program is distributed in the hope that it will be useful,
|
||||
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
* GNU Affero General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Affero General Public License
|
||||
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
*/
|
||||
|
||||
package dev.dnpm.etl.processor.web
|
||||
|
||||
import dev.dnpm.etl.processor.config.AppConfiguration
|
||||
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||
import dev.dnpm.etl.processor.security.TokenService
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.htmlunit.WebClient
|
||||
import org.htmlunit.html.HtmlPage
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.springframework.beans.factory.annotation.Autowired
|
||||
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
||||
import org.springframework.test.context.ContextConfiguration
|
||||
import org.springframework.test.context.TestPropertySource
|
||||
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||
import org.springframework.test.web.servlet.MockMvc
|
||||
import org.springframework.test.web.servlet.get
|
||||
import org.springframework.test.web.servlet.htmlunit.MockMvcWebClientBuilder
|
||||
|
||||
@WebMvcTest(controllers = [LoginController::class])
|
||||
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
|
||||
@ContextConfiguration(
|
||||
classes = [
|
||||
LoginController::class,
|
||||
AppConfiguration::class,
|
||||
AppSecurityConfiguration::class
|
||||
]
|
||||
)
|
||||
@TestPropertySource(
|
||||
properties = [
|
||||
"app.pseudonymize.generator=BUILDIN",
|
||||
"app.security.admin-user=admin",
|
||||
"app.security.admin-password={noop}very-secret",
|
||||
"app.security.enable-tokens=true"
|
||||
]
|
||||
)
|
||||
@MockitoBean(
|
||||
types = [TokenService::class]
|
||||
)
|
||||
class LoginControllerTest {
|
||||
|
||||
private lateinit var mockMvc: MockMvc
|
||||
private lateinit var webClient: WebClient
|
||||
|
||||
@BeforeEach
|
||||
fun setup(@Autowired mockMvc: MockMvc) {
|
||||
this.mockMvc = mockMvc
|
||||
this.webClient = MockMvcWebClientBuilder.mockMvcSetup(mockMvc).build()
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldRequestLoginPage() {
|
||||
mockMvc.get("/login").andExpect {
|
||||
status { isOk() }
|
||||
view { name("login") }
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldShowLoginForm() {
|
||||
val page = webClient.getPage<HtmlPage>("http://localhost/login")
|
||||
assertThat(
|
||||
page.getElementsByTagName("main").first().firstElementChild.getAttribute("class")
|
||||
).isEqualTo("login-form")
|
||||
}
|
||||
}
|
@ -0,0 +1,73 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
* by the Free Software Foundation, either version 3 of the License, or
|
||||
* (at your option) any later version.
|
||||
*
|
||||
* This program is distributed in the hope that it will be useful,
|
||||
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
* GNU Affero General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Affero General Public License
|
||||
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
*/
|
||||
|
||||
package dev.dnpm.etl.processor.web
|
||||
|
||||
import dev.dnpm.etl.processor.config.AppConfiguration
|
||||
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||
import org.htmlunit.WebClient
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.springframework.beans.factory.annotation.Autowired
|
||||
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
||||
import org.springframework.test.context.ContextConfiguration
|
||||
import org.springframework.test.context.TestPropertySource
|
||||
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||
import org.springframework.test.web.servlet.MockMvc
|
||||
import org.springframework.test.web.servlet.get
|
||||
import org.springframework.test.web.servlet.htmlunit.MockMvcWebClientBuilder
|
||||
|
||||
@WebMvcTest(controllers = [StatisticsController::class])
|
||||
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
|
||||
@ContextConfiguration(
|
||||
classes = [
|
||||
StatisticsController::class,
|
||||
AppConfiguration::class,
|
||||
AppSecurityConfiguration::class
|
||||
]
|
||||
)
|
||||
@TestPropertySource(
|
||||
properties = [
|
||||
"app.pseudonymize.generator=BUILDIN",
|
||||
"app.security.admin-user=admin",
|
||||
"app.security.admin-password={noop}very-secret"
|
||||
]
|
||||
)
|
||||
class StatisticsControllerTest {
|
||||
|
||||
private lateinit var mockMvc: MockMvc
|
||||
private lateinit var webClient: WebClient
|
||||
|
||||
@BeforeEach
|
||||
fun setup(@Autowired mockMvc: MockMvc) {
|
||||
this.mockMvc = mockMvc
|
||||
this.webClient = MockMvcWebClientBuilder.mockMvcSetup(mockMvc).build()
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldRequestLoginPage() {
|
||||
mockMvc.get("/statistics").andExpect {
|
||||
status { isOk() }
|
||||
view { name("statistics") }
|
||||
}
|
||||
}
|
||||
|
||||
}
|
@ -0,0 +1,314 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
* by the Free Software Foundation, either version 3 of the License, or
|
||||
* (at your option) any later version.
|
||||
*
|
||||
* This program is distributed in the hope that it will be useful,
|
||||
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
* GNU Affero General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Affero General Public License
|
||||
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
*/
|
||||
|
||||
package dev.dnpm.etl.processor.web
|
||||
|
||||
import dev.dnpm.etl.processor.Fingerprint
|
||||
import dev.dnpm.etl.processor.PatientId
|
||||
import dev.dnpm.etl.processor.PatientPseudonym
|
||||
import dev.dnpm.etl.processor.config.AppConfiguration
|
||||
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||
import dev.dnpm.etl.processor.monitoring.CountedState
|
||||
import dev.dnpm.etl.processor.monitoring.Request
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import dev.dnpm.etl.processor.monitoring.RequestType
|
||||
import dev.dnpm.etl.processor.randomRequestId
|
||||
import dev.dnpm.etl.processor.services.RequestService
|
||||
import org.hamcrest.Matchers.equalTo
|
||||
import org.hamcrest.Matchers.hasSize
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Nested
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.mockito.kotlin.doAnswer
|
||||
import org.mockito.kotlin.whenever
|
||||
import org.springframework.beans.factory.annotation.Autowired
|
||||
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
||||
import org.springframework.http.MediaType.TEXT_EVENT_STREAM
|
||||
import org.springframework.test.context.ContextConfiguration
|
||||
import org.springframework.test.context.TestPropertySource
|
||||
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||
import org.springframework.test.web.reactive.server.WebTestClient
|
||||
import org.springframework.test.web.servlet.MockMvc
|
||||
import org.springframework.test.web.servlet.client.MockMvcWebTestClient
|
||||
import org.springframework.test.web.servlet.get
|
||||
import org.springframework.web.context.WebApplicationContext
|
||||
import reactor.core.publisher.Sinks
|
||||
import reactor.test.StepVerifier
|
||||
import java.time.Instant
|
||||
import java.time.ZoneId
|
||||
import java.time.temporal.ChronoUnit
|
||||
|
||||
|
||||
@WebMvcTest(controllers = [StatisticsRestController::class])
|
||||
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
|
||||
@ContextConfiguration(
|
||||
classes = [
|
||||
StatisticsRestController::class,
|
||||
AppConfiguration::class,
|
||||
AppSecurityConfiguration::class
|
||||
]
|
||||
)
|
||||
@TestPropertySource(
|
||||
properties = [
|
||||
"app.pseudonymize.generator=BUILDIN",
|
||||
"app.security.admin-user=admin",
|
||||
"app.security.admin-password={noop}very-secret"
|
||||
]
|
||||
)
|
||||
@MockitoBean(
|
||||
types = [RequestService::class]
|
||||
)
|
||||
class StatisticsRestControllerTest {
|
||||
|
||||
private lateinit var mockMvc: MockMvc
|
||||
|
||||
private lateinit var statisticsUpdateProducer: Sinks.Many<Any>
|
||||
private lateinit var requestService: RequestService
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Autowired mockMvc: MockMvc,
|
||||
@Autowired statisticsUpdateProducer: Sinks.Many<Any>,
|
||||
@Autowired requestService: RequestService
|
||||
) {
|
||||
this.mockMvc = mockMvc
|
||||
this.statisticsUpdateProducer = statisticsUpdateProducer
|
||||
this.requestService = requestService
|
||||
}
|
||||
|
||||
@Nested
|
||||
inner class RequestStatesTest {
|
||||
@Test
|
||||
fun testShouldRequestStatesForMtbFiles() {
|
||||
doAnswer { _ ->
|
||||
listOf(
|
||||
CountedState(42, RequestStatus.WARNING),
|
||||
CountedState(1, RequestStatus.UNKNOWN)
|
||||
)
|
||||
}.whenever(requestService).countStates()
|
||||
|
||||
mockMvc.get("/statistics/requeststates").andExpect {
|
||||
status { isOk() }.also {
|
||||
jsonPath("$", hasSize<Int>(2))
|
||||
jsonPath("$[0].name", equalTo(RequestStatus.WARNING.name))
|
||||
jsonPath("$[0].value", equalTo(42))
|
||||
jsonPath("$[1].name", equalTo(RequestStatus.UNKNOWN.name))
|
||||
jsonPath("$[1].value", equalTo(1))
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldRequestStatesForDeletes() {
|
||||
doAnswer { _ ->
|
||||
listOf(
|
||||
CountedState(42, RequestStatus.SUCCESS),
|
||||
CountedState(1, RequestStatus.ERROR)
|
||||
)
|
||||
}.whenever(requestService).countDeleteStates()
|
||||
|
||||
mockMvc.get("/statistics/requeststates?delete=true").andExpect {
|
||||
status { isOk() }.also {
|
||||
jsonPath("$", hasSize<Int>(2))
|
||||
jsonPath("$[0].name", equalTo(RequestStatus.SUCCESS.name))
|
||||
jsonPath("$[0].value", equalTo(42))
|
||||
jsonPath("$[1].name", equalTo(RequestStatus.ERROR.name))
|
||||
jsonPath("$[1].value", equalTo(1))
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@Nested
|
||||
inner class PatientRequestStatesTest {
|
||||
@Test
|
||||
fun testShouldRequestPatientStatesForMtbFiles() {
|
||||
doAnswer { _ ->
|
||||
listOf(
|
||||
CountedState(42, RequestStatus.WARNING),
|
||||
CountedState(1, RequestStatus.UNKNOWN)
|
||||
)
|
||||
}.whenever(requestService).findPatientUniqueStates()
|
||||
|
||||
mockMvc.get("/statistics/requestpatientstates").andExpect {
|
||||
status { isOk() }.also {
|
||||
jsonPath("$", hasSize<Int>(2))
|
||||
jsonPath("$[0].name", equalTo(RequestStatus.WARNING.name))
|
||||
jsonPath("$[0].value", equalTo(42))
|
||||
jsonPath("$[1].name", equalTo(RequestStatus.UNKNOWN.name))
|
||||
jsonPath("$[1].value", equalTo(1))
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldRequestPatientStatesForDeletes() {
|
||||
doAnswer { _ ->
|
||||
listOf(
|
||||
CountedState(42, RequestStatus.SUCCESS),
|
||||
CountedState(1, RequestStatus.ERROR)
|
||||
)
|
||||
}.whenever(requestService).findPatientUniqueDeleteStates()
|
||||
|
||||
mockMvc.get("/statistics/requestpatientstates?delete=true").andExpect {
|
||||
status { isOk() }.also {
|
||||
jsonPath("$", hasSize<Int>(2))
|
||||
jsonPath("$[0].name", equalTo(RequestStatus.SUCCESS.name))
|
||||
jsonPath("$[0].value", equalTo(42))
|
||||
jsonPath("$[1].name", equalTo(RequestStatus.ERROR.name))
|
||||
jsonPath("$[1].value", equalTo(1))
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@Nested
|
||||
inner class LastMonthStatesTest {
|
||||
|
||||
@BeforeEach
|
||||
fun setup() {
|
||||
val zoneId = ZoneId.of("Europe/Berlin")
|
||||
doAnswer { _ ->
|
||||
listOf(
|
||||
Request(
|
||||
1,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678901"),
|
||||
PatientId("P1"),
|
||||
Fingerprint("0123456789abcdef1"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.SUCCESS,
|
||||
Instant.now().atZone(zoneId).truncatedTo(ChronoUnit.DAYS).minus(2, ChronoUnit.DAYS).toInstant()
|
||||
),
|
||||
Request(
|
||||
2,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678902"),
|
||||
PatientId("P2"),
|
||||
Fingerprint("0123456789abcdef2"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.WARNING,
|
||||
Instant.now().atZone(zoneId).truncatedTo(ChronoUnit.DAYS).minus(2, ChronoUnit.DAYS).toInstant()
|
||||
),
|
||||
Request(
|
||||
3,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678901"),
|
||||
PatientId("P2"),
|
||||
Fingerprint("0123456789abcdee1"),
|
||||
RequestType.DELETE,
|
||||
RequestStatus.ERROR,
|
||||
Instant.now().atZone(zoneId).truncatedTo(ChronoUnit.DAYS).minus(1, ChronoUnit.DAYS).toInstant()
|
||||
),
|
||||
Request(
|
||||
4,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678902"),
|
||||
PatientId("P2"),
|
||||
Fingerprint("0123456789abcdef2"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.DUPLICATION,
|
||||
Instant.now().atZone(zoneId).truncatedTo(ChronoUnit.DAYS).minus(1, ChronoUnit.DAYS).toInstant()
|
||||
),
|
||||
Request(
|
||||
5,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678902"),
|
||||
PatientId("P2"),
|
||||
Fingerprint("0123456789abcdef2"),
|
||||
RequestType.DELETE,
|
||||
RequestStatus.UNKNOWN,
|
||||
Instant.now().atZone(zoneId).truncatedTo(ChronoUnit.DAYS).toInstant()
|
||||
),
|
||||
)
|
||||
}.whenever(requestService).findAll()
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldRequestLastMonthForMtbFiles() {
|
||||
mockMvc.get("/statistics/requestslastmonth").andExpect {
|
||||
status { isOk() }.also {
|
||||
jsonPath("$", hasSize<Int>(31))
|
||||
}.also {
|
||||
jsonPath("$[28].nameValues.error", equalTo(0))
|
||||
jsonPath("$[28].nameValues.warning", equalTo(1))
|
||||
jsonPath("$[28].nameValues.success", equalTo(1))
|
||||
jsonPath("$[28].nameValues.duplication", equalTo(0))
|
||||
jsonPath("$[28].nameValues.unknown", equalTo(0))
|
||||
jsonPath("$[29].nameValues.error", equalTo(0))
|
||||
jsonPath("$[29].nameValues.warning", equalTo(0))
|
||||
jsonPath("$[29].nameValues.success", equalTo(0))
|
||||
jsonPath("$[29].nameValues.duplication", equalTo(1))
|
||||
jsonPath("$[29].nameValues.unknown", equalTo(0))
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldRequestLastMonthForDeletes() {
|
||||
mockMvc.get("/statistics/requestslastmonth?delete=true").andExpect {
|
||||
status { isOk() }.also {
|
||||
jsonPath("$", hasSize<Int>(31))
|
||||
}.also {
|
||||
jsonPath("$[29].nameValues.error", equalTo(1))
|
||||
jsonPath("$[29].nameValues.warning", equalTo(0))
|
||||
jsonPath("$[29].nameValues.success", equalTo(0))
|
||||
jsonPath("$[29].nameValues.duplication", equalTo(0))
|
||||
jsonPath("$[29].nameValues.unknown", equalTo(0))
|
||||
jsonPath("$[30].nameValues.error", equalTo(0))
|
||||
jsonPath("$[30].nameValues.warning", equalTo(0))
|
||||
jsonPath("$[30].nameValues.success", equalTo(0))
|
||||
jsonPath("$[30].nameValues.duplication", equalTo(0))
|
||||
jsonPath("$[30].nameValues.unknown", equalTo(1))
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@Nested
|
||||
inner class SseTest {
|
||||
private lateinit var webClient: WebTestClient
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
applicationContext: WebApplicationContext,
|
||||
) {
|
||||
this.webClient = MockMvcWebTestClient
|
||||
.bindToApplicationContext(applicationContext).build()
|
||||
}
|
||||
|
||||
@Test
|
||||
fun testShouldRequestSSE() {
|
||||
statisticsUpdateProducer.emitComplete { _, _ -> true }
|
||||
|
||||
val result = webClient.get().uri("http://localhost/statistics/events").accept(TEXT_EVENT_STREAM).exchange()
|
||||
.expectStatus().isOk()
|
||||
.expectHeader().contentType(TEXT_EVENT_STREAM)
|
||||
.returnResult(String::class.java)
|
||||
|
||||
StepVerifier.create(result.responseBody)
|
||||
.expectComplete()
|
||||
.verify()
|
||||
}
|
||||
}
|
||||
|
||||
}
|
@ -0,0 +1,18 @@
|
||||
package dev.dnpm.etl.processor.consent;
|
||||
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
public class ConsentCheckFileBased implements ICheckConsent{
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(ConsentCheckFileBased.class);
|
||||
|
||||
public ConsentCheckFileBased() {
|
||||
log.info("ConsentCheckFileBased initialized...");
|
||||
}
|
||||
|
||||
@Override
|
||||
public TtpConsentStatus getTtpConsentStatus(String personIdentifierValue) {
|
||||
return TtpConsentStatus.UNKNOWN_CHECK_FILE;
|
||||
}
|
||||
}
|
@ -0,0 +1,6 @@
|
||||
package dev.dnpm.etl.processor.consent;
|
||||
|
||||
public enum ConsentDomain {
|
||||
BroadConsent,
|
||||
Modelvorhaben64e
|
||||
}
|
@ -0,0 +1,281 @@
|
||||
package dev.dnpm.etl.processor.consent;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.parser.DataFormatException;
|
||||
import dev.dnpm.etl.processor.config.AppFhirConfig;
|
||||
import dev.dnpm.etl.processor.config.GIcsConfigProperties;
|
||||
import java.util.Date;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.r4.model.BooleanType;
|
||||
import org.hl7.fhir.r4.model.Bundle;
|
||||
import org.hl7.fhir.r4.model.Coding;
|
||||
import org.hl7.fhir.r4.model.DateType;
|
||||
import org.hl7.fhir.r4.model.Identifier;
|
||||
import org.hl7.fhir.r4.model.OperationOutcome;
|
||||
import org.hl7.fhir.r4.model.Parameters;
|
||||
import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
|
||||
import org.hl7.fhir.r4.model.StringType;
|
||||
import org.jetbrains.annotations.NotNull;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.springframework.http.HttpEntity;
|
||||
import org.springframework.http.HttpHeaders;
|
||||
import org.springframework.http.HttpMethod;
|
||||
import org.springframework.http.MediaType;
|
||||
import org.springframework.http.ResponseEntity;
|
||||
import org.springframework.retry.TerminatedRetryException;
|
||||
import org.springframework.retry.support.RetryTemplate;
|
||||
import org.springframework.web.client.RestClientException;
|
||||
import org.springframework.web.client.RestTemplate;
|
||||
import org.springframework.web.util.UriComponentsBuilder;
|
||||
|
||||
|
||||
public class GicsConsentService implements ICheckConsent {
|
||||
|
||||
private final Logger log = LoggerFactory.getLogger(GicsConsentService.class);
|
||||
|
||||
private final GIcsConfigProperties gIcsConfigProperties;
|
||||
|
||||
public static final String IS_CONSENTED_ENDPOINT = "/$isConsented";
|
||||
public static final String IS_POLICY_STATES_FOR_PERSON_ENDPOINT = "/$currentPolicyStatesForPerson";
|
||||
private final RetryTemplate retryTemplate;
|
||||
private final RestTemplate restTemplate;
|
||||
private final FhirContext fhirContext;
|
||||
private final HttpHeaders httpHeader;
|
||||
private String url;
|
||||
|
||||
public GicsConsentService(GIcsConfigProperties gIcsConfigProperties,
|
||||
RetryTemplate retryTemplate, RestTemplate restTemplate, AppFhirConfig appFhirConfig) {
|
||||
this.gIcsConfigProperties = gIcsConfigProperties;
|
||||
this.retryTemplate = retryTemplate;
|
||||
this.restTemplate = restTemplate;
|
||||
this.fhirContext = appFhirConfig.fhirContext();
|
||||
httpHeader = buildHeader(gIcsConfigProperties.getUsername(),
|
||||
gIcsConfigProperties.getPassword());
|
||||
log.info("GicsConsentService initialized...");
|
||||
}
|
||||
|
||||
public String getGicsUri(String endpoint) {
|
||||
if (url == null) {
|
||||
final String gIcsBaseUri = gIcsConfigProperties.getUri();
|
||||
if (StringUtils.isBlank(gIcsBaseUri)) {
|
||||
throw new IllegalArgumentException(
|
||||
"gICS base URL is empty - should call gICS with false configuration.");
|
||||
}
|
||||
url = UriComponentsBuilder.fromUriString(gIcsBaseUri).path(IS_CONSENTED_ENDPOINT)
|
||||
.toUriString();
|
||||
}
|
||||
return url;
|
||||
}
|
||||
|
||||
@NotNull
|
||||
private static HttpHeaders buildHeader(String gPasUserName, String gPasPassword) {
|
||||
var headers = new HttpHeaders();
|
||||
headers.setContentType(MediaType.APPLICATION_XML);
|
||||
|
||||
if (StringUtils.isBlank(gPasUserName) || StringUtils.isBlank(gPasPassword)) {
|
||||
return headers;
|
||||
}
|
||||
|
||||
headers.setBasicAuth(gPasUserName, gPasPassword);
|
||||
return headers;
|
||||
}
|
||||
|
||||
protected static Parameters getIsConsentedRequestParam(GIcsConfigProperties configProperties,
|
||||
String personIdentifierValue) {
|
||||
var result = new Parameters();
|
||||
result.addParameter(new ParametersParameterComponent().setName("personIdentifier").setValue(
|
||||
new Identifier().setValue(personIdentifierValue)
|
||||
.setSystem(configProperties.getPersonIdentifierSystem())));
|
||||
result.addParameter(new ParametersParameterComponent().setName("domain")
|
||||
.setValue(new StringType().setValue(configProperties.getBroadConsentDomainName())));
|
||||
result.addParameter(new ParametersParameterComponent().setName("policy").setValue(
|
||||
new Coding().setCode(configProperties.getPolicyCode())
|
||||
.setSystem(configProperties.getPolicySystem())));
|
||||
|
||||
/*
|
||||
* is mandatory parameter, but we ignore it via additional configuration parameter
|
||||
* 'ignoreVersionNumber'.
|
||||
*/
|
||||
result.addParameter(new ParametersParameterComponent().setName("version")
|
||||
.setValue(new StringType().setValue("1.1")));
|
||||
|
||||
/* add config parameter with:
|
||||
* ignoreVersionNumber -> true ->> Reason is we cannot know which policy version each patient
|
||||
* has possibly signed or not, therefore we are happy with any version found.
|
||||
* unknownStateIsConsideredAsDecline -> true
|
||||
*/
|
||||
var config = new ParametersParameterComponent().setName("config").addPart(
|
||||
new ParametersParameterComponent().setName("ignoreVersionNumber")
|
||||
.setValue(new BooleanType().setValue(true))).addPart(
|
||||
new ParametersParameterComponent().setName("unknownStateIsConsideredAsDecline")
|
||||
.setValue(new BooleanType().setValue(false)));
|
||||
result.addParameter(config);
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
protected String callGicsApi(Parameters parameter, String endpoint) {
|
||||
var parameterAsXml = fhirContext.newXmlParser().encodeResourceToString(parameter);
|
||||
|
||||
HttpEntity<String> requestEntity = new HttpEntity<>(parameterAsXml, this.httpHeader);
|
||||
ResponseEntity<String> responseEntity;
|
||||
try {
|
||||
var url = getGicsUri(endpoint);
|
||||
|
||||
responseEntity = retryTemplate.execute(
|
||||
ctx -> restTemplate.exchange(url, HttpMethod.POST, requestEntity, String.class));
|
||||
} catch (RestClientException e) {
|
||||
var msg = String.format("Get consents status request failed reason: '%s",
|
||||
e.getMessage());
|
||||
log.error(msg);
|
||||
return null;
|
||||
|
||||
} catch (TerminatedRetryException terminatedRetryException) {
|
||||
var msg = String.format(
|
||||
"Get consents status process has been terminated. termination reason: '%s",
|
||||
terminatedRetryException.getMessage());
|
||||
log.error(msg);
|
||||
return null;
|
||||
|
||||
}
|
||||
if (responseEntity.getStatusCode().is2xxSuccessful()) {
|
||||
return responseEntity.getBody();
|
||||
} else {
|
||||
var msg = String.format(
|
||||
"Trusted party system reached but request failed! code: '%s' response: '%s'",
|
||||
responseEntity.getStatusCode(), responseEntity.getBody());
|
||||
log.error(msg);
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public TtpConsentStatus getTtpConsentStatus(String personIdentifierValue) {
|
||||
var parameter = GicsConsentService.getIsConsentedRequestParam(gIcsConfigProperties,
|
||||
personIdentifierValue);
|
||||
|
||||
var consentStatusResponse = callGicsApi(parameter,
|
||||
GicsConsentService.IS_CONSENTED_ENDPOINT);
|
||||
return evaluateConsentResponse(consentStatusResponse);
|
||||
}
|
||||
|
||||
public Bundle currentConsentForPersonAndTemplate(String personIdentifierValue,
|
||||
ConsentDomain targetConsentDomain, Date requestDate) {
|
||||
|
||||
String consentDomain = getConsentDomain(targetConsentDomain);
|
||||
|
||||
var requestParameter = GicsConsentService.buildRequestParameterCurrentPolicyStatesForPerson(
|
||||
gIcsConfigProperties, personIdentifierValue, requestDate, consentDomain);
|
||||
|
||||
var consentDataSerialized = callGicsApi(requestParameter,
|
||||
GicsConsentService.IS_POLICY_STATES_FOR_PERSON_ENDPOINT);
|
||||
|
||||
if (consentDataSerialized == null) {
|
||||
// error occurred - should not process further!
|
||||
throw new IllegalStateException(
|
||||
"consent data request failed - stopping processing! - try again or fix other problems first.");
|
||||
}
|
||||
IBaseResource iBaseResource = fhirContext.newXmlParser()
|
||||
.parseResource(consentDataSerialized);
|
||||
if (iBaseResource instanceof OperationOutcome) {
|
||||
// log error - very likely a configuration error
|
||||
String errorMessage =
|
||||
"Consent request failed! Check outcome:\n " + consentDataSerialized;
|
||||
log.error(errorMessage);
|
||||
throw new IllegalStateException(errorMessage);
|
||||
} else if (iBaseResource instanceof Bundle) {
|
||||
return (Bundle) iBaseResource;
|
||||
} else {
|
||||
String errorMessage = "Consent request failed! Unexpected response received! -> "
|
||||
+ consentDataSerialized;
|
||||
log.error(errorMessage);
|
||||
throw new IllegalStateException(errorMessage);
|
||||
}
|
||||
}
|
||||
|
||||
@NotNull
|
||||
private String getConsentDomain(ConsentDomain targetConsentDomain) {
|
||||
String consentDomain;
|
||||
switch (targetConsentDomain) {
|
||||
case BroadConsent -> {
|
||||
consentDomain = gIcsConfigProperties.getBroadConsentDomainName();
|
||||
}
|
||||
case Modelvorhaben64e -> {
|
||||
consentDomain = gIcsConfigProperties.getGnomDeConsentDomainName();
|
||||
}
|
||||
default -> {
|
||||
throw new IllegalArgumentException(
|
||||
"target ConsentDomain is missing but must be provided!");
|
||||
}
|
||||
}
|
||||
return consentDomain;
|
||||
}
|
||||
|
||||
public Bundle getBroadConsent(String personIdentifierValue, Date requestDate) {
|
||||
return currentConsentForPersonAndTemplate(personIdentifierValue, ConsentDomain.BroadConsent,
|
||||
requestDate);
|
||||
}
|
||||
|
||||
public Bundle getGenomDeConsent(String personIdentifierValue, Date requestDate) {
|
||||
return currentConsentForPersonAndTemplate(personIdentifierValue,
|
||||
ConsentDomain.Modelvorhaben64e, requestDate);
|
||||
}
|
||||
|
||||
protected static Parameters buildRequestParameterCurrentPolicyStatesForPerson(
|
||||
GIcsConfigProperties gIcsConfigProperties, String personIdentifierValue, Date requestDate,
|
||||
String targetDomain) {
|
||||
var requestParameter = new Parameters();
|
||||
requestParameter.addParameter(new ParametersParameterComponent().setName("personIdentifier")
|
||||
.setValue(new Identifier().setValue(personIdentifierValue)
|
||||
.setSystem(gIcsConfigProperties.getPersonIdentifierSystem())));
|
||||
|
||||
requestParameter.addParameter(new ParametersParameterComponent().setName("domain")
|
||||
.setValue(new StringType().setValue(targetDomain)));
|
||||
|
||||
Parameters nestedConfigParameters = new Parameters();
|
||||
nestedConfigParameters.addParameter(
|
||||
new ParametersParameterComponent().setName("idMatchingType").setValue(
|
||||
new Coding().setSystem(
|
||||
"https://ths-greifswald.de/fhir/CodeSystem/gics/IdMatchingType")
|
||||
.setCode("AT_LEAST_ONE"))).addParameter("ignoreVersionNumber", false)
|
||||
.addParameter("unknownStateIsConsideredAsDecline", false)
|
||||
.addParameter("requestDate", new DateType().setValue(requestDate));
|
||||
|
||||
requestParameter.addParameter(new ParametersParameterComponent().setName("config").addPart()
|
||||
.setResource(nestedConfigParameters));
|
||||
|
||||
return requestParameter;
|
||||
}
|
||||
|
||||
private TtpConsentStatus evaluateConsentResponse(String consentStatusResponse) {
|
||||
if (consentStatusResponse == null) {
|
||||
return TtpConsentStatus.FAILED_TO_ASK;
|
||||
}
|
||||
try {
|
||||
var response = fhirContext.newJsonParser().parseResource(consentStatusResponse);
|
||||
|
||||
if (response instanceof Parameters responseParameters) {
|
||||
|
||||
var responseValue = responseParameters.getParameter("consented").getValue();
|
||||
var isConsented = responseValue.castToBoolean(responseValue);
|
||||
if (!isConsented.hasValue()) {
|
||||
return TtpConsentStatus.FAILED_TO_ASK;
|
||||
}
|
||||
if (isConsented.booleanValue()) {
|
||||
return TtpConsentStatus.CONSENTED;
|
||||
} else {
|
||||
return TtpConsentStatus.CONSENT_MISSING_OR_REJECTED;
|
||||
}
|
||||
} else if (response instanceof OperationOutcome outcome) {
|
||||
log.error("failed to get consent status from ttp. probably configuration error. "
|
||||
+ "outcome: '{}'", fhirContext.newJsonParser().encodeToString(outcome));
|
||||
|
||||
}
|
||||
} catch (DataFormatException dfe) {
|
||||
log.error("failed to parse response to FHIR R4 resource.", dfe);
|
||||
}
|
||||
return TtpConsentStatus.FAILED_TO_ASK;
|
||||
}
|
||||
}
|
@ -0,0 +1,8 @@
|
||||
package dev.dnpm.etl.processor.consent;
|
||||
|
||||
|
||||
public interface ICheckConsent {
|
||||
|
||||
TtpConsentStatus getTtpConsentStatus(String personIdentifierValue);
|
||||
|
||||
}
|
@ -0,0 +1,20 @@
|
||||
package dev.dnpm.etl.processor.consent;
|
||||
|
||||
public enum TtpConsentStatus {
|
||||
/**
|
||||
* Valid consent found
|
||||
*/
|
||||
CONSENTED,
|
||||
|
||||
CONSENT_MISSING_OR_REJECTED,
|
||||
|
||||
/**
|
||||
* Due technical problems consent status is unknown
|
||||
*/
|
||||
FAILED_TO_ASK,
|
||||
|
||||
/**
|
||||
* Consent status is validate via file property 'consent.status'
|
||||
*/
|
||||
UNKNOWN_CHECK_FILE
|
||||
}
|
@ -21,73 +21,40 @@ package dev.dnpm.etl.processor.pseudonym;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.parser.IParser;
|
||||
import dev.dnpm.etl.processor.config.AppFhirConfig;
|
||||
import dev.dnpm.etl.processor.config.GPasConfigProperties;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.apache.hc.client5.http.impl.classic.CloseableHttpClient;
|
||||
import org.apache.hc.client5.http.impl.classic.HttpClients;
|
||||
import org.apache.hc.client5.http.impl.io.BasicHttpClientConnectionManager;
|
||||
import org.apache.hc.client5.http.socket.ConnectionSocketFactory;
|
||||
import org.apache.hc.client5.http.socket.PlainConnectionSocketFactory;
|
||||
import org.apache.hc.client5.http.ssl.SSLConnectionSocketFactory;
|
||||
import org.apache.hc.core5.http.config.Registry;
|
||||
import org.apache.hc.core5.http.config.RegistryBuilder;
|
||||
import org.hl7.fhir.r4.model.Identifier;
|
||||
import org.hl7.fhir.r4.model.Parameters;
|
||||
import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
|
||||
import org.hl7.fhir.r4.model.StringType;
|
||||
import org.jetbrains.annotations.NotNull;
|
||||
import org.jetbrains.annotations.Nullable;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.springframework.http.*;
|
||||
import org.springframework.http.client.HttpComponentsClientHttpRequestFactory;
|
||||
import org.springframework.retry.support.RetryTemplate;
|
||||
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 FhirContext r4Context;
|
||||
private final String gPasUrl;
|
||||
private final String psnTargetDomain;
|
||||
private final HttpHeaders httpHeader;
|
||||
private final RetryTemplate retryTemplate;
|
||||
private final Logger log = LoggerFactory.getLogger(GpasPseudonymGenerator.class);
|
||||
|
||||
private SSLContext customSslContext;
|
||||
private RestTemplate restTemplate;
|
||||
private final RestTemplate restTemplate;
|
||||
|
||||
public GpasPseudonymGenerator(GPasConfigProperties gpasCfg, RetryTemplate retryTemplate) {
|
||||
public GpasPseudonymGenerator(GPasConfigProperties gpasCfg, RetryTemplate retryTemplate,
|
||||
RestTemplate restTemplate, AppFhirConfig appFhirConfig) {
|
||||
this.retryTemplate = retryTemplate;
|
||||
|
||||
this.restTemplate = restTemplate;
|
||||
this.gPasUrl = gpasCfg.getUri();
|
||||
this.psnTargetDomain = gpasCfg.getTarget();
|
||||
this.r4Context = appFhirConfig.fhirContext();
|
||||
httpHeader = getHttpHeaders(gpasCfg.getUsername(), gpasCfg.getPassword());
|
||||
|
||||
try {
|
||||
if (StringUtils.isNotBlank(gpasCfg.getSslCaLocation())) {
|
||||
customSslContext = getSslContext(gpasCfg.getSslCaLocation());
|
||||
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 |
|
||||
NoSuchAlgorithmException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
|
||||
log.debug(String.format("%s has been initialized", this.getClass().getName()));
|
||||
|
||||
}
|
||||
@ -133,13 +100,11 @@ public class GpasPseudonymGenerator implements Generator {
|
||||
return psnValue.replaceAll(forbiddenCharsRegex, "_");
|
||||
}
|
||||
|
||||
|
||||
@NotNull
|
||||
protected ResponseEntity<String> getGpasPseudonym(String gPasRequestBody) {
|
||||
|
||||
HttpEntity<String> requestEntity = new HttpEntity<>(gPasRequestBody, this.httpHeader);
|
||||
ResponseEntity<String> responseEntity;
|
||||
var restTemplate = getRestTemplete();
|
||||
|
||||
try {
|
||||
responseEntity = retryTemplate.execute(
|
||||
@ -179,74 +144,7 @@ public class GpasPseudonymGenerator implements Generator {
|
||||
return headers;
|
||||
}
|
||||
|
||||
String authHeader = gPasUserName + ":" + gPasPassword;
|
||||
byte[] authHeaderBytes = authHeader.getBytes();
|
||||
byte[] encodedAuthHeaderBytes = Base64.getEncoder().encode(authHeaderBytes);
|
||||
String encodedAuthHeader = new String(encodedAuthHeaderBytes);
|
||||
|
||||
if (StringUtils.isNotBlank(gPasUserName) && StringUtils.isNotBlank(gPasPassword)) {
|
||||
headers.set("Authorization", "Basic " + encodedAuthHeader);
|
||||
}
|
||||
|
||||
headers.setBasicAuth(gPasUserName, gPasPassword);
|
||||
return headers;
|
||||
}
|
||||
|
||||
/**
|
||||
* Read SSL root certificate and return SSLContext
|
||||
*
|
||||
* @param certificateLocation file location to root certificate (PEM)
|
||||
* @return initialized SSLContext
|
||||
* @throws IOException file cannot be read
|
||||
* @throws CertificateException in case we have an invalid certificate of type X.509
|
||||
* @throws KeyStoreException keystore cannot be initialized
|
||||
* @throws NoSuchAlgorithmException missing trust manager algorithmus
|
||||
* @throws KeyManagementException key management failed at init SSLContext
|
||||
*/
|
||||
@Nullable
|
||||
protected SSLContext getSslContext(String certificateLocation)
|
||||
throws IOException, CertificateException, KeyStoreException, KeyManagementException, NoSuchAlgorithmException {
|
||||
|
||||
KeyStore ks = KeyStore.getInstance(KeyStore.getDefaultType());
|
||||
|
||||
FileInputStream fis = new FileInputStream(certificateLocation);
|
||||
X509Certificate ca = (X509Certificate) CertificateFactory.getInstance("X.509")
|
||||
.generateCertificate(new BufferedInputStream(fis));
|
||||
|
||||
ks.load(null, null);
|
||||
ks.setCertificateEntry(Integer.toString(1), ca);
|
||||
|
||||
TrustManagerFactory tmf = TrustManagerFactory.getInstance(
|
||||
TrustManagerFactory.getDefaultAlgorithm());
|
||||
tmf.init(ks);
|
||||
|
||||
SSLContext sslContext = SSLContext.getInstance("TLS");
|
||||
sslContext.init(null, tmf.getTrustManagers(), null);
|
||||
|
||||
return sslContext;
|
||||
}
|
||||
|
||||
protected RestTemplate getRestTemplete() {
|
||||
|
||||
if (restTemplate != null) {
|
||||
return restTemplate;
|
||||
}
|
||||
|
||||
if (customSslContext == null) {
|
||||
restTemplate = new RestTemplate();
|
||||
return restTemplate;
|
||||
}
|
||||
final var sslsf = new SSLConnectionSocketFactory(customSslContext);
|
||||
final Registry<ConnectionSocketFactory> socketFactoryRegistry = RegistryBuilder.<ConnectionSocketFactory>create()
|
||||
.register("https", sslsf).register("http", new PlainConnectionSocketFactory()).build();
|
||||
|
||||
final BasicHttpClientConnectionManager connectionManager = new BasicHttpClientConnectionManager(
|
||||
socketFactoryRegistry);
|
||||
final CloseableHttpClient httpClient = HttpClients.custom()
|
||||
.setConnectionManager(connectionManager).build();
|
||||
|
||||
final HttpComponentsClientHttpRequestFactory requestFactory = new HttpComponentsClientHttpRequestFactory(
|
||||
httpClient);
|
||||
restTemplate = new RestTemplate(requestFactory);
|
||||
return restTemplate;
|
||||
}
|
||||
}
|
||||
|
@ -1,7 +1,7 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
@ -21,16 +21,10 @@ 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?,
|
||||
@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
|
||||
@ -56,19 +50,66 @@ data class GPasConfigProperties(
|
||||
val target: String = "etl-processor",
|
||||
val username: String?,
|
||||
val password: String?,
|
||||
@get:DeprecatedConfigurationProperty(
|
||||
reason = "Deprecated in favor of including Root CA"
|
||||
)
|
||||
val sslCaLocation: String?
|
||||
) {
|
||||
companion object {
|
||||
const val NAME = "app.pseudonymize.gpas"
|
||||
}
|
||||
}
|
||||
|
||||
@ConfigurationProperties(GIcsConfigProperties.NAME)
|
||||
data class GIcsConfigProperties(
|
||||
/**
|
||||
* Base URL to gICS System
|
||||
*
|
||||
*/
|
||||
val uri: String?,
|
||||
val username: String?,
|
||||
val password: String?,
|
||||
|
||||
/**
|
||||
* If value is 'true' valid consent at processing time is mandatory for transmission of DNPM
|
||||
* files otherwise they will be flagged and skipped.
|
||||
* If value 'false' or missing consent status is assumed to be valid.
|
||||
*/
|
||||
val enabled: Boolean?,
|
||||
|
||||
/**
|
||||
* gICS specific system
|
||||
* **/
|
||||
val personIdentifierSystem: String =
|
||||
"https://ths-greifswald.de/fhir/gics/identifiers/Patienten-ID",
|
||||
|
||||
/**
|
||||
* Domain of broad consent resources
|
||||
**/
|
||||
val broadConsentDomainName: String = "MII",
|
||||
|
||||
/**
|
||||
* Domain of Modelvorhaben 64e consent resources
|
||||
**/
|
||||
val gnomDeConsentDomainName: String = "GenomDE_MV",
|
||||
|
||||
/**
|
||||
* Value to expect in case of positiv consent
|
||||
*/
|
||||
val policyCode: String = "2.16.840.1.113883.3.1937.777.24.5.3.6",
|
||||
|
||||
/**
|
||||
* Consent Policy which should be used for consent check
|
||||
*/
|
||||
val policySystem: String = "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3"
|
||||
) {
|
||||
companion object {
|
||||
const val NAME = "app.consent.gics"
|
||||
}
|
||||
}
|
||||
|
||||
@ConfigurationProperties(RestTargetProperties.NAME)
|
||||
data class RestTargetProperties(
|
||||
val uri: String?,
|
||||
val username: String?,
|
||||
val password: String?,
|
||||
val isBwhc: Boolean = false,
|
||||
) {
|
||||
companion object {
|
||||
const val NAME = "app.rest"
|
||||
@ -79,18 +120,8 @@ data class RestTargetProperties(
|
||||
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 groupId: String = "${outputTopic}_group",
|
||||
val servers: String = ""
|
||||
) {
|
||||
companion object {
|
||||
|
@ -1,7 +1,7 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
@ -20,13 +20,16 @@
|
||||
package dev.dnpm.etl.processor.config
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import dev.dnpm.etl.processor.monitoring.ReportService
|
||||
import dev.dnpm.etl.processor.consent.ConsentCheckFileBased
|
||||
import dev.dnpm.etl.processor.consent.ICheckConsent
|
||||
import dev.dnpm.etl.processor.consent.GicsConsentService
|
||||
import dev.dnpm.etl.processor.monitoring.*
|
||||
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.security.TokenRepository
|
||||
import dev.dnpm.etl.processor.security.TokenService
|
||||
import dev.dnpm.etl.processor.services.Transformation
|
||||
import dev.dnpm.etl.processor.services.TransformationService
|
||||
import org.slf4j.LoggerFactory
|
||||
@ -35,6 +38,7 @@ import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty
|
||||
import org.springframework.boot.context.properties.EnableConfigurationProperties
|
||||
import org.springframework.context.annotation.Bean
|
||||
import org.springframework.context.annotation.Configuration
|
||||
import org.springframework.data.jdbc.repository.config.AbstractJdbcConfiguration
|
||||
import org.springframework.retry.RetryCallback
|
||||
import org.springframework.retry.RetryContext
|
||||
import org.springframework.retry.RetryListener
|
||||
@ -44,6 +48,8 @@ import org.springframework.retry.support.RetryTemplateBuilder
|
||||
import org.springframework.scheduling.annotation.EnableScheduling
|
||||
import org.springframework.security.crypto.password.PasswordEncoder
|
||||
import org.springframework.security.provisioning.InMemoryUserDetailsManager
|
||||
import org.springframework.web.client.HttpClientErrorException
|
||||
import org.springframework.web.client.RestTemplate
|
||||
import reactor.core.publisher.Sinks
|
||||
import kotlin.time.Duration.Companion.seconds
|
||||
import kotlin.time.toJavaDuration
|
||||
@ -54,7 +60,8 @@ import kotlin.time.toJavaDuration
|
||||
value = [
|
||||
AppConfigProperties::class,
|
||||
PseudonymizeConfigProperties::class,
|
||||
GPasConfigProperties::class
|
||||
GPasConfigProperties::class,
|
||||
GIcsConfigProperties::class
|
||||
]
|
||||
)
|
||||
@EnableScheduling
|
||||
@ -62,10 +69,20 @@ class AppConfiguration {
|
||||
|
||||
private val logger = LoggerFactory.getLogger(AppConfiguration::class.java)
|
||||
|
||||
@Bean
|
||||
fun restTemplate(): RestTemplate {
|
||||
return RestTemplate()
|
||||
}
|
||||
|
||||
@Bean
|
||||
fun appFhirConfig(): AppFhirConfig{
|
||||
return AppFhirConfig()
|
||||
}
|
||||
|
||||
@ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "GPAS")
|
||||
@Bean
|
||||
fun gpasPseudonymGenerator(configProperties: GPasConfigProperties, retryTemplate: RetryTemplate): Generator {
|
||||
return GpasPseudonymGenerator(configProperties, retryTemplate)
|
||||
fun gpasPseudonymGenerator(configProperties: GPasConfigProperties, retryTemplate: RetryTemplate, restTemplate: RestTemplate, appFhirConfig: AppFhirConfig): Generator {
|
||||
return GpasPseudonymGenerator(configProperties, retryTemplate, restTemplate, appFhirConfig)
|
||||
}
|
||||
|
||||
@ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "BUILDIN", matchIfMissing = true)
|
||||
@ -74,20 +91,6 @@ class AppConfiguration {
|
||||
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,
|
||||
@ -97,17 +100,21 @@ class AppConfiguration {
|
||||
}
|
||||
|
||||
@Bean
|
||||
fun reportService(objectMapper: ObjectMapper): ReportService {
|
||||
return ReportService(objectMapper)
|
||||
fun reportService(): ReportService {
|
||||
return ReportService(getObjectMapper())
|
||||
}
|
||||
|
||||
@Bean
|
||||
fun getObjectMapper () : ObjectMapper{
|
||||
return JacksonConfig().objectMapper()
|
||||
}
|
||||
|
||||
@Bean
|
||||
fun transformationService(
|
||||
objectMapper: ObjectMapper,
|
||||
configProperties: AppConfigProperties
|
||||
): TransformationService {
|
||||
logger.info("Apply ${configProperties.transformations.size} transformation rules")
|
||||
return TransformationService(objectMapper, configProperties.transformations.map {
|
||||
return TransformationService(getObjectMapper(), configProperties.transformations.map {
|
||||
Transformation.of(it.path) from it.from to it.to
|
||||
})
|
||||
}
|
||||
@ -116,6 +123,8 @@ class AppConfiguration {
|
||||
fun retryTemplate(configProperties: AppConfigProperties): RetryTemplate {
|
||||
return RetryTemplateBuilder()
|
||||
.notRetryOn(IllegalArgumentException::class.java)
|
||||
.notRetryOn(HttpClientErrorException.BadRequest::class.java)
|
||||
.notRetryOn(HttpClientErrorException.UnprocessableEntity::class.java)
|
||||
.exponentialBackoff(2.seconds.toJavaDuration(), 1.25, 5.seconds.toJavaDuration())
|
||||
.customPolicy(SimpleRetryPolicy(configProperties.maxRetryAttempts))
|
||||
.withListener(object : RetryListener {
|
||||
@ -142,9 +151,62 @@ class AppConfiguration {
|
||||
}
|
||||
|
||||
@Bean
|
||||
fun configsUpdateProducer(): Sinks.Many<Boolean> {
|
||||
return Sinks.many().multicast().directBestEffort()
|
||||
fun connectionCheckUpdateProducer(): Sinks.Many<ConnectionCheckResult> {
|
||||
return Sinks.many().multicast().onBackpressureBuffer()
|
||||
}
|
||||
|
||||
@ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "GPAS")
|
||||
@Bean
|
||||
fun gPasConnectionCheckService(
|
||||
restTemplate: RestTemplate,
|
||||
gPasConfigProperties: GPasConfigProperties,
|
||||
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||
): ConnectionCheckService {
|
||||
return GPasConnectionCheckService(restTemplate, gPasConfigProperties, connectionCheckUpdateProducer)
|
||||
}
|
||||
|
||||
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS")
|
||||
@ConditionalOnMissingBean
|
||||
@Bean
|
||||
fun gPasConnectionCheckServiceOnDeprecatedProperty(
|
||||
restTemplate: RestTemplate,
|
||||
gPasConfigProperties: GPasConfigProperties,
|
||||
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||
): ConnectionCheckService {
|
||||
return GPasConnectionCheckService(restTemplate, gPasConfigProperties, connectionCheckUpdateProducer)
|
||||
}
|
||||
|
||||
@Bean
|
||||
fun jdbcConfiguration(): AbstractJdbcConfiguration {
|
||||
return AppJdbcConfiguration()
|
||||
}
|
||||
|
||||
@Bean
|
||||
@ConditionalOnProperty(name = ["app.consent.gics.enabled"], havingValue = "true")
|
||||
fun gicsConsentService( gIcsConfigProperties: GIcsConfigProperties,
|
||||
retryTemplate: RetryTemplate, restTemplate: RestTemplate, appFhirConfig: AppFhirConfig): ICheckConsent {
|
||||
return GicsConsentService(
|
||||
gIcsConfigProperties,
|
||||
retryTemplate,
|
||||
restTemplate,
|
||||
appFhirConfig
|
||||
)
|
||||
}
|
||||
|
||||
@ConditionalOnProperty(name = ["app.consent.gics.enabled"], havingValue = "true")
|
||||
@Bean
|
||||
fun gIcsConnectionCheckService(
|
||||
restTemplate: RestTemplate,
|
||||
gIcsConfigProperties: GIcsConfigProperties,
|
||||
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||
): ConnectionCheckService {
|
||||
return GIcsConnectionCheckService(restTemplate, gIcsConfigProperties, connectionCheckUpdateProducer)
|
||||
}
|
||||
|
||||
@Bean
|
||||
@ConditionalOnMissingBean
|
||||
fun constService(): ICheckConsent {
|
||||
return ConsentCheckFileBased()
|
||||
}
|
||||
}
|
||||
|
||||
|
@ -0,0 +1,16 @@
|
||||
package dev.dnpm.etl.processor.config
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext
|
||||
import org.springframework.context.annotation.Bean
|
||||
import org.springframework.context.annotation.Configuration
|
||||
|
||||
|
||||
@Configuration
|
||||
class AppFhirConfig {
|
||||
private val fhirCtx: FhirContext = FhirContext.forR4()
|
||||
|
||||
@Bean
|
||||
fun fhirContext(): FhirContext {
|
||||
return fhirCtx
|
||||
}
|
||||
}
|
@ -0,0 +1,25 @@
|
||||
package dev.dnpm.etl.processor.config
|
||||
|
||||
import dev.dnpm.etl.processor.Fingerprint
|
||||
import org.springframework.context.annotation.Configuration
|
||||
import org.springframework.core.convert.converter.Converter
|
||||
import org.springframework.data.jdbc.repository.config.AbstractJdbcConfiguration
|
||||
|
||||
@Configuration
|
||||
class AppJdbcConfiguration : AbstractJdbcConfiguration() {
|
||||
override fun userConverters(): MutableList<*> {
|
||||
return mutableListOf(StringToFingerprintConverter(), FingerprintToStringConverter())
|
||||
}
|
||||
}
|
||||
|
||||
class StringToFingerprintConverter : Converter<String, Fingerprint> {
|
||||
override fun convert(source: String): Fingerprint {
|
||||
return Fingerprint(source)
|
||||
}
|
||||
}
|
||||
|
||||
class FingerprintToStringConverter : Converter<Fingerprint, String> {
|
||||
override fun convert(source: Fingerprint): String {
|
||||
return source.value
|
||||
}
|
||||
}
|
@ -1,7 +1,7 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
@ -21,6 +21,7 @@ package dev.dnpm.etl.processor.config
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import dev.dnpm.etl.processor.input.KafkaInputListener
|
||||
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
|
||||
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
|
||||
import dev.dnpm.etl.processor.monitoring.KafkaConnectionCheckService
|
||||
import dev.dnpm.etl.processor.output.KafkaMtbFileSender
|
||||
@ -70,7 +71,7 @@ class AppKafkaConfiguration {
|
||||
kafkaProperties: KafkaProperties,
|
||||
kafkaResponseProcessor: KafkaResponseProcessor
|
||||
): KafkaMessageListenerContainer<String, String> {
|
||||
val containerProperties = ContainerProperties(kafkaProperties.responseTopic)
|
||||
val containerProperties = ContainerProperties(kafkaProperties.outputResponseTopic)
|
||||
containerProperties.messageListener = kafkaResponseProcessor
|
||||
return KafkaMessageListenerContainer(consumerFactory, containerProperties)
|
||||
}
|
||||
@ -105,8 +106,11 @@ class AppKafkaConfiguration {
|
||||
}
|
||||
|
||||
@Bean
|
||||
fun connectionCheckService(consumerFactory: ConsumerFactory<String, String>, configsUpdateProducer: Sinks.Many<Boolean>): ConnectionCheckService {
|
||||
return KafkaConnectionCheckService(consumerFactory.createConsumer(), configsUpdateProducer)
|
||||
fun kafkaConnectionCheckService(
|
||||
consumerFactory: ConsumerFactory<String, String>,
|
||||
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||
): ConnectionCheckService {
|
||||
return KafkaConnectionCheckService(consumerFactory.createConsumer(), connectionCheckUpdateProducer)
|
||||
}
|
||||
|
||||
}
|
@ -1,7 +1,7 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
@ -19,10 +19,13 @@
|
||||
|
||||
package dev.dnpm.etl.processor.config
|
||||
|
||||
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
|
||||
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
|
||||
import dev.dnpm.etl.processor.monitoring.ReportService
|
||||
import dev.dnpm.etl.processor.monitoring.RestConnectionCheckService
|
||||
import dev.dnpm.etl.processor.output.MtbFileSender
|
||||
import dev.dnpm.etl.processor.output.RestMtbFileSender
|
||||
import dev.dnpm.etl.processor.output.RestBwhcMtbFileSender
|
||||
import dev.dnpm.etl.processor.output.RestDipMtbFileSender
|
||||
import org.slf4j.LoggerFactory
|
||||
import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean
|
||||
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty
|
||||
@ -47,28 +50,29 @@ class AppRestConfiguration {
|
||||
|
||||
private val logger = LoggerFactory.getLogger(AppRestConfiguration::class.java)
|
||||
|
||||
@Bean
|
||||
fun restTemplate(): RestTemplate {
|
||||
return RestTemplate()
|
||||
}
|
||||
|
||||
@Bean
|
||||
fun restMtbFileSender(
|
||||
restTemplate: RestTemplate,
|
||||
restTargetProperties: RestTargetProperties,
|
||||
retryTemplate: RetryTemplate
|
||||
retryTemplate: RetryTemplate,
|
||||
reportService: ReportService,
|
||||
): MtbFileSender {
|
||||
logger.info("Selected 'RestMtbFileSender'")
|
||||
return RestMtbFileSender(restTemplate, restTargetProperties, retryTemplate)
|
||||
if (restTargetProperties.isBwhc) {
|
||||
logger.info("Selected 'RestBwhcMtbFileSender'")
|
||||
return RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
|
||||
}
|
||||
|
||||
logger.info("Selected 'RestDipMtbFileSender'")
|
||||
return RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
|
||||
}
|
||||
|
||||
@Bean
|
||||
fun connectionCheckService(
|
||||
fun restConnectionCheckService(
|
||||
restTemplate: RestTemplate,
|
||||
restTargetProperties: RestTargetProperties,
|
||||
configsUpdateProducer: Sinks.Many<Boolean>
|
||||
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||
): ConnectionCheckService {
|
||||
return RestConnectionCheckService(restTemplate, restTargetProperties, configsUpdateProducer)
|
||||
return RestConnectionCheckService(restTemplate, restTargetProperties, connectionCheckUpdateProducer)
|
||||
}
|
||||
|
||||
}
|
||||
|
@ -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) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
@ -21,7 +21,7 @@ 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 dev.dnpm.etl.processor.security.UserRoleService
|
||||
import org.slf4j.LoggerFactory
|
||||
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty
|
||||
import org.springframework.boot.context.properties.EnableConfigurationProperties
|
||||
@ -44,6 +44,8 @@ import org.springframework.security.web.SecurityFilterChain
|
||||
import java.util.*
|
||||
|
||||
|
||||
private const val LOGIN_PATH = "/login"
|
||||
|
||||
@Configuration
|
||||
@EnableConfigurationProperties(
|
||||
value = [
|
||||
@ -85,11 +87,16 @@ class AppSecurityConfiguration(
|
||||
|
||||
@Bean
|
||||
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "true")
|
||||
fun filterChainOidc(http: HttpSecurity, passwordEncoder: PasswordEncoder, userRoleRepository: UserRoleRepository, sessionRegistry: SessionRegistry): SecurityFilterChain {
|
||||
fun filterChainOidc(
|
||||
http: HttpSecurity,
|
||||
passwordEncoder: PasswordEncoder,
|
||||
userRoleRepository: UserRoleRepository,
|
||||
sessionRegistry: SessionRegistry
|
||||
): SecurityFilterChain {
|
||||
http {
|
||||
authorizeRequests {
|
||||
authorizeHttpRequests {
|
||||
authorize("/configs/**", hasRole("ADMIN"))
|
||||
authorize("/mtbfile/**", hasAnyRole("MTBFILE"))
|
||||
authorize("/mtbfile/**", hasAnyRole("MTBFILE", "ADMIN", "USER"))
|
||||
authorize("/report/**", hasAnyRole("ADMIN", "USER"))
|
||||
authorize("*.css", permitAll)
|
||||
authorize("*.ico", permitAll)
|
||||
@ -104,15 +111,15 @@ class AppSecurityConfiguration(
|
||||
realmName = "ETL-Processor"
|
||||
}
|
||||
formLogin {
|
||||
loginPage = "/login"
|
||||
loginPage = LOGIN_PATH
|
||||
}
|
||||
oauth2Login {
|
||||
loginPage = "/login"
|
||||
loginPage = LOGIN_PATH
|
||||
}
|
||||
sessionManagement {
|
||||
sessionConcurrency {
|
||||
maximumSessions = 1
|
||||
expiredUrl = "/login?expired"
|
||||
expiredUrl = "$LOGIN_PATH?expired"
|
||||
}
|
||||
sessionFixation {
|
||||
newSession()
|
||||
@ -125,13 +132,22 @@ class AppSecurityConfiguration(
|
||||
|
||||
@Bean
|
||||
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "true")
|
||||
fun grantedAuthoritiesMapper(userRoleRepository: UserRoleRepository, appSecurityConfigProperties: SecurityConfigProperties): GrantedAuthoritiesMapper {
|
||||
fun grantedAuthoritiesMapper(
|
||||
userRoleRepository: UserRoleRepository,
|
||||
appSecurityConfigProperties: SecurityConfigProperties
|
||||
): GrantedAuthoritiesMapper {
|
||||
return GrantedAuthoritiesMapper { grantedAuthority ->
|
||||
grantedAuthority.filterIsInstance<OidcUserAuthority>()
|
||||
.onEach {
|
||||
val userRole = userRoleRepository.findByUsername(it.userInfo.preferredUsername)
|
||||
if (userRole.isEmpty) {
|
||||
userRoleRepository.save(UserRole(null, it.userInfo.preferredUsername, appSecurityConfigProperties.defaultNewUserRole))
|
||||
userRoleRepository.save(
|
||||
UserRole(
|
||||
null,
|
||||
it.userInfo.preferredUsername,
|
||||
appSecurityConfigProperties.defaultNewUserRole
|
||||
)
|
||||
)
|
||||
}
|
||||
}
|
||||
.map {
|
||||
@ -145,9 +161,9 @@ class AppSecurityConfiguration(
|
||||
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "false", matchIfMissing = true)
|
||||
fun filterChain(http: HttpSecurity, passwordEncoder: PasswordEncoder): SecurityFilterChain {
|
||||
http {
|
||||
authorizeRequests {
|
||||
authorizeHttpRequests {
|
||||
authorize("/configs/**", hasRole("ADMIN"))
|
||||
authorize("/mtbfile/**", hasAnyRole("MTBFILE"))
|
||||
authorize("/mtbfile/**", hasAnyRole("MTBFILE", "ADMIN"))
|
||||
authorize("/report/**", hasRole("ADMIN"))
|
||||
authorize(anyRequest, permitAll)
|
||||
}
|
||||
@ -155,7 +171,7 @@ class AppSecurityConfiguration(
|
||||
realmName = "ETL-Processor"
|
||||
}
|
||||
formLogin {
|
||||
loginPage = "/login"
|
||||
loginPage = LOGIN_PATH
|
||||
}
|
||||
csrf { disable() }
|
||||
}
|
||||
|
@ -0,0 +1,12 @@
|
||||
package dev.dnpm.etl.processor.config
|
||||
|
||||
|
||||
import com.fasterxml.jackson.databind.module.SimpleModule
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource
|
||||
|
||||
class FhirResourceModule : SimpleModule() {
|
||||
init {
|
||||
addSerializer(IBaseResource::class.java, IBaseResourceSerializer())
|
||||
addDeserializer(IBaseResource::class.java, IBaseResourceDeserializer())
|
||||
}
|
||||
}
|
@ -0,0 +1,20 @@
|
||||
package dev.dnpm.etl.processor.config
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext
|
||||
import com.fasterxml.jackson.core.JsonParser
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationContext
|
||||
import com.fasterxml.jackson.databind.JsonDeserializer
|
||||
import com.fasterxml.jackson.databind.JsonNode
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource
|
||||
|
||||
class IBaseResourceDeserializer : JsonDeserializer<IBaseResource>() {
|
||||
override fun deserialize(p: JsonParser?, ctxt: DeserializationContext?): IBaseResource {
|
||||
val fhirContext = FhirContext.forR4()
|
||||
|
||||
val jsonNode = p?.readValueAsTree<JsonNode>()
|
||||
val json = jsonNode?.toString()
|
||||
|
||||
return fhirContext.newJsonParser().parseResource(json) as IBaseResource
|
||||
}
|
||||
}
|
@ -0,0 +1,19 @@
|
||||
package dev.dnpm.etl.processor.config
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext
|
||||
import com.fasterxml.jackson.core.JsonGenerator
|
||||
import com.fasterxml.jackson.databind.JsonSerializer
|
||||
import com.fasterxml.jackson.databind.SerializerProvider
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource
|
||||
|
||||
class IBaseResourceSerializer : JsonSerializer<IBaseResource>() {
|
||||
override fun serialize(
|
||||
value: IBaseResource,
|
||||
gen: JsonGenerator,
|
||||
serializers: SerializerProvider
|
||||
) {
|
||||
val fhirContext = FhirContext.forR4()
|
||||
val json = fhirContext.newJsonParser().encodeResourceToString(value)
|
||||
gen.writeRawValue(json)
|
||||
}
|
||||
}
|
@ -0,0 +1,19 @@
|
||||
package dev.dnpm.etl.processor.config
|
||||
|
||||
import org.springframework.context.annotation.Bean
|
||||
import org.springframework.context.annotation.Configuration
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import com.fasterxml.jackson.databind.SerializationFeature
|
||||
import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule
|
||||
|
||||
@Configuration
|
||||
class JacksonConfig {
|
||||
|
||||
@Bean
|
||||
fun objectMapper(): ObjectMapper =
|
||||
ObjectMapper()
|
||||
.registerModule(FhirResourceModule())
|
||||
.disable(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS).registerModule(
|
||||
JavaTimeModule()
|
||||
);
|
||||
}
|
@ -1,7 +1,7 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
@ -22,9 +22,14 @@ package dev.dnpm.etl.processor.input
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import de.ukw.ccc.bwhc.dto.Consent
|
||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import dev.dnpm.etl.processor.CustomMediaType
|
||||
import dev.dnpm.etl.processor.PatientId
|
||||
import dev.dnpm.etl.processor.RequestId
|
||||
import dev.dnpm.etl.processor.consent.TtpConsentStatus
|
||||
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||
import org.apache.kafka.clients.consumer.ConsumerRecord
|
||||
import org.slf4j.LoggerFactory
|
||||
import org.springframework.http.MediaType
|
||||
import org.springframework.kafka.listener.MessageListener
|
||||
|
||||
class KafkaInputListener(
|
||||
@ -33,14 +38,59 @@ class KafkaInputListener(
|
||||
) : 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)
|
||||
override fun onMessage(record: ConsumerRecord<String, String>) {
|
||||
when (guessMimeType(record)) {
|
||||
MediaType.APPLICATION_JSON_VALUE -> handleBwhcMessage(record)
|
||||
CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE -> handleDnpmV2Message(record)
|
||||
else -> {
|
||||
/* ignore other messages */
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private fun guessMimeType(record: ConsumerRecord<String, String>): String {
|
||||
if (record.headers().headers("contentType").toList().isEmpty()) {
|
||||
// Fallback if no contentType set (old behavior)
|
||||
return MediaType.APPLICATION_JSON_VALUE
|
||||
}
|
||||
|
||||
return record.headers().headers("contentType")?.firstOrNull()?.value().contentToString()
|
||||
}
|
||||
|
||||
private fun handleBwhcMessage(record: ConsumerRecord<String, String>) {
|
||||
val mtbFile = objectMapper.readValue(record.value(), MtbFile::class.java)
|
||||
val patientId = PatientId(mtbFile.patient.id)
|
||||
val firstRequestIdHeader = record.headers().headers("requestId")?.firstOrNull()
|
||||
val requestId = if (null != firstRequestIdHeader) {
|
||||
RequestId(String(firstRequestIdHeader.value()))
|
||||
} else {
|
||||
RequestId("")
|
||||
}
|
||||
|
||||
if (mtbFile.consent.status == Consent.Status.ACTIVE) {
|
||||
logger.debug("Accepted MTB File for processing")
|
||||
if (requestId.isBlank()) {
|
||||
requestProcessor.processMtbFile(mtbFile)
|
||||
} else {
|
||||
requestProcessor.processMtbFile(mtbFile, requestId)
|
||||
}
|
||||
} else {
|
||||
logger.debug("Accepted MTB File and process deletion")
|
||||
if (requestId.isBlank()) {
|
||||
requestProcessor.processDeletion(patientId, TtpConsentStatus.UNKNOWN_CHECK_FILE)
|
||||
} else {
|
||||
requestProcessor.processDeletion(
|
||||
patientId,
|
||||
requestId,
|
||||
TtpConsentStatus.UNKNOWN_CHECK_FILE
|
||||
)
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private fun handleDnpmV2Message(record: ConsumerRecord<String, String>) {
|
||||
// Do not handle DNPM-V2 for now
|
||||
logger.warn("Ignoring MTB File in DNPM V2 format: Not implemented yet")
|
||||
}
|
||||
|
||||
}
|
@ -1,7 +1,7 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
@ -21,15 +21,21 @@ package dev.dnpm.etl.processor.input
|
||||
|
||||
import de.ukw.ccc.bwhc.dto.Consent
|
||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import dev.dnpm.etl.processor.CustomMediaType
|
||||
import dev.dnpm.etl.processor.PatientId
|
||||
import dev.dnpm.etl.processor.consent.ICheckConsent
|
||||
import dev.dnpm.etl.processor.consent.TtpConsentStatus
|
||||
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||
import org.slf4j.LoggerFactory
|
||||
import org.springframework.http.MediaType
|
||||
import org.springframework.http.ResponseEntity
|
||||
import org.springframework.web.bind.annotation.*
|
||||
|
||||
@RestController
|
||||
@RequestMapping(path = ["mtbfile"])
|
||||
@RequestMapping(path = ["mtbfile", "mtb"])
|
||||
class MtbFileRestController(
|
||||
private val requestProcessor: RequestProcessor,
|
||||
private val requestProcessor: RequestProcessor, private val iCheckConsent: ICheckConsent
|
||||
) {
|
||||
|
||||
private val logger = LoggerFactory.getLogger(MtbFileRestController::class.java)
|
||||
@ -39,22 +45,49 @@ class MtbFileRestController(
|
||||
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")
|
||||
@PostMapping(consumes = [MediaType.APPLICATION_JSON_VALUE])
|
||||
fun mtbFile(@RequestBody mtbFile: MtbFile): ResponseEntity<Unit> {
|
||||
val consentStatusBooleanPair = checkConsentStatus(mtbFile)
|
||||
val ttpConsentStatus = consentStatusBooleanPair.first
|
||||
val isConsentOK = consentStatusBooleanPair.second
|
||||
if (isConsentOK) {
|
||||
logger.debug("Accepted MTB File (bwHC V1) for processing")
|
||||
requestProcessor.processMtbFile(mtbFile)
|
||||
} else {
|
||||
logger.debug("Accepted MTB File and process deletion")
|
||||
requestProcessor.processDeletion(mtbFile.patient.id)
|
||||
|
||||
logger.debug("Accepted MTB File (bwHC V1) and process deletion")
|
||||
val patientId = PatientId(mtbFile.patient.id)
|
||||
requestProcessor.processDeletion(patientId, ttpConsentStatus)
|
||||
}
|
||||
return ResponseEntity.accepted().build()
|
||||
}
|
||||
|
||||
private fun checkConsentStatus(mtbFile: MtbFile): Pair<TtpConsentStatus, Boolean> {
|
||||
var ttpConsentStatus = iCheckConsent.getTtpConsentStatus(mtbFile.patient.id)
|
||||
|
||||
val isConsentOK =
|
||||
(ttpConsentStatus.equals(TtpConsentStatus.UNKNOWN_CHECK_FILE) && mtbFile.consent.status == Consent.Status.ACTIVE) ||
|
||||
ttpConsentStatus.equals(
|
||||
TtpConsentStatus.CONSENTED
|
||||
)
|
||||
if (ttpConsentStatus.equals(TtpConsentStatus.UNKNOWN_CHECK_FILE) && mtbFile.consent.status == Consent.Status.REJECTED) {
|
||||
// in case ttp check is disabled - we propagate rejected status anyway
|
||||
ttpConsentStatus = TtpConsentStatus.CONSENT_MISSING_OR_REJECTED
|
||||
}
|
||||
return Pair(ttpConsentStatus, isConsentOK)
|
||||
}
|
||||
|
||||
@PostMapping(consumes = [CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE])
|
||||
fun mtbFile(@RequestBody mtbFile: Mtb): ResponseEntity<Unit> {
|
||||
logger.debug("Accepted MTB File (DNPM V2) for processing")
|
||||
requestProcessor.processMtbFile(mtbFile)
|
||||
return ResponseEntity.accepted().build()
|
||||
}
|
||||
|
||||
@DeleteMapping(path = ["{patientId}"])
|
||||
fun deleteData(@PathVariable patientId: String): ResponseEntity<Void> {
|
||||
fun deleteData(@PathVariable patientId: String): ResponseEntity<Unit> {
|
||||
logger.debug("Accepted patient ID to process deletion")
|
||||
requestProcessor.processDeletion(patientId)
|
||||
requestProcessor.processDeletion(PatientId(patientId), TtpConsentStatus.UNKNOWN_CHECK_FILE)
|
||||
return ResponseEntity.accepted().build()
|
||||
}
|
||||
|
||||
|
@ -20,46 +20,96 @@
|
||||
|
||||
package dev.dnpm.etl.processor.monitoring
|
||||
|
||||
import dev.dnpm.etl.processor.config.GIcsConfigProperties
|
||||
import dev.dnpm.etl.processor.config.GPasConfigProperties
|
||||
import dev.dnpm.etl.processor.config.RestTargetProperties
|
||||
import jakarta.annotation.PostConstruct
|
||||
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.http.*
|
||||
import org.springframework.scheduling.annotation.Scheduled
|
||||
import org.springframework.web.client.RestTemplate
|
||||
import org.springframework.web.util.UriComponentsBuilder
|
||||
import reactor.core.publisher.Sinks
|
||||
import java.time.Instant
|
||||
import kotlin.time.Duration.Companion.seconds
|
||||
import kotlin.time.toJavaDuration
|
||||
|
||||
interface ConnectionCheckService {
|
||||
fun interface ConnectionCheckService {
|
||||
|
||||
fun connectionAvailable(): Boolean
|
||||
fun connectionAvailable(): ConnectionCheckResult
|
||||
|
||||
}
|
||||
|
||||
interface OutputConnectionCheckService : ConnectionCheckService
|
||||
|
||||
sealed class ConnectionCheckResult {
|
||||
|
||||
abstract val available: Boolean
|
||||
|
||||
abstract val timestamp: Instant
|
||||
|
||||
abstract val lastChange: Instant
|
||||
|
||||
data class KafkaConnectionCheckResult(
|
||||
override val available: Boolean,
|
||||
override val timestamp: Instant,
|
||||
override val lastChange: Instant
|
||||
) : ConnectionCheckResult()
|
||||
|
||||
data class RestConnectionCheckResult(
|
||||
override val available: Boolean,
|
||||
override val timestamp: Instant,
|
||||
override val lastChange: Instant
|
||||
) : ConnectionCheckResult()
|
||||
|
||||
data class GPasConnectionCheckResult(
|
||||
override val available: Boolean,
|
||||
override val timestamp: Instant,
|
||||
override val lastChange: Instant
|
||||
) : ConnectionCheckResult()
|
||||
|
||||
data class GIcsConnectionCheckResult(
|
||||
override val available: Boolean,
|
||||
override val timestamp: Instant,
|
||||
override val lastChange: Instant
|
||||
) : ConnectionCheckResult()
|
||||
}
|
||||
|
||||
class KafkaConnectionCheckService(
|
||||
private val consumer: Consumer<String, String>,
|
||||
@Qualifier("configsUpdateProducer")
|
||||
private val configsUpdateProducer: Sinks.Many<Boolean>
|
||||
) : ConnectionCheckService {
|
||||
|
||||
private var connectionAvailable: Boolean = false
|
||||
@Qualifier("connectionCheckUpdateProducer")
|
||||
private val connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||
) : OutputConnectionCheckService {
|
||||
|
||||
private var result = ConnectionCheckResult.KafkaConnectionCheckResult(false, Instant.now(), Instant.now())
|
||||
|
||||
@PostConstruct
|
||||
@Scheduled(cron = "0 * * * * *")
|
||||
fun check() {
|
||||
connectionAvailable = try {
|
||||
null != consumer.listTopics(5.seconds.toJavaDuration())
|
||||
} catch (e: TimeoutException) {
|
||||
false
|
||||
result = try {
|
||||
val available = null != consumer.listTopics(5.seconds.toJavaDuration())
|
||||
ConnectionCheckResult.KafkaConnectionCheckResult(
|
||||
available,
|
||||
Instant.now(),
|
||||
if (result.available == available) { result.lastChange } else { Instant.now() }
|
||||
)
|
||||
} catch (_: TimeoutException) {
|
||||
ConnectionCheckResult.KafkaConnectionCheckResult(
|
||||
false,
|
||||
Instant.now(),
|
||||
if (!result.available) { result.lastChange } else { Instant.now() }
|
||||
)
|
||||
}
|
||||
configsUpdateProducer.emitNext(connectionAvailable, Sinks.EmitFailureHandler.FAIL_FAST)
|
||||
connectionCheckUpdateProducer.emitNext(
|
||||
result,
|
||||
Sinks.EmitFailureHandler.FAIL_FAST
|
||||
)
|
||||
}
|
||||
|
||||
override fun connectionAvailable(): Boolean {
|
||||
return this.connectionAvailable
|
||||
override fun connectionAvailable(): ConnectionCheckResult.KafkaConnectionCheckResult {
|
||||
return this.result
|
||||
}
|
||||
|
||||
}
|
||||
@ -67,27 +117,154 @@ class KafkaConnectionCheckService(
|
||||
class RestConnectionCheckService(
|
||||
private val restTemplate: RestTemplate,
|
||||
private val restTargetProperties: RestTargetProperties,
|
||||
@Qualifier("configsUpdateProducer")
|
||||
private val configsUpdateProducer: Sinks.Many<Boolean>
|
||||
) : ConnectionCheckService {
|
||||
@Qualifier("connectionCheckUpdateProducer")
|
||||
private val connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||
) : OutputConnectionCheckService {
|
||||
|
||||
private var connectionAvailable: Boolean = false
|
||||
private var result = ConnectionCheckResult.RestConnectionCheckResult(false, Instant.now(), Instant.now())
|
||||
|
||||
@PostConstruct
|
||||
@Scheduled(cron = "0 * * * * *")
|
||||
fun check() {
|
||||
connectionAvailable = try {
|
||||
restTemplate.getForEntity(
|
||||
restTargetProperties.uri?.replace("/etl/api", "").toString(),
|
||||
result = try {
|
||||
val available = restTemplate.getForEntity(
|
||||
if (restTargetProperties.isBwhc) {
|
||||
UriComponentsBuilder.fromUriString(restTargetProperties.uri.toString()).path("").toUriString()
|
||||
} else {
|
||||
UriComponentsBuilder.fromUriString(restTargetProperties.uri.toString())
|
||||
.pathSegment("mtb")
|
||||
.pathSegment("kaplan-meier")
|
||||
.pathSegment("config")
|
||||
.toUriString()
|
||||
},
|
||||
String::class.java
|
||||
).statusCode == HttpStatus.OK
|
||||
} catch (e: Exception) {
|
||||
false
|
||||
|
||||
ConnectionCheckResult.RestConnectionCheckResult(
|
||||
available,
|
||||
Instant.now(),
|
||||
if (result.available == available) { result.lastChange } else { Instant.now() }
|
||||
)
|
||||
} catch (_: Exception) {
|
||||
ConnectionCheckResult.RestConnectionCheckResult(
|
||||
false,
|
||||
Instant.now(),
|
||||
if (!result.available) { result.lastChange } else { Instant.now() }
|
||||
)
|
||||
}
|
||||
configsUpdateProducer.emitNext(connectionAvailable, Sinks.EmitFailureHandler.FAIL_FAST)
|
||||
connectionCheckUpdateProducer.emitNext(
|
||||
result,
|
||||
Sinks.EmitFailureHandler.FAIL_FAST
|
||||
)
|
||||
}
|
||||
|
||||
override fun connectionAvailable(): Boolean {
|
||||
return this.connectionAvailable
|
||||
override fun connectionAvailable(): ConnectionCheckResult.RestConnectionCheckResult {
|
||||
return this.result
|
||||
}
|
||||
}
|
||||
|
||||
class GPasConnectionCheckService(
|
||||
private val restTemplate: RestTemplate,
|
||||
private val gPasConfigProperties: GPasConfigProperties,
|
||||
@Qualifier("connectionCheckUpdateProducer")
|
||||
private val connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||
) : ConnectionCheckService {
|
||||
|
||||
private var result = ConnectionCheckResult.GPasConnectionCheckResult(false, Instant.now(), Instant.now())
|
||||
|
||||
@PostConstruct
|
||||
@Scheduled(cron = "0 * * * * *")
|
||||
fun check() {
|
||||
result = try {
|
||||
val uri = UriComponentsBuilder.fromUriString(
|
||||
gPasConfigProperties.uri?.replace("/\$pseudonymizeAllowCreate", "/metadata").toString()
|
||||
).build().toUri()
|
||||
|
||||
val headers = HttpHeaders()
|
||||
headers.contentType = MediaType.APPLICATION_JSON
|
||||
if (!gPasConfigProperties.username.isNullOrBlank() && !gPasConfigProperties.password.isNullOrBlank()) {
|
||||
headers.setBasicAuth(gPasConfigProperties.username, gPasConfigProperties.password)
|
||||
}
|
||||
|
||||
val available = restTemplate.exchange(
|
||||
uri,
|
||||
HttpMethod.GET,
|
||||
HttpEntity<Void>(headers),
|
||||
Void::class.java
|
||||
).statusCode == HttpStatus.OK
|
||||
|
||||
ConnectionCheckResult.GPasConnectionCheckResult(
|
||||
available,
|
||||
Instant.now(),
|
||||
if (result.available == available) { result.lastChange } else { Instant.now() }
|
||||
)
|
||||
} catch (_: Exception) {
|
||||
ConnectionCheckResult.GPasConnectionCheckResult(
|
||||
false,
|
||||
Instant.now(),
|
||||
if (!result.available) { result.lastChange } else { Instant.now() }
|
||||
)
|
||||
}
|
||||
connectionCheckUpdateProducer.emitNext(
|
||||
result,
|
||||
Sinks.EmitFailureHandler.FAIL_FAST
|
||||
)
|
||||
}
|
||||
|
||||
override fun connectionAvailable(): ConnectionCheckResult.GPasConnectionCheckResult {
|
||||
return this.result
|
||||
}
|
||||
}
|
||||
|
||||
class GIcsConnectionCheckService(
|
||||
private val restTemplate: RestTemplate,
|
||||
private val gIcsConfigProperties: GIcsConfigProperties,
|
||||
@Qualifier("connectionCheckUpdateProducer")
|
||||
private val connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||
) : ConnectionCheckService {
|
||||
|
||||
private var result = ConnectionCheckResult.GIcsConnectionCheckResult(false, Instant.now(), Instant.now())
|
||||
|
||||
@PostConstruct
|
||||
@Scheduled(cron = "0 * * * * *")
|
||||
fun check() {
|
||||
result = try {
|
||||
|
||||
val uri = UriComponentsBuilder.fromUriString(
|
||||
gIcsConfigProperties.uri.toString()).path("/metadata").build().toUri()
|
||||
|
||||
val headers = HttpHeaders()
|
||||
headers.contentType = MediaType.APPLICATION_JSON
|
||||
if (!gIcsConfigProperties.username.isNullOrBlank() && !gIcsConfigProperties.password.isNullOrBlank()) {
|
||||
headers.setBasicAuth(gIcsConfigProperties.username, gIcsConfigProperties.password)
|
||||
}
|
||||
|
||||
val available = restTemplate.exchange(
|
||||
uri,
|
||||
HttpMethod.GET,
|
||||
HttpEntity<Void>(headers),
|
||||
Void::class.java
|
||||
).statusCode == HttpStatus.OK
|
||||
|
||||
ConnectionCheckResult.GIcsConnectionCheckResult(
|
||||
available,
|
||||
Instant.now(),
|
||||
if (result.available == available) { result.lastChange } else { Instant.now() }
|
||||
)
|
||||
} catch (_: Exception) {
|
||||
ConnectionCheckResult.GIcsConnectionCheckResult(
|
||||
false,
|
||||
Instant.now(),
|
||||
if (!result.available) { result.lastChange } else { Instant.now() }
|
||||
)
|
||||
}
|
||||
connectionCheckUpdateProducer.emitNext(
|
||||
result,
|
||||
Sinks.EmitFailureHandler.FAIL_FAST
|
||||
)
|
||||
}
|
||||
|
||||
override fun connectionAvailable(): ConnectionCheckResult.GIcsConnectionCheckResult {
|
||||
return this.result
|
||||
}
|
||||
}
|
@ -19,11 +19,15 @@
|
||||
|
||||
package dev.dnpm.etl.processor.monitoring
|
||||
|
||||
import com.fasterxml.jackson.annotation.JsonAlias
|
||||
import com.fasterxml.jackson.annotation.JsonIgnoreProperties
|
||||
import com.fasterxml.jackson.annotation.JsonValue
|
||||
import com.fasterxml.jackson.core.JsonParseException
|
||||
import com.fasterxml.jackson.databind.JsonMappingException
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import dev.dnpm.etl.processor.monitoring.ReportService.Issue
|
||||
import dev.dnpm.etl.processor.monitoring.ReportService.Severity
|
||||
import java.util.Optional
|
||||
|
||||
class ReportService(
|
||||
private val objectMapper: ObjectMapper
|
||||
@ -54,11 +58,25 @@ class ReportService(
|
||||
private data class DataQualityReport(val issues: List<Issue>)
|
||||
|
||||
@JsonIgnoreProperties(ignoreUnknown = true)
|
||||
data class Issue(val severity: Severity, val message: String)
|
||||
data class Issue(
|
||||
val severity: Severity,
|
||||
@JsonAlias("details") val message: String,
|
||||
val path: Optional<String> = Optional.empty()
|
||||
)
|
||||
|
||||
enum class Severity(@JsonValue val value: String) {
|
||||
FATAL("fatal"),
|
||||
ERROR("error"),
|
||||
WARNING("warning"),
|
||||
INFO("info")
|
||||
}
|
||||
}
|
||||
|
||||
fun List<Issue>.asRequestStatus(): RequestStatus {
|
||||
val severity = this.minOfOrNull { it.severity }
|
||||
return when (severity) {
|
||||
Severity.FATAL, Severity.ERROR -> RequestStatus.ERROR
|
||||
Severity.WARNING -> RequestStatus.WARNING
|
||||
else -> RequestStatus.SUCCESS
|
||||
}
|
||||
}
|
@ -19,10 +19,12 @@
|
||||
|
||||
package dev.dnpm.etl.processor.monitoring
|
||||
|
||||
import dev.dnpm.etl.processor.*
|
||||
import org.springframework.data.annotation.Id
|
||||
import org.springframework.data.domain.Page
|
||||
import org.springframework.data.domain.Pageable
|
||||
import org.springframework.data.jdbc.repository.query.Query
|
||||
import org.springframework.data.relational.core.mapping.Column
|
||||
import org.springframework.data.relational.core.mapping.Embedded
|
||||
import org.springframework.data.relational.core.mapping.Table
|
||||
import org.springframework.data.repository.CrudRepository
|
||||
@ -30,26 +32,48 @@ import org.springframework.data.repository.PagingAndSortingRepository
|
||||
import java.time.Instant
|
||||
import java.util.*
|
||||
|
||||
typealias RequestId = UUID
|
||||
|
||||
@Table("request")
|
||||
data class Request(
|
||||
@Id val id: Long? = null,
|
||||
val uuid: String = RequestId.randomUUID().toString(),
|
||||
val patientId: String,
|
||||
val pid: String,
|
||||
val fingerprint: String,
|
||||
val uuid: RequestId = randomRequestId(),
|
||||
val patientPseudonym: PatientPseudonym,
|
||||
val pid: PatientId,
|
||||
@Column("fingerprint")
|
||||
val fingerprint: Fingerprint,
|
||||
val type: RequestType,
|
||||
var status: RequestStatus,
|
||||
var processedAt: Instant = Instant.now(),
|
||||
@Embedded.Nullable var report: Report? = null
|
||||
)
|
||||
) {
|
||||
constructor(
|
||||
uuid: RequestId,
|
||||
patientPseudonym: PatientPseudonym,
|
||||
pid: PatientId,
|
||||
fingerprint: Fingerprint,
|
||||
type: RequestType,
|
||||
status: RequestStatus
|
||||
) :
|
||||
this(null, uuid, patientPseudonym, pid, fingerprint, type, status, Instant.now())
|
||||
|
||||
constructor(
|
||||
uuid: RequestId,
|
||||
patientPseudonym: PatientPseudonym,
|
||||
pid: PatientId,
|
||||
fingerprint: Fingerprint,
|
||||
type: RequestType,
|
||||
status: RequestStatus,
|
||||
processedAt: Instant
|
||||
) :
|
||||
this(null, uuid, patientPseudonym, pid, fingerprint, type, status, processedAt)
|
||||
}
|
||||
|
||||
@JvmRecord
|
||||
data class Report(
|
||||
val description: String,
|
||||
val dataQualityReport: String = ""
|
||||
)
|
||||
|
||||
@JvmRecord
|
||||
data class CountedState(
|
||||
val count: Int,
|
||||
val status: RequestStatus,
|
||||
@ -57,17 +81,17 @@ data class CountedState(
|
||||
|
||||
interface RequestRepository : CrudRepository<Request, Long>, PagingAndSortingRepository<Request, Long> {
|
||||
|
||||
fun findAllByPatientIdOrderByProcessedAtDesc(patientId: String): List<Request>
|
||||
fun findAllByPatientPseudonymOrderByProcessedAtDesc(patientId: PatientPseudonym): List<Request>
|
||||
|
||||
fun findByUuidEquals(uuid: String): Optional<Request>
|
||||
fun findByUuidEquals(uuid: RequestId): Optional<Request>
|
||||
|
||||
fun findRequestByPatientId(patientId: String, pageable: Pageable): Page<Request>
|
||||
fun findRequestByPatientPseudonym(patientPseudonym: PatientPseudonym, 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>
|
||||
|
||||
@Query("SELECT count(*) AS count, status FROM (" +
|
||||
"SELECT status, rank() OVER (PARTITION BY patient_id ORDER BY processed_at DESC) AS rank FROM request " +
|
||||
"SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " +
|
||||
"WHERE type = 'MTB_FILE' AND status NOT IN ('DUPLICATION') " +
|
||||
") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;")
|
||||
fun findPatientUniqueStates(): List<CountedState>
|
||||
@ -76,7 +100,7 @@ interface RequestRepository : CrudRepository<Request, Long>, PagingAndSortingRep
|
||||
fun countDeleteStates(): List<CountedState>
|
||||
|
||||
@Query("SELECT count(*) AS count, status FROM (" +
|
||||
"SELECT status, rank() OVER (PARTITION BY patient_id ORDER BY processed_at DESC) AS rank FROM request " +
|
||||
"SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " +
|
||||
"WHERE type = 'DELETE'" +
|
||||
") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;")
|
||||
fun findPatientUniqueDeleteStates(): List<CountedState>
|
||||
|
@ -24,5 +24,6 @@ enum class RequestStatus(val value: String) {
|
||||
WARNING("warning"),
|
||||
ERROR("error"),
|
||||
UNKNOWN("unknown"),
|
||||
DUPLICATION("duplication")
|
||||
DUPLICATION("duplication"),
|
||||
NO_CONSENT("no-consent")
|
||||
}
|
@ -1,7 +1,7 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
@ -22,9 +22,12 @@ package dev.dnpm.etl.processor.output
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import de.ukw.ccc.bwhc.dto.Consent
|
||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import dev.dnpm.etl.processor.CustomMediaType
|
||||
import dev.dnpm.etl.processor.config.KafkaProperties
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import org.apache.kafka.clients.producer.ProducerRecord
|
||||
import org.slf4j.LoggerFactory
|
||||
import org.springframework.http.MediaType
|
||||
import org.springframework.kafka.core.KafkaTemplate
|
||||
import org.springframework.retry.support.RetryTemplate
|
||||
|
||||
@ -37,14 +40,20 @@ class KafkaMtbFileSender(
|
||||
|
||||
private val logger = LoggerFactory.getLogger(KafkaMtbFileSender::class.java)
|
||||
|
||||
override fun send(request: MtbFileSender.MtbFileRequest): MtbFileSender.Response {
|
||||
override fun <T> send(request: MtbFileRequest<T>): MtbFileSender.Response {
|
||||
return try {
|
||||
return retryTemplate.execute<MtbFileSender.Response, Exception> {
|
||||
val result = kafkaTemplate.send(
|
||||
kafkaProperties.topic,
|
||||
key(request),
|
||||
objectMapper.writeValueAsString(Data(request.requestId, request.mtbFile))
|
||||
)
|
||||
val record =
|
||||
ProducerRecord(kafkaProperties.outputTopic, key(request), objectMapper.writeValueAsString(request))
|
||||
when (request) {
|
||||
is BwhcV1MtbFileRequest -> record.headers()
|
||||
.add("contentType", MediaType.APPLICATION_JSON_VALUE.toByteArray())
|
||||
|
||||
is DnpmV2MtbFileRequest -> record.headers()
|
||||
.add("contentType", CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE.toByteArray())
|
||||
}
|
||||
|
||||
val result = kafkaTemplate.send(record)
|
||||
if (result.get() != null) {
|
||||
logger.debug("Sent file via KafkaMtbFileSender")
|
||||
MtbFileSender.Response(RequestStatus.UNKNOWN)
|
||||
@ -58,11 +67,11 @@ class KafkaMtbFileSender(
|
||||
}
|
||||
}
|
||||
|
||||
override fun send(request: MtbFileSender.DeleteRequest): MtbFileSender.Response {
|
||||
override fun send(request: DeleteRequest): MtbFileSender.Response {
|
||||
val dummyMtbFile = MtbFile.builder()
|
||||
.withConsent(
|
||||
Consent.builder()
|
||||
.withPatient(request.patientId)
|
||||
.withPatient(request.patientId.value)
|
||||
.withStatus(Consent.Status.REJECTED)
|
||||
.build()
|
||||
)
|
||||
@ -70,12 +79,15 @@ class KafkaMtbFileSender(
|
||||
|
||||
return try {
|
||||
return retryTemplate.execute<MtbFileSender.Response, Exception> {
|
||||
val result = kafkaTemplate.send(
|
||||
kafkaProperties.topic,
|
||||
key(request),
|
||||
objectMapper.writeValueAsString(Data(request.requestId, dummyMtbFile))
|
||||
)
|
||||
val record =
|
||||
ProducerRecord(
|
||||
kafkaProperties.outputTopic,
|
||||
key(request),
|
||||
// Always use old BwhcV1FileRequest with Consent REJECT
|
||||
objectMapper.writeValueAsString(BwhcV1MtbFileRequest(request.requestId, dummyMtbFile))
|
||||
)
|
||||
|
||||
val result = kafkaTemplate.send(record)
|
||||
if (result.get() != null) {
|
||||
logger.debug("Sent deletion request via KafkaMtbFileSender")
|
||||
MtbFileSender.Response(RequestStatus.UNKNOWN)
|
||||
@ -90,17 +102,15 @@ class KafkaMtbFileSender(
|
||||
}
|
||||
|
||||
override fun endpoint(): String {
|
||||
return "${this.kafkaProperties.servers} (${this.kafkaProperties.topic}/${this.kafkaProperties.responseTopic})"
|
||||
return "${this.kafkaProperties.servers} (${this.kafkaProperties.outputTopic}/${this.kafkaProperties.outputResponseTopic})"
|
||||
}
|
||||
|
||||
private fun key(request: MtbFileSender.MtbFileRequest): String {
|
||||
return "{\"pid\": \"${request.mtbFile.patient.id}\", " +
|
||||
"\"eid\": \"${request.mtbFile.episode.id}\"}"
|
||||
private fun key(request: MtbRequest): String {
|
||||
return when (request) {
|
||||
is BwhcV1MtbFileRequest -> "{\"pid\": \"${request.content.patient.id}\"}"
|
||||
is DnpmV2MtbFileRequest -> "{\"pid\": \"${request.content.patient.id}\"}"
|
||||
is DeleteRequest -> "{\"pid\": \"${request.patientId.value}\"}"
|
||||
else -> throw IllegalArgumentException("Unsupported request type: ${request::class.simpleName}")
|
||||
}
|
||||
}
|
||||
|
||||
private fun key(request: MtbFileSender.DeleteRequest): String {
|
||||
return "{\"pid\": \"${request.patientId}\"}"
|
||||
}
|
||||
|
||||
data class Data(val requestId: String, val content: MtbFile)
|
||||
}
|
@ -19,23 +19,17 @@
|
||||
|
||||
package dev.dnpm.etl.processor.output
|
||||
|
||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import org.springframework.http.HttpStatusCode
|
||||
|
||||
interface MtbFileSender {
|
||||
fun send(request: MtbFileRequest): Response
|
||||
fun <T> send(request: MtbFileRequest<T>): Response
|
||||
|
||||
fun send(request: DeleteRequest): Response
|
||||
|
||||
fun endpoint(): String
|
||||
|
||||
data class Response(val status: RequestStatus, val body: String = "")
|
||||
|
||||
data class MtbFileRequest(val requestId: String, val mtbFile: MtbFile)
|
||||
|
||||
data class DeleteRequest(val requestId: String, val patientId: String)
|
||||
|
||||
}
|
||||
|
||||
fun Int.asRequestStatus(): RequestStatus {
|
||||
|
59
src/main/kotlin/dev/dnpm/etl/processor/output/MtbRequest.kt
Normal file
59
src/main/kotlin/dev/dnpm/etl/processor/output/MtbRequest.kt
Normal file
@ -0,0 +1,59 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
* by the Free Software Foundation, either version 3 of the License, or
|
||||
* (at your option) any later version.
|
||||
*
|
||||
* This program is distributed in the hope that it will be useful,
|
||||
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
* GNU Affero General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Affero General Public License
|
||||
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
*/
|
||||
|
||||
package dev.dnpm.etl.processor.output
|
||||
|
||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import dev.dnpm.etl.processor.PatientPseudonym
|
||||
import dev.dnpm.etl.processor.RequestId
|
||||
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||
|
||||
interface MtbRequest {
|
||||
val requestId: RequestId
|
||||
}
|
||||
|
||||
sealed interface MtbFileRequest<out T> : MtbRequest {
|
||||
override val requestId: RequestId
|
||||
val content: T
|
||||
|
||||
fun patientPseudonym(): PatientPseudonym
|
||||
}
|
||||
|
||||
data class BwhcV1MtbFileRequest(
|
||||
override val requestId: RequestId,
|
||||
override val content: MtbFile
|
||||
) : MtbFileRequest<MtbFile> {
|
||||
override fun patientPseudonym(): PatientPseudonym {
|
||||
return PatientPseudonym(content.patient.id)
|
||||
}
|
||||
}
|
||||
|
||||
data class DnpmV2MtbFileRequest(
|
||||
override val requestId: RequestId,
|
||||
override val content: Mtb
|
||||
) : MtbFileRequest<Mtb> {
|
||||
override fun patientPseudonym(): PatientPseudonym {
|
||||
return PatientPseudonym(content.patient.id)
|
||||
}
|
||||
}
|
||||
|
||||
data class DeleteRequest(
|
||||
override val requestId: RequestId,
|
||||
val patientId: PatientPseudonym
|
||||
) : MtbRequest
|
@ -0,0 +1,51 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
* by the Free Software Foundation, either version 3 of the License, or
|
||||
* (at your option) any later version.
|
||||
*
|
||||
* This program is distributed in the hope that it will be useful,
|
||||
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
* GNU Affero General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Affero General Public License
|
||||
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
*/
|
||||
|
||||
package dev.dnpm.etl.processor.output
|
||||
|
||||
import dev.dnpm.etl.processor.PatientPseudonym
|
||||
import dev.dnpm.etl.processor.config.RestTargetProperties
|
||||
import dev.dnpm.etl.processor.monitoring.ReportService
|
||||
import org.springframework.retry.support.RetryTemplate
|
||||
import org.springframework.web.client.RestTemplate
|
||||
import org.springframework.web.util.UriComponentsBuilder
|
||||
|
||||
class RestBwhcMtbFileSender(
|
||||
restTemplate: RestTemplate,
|
||||
private val restTargetProperties: RestTargetProperties,
|
||||
retryTemplate: RetryTemplate,
|
||||
reportService: ReportService,
|
||||
) : RestMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService) {
|
||||
|
||||
override fun sendUrl(): String {
|
||||
return UriComponentsBuilder
|
||||
.fromUriString(restTargetProperties.uri.toString())
|
||||
.pathSegment("MTBFile")
|
||||
.toUriString()
|
||||
}
|
||||
|
||||
override fun deleteUrl(patientId: PatientPseudonym): String {
|
||||
return UriComponentsBuilder
|
||||
.fromUriString(restTargetProperties.uri.toString())
|
||||
.pathSegment("Patient")
|
||||
.pathSegment(patientId.value)
|
||||
.toUriString()
|
||||
}
|
||||
|
||||
}
|
@ -0,0 +1,55 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
* by the Free Software Foundation, either version 3 of the License, or
|
||||
* (at your option) any later version.
|
||||
*
|
||||
* This program is distributed in the hope that it will be useful,
|
||||
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
* GNU Affero General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Affero General Public License
|
||||
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
*/
|
||||
|
||||
package dev.dnpm.etl.processor.output
|
||||
|
||||
import dev.dnpm.etl.processor.PatientPseudonym
|
||||
import dev.dnpm.etl.processor.config.RestTargetProperties
|
||||
import dev.dnpm.etl.processor.monitoring.ReportService
|
||||
import org.springframework.retry.support.RetryTemplate
|
||||
import org.springframework.web.client.RestTemplate
|
||||
import org.springframework.web.util.UriComponentsBuilder
|
||||
|
||||
class RestDipMtbFileSender(
|
||||
restTemplate: RestTemplate,
|
||||
private val restTargetProperties: RestTargetProperties,
|
||||
retryTemplate: RetryTemplate,
|
||||
reportService: ReportService
|
||||
) : RestMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService) {
|
||||
|
||||
override fun sendUrl(): String {
|
||||
return UriComponentsBuilder
|
||||
.fromUriString(restTargetProperties.uri.toString())
|
||||
.pathSegment("mtb")
|
||||
.pathSegment("etl")
|
||||
.pathSegment("patient-record")
|
||||
.toUriString()
|
||||
}
|
||||
|
||||
override fun deleteUrl(patientId: PatientPseudonym): String {
|
||||
return UriComponentsBuilder
|
||||
.fromUriString(restTargetProperties.uri.toString())
|
||||
.pathSegment("mtb")
|
||||
.pathSegment("etl")
|
||||
.pathSegment("patient")
|
||||
.pathSegment(patientId.value)
|
||||
.toUriString()
|
||||
}
|
||||
|
||||
}
|
@ -1,7 +1,7 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
@ -19,62 +19,71 @@
|
||||
|
||||
package dev.dnpm.etl.processor.output
|
||||
|
||||
import dev.dnpm.etl.processor.CustomMediaType
|
||||
import dev.dnpm.etl.processor.PatientPseudonym
|
||||
import dev.dnpm.etl.processor.config.RestTargetProperties
|
||||
import dev.dnpm.etl.processor.monitoring.ReportService
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import dev.dnpm.etl.processor.monitoring.asRequestStatus
|
||||
import org.slf4j.LoggerFactory
|
||||
import org.springframework.http.HttpEntity
|
||||
import org.springframework.http.HttpHeaders
|
||||
import org.springframework.http.MediaType
|
||||
import org.springframework.retry.support.RetryTemplate
|
||||
import org.springframework.web.client.RestClientException
|
||||
import org.springframework.web.client.RestClientResponseException
|
||||
import org.springframework.web.client.RestTemplate
|
||||
|
||||
class RestMtbFileSender(
|
||||
abstract class RestMtbFileSender(
|
||||
private val restTemplate: RestTemplate,
|
||||
private val restTargetProperties: RestTargetProperties,
|
||||
private val retryTemplate: RetryTemplate
|
||||
private val retryTemplate: RetryTemplate,
|
||||
private val reportService: ReportService
|
||||
) : MtbFileSender {
|
||||
|
||||
private val logger = LoggerFactory.getLogger(RestMtbFileSender::class.java)
|
||||
|
||||
override fun send(request: MtbFileSender.MtbFileRequest): MtbFileSender.Response {
|
||||
abstract fun sendUrl(): String
|
||||
|
||||
abstract fun deleteUrl(patientId: PatientPseudonym): String
|
||||
|
||||
override fun <T> send(request: MtbFileRequest<T>): MtbFileSender.Response {
|
||||
try {
|
||||
return retryTemplate.execute<MtbFileSender.Response, Exception> {
|
||||
val headers = HttpHeaders()
|
||||
headers.contentType = MediaType.APPLICATION_JSON
|
||||
val entityReq = HttpEntity(request.mtbFile, headers)
|
||||
val headers = getHttpHeaders(request)
|
||||
val entityReq = HttpEntity(request.content, headers)
|
||||
val response = restTemplate.postForEntity(
|
||||
"${restTargetProperties.uri}/MTBFile",
|
||||
sendUrl(),
|
||||
entityReq,
|
||||
String::class.java
|
||||
)
|
||||
if (!response.statusCode.is2xxSuccessful) {
|
||||
logger.warn("Error sending to remote system: {}", response.body)
|
||||
return@execute MtbFileSender.Response(
|
||||
response.statusCode.asRequestStatus(),
|
||||
reportService.deserialize(response.body).asRequestStatus(),
|
||||
"Status-Code: ${response.statusCode.value()}"
|
||||
)
|
||||
}
|
||||
logger.debug("Sent file via RestMtbFileSender")
|
||||
return@execute MtbFileSender.Response(response.statusCode.asRequestStatus(), response.body.orEmpty())
|
||||
return@execute MtbFileSender.Response(reportService.deserialize(response.body).asRequestStatus(), response.body.orEmpty())
|
||||
}
|
||||
} catch (e: IllegalArgumentException) {
|
||||
logger.error("Not a valid URI to export to: '{}'", restTargetProperties.uri!!)
|
||||
} catch (e: RestClientException) {
|
||||
} catch (e: RestClientResponseException) {
|
||||
logger.info(restTargetProperties.uri!!.toString())
|
||||
logger.error("Cannot send data to remote system", e)
|
||||
logger.error("Request data not accepted by remote system", e)
|
||||
return MtbFileSender.Response(reportService.deserialize(e.responseBodyAsString).asRequestStatus(), e.responseBodyAsString)
|
||||
}
|
||||
return MtbFileSender.Response(RequestStatus.ERROR, "Sonstiger Fehler bei der Übertragung")
|
||||
}
|
||||
|
||||
override fun send(request: MtbFileSender.DeleteRequest): MtbFileSender.Response {
|
||||
override fun send(request: DeleteRequest): MtbFileSender.Response {
|
||||
try {
|
||||
return retryTemplate.execute<MtbFileSender.Response, Exception> {
|
||||
val headers = HttpHeaders()
|
||||
headers.contentType = MediaType.APPLICATION_JSON
|
||||
val headers = getHttpHeaders(request)
|
||||
val entityReq = HttpEntity(null, headers)
|
||||
restTemplate.delete(
|
||||
"${restTargetProperties.uri}/Patient/${request.patientId}",
|
||||
deleteUrl(request.patientId),
|
||||
entityReq,
|
||||
String::class.java
|
||||
)
|
||||
@ -94,4 +103,22 @@ class RestMtbFileSender(
|
||||
return this.restTargetProperties.uri.orEmpty()
|
||||
}
|
||||
|
||||
private fun getHttpHeaders(request: MtbRequest): HttpHeaders {
|
||||
val username = restTargetProperties.username
|
||||
val password = restTargetProperties.password
|
||||
val headers = HttpHeaders()
|
||||
headers.contentType = when (request) {
|
||||
is BwhcV1MtbFileRequest -> MediaType.APPLICATION_JSON
|
||||
is DnpmV2MtbFileRequest -> CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON
|
||||
else -> MediaType.APPLICATION_JSON
|
||||
}
|
||||
|
||||
if (username.isNullOrBlank() || password.isNullOrBlank()) {
|
||||
return headers
|
||||
}
|
||||
|
||||
headers.setBasicAuth(username, password)
|
||||
return headers
|
||||
}
|
||||
|
||||
}
|
@ -19,6 +19,8 @@
|
||||
|
||||
package dev.dnpm.etl.processor.pseudonym
|
||||
|
||||
import dev.dnpm.etl.processor.PatientId
|
||||
import dev.dnpm.etl.processor.PatientPseudonym
|
||||
import dev.dnpm.etl.processor.config.PseudonymizeConfigProperties
|
||||
|
||||
class PseudonymizeService(
|
||||
@ -26,11 +28,15 @@ class PseudonymizeService(
|
||||
private val configProperties: PseudonymizeConfigProperties
|
||||
) {
|
||||
|
||||
fun patientPseudonym(patientId: String): String {
|
||||
fun patientPseudonym(patientId: PatientId): PatientPseudonym {
|
||||
return when (generator) {
|
||||
is GpasPseudonymGenerator -> generator.generate(patientId)
|
||||
else -> "${configProperties.prefix}_${generator.generate(patientId)}"
|
||||
is GpasPseudonymGenerator -> PatientPseudonym(generator.generate(patientId.value))
|
||||
else -> PatientPseudonym("${configProperties.prefix}_${generator.generate(patientId.value)}")
|
||||
}
|
||||
}
|
||||
|
||||
fun prefix(): String {
|
||||
return configProperties.prefix
|
||||
}
|
||||
|
||||
}
|
@ -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
|
||||
@ -20,34 +20,308 @@
|
||||
package dev.dnpm.etl.processor.pseudonym
|
||||
|
||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import dev.dnpm.etl.processor.PatientId
|
||||
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||
import org.apache.commons.codec.digest.DigestUtils
|
||||
import org.hl7.fhir.r4.model.Consent
|
||||
|
||||
/** Replaces patient ID with generated patient pseudonym
|
||||
*
|
||||
* @param pseudonymizeService The pseudonymizeService to be used
|
||||
* @return The MTB file containing patient pseudonymes
|
||||
*/
|
||||
infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
|
||||
val patientPseudonym = pseudonymizeService.patientPseudonym(this.patient.id)
|
||||
val patientPseudonym = pseudonymizeService.patientPseudonym(PatientId(this.patient.id)).value
|
||||
|
||||
this.episode.patient = patientPseudonym
|
||||
this.carePlans.forEach { it.patient = patientPseudonym }
|
||||
this.episode?.patient = patientPseudonym
|
||||
this.carePlans?.forEach { it.patient = patientPseudonym }
|
||||
this.patient.id = patientPseudonym
|
||||
this.claims.forEach { it.patient = patientPseudonym }
|
||||
this.consent.patient = patientPseudonym
|
||||
this.claimResponses.forEach { it.patient = patientPseudonym }
|
||||
this.diagnoses.forEach { it.patient = patientPseudonym }
|
||||
this.ecogStatus.forEach { it.patient = patientPseudonym }
|
||||
this.familyMemberDiagnoses.forEach { it.patient = patientPseudonym }
|
||||
this.geneticCounsellingRequests.forEach { it.patient = patientPseudonym }
|
||||
this.histologyReevaluationRequests.forEach { it.patient = patientPseudonym }
|
||||
this.histologyReports.forEach {
|
||||
this.claims?.forEach { it.patient = patientPseudonym }
|
||||
this.consent?.patient = patientPseudonym
|
||||
this.claimResponses?.forEach { it.patient = patientPseudonym }
|
||||
this.diagnoses?.forEach { it.patient = patientPseudonym }
|
||||
this.ecogStatus?.forEach { it.patient = patientPseudonym }
|
||||
this.familyMemberDiagnoses?.forEach { it.patient = patientPseudonym }
|
||||
this.geneticCounsellingRequests?.forEach { it.patient = patientPseudonym }
|
||||
this.histologyReevaluationRequests?.forEach { it.patient = patientPseudonym }
|
||||
this.histologyReports?.forEach {
|
||||
it.patient = patientPseudonym
|
||||
it.tumorMorphology.patient = patientPseudonym
|
||||
it.tumorMorphology?.patient = patientPseudonym
|
||||
}
|
||||
this.lastGuidelineTherapies.forEach { it.patient = patientPseudonym }
|
||||
this.molecularPathologyFindings.forEach { it.patient = patientPseudonym }
|
||||
this.molecularTherapies.forEach { molecularTherapy -> molecularTherapy.history.forEach { it.patient = patientPseudonym } }
|
||||
this.ngsReports.forEach { it.patient = patientPseudonym }
|
||||
this.previousGuidelineTherapies.forEach { it.patient = patientPseudonym }
|
||||
this.rebiopsyRequests.forEach { it.patient = patientPseudonym }
|
||||
this.recommendations.forEach { it.patient = patientPseudonym }
|
||||
this.recommendations.forEach { it.patient = patientPseudonym }
|
||||
this.responses.forEach { it.patient = patientPseudonym }
|
||||
this.studyInclusionRequests.forEach { it.patient = patientPseudonym }
|
||||
this.specimens.forEach { it.patient = patientPseudonym }
|
||||
this.lastGuidelineTherapies?.forEach { it.patient = patientPseudonym }
|
||||
this.molecularPathologyFindings?.forEach { it.patient = patientPseudonym }
|
||||
this.molecularTherapies?.forEach { molecularTherapy ->
|
||||
molecularTherapy.history.forEach {
|
||||
it.patient = patientPseudonym
|
||||
}
|
||||
}
|
||||
this.ngsReports?.forEach { it.patient = patientPseudonym }
|
||||
this.previousGuidelineTherapies?.forEach { it.patient = patientPseudonym }
|
||||
this.rebiopsyRequests?.forEach { it.patient = patientPseudonym }
|
||||
this.recommendations?.forEach { it.patient = patientPseudonym }
|
||||
this.responses?.forEach { it.patient = patientPseudonym }
|
||||
this.studyInclusionRequests?.forEach { it.patient = patientPseudonym }
|
||||
this.specimens?.forEach { it.patient = patientPseudonym }
|
||||
}
|
||||
|
||||
/**
|
||||
* Creates new hash of content IDs with given prefix except for patient IDs
|
||||
*
|
||||
* @param pseudonymizeService The pseudonymizeService to be used
|
||||
* @return The MTB file containing rehashed content IDs
|
||||
*/
|
||||
infix fun MtbFile.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
|
||||
val prefix = pseudonymizeService.prefix()
|
||||
|
||||
fun anonymize(id: String): String {
|
||||
val hash = DigestUtils.sha256Hex("$prefix-$id").substring(0, 41).lowercase()
|
||||
return "$prefix$hash"
|
||||
}
|
||||
|
||||
this.episode?.apply {
|
||||
id = id?.let {
|
||||
anonymize(it)
|
||||
}
|
||||
}
|
||||
this.carePlans?.onEach { carePlan ->
|
||||
carePlan?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
diagnosis = diagnosis?.let { anonymize(it) }
|
||||
geneticCounsellingRequest = geneticCounsellingRequest?.let { anonymize(it) }
|
||||
rebiopsyRequests = rebiopsyRequests.map { it?.let { anonymize(it) } }
|
||||
recommendations = recommendations.map { it?.let { anonymize(it) } }
|
||||
studyInclusionRequests = studyInclusionRequests.map { it?.let { anonymize(it) } }
|
||||
}
|
||||
}
|
||||
this.claims?.onEach { claim ->
|
||||
claim?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
therapy = therapy?.let { anonymize(it) }
|
||||
}
|
||||
}
|
||||
this.claimResponses?.onEach { claimResponse ->
|
||||
claimResponse?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
claim = claim?.let { anonymize(it) }
|
||||
}
|
||||
}
|
||||
this.consent?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
}
|
||||
this.diagnoses?.onEach { diagnosis ->
|
||||
diagnosis?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
histologyResults = histologyResults?.map { it?.let { anonymize(it) } }
|
||||
}
|
||||
}
|
||||
this.ecogStatus?.onEach { ecogStatus ->
|
||||
ecogStatus?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
}
|
||||
}
|
||||
this.familyMemberDiagnoses?.onEach { familyMemberDiagnosis ->
|
||||
familyMemberDiagnosis?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
}
|
||||
}
|
||||
this.geneticCounsellingRequests?.onEach { geneticCounsellingRequest ->
|
||||
geneticCounsellingRequest?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
}
|
||||
}
|
||||
this.histologyReevaluationRequests?.onEach { histologyReevaluationRequest ->
|
||||
histologyReevaluationRequest?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
specimen = specimen?.let { anonymize(it) }
|
||||
}
|
||||
}
|
||||
this.histologyReports?.onEach { histologyReport ->
|
||||
histologyReport?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
specimen = specimen?.let { anonymize(it) }
|
||||
tumorMorphology?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
specimen = specimen?.let { anonymize(it) }
|
||||
}
|
||||
tumorCellContent?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
specimen = specimen?.let { anonymize(it) }
|
||||
}
|
||||
}
|
||||
}
|
||||
this.lastGuidelineTherapies?.onEach { lastGuidelineTherapy ->
|
||||
lastGuidelineTherapy?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
diagnosis = diagnosis?.let { anonymize(it) }
|
||||
}
|
||||
}
|
||||
this.molecularPathologyFindings?.onEach { molecularPathologyFinding ->
|
||||
molecularPathologyFinding?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
specimen = specimen?.let { anonymize(it) }
|
||||
}
|
||||
}
|
||||
this.molecularTherapies?.onEach { molecularTherapy ->
|
||||
molecularTherapy?.apply {
|
||||
history?.onEach { history ->
|
||||
history?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
basedOn = basedOn?.let { anonymize(it) }
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
this.ngsReports?.onEach { ngsReport ->
|
||||
ngsReport?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
specimen = specimen?.let { anonymize(it) }
|
||||
tumorCellContent?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
specimen = specimen?.let { anonymize(it) }
|
||||
}
|
||||
simpleVariants?.onEach { simpleVariant ->
|
||||
simpleVariant?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
this.previousGuidelineTherapies?.onEach { previousGuidelineTherapy ->
|
||||
previousGuidelineTherapy?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
diagnosis = diagnosis?.let { anonymize(it) }
|
||||
medication.forEach { medication ->
|
||||
medication?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
this.rebiopsyRequests?.onEach { rebiopsyRequest ->
|
||||
rebiopsyRequest?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
specimen = specimen?.let { anonymize(it) }
|
||||
}
|
||||
}
|
||||
this.recommendations?.onEach { recommendation ->
|
||||
recommendation?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
diagnosis = diagnosis?.let { anonymize(it) }
|
||||
ngsReport = ngsReport?.let { anonymize(it) }
|
||||
}
|
||||
}
|
||||
this.responses?.onEach { response ->
|
||||
response?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
therapy = therapy?.let { anonymize(it) }
|
||||
}
|
||||
}
|
||||
this.studyInclusionRequests?.onEach { studyInclusionRequest ->
|
||||
studyInclusionRequest?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
reason = reason?.let { anonymize(it) }
|
||||
}
|
||||
}
|
||||
this.specimens?.onEach { specimen ->
|
||||
specimen?.apply {
|
||||
id = id?.let { anonymize(it) }
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/** Replaces patient ID with generated patient pseudonym
|
||||
*
|
||||
* @since 0.11.0
|
||||
*
|
||||
* @param pseudonymizeService The pseudonymizeService to be used
|
||||
* @return The MTB file containing patient pseudonymes
|
||||
*/
|
||||
infix fun Mtb.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
|
||||
val patientPseudonym = pseudonymizeService.patientPseudonym(PatientId(this.patient.id)).value
|
||||
|
||||
this.episodesOfCare?.forEach { it.patient.id = patientPseudonym }
|
||||
this.carePlans?.forEach {
|
||||
it.patient.id = patientPseudonym
|
||||
it.rebiopsyRequests?.forEach { it.patient.id = patientPseudonym }
|
||||
it.histologyReevaluationRequests?.forEach { it.patient.id = patientPseudonym }
|
||||
it.medicationRecommendations.forEach { it.patient.id = patientPseudonym }
|
||||
it.studyEnrollmentRecommendations?.forEach { it.patient.id = patientPseudonym }
|
||||
it.procedureRecommendations?.forEach { it.patient.id = patientPseudonym }
|
||||
it.geneticCounselingRecommendation.patient.id = patientPseudonym
|
||||
}
|
||||
this.diagnoses?.forEach { it.patient.id = patientPseudonym }
|
||||
this.guidelineTherapies?.forEach { it.patient.id = patientPseudonym }
|
||||
this.guidelineProcedures?.forEach { it.patient.id = patientPseudonym }
|
||||
this.patient.id = patientPseudonym
|
||||
this.claims?.forEach { it.patient.id = patientPseudonym }
|
||||
this.claimResponses?.forEach { it.patient.id = patientPseudonym }
|
||||
this.diagnoses?.forEach { it.patient.id = patientPseudonym }
|
||||
this.histologyReports?.forEach {
|
||||
it.patient.id = patientPseudonym
|
||||
it.results.tumorMorphology?.patient?.id = patientPseudonym
|
||||
it.results.tumorCellContent?.patient?.id = patientPseudonym
|
||||
}
|
||||
this.ngsReports?.forEach {
|
||||
it.patient.id = patientPseudonym
|
||||
it.results.simpleVariants?.forEach { it.patient.id = patientPseudonym }
|
||||
it.results.copyNumberVariants?.forEach { it.patient.id = patientPseudonym }
|
||||
it.results.dnaFusions?.forEach { it.patient.id = patientPseudonym }
|
||||
it.results.rnaFusions?.forEach { it.patient.id = patientPseudonym }
|
||||
it.results.tumorCellContent?.patient?.id = patientPseudonym
|
||||
it.results.brcaness?.patient?.id = patientPseudonym
|
||||
it.results.tmb?.patient?.id = patientPseudonym
|
||||
it.results.hrdScore?.patient?.id = patientPseudonym
|
||||
}
|
||||
this.ihcReports?.forEach {
|
||||
it.patient.id = patientPseudonym
|
||||
it.results.msiMmr?.forEach { it.patient.id = patientPseudonym }
|
||||
it.results.proteinExpression?.forEach { it.patient.id = patientPseudonym }
|
||||
}
|
||||
this.responses?.forEach { it.patient.id = patientPseudonym }
|
||||
this.specimens?.forEach { it.patient.id = patientPseudonym }
|
||||
this.priorDiagnosticReports?.forEach { it.patient.id = patientPseudonym }
|
||||
this.performanceStatus?.forEach { it.patient.id = patientPseudonym }
|
||||
this.systemicTherapies?.forEach {
|
||||
it.history?.forEach {
|
||||
it.patient.id = patientPseudonym
|
||||
}
|
||||
}
|
||||
this.followUps?.forEach {
|
||||
it.patient.id = patientPseudonym
|
||||
}
|
||||
|
||||
// FIXME: MUST CREATE TESTCASE - NEEDS TESTING!!
|
||||
this.metadata?.researchConsents?.forEach { it -> {
|
||||
val consent = it as? Consent
|
||||
consent?.patient?.reference = "Patient/$patientPseudonym"
|
||||
consent?.patient?.display = null
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Creates new hash of content IDs with given prefix except for patient IDs
|
||||
*
|
||||
* @since 0.11.0
|
||||
*
|
||||
* @param pseudonymizeService The pseudonymizeService to be used
|
||||
* @return The MTB file containing rehashed content IDs
|
||||
*/
|
||||
infix fun Mtb.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
|
||||
val prefix = pseudonymizeService.prefix()
|
||||
|
||||
fun anonymize(id: String): String {
|
||||
val hash = DigestUtils.sha256Hex("$prefix-$id").substring(0, 41).lowercase()
|
||||
return "$prefix$hash"
|
||||
}
|
||||
|
||||
this.episodesOfCare?.forEach {
|
||||
it?.apply {
|
||||
id = id?.let {
|
||||
anonymize(it)
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// TODO all other properties
|
||||
}
|
@ -17,7 +17,7 @@
|
||||
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
*/
|
||||
|
||||
package dev.dnpm.etl.processor.services
|
||||
package dev.dnpm.etl.processor.security
|
||||
|
||||
import jakarta.annotation.PostConstruct
|
||||
import org.springframework.data.annotation.Id
|
@ -17,11 +17,8 @@
|
||||
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
*/
|
||||
|
||||
package dev.dnpm.etl.processor.services
|
||||
package dev.dnpm.etl.processor.security
|
||||
|
||||
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
|
@ -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) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
@ -21,16 +21,29 @@ package dev.dnpm.etl.processor.services
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import dev.dnpm.etl.processor.*
|
||||
import dev.dnpm.etl.processor.config.AppConfigProperties
|
||||
import dev.dnpm.etl.processor.consent.GicsConsentService
|
||||
import dev.dnpm.etl.processor.consent.TtpConsentStatus
|
||||
import dev.dnpm.etl.processor.monitoring.Report
|
||||
import dev.dnpm.etl.processor.monitoring.Request
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import dev.dnpm.etl.processor.monitoring.RequestType
|
||||
import dev.dnpm.etl.processor.output.MtbFileSender
|
||||
import dev.dnpm.etl.processor.output.*
|
||||
import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
|
||||
import dev.dnpm.etl.processor.pseudonym.anonymizeContentWith
|
||||
import dev.dnpm.etl.processor.pseudonym.pseudonymizeWith
|
||||
import dev.pcvolkmer.mv64e.mtb.ConsentProvision
|
||||
import dev.pcvolkmer.mv64e.mtb.ModelProjectConsent
|
||||
import dev.pcvolkmer.mv64e.mtb.ModelProjectConsentPurpose
|
||||
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||
import dev.pcvolkmer.mv64e.mtb.MvhMetadata
|
||||
import dev.pcvolkmer.mv64e.mtb.Provision
|
||||
import org.apache.commons.codec.binary.Base32
|
||||
import org.apache.commons.codec.digest.DigestUtils
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource
|
||||
import org.hl7.fhir.r4.model.Bundle
|
||||
import org.hl7.fhir.r4.model.Consent
|
||||
import org.springframework.context.ApplicationEventPublisher
|
||||
import org.springframework.stereotype.Service
|
||||
import java.time.Instant
|
||||
@ -44,32 +57,122 @@ class RequestProcessor(
|
||||
private val requestService: RequestService,
|
||||
private val objectMapper: ObjectMapper,
|
||||
private val applicationEventPublisher: ApplicationEventPublisher,
|
||||
private val appConfigProperties: AppConfigProperties
|
||||
private val appConfigProperties: AppConfigProperties,
|
||||
private val gicsConsentService: GicsConsentService?
|
||||
) {
|
||||
|
||||
fun processMtbFile(mtbFile: MtbFile) {
|
||||
val requestId = UUID.randomUUID().toString()
|
||||
val pid = mtbFile.patient.id
|
||||
processMtbFile(mtbFile, randomRequestId())
|
||||
}
|
||||
|
||||
fun processMtbFile(mtbFile: MtbFile, requestId: RequestId) {
|
||||
val pid = PatientId(mtbFile.patient.id)
|
||||
mtbFile pseudonymizeWith pseudonymizeService
|
||||
mtbFile anonymizeContentWith pseudonymizeService
|
||||
val request = BwhcV1MtbFileRequest(requestId, transformationService.transform(mtbFile))
|
||||
saveAndSend(request, pid)
|
||||
}
|
||||
|
||||
val request = MtbFileSender.MtbFileRequest(requestId, transformationService.transform(mtbFile))
|
||||
fun processMtbFile(mtbFile: Mtb) {
|
||||
processMtbFile(mtbFile, randomRequestId())
|
||||
}
|
||||
|
||||
fun processMtbFile(mtbFile: Mtb, requestId: RequestId) {
|
||||
val pid = PatientId(mtbFile.patient.id)
|
||||
|
||||
addConsentToMtb(mtbFile)
|
||||
mtbFile pseudonymizeWith pseudonymizeService
|
||||
mtbFile anonymizeContentWith pseudonymizeService
|
||||
val request = DnpmV2MtbFileRequest(requestId, transformationService.transform(mtbFile))
|
||||
saveAndSend(request, pid)
|
||||
}
|
||||
|
||||
fun addConsentToMtb(mtbFile: Mtb) {
|
||||
if (gicsConsentService == null) return
|
||||
// init metadata if necessary
|
||||
if (mtbFile.metadata == null) {
|
||||
val mvhMetadata = MvhMetadata.builder().build();
|
||||
mtbFile.metadata = mvhMetadata
|
||||
if (mtbFile.metadata.researchConsents == null) {
|
||||
mtbFile.metadata.researchConsents = mutableListOf()
|
||||
}
|
||||
if (mtbFile.metadata.modelProjectConsent == null) {
|
||||
mtbFile.metadata.modelProjectConsent = ModelProjectConsent()
|
||||
mtbFile.metadata.modelProjectConsent.provisions = mutableListOf()
|
||||
}
|
||||
}
|
||||
|
||||
// fixme Date should be extracted from mtbFile
|
||||
val consentGnomeDe =
|
||||
gicsConsentService.getGenomDeConsent(mtbFile.patient.id, Date.from(Instant.now()))
|
||||
addGenomeDbProvisions(mtbFile, consentGnomeDe)
|
||||
|
||||
// fixme Date should be extracted from mtbFile
|
||||
val broadConsent =
|
||||
gicsConsentService.getBroadConsent(mtbFile.patient.id, Date.from(Instant.now()))
|
||||
embedBroadConsentResources(mtbFile, broadConsent)
|
||||
}
|
||||
|
||||
fun embedBroadConsentResources(
|
||||
mtbFile: Mtb,
|
||||
broadConsent: Bundle
|
||||
) {
|
||||
broadConsent.entry.forEach { it ->
|
||||
mtbFile.metadata.researchConsents.add(mapOf(it.resource.id to it as IBaseResource))
|
||||
}
|
||||
}
|
||||
|
||||
fun addGenomeDbProvisions(
|
||||
mtbFile: Mtb,
|
||||
consentGnomeDe: Bundle
|
||||
) {
|
||||
consentGnomeDe.entry.forEach { it ->
|
||||
{
|
||||
val consent = it.resource as Consent
|
||||
val provisionComponent = consent.provision.provision.firstOrNull()
|
||||
val provisionCode =
|
||||
provisionComponent?.code?.firstOrNull()?.coding?.firstOrNull()?.code
|
||||
var isValidCode = true
|
||||
if (provisionCode != null) {
|
||||
var modelProjectConsentPurpose: ModelProjectConsentPurpose =
|
||||
ModelProjectConsentPurpose.SEQUENCING
|
||||
if (provisionCode == "Teilnahme") {
|
||||
modelProjectConsentPurpose = ModelProjectConsentPurpose.SEQUENCING
|
||||
} else if (provisionCode == "Fallidentifizierung") {
|
||||
modelProjectConsentPurpose = ModelProjectConsentPurpose.CASE_IDENTIFICATION
|
||||
} else if (provisionCode == "Rekontaktierung") {
|
||||
modelProjectConsentPurpose = ModelProjectConsentPurpose.REIDENTIFICATION
|
||||
} else {
|
||||
isValidCode = false
|
||||
}
|
||||
if (isValidCode) mtbFile.metadata.modelProjectConsent.provisions.add(
|
||||
Provision.builder().type(
|
||||
ConsentProvision.forValue(provisionComponent.type.name)
|
||||
).date(provisionComponent.period.start).purpose(
|
||||
modelProjectConsentPurpose
|
||||
).build()
|
||||
)
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private fun <T> saveAndSend(request: MtbFileRequest<T>, pid: PatientId) {
|
||||
requestService.save(
|
||||
Request(
|
||||
uuid = requestId,
|
||||
patientId = request.mtbFile.patient.id,
|
||||
pid = pid,
|
||||
fingerprint = fingerprint(request.mtbFile),
|
||||
status = RequestStatus.UNKNOWN,
|
||||
type = RequestType.MTB_FILE
|
||||
request.requestId,
|
||||
request.patientPseudonym(),
|
||||
pid,
|
||||
fingerprint(request),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.UNKNOWN
|
||||
)
|
||||
)
|
||||
|
||||
if (appConfigProperties.duplicationDetection && isDuplication(mtbFile)) {
|
||||
if (appConfigProperties.duplicationDetection && isDuplication(request)) {
|
||||
applicationEventPublisher.publishEvent(
|
||||
ResponseEvent(
|
||||
requestId,
|
||||
request.requestId,
|
||||
Instant.now(),
|
||||
RequestStatus.DUPLICATION
|
||||
)
|
||||
@ -81,45 +184,61 @@ class RequestProcessor(
|
||||
|
||||
applicationEventPublisher.publishEvent(
|
||||
ResponseEvent(
|
||||
requestId,
|
||||
request.requestId,
|
||||
Instant.now(),
|
||||
responseStatus.status,
|
||||
when (responseStatus.status) {
|
||||
RequestStatus.WARNING -> Optional.of(responseStatus.body)
|
||||
RequestStatus.ERROR, RequestStatus.WARNING -> Optional.of(responseStatus.body)
|
||||
else -> Optional.empty()
|
||||
}
|
||||
)
|
||||
)
|
||||
}
|
||||
|
||||
private fun isDuplication(pseudonymizedMtbFile: MtbFile): Boolean {
|
||||
private fun <T> isDuplication(pseudonymizedMtbFileRequest: MtbFileRequest<T>): Boolean {
|
||||
val patientPseudonym = when (pseudonymizedMtbFileRequest) {
|
||||
is BwhcV1MtbFileRequest -> PatientPseudonym(pseudonymizedMtbFileRequest.content.patient.id)
|
||||
is DnpmV2MtbFileRequest -> PatientPseudonym(pseudonymizedMtbFileRequest.content.patient.id)
|
||||
}
|
||||
|
||||
val lastMtbFileRequestForPatient =
|
||||
requestService.lastMtbFileRequestForPatientPseudonym(pseudonymizedMtbFile.patient.id)
|
||||
val isLastRequestDeletion = requestService.isLastRequestWithKnownStatusDeletion(pseudonymizedMtbFile.patient.id)
|
||||
requestService.lastMtbFileRequestForPatientPseudonym(patientPseudonym)
|
||||
val isLastRequestDeletion =
|
||||
requestService.isLastRequestWithKnownStatusDeletion(patientPseudonym)
|
||||
|
||||
return null != lastMtbFileRequestForPatient
|
||||
&& !isLastRequestDeletion
|
||||
&& lastMtbFileRequestForPatient.fingerprint == fingerprint(pseudonymizedMtbFile)
|
||||
&& lastMtbFileRequestForPatient.fingerprint == fingerprint(
|
||||
pseudonymizedMtbFileRequest
|
||||
)
|
||||
}
|
||||
|
||||
fun processDeletion(patientId: String) {
|
||||
val requestId = UUID.randomUUID().toString()
|
||||
fun processDeletion(patientId: PatientId, isConsented: TtpConsentStatus) {
|
||||
processDeletion(patientId, randomRequestId(), isConsented)
|
||||
}
|
||||
|
||||
fun processDeletion(patientId: PatientId, requestId: RequestId, isConsented: TtpConsentStatus) {
|
||||
try {
|
||||
val patientPseudonym = pseudonymizeService.patientPseudonym(patientId)
|
||||
|
||||
val requestStatus: RequestStatus = when (isConsented) {
|
||||
TtpConsentStatus.CONSENT_MISSING_OR_REJECTED -> RequestStatus.NO_CONSENT
|
||||
TtpConsentStatus.FAILED_TO_ASK -> RequestStatus.ERROR
|
||||
TtpConsentStatus.CONSENTED, TtpConsentStatus.UNKNOWN_CHECK_FILE -> RequestStatus.UNKNOWN
|
||||
}
|
||||
|
||||
requestService.save(
|
||||
Request(
|
||||
uuid = requestId,
|
||||
patientId = patientPseudonym,
|
||||
pid = patientId,
|
||||
fingerprint = fingerprint(patientPseudonym),
|
||||
status = RequestStatus.UNKNOWN,
|
||||
type = RequestType.DELETE
|
||||
requestId,
|
||||
patientPseudonym,
|
||||
patientId,
|
||||
fingerprint(patientPseudonym.value),
|
||||
RequestType.DELETE,
|
||||
requestStatus
|
||||
)
|
||||
)
|
||||
|
||||
val responseStatus = sender.send(MtbFileSender.DeleteRequest(requestId, patientPseudonym))
|
||||
val responseStatus = sender.send(DeleteRequest(requestId, patientPseudonym))
|
||||
|
||||
applicationEventPublisher.publishEvent(
|
||||
ResponseEvent(
|
||||
@ -137,9 +256,9 @@ class RequestProcessor(
|
||||
requestService.save(
|
||||
Request(
|
||||
uuid = requestId,
|
||||
patientId = "???",
|
||||
patientPseudonym = emptyPatientPseudonym(),
|
||||
pid = patientId,
|
||||
fingerprint = "",
|
||||
fingerprint = Fingerprint.empty(),
|
||||
status = RequestStatus.ERROR,
|
||||
type = RequestType.DELETE,
|
||||
report = Report("Fehler bei der Pseudonymisierung")
|
||||
@ -148,14 +267,19 @@ class RequestProcessor(
|
||||
}
|
||||
}
|
||||
|
||||
private fun fingerprint(mtbFile: MtbFile): String {
|
||||
return fingerprint(objectMapper.writeValueAsString(mtbFile))
|
||||
private fun <T> fingerprint(request: MtbFileRequest<T>): Fingerprint {
|
||||
return when (request) {
|
||||
is BwhcV1MtbFileRequest -> fingerprint(objectMapper.writeValueAsString(request.content))
|
||||
is DnpmV2MtbFileRequest -> fingerprint(objectMapper.writeValueAsString(request.content))
|
||||
}
|
||||
}
|
||||
|
||||
private fun fingerprint(s: String): String {
|
||||
return Base32().encodeAsString(DigestUtils.sha256(s))
|
||||
.replace("=", "")
|
||||
.lowercase()
|
||||
private fun fingerprint(s: String): Fingerprint {
|
||||
return Fingerprint(
|
||||
Base32().encodeAsString(DigestUtils.sha256(s))
|
||||
.replace("=", "")
|
||||
.lowercase()
|
||||
)
|
||||
}
|
||||
|
||||
}
|
@ -19,11 +19,13 @@
|
||||
|
||||
package dev.dnpm.etl.processor.services
|
||||
|
||||
import dev.dnpm.etl.processor.monitoring.Request
|
||||
import dev.dnpm.etl.processor.monitoring.RequestRepository
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import dev.dnpm.etl.processor.monitoring.RequestType
|
||||
import dev.dnpm.etl.processor.PatientPseudonym
|
||||
import dev.dnpm.etl.processor.RequestId
|
||||
import dev.dnpm.etl.processor.monitoring.*
|
||||
import org.springframework.data.domain.Page
|
||||
import org.springframework.data.domain.Pageable
|
||||
import org.springframework.stereotype.Service
|
||||
import java.util.*
|
||||
|
||||
@Service
|
||||
class RequestService(
|
||||
@ -32,15 +34,32 @@ class RequestService(
|
||||
|
||||
fun save(request: Request) = requestRepository.save(request)
|
||||
|
||||
fun allRequestsByPatientPseudonym(patientPseudonym: String) = requestRepository
|
||||
.findAllByPatientIdOrderByProcessedAtDesc(patientPseudonym)
|
||||
fun findAll(): Iterable<Request> = requestRepository.findAll()
|
||||
|
||||
fun lastMtbFileRequestForPatientPseudonym(patientPseudonym: String) =
|
||||
fun findAll(pageable: Pageable): Page<Request> = requestRepository.findAll(pageable)
|
||||
|
||||
fun findByUuid(uuid: RequestId): Optional<Request> =
|
||||
requestRepository.findByUuidEquals(uuid)
|
||||
|
||||
fun findRequestByPatientId(patientPseudonym: PatientPseudonym, pageable: Pageable): Page<Request> = requestRepository.findRequestByPatientPseudonym(patientPseudonym, pageable)
|
||||
|
||||
fun allRequestsByPatientPseudonym(patientPseudonym: PatientPseudonym) = requestRepository
|
||||
.findAllByPatientPseudonymOrderByProcessedAtDesc(patientPseudonym)
|
||||
|
||||
fun lastMtbFileRequestForPatientPseudonym(patientPseudonym: PatientPseudonym) =
|
||||
Companion.lastMtbFileRequestForPatientPseudonym(allRequestsByPatientPseudonym(patientPseudonym))
|
||||
|
||||
fun isLastRequestWithKnownStatusDeletion(patientPseudonym: String) =
|
||||
fun isLastRequestWithKnownStatusDeletion(patientPseudonym: PatientPseudonym) =
|
||||
Companion.isLastRequestWithKnownStatusDeletion(allRequestsByPatientPseudonym(patientPseudonym))
|
||||
|
||||
fun countStates(): Iterable<CountedState> = requestRepository.countStates()
|
||||
|
||||
fun countDeleteStates(): Iterable<CountedState> = requestRepository.countDeleteStates()
|
||||
|
||||
fun findPatientUniqueStates(): List<CountedState> = requestRepository.findPatientUniqueStates()
|
||||
|
||||
fun findPatientUniqueDeleteStates(): List<CountedState> = requestRepository.findPatientUniqueDeleteStates()
|
||||
|
||||
companion object {
|
||||
|
||||
fun lastMtbFileRequestForPatientPseudonym(allRequests: List<Request>) = allRequests
|
||||
|
@ -19,8 +19,8 @@
|
||||
|
||||
package dev.dnpm.etl.processor.services
|
||||
|
||||
import dev.dnpm.etl.processor.RequestId
|
||||
import dev.dnpm.etl.processor.monitoring.Report
|
||||
import dev.dnpm.etl.processor.monitoring.RequestRepository
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import org.slf4j.LoggerFactory
|
||||
import org.springframework.context.event.EventListener
|
||||
@ -31,7 +31,7 @@ import java.util.*
|
||||
|
||||
@Service
|
||||
class ResponseProcessor(
|
||||
private val requestRepository: RequestRepository,
|
||||
private val requestService: RequestService,
|
||||
private val statisticsUpdateProducer: Sinks.Many<Any>
|
||||
) {
|
||||
|
||||
@ -39,7 +39,7 @@ class ResponseProcessor(
|
||||
|
||||
@EventListener(classes = [ResponseEvent::class])
|
||||
fun handleResponseEvent(event: ResponseEvent) {
|
||||
requestRepository.findByUuidEquals(event.requestUuid).ifPresentOrElse({
|
||||
requestService.findByUuid(event.requestUuid).ifPresentOrElse({
|
||||
it.processedAt = event.timestamp
|
||||
it.status = event.status
|
||||
|
||||
@ -70,13 +70,19 @@ class ResponseProcessor(
|
||||
)
|
||||
}
|
||||
|
||||
RequestStatus.NO_CONSENT -> {
|
||||
it.report = Report(
|
||||
"Einwilligung Status fehlt, widerrufen oder ungeklärt."
|
||||
)
|
||||
}
|
||||
|
||||
else -> {
|
||||
logger.error("Cannot process response: Unknown response!")
|
||||
return@ifPresentOrElse
|
||||
}
|
||||
}
|
||||
|
||||
requestRepository.save(it)
|
||||
requestService.save(it)
|
||||
|
||||
statisticsUpdateProducer.emitNext("", Sinks.EmitFailureHandler.FAIL_FAST)
|
||||
}, {
|
||||
@ -87,7 +93,7 @@ class ResponseProcessor(
|
||||
}
|
||||
|
||||
data class ResponseEvent(
|
||||
val requestUuid: String,
|
||||
val requestUuid: RequestId,
|
||||
val timestamp: Instant,
|
||||
val status: RequestStatus,
|
||||
val body: Optional<String> = Optional.empty()
|
||||
|
@ -23,10 +23,21 @@ import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import com.jayway.jsonpath.JsonPath
|
||||
import com.jayway.jsonpath.PathNotFoundException
|
||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||
|
||||
class TransformationService(private val objectMapper: ObjectMapper, private val transformations: List<Transformation>) {
|
||||
fun transform(mtbFile: MtbFile): MtbFile {
|
||||
var json = objectMapper.writeValueAsString(mtbFile)
|
||||
val json = transform(objectMapper.writeValueAsString(mtbFile))
|
||||
return objectMapper.readValue(json, MtbFile::class.java)
|
||||
}
|
||||
|
||||
fun transform(mtbFile: Mtb): Mtb {
|
||||
val json = transform(objectMapper.writeValueAsString(mtbFile))
|
||||
return objectMapper.readValue(json, Mtb::class.java)
|
||||
}
|
||||
|
||||
private fun transform(content: String): String {
|
||||
var json = content
|
||||
|
||||
transformations.forEach { transformation ->
|
||||
val jsonPath = JsonPath.parse(json)
|
||||
@ -48,7 +59,7 @@ class TransformationService(private val objectMapper: ObjectMapper, private val
|
||||
json = jsonPath.jsonString()
|
||||
}
|
||||
|
||||
return objectMapper.readValue(json, MtbFile::class.java)
|
||||
return json
|
||||
}
|
||||
|
||||
fun getTransformations(): List<Transformation> {
|
||||
|
@ -22,6 +22,7 @@ package dev.dnpm.etl.processor.services.kafka
|
||||
import com.fasterxml.jackson.annotation.JsonAlias
|
||||
import com.fasterxml.jackson.annotation.JsonProperty
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import dev.dnpm.etl.processor.RequestId
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import dev.dnpm.etl.processor.output.asRequestStatus
|
||||
import dev.dnpm.etl.processor.services.ResponseEvent
|
||||
@ -47,7 +48,7 @@ class KafkaResponseProcessor(
|
||||
Optional.empty()
|
||||
}.ifPresentOrElse({ responseBody ->
|
||||
val event = ResponseEvent(
|
||||
responseBody.requestId,
|
||||
RequestId(responseBody.requestId),
|
||||
Instant.ofEpochMilli(data.timestamp()),
|
||||
responseBody.statusCode.asRequestStatus(),
|
||||
when (responseBody.statusCode.asRequestStatus()) {
|
||||
|
63
src/main/kotlin/dev/dnpm/etl/processor/types.kt
Normal file
63
src/main/kotlin/dev/dnpm/etl/processor/types.kt
Normal file
@ -0,0 +1,63 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
* by the Free Software Foundation, either version 3 of the License, or
|
||||
* (at your option) any later version.
|
||||
*
|
||||
* This program is distributed in the hope that it will be useful,
|
||||
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
* GNU Affero General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Affero General Public License
|
||||
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
*/
|
||||
|
||||
package dev.dnpm.etl.processor
|
||||
|
||||
import org.springframework.http.MediaType
|
||||
import java.util.*
|
||||
|
||||
class Fingerprint(val value: String) {
|
||||
override fun hashCode() = value.hashCode()
|
||||
|
||||
override fun equals(other: Any?) = other is Fingerprint && other.value == value
|
||||
|
||||
companion object {
|
||||
fun empty() = Fingerprint("")
|
||||
}
|
||||
}
|
||||
|
||||
@JvmInline
|
||||
value class RequestId(val value: String) {
|
||||
|
||||
fun isBlank() = value.isBlank()
|
||||
|
||||
}
|
||||
|
||||
fun randomRequestId() = RequestId(UUID.randomUUID().toString())
|
||||
|
||||
@JvmInline
|
||||
value class PatientId(val value: String)
|
||||
|
||||
@JvmInline
|
||||
value class PatientPseudonym(val value: String)
|
||||
|
||||
fun emptyPatientPseudonym() = PatientPseudonym("")
|
||||
|
||||
/**
|
||||
* Custom MediaTypes
|
||||
*
|
||||
* @since 0.11.0
|
||||
*/
|
||||
object CustomMediaType {
|
||||
val APPLICATION_VND_DNPM_V2_MTB_JSON = MediaType("application", "vnd.dnpm.v2.mtb+json")
|
||||
const val APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE = "application/vnd.dnpm.v2.mtb+json"
|
||||
|
||||
val APPLICATION_VND_DNPM_V2_RD_JSON = MediaType("application", "vnd.dnpm.v2.rd+json")
|
||||
const val APPLICATION_VND_DNPM_V2_RD_JSON_VALUE = "application/vnd.dnpm.v2.rd+json"
|
||||
}
|
@ -19,15 +19,15 @@
|
||||
|
||||
package dev.dnpm.etl.processor.web
|
||||
|
||||
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
|
||||
import dev.dnpm.etl.processor.monitoring.*
|
||||
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.security.Token
|
||||
import dev.dnpm.etl.processor.security.TokenService
|
||||
import dev.dnpm.etl.processor.services.TransformationService
|
||||
import dev.dnpm.etl.processor.services.UserRoleService
|
||||
import dev.dnpm.etl.processor.security.UserRoleService
|
||||
import org.springframework.beans.factory.annotation.Qualifier
|
||||
import org.springframework.http.MediaType
|
||||
import org.springframework.http.codec.ServerSentEvent
|
||||
@ -40,22 +40,33 @@ import reactor.core.publisher.Sinks
|
||||
@Controller
|
||||
@RequestMapping(path = ["configs"])
|
||||
class ConfigController(
|
||||
@Qualifier("configsUpdateProducer")
|
||||
private val configsUpdateProducer: Sinks.Many<Boolean>,
|
||||
@Qualifier("connectionCheckUpdateProducer")
|
||||
private val connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>,
|
||||
private val transformationService: TransformationService,
|
||||
private val pseudonymGenerator: Generator,
|
||||
private val mtbFileSender: MtbFileSender,
|
||||
private val connectionCheckService: ConnectionCheckService,
|
||||
private val connectionCheckServices: List<ConnectionCheckService>,
|
||||
private val tokenService: TokenService?,
|
||||
private val userRoleService: UserRoleService?
|
||||
) {
|
||||
|
||||
@GetMapping
|
||||
fun index(model: Model): String {
|
||||
val outputConnectionAvailable =
|
||||
connectionCheckServices.filterIsInstance<OutputConnectionCheckService>().firstOrNull()?.connectionAvailable()
|
||||
|
||||
val gPasConnectionAvailable =
|
||||
connectionCheckServices.filterIsInstance<GPasConnectionCheckService>().firstOrNull()?.connectionAvailable()
|
||||
|
||||
val gIcsConnectionAvailable =
|
||||
connectionCheckServices.filterIsInstance<GIcsConnectionCheckService>().firstOrNull()?.connectionAvailable()
|
||||
|
||||
model.addAttribute("pseudonymGenerator", pseudonymGenerator.javaClass.simpleName)
|
||||
model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName)
|
||||
model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint())
|
||||
model.addAttribute("connectionAvailable", connectionCheckService.connectionAvailable())
|
||||
model.addAttribute("outputConnectionAvailable", outputConnectionAvailable)
|
||||
model.addAttribute("gPasConnectionAvailable", gPasConnectionAvailable)
|
||||
model.addAttribute("gIcsConnectionAvailable", gIcsConnectionAvailable)
|
||||
model.addAttribute("tokensEnabled", tokenService != null)
|
||||
if (tokenService != null) {
|
||||
model.addAttribute("tokens", tokenService.findAll())
|
||||
@ -73,11 +84,14 @@ class ConfigController(
|
||||
return "configs"
|
||||
}
|
||||
|
||||
@GetMapping(params = ["connectionAvailable"])
|
||||
fun connectionAvailable(model: Model): String {
|
||||
@GetMapping(params = ["outputConnectionAvailable"])
|
||||
fun outputConnectionAvailable(model: Model): String {
|
||||
val outputConnectionAvailable =
|
||||
connectionCheckServices.filterIsInstance<OutputConnectionCheckService>().first().connectionAvailable()
|
||||
|
||||
model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName)
|
||||
model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint())
|
||||
model.addAttribute("connectionAvailable", connectionCheckService.connectionAvailable())
|
||||
model.addAttribute("outputConnectionAvailable", outputConnectionAvailable)
|
||||
if (tokenService != null) {
|
||||
model.addAttribute("tokensEnabled", true)
|
||||
model.addAttribute("tokens", tokenService.findAll())
|
||||
@ -85,7 +99,43 @@ class ConfigController(
|
||||
model.addAttribute("tokens", listOf<Token>())
|
||||
}
|
||||
|
||||
return "configs/connectionAvailable"
|
||||
return "configs/outputConnectionAvailable"
|
||||
}
|
||||
|
||||
@GetMapping(params = ["gPasConnectionAvailable"])
|
||||
fun gPasConnectionAvailable(model: Model): String {
|
||||
val gPasConnectionAvailable =
|
||||
connectionCheckServices.filterIsInstance<GPasConnectionCheckService>().firstOrNull()?.connectionAvailable()
|
||||
|
||||
model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName)
|
||||
model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint())
|
||||
model.addAttribute("gPasConnectionAvailable", gPasConnectionAvailable)
|
||||
if (tokenService != null) {
|
||||
model.addAttribute("tokensEnabled", true)
|
||||
model.addAttribute("tokens", tokenService.findAll())
|
||||
} else {
|
||||
model.addAttribute("tokens", listOf<Token>())
|
||||
}
|
||||
|
||||
return "configs/gPasConnectionAvailable"
|
||||
}
|
||||
|
||||
@GetMapping(params = ["gIcsConnectionAvailable"])
|
||||
fun gIcsConnectionAvailable(model: Model): String {
|
||||
val gIcsConnectionAvailable =
|
||||
connectionCheckServices.filterIsInstance<GIcsConnectionCheckService>().firstOrNull()?.connectionAvailable()
|
||||
|
||||
model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName)
|
||||
model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint())
|
||||
model.addAttribute("gIcsConnectionAvailable", gIcsConnectionAvailable)
|
||||
if (tokenService != null) {
|
||||
model.addAttribute("tokensEnabled", true)
|
||||
model.addAttribute("tokens", tokenService.findAll())
|
||||
} else {
|
||||
model.addAttribute("tokens", listOf<Token>())
|
||||
}
|
||||
|
||||
return "configs/gIcsConnectionAvailable"
|
||||
}
|
||||
|
||||
@PostMapping(path = ["tokens"])
|
||||
@ -96,10 +146,11 @@ class ConfigController(
|
||||
} else {
|
||||
model.addAttribute("tokensEnabled", true)
|
||||
val result = tokenService.addToken(name)
|
||||
if (result.isSuccess) {
|
||||
model.addAttribute("newTokenValue", result.getOrDefault(""))
|
||||
result.onSuccess {
|
||||
model.addAttribute("newTokenValue", it)
|
||||
model.addAttribute("success", true)
|
||||
} else {
|
||||
}
|
||||
result.onFailure {
|
||||
model.addAttribute("success", false)
|
||||
}
|
||||
model.addAttribute("tokens", tokenService.findAll())
|
||||
@ -151,10 +202,18 @@ class ConfigController(
|
||||
}
|
||||
|
||||
@GetMapping(path = ["events"], produces = [MediaType.TEXT_EVENT_STREAM_VALUE])
|
||||
@ResponseBody
|
||||
fun events(): Flux<ServerSentEvent<Any>> {
|
||||
return configsUpdateProducer.asFlux().map {
|
||||
return connectionCheckUpdateProducer.asFlux().map {
|
||||
val event = when (it) {
|
||||
is ConnectionCheckResult.KafkaConnectionCheckResult -> "output-connection-check"
|
||||
is ConnectionCheckResult.RestConnectionCheckResult -> "output-connection-check"
|
||||
is ConnectionCheckResult.GPasConnectionCheckResult -> "gpas-connection-check"
|
||||
is ConnectionCheckResult.GIcsConnectionCheckResult -> "gics-connection-check"
|
||||
}
|
||||
|
||||
ServerSentEvent.builder<Any>()
|
||||
.event("connection-available").id("none").data("")
|
||||
.event(event).id("none").data(it)
|
||||
.build()
|
||||
}
|
||||
}
|
||||
|
@ -20,9 +20,10 @@
|
||||
package dev.dnpm.etl.processor.web
|
||||
|
||||
import dev.dnpm.etl.processor.NotFoundException
|
||||
import dev.dnpm.etl.processor.PatientPseudonym
|
||||
import dev.dnpm.etl.processor.RequestId
|
||||
import dev.dnpm.etl.processor.monitoring.ReportService
|
||||
import dev.dnpm.etl.processor.monitoring.RequestId
|
||||
import dev.dnpm.etl.processor.monitoring.RequestRepository
|
||||
import dev.dnpm.etl.processor.services.RequestService
|
||||
import org.springframework.data.domain.Pageable
|
||||
import org.springframework.data.domain.Sort
|
||||
import org.springframework.data.web.PageableDefault
|
||||
@ -35,7 +36,7 @@ import org.springframework.web.bind.annotation.RequestMapping
|
||||
@Controller
|
||||
@RequestMapping(path = ["/"])
|
||||
class HomeController(
|
||||
private val requestRepository: RequestRepository,
|
||||
private val requestService: RequestService,
|
||||
private val reportService: ReportService
|
||||
) {
|
||||
|
||||
@ -44,20 +45,20 @@ class HomeController(
|
||||
@PageableDefault(page = 0, size = 20, sort = ["processedAt"], direction = Sort.Direction.DESC) pageable: Pageable,
|
||||
model: Model
|
||||
): String {
|
||||
val requests = requestRepository.findAll(pageable)
|
||||
val requests = requestService.findAll(pageable)
|
||||
model.addAttribute("requests", requests)
|
||||
|
||||
return "index"
|
||||
}
|
||||
|
||||
@GetMapping(path = ["patient/{patientId}"])
|
||||
@GetMapping(path = ["patient/{patientPseudonym}"])
|
||||
fun byPatient(
|
||||
@PathVariable patientId: String,
|
||||
@PathVariable patientPseudonym: PatientPseudonym,
|
||||
@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)
|
||||
val requests = requestService.findRequestByPatientId(patientPseudonym, pageable)
|
||||
model.addAttribute("patientPseudonym", patientPseudonym.value)
|
||||
model.addAttribute("requests", requests)
|
||||
|
||||
return "index"
|
||||
@ -65,7 +66,7 @@ class HomeController(
|
||||
|
||||
@GetMapping(path = ["/report/{id}"])
|
||||
fun report(@PathVariable id: RequestId, model: Model): String {
|
||||
val request = requestRepository.findByUuidEquals(id.toString()).orElse(null) ?: throw NotFoundException()
|
||||
val request = requestService.findByUuid(id).orElse(null) ?: throw NotFoundException()
|
||||
model.addAttribute("request", request)
|
||||
model.addAttribute("issues", reportService.deserialize(request.report?.dataQualityReport))
|
||||
|
||||
|
@ -19,9 +19,9 @@
|
||||
|
||||
package dev.dnpm.etl.processor.web
|
||||
|
||||
import dev.dnpm.etl.processor.monitoring.RequestRepository
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import dev.dnpm.etl.processor.monitoring.RequestType
|
||||
import dev.dnpm.etl.processor.services.RequestService
|
||||
import org.springframework.beans.factory.annotation.Qualifier
|
||||
import org.springframework.http.MediaType
|
||||
import org.springframework.http.codec.ServerSentEvent
|
||||
@ -41,15 +41,15 @@ import java.time.temporal.ChronoUnit
|
||||
class StatisticsRestController(
|
||||
@Qualifier("statisticsUpdateProducer")
|
||||
private val statisticsUpdateProducer: Sinks.Many<Any>,
|
||||
private val requestRepository: RequestRepository
|
||||
private val requestService: RequestService
|
||||
) {
|
||||
|
||||
@GetMapping(path = ["requeststates"])
|
||||
fun requestStates(@RequestParam(required = false, defaultValue = "false") delete: Boolean): List<NameValue> {
|
||||
val states = if (delete) {
|
||||
requestRepository.countDeleteStates()
|
||||
requestService.countDeleteStates()
|
||||
} else {
|
||||
requestRepository.countStates()
|
||||
requestService.countStates()
|
||||
}
|
||||
|
||||
return states
|
||||
@ -79,7 +79,7 @@ class StatisticsRestController(
|
||||
}
|
||||
|
||||
val formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd").withZone(ZoneId.of("Europe/Berlin"))
|
||||
val data = requestRepository.findAll()
|
||||
val data = requestService.findAll()
|
||||
.filter { it.type == requestType }
|
||||
.filter { it.processedAt.isAfter(Instant.now().minus(30, ChronoUnit.DAYS)) }
|
||||
.groupBy { formatter.format(it.processedAt) }
|
||||
@ -115,9 +115,9 @@ class StatisticsRestController(
|
||||
@GetMapping(path = ["requestpatientstates"])
|
||||
fun requestPatientStates(@RequestParam(required = false, defaultValue = "false") delete: Boolean): List<NameValue> {
|
||||
val states = if (delete) {
|
||||
requestRepository.findPatientUniqueDeleteStates()
|
||||
requestService.findPatientUniqueDeleteStates()
|
||||
} else {
|
||||
requestRepository.findPatientUniqueStates()
|
||||
requestService.findPatientUniqueStates()
|
||||
}
|
||||
|
||||
return states.map {
|
||||
@ -134,7 +134,6 @@ 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>()
|
||||
|
@ -3,17 +3,34 @@ spring:
|
||||
compose:
|
||||
file: ./dev-compose.yml
|
||||
|
||||
security:
|
||||
oauth2:
|
||||
client:
|
||||
registration:
|
||||
custom:
|
||||
client-name: App-Dev
|
||||
client-id: app-dev
|
||||
client-secret: very-secret-ae3f7a-5a9f-1190
|
||||
scope:
|
||||
- openid
|
||||
provider:
|
||||
custom:
|
||||
issuer-uri: https://dnpm.dev/auth/realms/intern
|
||||
user-name-attribute: name
|
||||
|
||||
app:
|
||||
#rest:
|
||||
# uri: http://localhost:9000/bwhc/etl/api
|
||||
kafka:
|
||||
topic: test
|
||||
response-topic: test_response
|
||||
servers: localhost:9094
|
||||
#security:
|
||||
# admin-user: admin
|
||||
# admin-password: "{noop}very-secret"
|
||||
rest:
|
||||
uri: http://localhost:9000/bwhc/etl/api
|
||||
#kafka:
|
||||
# topic: test
|
||||
# response-topic: test_response
|
||||
# servers: localhost:9094
|
||||
security:
|
||||
admin-user: admin
|
||||
admin-password: "{noop}very-secret"
|
||||
enable-oidc: "true"
|
||||
|
||||
server:
|
||||
port: 8000
|
||||
|
||||
|
||||
|
@ -0,0 +1 @@
|
||||
ALTER TABLE request RENAME COLUMN patient_id TO patient_pseudonym;
|
@ -0,0 +1 @@
|
||||
ALTER TABLE request RENAME COLUMN patient_id TO patient_pseudonym;
|
@ -22,6 +22,10 @@
|
||||
--bg-gray-op: rgba(112, 128, 144, .35);
|
||||
}
|
||||
|
||||
* {
|
||||
font-family: sans-serif;
|
||||
}
|
||||
|
||||
html {
|
||||
background: linear-gradient(-5deg, var(--bg-blue-op), transparent 10em);
|
||||
min-height: 100vh;
|
||||
@ -30,7 +34,6 @@ html {
|
||||
|
||||
body {
|
||||
margin: 0 0 5em 0;
|
||||
font-family: sans-serif;
|
||||
font-size: .8rem;
|
||||
color: var(--text);
|
||||
|
||||
@ -257,6 +260,10 @@ form.samplecode-input input:focus-visible {
|
||||
display: block;
|
||||
}
|
||||
|
||||
.userrole-form {
|
||||
display: inline-block;
|
||||
}
|
||||
|
||||
.userrole-form form {
|
||||
margin: 0;
|
||||
padding: 0;
|
||||
@ -321,6 +328,15 @@ table {
|
||||
font-family: sans-serif;
|
||||
}
|
||||
|
||||
table.config-table td:first-child {
|
||||
width: 24em;
|
||||
min-width: fit-content;
|
||||
}
|
||||
|
||||
table.config-table td > button:last-of-type {
|
||||
float: right;
|
||||
}
|
||||
|
||||
.border > table {
|
||||
padding: 0;
|
||||
border: none;
|
||||
@ -490,7 +506,7 @@ td.clipboard.clipped {
|
||||
|
||||
.btn:active,
|
||||
.btn:hover {
|
||||
filter: drop-shadow(1px 1px 1px gray) var(--dark);
|
||||
filter: drop-shadow(0px 1px 1px var(--bg-gray)) var(--dark);
|
||||
}
|
||||
|
||||
.btn:active {
|
||||
@ -555,15 +571,24 @@ input.inline:focus-visible {
|
||||
font-weight: bold;
|
||||
}
|
||||
|
||||
.chart {
|
||||
width: calc(100% - 2.4rem - 4px);
|
||||
height: 320px;
|
||||
|
||||
display: inline-block;
|
||||
.charts {
|
||||
display: grid;
|
||||
grid-gap: 1em;
|
||||
grid-template:
|
||||
"a b" 28em
|
||||
"c c" 28em / 1fr 1fr;
|
||||
}
|
||||
|
||||
.chart-50pc {
|
||||
width: calc(50% - 2.4rem - 4px);
|
||||
.charts > .grid-left {
|
||||
grid-area: a;
|
||||
}
|
||||
|
||||
.charts > .grid-right {
|
||||
grid-area: b;
|
||||
}
|
||||
|
||||
.charts > .grid-full {
|
||||
grid-area: c;
|
||||
}
|
||||
|
||||
.connection-display {
|
||||
@ -571,7 +596,7 @@ input.inline:focus-visible {
|
||||
grid-template-columns: 10em 16em 10em;
|
||||
place-items: center;
|
||||
width: fit-content;
|
||||
margin: 1em 0;
|
||||
margin: 1em auto;
|
||||
}
|
||||
|
||||
.connection-display > * {
|
||||
@ -597,6 +622,10 @@ input.inline:focus-visible {
|
||||
text-align: center;
|
||||
}
|
||||
|
||||
.notification.info {
|
||||
color: var(--bg-blue);
|
||||
}
|
||||
|
||||
.notification.success {
|
||||
color: var(--bg-green);
|
||||
}
|
||||
@ -609,6 +638,34 @@ input.inline:focus-visible {
|
||||
color: var(--bg-red);
|
||||
}
|
||||
|
||||
.tab {
|
||||
padding: 1em;
|
||||
border: none;
|
||||
border-radius: 3px 3px 0 0;
|
||||
cursor: pointer;
|
||||
transition: all 0.2s;
|
||||
|
||||
font-weight: bold;
|
||||
}
|
||||
|
||||
.tab:hover,
|
||||
.tab.active {
|
||||
background: var(--bg-gray);
|
||||
color: white;
|
||||
}
|
||||
|
||||
.tabcontent {
|
||||
border: 2px solid var(--bg-gray);
|
||||
border-radius: 0 .5em .5em .5em;
|
||||
display: none;
|
||||
padding: 1em;
|
||||
background: white;
|
||||
}
|
||||
|
||||
.tabcontent.active {
|
||||
display: block;
|
||||
}
|
||||
|
||||
a.reload {
|
||||
display: none;
|
||||
position: absolute;
|
||||
@ -641,3 +698,13 @@ a.reload {
|
||||
padding: 1em;
|
||||
background: var(--bg-red-op);
|
||||
}
|
||||
|
||||
.issue-message {
|
||||
font-family: monospace;
|
||||
font-weight: bolder;
|
||||
}
|
||||
|
||||
.issue-path {
|
||||
font-family: monospace;
|
||||
line-height: 1rem;
|
||||
}
|
@ -10,90 +10,121 @@
|
||||
<main>
|
||||
<h1>Konfiguration</h1>
|
||||
|
||||
<section>
|
||||
<h2>🔧 Allgemeine Konfiguration</h2>
|
||||
<table>
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Name</th>
|
||||
<th>Wert</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<div class="tabs">
|
||||
<button class="tab active" onclick="selectTab(this, 'common');">Allgemeine Informationen</button>
|
||||
<button class="tab" onclick="selectTab(this, 'security');">Sicherheit</button>
|
||||
<button class="tab" onclick="selectTab(this, 'transformation');">Transformationen</button>
|
||||
</div>
|
||||
|
||||
<div id="common" class="tabcontent active">
|
||||
<section>
|
||||
<h2>🔧 Allgemeine Konfiguration</h2>
|
||||
<table class="config-table">
|
||||
<thead>
|
||||
<tr>
|
||||
<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>[[ ${mtbFileEndpoint} ]]</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</section>
|
||||
|
||||
<section hx-ext="sse" th:sse-connect="@{/configs/events}">
|
||||
<div th:insert="~{configs/gPasConnectionAvailable.html}" th:hx-get="@{/configs?gPasConnectionAvailable}" hx-trigger="sse:gpas-connection-check">
|
||||
</div>
|
||||
</section>
|
||||
|
||||
<section hx-ext="sse" th:sse-connect="@{/configs/events}">
|
||||
<div th:insert="~{configs/gIcsConnectionAvailable.html}" th:hx-get="@{/configs?gIcsConnectionAvailable}" hx-trigger="sse:gics-connection-check">
|
||||
</div>
|
||||
</section>
|
||||
|
||||
<section hx-ext="sse" th:sse-connect="@{/configs/events}">
|
||||
<div th:insert="~{configs/outputConnectionAvailable.html}" th:hx-get="@{/configs?outputConnectionAvailable}" hx-trigger="sse:output-connection-check">
|
||||
</div>
|
||||
</section>
|
||||
</div>
|
||||
|
||||
<div id="security" class="tabcontent">
|
||||
<section th:insert="~{configs/tokens.html}">
|
||||
</section>
|
||||
|
||||
<section th:insert="~{configs/userroles.html}">
|
||||
</section>
|
||||
</div>
|
||||
|
||||
<div id="transformation" class="tabcontent">
|
||||
<section>
|
||||
<h2><span th:if="${not transformations.isEmpty()}">✅</span><span th:if="${transformations.isEmpty()}">⛔</span> Transformationen</h2>
|
||||
|
||||
<h3>Syntax</h3>
|
||||
Hier einige Beispiele zum Syntax des JSON-Path
|
||||
<ul>
|
||||
<li style="padding: 0.6rem 0;"><span class="bg-path">diagnoses[*].icdO3T.version</span>: Ersetze die ICD-O3T-Version in allen Diagnosen, z.B. zur Version der deutschen Übersetzung</li>
|
||||
<li style="padding: 0.6rem 0;"><span class="bg-path">patient.gender</span>: Ersetze das Geschlecht des Patienten, z.B. in das von bwHC verlangte Format</li>
|
||||
</ul>
|
||||
|
||||
<h3>Konfigurierte Transformationen</h3>
|
||||
<th:block th:if="${transformations.isEmpty()}">
|
||||
<p>
|
||||
Keine konfigurierten Transformationen.
|
||||
</p>
|
||||
</th:block>
|
||||
<th:block th:if="${not transformations.isEmpty()}">
|
||||
<p>
|
||||
Hier sehen Sie eine Übersicht der konfigurierten Transformationen.
|
||||
</p>
|
||||
|
||||
<table class="config-table">
|
||||
<thead>
|
||||
<tr>
|
||||
<td>MTBFile-Sender</td>
|
||||
<td>[[ ${mtbFileSender} ]]</td>
|
||||
<th>JSON-Path</th>
|
||||
<th>Transformation von ⇒ nach</th>
|
||||
</tr>
|
||||
<tr>
|
||||
<td th:if="${mtbFileSender.startsWith('Rest')}">REST-Endpunkt</td>
|
||||
<td th:if="${mtbFileSender.startsWith('Kafka')}">Kafka-Broker und Topics</td>
|
||||
<td>[[ ${mtbFileEndpoint} ]]</td>
|
||||
</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>⇒</strong>
|
||||
<span class="bg-to" title="Ersetze durch diesen Wert">[[ ${transformation.newValue} ]]</span>
|
||||
</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</section>
|
||||
|
||||
<section th:insert="~{configs/tokens.html}">
|
||||
</section>
|
||||
|
||||
<section th:insert="~{configs/userroles.html}">
|
||||
</section>
|
||||
|
||||
<section hx-ext="sse" th:sse-connect="@{/configs/events}">
|
||||
<div th:insert="~{configs/connectionAvailable.html}" th:hx-get="@{/configs?connectionAvailable}" hx-trigger="sse:connection-available">
|
||||
</div>
|
||||
</section>
|
||||
|
||||
<section>
|
||||
<h2><span th:if="${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>
|
||||
<th>JSON-Path</th>
|
||||
<th>Transformation von ⇒ 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>⇒</strong>
|
||||
<span class="bg-to" title="Ersetze durch diesen Wert">[[ ${transformation.newValue} ]]</span>
|
||||
</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</th:block>
|
||||
</section>
|
||||
</tbody>
|
||||
</table>
|
||||
</th:block>
|
||||
</section>
|
||||
</div>
|
||||
</main>
|
||||
<script th:src="@{/scripts.js}"></script>
|
||||
<script th:src="@{/webjars/htmx.org/dist/htmx.min.js}"></script>
|
||||
<script th:src="@{/webjars/htmx.org/dist/ext/sse.js}"></script>
|
||||
<script>
|
||||
function selectTab(self, elem) {
|
||||
Array.from(document.getElementsByClassName('tab')).forEach(e => e.className = 'tab');
|
||||
self.className = 'tab active';
|
||||
|
||||
Array.from(document.getElementsByClassName('tabcontent')).forEach(e => e.className = 'tabcontent');
|
||||
document.getElementById(elem).className = 'tabcontent active';
|
||||
}
|
||||
</script>
|
||||
</body>
|
||||
</html>
|
@ -1,16 +0,0 @@
|
||||
<h2><span th:if="${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>
|
@ -0,0 +1,24 @@
|
||||
<th:block th:if="${gIcsConnectionAvailable == null}">
|
||||
<h2><span>🟦</span> gICS nicht konfiguriert - Einwilligung wird über Dateiinhalt geprüft</h2>
|
||||
</th:block>
|
||||
<th:block th:if="${gIcsConnectionAvailable != null}">
|
||||
<h2><span th:if="${gIcsConnectionAvailable.available}">✅</span><span th:if="${not(gIcsConnectionAvailable.available)}">⚡</span> Verbindung zu gICS</h2>
|
||||
<div>
|
||||
Stand: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(gIcsConnectionAvailable.timestamp)}" th:text="${#temporals.formatISO(gIcsConnectionAvailable.timestamp)}"></time>
|
||||
|
|
||||
Letzte Änderung: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(gIcsConnectionAvailable.lastChange)}" th:text="${#temporals.formatISO(gIcsConnectionAvailable.lastChange)}"></time>
|
||||
</div>
|
||||
<div>
|
||||
<span>Die Verbindung ist aktuell</span>
|
||||
<strong th:if="${gIcsConnectionAvailable.available}" style="color: green">verfügbar.</strong>
|
||||
<strong th:if="${not(gIcsConnectionAvailable.available)}" style="color: red">nicht verfügbar.</strong>
|
||||
</div>
|
||||
<div class="connection-display border">
|
||||
<img th:src="@{/server.png}" alt="ETL-Processor" />
|
||||
<span class="connection" th:classappend="${gIcsConnectionAvailable.available ? 'available' : ''}"></span>
|
||||
<img th:src="@{/server.png}" alt="gICS" />
|
||||
<span>ETL-Processor</span>
|
||||
<span></span>
|
||||
<span>gICS</span>
|
||||
</div>
|
||||
</th:block>
|
@ -0,0 +1,24 @@
|
||||
<th:block th:if="${gPasConnectionAvailable == null}">
|
||||
<h2><span>🟦</span> gPAS nicht konfiguriert - Patienten-IDs werden intern anonymisiert</h2>
|
||||
</th:block>
|
||||
<th:block th:if="${gPasConnectionAvailable != null}">
|
||||
<h2><span th:if="${gPasConnectionAvailable.available}">✅</span><span th:if="${not(gPasConnectionAvailable.available)}">⚡</span> Verbindung zu gPAS</h2>
|
||||
<div>
|
||||
Stand: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(gPasConnectionAvailable.timestamp)}" th:text="${#temporals.formatISO(gPasConnectionAvailable.timestamp)}"></time>
|
||||
|
|
||||
Letzte Änderung: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(gPasConnectionAvailable.lastChange)}" th:text="${#temporals.formatISO(gPasConnectionAvailable.lastChange)}"></time>
|
||||
</div>
|
||||
<div>
|
||||
<span>Die Verbindung ist aktuell</span>
|
||||
<strong th:if="${gPasConnectionAvailable.available}" style="color: green">verfügbar.</strong>
|
||||
<strong th:if="${not(gPasConnectionAvailable.available)}" style="color: red">nicht verfügbar.</strong>
|
||||
</div>
|
||||
<div class="connection-display border">
|
||||
<img th:src="@{/server.png}" alt="ETL-Processor" />
|
||||
<span class="connection" th:classappend="${gPasConnectionAvailable.available ? 'available' : ''}"></span>
|
||||
<img th:src="@{/server.png}" alt="gPAS" />
|
||||
<span>ETL-Processor</span>
|
||||
<span></span>
|
||||
<span>gPAS</span>
|
||||
</div>
|
||||
</th:block>
|
@ -0,0 +1,27 @@
|
||||
<th:block th:if="${outputConnectionAvailable == null}">
|
||||
<h2><span>🟦</span> Keine Ausgabenkonfiguration</h2>
|
||||
</th:block>
|
||||
<th:block th:if="${outputConnectionAvailable != null}">
|
||||
<h2><span th:if="${outputConnectionAvailable.available}">✅</span><span th:if="${not(outputConnectionAvailable.available)}">⚡</span> MTB-File Verbindung</h2>
|
||||
<div>
|
||||
Stand: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(outputConnectionAvailable.timestamp)}" th:text="${#temporals.formatISO(outputConnectionAvailable.timestamp)}"></time>
|
||||
|
|
||||
Letzte Änderung: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(outputConnectionAvailable.lastChange)}" th:text="${#temporals.formatISO(outputConnectionAvailable.lastChange)}"></time>
|
||||
</div>
|
||||
<div>
|
||||
Verbindung über <code>[[ ${mtbFileSender} ]]</code>. Die Verbindung ist aktuell
|
||||
<strong th:if="${outputConnectionAvailable.available}" style="color: green">verfügbar.</strong>
|
||||
<strong th:if="${not(outputConnectionAvailable.available)}" style="color: red">nicht verfügbar.</strong>
|
||||
</div>
|
||||
<div class="connection-display border">
|
||||
<img th:src="@{/server.png}" alt="ETL-Processor" />
|
||||
<span class="connection" th:classappend="${outputConnectionAvailable.available ? 'available' : ''}"></span>
|
||||
<img th:if="${mtbFileSender.startsWith('Rest')}" th:src="@{/server.png}" alt="bwHC-Backend" />
|
||||
<img th:if="${mtbFileSender.startsWith('Kafka')}" th:src="@{/kafka.png}" alt="Kafka-Broker" />
|
||||
<span>ETL-Processor</span>
|
||||
<span></span>
|
||||
<span th:if="${mtbFileSender.startsWith('RestBwhc')}">bwHC-Backend</span>
|
||||
<span th:if="${mtbFileSender.startsWith('RestDip')}">DNPM:DIP-Backend</span>
|
||||
<span th:if="${mtbFileSender.startsWith('Kafka')}">Kafka-Broker</span>
|
||||
</div>
|
||||
</th:block>
|
@ -7,19 +7,20 @@
|
||||
<h2><span>✅</span> Tokens</h2>
|
||||
<div class="border">
|
||||
<div th:if="${tokens.isEmpty()}">Noch keine Tokens vorhanden.</div>
|
||||
<table th:if="${not tokens.isEmpty()}">
|
||||
<table th:if="${not tokens.isEmpty()}" class="config-table">
|
||||
<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>
|
||||
<td>
|
||||
<time th:datetime="${token.createdAt}">[[ ${token.createdAt} ]]</time>
|
||||
<button class="btn btn-red" th:hx-delete="@{/configs/tokens/{id}(id=${token.id})}" hx-target="#tokens">Löschen</button>
|
||||
</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
@ -7,12 +7,11 @@
|
||||
<h2><span>✅</span> Benutzerberechtigungen</h2>
|
||||
<div class="border">
|
||||
<div th:if="${userRoles.isEmpty()}">Noch keine Benutzerberechtigungen vorhanden.</div>
|
||||
<table th:if="${not userRoles.isEmpty()}">
|
||||
<table th:if="${not userRoles.isEmpty()}" class="config-table">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Benutzername</th>
|
||||
<th>Rolle</th>
|
||||
<th></th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
@ -29,8 +28,6 @@
|
||||
<button class="btn btn-blue" th:disabled="${#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>
|
||||
|
@ -12,26 +12,30 @@
|
||||
<h1>Alle Anfragen<a id="reload-notify" class="reload" title="Neue Anfragen" th:href="@{/}">⟳</a></h1>
|
||||
|
||||
<div>
|
||||
<h2 th:if="${patientId != null}">
|
||||
Betreffend Patienten-Pseudonym <span class="monospace" th:text="${patientId}">***</span>
|
||||
<a class="btn btn-blue" th:if="${patientId != null}" th:href="@{/}">Alle anzeigen</a>
|
||||
<h2 th:if="${patientPseudonym != null}">
|
||||
Betreffend Patienten-Pseudonym <span class="monospace" th:text="${patientPseudonym}">***</span>
|
||||
<a class="btn btn-blue" th:if="${patientPseudonym != null}" th:href="@{/}">Alle anzeigen</a>
|
||||
</h2>
|
||||
</div>
|
||||
|
||||
<div class="border">
|
||||
<div th:if="${patientId == null}" class="page-control">
|
||||
<div class="border" th:if="${requests.totalElements == 0}">
|
||||
<div class="notification info">Noch keine Anfragen eingegangen</div>
|
||||
</div>
|
||||
|
||||
<div class="border" th:if="${requests.totalElements > 0}">
|
||||
<div th:if="${patientPseudonym == null}" class="page-control">
|
||||
<a id="first-page-link" th:href="@{/(page=${0})}" title="Zum Anfang: Taste W" th:if="${not requests.isFirst()}">⇤</a><a th:if="${requests.isFirst()}">⇤</a>
|
||||
<a id="prev-page-link" th:href="@{/(page=${requests.getNumber() - 1})}" title="Seite zurück: Taste A" th:if="${not requests.isFirst()}">←</a><a th:if="${requests.isFirst()}">←</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="${not requests.isLast()}">→</a><a th:if="${requests.isLast()}">→</a>
|
||||
<a id="last-page-link" th:href="@{/(page=${requests.getTotalPages() - 1})}" title="Zum Ende: Taste S" th:if="${not requests.isLast()}">⇥</a><a th:if="${requests.isLast()}">⇥</a>
|
||||
</div>
|
||||
<div th:if="${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="${not requests.isFirst()}">⇤</a><a th:if="${requests.isFirst()}">⇤</a>
|
||||
<a id="prev-page-link" th:href="@{/patient/{patientId}(patientId=${patientId},page=${requests.getNumber() - 1})}" title="Seite zurück: Taste A" th:if="${not requests.isFirst()}">←</a><a th:if="${requests.isFirst()}">←</a>
|
||||
<div th:if="${patientPseudonym != null}" class="page-control">
|
||||
<a id="first-page-link" th:href="@{/patient/{patientPseudonym}(patientPseudonym=${patientPseudonym},page=${0})}" title="Zum Anfang: Taste W" th:if="${not requests.isFirst()}">⇤</a><a th:if="${requests.isFirst()}">⇤</a>
|
||||
<a id="prev-page-link" th:href="@{/patient/{patientPseudonym}(patientPseudonym=${patientPseudonym},page=${requests.getNumber() - 1})}" title="Seite zurück: Taste A" th:if="${not requests.isFirst()}">←</a><a th:if="${requests.isFirst()}">←</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()}">→</a><a th:if="${requests.isLast()}">→</a>
|
||||
<a id="last-page-link" th:href="@{/patient/{patientId}(patientId=${patientId},page=${requests.getTotalPages() - 1})}" title="Zum Ende: Taste S" th:if="${not requests.isLast()}">⇥</a><a th:if="${requests.isLast()}">⇥</a>
|
||||
<a id="next-page-link" th:href="@{/patient/{patientPseudonym}(patientPseudonym=${patientPseudonym},page=${requests.getNumber() + 1})}" title="Seite vor: Taste D" th:if="${not requests.isLast()}">→</a><a th:if="${requests.isLast()}">→</a>
|
||||
<a id="last-page-link" th:href="@{/patient/{patientPseudonym}(patientPseudonym=${patientPseudonym},page=${requests.getTotalPages() - 1})}" title="Zum Ende: Taste S" th:if="${not requests.isLast()}">⇥</a><a th:if="${requests.isLast()}">⇥</a>
|
||||
</div>
|
||||
<table class="paged">
|
||||
<thead>
|
||||
@ -57,11 +61,11 @@
|
||||
<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')">
|
||||
[[ ${request.patientId} ]]
|
||||
<td class="patient-id" th:if="${patientPseudonym != null}" sec:authorize="hasRole('USER') or hasRole('ADMIN')">
|
||||
[[ ${request.patientPseudonym} ]]
|
||||
</td>
|
||||
<td class="patient-id" th:if="${patientId == null}" sec:authorize="hasRole('USER') or hasRole('ADMIN')">
|
||||
<a th:href="@{/patient/{pid}(pid=${request.patientId})}">[[ ${request.patientId} ]]</a>
|
||||
<td class="patient-id" th:if="${patientPseudonym == null}" sec:authorize="hasRole('USER') or hasRole('ADMIN')">
|
||||
<a th:href="@{/patient/{pid}(pid=${request.patientPseudonym})}">[[ ${request.patientPseudonym} ]]</a>
|
||||
</td>
|
||||
<td class="patient-id" sec:authorize="not (hasRole('USER') or hasRole('ADMIN'))">***</td>
|
||||
</tr>
|
||||
|
@ -31,7 +31,7 @@
|
||||
<td th:style="${request.type.value == 'delete'} ? 'color: red;'"><small>[[ ${request.type} ]]</small></td>
|
||||
<td>[[ ${request.uuid} ]]</td>
|
||||
<td><time th:datetime="${request.processedAt}">[[ ${request.processedAt} ]]</time></td>
|
||||
<td class="patient-id" sec:authorize="authenticated">[[ ${request.patientId} ]]</td>
|
||||
<td class="patient-id" sec:authorize="authenticated">[[ ${request.patientPseudonym} ]]</td>
|
||||
<td class="patient-id" sec:authorize="not authenticated">***</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@ -47,7 +47,7 @@
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Schweregrad</th>
|
||||
<th>Beschreibung</th>
|
||||
<th>Beschreibung und Pfad</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
@ -55,7 +55,12 @@
|
||||
<td th:if="${issue.severity.value == 'info'}" class="bg-blue"><small>[[ ${issue.severity} ]]</small></td>
|
||||
<td th:if="${issue.severity.value == 'warning'}" class="bg-yellow"><small>[[ ${issue.severity} ]]</small></td>
|
||||
<td th:if="${issue.severity.value == 'error'}" class="bg-red"><small>[[ ${issue.severity} ]]</small></td>
|
||||
<td>[[ ${issue.message} ]]</td>
|
||||
<td th:if="${issue.severity.value == 'fatal'}" class="bg-red"><small>[[ ${issue.severity} ]]</small></td>
|
||||
<td>
|
||||
<div class="issue-message">[[ ${issue.message} ]]</div>
|
||||
<div class="issue-path" th:if="${issue.path.isPresent()}">[[ ${issue.path.get()} ]]</div>
|
||||
<div class="issue-path" th:if="${issue.path.isEmpty()}"><i>Keine Angabe</i></div>
|
||||
</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
@ -18,11 +18,11 @@
|
||||
<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 class="charts">
|
||||
<div id="piechart1" class="chart grid-left"></div>
|
||||
<div id="piechart2" class="chart grid-right"></div>
|
||||
<div id="barchart" class="chart grid-full"></div>
|
||||
</div>
|
||||
<div id="barchart" class="chart"></div>
|
||||
</section>
|
||||
|
||||
<section>
|
||||
@ -30,11 +30,11 @@
|
||||
<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 class="charts">
|
||||
<div id="piechartdel1" class="chart grid-left"></div>
|
||||
<div id="piechartdel2" class="chart grid-right"></div>
|
||||
<div id="barchartdel" class="chart grid-full"></div>
|
||||
</div>
|
||||
<div id="barchartdel" class="chart"></div>
|
||||
</section>
|
||||
|
||||
</main>
|
||||
|
@ -0,0 +1,124 @@
|
||||
package dev.dnpm.etl.processor.consent;
|
||||
|
||||
import static org.assertj.core.api.Assertions.assertThat;
|
||||
import static org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo;
|
||||
import static org.springframework.test.web.client.response.MockRestResponseCreators.withSuccess;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import dev.dnpm.etl.processor.config.AppConfiguration;
|
||||
import dev.dnpm.etl.processor.config.AppFhirConfig;
|
||||
import dev.dnpm.etl.processor.config.GIcsConfigProperties;
|
||||
import java.time.Instant;
|
||||
import java.util.Date;
|
||||
import org.hl7.fhir.r4.model.BooleanType;
|
||||
import org.hl7.fhir.r4.model.Identifier;
|
||||
import org.hl7.fhir.r4.model.OperationOutcome;
|
||||
import org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity;
|
||||
import org.hl7.fhir.r4.model.OperationOutcome.IssueType;
|
||||
import org.hl7.fhir.r4.model.OperationOutcome.OperationOutcomeIssueComponent;
|
||||
import org.hl7.fhir.r4.model.Parameters;
|
||||
import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
|
||||
import org.hl7.fhir.r4.model.StringType;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.boot.test.autoconfigure.web.client.RestClientTest;
|
||||
import org.springframework.http.MediaType;
|
||||
import org.springframework.test.context.ContextConfiguration;
|
||||
import org.springframework.test.context.TestPropertySource;
|
||||
import org.springframework.test.web.client.MockRestServiceServer;
|
||||
|
||||
|
||||
@ContextConfiguration(classes = {AppConfiguration.class, ObjectMapper.class})
|
||||
@TestPropertySource(properties = {"app.consent.gics.enabled=true",
|
||||
"app.consent.gics.uri=http://localhost:8090/ttp-fhir/fhir/gics"})
|
||||
@RestClientTest
|
||||
public class GicsConsentServiceTest {
|
||||
|
||||
public static final String GICS_BASE_URI = "http://localhost:8090/ttp-fhir/fhir/gics";
|
||||
@Autowired
|
||||
MockRestServiceServer mockRestServiceServer;
|
||||
|
||||
@Autowired
|
||||
GicsConsentService gicsConsentService;
|
||||
|
||||
@Autowired
|
||||
AppConfiguration appConfiguration;
|
||||
|
||||
@Autowired
|
||||
AppFhirConfig appFhirConfig;
|
||||
|
||||
@Autowired
|
||||
GIcsConfigProperties gIcsConfigProperties;
|
||||
|
||||
@BeforeEach
|
||||
public void setUp() {
|
||||
mockRestServiceServer = MockRestServiceServer.createServer(appConfiguration.restTemplate());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
void getTtpConsentStatus() {
|
||||
final Parameters responseConsented = new Parameters().addParameter(
|
||||
new ParametersParameterComponent().setName("consented")
|
||||
.setValue(new BooleanType().setValue(true)));
|
||||
|
||||
mockRestServiceServer.expect(
|
||||
requestTo("http://localhost:8090/ttp-fhir/fhir/gics"
|
||||
+ GicsConsentService.IS_CONSENTED_ENDPOINT)).andRespond(
|
||||
withSuccess(appFhirConfig.fhirContext().newJsonParser()
|
||||
.encodeResourceToString(responseConsented),
|
||||
MediaType.APPLICATION_JSON));
|
||||
|
||||
var consentStatus = gicsConsentService.getTtpConsentStatus("123456");
|
||||
assertThat(consentStatus).isEqualTo(TtpConsentStatus.CONSENTED);
|
||||
}
|
||||
|
||||
@Test
|
||||
void consentRevoced() {
|
||||
final Parameters responseRevoced = new Parameters().addParameter(
|
||||
new ParametersParameterComponent().setName("consented")
|
||||
.setValue(new BooleanType().setValue(false)));
|
||||
|
||||
mockRestServiceServer.expect(
|
||||
requestTo("http://localhost:8090/ttp-fhir/fhir/gics"
|
||||
+ GicsConsentService.IS_CONSENTED_ENDPOINT)).andRespond(
|
||||
withSuccess(appFhirConfig.fhirContext().newJsonParser()
|
||||
.encodeResourceToString(responseRevoced),
|
||||
MediaType.APPLICATION_JSON));
|
||||
|
||||
var consentStatus = gicsConsentService.getTtpConsentStatus("123456");
|
||||
assertThat(consentStatus).isEqualTo(TtpConsentStatus.CONSENT_MISSING_OR_REJECTED);
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
void gicsParameterInvalid() {
|
||||
final OperationOutcome responseErrorOutcome = new OperationOutcome().addIssue(
|
||||
new OperationOutcomeIssueComponent().setSeverity(
|
||||
IssueSeverity.ERROR).setCode(IssueType.PROCESSING)
|
||||
.setDiagnostics("Invalid policy parameter..."));
|
||||
|
||||
mockRestServiceServer.expect(
|
||||
requestTo(GICS_BASE_URI + GicsConsentService.IS_CONSENTED_ENDPOINT)).andRespond(
|
||||
withSuccess(appFhirConfig.fhirContext().newJsonParser()
|
||||
.encodeResourceToString(responseErrorOutcome),
|
||||
MediaType.APPLICATION_JSON));
|
||||
|
||||
var consentStatus = gicsConsentService.getTtpConsentStatus("123456");
|
||||
assertThat(consentStatus).isEqualTo(TtpConsentStatus.FAILED_TO_ASK);
|
||||
}
|
||||
|
||||
@Test
|
||||
void buildRequestParameterCurrentPolicyStatesForPersonTest() {
|
||||
|
||||
String pid = "12345678";
|
||||
var result = GicsConsentService.buildRequestParameterCurrentPolicyStatesForPerson(gIcsConfigProperties,
|
||||
pid, Date.from(Instant.now()),gIcsConfigProperties.getGnomDeConsentDomainName());
|
||||
|
||||
assertThat(result.getParameter().size()).as("should contain 3 parameter resources").isEqualTo(3);
|
||||
|
||||
assertThat(((StringType)result.getParameter("domain").getValue()).getValue()).isEqualTo(gIcsConfigProperties.getGnomDeConsentDomainName());
|
||||
assertThat(((Identifier)result.getParameter("personIdentifier").getValue()).getValue()).isEqualTo(pid);
|
||||
}
|
||||
}
|
20
src/test/kotlin/dev/dnpm/etl/processor/helpers.kt
Normal file
20
src/test/kotlin/dev/dnpm/etl/processor/helpers.kt
Normal file
@ -0,0 +1,20 @@
|
||||
/*
|
||||
* 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
|
@ -1,7 +1,7 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
@ -23,17 +23,20 @@ import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import de.ukw.ccc.bwhc.dto.Consent
|
||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import de.ukw.ccc.bwhc.dto.Patient
|
||||
import dev.dnpm.etl.processor.consent.TtpConsentStatus
|
||||
import dev.dnpm.etl.processor.CustomMediaType
|
||||
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||
import org.apache.kafka.clients.consumer.ConsumerRecord
|
||||
import org.apache.kafka.common.header.internals.RecordHeader
|
||||
import org.apache.kafka.common.header.internals.RecordHeaders
|
||||
import org.apache.kafka.common.record.TimestampType
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.mockito.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
|
||||
import org.mockito.kotlin.*
|
||||
import java.util.*
|
||||
|
||||
@ExtendWith(MockitoExtension::class)
|
||||
class KafkaInputListenerTest {
|
||||
@ -44,7 +47,7 @@ class KafkaInputListenerTest {
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Mock requestProcessor: RequestProcessor
|
||||
@Mock requestProcessor: RequestProcessor,
|
||||
) {
|
||||
this.requestProcessor = requestProcessor
|
||||
this.objectMapper = ObjectMapper()
|
||||
@ -59,9 +62,17 @@ class KafkaInputListenerTest {
|
||||
.withConsent(Consent.builder().withStatus(Consent.Status.ACTIVE).build())
|
||||
.build()
|
||||
|
||||
kafkaInputListener.onMessage(ConsumerRecord("testtopic", 0, 0, "", this.objectMapper.writeValueAsString(mtbFile)))
|
||||
kafkaInputListener.onMessage(
|
||||
ConsumerRecord(
|
||||
"testtopic",
|
||||
0,
|
||||
0,
|
||||
"",
|
||||
this.objectMapper.writeValueAsString(mtbFile)
|
||||
)
|
||||
)
|
||||
|
||||
verify(requestProcessor, times(1)).processMtbFile(any())
|
||||
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
|
||||
}
|
||||
|
||||
@Test
|
||||
@ -71,9 +82,106 @@ class KafkaInputListenerTest {
|
||||
.withConsent(Consent.builder().withStatus(Consent.Status.REJECTED).build())
|
||||
.build()
|
||||
|
||||
kafkaInputListener.onMessage(ConsumerRecord("testtopic", 0, 0, "", this.objectMapper.writeValueAsString(mtbFile)))
|
||||
kafkaInputListener.onMessage(
|
||||
ConsumerRecord(
|
||||
"testtopic",
|
||||
0,
|
||||
0,
|
||||
"",
|
||||
this.objectMapper.writeValueAsString(mtbFile)
|
||||
)
|
||||
)
|
||||
|
||||
verify(requestProcessor, times(1)).processDeletion(anyString())
|
||||
verify(requestProcessor, times(1)).processDeletion(
|
||||
anyValueClass(),
|
||||
eq(TtpConsentStatus.UNKNOWN_CHECK_FILE)
|
||||
)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldProcessMtbFileRequestWithExistingRequestId() {
|
||||
val mtbFile = MtbFile.builder()
|
||||
.withPatient(Patient.builder().withId("DUMMY_12345678").build())
|
||||
.withConsent(Consent.builder().withStatus(Consent.Status.ACTIVE).build())
|
||||
.build()
|
||||
|
||||
val headers = RecordHeaders(listOf(RecordHeader("requestId", UUID.randomUUID().toString().toByteArray())))
|
||||
kafkaInputListener.onMessage(
|
||||
ConsumerRecord(
|
||||
"testtopic",
|
||||
0,
|
||||
0,
|
||||
-1L,
|
||||
TimestampType.NO_TIMESTAMP_TYPE,
|
||||
-1,
|
||||
-1,
|
||||
"",
|
||||
this.objectMapper.writeValueAsString(mtbFile),
|
||||
headers,
|
||||
Optional.empty()
|
||||
)
|
||||
)
|
||||
|
||||
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>(), anyValueClass())
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldProcessDeleteRequestWithExistingRequestId() {
|
||||
val mtbFile = MtbFile.builder()
|
||||
.withPatient(Patient.builder().withId("DUMMY_12345678").build())
|
||||
.withConsent(Consent.builder().withStatus(Consent.Status.REJECTED).build())
|
||||
.build()
|
||||
|
||||
val headers = RecordHeaders(listOf(RecordHeader("requestId", UUID.randomUUID().toString().toByteArray())))
|
||||
kafkaInputListener.onMessage(
|
||||
ConsumerRecord(
|
||||
"testtopic",
|
||||
0,
|
||||
0,
|
||||
-1L,
|
||||
TimestampType.NO_TIMESTAMP_TYPE,
|
||||
-1,
|
||||
-1,
|
||||
"",
|
||||
this.objectMapper.writeValueAsString(mtbFile),
|
||||
headers,
|
||||
Optional.empty()
|
||||
)
|
||||
)
|
||||
verify(requestProcessor, times(1)).processDeletion(anyValueClass(), anyValueClass(), eq(
|
||||
TtpConsentStatus.UNKNOWN_CHECK_FILE))
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldNotProcessDnpmV2Request() {
|
||||
val mtbFile = MtbFile.builder()
|
||||
.withPatient(Patient.builder().withId("DUMMY_12345678").build())
|
||||
.withConsent(Consent.builder().withStatus(Consent.Status.REJECTED).build())
|
||||
.build()
|
||||
|
||||
val headers = RecordHeaders(
|
||||
listOf(
|
||||
RecordHeader("requestId", UUID.randomUUID().toString().toByteArray()),
|
||||
RecordHeader("contentType", CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE.toByteArray())
|
||||
)
|
||||
)
|
||||
kafkaInputListener.onMessage(
|
||||
ConsumerRecord(
|
||||
"testtopic",
|
||||
0,
|
||||
0,
|
||||
-1L,
|
||||
TimestampType.NO_TIMESTAMP_TYPE,
|
||||
-1,
|
||||
-1,
|
||||
"",
|
||||
this.objectMapper.writeValueAsString(mtbFile),
|
||||
headers,
|
||||
Optional.empty()
|
||||
)
|
||||
)
|
||||
verify(requestProcessor, times(0)).processDeletion(anyValueClass(), anyValueClass(), eq(
|
||||
TtpConsentStatus.UNKNOWN_CHECK_FILE))
|
||||
}
|
||||
|
||||
}
|
@ -1,7 +1,7 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
@ -21,18 +21,29 @@ package dev.dnpm.etl.processor.input
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import de.ukw.ccc.bwhc.dto.*
|
||||
import de.ukw.ccc.bwhc.dto.Consent.Status
|
||||
import dev.dnpm.etl.processor.CustomMediaType
|
||||
import dev.dnpm.etl.processor.consent.ConsentCheckFileBased
|
||||
import dev.dnpm.etl.processor.consent.GicsConsentService
|
||||
import dev.dnpm.etl.processor.consent.TtpConsentStatus
|
||||
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Nested
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.junit.jupiter.params.ParameterizedTest
|
||||
import org.junit.jupiter.params.provider.ValueSource
|
||||
import org.mockito.Mock
|
||||
import org.mockito.Mockito.times
|
||||
import org.mockito.Mockito.verify
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.mockito.kotlin.any
|
||||
import org.mockito.kotlin.argumentCaptor
|
||||
import org.mockito.kotlin.anyValueClass
|
||||
import org.mockito.kotlin.whenever
|
||||
import org.springframework.core.io.ClassPathResource
|
||||
import org.springframework.http.MediaType
|
||||
import org.springframework.test.context.TestPropertySource
|
||||
import org.springframework.test.web.servlet.MockMvc
|
||||
import org.springframework.test.web.servlet.delete
|
||||
import org.springframework.test.web.servlet.post
|
||||
@ -41,24 +52,268 @@ import org.springframework.test.web.servlet.setup.MockMvcBuilders
|
||||
@ExtendWith(MockitoExtension::class)
|
||||
class MtbFileRestControllerTest {
|
||||
|
||||
private lateinit var mockMvc: MockMvc
|
||||
|
||||
private lateinit var requestProcessor: RequestProcessor
|
||||
|
||||
private val objectMapper = ObjectMapper()
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Mock requestProcessor: RequestProcessor
|
||||
) {
|
||||
this.requestProcessor = requestProcessor
|
||||
val controller = MtbFileRestController(requestProcessor)
|
||||
this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build()
|
||||
@Nested
|
||||
inner class BwhcRequests {
|
||||
|
||||
private lateinit var mockMvc: MockMvc
|
||||
|
||||
private lateinit var requestProcessor: RequestProcessor
|
||||
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Mock requestProcessor: RequestProcessor
|
||||
) {
|
||||
this.requestProcessor = requestProcessor
|
||||
val controller = MtbFileRestController(requestProcessor,
|
||||
ConsentCheckFileBased()
|
||||
)
|
||||
this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build()
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldProcessPostRequest() {
|
||||
mockMvc.post("/mtbfile") {
|
||||
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Status.ACTIVE))
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
}.andExpect {
|
||||
status {
|
||||
isAccepted()
|
||||
}
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldProcessPostRequestWithRejectedConsent() {
|
||||
mockMvc.post("/mtbfile") {
|
||||
content =
|
||||
objectMapper.writeValueAsString(bwhcMtbFileContent(Status.REJECTED))
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
}.andExpect {
|
||||
status {
|
||||
isAccepted()
|
||||
}
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processDeletion(
|
||||
anyValueClass(),
|
||||
org.mockito.kotlin.eq(TtpConsentStatus.CONSENT_MISSING_OR_REJECTED)
|
||||
)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldProcessDeleteRequest() {
|
||||
mockMvc.delete("/mtbfile/TEST_12345678").andExpect {
|
||||
status {
|
||||
isAccepted()
|
||||
}
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processDeletion(
|
||||
anyValueClass(),
|
||||
org.mockito.kotlin.eq(TtpConsentStatus.UNKNOWN_CHECK_FILE)
|
||||
)
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldProcessMtbFilePostRequest() {
|
||||
val mtbFile = MtbFile.builder()
|
||||
@TestPropertySource(
|
||||
properties = ["app.consent.gics.enabled=true",
|
||||
"app.consent.gics.gIcsBaseUri=http://localhost:8090/ttp-fhir/fhir/gics"]
|
||||
)
|
||||
@Nested
|
||||
inner class BwhcRequestsCheckConsentViaTtp {
|
||||
|
||||
private lateinit var mockMvc: MockMvc
|
||||
|
||||
private lateinit var requestProcessor: RequestProcessor
|
||||
|
||||
private lateinit var gicsConsentService: GicsConsentService
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Mock requestProcessor: RequestProcessor,
|
||||
@Mock gicsConsentService: GicsConsentService
|
||||
) {
|
||||
this.requestProcessor = requestProcessor
|
||||
val controller = MtbFileRestController(requestProcessor, gicsConsentService)
|
||||
this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build()
|
||||
this.gicsConsentService = gicsConsentService
|
||||
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@ValueSource(strings = ["ACTIVE", "REJECTED"])
|
||||
fun shouldProcessPostRequest(status: String) {
|
||||
|
||||
whenever(gicsConsentService.getTtpConsentStatus(any())).thenReturn(TtpConsentStatus.CONSENTED)
|
||||
|
||||
mockMvc.post("/mtbfile") {
|
||||
content =
|
||||
objectMapper.writeValueAsString(bwhcMtbFileContent(Status.valueOf(status)))
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
}.andExpect {
|
||||
status {
|
||||
isAccepted()
|
||||
}
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
|
||||
}
|
||||
|
||||
|
||||
@ParameterizedTest
|
||||
@ValueSource(strings = ["ACTIVE", "REJECTED"])
|
||||
fun shouldProcessPostRequestWithRejectedConsent(status: String) {
|
||||
|
||||
whenever(gicsConsentService.getTtpConsentStatus(any())).thenReturn(TtpConsentStatus.CONSENT_MISSING_OR_REJECTED)
|
||||
|
||||
mockMvc.post("/mtbfile") {
|
||||
content =
|
||||
objectMapper.writeValueAsString(bwhcMtbFileContent(Status.valueOf(status)))
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
}.andExpect {
|
||||
status {
|
||||
isAccepted()
|
||||
}
|
||||
}
|
||||
|
||||
// consent status from ttp should override file consent value
|
||||
verify(requestProcessor, times(1)).processDeletion(
|
||||
anyValueClass(),
|
||||
org.mockito.kotlin.eq(TtpConsentStatus.CONSENT_MISSING_OR_REJECTED)
|
||||
)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldProcessDeleteRequest() {
|
||||
|
||||
mockMvc.delete("/mtbfile/TEST_12345678").andExpect {
|
||||
status {
|
||||
isAccepted()
|
||||
}
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processDeletion(
|
||||
anyValueClass(),
|
||||
org.mockito.kotlin.eq(TtpConsentStatus.UNKNOWN_CHECK_FILE)
|
||||
)
|
||||
verify(gicsConsentService, times(0)).getTtpConsentStatus(any())
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@Nested
|
||||
inner class BwhcRequestsWithAlias {
|
||||
|
||||
private lateinit var mockMvc: MockMvc
|
||||
|
||||
private lateinit var requestProcessor: RequestProcessor
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Mock requestProcessor: RequestProcessor
|
||||
) {
|
||||
this.requestProcessor = requestProcessor
|
||||
val controller = MtbFileRestController(requestProcessor,
|
||||
ConsentCheckFileBased()
|
||||
)
|
||||
this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build()
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldProcessPostRequest() {
|
||||
mockMvc.post("/mtb") {
|
||||
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Status.ACTIVE))
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
}.andExpect {
|
||||
status {
|
||||
isAccepted()
|
||||
}
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processMtbFile(any<MtbFile>())
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldProcessPostRequestWithRejectedConsent() {
|
||||
mockMvc.post("/mtb") {
|
||||
content =
|
||||
objectMapper.writeValueAsString(bwhcMtbFileContent(Status.REJECTED))
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
}.andExpect {
|
||||
status {
|
||||
isAccepted()
|
||||
}
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processDeletion(
|
||||
anyValueClass(), org.mockito.kotlin.eq(
|
||||
TtpConsentStatus.CONSENT_MISSING_OR_REJECTED
|
||||
)
|
||||
)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldProcessDeleteRequest() {
|
||||
mockMvc.delete("/mtb/TEST_12345678").andExpect {
|
||||
status {
|
||||
isAccepted()
|
||||
}
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processDeletion(
|
||||
anyValueClass(), org.mockito.kotlin.eq(
|
||||
TtpConsentStatus.UNKNOWN_CHECK_FILE
|
||||
)
|
||||
)
|
||||
}
|
||||
}
|
||||
|
||||
@Nested
|
||||
inner class RequestsForDnpmDataModel21 {
|
||||
|
||||
private lateinit var mockMvc: MockMvc
|
||||
|
||||
private lateinit var requestProcessor: RequestProcessor
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Mock requestProcessor: RequestProcessor
|
||||
) {
|
||||
this.requestProcessor = requestProcessor
|
||||
val controller = MtbFileRestController(requestProcessor,
|
||||
ConsentCheckFileBased()
|
||||
)
|
||||
this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build()
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldRespondPostRequest() {
|
||||
val mtbFileContent =
|
||||
ClassPathResource("mv64e-mtb-fake-patient.json").inputStream.readAllBytes()
|
||||
.toString(Charsets.UTF_8)
|
||||
|
||||
mockMvc.post("/mtb") {
|
||||
content = mtbFileContent
|
||||
contentType = CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON
|
||||
}.andExpect {
|
||||
status {
|
||||
isAccepted()
|
||||
}
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
companion object {
|
||||
fun bwhcMtbFileContent(consentStatus: Status) = MtbFile.builder()
|
||||
.withPatient(
|
||||
Patient.builder()
|
||||
.withId("TEST_12345678")
|
||||
@ -69,7 +324,7 @@ class MtbFileRestControllerTest {
|
||||
.withConsent(
|
||||
Consent.builder()
|
||||
.withId("1")
|
||||
.withStatus(Consent.Status.ACTIVE)
|
||||
.withStatus(consentStatus)
|
||||
.withPatient("TEST_12345678")
|
||||
.build()
|
||||
)
|
||||
@ -81,70 +336,5 @@ class MtbFileRestControllerTest {
|
||||
.build()
|
||||
)
|
||||
.build()
|
||||
|
||||
mockMvc.post("/mtbfile") {
|
||||
content = objectMapper.writeValueAsString(mtbFile)
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
}.andExpect {
|
||||
status {
|
||||
isAccepted()
|
||||
}
|
||||
}
|
||||
|
||||
verify(requestProcessor, times(1)).processMtbFile(any())
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldProcessMtbFilePostRequestWithRejectedConsent() {
|
||||
val mtbFile = MtbFile.builder()
|
||||
.withPatient(
|
||||
Patient.builder()
|
||||
.withId("TEST_12345678")
|
||||
.withBirthDate("2000-08-08")
|
||||
.withGender(Patient.Gender.MALE)
|
||||
.build()
|
||||
)
|
||||
.withConsent(
|
||||
Consent.builder()
|
||||
.withId("1")
|
||||
.withStatus(Consent.Status.REJECTED)
|
||||
.withPatient("TEST_12345678")
|
||||
.build()
|
||||
)
|
||||
.withEpisode(
|
||||
Episode.builder()
|
||||
.withId("1")
|
||||
.withPatient("TEST_12345678")
|
||||
.withPeriod(PeriodStart("2023-08-08"))
|
||||
.build()
|
||||
)
|
||||
.build()
|
||||
|
||||
mockMvc.post("/mtbfile") {
|
||||
content = objectMapper.writeValueAsString(mtbFile)
|
||||
contentType = MediaType.APPLICATION_JSON
|
||||
}.andExpect {
|
||||
status {
|
||||
isAccepted()
|
||||
}
|
||||
}
|
||||
|
||||
val captor = argumentCaptor<String>()
|
||||
verify(requestProcessor, times(1)).processDeletion(captor.capture())
|
||||
assertThat(captor.firstValue).isEqualTo("TEST_12345678")
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldProcessMtbFileDeleteRequest() {
|
||||
mockMvc.delete("/mtbfile/TEST_12345678").andExpect {
|
||||
status {
|
||||
isAccepted()
|
||||
}
|
||||
}
|
||||
|
||||
val captor = argumentCaptor<String>()
|
||||
verify(requestProcessor, times(1)).processDeletion(captor.capture())
|
||||
assertThat(captor.firstValue).isEqualTo("TEST_12345678")
|
||||
}
|
||||
|
||||
}
|
@ -1,7 +1,7 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
@ -21,161 +21,262 @@ package dev.dnpm.etl.processor.output
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import de.ukw.ccc.bwhc.dto.*
|
||||
import de.ukw.ccc.bwhc.dto.Patient
|
||||
import dev.dnpm.etl.processor.CustomMediaType
|
||||
import dev.dnpm.etl.processor.PatientPseudonym
|
||||
import dev.dnpm.etl.processor.RequestId
|
||||
import dev.dnpm.etl.processor.config.KafkaProperties
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import dev.pcvolkmer.mv64e.mtb.*
|
||||
import org.apache.kafka.clients.producer.ProducerRecord
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Nested
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.junit.jupiter.params.ParameterizedTest
|
||||
import org.junit.jupiter.params.provider.MethodSource
|
||||
import org.mockito.ArgumentMatchers.anyString
|
||||
import org.mockito.Mock
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.mockito.kotlin.*
|
||||
import org.springframework.http.MediaType
|
||||
import org.springframework.kafka.core.KafkaTemplate
|
||||
import org.springframework.kafka.support.SendResult
|
||||
import org.springframework.retry.policy.SimpleRetryPolicy
|
||||
import org.springframework.retry.support.RetryTemplateBuilder
|
||||
import java.time.Instant
|
||||
import java.util.*
|
||||
import java.util.concurrent.CompletableFuture.completedFuture
|
||||
import java.util.concurrent.ExecutionException
|
||||
|
||||
@ExtendWith(MockitoExtension::class)
|
||||
class KafkaMtbFileSenderTest {
|
||||
|
||||
private lateinit var kafkaTemplate: KafkaTemplate<String, String>
|
||||
@Nested
|
||||
inner class BwhcV1Record {
|
||||
|
||||
private lateinit var kafkaMtbFileSender: KafkaMtbFileSender
|
||||
private lateinit var kafkaTemplate: KafkaTemplate<String, String>
|
||||
|
||||
private lateinit var objectMapper: ObjectMapper
|
||||
private lateinit var kafkaMtbFileSender: KafkaMtbFileSender
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Mock kafkaTemplate: KafkaTemplate<String, String>
|
||||
) {
|
||||
val kafkaProperties = KafkaProperties("testtopic")
|
||||
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
|
||||
private lateinit var objectMapper: ObjectMapper
|
||||
|
||||
this.objectMapper = ObjectMapper()
|
||||
this.kafkaTemplate = kafkaTemplate
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Mock kafkaTemplate: KafkaTemplate<String, String>
|
||||
) {
|
||||
val kafkaProperties = KafkaProperties("testtopic")
|
||||
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
|
||||
|
||||
this.kafkaMtbFileSender = KafkaMtbFileSender(kafkaTemplate, kafkaProperties, retryTemplate, objectMapper)
|
||||
}
|
||||
this.objectMapper = ObjectMapper()
|
||||
this.kafkaTemplate = kafkaTemplate
|
||||
|
||||
@ParameterizedTest
|
||||
@MethodSource("requestWithResponseSource")
|
||||
fun shouldSendMtbFileRequestAndReturnExpectedState(testData: TestData) {
|
||||
doAnswer {
|
||||
if (null != testData.exception) {
|
||||
throw testData.exception
|
||||
}
|
||||
completedFuture(SendResult<String, String>(null, null))
|
||||
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
|
||||
|
||||
val response = kafkaMtbFileSender.send(MtbFileSender.MtbFileRequest("TestID", mtbFile(Consent.Status.ACTIVE)))
|
||||
assertThat(response.status).isEqualTo(testData.requestStatus)
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@MethodSource("requestWithResponseSource")
|
||||
fun shouldSendDeleteRequestAndReturnExpectedState(testData: TestData) {
|
||||
doAnswer {
|
||||
if (null != testData.exception) {
|
||||
throw testData.exception
|
||||
}
|
||||
completedFuture(SendResult<String, String>(null, null))
|
||||
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
|
||||
|
||||
val response = kafkaMtbFileSender.send(MtbFileSender.DeleteRequest("TestID", "PID"))
|
||||
assertThat(response.status).isEqualTo(testData.requestStatus)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldSendMtbFileRequestWithCorrectKeyAndBody() {
|
||||
doAnswer {
|
||||
completedFuture(SendResult<String, String>(null, null))
|
||||
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
|
||||
|
||||
kafkaMtbFileSender.send(MtbFileSender.MtbFileRequest("TestID", mtbFile(Consent.Status.ACTIVE)))
|
||||
|
||||
val captor = argumentCaptor<String>()
|
||||
verify(kafkaTemplate, times(1)).send(anyString(), captor.capture(), captor.capture())
|
||||
assertThat(captor.firstValue).isNotNull
|
||||
assertThat(captor.firstValue).isEqualTo("{\"pid\": \"PID\", \"eid\": \"1\"}")
|
||||
assertThat(captor.secondValue).isNotNull
|
||||
assertThat(captor.secondValue).isEqualTo(objectMapper.writeValueAsString(kafkaRecordData("TestID", Consent.Status.ACTIVE)))
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldSendDeleteRequestWithCorrectKeyAndBody() {
|
||||
doAnswer {
|
||||
completedFuture(SendResult<String, String>(null, null))
|
||||
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
|
||||
|
||||
kafkaMtbFileSender.send(MtbFileSender.DeleteRequest("TestID", "PID"))
|
||||
|
||||
val captor = argumentCaptor<String>()
|
||||
verify(kafkaTemplate, times(1)).send(anyString(), captor.capture(), captor.capture())
|
||||
assertThat(captor.firstValue).isNotNull
|
||||
assertThat(captor.firstValue).isEqualTo("{\"pid\": \"PID\"}")
|
||||
assertThat(captor.secondValue).isNotNull
|
||||
assertThat(captor.secondValue).isEqualTo(objectMapper.writeValueAsString(kafkaRecordData("TestID", Consent.Status.REJECTED)))
|
||||
}
|
||||
|
||||
@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)
|
||||
this.kafkaMtbFileSender = KafkaMtbFileSender(kafkaTemplate, kafkaProperties, retryTemplate, objectMapper)
|
||||
}
|
||||
|
||||
verify(kafkaTemplate, expectedCount).send(anyString(), anyString(), anyString())
|
||||
}
|
||||
@ParameterizedTest
|
||||
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
|
||||
fun shouldSendMtbFileRequestAndReturnExpectedState(testData: TestData) {
|
||||
doAnswer {
|
||||
if (null != testData.exception) {
|
||||
throw testData.exception
|
||||
}
|
||||
completedFuture(SendResult<String, String>(null, null))
|
||||
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
|
||||
|
||||
@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)
|
||||
val response = kafkaMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1MtbFile(Consent.Status.ACTIVE)))
|
||||
assertThat(response.status).isEqualTo(testData.requestStatus)
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
|
||||
fun shouldSendDeleteRequestAndReturnExpectedState(testData: TestData) {
|
||||
doAnswer {
|
||||
if (null != testData.exception) {
|
||||
throw testData.exception
|
||||
}
|
||||
completedFuture(SendResult<String, String>(null, null))
|
||||
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
|
||||
|
||||
val response = kafkaMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
||||
assertThat(response.status).isEqualTo(testData.requestStatus)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldSendMtbFileRequestWithCorrectKeyAndHeaderAndBody() {
|
||||
doAnswer {
|
||||
completedFuture(SendResult<String, String>(null, null))
|
||||
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
|
||||
|
||||
kafkaMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1MtbFile(Consent.Status.ACTIVE)))
|
||||
|
||||
val captor = argumentCaptor<ProducerRecord<String, String>>()
|
||||
verify(kafkaTemplate, times(1)).send(captor.capture())
|
||||
assertThat(captor.firstValue.key()).isNotNull
|
||||
assertThat(captor.firstValue.key()).isEqualTo("{\"pid\": \"PID\"}")
|
||||
assertThat(captor.firstValue.headers().headers("contentType")).isNotNull
|
||||
assertThat(captor.firstValue.headers().headers("contentType")?.firstOrNull()?.value()).isEqualTo(MediaType.APPLICATION_JSON_VALUE.toByteArray())
|
||||
assertThat(captor.firstValue.value()).isNotNull
|
||||
assertThat(captor.firstValue.value()).isEqualTo(objectMapper.writeValueAsString(bwhcV1kafkaRecordData(TEST_REQUEST_ID, Consent.Status.ACTIVE)))
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldSendDeleteRequestWithCorrectKeyAndBody() {
|
||||
doAnswer {
|
||||
completedFuture(SendResult<String, String>(null, null))
|
||||
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
|
||||
|
||||
kafkaMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
||||
|
||||
val captor = argumentCaptor<ProducerRecord<String, String>>()
|
||||
verify(kafkaTemplate, times(1)).send(captor.capture())
|
||||
assertThat(captor.firstValue.key()).isNotNull
|
||||
assertThat(captor.firstValue.key()).isEqualTo("{\"pid\": \"PID\"}")
|
||||
assertThat(captor.firstValue.value()).isNotNull
|
||||
assertThat(captor.firstValue.value()).isEqualTo(objectMapper.writeValueAsString(bwhcV1kafkaRecordData(TEST_REQUEST_ID, Consent.Status.REJECTED)))
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
|
||||
fun shouldRetryOnMtbFileKafkaSendError(testData: TestData) {
|
||||
val kafkaProperties = KafkaProperties("testtopic")
|
||||
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
|
||||
this.kafkaMtbFileSender = KafkaMtbFileSender(this.kafkaTemplate, kafkaProperties, retryTemplate, this.objectMapper)
|
||||
|
||||
doAnswer {
|
||||
if (null != testData.exception) {
|
||||
throw testData.exception
|
||||
}
|
||||
completedFuture(SendResult<String, String>(null, null))
|
||||
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
|
||||
|
||||
kafkaMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1MtbFile(Consent.Status.ACTIVE)))
|
||||
|
||||
val expectedCount = when (testData.exception) {
|
||||
// OK - No Retry
|
||||
null -> times(1)
|
||||
// Request failed - Retry max 3 times
|
||||
else -> times(3)
|
||||
}
|
||||
|
||||
verify(kafkaTemplate, expectedCount).send(any<ProducerRecord<String, String>>())
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
|
||||
fun shouldRetryOnDeleteKafkaSendError(testData: TestData) {
|
||||
val kafkaProperties = KafkaProperties("testtopic")
|
||||
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
|
||||
this.kafkaMtbFileSender = KafkaMtbFileSender(this.kafkaTemplate, kafkaProperties, retryTemplate, this.objectMapper)
|
||||
|
||||
doAnswer {
|
||||
if (null != testData.exception) {
|
||||
throw testData.exception
|
||||
}
|
||||
completedFuture(SendResult<String, String>(null, null))
|
||||
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
|
||||
|
||||
kafkaMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
||||
|
||||
val expectedCount = when (testData.exception) {
|
||||
// OK - No Retry
|
||||
null -> times(1)
|
||||
// Request failed - Retry max 3 times
|
||||
else -> times(3)
|
||||
}
|
||||
|
||||
verify(kafkaTemplate, expectedCount).send(any<ProducerRecord<String, String>>())
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Nested
|
||||
inner class DnpmV2Record {
|
||||
|
||||
private lateinit var kafkaTemplate: KafkaTemplate<String, String>
|
||||
|
||||
private lateinit var kafkaMtbFileSender: KafkaMtbFileSender
|
||||
|
||||
private lateinit var objectMapper: ObjectMapper
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Mock kafkaTemplate: KafkaTemplate<String, String>
|
||||
) {
|
||||
val kafkaProperties = KafkaProperties("testtopic")
|
||||
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
|
||||
|
||||
this.objectMapper = ObjectMapper()
|
||||
this.kafkaTemplate = kafkaTemplate
|
||||
|
||||
this.kafkaMtbFileSender = KafkaMtbFileSender(kafkaTemplate, kafkaProperties, retryTemplate, objectMapper)
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
|
||||
fun shouldSendMtbFileRequestAndReturnExpectedState(testData: TestData) {
|
||||
doAnswer {
|
||||
if (null != testData.exception) {
|
||||
throw testData.exception
|
||||
}
|
||||
completedFuture(SendResult<String, String>(null, null))
|
||||
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
|
||||
|
||||
val response = kafkaMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile()))
|
||||
assertThat(response.status).isEqualTo(testData.requestStatus)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldSendMtbFileRequestWithCorrectKeyAndHeaderAndBody() {
|
||||
doAnswer {
|
||||
completedFuture(SendResult<String, String>(null, null))
|
||||
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
|
||||
|
||||
kafkaMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile()))
|
||||
|
||||
val captor = argumentCaptor<ProducerRecord<String, String>>()
|
||||
verify(kafkaTemplate, times(1)).send(captor.capture())
|
||||
assertThat(captor.firstValue.key()).isNotNull
|
||||
assertThat(captor.firstValue.key()).isEqualTo("{\"pid\": \"PID\"}")
|
||||
assertThat(captor.firstValue.headers().headers("contentType")).isNotNull
|
||||
assertThat(captor.firstValue.headers().headers("contentType")?.firstOrNull()?.value()).isEqualTo(CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE.toByteArray())
|
||||
assertThat(captor.firstValue.value()).isNotNull
|
||||
assertThat(captor.firstValue.value()).isEqualTo(objectMapper.writeValueAsString(dnmpV2kafkaRecordData(TEST_REQUEST_ID)))
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
|
||||
fun shouldRetryOnMtbFileKafkaSendError(testData: TestData) {
|
||||
val kafkaProperties = KafkaProperties("testtopic")
|
||||
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
|
||||
this.kafkaMtbFileSender = KafkaMtbFileSender(this.kafkaTemplate, kafkaProperties, retryTemplate, this.objectMapper)
|
||||
|
||||
doAnswer {
|
||||
if (null != testData.exception) {
|
||||
throw testData.exception
|
||||
}
|
||||
completedFuture(SendResult<String, String>(null, null))
|
||||
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
|
||||
|
||||
kafkaMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile()))
|
||||
|
||||
val expectedCount = when (testData.exception) {
|
||||
// OK - No Retry
|
||||
null -> times(1)
|
||||
// Request failed - Retry max 3 times
|
||||
else -> times(3)
|
||||
}
|
||||
|
||||
verify(kafkaTemplate, expectedCount).send(any<ProducerRecord<String, String>>())
|
||||
}
|
||||
|
||||
verify(kafkaTemplate, expectedCount).send(anyString(), anyString(), anyString())
|
||||
}
|
||||
|
||||
companion object {
|
||||
fun mtbFile(consentStatus: Consent.Status): MtbFile {
|
||||
val TEST_REQUEST_ID = RequestId("TestId")
|
||||
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID")
|
||||
|
||||
fun bwhcV1MtbFile(consentStatus: Consent.Status): MtbFile {
|
||||
return if (consentStatus == Consent.Status.ACTIVE) {
|
||||
MtbFile.builder()
|
||||
.withPatient(
|
||||
@ -210,8 +311,35 @@ class KafkaMtbFileSenderTest {
|
||||
}.build()
|
||||
}
|
||||
|
||||
fun kafkaRecordData(requestId: String, consentStatus: Consent.Status): KafkaMtbFileSender.Data {
|
||||
return KafkaMtbFileSender.Data(requestId, mtbFile(consentStatus))
|
||||
fun dnpmV2MtbFile(): Mtb {
|
||||
return Mtb().apply {
|
||||
this.patient = dev.pcvolkmer.mv64e.mtb.Patient().apply {
|
||||
this.id = "PID"
|
||||
this.birthDate = Date.from(Instant.now())
|
||||
this.gender = GenderCoding().apply {
|
||||
this.code = GenderCodingCode.MALE
|
||||
}
|
||||
}
|
||||
this.episodesOfCare = listOf(
|
||||
MtbEpisodeOfCare().apply {
|
||||
this.id = "1"
|
||||
this.patient = Reference().apply {
|
||||
this.id = "PID"
|
||||
}
|
||||
this.period = PeriodDate().apply {
|
||||
this.start = Date.from(Instant.now())
|
||||
}
|
||||
}
|
||||
)
|
||||
}
|
||||
}
|
||||
|
||||
fun bwhcV1kafkaRecordData(requestId: RequestId, consentStatus: Consent.Status): MtbRequest {
|
||||
return BwhcV1MtbFileRequest(requestId, bwhcV1MtbFile(consentStatus))
|
||||
}
|
||||
|
||||
fun dnmpV2kafkaRecordData(requestId: RequestId): MtbRequest {
|
||||
return DnpmV2MtbFileRequest(requestId, dnpmV2MtbFile())
|
||||
}
|
||||
|
||||
data class TestData(val requestStatus: RequestStatus, val exception: Throwable? = null)
|
||||
|
@ -1,7 +1,7 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
@ -19,52 +19,61 @@
|
||||
|
||||
package dev.dnpm.etl.processor.output
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import com.fasterxml.jackson.module.kotlin.KotlinModule
|
||||
import de.ukw.ccc.bwhc.dto.*
|
||||
import dev.dnpm.etl.processor.PatientPseudonym
|
||||
import dev.dnpm.etl.processor.RequestId
|
||||
import dev.dnpm.etl.processor.config.RestTargetProperties
|
||||
import dev.dnpm.etl.processor.monitoring.ReportService
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.params.ParameterizedTest
|
||||
import org.junit.jupiter.params.provider.MethodSource
|
||||
import org.springframework.http.HttpHeaders
|
||||
import org.springframework.http.HttpMethod
|
||||
import org.springframework.http.HttpStatus
|
||||
import org.springframework.http.MediaType
|
||||
import org.springframework.retry.policy.SimpleRetryPolicy
|
||||
import org.springframework.retry.support.RetryTemplateBuilder
|
||||
import org.springframework.test.web.client.ExpectedCount
|
||||
import org.springframework.test.web.client.MockRestServiceServer
|
||||
import org.springframework.test.web.client.match.MockRestRequestMatchers.method
|
||||
import org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo
|
||||
import org.springframework.test.web.client.match.MockRestRequestMatchers.*
|
||||
import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus
|
||||
import org.springframework.web.client.RestTemplate
|
||||
|
||||
class RestMtbFileSenderTest {
|
||||
class RestBwhcMtbFileSenderTest {
|
||||
|
||||
private lateinit var mockRestServiceServer: MockRestServiceServer
|
||||
|
||||
private lateinit var restMtbFileSender: RestMtbFileSender
|
||||
|
||||
private var reportService = ReportService(ObjectMapper().registerModule(KotlinModule.Builder().build()))
|
||||
|
||||
@BeforeEach
|
||||
fun setup() {
|
||||
val restTemplate = RestTemplate()
|
||||
val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile")
|
||||
val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile", null, null)
|
||||
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
|
||||
|
||||
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
|
||||
|
||||
this.restMtbFileSender = RestMtbFileSender(restTemplate, restTargetProperties, retryTemplate)
|
||||
this.restMtbFileSender =
|
||||
RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@MethodSource("deleteRequestWithResponseSource")
|
||||
fun shouldReturnExpectedResponseForDelete(requestWithResponse: RequestWithResponse) {
|
||||
this.mockRestServiceServer.expect {
|
||||
method(HttpMethod.DELETE)
|
||||
requestTo("/mtbfile")
|
||||
}.andRespond {
|
||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||
}
|
||||
this.mockRestServiceServer
|
||||
.expect(method(HttpMethod.DELETE))
|
||||
.andExpect(requestTo("http://localhost:9000/mtbfile/Patient/${TEST_PATIENT_PSEUDONYM.value}"))
|
||||
.andRespond {
|
||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||
}
|
||||
|
||||
val response = restMtbFileSender.send(MtbFileSender.DeleteRequest("TestID", "PID"))
|
||||
val response = restMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
||||
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
||||
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
||||
}
|
||||
@ -72,14 +81,15 @@ class RestMtbFileSenderTest {
|
||||
@ParameterizedTest
|
||||
@MethodSource("mtbFileRequestWithResponseSource")
|
||||
fun shouldReturnExpectedResponseForMtbFilePost(requestWithResponse: RequestWithResponse) {
|
||||
this.mockRestServiceServer.expect {
|
||||
method(HttpMethod.POST)
|
||||
requestTo("/mtbfile")
|
||||
}.andRespond {
|
||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||
}
|
||||
this.mockRestServiceServer
|
||||
.expect(method(HttpMethod.POST))
|
||||
.andExpect(requestTo("http://localhost:9000/mtbfile/MTBFile"))
|
||||
.andExpect(header(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE))
|
||||
.andRespond {
|
||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||
}
|
||||
|
||||
val response = restMtbFileSender.send(MtbFileSender.MtbFileRequest("TestID", mtbFile))
|
||||
val response = restMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, mtbFile))
|
||||
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
||||
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
||||
}
|
||||
@ -88,11 +98,12 @@ class RestMtbFileSenderTest {
|
||||
@MethodSource("mtbFileRequestWithResponseSource")
|
||||
fun shouldRetryOnMtbFileHttpRequestError(requestWithResponse: RequestWithResponse) {
|
||||
val restTemplate = RestTemplate()
|
||||
val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile")
|
||||
val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile", null, null)
|
||||
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
|
||||
|
||||
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
|
||||
this.restMtbFileSender = RestMtbFileSender(restTemplate, restTargetProperties, retryTemplate)
|
||||
this.restMtbFileSender =
|
||||
RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
|
||||
|
||||
val expectedCount = when (requestWithResponse.httpStatus) {
|
||||
// OK - No Retry
|
||||
@ -101,14 +112,14 @@ class RestMtbFileSenderTest {
|
||||
else -> ExpectedCount.max(3)
|
||||
}
|
||||
|
||||
this.mockRestServiceServer.expect(expectedCount) {
|
||||
method(HttpMethod.POST)
|
||||
requestTo("/mtbfile")
|
||||
}.andRespond {
|
||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||
}
|
||||
this.mockRestServiceServer
|
||||
.expect(expectedCount, method(HttpMethod.POST))
|
||||
.andExpect(requestTo("http://localhost:9000/mtbfile/MTBFile"))
|
||||
.andRespond {
|
||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||
}
|
||||
|
||||
val response = restMtbFileSender.send(MtbFileSender.MtbFileRequest("TestID", mtbFile))
|
||||
val response = restMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, mtbFile))
|
||||
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
||||
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
||||
}
|
||||
@ -117,11 +128,12 @@ class RestMtbFileSenderTest {
|
||||
@MethodSource("deleteRequestWithResponseSource")
|
||||
fun shouldRetryOnDeleteHttpRequestError(requestWithResponse: RequestWithResponse) {
|
||||
val restTemplate = RestTemplate()
|
||||
val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile")
|
||||
val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile", null, null)
|
||||
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
|
||||
|
||||
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
|
||||
this.restMtbFileSender = RestMtbFileSender(restTemplate, restTargetProperties, retryTemplate)
|
||||
this.restMtbFileSender =
|
||||
RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
|
||||
|
||||
val expectedCount = when (requestWithResponse.httpStatus) {
|
||||
// OK - No Retry
|
||||
@ -130,14 +142,14 @@ class RestMtbFileSenderTest {
|
||||
else -> ExpectedCount.max(3)
|
||||
}
|
||||
|
||||
this.mockRestServiceServer.expect(expectedCount) {
|
||||
method(HttpMethod.DELETE)
|
||||
requestTo("/mtbfile")
|
||||
}.andRespond {
|
||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||
}
|
||||
this.mockRestServiceServer
|
||||
.expect(expectedCount, method(HttpMethod.DELETE))
|
||||
.andExpect(requestTo("http://localhost:9000/mtbfile/Patient/${TEST_PATIENT_PSEUDONYM.value}"))
|
||||
.andRespond {
|
||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||
}
|
||||
|
||||
val response = restMtbFileSender.send(MtbFileSender.DeleteRequest("TestID", "PID"))
|
||||
val response = restMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
||||
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
||||
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
||||
}
|
||||
@ -149,23 +161,8 @@ class RestMtbFileSenderTest {
|
||||
val response: MtbFileSender.Response
|
||||
)
|
||||
|
||||
private val warningBody = """
|
||||
{
|
||||
"patient_id": "PID",
|
||||
"issues": [
|
||||
{ "severity": "warning", "message": "Something is not right" }
|
||||
]
|
||||
}
|
||||
""".trimIndent()
|
||||
|
||||
private val errorBody = """
|
||||
{
|
||||
"patient_id": "PID",
|
||||
"issues": [
|
||||
{ "severity": "error", "message": "Something is very bad" }
|
||||
]
|
||||
}
|
||||
""".trimIndent()
|
||||
val TEST_REQUEST_ID = RequestId("TestId")
|
||||
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID")
|
||||
|
||||
val mtbFile: MtbFile = MtbFile.builder()
|
||||
.withPatient(
|
||||
@ -200,31 +197,44 @@ class RestMtbFileSenderTest {
|
||||
@JvmStatic
|
||||
fun mtbFileRequestWithResponseSource(): Set<RequestWithResponse> {
|
||||
return setOf(
|
||||
RequestWithResponse(HttpStatus.OK, "{}", MtbFileSender.Response(RequestStatus.SUCCESS, "{}")),
|
||||
RequestWithResponse(
|
||||
HttpStatus.OK,
|
||||
responseBodyWithMaxSeverity(ReportService.Severity.INFO),
|
||||
MtbFileSender.Response(
|
||||
RequestStatus.SUCCESS,
|
||||
responseBodyWithMaxSeverity(ReportService.Severity.INFO)
|
||||
)
|
||||
),
|
||||
RequestWithResponse(
|
||||
HttpStatus.CREATED,
|
||||
warningBody,
|
||||
MtbFileSender.Response(RequestStatus.WARNING, warningBody)
|
||||
responseBodyWithMaxSeverity(ReportService.Severity.WARNING),
|
||||
MtbFileSender.Response(
|
||||
RequestStatus.WARNING,
|
||||
responseBodyWithMaxSeverity(ReportService.Severity.WARNING)
|
||||
)
|
||||
),
|
||||
RequestWithResponse(
|
||||
HttpStatus.BAD_REQUEST,
|
||||
"??",
|
||||
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
|
||||
responseBodyWithMaxSeverity(ReportService.Severity.ERROR),
|
||||
MtbFileSender.Response(RequestStatus.ERROR, responseBodyWithMaxSeverity(ReportService.Severity.ERROR))
|
||||
),
|
||||
RequestWithResponse(
|
||||
HttpStatus.UNPROCESSABLE_ENTITY,
|
||||
errorBody,
|
||||
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
|
||||
responseBodyWithMaxSeverity(ReportService.Severity.FATAL),
|
||||
MtbFileSender.Response(
|
||||
RequestStatus.ERROR,
|
||||
responseBodyWithMaxSeverity(ReportService.Severity.FATAL)
|
||||
)
|
||||
),
|
||||
// Some more errors not mentioned in documentation
|
||||
RequestWithResponse(
|
||||
HttpStatus.NOT_FOUND,
|
||||
"what????",
|
||||
ERROR_RESPONSE_BODY,
|
||||
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
|
||||
),
|
||||
RequestWithResponse(
|
||||
HttpStatus.INTERNAL_SERVER_ERROR,
|
||||
"what????",
|
||||
ERROR_RESPONSE_BODY,
|
||||
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
|
||||
)
|
||||
)
|
||||
@ -251,6 +261,52 @@ class RestMtbFileSenderTest {
|
||||
)
|
||||
)
|
||||
}
|
||||
|
||||
fun responseBodyWithMaxSeverity(severity: ReportService.Severity): String {
|
||||
return when (severity) {
|
||||
ReportService.Severity.INFO -> """
|
||||
{
|
||||
"patient": "PID",
|
||||
"issues": [
|
||||
{ "severity": "info", "message": "Info Message" }
|
||||
]
|
||||
}
|
||||
"""
|
||||
|
||||
ReportService.Severity.WARNING -> """
|
||||
{
|
||||
"patient": "PID",
|
||||
"issues": [
|
||||
{ "severity": "info", "message": "Info Message" },
|
||||
{ "severity": "warning", "message": "Warning Message" }
|
||||
]
|
||||
}
|
||||
"""
|
||||
|
||||
ReportService.Severity.ERROR -> """
|
||||
{
|
||||
"patient": "PID",
|
||||
"issues": [
|
||||
{ "severity": "info", "message": "Info Message" },
|
||||
{ "severity": "warning", "message": "Warning Message" },
|
||||
{ "severity": "error", "message": "Error Message" }
|
||||
]
|
||||
}
|
||||
"""
|
||||
|
||||
ReportService.Severity.FATAL -> """
|
||||
{
|
||||
"patient": "PID",
|
||||
"issues": [
|
||||
{ "severity": "info", "message": "Info Message" },
|
||||
{ "severity": "warning", "message": "Warning Message" },
|
||||
{ "severity": "error", "message": "Error Message" },
|
||||
{ "severity": "fatal", "message": "Fatal Message" }
|
||||
]
|
||||
}
|
||||
"""
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
@ -0,0 +1,411 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
* by the Free Software Foundation, either version 3 of the License, or
|
||||
* (at your option) any later version.
|
||||
*
|
||||
* This program is distributed in the hope that it will be useful,
|
||||
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
* GNU Affero General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Affero General Public License
|
||||
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
*/
|
||||
|
||||
package dev.dnpm.etl.processor.output
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import com.fasterxml.jackson.module.kotlin.KotlinModule
|
||||
import de.ukw.ccc.bwhc.dto.*
|
||||
import de.ukw.ccc.bwhc.dto.Patient
|
||||
import dev.dnpm.etl.processor.CustomMediaType
|
||||
import dev.dnpm.etl.processor.PatientPseudonym
|
||||
import dev.dnpm.etl.processor.RequestId
|
||||
import dev.dnpm.etl.processor.config.AppConfigProperties
|
||||
import dev.dnpm.etl.processor.config.AppConfiguration
|
||||
import dev.dnpm.etl.processor.config.RestTargetProperties
|
||||
import dev.dnpm.etl.processor.monitoring.ReportService
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import dev.pcvolkmer.mv64e.mtb.*
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Nested
|
||||
import org.junit.jupiter.params.ParameterizedTest
|
||||
import org.junit.jupiter.params.provider.MethodSource
|
||||
import org.springframework.http.HttpHeaders
|
||||
import org.springframework.http.HttpMethod
|
||||
import org.springframework.http.HttpStatus
|
||||
import org.springframework.http.MediaType
|
||||
import org.springframework.retry.backoff.NoBackOffPolicy
|
||||
import org.springframework.retry.policy.SimpleRetryPolicy
|
||||
import org.springframework.retry.support.RetryTemplateBuilder
|
||||
import org.springframework.test.web.client.ExpectedCount
|
||||
import org.springframework.test.web.client.MockRestServiceServer
|
||||
import org.springframework.test.web.client.match.MockRestRequestMatchers.*
|
||||
import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus
|
||||
import org.springframework.web.client.RestTemplate
|
||||
import java.time.Instant
|
||||
import java.util.*
|
||||
|
||||
class RestDipMtbFileSenderTest {
|
||||
|
||||
@Nested
|
||||
inner class BwhcV1ContentRequest {
|
||||
|
||||
private lateinit var mockRestServiceServer: MockRestServiceServer
|
||||
|
||||
private lateinit var restMtbFileSender: RestMtbFileSender
|
||||
|
||||
private var reportService = ReportService(ObjectMapper().registerModule(KotlinModule.Builder().build()))
|
||||
|
||||
@BeforeEach
|
||||
fun setup() {
|
||||
val restTemplate = RestTemplate()
|
||||
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false)
|
||||
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
|
||||
|
||||
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
|
||||
|
||||
this.restMtbFileSender =
|
||||
RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#mtbFileRequestWithResponseSource")
|
||||
fun shouldReturnExpectedResponseForMtbFilePost(requestWithResponse: RequestWithResponse) {
|
||||
this.mockRestServiceServer
|
||||
.expect(method(HttpMethod.POST))
|
||||
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient-record"))
|
||||
.andExpect(header(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON_VALUE))
|
||||
.andRespond {
|
||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||
}
|
||||
|
||||
val response = restMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1mtbFile))
|
||||
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
||||
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#mtbFileRequestWithResponseSource")
|
||||
fun shouldRetryOnMtbFileHttpRequestError(requestWithResponse: RequestWithResponse) {
|
||||
val restTemplate = RestTemplate()
|
||||
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false)
|
||||
val retryTemplate = AppConfiguration().retryTemplate(AppConfigProperties("http://localhost:9000"))
|
||||
retryTemplate.setBackOffPolicy(NoBackOffPolicy())
|
||||
|
||||
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
|
||||
this.restMtbFileSender =
|
||||
RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
|
||||
|
||||
val expectedCount = when (requestWithResponse.httpStatus) {
|
||||
// OK - No Retry
|
||||
HttpStatus.OK, HttpStatus.CREATED, HttpStatus.UNPROCESSABLE_ENTITY, HttpStatus.BAD_REQUEST -> ExpectedCount.max(
|
||||
1
|
||||
)
|
||||
// Request failed - Retry max 3 times
|
||||
else -> ExpectedCount.max(3)
|
||||
}
|
||||
|
||||
this.mockRestServiceServer
|
||||
.expect(expectedCount, method(HttpMethod.POST))
|
||||
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient-record"))
|
||||
.andRespond {
|
||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||
}
|
||||
|
||||
val response = restMtbFileSender.send(BwhcV1MtbFileRequest(TEST_REQUEST_ID, bwhcV1mtbFile))
|
||||
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
||||
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Nested
|
||||
inner class DnpmV2ContentRequest {
|
||||
|
||||
private lateinit var mockRestServiceServer: MockRestServiceServer
|
||||
|
||||
private lateinit var restMtbFileSender: RestMtbFileSender
|
||||
|
||||
private var reportService = ReportService(ObjectMapper().registerModule(KotlinModule.Builder().build()))
|
||||
|
||||
@BeforeEach
|
||||
fun setup() {
|
||||
val restTemplate = RestTemplate()
|
||||
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false)
|
||||
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
|
||||
|
||||
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
|
||||
|
||||
this.restMtbFileSender = RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#mtbFileRequestWithResponseSource")
|
||||
fun shouldReturnExpectedResponseForDnpmV2MtbFilePost(requestWithResponse: RequestWithResponse) {
|
||||
this.mockRestServiceServer
|
||||
.expect(method(HttpMethod.POST))
|
||||
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient-record"))
|
||||
.andExpect(header(HttpHeaders.CONTENT_TYPE, CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE))
|
||||
.andRespond {
|
||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||
}
|
||||
|
||||
val response = restMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile()))
|
||||
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
||||
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Nested
|
||||
inner class DeleteRequest {
|
||||
|
||||
private lateinit var mockRestServiceServer: MockRestServiceServer
|
||||
|
||||
private lateinit var restMtbFileSender: RestMtbFileSender
|
||||
|
||||
private var reportService = ReportService(ObjectMapper().registerModule(KotlinModule.Builder().build()))
|
||||
|
||||
@BeforeEach
|
||||
fun setup() {
|
||||
val restTemplate = RestTemplate()
|
||||
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false)
|
||||
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
|
||||
|
||||
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
|
||||
|
||||
this.restMtbFileSender =
|
||||
RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#deleteRequestWithResponseSource")
|
||||
fun shouldReturnExpectedResponseForDelete(requestWithResponse: RequestWithResponse) {
|
||||
this.mockRestServiceServer
|
||||
.expect(method(HttpMethod.DELETE))
|
||||
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient/${TEST_PATIENT_PSEUDONYM.value}"))
|
||||
.andRespond {
|
||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||
}
|
||||
|
||||
val response = restMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
||||
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
||||
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#deleteRequestWithResponseSource")
|
||||
fun shouldRetryOnDeleteHttpRequestError(requestWithResponse: RequestWithResponse) {
|
||||
val restTemplate = RestTemplate()
|
||||
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false)
|
||||
val retryTemplate = AppConfiguration().retryTemplate(AppConfigProperties("http://localhost:9000"))
|
||||
retryTemplate.setBackOffPolicy(NoBackOffPolicy())
|
||||
|
||||
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
|
||||
this.restMtbFileSender =
|
||||
RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
|
||||
|
||||
val expectedCount = when (requestWithResponse.httpStatus) {
|
||||
// OK - No Retry
|
||||
HttpStatus.OK, HttpStatus.CREATED, HttpStatus.UNPROCESSABLE_ENTITY, HttpStatus.BAD_REQUEST -> ExpectedCount.max(
|
||||
1
|
||||
)
|
||||
// Request failed - Retry max 3 times
|
||||
else -> ExpectedCount.max(3)
|
||||
}
|
||||
|
||||
this.mockRestServiceServer
|
||||
.expect(expectedCount, method(HttpMethod.DELETE))
|
||||
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient/${TEST_PATIENT_PSEUDONYM.value}"))
|
||||
.andRespond {
|
||||
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
|
||||
}
|
||||
|
||||
val response = restMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
|
||||
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
|
||||
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
companion object {
|
||||
data class RequestWithResponse(
|
||||
val httpStatus: HttpStatus,
|
||||
val body: String,
|
||||
val response: MtbFileSender.Response
|
||||
)
|
||||
|
||||
val TEST_REQUEST_ID = RequestId("TestId")
|
||||
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID")
|
||||
|
||||
val bwhcV1mtbFile: MtbFile = MtbFile.builder()
|
||||
.withPatient(
|
||||
Patient.builder()
|
||||
.withId("PID")
|
||||
.withBirthDate("2000-08-08")
|
||||
.withGender(Patient.Gender.MALE)
|
||||
.build()
|
||||
)
|
||||
.withConsent(
|
||||
Consent.builder()
|
||||
.withId("1")
|
||||
.withStatus(Consent.Status.ACTIVE)
|
||||
.withPatient("PID")
|
||||
.build()
|
||||
)
|
||||
.withEpisode(
|
||||
Episode.builder()
|
||||
.withId("1")
|
||||
.withPatient("PID")
|
||||
.withPeriod(PeriodStart("2023-08-08"))
|
||||
.build()
|
||||
)
|
||||
.build()
|
||||
|
||||
fun dnpmV2MtbFile(): Mtb {
|
||||
return Mtb().apply {
|
||||
this.patient = dev.pcvolkmer.mv64e.mtb.Patient().apply {
|
||||
this.id = "PID"
|
||||
this.birthDate = Date.from(Instant.now())
|
||||
this.gender = GenderCoding().apply {
|
||||
this.code = GenderCodingCode.MALE
|
||||
}
|
||||
}
|
||||
this.episodesOfCare = listOf(
|
||||
MtbEpisodeOfCare().apply {
|
||||
this.id = "1"
|
||||
this.patient = Reference().apply {
|
||||
this.id = "PID"
|
||||
}
|
||||
this.period = PeriodDate().apply {
|
||||
this.start = Date.from(Instant.now())
|
||||
}
|
||||
}
|
||||
)
|
||||
}
|
||||
}
|
||||
|
||||
private const val ERROR_RESPONSE_BODY = "Sonstiger Fehler bei der Übertragung"
|
||||
|
||||
/**
|
||||
* Synthetic http responses with related request status
|
||||
* Also see: https://ibmi-intra.cs.uni-tuebingen.de/display/ZPM/bwHC+REST+API
|
||||
*/
|
||||
@JvmStatic
|
||||
fun mtbFileRequestWithResponseSource(): Set<RequestWithResponse> {
|
||||
return setOf(
|
||||
RequestWithResponse(
|
||||
HttpStatus.OK,
|
||||
responseBodyWithMaxSeverity(ReportService.Severity.INFO),
|
||||
MtbFileSender.Response(
|
||||
RequestStatus.SUCCESS,
|
||||
responseBodyWithMaxSeverity(ReportService.Severity.INFO)
|
||||
)
|
||||
),
|
||||
RequestWithResponse(
|
||||
HttpStatus.CREATED,
|
||||
responseBodyWithMaxSeverity(ReportService.Severity.WARNING),
|
||||
MtbFileSender.Response(RequestStatus.WARNING, responseBodyWithMaxSeverity(ReportService.Severity.WARNING))
|
||||
),
|
||||
RequestWithResponse(
|
||||
HttpStatus.BAD_REQUEST,
|
||||
responseBodyWithMaxSeverity(ReportService.Severity.ERROR),
|
||||
MtbFileSender.Response(RequestStatus.ERROR, responseBodyWithMaxSeverity(ReportService.Severity.ERROR))
|
||||
),
|
||||
RequestWithResponse(
|
||||
HttpStatus.UNPROCESSABLE_ENTITY,
|
||||
responseBodyWithMaxSeverity(ReportService.Severity.ERROR),
|
||||
MtbFileSender.Response(RequestStatus.ERROR, responseBodyWithMaxSeverity(ReportService.Severity.ERROR))
|
||||
),
|
||||
// Some more errors not mentioned in documentation
|
||||
RequestWithResponse(
|
||||
HttpStatus.NOT_FOUND,
|
||||
ERROR_RESPONSE_BODY,
|
||||
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
|
||||
),
|
||||
RequestWithResponse(
|
||||
HttpStatus.INTERNAL_SERVER_ERROR,
|
||||
ERROR_RESPONSE_BODY,
|
||||
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
|
||||
)
|
||||
)
|
||||
}
|
||||
|
||||
/**
|
||||
* Synthetic http responses with related request status
|
||||
* Also see: https://ibmi-intra.cs.uni-tuebingen.de/display/ZPM/bwHC+REST+API
|
||||
*/
|
||||
@JvmStatic
|
||||
fun deleteRequestWithResponseSource(): Set<RequestWithResponse> {
|
||||
return setOf(
|
||||
RequestWithResponse(HttpStatus.OK, "", MtbFileSender.Response(RequestStatus.SUCCESS)),
|
||||
// Some more errors not mentioned in documentation
|
||||
RequestWithResponse(
|
||||
HttpStatus.NOT_FOUND,
|
||||
"what????",
|
||||
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
|
||||
),
|
||||
RequestWithResponse(
|
||||
HttpStatus.INTERNAL_SERVER_ERROR,
|
||||
"what????",
|
||||
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
|
||||
)
|
||||
)
|
||||
}
|
||||
|
||||
fun responseBodyWithMaxSeverity(severity: ReportService.Severity): String {
|
||||
return when (severity) {
|
||||
ReportService.Severity.INFO -> """
|
||||
{
|
||||
"patient": "PID",
|
||||
"issues": [
|
||||
{ "severity": "info", "message": "Info Message" }
|
||||
]
|
||||
}
|
||||
"""
|
||||
|
||||
ReportService.Severity.WARNING -> """
|
||||
{
|
||||
"patient": "PID",
|
||||
"issues": [
|
||||
{ "severity": "info", "message": "Info Message" },
|
||||
{ "severity": "warning", "message": "Warning Message" }
|
||||
]
|
||||
}
|
||||
"""
|
||||
|
||||
ReportService.Severity.ERROR -> """
|
||||
{
|
||||
"patient": "PID",
|
||||
"issues": [
|
||||
{ "severity": "info", "message": "Info Message" },
|
||||
{ "severity": "warning", "message": "Warning Message" },
|
||||
{ "severity": "error", "message": "Error Message" }
|
||||
]
|
||||
}
|
||||
"""
|
||||
|
||||
ReportService.Severity.FATAL -> """
|
||||
{
|
||||
"patient": "PID",
|
||||
"issues": [
|
||||
{ "severity": "info", "message": "Info Message" },
|
||||
{ "severity": "warning", "message": "Warning Message" },
|
||||
{ "severity": "error", "message": "Error Message" },
|
||||
{ "severity": "fatal", "message": "Fatal Message" }
|
||||
]
|
||||
}
|
||||
"""
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
}
|
@ -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) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
@ -20,45 +20,261 @@
|
||||
package dev.dnpm.etl.processor.pseudonym
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import de.ukw.ccc.bwhc.dto.*
|
||||
import de.ukw.ccc.bwhc.dto.Patient
|
||||
import dev.dnpm.etl.processor.config.JacksonConfig
|
||||
import dev.pcvolkmer.mv64e.mtb.*
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.junit.jupiter.api.Nested
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.assertThrows
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.mockito.ArgumentMatchers
|
||||
import org.mockito.Mock
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.mockito.kotlin.anyValueClass
|
||||
import org.mockito.kotlin.doAnswer
|
||||
import org.mockito.kotlin.whenever
|
||||
import org.springframework.core.io.ClassPathResource
|
||||
|
||||
const val FAKE_MTB_FILE_PATH = "fake_MTBFile.json"
|
||||
const val CLEAN_PATIENT_ID = "5dad2f0b-49c6-47d8-a952-7b9e9e0f7549"
|
||||
import java.time.Instant
|
||||
import java.util.*
|
||||
|
||||
@ExtendWith(MockitoExtension::class)
|
||||
class ExtensionsTest {
|
||||
|
||||
private fun fakeMtbFile(): MtbFile {
|
||||
val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
|
||||
return ObjectMapper().readValue(mtbFile, MtbFile::class.java)
|
||||
fun getObjectMapper() : ObjectMapper {
|
||||
return JacksonConfig().objectMapper()
|
||||
}
|
||||
|
||||
private fun MtbFile.serialized(): String {
|
||||
return ObjectMapper().writeValueAsString(this)
|
||||
@Nested
|
||||
inner class UsingBwhcDatamodel {
|
||||
|
||||
val FAKE_MTB_FILE_PATH = "fake_MTBFile.json"
|
||||
val CLEAN_PATIENT_ID = "5dad2f0b-49c6-47d8-a952-7b9e9e0f7549"
|
||||
|
||||
|
||||
private fun fakeMtbFile(): MtbFile {
|
||||
val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
|
||||
return getObjectMapper().readValue(mtbFile, MtbFile::class.java)
|
||||
}
|
||||
|
||||
private fun MtbFile.serialized(): String {
|
||||
return getObjectMapper().writeValueAsString(this)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldNotContainCleanPatientId(@Mock pseudonymizeService: PseudonymizeService) {
|
||||
doAnswer {
|
||||
it.arguments[0]
|
||||
"PSEUDO-ID"
|
||||
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||
|
||||
val mtbFile = fakeMtbFile()
|
||||
|
||||
mtbFile.pseudonymizeWith(pseudonymizeService)
|
||||
|
||||
assertThat(mtbFile.patient.id).isEqualTo("PSEUDO-ID")
|
||||
assertThat(mtbFile.serialized()).doesNotContain(CLEAN_PATIENT_ID)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldNotContainAnyUuidAfterRehashingOfIds(@Mock pseudonymizeService: PseudonymizeService) {
|
||||
doAnswer {
|
||||
it.arguments[0]
|
||||
"PSEUDO-ID"
|
||||
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
"TESTDOMAIN"
|
||||
}.whenever(pseudonymizeService).prefix()
|
||||
|
||||
val mtbFile = fakeMtbFile()
|
||||
|
||||
mtbFile.pseudonymizeWith(pseudonymizeService)
|
||||
mtbFile.anonymizeContentWith(pseudonymizeService)
|
||||
|
||||
val pattern = "\"[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}\"".toRegex().toPattern()
|
||||
val matcher = pattern.matcher(mtbFile.serialized())
|
||||
|
||||
assertThrows<IllegalStateException> {
|
||||
matcher.find()
|
||||
matcher.group()
|
||||
}.also {
|
||||
assertThat(it.message).isEqualTo("No match found")
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldRehashIdsWithPrefix(@Mock pseudonymizeService: PseudonymizeService) {
|
||||
doAnswer {
|
||||
it.arguments[0]
|
||||
"PSEUDO-ID"
|
||||
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
"TESTDOMAIN"
|
||||
}.whenever(pseudonymizeService).prefix()
|
||||
|
||||
val mtbFile = MtbFile.builder()
|
||||
.withPatient(
|
||||
Patient.builder()
|
||||
.withId("1")
|
||||
.withBirthDate("2000-08-08")
|
||||
.withGender(Patient.Gender.MALE)
|
||||
.build()
|
||||
)
|
||||
.withConsent(
|
||||
Consent.builder()
|
||||
.withId("1")
|
||||
.withStatus(Consent.Status.ACTIVE)
|
||||
.withPatient("123")
|
||||
.build()
|
||||
)
|
||||
.withEpisode(
|
||||
Episode.builder()
|
||||
.withId("1")
|
||||
.withPatient("1")
|
||||
.withPeriod(PeriodStart("2023-08-08"))
|
||||
.build()
|
||||
)
|
||||
.build()
|
||||
|
||||
mtbFile.pseudonymizeWith(pseudonymizeService)
|
||||
mtbFile.anonymizeContentWith(pseudonymizeService)
|
||||
|
||||
|
||||
assertThat(mtbFile.episode.id)
|
||||
// TESTDOMAIN<sha256(TESTDOMAIN-1)[0-41]>
|
||||
.isEqualTo("TESTDOMAIN44e20a53bbbf9f3ae39626d05df7014dcd77d6098")
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldNotThrowExceptionOnNullValues(@Mock pseudonymizeService: PseudonymizeService) {
|
||||
doAnswer {
|
||||
it.arguments[0]
|
||||
"PSEUDO-ID"
|
||||
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
"TESTDOMAIN"
|
||||
}.whenever(pseudonymizeService).prefix()
|
||||
|
||||
val mtbFile = MtbFile.builder()
|
||||
.withPatient(
|
||||
Patient.builder()
|
||||
.withId("1")
|
||||
.withBirthDate("2000-08-08")
|
||||
.withGender(Patient.Gender.MALE)
|
||||
.build()
|
||||
)
|
||||
.withConsent(
|
||||
Consent.builder()
|
||||
.withId("1")
|
||||
.withStatus(Consent.Status.ACTIVE)
|
||||
.withPatient("123")
|
||||
.build()
|
||||
)
|
||||
.withEpisode(
|
||||
Episode.builder()
|
||||
.withId("1")
|
||||
.withPatient("1")
|
||||
.withPeriod(PeriodStart("2023-08-08"))
|
||||
.build()
|
||||
)
|
||||
.withClaims(null)
|
||||
.withDiagnoses(null)
|
||||
.withCarePlans(null)
|
||||
.withClaimResponses(null)
|
||||
.withEcogStatus(null)
|
||||
.withFamilyMemberDiagnoses(null)
|
||||
.withGeneticCounsellingRequests(null)
|
||||
.withHistologyReevaluationRequests(null)
|
||||
.withHistologyReports(null)
|
||||
.withLastGuidelineTherapies(null)
|
||||
.withMolecularPathologyFindings(null)
|
||||
.withMolecularTherapies(null)
|
||||
.withNgsReports(null)
|
||||
.withPreviousGuidelineTherapies(null)
|
||||
.withRebiopsyRequests(null)
|
||||
.withRecommendations(null)
|
||||
.withResponses(null)
|
||||
.withStudyInclusionRequests(null)
|
||||
.withSpecimens(null)
|
||||
.build()
|
||||
|
||||
mtbFile.pseudonymizeWith(pseudonymizeService)
|
||||
mtbFile.anonymizeContentWith(pseudonymizeService)
|
||||
|
||||
assertThat(mtbFile.episode.id).isNotNull()
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldNotContainCleanPatientId(@Mock pseudonymizeService: PseudonymizeService) {
|
||||
doAnswer {
|
||||
it.arguments[0]
|
||||
"PSEUDO-ID"
|
||||
}.whenever(pseudonymizeService).patientPseudonym(ArgumentMatchers.anyString())
|
||||
@Nested
|
||||
inner class UsingDnpmV2Datamodel {
|
||||
|
||||
val mtbFile = fakeMtbFile()
|
||||
val FAKE_MTB_FILE_PATH = "mv64e-mtb-fake-patient.json"
|
||||
val CLEAN_PATIENT_ID = "e14bf9b6-7982-4933-a648-cfdea6484f1c"
|
||||
|
||||
mtbFile.pseudonymizeWith(pseudonymizeService)
|
||||
private fun fakeMtbFile(): Mtb {
|
||||
val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
|
||||
return getObjectMapper().readValue(mtbFile, Mtb::class.java)
|
||||
}
|
||||
|
||||
assertThat(mtbFile.patient.id).isEqualTo("PSEUDO-ID")
|
||||
assertThat(mtbFile.serialized()).doesNotContain(CLEAN_PATIENT_ID)
|
||||
private fun Mtb.serialized(): String {
|
||||
return getObjectMapper().writeValueAsString(this)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldNotContainCleanPatientId(@Mock pseudonymizeService: PseudonymizeService) {
|
||||
doAnswer {
|
||||
it.arguments[0]
|
||||
"PSEUDO-ID"
|
||||
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||
|
||||
val mtbFile = fakeMtbFile()
|
||||
|
||||
mtbFile.pseudonymizeWith(pseudonymizeService)
|
||||
|
||||
assertThat(mtbFile.patient.id).isEqualTo("PSEUDO-ID")
|
||||
assertThat(mtbFile.serialized()).doesNotContain(CLEAN_PATIENT_ID)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldNotThrowExceptionOnNullValues(@Mock pseudonymizeService: PseudonymizeService) {
|
||||
doAnswer {
|
||||
it.arguments[0]
|
||||
"PSEUDO-ID"
|
||||
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
"TESTDOMAIN"
|
||||
}.whenever(pseudonymizeService).prefix()
|
||||
|
||||
val mtbFile = Mtb().apply {
|
||||
this.patient = dev.pcvolkmer.mv64e.mtb.Patient().apply {
|
||||
this.id = "PID"
|
||||
this.birthDate = Date.from(Instant.now())
|
||||
this.gender = GenderCoding().apply {
|
||||
this.code = GenderCodingCode.MALE
|
||||
}
|
||||
}
|
||||
this.episodesOfCare = listOf(
|
||||
MtbEpisodeOfCare().apply {
|
||||
this.id = "1"
|
||||
this.patient = Reference().apply {
|
||||
this.id = "PID"
|
||||
}
|
||||
this.period = PeriodDate().apply {
|
||||
this.start = Date.from(Instant.now())
|
||||
}
|
||||
}
|
||||
)
|
||||
}
|
||||
|
||||
mtbFile.pseudonymizeWith(pseudonymizeService)
|
||||
mtbFile.anonymizeContentWith(pseudonymizeService)
|
||||
|
||||
assertThat(mtbFile.episodesOfCare).hasSize(1)
|
||||
assertThat(mtbFile.episodesOfCare.map { it.id }).isNotNull
|
||||
}
|
||||
}
|
||||
|
||||
}
|
@ -17,13 +17,12 @@
|
||||
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
*/
|
||||
|
||||
package dev.dnpm.etl.processor.services
|
||||
package dev.dnpm.etl.processor.security
|
||||
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.mockito.ArgumentCaptor
|
||||
import org.mockito.ArgumentMatchers.anyLong
|
||||
import org.mockito.ArgumentMatchers.anyString
|
||||
import org.mockito.Mock
|
||||
@ -96,11 +95,11 @@ class TokenServiceTest {
|
||||
|
||||
val actual = this.tokenService.addToken("Test Token")
|
||||
|
||||
val captor = ArgumentCaptor.forClass(Token::class.java)
|
||||
val captor = argumentCaptor<Token>()
|
||||
verify(tokenRepository, times(1)).save(captor.capture())
|
||||
|
||||
assertThat(actual).satisfies(Consumer { assertThat(it.isSuccess).isTrue() })
|
||||
assertThat(captor.value).satisfies(
|
||||
assertThat(captor.firstValue).satisfies(
|
||||
Consumer { assertThat(it.name).isEqualTo("Test Token") },
|
||||
Consumer { assertThat(it.username).isEqualTo("testtoken") },
|
||||
Consumer { assertThat(it.password).isEqualTo("{test}verysecret") }
|
||||
@ -116,13 +115,13 @@ class TokenServiceTest {
|
||||
|
||||
this.tokenService.deleteToken(42)
|
||||
|
||||
val stringCaptor = ArgumentCaptor.forClass(String::class.java)
|
||||
val stringCaptor = argumentCaptor<String>()
|
||||
verify(userDetailsManager, times(1)).deleteUser(stringCaptor.capture())
|
||||
assertThat(stringCaptor.value).isEqualTo("testtoken")
|
||||
assertThat(stringCaptor.firstValue).isEqualTo("testtoken")
|
||||
|
||||
val tokenCaptor = ArgumentCaptor.forClass(Token::class.java)
|
||||
val tokenCaptor = argumentCaptor<Token>()
|
||||
verify(tokenRepository, times(1)).delete(tokenCaptor.capture())
|
||||
assertThat(tokenCaptor.value.id).isEqualTo(42)
|
||||
assertThat(tokenCaptor.firstValue.id).isEqualTo(42)
|
||||
}
|
||||
|
||||
@Test
|
@ -0,0 +1,202 @@
|
||||
/*
|
||||
* This file is part of ETL-Processor
|
||||
*
|
||||
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
* by the Free Software Foundation, either version 3 of the License, or
|
||||
* (at your option) any later version.
|
||||
*
|
||||
* This program is distributed in the hope that it will be useful,
|
||||
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
* GNU Affero General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU Affero General Public License
|
||||
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
*/
|
||||
|
||||
package dev.dnpm.etl.processor.security
|
||||
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Nested
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.mockito.Mock
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.mockito.kotlin.*
|
||||
import org.springframework.security.core.session.SessionInformation
|
||||
import org.springframework.security.core.session.SessionRegistry
|
||||
import org.springframework.security.oauth2.core.oidc.OidcIdToken
|
||||
import org.springframework.security.oauth2.core.oidc.user.DefaultOidcUser
|
||||
import org.springframework.security.oauth2.core.oidc.user.OidcUser
|
||||
import java.time.Instant
|
||||
import java.util.*
|
||||
|
||||
@ExtendWith(MockitoExtension::class)
|
||||
class UserRoleServiceTest {
|
||||
|
||||
private lateinit var userRoleRepository: UserRoleRepository
|
||||
private lateinit var sessionRegistry: SessionRegistry
|
||||
|
||||
private lateinit var userRoleService: UserRoleService
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Mock userRoleRepository: UserRoleRepository,
|
||||
@Mock sessionRegistry: SessionRegistry
|
||||
) {
|
||||
this.userRoleRepository = userRoleRepository
|
||||
this.sessionRegistry = sessionRegistry
|
||||
|
||||
this.userRoleService = UserRoleService(userRoleRepository, sessionRegistry)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldDelegateFindAllToRepository() {
|
||||
userRoleService.findAll()
|
||||
|
||||
verify(userRoleRepository, times(1)).findAll()
|
||||
}
|
||||
|
||||
@Nested
|
||||
inner class WithExistingUserRole {
|
||||
|
||||
@BeforeEach
|
||||
fun setup() {
|
||||
doAnswer { invocation ->
|
||||
Optional.of(
|
||||
UserRole(invocation.getArgument(0), "patrick.tester", Role.USER)
|
||||
)
|
||||
}.whenever(userRoleRepository).findById(any<Long>())
|
||||
|
||||
doAnswer { _ ->
|
||||
listOf(
|
||||
dummyPrincipal()
|
||||
)
|
||||
}.whenever(sessionRegistry).allPrincipals
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldUpdateUserRole() {
|
||||
userRoleService.updateUserRole(1, Role.ADMIN)
|
||||
|
||||
val userRoleCaptor = argumentCaptor<UserRole>()
|
||||
verify(userRoleRepository, times(1)).save(userRoleCaptor.capture())
|
||||
|
||||
assertThat(userRoleCaptor.firstValue.id).isEqualTo(1L)
|
||||
assertThat(userRoleCaptor.firstValue.role).isEqualTo(Role.ADMIN)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldExpireSessionOnUpdate() {
|
||||
val dummySessions = dummySessions()
|
||||
whenever(sessionRegistry.getAllSessions(any(), any<Boolean>())).thenReturn(
|
||||
dummySessions
|
||||
)
|
||||
|
||||
assertThat(dummySessions.filter { it.isExpired }).hasSize(0)
|
||||
|
||||
userRoleService.updateUserRole(1, Role.ADMIN)
|
||||
|
||||
verify(sessionRegistry, times(1)).getAllSessions(any<OidcUser>(), any<Boolean>())
|
||||
|
||||
assertThat(dummySessions.filter { it.isExpired }).hasSize(2)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldDeleteUserRole() {
|
||||
userRoleService.deleteUserRole(1)
|
||||
|
||||
val userRoleCaptor = argumentCaptor<UserRole>()
|
||||
verify(userRoleRepository, times(1)).delete(userRoleCaptor.capture())
|
||||
|
||||
assertThat(userRoleCaptor.firstValue.id).isEqualTo(1L)
|
||||
assertThat(userRoleCaptor.firstValue.role).isEqualTo(Role.USER)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldExpireSessionOnDelete() {
|
||||
val dummySessions = dummySessions()
|
||||
whenever(sessionRegistry.getAllSessions(any(), any<Boolean>())).thenReturn(
|
||||
dummySessions
|
||||
)
|
||||
|
||||
assertThat(dummySessions.filter { it.isExpired }).hasSize(0)
|
||||
|
||||
userRoleService.deleteUserRole(1)
|
||||
|
||||
verify(sessionRegistry, times(1)).getAllSessions(any<OidcUser>(), any<Boolean>())
|
||||
|
||||
assertThat(dummySessions.filter { it.isExpired }).hasSize(2)
|
||||
}
|
||||
}
|
||||
|
||||
@Nested
|
||||
inner class WithoutExistingUserRole {
|
||||
|
||||
@BeforeEach
|
||||
fun setup() {
|
||||
doAnswer { _ ->
|
||||
Optional.empty<UserRole>()
|
||||
}.whenever(userRoleRepository).findById(any<Long>())
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldNotUpdateUserRole() {
|
||||
userRoleService.updateUserRole(1, Role.ADMIN)
|
||||
|
||||
verify(userRoleRepository, never()).save(any<UserRole>())
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldNotExpireSessionOnUpdate() {
|
||||
userRoleService.updateUserRole(1, Role.ADMIN)
|
||||
|
||||
verify(sessionRegistry, never()).getAllSessions(any<OidcUser>(), any<Boolean>())
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldNotDeleteUserRole() {
|
||||
userRoleService.deleteUserRole(1)
|
||||
|
||||
verify(userRoleRepository, never()).delete(any<UserRole>())
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldNotExpireSessionOnDelete() {
|
||||
userRoleService.deleteUserRole(1)
|
||||
|
||||
verify(sessionRegistry, never()).getAllSessions(any<OidcUser>(), any<Boolean>())
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
companion object {
|
||||
private fun dummyPrincipal() = DefaultOidcUser(
|
||||
listOf(),
|
||||
OidcIdToken(
|
||||
"anytokenvalue",
|
||||
Instant.now(),
|
||||
Instant.now().plusSeconds(10),
|
||||
mapOf("sub" to "testsub", "preferred_username" to "patrick.tester")
|
||||
)
|
||||
)
|
||||
|
||||
private fun dummySessions() = listOf(
|
||||
SessionInformation(
|
||||
dummyPrincipal(),
|
||||
"SESSIONID1",
|
||||
Date.from(Instant.now()),
|
||||
),
|
||||
SessionInformation(
|
||||
dummyPrincipal(),
|
||||
"SESSIONID2",
|
||||
Date.from(Instant.now()),
|
||||
)
|
||||
)
|
||||
}
|
||||
}
|
@ -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) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||
*
|
||||
* This program is free software: you can redistribute it and/or modify
|
||||
* it under the terms of the GNU Affero General Public License as published
|
||||
@ -22,9 +22,14 @@ package dev.dnpm.etl.processor.services
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import com.fasterxml.jackson.module.kotlin.KotlinModule
|
||||
import dev.dnpm.etl.processor.monitoring.ReportService
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import dev.dnpm.etl.processor.monitoring.asRequestStatus
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.params.ParameterizedTest
|
||||
import org.junit.jupiter.params.provider.Arguments
|
||||
import org.junit.jupiter.params.provider.MethodSource
|
||||
|
||||
class ReportServiceTest {
|
||||
|
||||
@ -43,20 +48,32 @@ class ReportServiceTest {
|
||||
"issues": [
|
||||
{ "severity": "info", "message": "Info Message" },
|
||||
{ "severity": "warning", "message": "Warning Message" },
|
||||
{ "severity": "error", "message": "Error Message" }
|
||||
{ "severity": "error", "message": "Error Message" },
|
||||
{ "severity": "fatal", "message": "Fatal Message" }
|
||||
]
|
||||
}
|
||||
""".trimIndent()
|
||||
|
||||
val actual = this.reportService.deserialize(json)
|
||||
|
||||
assertThat(actual).hasSize(3)
|
||||
assertThat(actual[0].severity).isEqualTo(ReportService.Severity.ERROR)
|
||||
assertThat(actual[0].message).isEqualTo("Error Message")
|
||||
assertThat(actual[1].severity).isEqualTo(ReportService.Severity.WARNING)
|
||||
assertThat(actual[1].message).isEqualTo("Warning Message")
|
||||
assertThat(actual[2].severity).isEqualTo(ReportService.Severity.INFO)
|
||||
assertThat(actual[2].message).isEqualTo("Info Message")
|
||||
assertThat(actual).hasSize(4)
|
||||
assertThat(actual[0].severity).isEqualTo(ReportService.Severity.FATAL)
|
||||
assertThat(actual[0].message).isEqualTo("Fatal Message")
|
||||
assertThat(actual[1].severity).isEqualTo(ReportService.Severity.ERROR)
|
||||
assertThat(actual[1].message).isEqualTo("Error Message")
|
||||
assertThat(actual[2].severity).isEqualTo(ReportService.Severity.WARNING)
|
||||
assertThat(actual[2].message).isEqualTo("Warning Message")
|
||||
assertThat(actual[3].severity).isEqualTo(ReportService.Severity.INFO)
|
||||
assertThat(actual[3].message).isEqualTo("Info Message")
|
||||
|
||||
assertThat(actual.asRequestStatus()).isEqualTo(RequestStatus.ERROR)
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@MethodSource("testData")
|
||||
fun shouldParseDataQualityReport(json: String, requestStatus: RequestStatus) {
|
||||
val actual = this.reportService.deserialize(json)
|
||||
assertThat(actual.asRequestStatus()).isEqualTo(requestStatus)
|
||||
}
|
||||
|
||||
@Test
|
||||
@ -70,4 +87,75 @@ class ReportServiceTest {
|
||||
assertThat(actual[0].message).isEqualTo("Not parsable data quality report '$invalidResponse'")
|
||||
}
|
||||
|
||||
companion object {
|
||||
|
||||
@JvmStatic
|
||||
fun testData(): Set<Arguments> {
|
||||
return setOf(
|
||||
Arguments.of(
|
||||
"""
|
||||
{
|
||||
"patient": "4711",
|
||||
"issues": [
|
||||
{ "severity": "info", "message": "Info Message" },
|
||||
{ "severity": "warning", "message": "Warning Message" },
|
||||
{ "severity": "error", "message": "Error Message" },
|
||||
{ "severity": "fatal", "message": "Fatal Message" }
|
||||
]
|
||||
}
|
||||
""".trimIndent(),
|
||||
RequestStatus.ERROR
|
||||
),
|
||||
Arguments.of(
|
||||
"""
|
||||
{
|
||||
"patient": "4711",
|
||||
"issues": [
|
||||
{ "severity": "info", "message": "Info Message" },
|
||||
{ "severity": "warning", "message": "Warning Message" },
|
||||
{ "severity": "error", "message": "Error Message" }
|
||||
]
|
||||
}
|
||||
""".trimIndent(),
|
||||
RequestStatus.ERROR
|
||||
),
|
||||
Arguments.of(
|
||||
"""
|
||||
{
|
||||
"patient": "4711",
|
||||
"issues": [
|
||||
{ "severity": "error", "message": "Error Message" }
|
||||
{ "severity": "info", "message": "Info Message" }
|
||||
]
|
||||
}
|
||||
""".trimIndent(),
|
||||
RequestStatus.ERROR
|
||||
),
|
||||
Arguments.of(
|
||||
"""
|
||||
{
|
||||
"patient": "4711",
|
||||
"issues": [
|
||||
{ "severity": "info", "message": "Info Message" },
|
||||
{ "severity": "warning", "message": "Warning Message" }
|
||||
]
|
||||
}
|
||||
""".trimIndent(),
|
||||
RequestStatus.WARNING
|
||||
),
|
||||
Arguments.of(
|
||||
"""
|
||||
{
|
||||
"patient": "4711",
|
||||
"issues": [
|
||||
{ "severity": "info", "message": "Info Message" }
|
||||
]
|
||||
}
|
||||
""".trimIndent(),
|
||||
RequestStatus.SUCCESS
|
||||
)
|
||||
)
|
||||
}
|
||||
}
|
||||
|
||||
}
|
@ -21,27 +21,34 @@ package dev.dnpm.etl.processor.services
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import de.ukw.ccc.bwhc.dto.*
|
||||
import dev.dnpm.etl.processor.Fingerprint
|
||||
import dev.dnpm.etl.processor.PatientId
|
||||
import dev.dnpm.etl.processor.PatientPseudonym
|
||||
import dev.dnpm.etl.processor.config.AppConfigProperties
|
||||
import dev.dnpm.etl.processor.consent.GicsConsentService
|
||||
import dev.dnpm.etl.processor.consent.TtpConsentStatus
|
||||
import dev.dnpm.etl.processor.monitoring.Request
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import dev.dnpm.etl.processor.monitoring.RequestType
|
||||
import dev.dnpm.etl.processor.output.BwhcV1MtbFileRequest
|
||||
import dev.dnpm.etl.processor.output.DeleteRequest
|
||||
import dev.dnpm.etl.processor.output.MtbFileSender
|
||||
import dev.dnpm.etl.processor.output.RestMtbFileSender
|
||||
import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
|
||||
import dev.dnpm.etl.processor.randomRequestId
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.mockito.ArgumentMatchers.anyString
|
||||
import org.mockito.Mock
|
||||
import org.mockito.Mockito.*
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.mockito.kotlin.any
|
||||
import org.mockito.kotlin.anyValueClass
|
||||
import org.mockito.kotlin.argumentCaptor
|
||||
import org.mockito.kotlin.whenever
|
||||
import org.springframework.context.ApplicationEventPublisher
|
||||
import java.time.Instant
|
||||
import java.util.*
|
||||
|
||||
|
||||
@ExtendWith(MockitoExtension::class)
|
||||
@ -53,7 +60,7 @@ class RequestProcessorTest {
|
||||
private lateinit var requestService: RequestService
|
||||
private lateinit var applicationEventPublisher: ApplicationEventPublisher
|
||||
private lateinit var appConfigProperties: AppConfigProperties
|
||||
|
||||
private lateinit var gicsConsentService : GicsConsentService
|
||||
private lateinit var requestProcessor: RequestProcessor
|
||||
|
||||
@BeforeEach
|
||||
@ -62,7 +69,8 @@ class RequestProcessorTest {
|
||||
@Mock transformationService: TransformationService,
|
||||
@Mock sender: RestMtbFileSender,
|
||||
@Mock requestService: RequestService,
|
||||
@Mock applicationEventPublisher: ApplicationEventPublisher
|
||||
@Mock applicationEventPublisher: ApplicationEventPublisher,
|
||||
@Mock gicsConsentService: GicsConsentService
|
||||
) {
|
||||
this.pseudonymizeService = pseudonymizeService
|
||||
this.transformationService = transformationService
|
||||
@ -70,6 +78,7 @@ class RequestProcessorTest {
|
||||
this.requestService = requestService
|
||||
this.applicationEventPublisher = applicationEventPublisher
|
||||
this.appConfigProperties = AppConfigProperties(null)
|
||||
this.gicsConsentService = gicsConsentService
|
||||
|
||||
val objectMapper = ObjectMapper()
|
||||
|
||||
@ -80,7 +89,8 @@ class RequestProcessorTest {
|
||||
requestService,
|
||||
objectMapper,
|
||||
applicationEventPublisher,
|
||||
appConfigProperties
|
||||
appConfigProperties,
|
||||
gicsConsentService
|
||||
)
|
||||
}
|
||||
|
||||
@ -88,28 +98,28 @@ class RequestProcessorTest {
|
||||
fun testShouldSendMtbFileDuplicationAndSaveUnknownRequestStatusAtFirst() {
|
||||
doAnswer {
|
||||
Request(
|
||||
id = 1L,
|
||||
uuid = UUID.randomUUID().toString(),
|
||||
patientId = "TEST_12345678901",
|
||||
pid = "P1",
|
||||
fingerprint = "xrysxpozhbs2lnrjgf3yq4fzj33kxr7xr5c2cbuskmelfdmckl3a",
|
||||
type = RequestType.MTB_FILE,
|
||||
status = RequestStatus.SUCCESS,
|
||||
processedAt = Instant.parse("2023-08-08T02:00:00Z")
|
||||
1L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678901"),
|
||||
PatientId("P1"),
|
||||
Fingerprint("zdlzv5s5ydmd4ktw2v5piohegc4jcyrm6j66bq6tv2uxuerndmga"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.SUCCESS,
|
||||
Instant.parse("2023-08-08T02:00:00Z")
|
||||
)
|
||||
}.`when`(requestService).lastMtbFileRequestForPatientPseudonym(anyString())
|
||||
}.whenever(requestService).lastMtbFileRequestForPatientPseudonym(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
false
|
||||
}.`when`(requestService).isLastRequestWithKnownStatusDeletion(anyString())
|
||||
}.whenever(requestService).isLastRequestWithKnownStatusDeletion(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
it.arguments[0] as String
|
||||
}.`when`(pseudonymizeService).patientPseudonym(any())
|
||||
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
it.arguments[0]
|
||||
}.whenever(transformationService).transform(any())
|
||||
}.whenever(transformationService).transform(any<MtbFile>())
|
||||
|
||||
val mtbFile = MtbFile.builder()
|
||||
.withPatient(
|
||||
@ -147,28 +157,28 @@ class RequestProcessorTest {
|
||||
fun testShouldDetectMtbFileDuplicationAndSendDuplicationEvent() {
|
||||
doAnswer {
|
||||
Request(
|
||||
id = 1L,
|
||||
uuid = UUID.randomUUID().toString(),
|
||||
patientId = "TEST_12345678901",
|
||||
pid = "P1",
|
||||
fingerprint = "xrysxpozhbs2lnrjgf3yq4fzj33kxr7xr5c2cbuskmelfdmckl3a",
|
||||
type = RequestType.MTB_FILE,
|
||||
status = RequestStatus.SUCCESS,
|
||||
processedAt = Instant.parse("2023-08-08T02:00:00Z")
|
||||
1L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678901"),
|
||||
PatientId("P1"),
|
||||
Fingerprint("zdlzv5s5ydmd4ktw2v5piohegc4jcyrm6j66bq6tv2uxuerndmga"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.SUCCESS,
|
||||
Instant.parse("2023-08-08T02:00:00Z")
|
||||
)
|
||||
}.`when`(requestService).lastMtbFileRequestForPatientPseudonym(anyString())
|
||||
}.whenever(requestService).lastMtbFileRequestForPatientPseudonym(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
false
|
||||
}.`when`(requestService).isLastRequestWithKnownStatusDeletion(anyString())
|
||||
}.whenever(requestService).isLastRequestWithKnownStatusDeletion(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
it.arguments[0] as String
|
||||
}.`when`(pseudonymizeService).patientPseudonym(any())
|
||||
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
it.arguments[0]
|
||||
}.whenever(transformationService).transform(any())
|
||||
}.whenever(transformationService).transform(any<MtbFile>())
|
||||
|
||||
val mtbFile = MtbFile.builder()
|
||||
.withPatient(
|
||||
@ -206,32 +216,32 @@ class RequestProcessorTest {
|
||||
fun testShouldSendMtbFileAndSendSuccessEvent() {
|
||||
doAnswer {
|
||||
Request(
|
||||
id = 1L,
|
||||
uuid = UUID.randomUUID().toString(),
|
||||
patientId = "TEST_12345678901",
|
||||
pid = "P1",
|
||||
fingerprint = "different",
|
||||
type = RequestType.MTB_FILE,
|
||||
status = RequestStatus.SUCCESS,
|
||||
processedAt = Instant.parse("2023-08-08T02:00:00Z")
|
||||
1L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678901"),
|
||||
PatientId("P1"),
|
||||
Fingerprint("different"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.SUCCESS,
|
||||
Instant.parse("2023-08-08T02:00:00Z")
|
||||
)
|
||||
}.`when`(requestService).lastMtbFileRequestForPatientPseudonym(anyString())
|
||||
}.whenever(requestService).lastMtbFileRequestForPatientPseudonym(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
false
|
||||
}.`when`(requestService).isLastRequestWithKnownStatusDeletion(anyString())
|
||||
}.whenever(requestService).isLastRequestWithKnownStatusDeletion(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
MtbFileSender.Response(status = RequestStatus.SUCCESS)
|
||||
}.`when`(sender).send(any<MtbFileSender.MtbFileRequest>())
|
||||
}.whenever(sender).send(any<BwhcV1MtbFileRequest>())
|
||||
|
||||
doAnswer {
|
||||
it.arguments[0] as String
|
||||
}.`when`(pseudonymizeService).patientPseudonym(any())
|
||||
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
it.arguments[0]
|
||||
}.whenever(transformationService).transform(any())
|
||||
}.whenever(transformationService).transform(any<MtbFile>())
|
||||
|
||||
val mtbFile = MtbFile.builder()
|
||||
.withPatient(
|
||||
@ -269,32 +279,32 @@ class RequestProcessorTest {
|
||||
fun testShouldSendMtbFileAndSendErrorEvent() {
|
||||
doAnswer {
|
||||
Request(
|
||||
id = 1L,
|
||||
uuid = UUID.randomUUID().toString(),
|
||||
patientId = "TEST_12345678901",
|
||||
pid = "P1",
|
||||
fingerprint = "different",
|
||||
type = RequestType.MTB_FILE,
|
||||
status = RequestStatus.SUCCESS,
|
||||
processedAt = Instant.parse("2023-08-08T02:00:00Z")
|
||||
1L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678901"),
|
||||
PatientId("P1"),
|
||||
Fingerprint("different"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.SUCCESS,
|
||||
Instant.parse("2023-08-08T02:00:00Z")
|
||||
)
|
||||
}.`when`(requestService).lastMtbFileRequestForPatientPseudonym(anyString())
|
||||
}.whenever(requestService).lastMtbFileRequestForPatientPseudonym(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
false
|
||||
}.`when`(requestService).isLastRequestWithKnownStatusDeletion(anyString())
|
||||
}.whenever(requestService).isLastRequestWithKnownStatusDeletion(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
MtbFileSender.Response(status = RequestStatus.ERROR)
|
||||
}.`when`(sender).send(any<MtbFileSender.MtbFileRequest>())
|
||||
}.whenever(sender).send(any<BwhcV1MtbFileRequest>())
|
||||
|
||||
doAnswer {
|
||||
it.arguments[0] as String
|
||||
}.`when`(pseudonymizeService).patientPseudonym(any())
|
||||
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
it.arguments[0]
|
||||
}.whenever(transformationService).transform(any())
|
||||
}.whenever(transformationService).transform(any<MtbFile>())
|
||||
|
||||
val mtbFile = MtbFile.builder()
|
||||
.withPatient(
|
||||
@ -332,13 +342,13 @@ class RequestProcessorTest {
|
||||
fun testShouldSendDeleteRequestAndSaveUnknownRequestStatusAtFirst() {
|
||||
doAnswer {
|
||||
"PSEUDONYM"
|
||||
}.`when`(pseudonymizeService).patientPseudonym(anyString())
|
||||
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
MtbFileSender.Response(status = RequestStatus.UNKNOWN)
|
||||
}.`when`(sender).send(any<MtbFileSender.DeleteRequest>())
|
||||
}.whenever(sender).send(any<DeleteRequest>())
|
||||
|
||||
this.requestProcessor.processDeletion("TEST_12345678901")
|
||||
this.requestProcessor.processDeletion(TEST_PATIENT_ID, isConsented = TtpConsentStatus.UNKNOWN_CHECK_FILE)
|
||||
|
||||
val requestCaptor = argumentCaptor<Request>()
|
||||
verify(requestService, times(1)).save(requestCaptor.capture())
|
||||
@ -350,13 +360,13 @@ class RequestProcessorTest {
|
||||
fun testShouldSendDeleteRequestAndSendSuccessEvent() {
|
||||
doAnswer {
|
||||
"PSEUDONYM"
|
||||
}.`when`(pseudonymizeService).patientPseudonym(anyString())
|
||||
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
MtbFileSender.Response(status = RequestStatus.SUCCESS)
|
||||
}.`when`(sender).send(any<MtbFileSender.DeleteRequest>())
|
||||
}.whenever(sender).send(any<DeleteRequest>())
|
||||
|
||||
this.requestProcessor.processDeletion("TEST_12345678901")
|
||||
this.requestProcessor.processDeletion(TEST_PATIENT_ID, isConsented = TtpConsentStatus.UNKNOWN_CHECK_FILE)
|
||||
|
||||
val eventCaptor = argumentCaptor<ResponseEvent>()
|
||||
verify(applicationEventPublisher, times(1)).publishEvent(eventCaptor.capture())
|
||||
@ -368,13 +378,13 @@ class RequestProcessorTest {
|
||||
fun testShouldSendDeleteRequestAndSendErrorEvent() {
|
||||
doAnswer {
|
||||
"PSEUDONYM"
|
||||
}.`when`(pseudonymizeService).patientPseudonym(anyString())
|
||||
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
MtbFileSender.Response(status = RequestStatus.ERROR)
|
||||
}.`when`(sender).send(any<MtbFileSender.DeleteRequest>())
|
||||
}.whenever(sender).send(any<DeleteRequest>())
|
||||
|
||||
this.requestProcessor.processDeletion("TEST_12345678901")
|
||||
this.requestProcessor.processDeletion(TEST_PATIENT_ID, isConsented = TtpConsentStatus.UNKNOWN_CHECK_FILE)
|
||||
|
||||
val eventCaptor = argumentCaptor<ResponseEvent>()
|
||||
verify(applicationEventPublisher, times(1)).publishEvent(eventCaptor.capture())
|
||||
@ -384,9 +394,9 @@ class RequestProcessorTest {
|
||||
|
||||
@Test
|
||||
fun testShouldSendDeleteRequestWithPseudonymErrorAndSaveErrorRequestStatus() {
|
||||
doThrow(RuntimeException()).`when`(pseudonymizeService).patientPseudonym(anyString())
|
||||
doThrow(RuntimeException()).whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||
|
||||
this.requestProcessor.processDeletion("TEST_12345678901")
|
||||
this.requestProcessor.processDeletion(TEST_PATIENT_ID, isConsented = TtpConsentStatus.UNKNOWN_CHECK_FILE)
|
||||
|
||||
val requestCaptor = argumentCaptor<Request>()
|
||||
verify(requestService, times(1)).save(requestCaptor.capture())
|
||||
@ -400,15 +410,15 @@ class RequestProcessorTest {
|
||||
|
||||
doAnswer {
|
||||
it.arguments[0] as String
|
||||
}.`when`(pseudonymizeService).patientPseudonym(any())
|
||||
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
|
||||
|
||||
doAnswer {
|
||||
it.arguments[0]
|
||||
}.whenever(transformationService).transform(any())
|
||||
}.whenever(transformationService).transform(any<MtbFile>())
|
||||
|
||||
doAnswer {
|
||||
MtbFileSender.Response(status = RequestStatus.SUCCESS)
|
||||
}.`when`(sender).send(any<MtbFileSender.MtbFileRequest>())
|
||||
}.whenever(sender).send(any<BwhcV1MtbFileRequest>())
|
||||
|
||||
val mtbFile = MtbFile.builder()
|
||||
.withPatient(
|
||||
@ -442,4 +452,8 @@ class RequestProcessorTest {
|
||||
assertThat(eventCaptor.firstValue.status).isEqualTo(RequestStatus.SUCCESS)
|
||||
}
|
||||
|
||||
companion object {
|
||||
val TEST_PATIENT_ID = PatientId("TEST_12345678901")
|
||||
}
|
||||
|
||||
}
|
@ -19,6 +19,7 @@
|
||||
|
||||
package dev.dnpm.etl.processor.services
|
||||
|
||||
import dev.dnpm.etl.processor.*
|
||||
import dev.dnpm.etl.processor.monitoring.Request
|
||||
import dev.dnpm.etl.processor.monitoring.RequestRepository
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
@ -30,8 +31,9 @@ import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.mockito.Mock
|
||||
import org.mockito.Mockito.*
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.mockito.kotlin.anyValueClass
|
||||
import org.mockito.kotlin.whenever
|
||||
import java.time.Instant
|
||||
import java.util.*
|
||||
|
||||
@ExtendWith(MockitoExtension::class)
|
||||
class RequestServiceTest {
|
||||
@ -41,14 +43,14 @@ class RequestServiceTest {
|
||||
private lateinit var requestService: RequestService
|
||||
|
||||
private fun anyRequest() = any(Request::class.java) ?: Request(
|
||||
id = 0L,
|
||||
uuid = UUID.randomUUID().toString(),
|
||||
patientId = "TEST_dummy",
|
||||
pid = "PX",
|
||||
fingerprint = "dummy",
|
||||
type = RequestType.MTB_FILE,
|
||||
status = RequestStatus.SUCCESS,
|
||||
processedAt = Instant.parse("2023-08-08T02:00:00Z")
|
||||
0L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_dummy"),
|
||||
PatientId("PX"),
|
||||
Fingerprint("dummy"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.SUCCESS,
|
||||
Instant.parse("2023-08-08T02:00:00Z")
|
||||
)
|
||||
|
||||
@BeforeEach
|
||||
@ -63,34 +65,34 @@ class RequestServiceTest {
|
||||
fun shouldIndicateLastRequestIsDeleteRequest() {
|
||||
val requests = listOf(
|
||||
Request(
|
||||
id = 1L,
|
||||
uuid = UUID.randomUUID().toString(),
|
||||
patientId = "TEST_12345678901",
|
||||
pid = "P1",
|
||||
fingerprint = "0123456789abcdef1",
|
||||
type = RequestType.MTB_FILE,
|
||||
status = RequestStatus.WARNING,
|
||||
processedAt = Instant.parse("2023-07-07T00:00:00Z")
|
||||
1L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678901"),
|
||||
PatientId("P1"),
|
||||
Fingerprint("0123456789abcdef1"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.WARNING,
|
||||
Instant.parse("2023-07-07T00:00:00Z")
|
||||
),
|
||||
Request(
|
||||
id = 2L,
|
||||
uuid = UUID.randomUUID().toString(),
|
||||
patientId = "TEST_12345678901",
|
||||
pid = "P1",
|
||||
fingerprint = "0123456789abcdefd",
|
||||
type = RequestType.DELETE,
|
||||
status = RequestStatus.WARNING,
|
||||
processedAt = Instant.parse("2023-07-07T02:00:00Z")
|
||||
2L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678901"),
|
||||
PatientId("P1"),
|
||||
Fingerprint("0123456789abcdefd"),
|
||||
RequestType.DELETE,
|
||||
RequestStatus.WARNING,
|
||||
Instant.parse("2023-07-07T02:00:00Z")
|
||||
),
|
||||
Request(
|
||||
id = 3L,
|
||||
uuid = UUID.randomUUID().toString(),
|
||||
patientId = "TEST_12345678901",
|
||||
pid = "P1",
|
||||
fingerprint = "0123456789abcdef1",
|
||||
type = RequestType.MTB_FILE,
|
||||
status = RequestStatus.UNKNOWN,
|
||||
processedAt = Instant.parse("2023-08-11T00:00:00Z")
|
||||
3L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678901"),
|
||||
PatientId("P1"),
|
||||
Fingerprint("0123456789abcdef1"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.UNKNOWN,
|
||||
Instant.parse("2023-08-11T00:00:00Z")
|
||||
)
|
||||
)
|
||||
|
||||
@ -103,34 +105,34 @@ class RequestServiceTest {
|
||||
fun shouldIndicateLastRequestIsNotDeleteRequest() {
|
||||
val requests = listOf(
|
||||
Request(
|
||||
id = 1L,
|
||||
uuid = UUID.randomUUID().toString(),
|
||||
patientId = "TEST_12345678901",
|
||||
pid = "P1",
|
||||
fingerprint = "0123456789abcdef1",
|
||||
type = RequestType.MTB_FILE,
|
||||
status = RequestStatus.WARNING,
|
||||
processedAt = Instant.parse("2023-07-07T00:00:00Z")
|
||||
1L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678901"),
|
||||
PatientId("P1"),
|
||||
Fingerprint("0123456789abcdef1"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.WARNING,
|
||||
Instant.parse("2023-07-07T00:00:00Z")
|
||||
),
|
||||
Request(
|
||||
id = 2L,
|
||||
uuid = UUID.randomUUID().toString(),
|
||||
patientId = "TEST_12345678901",
|
||||
pid = "P1",
|
||||
fingerprint = "0123456789abcdef1",
|
||||
type = RequestType.MTB_FILE,
|
||||
status = RequestStatus.WARNING,
|
||||
processedAt = Instant.parse("2023-07-07T02:00:00Z")
|
||||
2L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678901"),
|
||||
PatientId("P1"),
|
||||
Fingerprint("0123456789abcdef1"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.WARNING,
|
||||
Instant.parse("2023-07-07T02:00:00Z")
|
||||
),
|
||||
Request(
|
||||
id = 3L,
|
||||
uuid = UUID.randomUUID().toString(),
|
||||
patientId = "TEST_12345678901",
|
||||
pid = "P1",
|
||||
fingerprint = "0123456789abcdef1",
|
||||
type = RequestType.MTB_FILE,
|
||||
status = RequestStatus.UNKNOWN,
|
||||
processedAt = Instant.parse("2023-08-11T00:00:00Z")
|
||||
3L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678901"),
|
||||
PatientId("P1"),
|
||||
Fingerprint("0123456789abcdef1"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.UNKNOWN,
|
||||
Instant.parse("2023-08-11T00:00:00Z")
|
||||
)
|
||||
)
|
||||
|
||||
@ -143,31 +145,31 @@ class RequestServiceTest {
|
||||
fun shouldReturnPatientsLastRequest() {
|
||||
val requests = listOf(
|
||||
Request(
|
||||
id = 1L,
|
||||
uuid = UUID.randomUUID().toString(),
|
||||
patientId = "TEST_12345678901",
|
||||
pid = "P1",
|
||||
fingerprint = "0123456789abcdef1",
|
||||
type = RequestType.DELETE,
|
||||
status = RequestStatus.SUCCESS,
|
||||
processedAt = Instant.parse("2023-07-07T02:00:00Z")
|
||||
1L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678901"),
|
||||
PatientId("P1"),
|
||||
Fingerprint("0123456789abcdef1"),
|
||||
RequestType.DELETE,
|
||||
RequestStatus.SUCCESS,
|
||||
Instant.parse("2023-07-07T02:00:00Z")
|
||||
),
|
||||
Request(
|
||||
id = 1L,
|
||||
uuid = UUID.randomUUID().toString(),
|
||||
patientId = "TEST_12345678902",
|
||||
pid = "P2",
|
||||
fingerprint = "0123456789abcdef2",
|
||||
type = RequestType.MTB_FILE,
|
||||
status = RequestStatus.WARNING,
|
||||
processedAt = Instant.parse("2023-08-08T00:00:00Z")
|
||||
1L,
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678902"),
|
||||
PatientId("P2"),
|
||||
Fingerprint("0123456789abcdef2"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.WARNING,
|
||||
Instant.parse("2023-08-08T00:00:00Z")
|
||||
)
|
||||
)
|
||||
|
||||
val actual = RequestService.lastMtbFileRequestForPatientPseudonym(requests)
|
||||
|
||||
assertThat(actual).isInstanceOf(Request::class.java)
|
||||
assertThat(actual?.fingerprint).isEqualTo("0123456789abcdef2")
|
||||
assertThat(actual?.fingerprint).isEqualTo(Fingerprint("0123456789abcdef2"))
|
||||
}
|
||||
|
||||
@Test
|
||||
@ -184,16 +186,16 @@ class RequestServiceTest {
|
||||
doAnswer {
|
||||
val obj = it.arguments[0] as Request
|
||||
obj.copy(id = 1L)
|
||||
}.`when`(requestRepository).save(anyRequest())
|
||||
}.whenever(requestRepository).save(anyRequest())
|
||||
|
||||
val request = Request(
|
||||
uuid = UUID.randomUUID().toString(),
|
||||
patientId = "TEST_12345678901",
|
||||
pid = "P1",
|
||||
fingerprint = "0123456789abcdef1",
|
||||
type = RequestType.DELETE,
|
||||
status = RequestStatus.SUCCESS,
|
||||
processedAt = Instant.parse("2023-07-07T02:00:00Z")
|
||||
randomRequestId(),
|
||||
PatientPseudonym("TEST_12345678901"),
|
||||
PatientId("P1"),
|
||||
Fingerprint("0123456789abcdef1"),
|
||||
RequestType.DELETE,
|
||||
RequestStatus.SUCCESS,
|
||||
Instant.parse("2023-07-07T02:00:00Z")
|
||||
)
|
||||
|
||||
requestService.save(request)
|
||||
@ -203,23 +205,23 @@ class RequestServiceTest {
|
||||
|
||||
@Test
|
||||
fun allRequestsByPatientPseudonymShouldRequestAllRequestsForPatientPseudonym() {
|
||||
requestService.allRequestsByPatientPseudonym("TEST_12345678901")
|
||||
requestService.allRequestsByPatientPseudonym(PatientPseudonym("TEST_12345678901"))
|
||||
|
||||
verify(requestRepository, times(1)).findAllByPatientIdOrderByProcessedAtDesc(anyString())
|
||||
verify(requestRepository, times(1)).findAllByPatientPseudonymOrderByProcessedAtDesc(anyValueClass())
|
||||
}
|
||||
|
||||
@Test
|
||||
fun lastMtbFileRequestForPatientPseudonymShouldRequestAllRequestsForPatientPseudonym() {
|
||||
requestService.lastMtbFileRequestForPatientPseudonym("TEST_12345678901")
|
||||
requestService.lastMtbFileRequestForPatientPseudonym(PatientPseudonym("TEST_12345678901"))
|
||||
|
||||
verify(requestRepository, times(1)).findAllByPatientIdOrderByProcessedAtDesc(anyString())
|
||||
verify(requestRepository, times(1)).findAllByPatientPseudonymOrderByProcessedAtDesc(anyValueClass())
|
||||
}
|
||||
|
||||
@Test
|
||||
fun isLastRequestDeletionShouldRequestAllRequestsForPatientPseudonym() {
|
||||
requestService.isLastRequestWithKnownStatusDeletion("TEST_12345678901")
|
||||
requestService.isLastRequestWithKnownStatusDeletion(PatientPseudonym("TEST_12345678901"))
|
||||
|
||||
verify(requestRepository, times(1)).findAllByPatientIdOrderByProcessedAtDesc(anyString())
|
||||
verify(requestRepository, times(1)).findAllByPatientPseudonymOrderByProcessedAtDesc(anyValueClass())
|
||||
}
|
||||
|
||||
}
|
@ -19,8 +19,8 @@
|
||||
|
||||
package dev.dnpm.etl.processor.services
|
||||
|
||||
import dev.dnpm.etl.processor.*
|
||||
import dev.dnpm.etl.processor.monitoring.Request
|
||||
import dev.dnpm.etl.processor.monitoring.RequestRepository
|
||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||
import dev.dnpm.etl.processor.monitoring.RequestType
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
@ -29,7 +29,6 @@ import org.junit.jupiter.api.Test
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.junit.jupiter.params.ParameterizedTest
|
||||
import org.junit.jupiter.params.provider.MethodSource
|
||||
import org.mockito.ArgumentMatchers.anyString
|
||||
import org.mockito.Mock
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.mockito.kotlin.*
|
||||
@ -40,64 +39,64 @@ import java.util.*
|
||||
@ExtendWith(MockitoExtension::class)
|
||||
class ResponseProcessorTest {
|
||||
|
||||
private lateinit var requestRepository: RequestRepository
|
||||
private lateinit var requestService: RequestService
|
||||
private lateinit var statisticsUpdateProducer: Sinks.Many<Any>
|
||||
|
||||
private lateinit var responseProcessor: ResponseProcessor
|
||||
|
||||
private val testRequest = Request(
|
||||
1L,
|
||||
"TestID1234",
|
||||
"PSEUDONYM-A",
|
||||
"1",
|
||||
"dummyfingerprint",
|
||||
RequestId("TestID1234"),
|
||||
PatientPseudonym("PSEUDONYM-A"),
|
||||
PatientId("1"),
|
||||
Fingerprint("dummyfingerprint"),
|
||||
RequestType.MTB_FILE,
|
||||
RequestStatus.UNKNOWN
|
||||
)
|
||||
|
||||
@BeforeEach
|
||||
fun setup(
|
||||
@Mock requestRepository: RequestRepository,
|
||||
@Mock requestService: RequestService,
|
||||
@Mock statisticsUpdateProducer: Sinks.Many<Any>
|
||||
) {
|
||||
this.requestRepository = requestRepository
|
||||
this.requestService = requestService
|
||||
this.statisticsUpdateProducer = statisticsUpdateProducer
|
||||
|
||||
this.responseProcessor = ResponseProcessor(requestRepository, statisticsUpdateProducer)
|
||||
this.responseProcessor = ResponseProcessor(requestService, statisticsUpdateProducer)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldNotSaveStatusForUnknownRequest() {
|
||||
doAnswer {
|
||||
Optional.empty<Request>()
|
||||
}.whenever(requestRepository).findByUuidEquals(anyString())
|
||||
}.whenever(requestService).findByUuid(anyValueClass())
|
||||
|
||||
val event = ResponseEvent(
|
||||
"TestID1234",
|
||||
RequestId("TestID1234"),
|
||||
Instant.parse("2023-09-09T00:00:00Z"),
|
||||
RequestStatus.SUCCESS
|
||||
)
|
||||
|
||||
this.responseProcessor.handleResponseEvent(event)
|
||||
|
||||
verify(requestRepository, never()).save(any())
|
||||
verify(requestService, never()).save(any())
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldNotSaveStatusWithUnknownState() {
|
||||
doAnswer {
|
||||
Optional.of(testRequest)
|
||||
}.whenever(requestRepository).findByUuidEquals(anyString())
|
||||
}.whenever(requestService).findByUuid(anyValueClass())
|
||||
|
||||
val event = ResponseEvent(
|
||||
"TestID1234",
|
||||
RequestId("TestID1234"),
|
||||
Instant.parse("2023-09-09T00:00:00Z"),
|
||||
RequestStatus.UNKNOWN
|
||||
)
|
||||
|
||||
this.responseProcessor.handleResponseEvent(event)
|
||||
|
||||
verify(requestRepository, never()).save(any())
|
||||
verify(requestService, never()).save(any<Request>())
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@ -105,10 +104,10 @@ class ResponseProcessorTest {
|
||||
fun shouldSaveStatusForKnownRequest(requestStatus: RequestStatus) {
|
||||
doAnswer {
|
||||
Optional.of(testRequest)
|
||||
}.whenever(requestRepository).findByUuidEquals(anyString())
|
||||
}.whenever(requestService).findByUuid(anyValueClass())
|
||||
|
||||
val event = ResponseEvent(
|
||||
"TestID1234",
|
||||
RequestId("TestID1234"),
|
||||
Instant.parse("2023-09-09T00:00:00Z"),
|
||||
requestStatus
|
||||
)
|
||||
@ -116,7 +115,7 @@ class ResponseProcessorTest {
|
||||
this.responseProcessor.handleResponseEvent(event)
|
||||
|
||||
val captor = argumentCaptor<Request>()
|
||||
verify(requestRepository, times(1)).save(captor.capture())
|
||||
verify(requestService, times(1)).save(captor.capture())
|
||||
assertThat(captor.firstValue).isNotNull
|
||||
assertThat(captor.firstValue.status).isEqualTo(requestStatus)
|
||||
}
|
||||
|
@ -19,14 +19,22 @@
|
||||
|
||||
package dev.dnpm.etl.processor.services
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import de.ukw.ccc.bwhc.dto.Consent
|
||||
import de.ukw.ccc.bwhc.dto.Diagnosis
|
||||
import de.ukw.ccc.bwhc.dto.Icd10
|
||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
||||
import dev.dnpm.etl.processor.config.JacksonConfig
|
||||
import dev.pcvolkmer.mv64e.mtb.ModelProjectConsent
|
||||
import org.assertj.core.api.Assertions.assertThat
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Test
|
||||
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||
import dev.pcvolkmer.mv64e.mtb.MvhMetadata
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource
|
||||
import org.hl7.fhir.r4.model.CodeableConcept
|
||||
import org.hl7.fhir.r4.model.Coding
|
||||
import java.time.Instant
|
||||
import java.util.Date
|
||||
|
||||
class TransformationServiceTest {
|
||||
|
||||
@ -35,7 +43,7 @@ class TransformationServiceTest {
|
||||
@BeforeEach
|
||||
fun setup() {
|
||||
this.service = TransformationService(
|
||||
ObjectMapper(), listOf(
|
||||
JacksonConfig().objectMapper(), listOf(
|
||||
Transformation.of("consent.status") from Consent.Status.ACTIVE to Consent.Status.REJECTED,
|
||||
Transformation.of("diagnoses[*].icd10.version") from "2013" to "2014",
|
||||
)
|
||||
@ -92,4 +100,79 @@ class TransformationServiceTest {
|
||||
assertThat(actual.consent.status).isEqualTo(Consent.Status.REJECTED)
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldTransformConsentValues() {
|
||||
val mtbFile = MtbFile.builder().withDiagnoses(
|
||||
listOf(
|
||||
Diagnosis.builder().withId("1234").withIcd10(Icd10("F79.9").also {
|
||||
it.version = "2013"
|
||||
}).build(),
|
||||
Diagnosis.builder().withId("5678").withIcd10(Icd10("F79.8").also {
|
||||
it.version = "2019"
|
||||
}).build()
|
||||
)
|
||||
).build()
|
||||
|
||||
val actual = this.service.transform(mtbFile)
|
||||
|
||||
assertThat(actual).isNotNull
|
||||
assertThat(actual.diagnoses[0].icd10.code).isEqualTo("F79.9")
|
||||
assertThat(actual.diagnoses[0].icd10.version).isEqualTo("2014")
|
||||
assertThat(actual.diagnoses[1].icd10.code).isEqualTo("F79.8")
|
||||
assertThat(actual.diagnoses[1].icd10.version).isEqualTo("2019")
|
||||
}
|
||||
|
||||
@Test
|
||||
fun shouldTransformConsent() {
|
||||
val mvhMetadata = MvhMetadata.builder().transferTan("transfertan12345").build();
|
||||
|
||||
assertThat(mvhMetadata).isNotNull
|
||||
mvhMetadata.modelProjectConsent =
|
||||
ModelProjectConsent.builder().date(Date.from(Instant.now())).version("1").build()
|
||||
val consent1 = org.hl7.fhir.r4.model.Consent()
|
||||
consent1.id = "consent 1 id"
|
||||
consent1.patient.reference = "Patient/1234-pat1"
|
||||
|
||||
consent1.provision.setType(org.hl7.fhir.r4.model.Consent.ConsentProvisionType.fromCode("deny"))
|
||||
consent1.provision.period.start = Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
|
||||
consent1.provision.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
|
||||
|
||||
|
||||
val addProvision1 = consent1.provision.addProvision()
|
||||
addProvision1.setType(org.hl7.fhir.r4.model.Consent.ConsentProvisionType.fromCode("permit"))
|
||||
addProvision1.period.start = Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
|
||||
addProvision1.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
|
||||
addProvision1.code.addLast(
|
||||
CodeableConcept(
|
||||
Coding(
|
||||
"https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"Teilnahme",
|
||||
"Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
|
||||
)
|
||||
)
|
||||
)
|
||||
|
||||
val addProvision2 = consent1.provision.addProvision()
|
||||
addProvision2.setType(org.hl7.fhir.r4.model.Consent.ConsentProvisionType.fromCode("deny"))
|
||||
addProvision2.period.start = Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
|
||||
addProvision2.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
|
||||
addProvision2.code.addLast(
|
||||
CodeableConcept(
|
||||
Coding(
|
||||
"https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"Rekontaktierung",
|
||||
"Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
|
||||
)
|
||||
)
|
||||
)
|
||||
|
||||
mvhMetadata.researchConsents = mutableListOf()
|
||||
mvhMetadata.researchConsents.add(mapOf(consent1.id to consent1 as IBaseResource))
|
||||
|
||||
val mtbFile = Mtb.builder().metadata(mvhMetadata).build()
|
||||
|
||||
val transformed = service.transform(mtbFile)
|
||||
assertThat(transformed.metadata.modelProjectConsent.date).isNotNull
|
||||
|
||||
}
|
||||
}
|
File diff suppressed because one or more lines are too long
1631
src/test/resources/fake_broadConsent_gics_response_deny.json
Normal file
1631
src/test/resources/fake_broadConsent_gics_response_deny.json
Normal file
File diff suppressed because it is too large
Load Diff
1631
src/test/resources/fake_broadConsent_gics_response_permit.json
Normal file
1631
src/test/resources/fake_broadConsent_gics_response_permit.json
Normal file
File diff suppressed because it is too large
Load Diff
333
src/test/resources/fake_mv64e-gics-response_deny.json
Normal file
333
src/test/resources/fake_mv64e-gics-response_deny.json
Normal file
@ -0,0 +1,333 @@
|
||||
{
|
||||
"resourceType": "Bundle",
|
||||
"type": "collection",
|
||||
"entry": [
|
||||
{
|
||||
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/24673204-50e1-11f0-a144-661e92ac9503",
|
||||
"resource": {
|
||||
"resourceType": "Consent",
|
||||
"id": "24673204-50e1-11f0-a144-661e92ac9503",
|
||||
"meta": {
|
||||
"lastUpdated": "2025-06-24T11:58:27.178+02:00",
|
||||
"profile": [
|
||||
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
|
||||
]
|
||||
},
|
||||
"extension": [
|
||||
{
|
||||
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
|
||||
"extension": [
|
||||
{
|
||||
"url": "domain",
|
||||
"valueReference": {
|
||||
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
|
||||
}
|
||||
},
|
||||
{
|
||||
"url": "status",
|
||||
"valueCoding": {
|
||||
"system": "http://hl7.org/fhir/publication-status",
|
||||
"code": "active"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"status": "active",
|
||||
"scope": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
|
||||
"code": "research"
|
||||
}
|
||||
]
|
||||
},
|
||||
"category": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://loinc.org",
|
||||
"code": "59284-0"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
|
||||
"code": "policy"
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"patient": {
|
||||
"reference": "Patient/2466d49b-50e1-11f0-a144-661e92ac9503",
|
||||
"display": "Patienten-ID 999999"
|
||||
},
|
||||
"dateTime": "2025-06-24T00:00:00+02:00",
|
||||
"organization": [
|
||||
{
|
||||
"display": "GenomDE_MV"
|
||||
}
|
||||
],
|
||||
"sourceReference": {
|
||||
"reference": "QuestionnaireResponse/24670c77-50e1-11f0-a144-661e92ac9503"
|
||||
},
|
||||
"policyRule": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Teilnahme",
|
||||
"display": "Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
|
||||
}
|
||||
]
|
||||
},
|
||||
"provision": {
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"provision": [
|
||||
{
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"code": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Teilnahme",
|
||||
"display": "Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
},
|
||||
{
|
||||
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/24673913-50e1-11f0-a144-661e92ac9503",
|
||||
"resource": {
|
||||
"resourceType": "Consent",
|
||||
"id": "24673913-50e1-11f0-a144-661e92ac9503",
|
||||
"meta": {
|
||||
"lastUpdated": "2025-06-24T11:58:27.194+02:00",
|
||||
"profile": [
|
||||
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
|
||||
]
|
||||
},
|
||||
"extension": [
|
||||
{
|
||||
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
|
||||
"extension": [
|
||||
{
|
||||
"url": "domain",
|
||||
"valueReference": {
|
||||
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
|
||||
}
|
||||
},
|
||||
{
|
||||
"url": "status",
|
||||
"valueCoding": {
|
||||
"system": "http://hl7.org/fhir/publication-status",
|
||||
"code": "active"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"status": "active",
|
||||
"scope": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
|
||||
"code": "research"
|
||||
}
|
||||
]
|
||||
},
|
||||
"category": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://loinc.org",
|
||||
"code": "59284-0"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
|
||||
"code": "policy"
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"patient": {
|
||||
"reference": "Patient/2466d49b-50e1-11f0-a144-661e92ac9503",
|
||||
"display": "Patienten-ID 999999"
|
||||
},
|
||||
"dateTime": "2025-06-24T00:00:00+02:00",
|
||||
"organization": [
|
||||
{
|
||||
"display": "GenomDE_MV"
|
||||
}
|
||||
],
|
||||
"sourceReference": {
|
||||
"reference": "QuestionnaireResponse/24670c77-50e1-11f0-a144-661e92ac9503"
|
||||
},
|
||||
"policyRule": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Fallidentifizierung",
|
||||
"display": "Fallidentifizierung zum fachlichen Austausch unter Behandelnden"
|
||||
}
|
||||
]
|
||||
},
|
||||
"provision": {
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"provision": [
|
||||
{
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"code": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Fallidentifizierung",
|
||||
"display": "Fallidentifizierung zum fachlichen Austausch unter Behandelnden"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
},
|
||||
{
|
||||
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/24673da9-50e1-11f0-a144-661e92ac9503",
|
||||
"resource": {
|
||||
"resourceType": "Consent",
|
||||
"id": "24673da9-50e1-11f0-a144-661e92ac9503",
|
||||
"meta": {
|
||||
"lastUpdated": "2025-06-24T11:58:27.211+02:00",
|
||||
"profile": [
|
||||
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
|
||||
]
|
||||
},
|
||||
"extension": [
|
||||
{
|
||||
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
|
||||
"extension": [
|
||||
{
|
||||
"url": "domain",
|
||||
"valueReference": {
|
||||
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
|
||||
}
|
||||
},
|
||||
{
|
||||
"url": "status",
|
||||
"valueCoding": {
|
||||
"system": "http://hl7.org/fhir/publication-status",
|
||||
"code": "active"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"status": "active",
|
||||
"scope": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
|
||||
"code": "research"
|
||||
}
|
||||
]
|
||||
},
|
||||
"category": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://loinc.org",
|
||||
"code": "59284-0"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
|
||||
"code": "policy"
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"patient": {
|
||||
"reference": "Patient/2466d49b-50e1-11f0-a144-661e92ac9503",
|
||||
"display": "Patienten-ID 999999"
|
||||
},
|
||||
"dateTime": "2025-06-24T00:00:00+02:00",
|
||||
"organization": [
|
||||
{
|
||||
"display": "GenomDE_MV"
|
||||
}
|
||||
],
|
||||
"sourceReference": {
|
||||
"reference": "QuestionnaireResponse/24670c77-50e1-11f0-a144-661e92ac9503"
|
||||
},
|
||||
"policyRule": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Rekontaktierung",
|
||||
"display": "Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
|
||||
}
|
||||
]
|
||||
},
|
||||
"provision": {
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"provision": [
|
||||
{
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"code": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Rekontaktierung",
|
||||
"display": "Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
333
src/test/resources/fake_mv64e-gics-response_permit.json
Normal file
333
src/test/resources/fake_mv64e-gics-response_permit.json
Normal file
@ -0,0 +1,333 @@
|
||||
{
|
||||
"resourceType": "Bundle",
|
||||
"type": "collection",
|
||||
"entry": [
|
||||
{
|
||||
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/121a8368-50e1-11f0-a144-661e92ac9503",
|
||||
"resource": {
|
||||
"resourceType": "Consent",
|
||||
"id": "121a8368-50e1-11f0-a144-661e92ac9503",
|
||||
"meta": {
|
||||
"lastUpdated": "2025-06-24T11:55:42.079+02:00",
|
||||
"profile": [
|
||||
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
|
||||
]
|
||||
},
|
||||
"extension": [
|
||||
{
|
||||
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
|
||||
"extension": [
|
||||
{
|
||||
"url": "domain",
|
||||
"valueReference": {
|
||||
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
|
||||
}
|
||||
},
|
||||
{
|
||||
"url": "status",
|
||||
"valueCoding": {
|
||||
"system": "http://hl7.org/fhir/publication-status",
|
||||
"code": "active"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"status": "active",
|
||||
"scope": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
|
||||
"code": "research"
|
||||
}
|
||||
]
|
||||
},
|
||||
"category": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://loinc.org",
|
||||
"code": "59284-0"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
|
||||
"code": "policy"
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"patient": {
|
||||
"reference": "Patient/12194791-50e1-11f0-a144-661e92ac9503",
|
||||
"display": "Patienten-ID 12345678"
|
||||
},
|
||||
"dateTime": "2025-06-24T00:00:00+02:00",
|
||||
"organization": [
|
||||
{
|
||||
"display": "GenomDE_MV"
|
||||
}
|
||||
],
|
||||
"sourceReference": {
|
||||
"reference": "QuestionnaireResponse/1219ca42-50e1-11f0-a144-661e92ac9503"
|
||||
},
|
||||
"policyRule": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Teilnahme",
|
||||
"display": "Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
|
||||
}
|
||||
]
|
||||
},
|
||||
"provision": {
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"provision": [
|
||||
{
|
||||
"type": "permit",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"code": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Teilnahme",
|
||||
"display": "Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
},
|
||||
{
|
||||
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/121aad40-50e1-11f0-a144-661e92ac9503",
|
||||
"resource": {
|
||||
"resourceType": "Consent",
|
||||
"id": "121aad40-50e1-11f0-a144-661e92ac9503",
|
||||
"meta": {
|
||||
"lastUpdated": "2025-06-24T11:55:42.096+02:00",
|
||||
"profile": [
|
||||
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
|
||||
]
|
||||
},
|
||||
"extension": [
|
||||
{
|
||||
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
|
||||
"extension": [
|
||||
{
|
||||
"url": "domain",
|
||||
"valueReference": {
|
||||
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
|
||||
}
|
||||
},
|
||||
{
|
||||
"url": "status",
|
||||
"valueCoding": {
|
||||
"system": "http://hl7.org/fhir/publication-status",
|
||||
"code": "active"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"status": "active",
|
||||
"scope": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
|
||||
"code": "research"
|
||||
}
|
||||
]
|
||||
},
|
||||
"category": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://loinc.org",
|
||||
"code": "59284-0"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
|
||||
"code": "policy"
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"patient": {
|
||||
"reference": "Patient/12194791-50e1-11f0-a144-661e92ac9503",
|
||||
"display": "Patienten-ID 12345678"
|
||||
},
|
||||
"dateTime": "2025-06-24T00:00:00+02:00",
|
||||
"organization": [
|
||||
{
|
||||
"display": "GenomDE_MV"
|
||||
}
|
||||
],
|
||||
"sourceReference": {
|
||||
"reference": "QuestionnaireResponse/1219ca42-50e1-11f0-a144-661e92ac9503"
|
||||
},
|
||||
"policyRule": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Fallidentifizierung",
|
||||
"display": "Fallidentifizierung zum fachlichen Austausch unter Behandelnden"
|
||||
}
|
||||
]
|
||||
},
|
||||
"provision": {
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"provision": [
|
||||
{
|
||||
"type": "permit",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"code": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Fallidentifizierung",
|
||||
"display": "Fallidentifizierung zum fachlichen Austausch unter Behandelnden"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
},
|
||||
{
|
||||
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/121ac5f8-50e1-11f0-a144-661e92ac9503",
|
||||
"resource": {
|
||||
"resourceType": "Consent",
|
||||
"id": "121ac5f8-50e1-11f0-a144-661e92ac9503",
|
||||
"meta": {
|
||||
"lastUpdated": "2025-06-24T11:55:42.110+02:00",
|
||||
"profile": [
|
||||
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
|
||||
]
|
||||
},
|
||||
"extension": [
|
||||
{
|
||||
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
|
||||
"extension": [
|
||||
{
|
||||
"url": "domain",
|
||||
"valueReference": {
|
||||
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
|
||||
}
|
||||
},
|
||||
{
|
||||
"url": "status",
|
||||
"valueCoding": {
|
||||
"system": "http://hl7.org/fhir/publication-status",
|
||||
"code": "active"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"status": "active",
|
||||
"scope": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
|
||||
"code": "research"
|
||||
}
|
||||
]
|
||||
},
|
||||
"category": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://loinc.org",
|
||||
"code": "59284-0"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
|
||||
"code": "policy"
|
||||
}
|
||||
]
|
||||
}
|
||||
],
|
||||
"patient": {
|
||||
"reference": "Patient/12194791-50e1-11f0-a144-661e92ac9503",
|
||||
"display": "Patienten-ID 12345678"
|
||||
},
|
||||
"dateTime": "2025-06-24T00:00:00+02:00",
|
||||
"organization": [
|
||||
{
|
||||
"display": "GenomDE_MV"
|
||||
}
|
||||
],
|
||||
"sourceReference": {
|
||||
"reference": "QuestionnaireResponse/1219ca42-50e1-11f0-a144-661e92ac9503"
|
||||
},
|
||||
"policyRule": {
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Rekontaktierung",
|
||||
"display": "Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
|
||||
}
|
||||
]
|
||||
},
|
||||
"provision": {
|
||||
"type": "deny",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"provision": [
|
||||
{
|
||||
"type": "permit",
|
||||
"period": {
|
||||
"start": "2025-06-24T00:00:00+02:00",
|
||||
"end": "3000-01-01T00:00:00+01:00"
|
||||
},
|
||||
"code": [
|
||||
{
|
||||
"coding": [
|
||||
{
|
||||
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
|
||||
"code": "Rekontaktierung",
|
||||
"display": "Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user