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1 Commits
v0.11.0-rc ... v0.10.0

Author SHA1 Message Date
Paul-Christian Volkmer
ec096d9c81 chore: bump version 2025-04-04 14:57:28 +02:00
75 changed files with 1958 additions and 10397 deletions
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@@ -39,5 +39,3 @@ out/
.vscode/
/dev/gpas*
/deploy/.env
/dev/gICS*
/dev/gPAS*

344
README.md
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@@ -1,15 +1,12 @@
# ETL-Processor für das MV gem. §64e und DNPM:DIP
[![Run Tests](https://github.com/pcvolkmer/etl-processor/actions/workflows/test.yml/badge.svg)](https://github.com/pcvolkmer/etl-processor/actions/workflows/test.yml)
# ETL-Processor for DNPM:DIP [![Run Tests](https://github.com/pcvolkmer/etl-processor/actions/workflows/test.yml/badge.svg)](https://github.com/pcvolkmer/etl-processor/actions/workflows/test.yml)
Diese Anwendung pseudonymisiert/anonymisiert Daten im DNPM-Datenmodell 2.1 für das Modellvorhaben
Genomsequenzierung nach §64e unter Beachtung des Consents und sendet sie an DNPM:DIP.
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
Diese Anwendung erlaubt das Entgegennehmen von HTTP/REST-Anfragen aus dem Onkostar-Plugin
**[mv64e-onkostar-plugin-export](https://github.com/pcvolkmer/mv64e-onkostar-plugin-export)**.
Diese Anwendung erlaubt das Entgegennehmen von HTTP/REST-Anfragen aus dem Onkostar-Plugin **[onkostar-plugin-dnpmexport](https://github.com/CCC-MF/onkostar-plugin-dnpmexport)**.
Der Inhalt einer Anfrage, wenn ein MTB-File, wird pseudonymisiert und auf Duplikate geprüft.
Der Inhalt einer Anfrage, wenn ein bwHC-MTBFile, wird pseudonymisiert und auf Duplikate geprüft.
Duplikate werden verworfen, Änderungen werden weitergeleitet.
Löschanfragen werden immer als Löschanfrage an DNPM:DIP weitergeleitet.
@@ -18,48 +15,16 @@ Zudem ist eine minimalistische Weboberfläche integriert, die einen Einblick in
![Modell DNPM-ETL-Strecke](docs/etl.png)
### 🔥 Wichtige Änderungen in Version 0.11
Ab Version 0.11 wird ausschließlich [DNPM:DIP](https://github.com/dnpm-dip) unterstützt.
Zudem wurde der Name des Pakets in **mv64e-etl-processor** geändert.
## Funktionsweise
### Duplikaterkennung
Die Erkennung von Duplikaten ist normalerweise immer aktiv, kann jedoch über den
Konfigurationsparameter
Die Erkennung von Duplikaten ist normalerweise immer aktiv, kann jedoch über den Konfigurationsparameter
`APP_DUPLICATION_DETECTION=false` deaktiviert werden.
### Modelvorhaben genomDE §64e
#### Vorgangsummern
Zusätzlich zur Patienten Identifier Pseudonymisierung müssen Vorgangsummern generiert werden, die
jede Übertragung eindeutig identifizieren aber gleichzeitig dem Patienten zugeordnet werden können.
Dies lässt sich durch weitere Pseudonyme abbilden, allerdings werden pro Originalwert mehrere
Pseudonyme benötigt.
Zu diesem Zweck muss in gPas eine **Multi-Pseudonym-Domäne** konfiguriert werden (siehe auch
*APP_PSEUDONYMIZE_GPAS_CCDN*).
**WICHTIG:** Deaktivierte Pseudonymisierung ist nur für Tests nutzbar. Vorgangsummern sind zufällig
und werden anschließend verworfen.
#### Test Betriebsbereitschaft
Um die voll Betriebsbereitschaft herzustellen, muss eine erfolgreiche Übertragung mit dem
Submission-Typ *Test* erfolgt sein. Über die Umgebungsvariable wird dieser Übertragungsmodus
aktiviert. Alle Datensätze mit erteilter Teilnahme am Modelvorhaben werden mit der Test-Submission-Kennung
übertragen, unabhängig vom ursprünglichen Wert.
`APP_GENOM_DE_TEST_SUBMISSION` -> `true` | `false` (falls fehlt, wird `false` angenommen)
### Datenübermittlung über HTTP/REST
Anfragen werden, wenn nicht als Duplikat behandelt, nach der Pseudonymisierung direkt an DNPM:DIP
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:
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 |
|--------------|-----------------------------------------|-----------------------------|---------------------------------------------------------------------------------|
@@ -67,20 +32,34 @@ nachfolgende URLs gesendet werden:
| `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.
Anstelle des Pfads `/mtb` kann auch, wie in Version 0.9 und älter üblich, `/mtbfile` verwendet werden.
### Datenübermittlung mit Apache Kafka
Anfragen werden, wenn nicht als Duplikat behandelt, nach der Pseudonymisierung an Apache Kafka
übergeben.
Eine Antwort wird dabei ebenfalls mithilfe von Apache Kafka übermittelt und nach der Entgegennahme
verarbeitet.
Anfragen werden, wenn nicht als Duplikat behandelt, nach der Pseudonymisierung an Apache Kafka übergeben.
Eine Antwort wird dabei ebenfalls mithilfe von Apache Kafka übermittelt und nach der Entgegennahme verarbeitet.
Siehe hierzu auch: https://github.com/CCC-MF/kafka-to-bwhc
## Konfiguration
### 🔥 Wichtige Änderungen in Version 0.10
Ab Version 0.10 wird [DNPM:DIP](https://github.com/dnpm-dip) unterstützt und als Standardendpunkt verwendet.
Soll noch das alte bwHC-Backend verwendet werden, so ist die Umgebungsvariable `APP_REST_IS_BWHC` auf `true` zu setzen.
### 🔥 Breaking Changes nach Version 0.10
In Versionen des ETL-Processors **nach Version 0.10** werden die folgenden Konfigurationsoptionen entfernt:
* `APP_PSEUDONYMIZE_GPAS_SSLCALOCATION`: Nutzen Sie hier, wie unter [_Integration eines eigenen Root CA
Zertifikats_](#integration-eines-eigenen-root-ca-zertifikats) beschrieben, das Einbinden eigener Zertifikate.
* `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.
@@ -89,93 +68,40 @@ Ist diese nicht gesetzt. wird intern eine Anonymisierung der Patienten-ID vorgen
* `APP_PSEUDONYMIZE_PREFIX`: Standortbezogenes Präfix - `UNKNOWN`, wenn nicht gesetzt
* `APP_PSEUDONYMIZE_GENERATOR`: `BUILDIN` oder `GPAS` - `BUILDIN`, wenn nicht gesetzt
**Hinweis**
**Hinweise**:
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
* 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 IDs werden mithilfe des standortbezogenen Präfixes (erneut) anonymisiert, um für den aktuellen Kontext nicht
vergleichbare IDs bereitzustellen.
#### Eingebaute Anonymisierung
Wurde keine oder die Verwendung der eingebauten Anonymisierung konfiguriert, so wird für die
Patienten-ID der entsprechende SHA-256-Hash gebildet und Base64-codiert - hier ohne endende
"=" - zuzüglich des konfigurierten Präfixes als Patienten-Pseudonym verwendet.
Wurde keine oder die Verwendung der eingebauten Anonymisierung konfiguriert, so wird für die Patienten-ID der
entsprechende SHA-256-Hash gebildet und Base64-codiert - hier ohne endende "=" - zuzüglich des konfigurierten Präfixes
als Patienten-Pseudonym verwendet.
#### Pseudonymisierung mit gPAS
Wurde die Verwendung von gPAS konfiguriert, so sind weitere Angaben zu konfigurieren.
Ab Version 2025.1 (Multi-Pseudonym Support)
* `APP_PSEUDONYMIZE_GPAS_URI`: URI der gPAS-Instanz REST API (e.g. http://127.0.0.1:9990/ttp-fhir/fhir/gpas)
* `APP_PSEUDONYMIZE_GPAS_URI`: URI der gPAS-Instanz inklusive Endpoint (z.B. `http://localhost:8080/ttp-fhir/fhir/gpas/$$pseudonymizeAllowCreate`)
* `APP_PSEUDONYMIZE_GPAS_TARGET`: gPas Domänenname
* `APP_PSEUDONYMIZE_GPAS_USERNAME`: gPas Basic-Auth Benutzername
* `APP_PSEUDONYMIZE_GPAS_PASSWORD`: gPas Basic-Auth Passwort
* `APP_PSEUDONYMIZE_GPAS_PID_DOMAIN`: gPas Domänenname für Patienten ID
* `APP_PSEUDONYMIZE_GPAS_GENOM_DE_TAN_DOMAIN`: gPas Multi-Pseudonym-Domäne für genomDE Vorgangsnummern (
Clinical data node)
* ~~`APP_PSEUDONYMIZE_GPAS_SSLCALOCATION`~~: **Veraltet** - Root Zertifikat für gPas, falls es dediziert hinzugefügt werden muss.
**Wird in nach Version 0.10 entfernt**
### (Externe) Consent-Services
Consent-Services können konfiguriert werden.
* `APP_CONSENT_SERVICE`: Zu verwendender (externer) Consent-Service:
* `NONE`: Verwende Consent-Angaben im MTB-File v1 und ändere diese nicht. Für MTB-File v2 wird
die Prüfung übersprungen.
* `GICS`: Verwende gICS der Greiswalder Tools (siehe unten).
#### Einwilligung gICS
Ab gIcs Version 2.13.0 kann im ETL-Processor
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* (MTB-File v1) und *currentPolicyStatesForPerson* (MTB-File v2) 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_SERVICE`: Muss Wert `GICS` gesetzt sein um die Abfragen zu aktivieren. Der Wert
`NONE` deaktiviert die Abfrage in gICS.
* `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.
Der Konfigurationsparameter `APP_PSEUDONYMIZE_GPAS_SSLCALOCATION` sollte nicht mehr verwendet werden und wird nach
Version 0.10 entfernt.
Stattdessen sollte das Root Zertifikat wie unter [_Integration eines eigenen Root CA
Zertifikats_](#integration-eines-eigenen-root-ca-zertifikats) beschrieben eingebunden werden.
### Anmeldung mit einem Passwort
Ein initialer Administrator-Account kann optional konfiguriert werden und sorgt dafür, dass
bestimmte Bereiche nur nach einem erfolgreichen Login erreichbar sind.
Ein initialer Administrator-Account kann optional konfiguriert werden und sorgt dafür, dass bestimmte Bereiche nur nach
einem erfolgreichen Login erreichbar sind.
* `APP_SECURITY_ADMIN_USER`: Muss angegeben werden zur Aktivierung der Zugriffsbeschränkung.
* `APP_SECURITY_ADMIN_PASSWORD`: Das Passwort für den Administrator (Empfohlen).
@@ -188,34 +114,27 @@ Hier Beispiele für das Beispielpasswort `very-secret`:
* `{bcrypt}$2y$05$CCkfsMr/wbTleMyjVIK8g.Aa3RCvrvoLXVAsL.f6KeouS88vXD9b6`
* `{sha256}9a34717f0646b5e9cfcba70055de62edb026ff4f68671ba3db96aa29297d2df5f1a037d58c745657`
Wird kein Administrator-Passwort angegeben, wird ein zufälliger Wert generiert und beim Start der
Anwendung in den Logs
Wird kein Administrator-Passwort angegeben, wird ein zufälliger Wert generiert und beim Start der Anwendung in den Logs
angezeigt.
#### Weitere (nicht administrative) Nutzer mit OpenID Connect
Die folgenden Konfigurationsparameter werden benötigt, um die Authentifizierung weiterer Benutzer an
einen OIDC-Provider
Die folgenden Konfigurationsparameter werden benötigt, um die Authentifizierung weiterer Benutzer an einen OIDC-Provider
zu delegieren.
Ein Admin-Benutzer muss dabei konfiguriert sein.
* `APP_SECURITY_ENABLE_OIDC`: Aktiviert die Nutzung von OpenID Connect. Damit sind weitere Parameter
erforderlich
* `SPRING_SECURITY_OAUTH2_CLIENT_REGISTRATION_CUSTOM_CLIENT_NAME`: Name. Wird beim zusätzlichen
Loginbutton angezeigt.
* `APP_SECURITY_ENABLE_OIDC`: Aktiviert die Nutzung von OpenID Connect. Damit sind weitere Parameter erforderlich
* `SPRING_SECURITY_OAUTH2_CLIENT_REGISTRATION_CUSTOM_CLIENT_NAME`: Name. Wird beim zusätzlichen Loginbutton angezeigt.
* `SPRING_SECURITY_OAUTH2_CLIENT_REGISTRATION_CUSTOM_CLIENT_ID`: Client-ID
* `SPRING_SECURITY_OAUTH2_CLIENT_REGISTRATION_CUSTOM_CLIENT_SECRET`: Client-Secret
* `SPRING_SECURITY_OAUTH2_CLIENT_REGISTRATION_CUSTOM_CLIENT_SCOPE[0]`: Hier sollte immer `openid`
angegeben werden.
* `SPRING_SECURITY_OAUTH2_CLIENT_REGISTRATION_CUSTOM_CLIENT_SCOPE[0]`: Hier sollte immer `openid` angegeben werden.
* `SPRING_SECURITY_OAUTH2_CLIENT_PROVIDER_CUSTOM_ISSUER_URI`: Die URI des Providers,
z.B. `https://auth.example.com/realm/example`
* `SPRING_SECURITY_OAUTH2_CLIENT_PROVIDER_CUSTOM_USER_NAME_ATTRIBUTE`: Name des Attributes, welches
den Benutzernamen
* `SPRING_SECURITY_OAUTH2_CLIENT_PROVIDER_CUSTOM_USER_NAME_ATTRIBUTE`: Name des Attributes, welches den Benutzernamen
enthält.
Oft verwendet: `preferred_username`
Ist die Nutzung von OpenID Connect konfiguriert, erscheint ein zusätzlicher Login-Button zur Nutzung
mit OpenID Connect
Ist die Nutzung von OpenID Connect konfiguriert, erscheint ein zusätzlicher Login-Button zur Nutzung mit OpenID Connect
und dem konfigurierten `CLIENT_NAME`.
![Login mit OpenID Connect](docs/login.png)
@@ -228,73 +147,60 @@ zu finden.
Wird OpenID Connect verwendet, gibt es eine rollenbasierte Berechtigungszuweisung.
Die Standardrolle für neue OIDC-Benutzer kann mit der Option `APP_SECURITY_DEFAULT_USER_ROLE`
festgelegt werden.
Die Standardrolle für neue OIDC-Benutzer kann mit der Option `APP_SECURITY_DEFAULT_USER_ROLE` festgelegt werden.
Mögliche Werte sind `user` oder `guest`. Standardwert ist `user`.
Benutzer mit der Rolle "Gast" sehen nur die Inhalte, die auch nicht angemeldete Benutzer sehen.
Hierdurch ist es möglich, einzelne Benutzer einzuschränken oder durch Änderung der Standardrolle auf
`guest` nur
Hierdurch ist es möglich, einzelne Benutzer einzuschränken oder durch Änderung der Standardrolle auf `guest` nur
einzelne Benutzer als vollwertige Nutzer zuzulassen.
![Rollenverwaltung](docs/userroles.png)
Benutzer werden nach dem Entfernen oder der Änderung der vergebenen Rolle automatisch abgemeldet und
müssen sich neu anmelden.
Benutzer werden nach dem Entfernen oder der Änderung der vergebenen Rolle automatisch abgemeldet und müssen sich neu anmelden.
Sie bekommen dabei wieder die Standardrolle zugewiesen.
#### Auswirkungen auf den dargestellten Inhalt
Nur Administratoren haben Zugriff auf den Konfigurationsbereich, nur angemeldete Benutzer können die
anonymisierte oder
Nur Administratoren haben Zugriff auf den Konfigurationsbereich, nur angemeldete Benutzer können die anonymisierte oder
pseudonymisierte Patienten-ID sowie den Qualitätsbericht von DNPM:DIP einsehen.
Wurde kein Administrator-Account konfiguriert, sind diese Inhalte generell nicht verfügbar.
### Tokenbasierte Authentifizierung für MTBFile-Endpunkt
Die Anwendung unterstützt das Erstellen und Nutzen einer tokenbasierten Authentifizierung für den
MTB-File-Endpunkt.
Die Anwendung unterstützt das Erstellen und Nutzen einer tokenbasierten Authentifizierung für den MTB-File-Endpunkt.
Dies kann mit der Umgebungsvariable `APP_SECURITY_ENABLE_TOKENS` aktiviert (`true` oder `false`)
werden
Dies kann mit der Umgebungsvariable `APP_SECURITY_ENABLE_TOKENS` aktiviert (`true` oder `false`) werden
und ist als Standardeinstellung nicht aktiv.
Ist diese Einstellung aktiviert worden, ist es Administratoren möglich, Zugriffstokens für Onkostar
zu erstellen, die
Ist diese Einstellung aktiviert worden, ist es Administratoren möglich, Zugriffstokens für Onkostar zu erstellen, die
zur Nutzung des MTB-File-Endpunkts eine HTTP-Basic-Authentifizierung voraussetzen.
![Tokenverwaltung](docs/tokens.png)
In diesem Fall kann der Endpunkt für das Onkostar-Plugin *
*[onkostar-plugin-dnpmexport](https://github.com/CCC-MF/onkostar-plugin-dnpmexport)** wie folgt
konfiguriert werden:
In diesem Fall kann der Endpunkt für das Onkostar-Plugin **[onkostar-plugin-dnpmexport](https://github.com/CCC-MF/onkostar-plugin-dnpmexport)** wie folgt konfiguriert werden:
```
https://testonkostar:MTg1NTL...NGU4@etl.example.com/mtbfile
```
Ist die Verwendung von Tokens aktiv, werden Anfragen ohne die Angabe der Token-Information
abgelehnt.
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,
In Onkostar kann es vorkommen, dass ein Wert eines Merkmalskatalogs an einem Standort angepasst wurde und dadurch nicht dem Wert entspricht,
der von DNPM:DIP akzeptiert wird.
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.
Diese Anwendung bietet daher die Möglichkeit, eine Transformation vorzunehmen. Hierzu muss der "Pfad" innerhalb des JSON-MTB-Files angegeben werden und
welcher Wert wie ersetzt werden soll.
Hier ein Beispiel für die erste (Index 0 - weitere dann mit 1,2, ...) Transformationsregel:
* `APP_TRANSFORMATIONS_0_PATH`: Pfad zum Wert in der JSON-MTB-Datei. Beispiel:
`diagnoses[*].icd10.version` für **alle** Diagnosen
* `APP_TRANSFORMATIONS_0_FROM`: Angabe des Werts, der ersetzt werden soll. Andere Werte bleiben
dabei unverändert.
* `APP_TRANSFORMATIONS_0_PATH`: Pfad zum Wert in der JSON-MTB-Datei. Beispiel: `diagnoses[*].icd10.version` für **alle** Diagnosen
* `APP_TRANSFORMATIONS_0_FROM`: Angabe des Werts, der ersetzt werden soll. Andere Werte bleiben dabei unverändert.
* `APP_TRANSFORMATIONS_0_TO`: Angabe des neuen Werts.
### Mögliche Endpunkte zur Datenübermittlung
@@ -306,61 +212,56 @@ Werden sowohl REST als auch Kafka-Endpunkt konfiguriert, wird nur der REST-Endpu
#### REST
Folgende Umgebungsvariablen müssen gesetzt sein, damit ein MTB-File an DNPM:DIP 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 Backend-Instanz. Zum Beispiel `http://localhost:9000/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 MTB-File an ein Kafka-Topic
übermittelt wird:
Folgende Umgebungsvariablen müssen gesetzt sein, damit ein bwHC-MTB-File an ein Kafka-Topic übermittelt wird:
* `APP_KAFKA_OUTPUT_TOPIC`: Zu verwendendes Topic zum Versenden von Anfragen.
* `APP_KAFKA_OUTPUT_RESPONSE_TOPIC`: Topic mit Antworten über den Erfolg des Versendens.
Standardwert: `APP_KAFKA_TOPIC` mit Anhang "_response".
* `APP_KAFKA_GROUP_ID`: Kafka GroupID des Consumers. Standardwert: `APP_KAFKA_TOPIC` mit Anhang "_
group".
Ersetzt ~~`APP_KAFKA_TOPIC`~~, **welches nach Version 0.10 entfernt wird**.
* `APP_KAFKA_OUTPUT_RESPONSE_TOPIC`: Topic mit Antworten über den Erfolg des Versendens. Standardwert: `APP_KAFKA_TOPIC` mit Anhang "_response".
Ersetzt ~~`APP_KAFKA_RESPONSE_TOPIC`~~, **welches nach Version 0.10 entfernt wird**.
* `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
Wird keine Rückantwort über Apache Kafka empfangen und es gibt keine weitere Möglichkeit den Status
festzustellen, verbleibt der Status auf `UNKNOWN`.
Wird keine Rückantwort über Apache Kafka empfangen und es gibt keine weitere Möglichkeit den Status festzustellen, verbleibt der Status auf `UNKNOWN`.
Weitere Einstellungen können über die Parameter von Spring Kafka konfiguriert werden.
Lässt sich keine Verbindung zu dem Backend aufbauen, wird eine Rückantwort mit Status-Code `900`
erwartet, welchen es
Lässt sich keine Verbindung zu dem 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.
Wird die Umgebungsvariable `APP_KAFKA_INPUT_TOPIC` gesetzt, kann eine Nachricht auch über dieses Kafka-Topic an den ETL-Prozessor übermittelt werden.
##### Retention Time
Generell werden in Apache Kafka alle Records entsprechend der Konfiguration vorgehalten.
So wird ohne spezielle Konfiguration ein Record für 7 Tage in Apache Kafka gespeichert.
Es sind innerhalb dieses Zeitraums auch alte Informationen weiterhin enthalten, wenn der Consent
später abgelehnt wurde.
Es sind innerhalb dieses Zeitraums auch alte Informationen weiterhin enthalten, wenn der Consent später abgelehnt wurde.
Durch eine entsprechende Konfiguration des Topics kann dies verhindert werden.
Beispiel - auszuführen innerhalb des Kafka-Containers: Löschen alter Records nach einem Tag
```
kafka-configs.sh --bootstrap-server localhost:9092 --alter --topic test --add-config retention.ms=86400000
```
##### Key based Retention
Möchten Sie hingegen immer nur die letzte Meldung für einen Patienten und eine Erkrankung in Apache
Kafka vorhalten,
Möchten Sie hingegen immer nur die letzte Meldung für einen Patienten und eine Erkrankung in Apache Kafka vorhalten,
so ist die nachfolgend genannte Konfiguration der Kafka-Topics hilfreich.
* `retention.ms`: Möglichst kurze Zeit in der alte Records noch erhalten bleiben, z.B. 10 Sekunden
10000
* `cleanup.policy`: Löschen alter Records und Beibehalten des letzten Records zu einem
Key [delete,compact]
* `retention.ms`: Möglichst kurze Zeit in der alte Records noch erhalten bleiben, z.B. 10 Sekunden 10000
* `cleanup.policy`: Löschen alter Records und Beibehalten des letzten Records zu einem Key [delete,compact]
Beispiele für ein Topic `test`, hier bitte an die verwendeten Topics anpassen.
@@ -369,28 +270,32 @@ kafka-configs.sh --bootstrap-server localhost:9092 --alter --topic test --add-co
kafka-configs.sh --bootstrap-server localhost:9092 --alter --topic test --add-config cleanup.policy=[delete,compact]
```
Da als Key eines Records die (pseudonymisierte) Patienten-ID verwendet wird, stehen mit obiger
Konfiguration
der Kafka-Topics nach 10 Sekunden nur noch der jeweils letzte Eintrag für den entsprechenden Key zur
Verfügung.
Da als Key eines Records die (pseudonymisierte) Patienten-ID verwendet wird, stehen mit obiger Konfiguration
der Kafka-Topics nach 10 Sekunden nur noch der jeweils letzte Eintrag für den entsprechenden Key zur Verfügung.
Da der Key sowohl für die Records in Richtung DNPM:DIP, als auch für die Rückantwort identisch
aufgebaut ist, lassen sich so
auch im Falle eines Consent-Widerspruchs die enthaltenen Daten als auch die Offenlegung durch
Verifikationsdaten in der
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
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.
Dieses Vorgehen empfiehlt sich, wenn Sie gespeicherte Records nachgelagert für andere Auswertungen verwenden möchten.
### Antworten und Statusauswertung
Seit Version 0.10 wird die Issue-Liste der Antwort verwendet und die darion enthaltene höchste
Severity-Stufe als Ergebnis verwendet.
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 |
|------------------|-----------|
@@ -400,8 +305,7 @@ Severity-Stufe als Ergebnis verwendet.
## Docker-Images
Diese Anwendung ist auch als Docker-Image
verfügbar: https://github.com/pcvolkmer/etl-processor/pkgs/container/etl-processor
Diese Anwendung ist auch als Docker-Image verfügbar: https://github.com/pcvolkmer/etl-processor/pkgs/container/etl-processor
### Images lokal bauen
@@ -411,25 +315,20 @@ verfügbar: https://github.com/pcvolkmer/etl-processor/pkgs/container/etl-proces
### Integration eines eigenen Root CA Zertifikats
Wird eine eigene Root CA verwendet, die nicht offiziell signiert ist, wird es zu Problemen beim
SSL-Handshake kommen, wenn z.B. gPAS zur Generierung von Pseudonymen verwendet wird.
Wird eine eigene Root CA verwendet, die nicht offiziell signiert ist, wird es zu Problemen beim SSL-Handshake kommen, wenn z.B. gPAS zur Generierung von Pseudonymen verwendet wird.
Hier bietet es sich an, das Root CA Zertifikat in das Image zu integrieren.
#### Integration beim Bauen des Images
Hier muss die Zeile `"BP_EMBED_CERTS" to "true"` in der Datei `build.gradle.kts` verwendet werden
und darf nicht als Kommentar verwendet werden.
Hier muss die Zeile `"BP_EMBED_CERTS" to "true"` in der Datei `build.gradle.kts` verwendet werden und darf nicht als Kommentar verwendet werden.
Die PEM-Datei mit dem/den Root CA Zertifikat(en) muss dabei im vorbereiteten Verzeichnis [
`bindings/ca-certificates`](bindings/ca-certificates) enthalten sein.
Die PEM-Datei mit dem/den Root CA Zertifikat(en) muss dabei im vorbereiteten Verzeichnis [`bindings/ca-certificates`](bindings/ca-certificates) enthalten sein.
#### Integration zur Laufzeit
Hier muss die Umgebungsvariable `SERVICE_BINDING_ROOT` z.B. auf den Wert `/bindings` gesetzt sein.
Zudem muss ein Verzeichnis `bindings/ca-certificates` - analog zum Verzeichnis [
`bindings/ca-certificates`](bindings/ca-certificates) mit einer PEM-Datei als Docker-Volume
eingebunden werden.
Zudem muss ein Verzeichnis `bindings/ca-certificates` - analog zum Verzeichnis [`bindings/ca-certificates`](bindings/ca-certificates) mit einer PEM-Datei als Docker-Volume eingebunden werden.
Beispiel für Docker-Compose:
@@ -444,14 +343,12 @@ Beispiel für Docker-Compose:
```
## Deployment
*Ausführen als Docker Container:*
```bash
cd ./deploy
cp env-sample.env .env
```
Wenn gewünscht, Änderungen in der `.env` vornehmen.
```bash
@@ -460,19 +357,15 @@ docker compose up -d
### Einfaches Beispiel für ein eigenes Docker-Compose-File
Die Datei [`docs/docker-compose.yml`](docs/docker-compose.yml) zeigt eine einfache Konfiguration für
REST-Requests basierend
Die Datei [`docs/docker-compose.yml`](docs/docker-compose.yml) zeigt eine einfache Konfiguration für REST-Requests basierend
auf Docker-Compose mit der gestartet werden kann.
### Betrieb hinter einem Reverse-Proxy
Die Anwendung verarbeitet `X-Forwarded`-HTTP-Header und kann daher auch hinter einem Reverse-Proxy
betrieben werden.
Die Anwendung verarbeitet `X-Forwarded`-HTTP-Header und kann daher auch hinter einem Reverse-Proxy betrieben werden.
Dabei werden, je nachdem welche Header durch den Reverse-Proxy gesendet werden auch Protokoll, Host
oder auch Path-Präfix
automatisch erkannt und verwendet werden. Dadurch ist z.B. eine abweichende Angabe des Pfads
problemlos möglich.
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):
@@ -508,17 +401,13 @@ Das folgende Beispiel zeigt die Konfiguration einer _location_ in einer nginx-Ko
## Entwicklungssetup
Zum Starten einer lokalen Entwicklungs- und Testumgebung kann die beiliegende Datei
`dev-compose.yml` verwendet werden.
Zum Starten einer lokalen Entwicklungs- und Testumgebung kann die beiliegende Datei `dev-compose.yml` verwendet werden.
Diese kann zur Nutzung der Datenbanken **MariaDB** als auch **PostgreSQL** angepasst werden.
Zur Nutzung von Apache Kafka muss dazu ein Eintrag im hosts-File vorgenommen werden und der Hostname
`kafka` auf die lokale
IP-Adresse verweisen. Ohne diese Einstellung ist eine Nutzung von Apache Kafka außerhalb der
Docker-Umgebung nicht möglich.
Zur Nutzung von Apache Kafka muss dazu ein Eintrag im hosts-File vorgenommen werden und der Hostname `kafka` auf die lokale
IP-Adresse verweisen. Ohne diese Einstellung ist eine Nutzung von Apache Kafka außerhalb der Docker-Umgebung nicht möglich.
Beim Start der Anwendung mit dem Profil `dev` wird die in `dev-compose.yml` definierte Umgebung beim
Start der
Beim Start der Anwendung mit dem Profil `dev` wird die in `dev-compose.yml` definierte Umgebung beim Start der
Anwendung mit gestartet:
```
@@ -530,5 +419,4 @@ 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.
Ein einfaches Entwickler-Setup inklusive DNPM:DIP ist mit Hilfe von https://github.com/pcvolkmer/dnpmdip-devenv realisierbar.

35
build.gradle.kts
View File

@@ -5,7 +5,7 @@ import org.springframework.boot.gradle.tasks.bundling.BootBuildImage
plugins {
war
id("org.springframework.boot") version "3.5.3"
id("org.springframework.boot") version "3.3.10"
id("io.spring.dependency-management") version "1.1.7"
kotlin("jvm") version "1.9.25"
kotlin("plugin.spring") version "1.9.25"
@@ -13,11 +13,12 @@ plugins {
}
group = "dev.dnpm"
version = "0.11.0-SNAPSHOT"
version = "0.10.0"
var versions = mapOf(
"mtb-dto" to "0.1.0-SNAPSHOT",
"hapi-fhir" to "7.6.1",
"bwhc-dto-java" to "0.4.0",
"hapi-fhir" to "7.6.0",
"commons-compress" to "1.26.2",
"mockito-kotlin" to "5.4.0",
"archunit" to "1.3.0",
// Webjars
@@ -48,18 +49,9 @@ configurations {
compileOnly {
extendsFrom(configurations.annotationProcessor.get())
}
all {
resolutionStrategy {
cacheChangingModulesFor(5, "minutes")
}
}
}
repositories {
maven {
url = uri("https://git.dnpm.dev/api/packages/public-snapshots/maven")
}
maven {
url = uri("https://git.dnpm.dev/api/packages/public/maven")
}
@@ -80,7 +72,7 @@ dependencies {
implementation("org.flywaydb:flyway-mysql")
implementation("commons-codec:commons-codec")
implementation("io.projectreactor.kotlin:reactor-kotlin-extensions")
implementation("dev.pcvolkmer.mv64e:mtb-dto:${versions["mtb-dto"]}") { isChanging = true }
implementation("de.ukw.ccc:bwhc-dto-java:${versions["bwhc-dto-java"]}")
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")
@@ -88,8 +80,6 @@ dependencies {
implementation("org.webjars:webjars-locator:${versions["webjars-locator"]}")
implementation("org.webjars.npm:echarts:${versions["echarts"]}")
implementation("org.webjars.npm:htmx.org:${versions["htmx.org"]}")
// Fix for CVE-2025-48924
implementation("org.apache.commons:commons-lang3:3.18.0")
runtimeOnly("org.mariadb.jdbc:mariadb-java-client")
runtimeOnly("org.postgresql:postgresql")
@@ -109,8 +99,10 @@ dependencies {
integrationTestImplementation("org.testcontainers:junit-jupiter")
integrationTestImplementation("org.testcontainers:postgresql")
integrationTestImplementation("com.tngtech.archunit:archunit:${versions["archunit"]}")
integrationTestImplementation("org.htmlunit:htmlunit")
integrationTestImplementation("net.sourceforge.htmlunit:htmlunit")
integrationTestImplementation("org.springframework:spring-webflux")
// Override dependency version from org.testcontainers:junit-jupiter - CVE-2024-26308, CVE-2024-25710
integrationTestImplementation("org.apache.commons:commons-compress:${versions["commons-compress"]}")
}
tasks.withType<KotlinCompile> {
@@ -127,9 +119,8 @@ tasks.withType<Test> {
}
}
tasks.register<Test>("integrationTest") {
task<Test>("integrationTest") {
description = "Runs integration tests"
group = "verification"
testClassesDirs = sourceSets["integrationTest"].output.classesDirs
classpath = sourceSets["integrationTest"].runtimeClasspath
@@ -154,7 +145,7 @@ tasks.jacocoTestReport {
}
tasks.named<BootBuildImage>("bootBuildImage") {
imageName.set("ghcr.io/pcvolkmer/mv64e-etl-processor")
imageName.set("ghcr.io/pcvolkmer/etl-processor")
// Binding for CA Certs
bindings.set(listOf(
@@ -164,8 +155,8 @@ 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/pcvolkmer/mv64e-etl-processor",
"BP_OCI_SOURCE" to "https://github.com/pcvolkmer/etl-processor",
"BP_OCI_LICENSES" to "AGPLv3",
"BP_OCI_DESCRIPTION" to "ETL Processor for MV § 64e and DNPM:DIP"
"BP_OCI_DESCRIPTION" to "ETL Processor for bwHC MTB files"
))
}

5
dev-compose.yml
View File

@@ -16,11 +16,6 @@ services:
KAFKA_CFG_AUTO_CREATE_TOPICS_ENABLE: true
KAFKA_CFG_CONTROLLER_QUORUM_VOTERS: 0@kafka:9093
KAFKA_CFG_CONTROLLER_LISTENER_NAMES: CONTROLLER
healthcheck:
test: kafka-topics --bootstrap-server kafka:9092 --list
interval: 30s
timeout: 10s
retries: 3
## Use AKHQ as Kafka web frontend
akhq:

74
dev/docker-compose.dev.yml
View File

@@ -2,55 +2,31 @@ version: '3.7'
services:
zoo:
image: zookeeper:3.9.2
restart: unless-stopped
zoo1:
image: zookeeper:3.8.0
hostname: zoo1
ports:
- "2181:2181"
environment:
ZOO_MY_ID: 1
ZOO_PORT: 2181
ZOO_SERVERS: server.1=zoo:2888:3888;2181
ZOO_SERVERS: server.1=zoo1:2888:3888;2181
kafka:
image: confluentinc/cp-kafka:7.6.1
kafka1:
image: confluentinc/cp-kafka:7.2.1
hostname: kafka1
ports:
- "9092:9092"
environment:
KAFKA_ADVERTISED_LISTENERS: LISTENER_DOCKER_INTERNAL://kafka:19092,LISTENER_DOCKER_EXTERNAL://172.17.0.1:9093,LISTENER_EXTERNAL://127.0.0.1:9092
KAFKA_LISTENER_SECURITY_PROTOCOL_MAP: LISTENER_DOCKER_INTERNAL:PLAINTEXT,LISTENER_DOCKER_EXTERNAL:PLAINTEXT,LISTENER_EXTERNAL:PLAINTEXT
KAFKA_ADVERTISED_LISTENERS: LISTENER_DOCKER_INTERNAL://kafka1:19092,LISTENER_DOCKER_EXTERNAL://${DOCKER_HOST_IP:-127.0.0.1}:9092
KAFKA_LISTENER_SECURITY_PROTOCOL_MAP: LISTENER_DOCKER_INTERNAL:PLAINTEXT,LISTENER_DOCKER_EXTERNAL:PLAINTEXT
KAFKA_INTER_BROKER_LISTENER_NAME: LISTENER_DOCKER_INTERNAL
KAFKA_ZOOKEEPER_CONNECT: zoo:2181
KAFKA_ZOOKEEPER_CONNECT: "zoo1:2181"
KAFKA_BROKER_ID: 1
KAFKA_LOG4J_LOGGERS: kafka.controller=INFO,kafka.producer.async.DefaultEventHandler=INFO,state.change.logger=INFO
KAFKA_LOG4J_LOGGERS: "kafka.controller=INFO,kafka.producer.async.DefaultEventHandler=INFO,state.change.logger=INFO"
KAFKA_OFFSETS_TOPIC_REPLICATION_FACTOR: 1
KAFKA_MESSAGE_MAX_BYTES: 5242880
KAFKA_REPLICA_FETCH_MAX_BYTES: 5242880
KAFKA_COMPRESSION_TYPE: gzip
depends_on:
- zoo
healthcheck:
test: kafka-topics --bootstrap-server kafka:9092 --list
interval: 30s
timeout: 10s
retries: 3
akhq:
image: tchiotludo/akhq:0.25.0
environment:
AKHQ_CONFIGURATION: |
akhq:
ui-options:
topic.show-all-consumer-groups: true
topic-data.sort: NEWEST
connections:
docker-kafka-server:
properties:
bootstrap.servers: "kafka:19092"
ports:
- "9000:8080"
depends_on:
- kafka
- zoo1
kafka-rest-proxy:
image: confluentinc/cp-kafka-rest:7.2.1
@@ -64,8 +40,8 @@ services:
KAFKA_REST_HOST_NAME: kafka-rest-proxy
KAFKA_REST_BOOTSTRAP_SERVERS: PLAINTEXT://kafka1:19092
depends_on:
- zoo
- kafka
- zoo1
- kafka1
kafka-connect:
image: confluentinc/cp-kafka-connect:7.2.1
@@ -91,6 +67,24 @@ services:
#volumes:
# - ./connectors:/etc/kafka-connect/jars/
depends_on:
- zoo
- kafka
- zoo1
- kafka1
- kafka-rest-proxy
akhq:
image: tchiotludo/akhq:0.21.0
environment:
AKHQ_CONFIGURATION: |
akhq:
connections:
docker-kafka-server:
properties:
bootstrap.servers: "kafka1:19092"
connect:
- name: "kafka-connect"
url: "http://kafka-connect:8083"
ports:
- "8084:8080"
depends_on:
- kafka1
- kafka-connect

2
settings.gradle.kts
View File

@@ -1 +1 @@
rootProject.name = "mv64e-etl-processor"
rootProject.name = "etl-processor"

64
src/integrationTest/kotlin/dev/dnpm/etl/processor/EtlProcessorApplicationTests.kt
View File

@@ -20,11 +20,10 @@
package dev.dnpm.etl.processor
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.DnpmV2MtbFileRequest
import dev.dnpm.etl.processor.output.MtbFileSender
import dev.pcvolkmer.mv64e.mtb.*
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Nested
@@ -34,10 +33,10 @@ import org.mockito.kotlin.*
import org.springframework.beans.factory.annotation.Autowired
import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc
import org.springframework.boot.test.context.SpringBootTest
import org.springframework.boot.test.mock.mockito.MockBean
import org.springframework.context.ApplicationContext
import org.springframework.http.MediaType
import org.springframework.test.context.TestPropertySource
import org.springframework.test.context.bean.override.mockito.MockitoBean
import org.springframework.test.context.junit.jupiter.SpringExtension
import org.springframework.test.web.servlet.MockMvc
import org.springframework.test.web.servlet.post
@@ -46,12 +45,11 @@ import org.testcontainers.junit.jupiter.Testcontainers
@Testcontainers
@ExtendWith(SpringExtension::class)
@SpringBootTest
@MockitoBean(types = [MtbFileSender::class])
@MockBean(MtbFileSender::class)
@TestPropertySource(
properties = [
"app.rest.uri=http://example.com",
"app.pseudonymize.generator=buildin",
"app.consent.service=none"
"app.pseudonymize.generator=buildin"
]
)
class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
@@ -68,15 +66,14 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
@TestPropertySource(
properties = [
"app.pseudonymize.generator=buildin",
"app.consent.service=none",
"app.transformations[0].path=diagnoses[*].code.version",
"app.transformations[0].path=diagnoses[*].icd10.version",
"app.transformations[0].from=2013",
"app.transformations[0].to=2014",
]
)
inner class TransformationTest {
@MockitoBean
@MockBean
private lateinit var mtbFileSender: MtbFileSender
@Autowired
@@ -94,33 +91,36 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
fun mtbFileIsTransformed() {
doAnswer {
MtbFileSender.Response(RequestStatus.SUCCESS)
}.whenever(mtbFileSender).send(any<DnpmV2MtbFileRequest>())
}.whenever(mtbFileSender).send(any<MtbFileSender.MtbFileRequest>())
val mtbFile = Mtb.builder()
.patient(
val mtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.id("TEST_12345678")
.withId("TEST_12345678")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.metadata(
MvhMetadata
.builder()
.modelProjectConsent(
ModelProjectConsent
.builder()
.provisions(
listOf(Provision.builder().type(ConsentProvision.PERMIT).purpose(ModelProjectConsentPurpose.SEQUENCING).build())
).build()
)
.withConsent(
Consent.builder()
.withId("1")
.withStatus(Consent.Status.ACTIVE)
.withPatient("TEST_12345678")
.build()
)
.diagnoses(
.withEpisode(
Episode.builder()
.withId("1")
.withPatient("TEST_12345678")
.withPeriod(PeriodStart("2023-08-08"))
.build()
)
.withDiagnoses(
listOf(
MtbDiagnosis.builder()
.id("1234")
.patient(Reference.builder().id("TEST_12345678").build())
.code(Coding.builder().code("F79.9").version("2013").build())
.build(),
Diagnosis.builder()
.withId("1234")
.withIcd10(Icd10.builder().withCode("F79.9").withVersion("2013").build())
.build()
)
)
.build()
@@ -134,10 +134,10 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
}
}
val captor = argumentCaptor<DnpmV2MtbFileRequest>()
val captor = argumentCaptor<MtbFileSender.MtbFileRequest>()
verify(mtbFileSender).send(captor.capture())
assertThat(captor.firstValue.content.diagnoses).hasSize(1).allMatch { diagnosis ->
diagnosis.code.version == "2014"
assertThat(captor.firstValue.mtbFile.diagnoses).hasSize(1).allMatch { diagnosis ->
diagnosis.icd10.version == "2014"
}
}
}

111
src/integrationTest/kotlin/dev/dnpm/etl/processor/config/AppConfigurationTest.kt
View File

@@ -20,18 +20,15 @@
package dev.dnpm.etl.processor.config
import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.consent.ConsentEvaluator
import dev.dnpm.etl.processor.consent.GicsConsentService
import dev.dnpm.etl.processor.consent.MtbFileConsentService
import dev.dnpm.etl.processor.input.KafkaInputListener
import dev.dnpm.etl.processor.monitoring.RequestRepository
import dev.dnpm.etl.processor.output.KafkaMtbFileSender
import dev.dnpm.etl.processor.output.RestMtbFileSender
import dev.dnpm.etl.processor.pseudonym.AnonymizingGenerator
import dev.dnpm.etl.processor.pseudonym.GpasPseudonymGenerator
import dev.dnpm.etl.processor.services.RequestProcessor
import dev.dnpm.etl.processor.security.TokenRepository
import dev.dnpm.etl.processor.security.TokenService
import dev.dnpm.etl.processor.services.RequestProcessor
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.Nested
import org.junit.jupiter.api.Test
@@ -39,26 +36,24 @@ 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 = [
@ContextConfiguration(classes = [
AppConfiguration::class,
AppSecurityConfiguration::class,
KafkaAutoConfiguration::class,
AppKafkaConfiguration::class,
AppRestConfiguration::class,
ConsentEvaluator::class
]
)
@MockitoBean(types = [ObjectMapper::class])
AppRestConfiguration::class
])
@MockBean(ObjectMapper::class)
@TestPropertySource(
properties = [
"app.pseudonymize.generator=BUILDIN",
@@ -91,7 +86,7 @@ class AppConfigurationTest {
"app.kafka.group-id=test"
]
)
@MockitoBean(types = [RequestRepository::class])
@MockBean(RequestRepository::class)
inner class AppConfigurationKafkaTest(private val context: ApplicationContext) {
@Test
@@ -150,7 +145,7 @@ class AppConfigurationTest {
"app.kafka.group-id=test"
]
)
@MockitoBean(types = [RequestProcessor::class])
@MockBean(RequestProcessor::class)
inner class AppConfigurationUsingKafkaInputTest(private val context: ApplicationContext) {
@Test
@@ -186,7 +181,40 @@ class AppConfigurationTest {
@Nested
@TestPropertySource(
properties = [
"app.pseudonymize.generator=buildin"
"app.pseudonymize.generator=",
"app.pseudonymizer=buildin",
]
)
inner class AppConfigurationPseudonymizerBuildinTest(private val context: ApplicationContext) {
@Test
fun shouldUseConfiguredGenerator() {
assertThat(context.getBean(AnonymizingGenerator::class.java)).isNotNull
}
}
@Nested
@TestPropertySource(
properties = [
"app.pseudonymize.generator=",
"app.pseudonymizer=gpas",
]
)
inner class AppConfigurationPseudonymizerGpasTest(private val context: ApplicationContext) {
@Test
fun shouldUseConfiguredGenerator() {
assertThat(context.getBean(GpasPseudonymGenerator::class.java)).isNotNull
}
}
@Nested
@TestPropertySource(
properties = [
"app.pseudonymize.generator=buildin",
"app.pseudonymizer=",
]
)
inner class AppConfigurationPseudonymizeGeneratorBuildinTest(private val context: ApplicationContext) {
@@ -201,7 +229,8 @@ class AppConfigurationTest {
@Nested
@TestPropertySource(
properties = [
"app.pseudonymize.generator=gpas"
"app.pseudonymize.generator=gpas",
"app.pseudonymizer=",
]
)
inner class AppConfigurationPseudonymizeGeneratorGpasTest(private val context: ApplicationContext) {
@@ -219,13 +248,11 @@ class AppConfigurationTest {
"app.security.enable-tokens=true"
]
)
@MockitoBean(
types = [
InMemoryUserDetailsManager::class,
PasswordEncoder::class,
TokenRepository::class
]
)
@MockBeans(value = [
MockBean(InMemoryUserDetailsManager::class),
MockBean(PasswordEncoder::class),
MockBean(TokenRepository::class)
])
inner class AppConfigurationTokenEnabledTest(private val context: ApplicationContext) {
@Test
@@ -236,13 +263,11 @@ class AppConfigurationTest {
}
@Nested
@MockitoBean(
types = [
InMemoryUserDetailsManager::class,
PasswordEncoder::class,
TokenRepository::class
]
)
@MockBeans(value = [
MockBean(InMemoryUserDetailsManager::class),
MockBean(PasswordEncoder::class),
MockBean(TokenRepository::class)
])
inner class AppConfigurationTokenDisabledTest(private val context: ApplicationContext) {
@Test
@@ -280,30 +305,4 @@ class AppConfigurationTest {
}
@Nested
@TestPropertySource(
properties = [
"app.consent.service=GICS",
"app.consent.gics.uri=http://localhost:9000",
]
)
inner class AppConfigurationConsentGicsTest(private val context: ApplicationContext) {
@Test
fun shouldUseConfiguredGenerator() {
assertThat(context.getBean(GicsConsentService::class.java)).isNotNull
}
}
@Nested
inner class AppConfigurationConsentBuildinTest(private val context: ApplicationContext) {
@Test
fun shouldUseConfiguredGenerator() {
assertThat(context.getBean(MtbFileConsentService::class.java)).isNotNull
}
}
}

78
src/integrationTest/kotlin/dev/dnpm/etl/processor/input/MtbFileRestControllerTest.kt
View File

@@ -20,47 +20,44 @@
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.ConsentEvaluation
import dev.dnpm.etl.processor.consent.ConsentEvaluator
import dev.dnpm.etl.processor.consent.MtbFileConsentService
import dev.dnpm.etl.processor.consent.TtpConsentStatus
import dev.dnpm.etl.processor.security.TokenRepository
import dev.dnpm.etl.processor.security.UserRoleRepository
import dev.dnpm.etl.processor.services.RequestProcessor
import dev.pcvolkmer.mv64e.mtb.*
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Nested
import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith
import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.*
import org.mockito.kotlin.any
import org.mockito.kotlin.never
import org.mockito.kotlin.times
import org.mockito.kotlin.verify
import org.springframework.beans.factory.annotation.Autowired
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
import org.springframework.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
import org.springframework.test.web.servlet.post
import java.time.Instant
import java.util.*
@WebMvcTest(controllers = [MtbFileRestController::class])
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
@ContextConfiguration(
classes = [
MtbFileRestController::class,
AppSecurityConfiguration::class,
MtbFileConsentService::class
AppSecurityConfiguration::class
]
)
@MockitoBean(types = [TokenRepository::class, RequestProcessor::class, ConsentEvaluator::class])
@MockBean(TokenRepository::class, RequestProcessor::class)
@TestPropertySource(
properties = [
"app.pseudonymize.generator=BUILDIN",
@@ -71,23 +68,17 @@ import java.util.*
)
class MtbFileRestControllerTest {
lateinit var mockMvc: MockMvc
lateinit var requestProcessor: RequestProcessor
lateinit var consentEvaluator: ConsentEvaluator
private lateinit var mockMvc: MockMvc
private lateinit var requestProcessor: RequestProcessor
@BeforeEach
fun setup(
@Autowired mockMvc: MockMvc,
@Autowired requestProcessor: RequestProcessor,
@Autowired consentEvaluator: ConsentEvaluator
@Autowired requestProcessor: RequestProcessor
) {
this.mockMvc = mockMvc
this.requestProcessor = requestProcessor
this.consentEvaluator = consentEvaluator
doAnswer {
ConsentEvaluation(TtpConsentStatus.BROAD_CONSENT_GIVEN, true)
}.whenever(consentEvaluator).check(any())
}
@Test
@@ -100,7 +91,7 @@ class MtbFileRestControllerTest {
status { isAccepted() }
}
verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
verify(requestProcessor, times(1)).processMtbFile(any())
}
@Test
@@ -113,7 +104,7 @@ class MtbFileRestControllerTest {
status { isAccepted() }
}
verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
verify(requestProcessor, times(1)).processMtbFile(any())
}
@Test
@@ -126,7 +117,7 @@ class MtbFileRestControllerTest {
status { isUnauthorized() }
}
verify(requestProcessor, never()).processMtbFile(any<Mtb>())
verify(requestProcessor, never()).processMtbFile(any())
}
@Test
@@ -139,7 +130,7 @@ class MtbFileRestControllerTest {
status { isForbidden() }
}
verify(requestProcessor, never()).processMtbFile(any<Mtb>())
verify(requestProcessor, never()).processMtbFile(any())
}
@Test
@@ -150,7 +141,7 @@ class MtbFileRestControllerTest {
status { isAccepted() }
}
verify(requestProcessor, times(1)).processDeletion(anyValueClass(), eq(TtpConsentStatus.UNKNOWN_CHECK_FILE))
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
}
@Test
@@ -161,11 +152,11 @@ class MtbFileRestControllerTest {
status { isUnauthorized() }
}
verify(requestProcessor, never()).processDeletion(anyValueClass(), any())
verify(requestProcessor, never()).processDeletion(anyValueClass())
}
@Nested
@MockitoBean(types = [UserRoleRepository::class, ClientRegistrationRepository::class])
@MockBean(UserRoleRepository::class, ClientRegistrationRepository::class)
@TestPropertySource(
properties = [
"app.pseudonymize.generator=BUILDIN",
@@ -186,7 +177,7 @@ class MtbFileRestControllerTest {
status { isAccepted() }
}
verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
verify(requestProcessor, times(1)).processMtbFile(any())
}
@Test
@@ -199,26 +190,33 @@ class MtbFileRestControllerTest {
status { isAccepted() }
}
verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
verify(requestProcessor, times(1)).processMtbFile(any())
}
}
companion object {
val mtbFile = Mtb.builder()
.patient(
val mtbFile: MtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.id("PID")
.withId("PID")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.episodesOfCare(
listOf(
MtbEpisodeOfCare.builder()
.id("1")
.patient(Reference.builder().id("PID").build())
.period(PeriodDate.builder().start(Date.from(Instant.parse("2023-08-08T02:00:00.00Z"))).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()

4
src/integrationTest/kotlin/dev/dnpm/etl/processor/monitoring/RequestRepositoryTest.kt
View File

@@ -27,8 +27,8 @@ 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.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
@@ -39,7 +39,7 @@ import java.time.Instant
@DataJdbcTest
@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE)
@Transactional
@MockitoBean(types = [MtbFileSender::class])
@MockBean(MtbFileSender::class)
@TestPropertySource(
properties = [
"app.pseudonymize.generator=buildin",

31
src/integrationTest/kotlin/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGeneratorTest.kt
View File

@@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
@@ -19,7 +19,6 @@
package dev.dnpm.etl.processor.pseudonym
import dev.dnpm.etl.processor.config.AppFhirConfig
import dev.dnpm.etl.processor.config.GPasConfigProperties
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach
@@ -43,37 +42,30 @@ 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:9990/ttp-fhir/fhir/gpas",
"test", "test2",
"http://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate",
"test",
null,
null,
null
)
this.restTemplate = RestTemplate()
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.generator =
GpasPseudonymGenerator(gPasConfigProperties, retryTemplate, restTemplate, appFhirConfig)
this.generator = GpasPseudonymGenerator(gPasConfigProperties, retryTemplate, restTemplate)
}
@Test
fun shouldReturnExpectedPseudonym() {
this.mockRestServiceServer.expect {
method(HttpMethod.POST)
requestTo("https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
requestTo("http://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
}.andRespond {
withStatus(HttpStatus.OK).body(
getDummyResponseBody(
"1234",
"test",
"test1234ABCDEF567890"
)
)
withStatus(HttpStatus.OK).body(getDummyResponseBody("1234", "test", "test1234ABCDEF567890"))
.createResponse(it)
}
@@ -84,7 +76,7 @@ class GpasPseudonymGeneratorTest {
fun shouldThrowExceptionIfGpasNotAvailable() {
this.mockRestServiceServer.expect {
method(HttpMethod.POST)
requestTo("https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
requestTo("http://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
}.andRespond {
withException(IOException("Simulated IO error")).createResponse(it)
}
@@ -96,13 +88,10 @@ class GpasPseudonymGeneratorTest {
fun shouldThrowExceptionIfGpasDoesNotReturn2xxResponse() {
this.mockRestServiceServer.expect {
method(HttpMethod.POST)
requestTo("https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
requestTo("http://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
}.andRespond {
withStatus(HttpStatus.FOUND)
.header(
HttpHeaders.LOCATION,
"https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate"
)
.header(HttpHeaders.LOCATION, "https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
.createResponse(it)
}

4
src/integrationTest/kotlin/dev/dnpm/etl/processor/services/RequestServiceIntegrationTest.kt
View File

@@ -31,8 +31,8 @@ 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
@@ -42,7 +42,7 @@ import java.time.Instant
@ExtendWith(SpringExtension::class)
@SpringBootTest
@Transactional
@MockitoBean(types = [MtbFileSender::class])
@MockBean(MtbFileSender::class)
@TestPropertySource(
properties = [
"app.pseudonymize.generator=buildin",

50
src/integrationTest/kotlin/dev/dnpm/etl/processor/web/ConfigControllerTest.kt
View File

@@ -19,22 +19,21 @@
package dev.dnpm.etl.processor.web
import com.gargoylesoftware.htmlunit.WebClient
import com.gargoylesoftware.htmlunit.html.HtmlPage
import dev.dnpm.etl.processor.config.AppConfiguration
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
import dev.dnpm.etl.processor.monitoring.GIcsConnectionCheckService
import dev.dnpm.etl.processor.monitoring.GPasConnectionCheckService
import dev.dnpm.etl.processor.monitoring.RestConnectionCheckService
import dev.dnpm.etl.processor.output.MtbFileSender
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.security.TokenService
import dev.dnpm.etl.processor.services.TransformationService
import dev.dnpm.etl.processor.security.UserRoleService
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
@@ -47,6 +46,7 @@ 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
@@ -55,7 +55,6 @@ import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequ
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user
import org.springframework.test.context.ContextConfiguration
import org.springframework.test.context.TestPropertySource
import org.springframework.test.context.bean.override.mockito.MockitoBean
import org.springframework.test.context.junit.jupiter.SpringExtension
import org.springframework.test.web.reactive.server.WebTestClient
import org.springframework.test.web.servlet.*
@@ -82,17 +81,14 @@ abstract class MockSink : Sinks.Many<Boolean>
"app.pseudonymize.generator=BUILDIN"
]
)
@MockitoBean(name = "configsUpdateProducer", types = [MockSink::class])
@MockitoBean(
types = [
@MockBean(name = "configsUpdateProducer", classes = [MockSink::class])
@MockBean(
Generator::class,
MtbFileSender::class,
RequestProcessor::class,
TransformationService::class,
GPasConnectionCheckService::class,
RestConnectionCheckService::class,
GIcsConnectionCheckService::class
]
)
class ConfigControllerTest {
@@ -147,10 +143,8 @@ class ConfigControllerTest {
"app.security.admin-user=admin"
]
)
@MockitoBean(
types = [
@MockBean(
TokenService::class
]
)
inner class WithTokensEnabled {
private lateinit var tokenService: TokenService
@@ -184,13 +178,7 @@ class ConfigControllerTest {
@Test
fun testShouldNotSaveTokenWithExstingName() {
whenever(tokenService.addToken(anyString())).thenReturn(
Result.failure(
RuntimeException(
"Testfailure"
)
)
)
whenever(tokenService.addToken(anyString())).thenReturn(Result.failure(RuntimeException("Testfailure")))
mockMvc.post("/configs/tokens") {
with(user("admin").roles("ADMIN"))
@@ -264,10 +252,8 @@ class ConfigControllerTest {
"app.security.admin-password={noop}very-secret"
]
)
@MockitoBean(
types = [
@MockBean(
UserRoleService::class
]
)
inner class WithUserRolesEnabled {
private lateinit var userRoleService: UserRoleService
@@ -311,10 +297,7 @@ class ConfigControllerTest {
val idCaptor = argumentCaptor<Long>()
val roleCaptor = argumentCaptor<Role>()
verify(userRoleService, times(1)).updateUserRole(
idCaptor.capture(),
roleCaptor.capture()
)
verify(userRoleService, times(1)).updateUserRole(idCaptor.capture(), roleCaptor.capture())
assertThat(idCaptor.firstValue).isEqualTo(42)
assertThat(roleCaptor.firstValue).isEqualTo(Role.ADMIN)
@@ -352,23 +335,20 @@ class ConfigControllerTest {
@BeforeEach
fun setup(
applicationContext: WebApplicationContext
applicationContext: WebApplicationContext,
) {
this.webClient = MockMvcWebTestClient
.bindToApplicationContext(applicationContext).build()
}
@Test
fun testShouldRequestGPasSSE() {
val expectedEvent =
ConnectionCheckResult.GPasConnectionCheckResult(true, Instant.now(), Instant.now())
fun testShouldRequestSSE() {
val expectedEvent = ConnectionCheckResult.GPasConnectionCheckResult(true, Instant.now(), Instant.now())
connectionCheckUpdateProducer.tryEmitNext(expectedEvent)
connectionCheckUpdateProducer.emitComplete { _, _ -> true }
val result =
webClient.get().uri("http://localhost/configs/events").accept(TEXT_EVENT_STREAM)
.exchange()
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)

10
src/integrationTest/kotlin/dev/dnpm/etl/processor/web/HomeControllerTest.kt
View File

@@ -19,6 +19,8 @@
package dev.dnpm.etl.processor.web
import com.gargoylesoftware.htmlunit.WebClient
import com.gargoylesoftware.htmlunit.html.HtmlPage
import dev.dnpm.etl.processor.*
import dev.dnpm.etl.processor.config.AppConfiguration
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
@@ -28,8 +30,6 @@ 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
@@ -40,13 +40,13 @@ 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.boot.test.mock.mockito.MockBean
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
@@ -71,8 +71,8 @@ import java.util.*
"app.security.admin-password={noop}very-secret"
]
)
@MockitoBean(
types = [RequestService::class]
@MockBean(
RequestService::class
)
class HomeControllerTest {

10
src/integrationTest/kotlin/dev/dnpm/etl/processor/web/LoginControllerTest.kt
View File

@@ -19,21 +19,21 @@
package dev.dnpm.etl.processor.web
import com.gargoylesoftware.htmlunit.WebClient
import com.gargoylesoftware.htmlunit.html.HtmlPage
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.boot.test.mock.mockito.MockBean
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
@@ -56,8 +56,8 @@ import org.springframework.test.web.servlet.htmlunit.MockMvcWebClientBuilder
"app.security.enable-tokens=true"
]
)
@MockitoBean(
types = [TokenService::class]
@MockBean(
TokenService::class,
)
class LoginControllerTest {

2
src/integrationTest/kotlin/dev/dnpm/etl/processor/web/StatisticsControllerTest.kt
View File

@@ -19,9 +19,9 @@
package dev.dnpm.etl.processor.web
import com.gargoylesoftware.htmlunit.WebClient
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

6
src/integrationTest/kotlin/dev/dnpm/etl/processor/web/StatisticsRestControllerTest.kt
View File

@@ -41,10 +41,10 @@ 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.boot.test.mock.mockito.MockBean
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
@@ -74,8 +74,8 @@ import java.time.temporal.ChronoUnit
"app.security.admin-password={noop}very-secret"
]
)
@MockitoBean(
types = [RequestService::class]
@MockBean(
RequestService::class
)
class StatisticsRestControllerTest {

13
src/main/java/dev/dnpm/etl/processor/consent/ConsentDomain.java
View File

@@ -1,13 +0,0 @@
package dev.dnpm.etl.processor.consent;
public enum ConsentDomain {
/**
* MII Broad consent
*/
BROAD_CONSENT,
/**
* GenomDe Modellvorhaben §64e
*/
MODELLVORHABEN_64E
}

307
src/main/java/dev/dnpm/etl/processor/consent/GicsConsentService.java
View File

@@ -1,307 +0,0 @@
package dev.dnpm.etl.processor.consent;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.DataFormatException;
import dev.dnpm.etl.processor.config.AppFhirConfig;
import dev.dnpm.etl.processor.config.GIcsConfigProperties;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
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.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;
import java.net.URI;
import java.util.Date;
/**
* Service to request Consent from remote gICS installation
*
* @since 0.11
*/
public class GicsConsentService implements IConsentService {
private final Logger log = LoggerFactory.getLogger(GicsConsentService.class);
public static final String IS_CONSENTED_ENDPOINT = "/$isConsented";
public static final String IS_POLICY_STATES_FOR_PERSON_ENDPOINT = "/$currentPolicyStatesForPerson";
private final RetryTemplate retryTemplate;
private final RestTemplate restTemplate;
private final FhirContext fhirContext;
private final GIcsConfigProperties gIcsConfigProperties;
public GicsConsentService(
GIcsConfigProperties gIcsConfigProperties,
RetryTemplate retryTemplate,
RestTemplate restTemplate,
AppFhirConfig appFhirConfig
) {
this.retryTemplate = retryTemplate;
this.restTemplate = restTemplate;
this.fhirContext = appFhirConfig.fhirContext();
this.gIcsConfigProperties = gIcsConfigProperties;
log.info("GicsConsentService initialized...");
}
protected Parameters getFhirRequestParameters(
String personIdentifierValue
) {
var result = new Parameters();
result.addParameter(
new ParametersParameterComponent()
.setName("personIdentifier")
.setValue(
new Identifier()
.setValue(personIdentifierValue)
.setSystem(this.gIcsConfigProperties.getPersonIdentifierSystem())
)
);
result.addParameter(
new ParametersParameterComponent()
.setName("domain")
.setValue(
new StringType()
.setValue(this.gIcsConfigProperties.getBroadConsentDomainName())
)
);
result.addParameter(
new ParametersParameterComponent()
.setName("policy")
.setValue(
new Coding()
.setCode(this.gIcsConfigProperties.getBroadConsentPolicyCode())
.setSystem(this.gIcsConfigProperties.getBroadConsentPolicySystem())
)
);
/*
* is mandatory parameter, but we ignore it via additional configuration parameter
* 'ignoreVersionNumber'.
*/
result.addParameter(
new ParametersParameterComponent()
.setName("version")
.setValue(new StringType().setValue("1.1")
)
);
/* add config parameter with:
* ignoreVersionNumber -> true ->> Reason is we cannot know which policy version each patient
* has possibly signed or not, therefore we are happy with any version found.
* unknownStateIsConsideredAsDecline -> true
*/
var config = new ParametersParameterComponent()
.setName("config")
.addPart(
new ParametersParameterComponent()
.setName("ignoreVersionNumber")
.setValue(new BooleanType().setValue(true))
)
.addPart(
new ParametersParameterComponent()
.setName("unknownStateIsConsideredAsDecline")
.setValue(new BooleanType().setValue(false))
);
result.addParameter(config);
return result;
}
private URI endpointUri(String endpoint) {
assert this.gIcsConfigProperties.getUri() != null;
return UriComponentsBuilder.fromUriString(this.gIcsConfigProperties.getUri()).path(endpoint).build().toUri();
}
private HttpHeaders headersWithHttpBasicAuth() {
assert this.gIcsConfigProperties.getUri() != null;
var headers = new HttpHeaders();
headers.setContentType(MediaType.APPLICATION_XML);
if (
StringUtils.isBlank(this.gIcsConfigProperties.getUsername())
|| StringUtils.isBlank(this.gIcsConfigProperties.getPassword())
) {
return headers;
}
headers.setBasicAuth(this.gIcsConfigProperties.getUsername(), this.gIcsConfigProperties.getPassword());
return headers;
}
protected String callGicsApi(Parameters parameter, String endpoint) {
var parameterAsXml = fhirContext.newXmlParser().encodeResourceToString(parameter);
HttpEntity<String> requestEntity = new HttpEntity<>(parameterAsXml, this.headersWithHttpBasicAuth());
try {
var responseEntity = retryTemplate.execute(
ctx -> restTemplate.exchange(endpointUri(endpoint), HttpMethod.POST, requestEntity, String.class)
);
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;
}
} 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;
}
}
@Override
public TtpConsentStatus getTtpBroadConsentStatus(String personIdentifierValue) {
var consentStatusResponse = callGicsApi(
getFhirRequestParameters(personIdentifierValue),
GicsConsentService.IS_CONSENTED_ENDPOINT
);
return evaluateConsentResponse(consentStatusResponse);
}
protected Bundle currentConsentForPersonAndTemplate(
String personIdentifierValue,
ConsentDomain consentDomain,
Date requestDate
) {
var requestParameter = buildRequestParameterCurrentPolicyStatesForPerson(
personIdentifierValue,
requestDate,
consentDomain
);
var consentDataSerialized = callGicsApi(requestParameter,
GicsConsentService.IS_POLICY_STATES_FOR_PERSON_ENDPOINT);
if (consentDataSerialized == null) {
// error occurred - should not process further!
throw new IllegalStateException(
"consent data request failed - stopping processing! - try again or fix other problems first.");
}
var iBaseResource = fhirContext.newJsonParser()
.parseResource(consentDataSerialized);
if (iBaseResource instanceof OperationOutcome) {
// log error - very likely a configuration error
String errorMessage =
"Consent request failed! Check outcome:\n " + consentDataSerialized;
log.error(errorMessage);
throw new IllegalStateException(errorMessage);
} else if (iBaseResource instanceof Bundle bundle) {
return bundle;
} else {
String errorMessage = "Consent request failed! Unexpected response received! -> "
+ consentDataSerialized;
log.error(errorMessage);
throw new IllegalStateException(errorMessage);
}
}
@NotNull
private String getConsentDomainName(ConsentDomain targetConsentDomain) {
return switch (targetConsentDomain) {
case BROAD_CONSENT -> gIcsConfigProperties.getBroadConsentDomainName();
case MODELLVORHABEN_64E -> gIcsConfigProperties.getGenomDeConsentDomainName();
};
}
protected Parameters buildRequestParameterCurrentPolicyStatesForPerson(
String personIdentifierValue,
Date requestDate,
ConsentDomain consentDomain
) {
var requestParameter = new Parameters();
requestParameter.addParameter(
new ParametersParameterComponent()
.setName("personIdentifier")
.setValue(
new Identifier()
.setValue(personIdentifierValue)
.setSystem(this.gIcsConfigProperties.getPersonIdentifierSystem())
)
);
requestParameter.addParameter(
new ParametersParameterComponent()
.setName("domain")
.setValue(new StringType().setValue(getConsentDomainName(consentDomain)))
);
Parameters nestedConfigParameters = new Parameters();
nestedConfigParameters
.addParameter(
new ParametersParameterComponent()
.setName("idMatchingType")
.setValue(new Coding()
.setSystem("https://ths-greifswald.de/fhir/CodeSystem/gics/IdMatchingType")
.setCode("AT_LEAST_ONE")
)
)
.addParameter("ignoreVersionNumber", false)
.addParameter("unknownStateIsConsideredAsDecline", false)
.addParameter("requestDate", new DateType().setValue(requestDate));
requestParameter.addParameter(
new ParametersParameterComponent().setName("config").addPart().setResource(nestedConfigParameters)
);
return requestParameter;
}
private TtpConsentStatus evaluateConsentResponse(String consentStatusResponse) {
if (consentStatusResponse == null) {
return TtpConsentStatus.FAILED_TO_ASK;
}
try {
var response = fhirContext.newJsonParser().parseResource(consentStatusResponse);
if (response instanceof Parameters responseParameters) {
var responseValue = responseParameters.getParameter("consented").getValue();
var isConsented = responseValue.castToBoolean(responseValue);
if (!isConsented.hasValue()) {
return TtpConsentStatus.FAILED_TO_ASK;
}
if (isConsented.booleanValue()) {
return TtpConsentStatus.BROAD_CONSENT_GIVEN;
} else {
return TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED;
}
} else if (response instanceof OperationOutcome outcome) {
log.error("failed to get consent status from ttp. probably configuration error. "
+ "outcome: '{}'", fhirContext.newJsonParser().encodeToString(outcome));
}
} catch (DataFormatException dfe) {
log.error("failed to parse response to FHIR R4 resource.", dfe);
}
return TtpConsentStatus.FAILED_TO_ASK;
}
@Override
public Bundle getConsent(String patientId, Date requestDate, ConsentDomain consentDomain) {
return currentConsentForPersonAndTemplate(patientId, consentDomain, requestDate);
}
}

27
src/main/java/dev/dnpm/etl/processor/consent/IConsentService.java
View File

@@ -1,27 +0,0 @@
package dev.dnpm.etl.processor.consent;
import java.util.Date;
import org.hl7.fhir.r4.model.Bundle;
public interface IConsentService {
/**
* Get broad consent status for a patient identifier
*
* @param personIdentifierValue patient identifier used for consent data
* @return status of broad consent
* @apiNote cannot not differ between not asked and rejected
*
*/
TtpConsentStatus getTtpBroadConsentStatus(String personIdentifierValue);
/**
* Get broad consent policies with respect to a request date
*
* @param personIdentifierValue patient identifier used for consent data
* @param requestDate target date until consent data should be considered
* @return consent policies as bundle; <p>if empty patient has not been asked, yet.</p>
*/
Bundle getConsent(String personIdentifierValue, Date requestDate, ConsentDomain consentDomain);
}

31
src/main/java/dev/dnpm/etl/processor/consent/MtbFileConsentService.java
View File

@@ -1,31 +0,0 @@
package dev.dnpm.etl.processor.consent;
import java.util.Date;
import org.hl7.fhir.r4.model.Bundle;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class MtbFileConsentService implements IConsentService {
private static final Logger log = LoggerFactory.getLogger(MtbFileConsentService.class);
public MtbFileConsentService() {
log.info("ConsentCheckFileBased initialized...");
}
@Override
public TtpConsentStatus getTtpBroadConsentStatus(String personIdentifierValue) {
return TtpConsentStatus.UNKNOWN_CHECK_FILE;
}
/**
* EMPTY METHOD: NOT IMPLEMENTED
*
* @return empty bundle
*/
@Override
public Bundle getConsent(String personIdentifierValue, Date requestDate,
ConsentDomain consentDomain) {
return new Bundle();
}
}

38
src/main/java/dev/dnpm/etl/processor/consent/TtpConsentStatus.java
View File

@@ -1,38 +0,0 @@
package dev.dnpm.etl.processor.consent;
public enum TtpConsentStatus {
/**
* Valid consent found
*/
BROAD_CONSENT_GIVEN,
/**
* Missing or rejected...actually unknown
*/
BROAD_CONSENT_MISSING_OR_REJECTED,
/**
* No Broad consent policy found
*/
BROAD_CONSENT_MISSING,
/**
* Research policy has been rejected
*/
BROAD_CONSENT_REJECTED,
GENOM_DE_CONSENT_SEQUENCING_PERMIT,
/**
* No GenomDE consent policy found
*/
GENOM_DE_CONSENT_MISSING,
/**
* GenomDE consent policy found, but has been rejected
*/
GENOM_DE_SEQUENCING_REJECTED,
/**
* Consent status is validate via file property 'consent.status'
*/
UNKNOWN_CHECK_FILE,
/**
* Due technical problems consent status is unknown
*/
FAILED_TO_ASK
}

2
src/main/java/dev/dnpm/etl/processor/pseudonym/Generator.java
View File

@@ -23,6 +23,4 @@ public interface Generator {
String generate(String id);
String generateGenomDeTan(String id);
}

131
src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java
View File

@@ -21,13 +21,8 @@ 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 java.net.URI;
import java.net.URISyntaxException;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.StringUtils;
import org.apache.hc.core5.net.URIBuilder;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
@@ -37,76 +32,42 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.http.*;
import org.springframework.retry.support.RetryTemplate;
import org.springframework.web.client.HttpClientErrorException.BadRequest;
import org.springframework.web.client.HttpClientErrorException.Unauthorized;
import org.springframework.web.client.RestClientException;
import org.springframework.web.client.RestTemplate;
public class GpasPseudonymGenerator implements Generator {
private final FhirContext r4Context;
private final static FhirContext r4Context = FhirContext.forR4();
private final String gPasUrl;
private final String psnTargetDomain;
private final HttpHeaders httpHeader;
private final RetryTemplate retryTemplate;
private final Logger log = LoggerFactory.getLogger(GpasPseudonymGenerator.class);
private final RestTemplate restTemplate;
private final @NotNull String genomDeTanDomain;
private final @NotNull String pidPsnDomain;
protected final static String createOrGetPsn = "$pseudonymizeAllowCreate";
protected final static String createMultiDomainPsn = "$pseudonymize-secondary";
private final static String SINGLE_PSN_PART_NAME = "pseudonym";
private final static String MULTI_PSN_PART_NAME = "value";
public GpasPseudonymGenerator(GPasConfigProperties gpasCfg, RetryTemplate retryTemplate,
RestTemplate restTemplate, AppFhirConfig appFhirConfig) {
private final RestTemplate restTemplate;
public GpasPseudonymGenerator(GPasConfigProperties gpasCfg, RetryTemplate retryTemplate, RestTemplate restTemplate) {
this.retryTemplate = retryTemplate;
this.restTemplate = restTemplate;
this.gPasUrl = gpasCfg.getUri();
this.pidPsnDomain = gpasCfg.getPatientDomain();
this.genomDeTanDomain = gpasCfg.getGenomDeTanDomain();
this.r4Context = appFhirConfig.fhirContext();
this.psnTargetDomain = gpasCfg.getTarget();
httpHeader = getHttpHeaders(gpasCfg.getUsername(), gpasCfg.getPassword());
log.debug("{} has been initialized", this.getClass().getName());
log.debug(String.format("%s has been initialized", this.getClass().getName()));
}
@Override
public String generate(String id) {
return generate(id, PsnDomainType.SINGLE_PSN_DOMAIN);
}
@Override
public String generateGenomDeTan(String id) {
return generate(id, PsnDomainType.MULTI_PSN_DOMAIN);
}
protected String generate(String id, PsnDomainType domainType) {
switch (domainType) {
case SINGLE_PSN_DOMAIN -> {
final var requestBody = createSinglePsnRequestBody(id, pidPsnDomain);
final var responseEntity = getGpasPseudonym(requestBody, createOrGetPsn);
final var gPasPseudonymResult = (Parameters) r4Context.newJsonParser()
var gPasRequestBody = getGpasRequestBody(id);
var responseEntity = getGpasPseudonym(gPasRequestBody);
var gPasPseudonymResult = (Parameters) r4Context.newJsonParser()
.parseResource(responseEntity.getBody());
return unwrapPseudonym(gPasPseudonymResult, SINGLE_PSN_PART_NAME);
}
case MULTI_PSN_DOMAIN -> {
final var requestBody = createMultiPsnRequestBody(id, genomDeTanDomain);
final var responseEntity = getGpasPseudonym(requestBody, createMultiDomainPsn);
final var gPasPseudonymResult = (Parameters) r4Context.newJsonParser()
.parseResource(responseEntity.getBody());
return unwrapPseudonym(gPasPseudonymResult, MULTI_PSN_PART_NAME);
}
}
throw new NotImplementedException(
"give domain type '%s' is unexpected and is currently not supported!".formatted(
domainType));
return unwrapPseudonym(gPasPseudonymResult);
}
@NotNull
public static String unwrapPseudonym(Parameters gPasPseudonymResult, String targetPartName) {
public static String unwrapPseudonym(Parameters gPasPseudonymResult) {
final var parameters = gPasPseudonymResult.getParameter().stream().findFirst();
if (parameters.isEmpty()) {
@@ -114,7 +75,7 @@ public class GpasPseudonymGenerator implements Generator {
}
final var identifier = (Identifier) parameters.get().getPart().stream()
.filter(a -> a.getName().equals(targetPartName))
.filter(a -> a.getName().equals("pseudonym"))
.findFirst()
.orElseGet(ParametersParameterComponent::new).getValue();
@@ -136,80 +97,42 @@ public class GpasPseudonymGenerator implements Generator {
return psnValue.replaceAll(forbiddenCharsRegex, "_");
}
@NotNull
protected ResponseEntity<String> getGpasPseudonym(String gPasRequestBody, String apiEndpoint) {
protected ResponseEntity<String> getGpasPseudonym(String gPasRequestBody) {
HttpEntity<String> requestEntity = new HttpEntity<>(gPasRequestBody, this.httpHeader);
ResponseEntity<String> responseEntity;
try {
var targetUrl = buildRequestUrl(apiEndpoint);
ResponseEntity<String> responseEntity = retryTemplate.execute(
ctx -> restTemplate.exchange(targetUrl, HttpMethod.POST, requestEntity,
responseEntity = retryTemplate.execute(
ctx -> restTemplate.exchange(gPasUrl, HttpMethod.POST, requestEntity,
String.class));
if (responseEntity.getStatusCode().is2xxSuccessful()) {
log.debug("API request succeeded. Response: {}", responseEntity.getStatusCode());
} else {
log.warn("API request unsuccessful. Response: {}", requestEntity.getBody());
throw new PseudonymRequestFailed("API request unsuccessful gPas unsuccessful.");
}
return responseEntity;
}
} catch (RestClientException rce) {
if (rce instanceof BadRequest) {
String msg = "gPas or request configuration is incorrect. Please check both."
+ rce.getMessage();
log.debug(
msg);
throw new PseudonymRequestFailed(msg, rce);
}
if (rce instanceof Unauthorized) {
var msg = "gPas access credentials are invalid check your configuration. msg: '%s".formatted(
rce.getMessage());
log.error(msg);
throw new PseudonymRequestFailed(msg, rce);
}
} catch (Exception unexpected) {
throw new PseudonymRequestFailed(
"API request due unexpected error unsuccessful gPas unsuccessful.", unexpected);
}
throw new PseudonymRequestFailed(
"API request due unexpected error unsuccessful gPas unsuccessful.");
}
protected URI buildRequestUrl(String apiEndpoint) throws URISyntaxException {
var gPasUrl1 = gPasUrl;
if (gPasUrl.lastIndexOf("/") == gPasUrl.length() - 1) {
gPasUrl1 = gPasUrl.substring(0, gPasUrl.length() - 1);
}
var urlBuilder = new URIBuilder(new URI(gPasUrl1)).appendPath(apiEndpoint);
return urlBuilder.build();
}
protected String createSinglePsnRequestBody(String id, String targetDomain) {
final var requestParameters = new Parameters();
protected String getGpasRequestBody(String id) {
var requestParameters = new Parameters();
requestParameters.addParameter().setName("target")
.setValue(new StringType().setValue(targetDomain));
.setValue(new StringType().setValue(psnTargetDomain));
requestParameters.addParameter().setName("original")
.setValue(new StringType().setValue(id));
final IParser iParser = r4Context.newJsonParser();
return iParser.encodeResourceToString(requestParameters);
}
protected String createMultiPsnRequestBody(String id, String targetDomain) {
final var param = new Parameters();
ParametersParameterComponent targetParam = param.addParameter().setName("original");
targetParam.addPart(
new ParametersParameterComponent().setName("target")
.setValue(new StringType(targetDomain)));
targetParam.addPart(
new ParametersParameterComponent().setName("value").setValue(new StringType(id)));
targetParam
.addPart(new ParametersParameterComponent().setName("count").setValue(
new StringType("1")));
final IParser iParser = r4Context.newJsonParser();
return iParser.encodeResourceToString(param);
}
@NotNull
protected HttpHeaders getHttpHeaders(String gPasUserName, String gPasPassword) {
var headers = new HttpHeaders();

12
src/main/java/dev/dnpm/etl/processor/pseudonym/PsnDomainType.java
View File

@@ -1,12 +0,0 @@
package dev.dnpm.etl.processor.pseudonym;
public enum PsnDomainType {
/**
* one pseudonym per original value
*/
SINGLE_PSN_DOMAIN,
/**
* multiple pseudonymes for one original value
*/
MULTI_PSN_DOMAIN
}

105
src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt
View File

@@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
@@ -21,13 +21,19 @@ 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,
var genomDeTestSubmission: Boolean = false
var duplicationDetection: Boolean = true
) {
companion object {
const val NAME = "app"
@@ -47,87 +53,25 @@ data class PseudonymizeConfigProperties(
@ConfigurationProperties(GPasConfigProperties.NAME)
data class GPasConfigProperties(
val uri: String?,
val patientDomain: String = "etl-processor",
val genomDeTanDomain: String = "ccdn",
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(ConsentConfigProperties.NAME)
data class ConsentConfigProperties(
var service: ConsentService = ConsentService.NONE
) {
companion object {
const val NAME = "app.consent"
}
}
@ConfigurationProperties(GIcsConfigProperties.NAME)
data class GIcsConfigProperties(
/**
* Base URL to gICS System
*
*/
val uri: String?,
val username: String? = null,
val password: String? = null,
/**
* gICS specific system
* **/
val personIdentifierSystem: String =
"https://ths-greifswald.de/fhir/gics/identifiers/Patienten-ID",
/**
* Domain of broad consent resources
**/
val broadConsentDomainName: String = "MII",
/**
* Domain of Modelvorhaben 64e consent resources
**/
val genomDeConsentDomainName: String = "GenomDE_MV",
/**
* Value to expect in case of positiv consent
*/
val broadConsentPolicyCode: String = "2.16.840.1.113883.3.1937.777.24.5.3.6",
/**
* Consent Policy which should be used for consent check
*/
val broadConsentPolicySystem: String = "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3",
/**
* Value to expect in case of positiv consent
*/
val genomeDePolicyCode: String = "sequencing",
/**
* Consent Policy which should be used for consent check
*/
val genomeDePolicySystem: String = "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
/**
* Consent version (fixed version)
*
*/
val genomeDeConsentVersion: String = "2.0"
) {
companion object {
const val NAME = "app.consent.gics"
}
}
@ConfigurationProperties(RestTargetProperties.NAME)
data class RestTargetProperties(
val uri: String?,
val username: String?,
val password: String?
val password: String?,
val isBwhc: Boolean = false,
) {
companion object {
const val NAME = "app.rest"
@@ -138,8 +82,18 @@ 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 = "${outputTopic}_response",
val groupId: String = "${outputTopic}_group",
@get:DeprecatedConfigurationProperty(
reason = "Deprecated",
replacement = "outputResponseTopic"
)
val responseTopic: String = outputResponseTopic,
val groupId: String = "${topic}_group",
val servers: String = ""
) {
companion object {
@@ -165,11 +119,6 @@ enum class PseudonymGenerator {
GPAS
}
enum class ConsentService {
NONE,
GICS
}
data class TransformationProperties(
val path: String,
val from: String,

253
src/main/kotlin/dev/dnpm/etl/processor/config/AppConfiguration.kt
View File

@@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 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
@@ -20,29 +20,32 @@
package dev.dnpm.etl.processor.config
import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.consent.MtbFileConsentService
import dev.dnpm.etl.processor.consent.GicsConsentService
import dev.dnpm.etl.processor.consent.IConsentService
import dev.dnpm.etl.processor.monitoring.*
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
import dev.dnpm.etl.processor.monitoring.GPasConnectionCheckService
import dev.dnpm.etl.processor.monitoring.ReportService
import dev.dnpm.etl.processor.pseudonym.AnonymizingGenerator
import dev.dnpm.etl.processor.pseudonym.Generator
import dev.dnpm.etl.processor.pseudonym.GpasPseudonymGenerator
import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
import dev.dnpm.etl.processor.security.TokenRepository
import dev.dnpm.etl.processor.security.TokenService
import dev.dnpm.etl.processor.services.ConsentProcessor
import dev.dnpm.etl.processor.services.Transformation
import dev.dnpm.etl.processor.services.TransformationService
import org.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.RegistryBuilder
import org.slf4j.LoggerFactory
import org.springframework.boot.autoconfigure.condition.AnyNestedCondition
import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty
import org.springframework.boot.context.properties.EnableConfigurationProperties
import org.springframework.context.annotation.Bean
import org.springframework.context.annotation.Conditional
import org.springframework.context.annotation.Configuration
import org.springframework.context.annotation.ConfigurationCondition
import org.springframework.data.jdbc.repository.config.AbstractJdbcConfiguration
import org.springframework.http.client.HttpComponentsClientHttpRequestFactory
import org.springframework.retry.RetryCallback
import org.springframework.retry.RetryContext
import org.springframework.retry.RetryListener
@@ -55,6 +58,13 @@ import org.springframework.security.provisioning.InMemoryUserDetailsManager
import org.springframework.web.client.HttpClientErrorException
import org.springframework.web.client.RestTemplate
import reactor.core.publisher.Sinks
import java.io.BufferedInputStream
import java.io.FileInputStream
import java.security.KeyStore
import java.security.cert.CertificateFactory
import java.security.cert.X509Certificate
import javax.net.ssl.SSLContext
import javax.net.ssl.TrustManagerFactory
import kotlin.time.Duration.Companion.seconds
import kotlin.time.toJavaDuration
@@ -64,9 +74,7 @@ import kotlin.time.toJavaDuration
value = [
AppConfigProperties::class,
PseudonymizeConfigProperties::class,
GPasConfigProperties::class,
ConsentConfigProperties::class,
GIcsConfigProperties::class
GPasConfigProperties::class
]
)
@EnableScheduling
@@ -79,31 +87,113 @@ class AppConfiguration {
return RestTemplate()
}
@Bean
fun appFhirConfig(): AppFhirConfig {
return AppFhirConfig()
}
@ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "GPAS")
@Bean
fun gpasPseudonymGenerator(
configProperties: GPasConfigProperties,
retryTemplate: RetryTemplate,
restTemplate: RestTemplate,
appFhirConfig: AppFhirConfig
): Generator {
logger.info("Selected 'GpasPseudonym Generator'")
return GpasPseudonymGenerator(configProperties, retryTemplate, restTemplate, appFhirConfig)
fun gpasPseudonymGenerator(configProperties: GPasConfigProperties, retryTemplate: RetryTemplate, restTemplate: RestTemplate): Generator {
try {
if (!configProperties.sslCaLocation.isNullOrBlank()) {
return GpasPseudonymGenerator(
configProperties,
retryTemplate,
createCustomGpasRestTemplate(configProperties)
)
}
} catch (e: Exception) {
throw RuntimeException(e)
}
@ConditionalOnProperty(
value = ["app.pseudonymize.generator"],
havingValue = "BUILDIN",
matchIfMissing = true
)
return GpasPseudonymGenerator(configProperties, retryTemplate, restTemplate)
}
@ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "BUILDIN", matchIfMissing = true)
@Bean
fun buildinPseudonymGenerator(): Generator {
logger.info("Selected 'BUILDIN Pseudonym Generator'")
return AnonymizingGenerator()
}
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS")
@ConditionalOnMissingBean
@Bean
fun gpasPseudonymGeneratorOnDeprecatedProperty(configProperties: GPasConfigProperties, retryTemplate: RetryTemplate, restTemplate: RestTemplate): Generator {
try {
if (!configProperties.sslCaLocation.isNullOrBlank()) {
return GpasPseudonymGenerator(
configProperties,
retryTemplate,
createCustomGpasRestTemplate(configProperties)
)
}
} catch (e: Exception) {
throw RuntimeException(e)
}
return GpasPseudonymGenerator(configProperties, retryTemplate, restTemplate)
}
private fun createCustomGpasRestTemplate(configProperties: GPasConfigProperties): RestTemplate {
fun getSslContext(certificateLocation: String): SSLContext? {
val ks = KeyStore.getInstance(KeyStore.getDefaultType())
val fis = FileInputStream(certificateLocation)
val ca = CertificateFactory.getInstance("X.509")
.generateCertificate(BufferedInputStream(fis)) as X509Certificate
ks.load(null, null)
ks.setCertificateEntry(1.toString(), ca)
val tmf = TrustManagerFactory.getInstance(
TrustManagerFactory.getDefaultAlgorithm()
)
tmf.init(ks)
val sslContext = SSLContext.getInstance("TLS")
sslContext.init(null, tmf.trustManagers, null)
return sslContext
}
fun getCustomRestTemplate(customSslContext: SSLContext): RestTemplate {
val sslsf = SSLConnectionSocketFactory(customSslContext)
val socketFactoryRegistry = RegistryBuilder.create<ConnectionSocketFactory>()
.register("https", sslsf).register("http", PlainConnectionSocketFactory()).build()
val connectionManager = BasicHttpClientConnectionManager(
socketFactoryRegistry
)
val httpClient = HttpClients.custom()
.setConnectionManager(connectionManager).build()
val requestFactory = HttpComponentsClientHttpRequestFactory(
httpClient
)
return RestTemplate(requestFactory)
}
try {
if (!configProperties.sslCaLocation.isNullOrBlank()) {
val customSslContext = getSslContext(configProperties.sslCaLocation)
logger.warn(
String.format(
"%s has been initialized with SSL certificate %s. This is deprecated in favor of including Root CA.",
this.javaClass.name, configProperties.sslCaLocation
)
)
if (customSslContext != null) {
return getCustomRestTemplate(customSslContext)
}
}
} catch (e: Exception) {
throw RuntimeException(e)
}
throw RuntimeException("Custom SSL configuration for gPAS not usable")
}
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "BUILDIN")
@ConditionalOnMissingBean
@Bean
fun buildinPseudonymGeneratorOnDeprecatedProperty(): Generator {
return AnonymizingGenerator()
}
@@ -116,21 +206,17 @@ class AppConfiguration {
}
@Bean
fun reportService(): ReportService {
return ReportService(getObjectMapper())
}
@Bean
fun getObjectMapper(): ObjectMapper {
return JacksonConfig().objectMapper()
fun reportService(objectMapper: ObjectMapper): ReportService {
return ReportService(objectMapper)
}
@Bean
fun transformationService(
objectMapper: ObjectMapper,
configProperties: AppConfigProperties
): TransformationService {
logger.info("Apply ${configProperties.transformations.size} transformation rules")
return TransformationService(getObjectMapper(), configProperties.transformations.map {
return TransformationService(objectMapper, configProperties.transformations.map {
Transformation.of(it.path) from it.from to it.to
})
}
@@ -149,11 +235,7 @@ class AppConfiguration {
callback: RetryCallback<T, E>,
throwable: Throwable
) {
logger.warn(
"Error occured: {}. Retrying {}",
throwable.message,
context.retryCount
)
logger.warn("Error occured: {}. Retrying {}", throwable.message, context.retryCount)
}
})
.build()
@@ -161,11 +243,7 @@ class AppConfiguration {
@ConditionalOnProperty(value = ["app.security.enable-tokens"], havingValue = "true")
@Bean
fun tokenService(
userDetailsManager: InMemoryUserDetailsManager,
passwordEncoder: PasswordEncoder,
tokenRepository: TokenRepository
): TokenService {
fun tokenService(userDetailsManager: InMemoryUserDetailsManager, passwordEncoder: PasswordEncoder, tokenRepository: TokenRepository): TokenService {
return TokenService(userDetailsManager, passwordEncoder, tokenRepository)
}
@@ -186,11 +264,7 @@ class AppConfiguration {
gPasConfigProperties: GPasConfigProperties,
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
): ConnectionCheckService {
return GPasConnectionCheckService(
restTemplate,
gPasConfigProperties,
connectionCheckUpdateProducer
)
return GPasConnectionCheckService(restTemplate, gPasConfigProperties, connectionCheckUpdateProducer)
}
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS")
@@ -201,81 +275,12 @@ class AppConfiguration {
gPasConfigProperties: GPasConfigProperties,
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
): ConnectionCheckService {
return GPasConnectionCheckService(
restTemplate,
gPasConfigProperties,
connectionCheckUpdateProducer
)
return GPasConnectionCheckService(restTemplate, gPasConfigProperties, connectionCheckUpdateProducer)
}
@Bean
fun jdbcConfiguration(): AbstractJdbcConfiguration {
return AppJdbcConfiguration()
}
@Conditional(GicsEnabledCondition::class)
@Bean
fun gicsConsentService(
gIcsConfigProperties: GIcsConfigProperties,
retryTemplate: RetryTemplate,
restTemplate: RestTemplate,
appFhirConfig: AppFhirConfig
): IConsentService {
return GicsConsentService(
gIcsConfigProperties,
retryTemplate,
restTemplate,
appFhirConfig
)
}
@Conditional(GicsEnabledCondition::class)
@Bean
fun consentProcessor(
configProperties: AppConfigProperties,
gIcsConfigProperties: GIcsConfigProperties,
getObjectMapper: ObjectMapper,
appFhirConfig: AppFhirConfig,
gicsConsentService: IConsentService
): ConsentProcessor {
return ConsentProcessor(
configProperties,
gIcsConfigProperties,
getObjectMapper,
appFhirConfig.fhirContext(),
gicsConsentService
)
}
@Conditional(GicsEnabledCondition::class)
@Bean
fun gIcsConnectionCheckService(
restTemplate: RestTemplate,
gIcsConfigProperties: GIcsConfigProperties,
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
): ConnectionCheckService {
return GIcsConnectionCheckService(
restTemplate,
gIcsConfigProperties,
connectionCheckUpdateProducer
)
}
@Bean
@ConditionalOnMissingBean
fun iGetConsentService(): IConsentService {
return MtbFileConsentService()
}
}
class GicsEnabledCondition :
AnyNestedCondition(ConfigurationCondition.ConfigurationPhase.REGISTER_BEAN) {
@ConditionalOnProperty(name = ["app.consent.service"], havingValue = "gics")
@ConditionalOnProperty(name = ["app.consent.gics.uri"])
class OnGicsServiceSelected {
// Just for Condition
}
}

16
src/main/kotlin/dev/dnpm/etl/processor/config/AppFhirConfig.kt
View File

@@ -1,16 +0,0 @@
package dev.dnpm.etl.processor.config
import ca.uhn.fhir.context.FhirContext
import org.springframework.context.annotation.Bean
import org.springframework.context.annotation.Configuration
@Configuration
class AppFhirConfig {
private val fhirCtx: FhirContext = FhirContext.forR4()
@Bean
fun fhirContext(): FhirContext {
return fhirCtx
}
}

10
src/main/kotlin/dev/dnpm/etl/processor/config/AppKafkaConfiguration.kt
View File

@@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 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
@@ -20,7 +20,6 @@
package dev.dnpm.etl.processor.config
import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.consent.ConsentEvaluator
import dev.dnpm.etl.processor.input.KafkaInputListener
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
@@ -72,7 +71,7 @@ class AppKafkaConfiguration {
kafkaProperties: KafkaProperties,
kafkaResponseProcessor: KafkaResponseProcessor
): KafkaMessageListenerContainer<String, String> {
val containerProperties = ContainerProperties(kafkaProperties.outputResponseTopic)
val containerProperties = ContainerProperties(kafkaProperties.responseTopic)
containerProperties.messageListener = kafkaResponseProcessor
return KafkaMessageListenerContainer(consumerFactory, containerProperties)
}
@@ -101,10 +100,9 @@ class AppKafkaConfiguration {
@ConditionalOnProperty(value = ["app.kafka.input-topic"])
fun kafkaInputListener(
requestProcessor: RequestProcessor,
objectMapper: ObjectMapper,
consentEvaluator: ConsentEvaluator
objectMapper: ObjectMapper
): KafkaInputListener {
return KafkaInputListener(requestProcessor, consentEvaluator, objectMapper)
return KafkaInputListener(requestProcessor, objectMapper)
}
@Bean

6
src/main/kotlin/dev/dnpm/etl/processor/config/AppRestConfiguration.kt
View File

@@ -24,6 +24,7 @@ import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
import dev.dnpm.etl.processor.monitoring.ReportService
import dev.dnpm.etl.processor.monitoring.RestConnectionCheckService
import dev.dnpm.etl.processor.output.MtbFileSender
import dev.dnpm.etl.processor.output.RestBwhcMtbFileSender
import dev.dnpm.etl.processor.output.RestDipMtbFileSender
import org.slf4j.LoggerFactory
import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean
@@ -56,6 +57,11 @@ class AppRestConfiguration {
retryTemplate: RetryTemplate,
reportService: ReportService,
): MtbFileSender {
if (restTargetProperties.isBwhc) {
logger.info("Selected 'RestBwhcMtbFileSender'")
return RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
}
logger.info("Selected 'RestDipMtbFileSender'")
return RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
}

28
src/main/kotlin/dev/dnpm/etl/processor/config/AppSecurityConfiguration.kt
View File

@@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
@@ -87,17 +87,11 @@ 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 {
authorizeHttpRequests {
authorizeRequests {
authorize("/configs/**", hasRole("ADMIN"))
authorize("/mtbfile/**", hasAnyRole("MTBFILE", "ADMIN", "USER"))
authorize("/mtb/**", hasAnyRole("MTBFILE", "ADMIN", "USER"))
authorize("/report/**", hasAnyRole("ADMIN", "USER"))
authorize("*.css", permitAll)
authorize("*.ico", permitAll)
@@ -133,22 +127,13 @@ 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 {
@@ -162,10 +147,9 @@ class AppSecurityConfiguration(
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "false", matchIfMissing = true)
fun filterChain(http: HttpSecurity, passwordEncoder: PasswordEncoder): SecurityFilterChain {
http {
authorizeHttpRequests {
authorizeRequests {
authorize("/configs/**", hasRole("ADMIN"))
authorize("/mtbfile/**", hasAnyRole("MTBFILE", "ADMIN"))
authorize("/mtb/**", hasAnyRole("MTBFILE", "ADMIN"))
authorize("/report/**", hasRole("ADMIN"))
authorize(anyRequest, permitAll)
}

18
src/main/kotlin/dev/dnpm/etl/processor/config/ConsentResourceDeserializer.kt
View File

@@ -1,18 +0,0 @@
package dev.dnpm.etl.processor.config
import com.fasterxml.jackson.core.JsonParser
import com.fasterxml.jackson.databind.DeserializationContext
import com.fasterxml.jackson.databind.JsonDeserializer
import com.fasterxml.jackson.databind.JsonNode
import org.hl7.fhir.r4.model.Consent
class ConsentResourceDeserializer : JsonDeserializer<Consent>() {
override fun deserialize(p: JsonParser?, ctxt: DeserializationContext?): Consent {
val jsonNode = p?.readValueAsTree<JsonNode>()
val json = jsonNode?.toString()
return JacksonConfig.fhirContext().newJsonParser().parseResource(json) as Consent
}
}

15
src/main/kotlin/dev/dnpm/etl/processor/config/ConsentResourceSerializer.kt
View File

@@ -1,15 +0,0 @@
package dev.dnpm.etl.processor.config
import com.fasterxml.jackson.core.JsonGenerator
import com.fasterxml.jackson.databind.JsonSerializer
import com.fasterxml.jackson.databind.SerializerProvider
import org.hl7.fhir.r4.model.Consent
class ConsentResourceSerializer : JsonSerializer<Consent>() {
override fun serialize(
value: Consent, gen: JsonGenerator, serializers: SerializerProvider
) {
val json = JacksonConfig.fhirContext().newJsonParser().encodeResourceToString(value)
gen.writeRawValue(json)
}
}

12
src/main/kotlin/dev/dnpm/etl/processor/config/FhirResourceModule.kt
View File

@@ -1,12 +0,0 @@
package dev.dnpm.etl.processor.config
import com.fasterxml.jackson.databind.module.SimpleModule
import org.hl7.fhir.r4.model.Consent
class FhirResourceModule : SimpleModule() {
init {
addSerializer(Consent::class.java, ConsentResourceSerializer())
addDeserializer(Consent::class.java, ConsentResourceDeserializer())
}
}

27
src/main/kotlin/dev/dnpm/etl/processor/config/JacksonConfig.kt
View File

@@ -1,27 +0,0 @@
package dev.dnpm.etl.processor.config
import ca.uhn.fhir.context.FhirContext
import org.springframework.context.annotation.Bean
import org.springframework.context.annotation.Configuration
import com.fasterxml.jackson.databind.ObjectMapper
import com.fasterxml.jackson.databind.SerializationFeature
import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule
@Configuration
class JacksonConfig {
companion object {
var fhirContext: FhirContext = FhirContext.forR4()
@JvmStatic
fun fhirContext(): FhirContext {
return fhirContext
}
}
@Bean
fun objectMapper(): ObjectMapper = ObjectMapper().registerModule(FhirResourceModule())
.disable(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS).registerModule(
JavaTimeModule()
)
}

66
src/main/kotlin/dev/dnpm/etl/processor/consent/ConsentEvaluator.kt
View File

@@ -1,66 +0,0 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.consent
import dev.pcvolkmer.mv64e.mtb.ConsentProvision
import dev.pcvolkmer.mv64e.mtb.ModelProjectConsentPurpose
import dev.pcvolkmer.mv64e.mtb.Mtb
import org.springframework.stereotype.Service
/**
* Evaluates consent using provided consent service and file based consent information
*/
@Service
class ConsentEvaluator(
private val consentService: IConsentService
) {
fun check(mtbFile: Mtb): ConsentEvaluation {
val ttpConsentStatus = consentService.getTtpBroadConsentStatus(mtbFile.patient.id)
val consentGiven = ttpConsentStatus == TtpConsentStatus.BROAD_CONSENT_GIVEN
|| ttpConsentStatus == TtpConsentStatus.GENOM_DE_CONSENT_SEQUENCING_PERMIT
// Aktuell nur Modellvorhaben Consent im File
|| ttpConsentStatus == TtpConsentStatus.UNKNOWN_CHECK_FILE && mtbFile.metadata?.modelProjectConsent?.provisions?.any {
it.purpose == ModelProjectConsentPurpose.SEQUENCING
&& it.type == ConsentProvision.PERMIT
} == true
return ConsentEvaluation(ttpConsentStatus, consentGiven)
}
}
data class ConsentEvaluation(private val ttpConsentStatus: TtpConsentStatus, private val consentGiven: Boolean) {
/**
* Checks if any required consent is present
*/
fun hasConsent(): Boolean {
return consentGiven
}
/**
* Returns the consent status
*/
fun getStatus(): TtpConsentStatus {
if (ttpConsentStatus == TtpConsentStatus.UNKNOWN_CHECK_FILE) {
// in case ttp check is disabled - we propagate rejected status anyway
return TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED
}
return ttpConsentStatus
}
}

49
src/main/kotlin/dev/dnpm/etl/processor/input/KafkaInputListener.kt
View File

@@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 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
@@ -20,58 +20,32 @@
package dev.dnpm.etl.processor.input
import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.CustomMediaType
import de.ukw.ccc.bwhc.dto.Consent
import de.ukw.ccc.bwhc.dto.MtbFile
import dev.dnpm.etl.processor.PatientId
import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.consent.ConsentEvaluator
import dev.dnpm.etl.processor.consent.TtpConsentStatus
import dev.dnpm.etl.processor.services.RequestProcessor
import dev.pcvolkmer.mv64e.mtb.Mtb
import org.apache.kafka.clients.consumer.ConsumerRecord
import org.slf4j.LoggerFactory
import org.springframework.http.MediaType
import org.springframework.kafka.listener.MessageListener
class KafkaInputListener(
private val requestProcessor: RequestProcessor,
private val consentEvaluator: ConsentEvaluator,
private val objectMapper: ObjectMapper
) : MessageListener<String, String> {
private val logger = LoggerFactory.getLogger(KafkaInputListener::class.java)
override fun onMessage(record: ConsumerRecord<String, String>) {
when (guessMimeType(record)) {
MediaType.APPLICATION_JSON_VALUE -> handleDnpmV2Message(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 handleDnpmV2Message(record: ConsumerRecord<String, String>) {
// Do not handle DNPM-V2 for now
logger.warn("Ignoring MTB File in DNPM V2 format: Not implemented yet")
val mtbFile = objectMapper.readValue(record.value(), Mtb::class.java)
override fun onMessage(data: ConsumerRecord<String, String>) {
val mtbFile = objectMapper.readValue(data.value(), MtbFile::class.java)
val patientId = PatientId(mtbFile.patient.id)
val firstRequestIdHeader = record.headers().headers("requestId")?.firstOrNull()
val firstRequestIdHeader = data.headers().headers("requestId")?.firstOrNull()
val requestId = if (null != firstRequestIdHeader) {
RequestId(String(firstRequestIdHeader.value()))
} else {
RequestId("")
}
if (consentEvaluator.check(mtbFile).hasConsent()) {
if (mtbFile.consent.status == Consent.Status.ACTIVE) {
logger.debug("Accepted MTB File for processing")
if (requestId.isBlank()) {
requestProcessor.processMtbFile(mtbFile)
@@ -81,15 +55,10 @@ class KafkaInputListener(
} else {
logger.debug("Accepted MTB File and process deletion")
if (requestId.isBlank()) {
requestProcessor.processDeletion(patientId, TtpConsentStatus.UNKNOWN_CHECK_FILE)
requestProcessor.processDeletion(patientId)
} else {
requestProcessor.processDeletion(
patientId,
requestId,
TtpConsentStatus.UNKNOWN_CHECK_FILE
)
requestProcessor.processDeletion(patientId, requestId)
}
}
}
}

24
src/main/kotlin/dev/dnpm/etl/processor/input/MtbFileRestController.kt
View File

@@ -19,14 +19,11 @@
package dev.dnpm.etl.processor.input
import dev.dnpm.etl.processor.CustomMediaType
import de.ukw.ccc.bwhc.dto.Consent
import de.ukw.ccc.bwhc.dto.MtbFile
import dev.dnpm.etl.processor.PatientId
import dev.dnpm.etl.processor.consent.ConsentEvaluator
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.*
@@ -34,8 +31,8 @@ import org.springframework.web.bind.annotation.*
@RequestMapping(path = ["mtbfile", "mtb"])
class MtbFileRestController(
private val requestProcessor: RequestProcessor,
private val consentEvaluator: ConsentEvaluator
) {
private val logger = LoggerFactory.getLogger(MtbFileRestController::class.java)
@GetMapping
@@ -43,16 +40,15 @@ class MtbFileRestController(
return ResponseEntity.ok("Test")
}
@PostMapping(consumes = [MediaType.APPLICATION_JSON_VALUE, CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE])
fun mtbFile(@RequestBody mtbFile: Mtb): ResponseEntity<Unit> {
val consentEvaluation = consentEvaluator.check(mtbFile)
if (consentEvaluation.hasConsent()) {
logger.debug("Accepted MTB File (DNPM V2) for processing")
@PostMapping
fun mtbFile(@RequestBody mtbFile: MtbFile): ResponseEntity<Unit> {
if (mtbFile.consent.status == Consent.Status.ACTIVE) {
logger.debug("Accepted MTB File for processing")
requestProcessor.processMtbFile(mtbFile)
} else {
logger.debug("Accepted MTB File (DNPM V2) and process deletion")
logger.debug("Accepted MTB File and process deletion")
val patientId = PatientId(mtbFile.patient.id)
requestProcessor.processDeletion(patientId, consentEvaluation.getStatus())
requestProcessor.processDeletion(patientId)
}
return ResponseEntity.accepted().build()
}
@@ -60,7 +56,7 @@ class MtbFileRestController(
@DeleteMapping(path = ["{patientId}"])
fun deleteData(@PathVariable patientId: String): ResponseEntity<Unit> {
logger.debug("Accepted patient ID to process deletion")
requestProcessor.processDeletion(PatientId(patientId), TtpConsentStatus.UNKNOWN_CHECK_FILE)
requestProcessor.processDeletion(PatientId(patientId))
return ResponseEntity.accepted().build()
}

66
src/main/kotlin/dev/dnpm/etl/processor/monitoring/ConnectionCheckService.kt
View File

@@ -20,7 +20,6 @@
package dev.dnpm.etl.processor.monitoring
import dev.dnpm.etl.processor.config.GIcsConfigProperties
import dev.dnpm.etl.processor.config.GPasConfigProperties
import dev.dnpm.etl.processor.config.RestTargetProperties
import jakarta.annotation.PostConstruct
@@ -69,12 +68,6 @@ sealed class ConnectionCheckResult {
override val timestamp: Instant,
override val lastChange: Instant
) : ConnectionCheckResult()
data class GIcsConnectionCheckResult(
override val available: Boolean,
override val timestamp: Instant,
override val lastChange: Instant
) : ConnectionCheckResult()
}
class KafkaConnectionCheckService(
@@ -128,11 +121,15 @@ class RestConnectionCheckService(
fun check() {
result = try {
val available = restTemplate.getForEntity(
if (restTargetProperties.isBwhc) {
UriComponentsBuilder.fromUriString(restTargetProperties.uri.toString()).path("").toUriString()
} else {
UriComponentsBuilder.fromUriString(restTargetProperties.uri.toString())
.pathSegment("mtb")
.pathSegment("kaplan-meier")
.pathSegment("config")
.toUriString(),
.toUriString()
},
String::class.java
).statusCode == HttpStatus.OK
@@ -211,56 +208,3 @@ class GPasConnectionCheckService(
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
}
}

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

@@ -24,6 +24,5 @@ enum class RequestStatus(val value: String) {
WARNING("warning"),
ERROR("error"),
UNKNOWN("unknown"),
DUPLICATION("duplication"),
NO_CONSENT("no-consent")
DUPLICATION("duplication")
}

67
src/main/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSender.kt
View File

@@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 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
@@ -20,14 +20,12 @@
package dev.dnpm.etl.processor.output
import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.CustomMediaType
import de.ukw.ccc.bwhc.dto.Consent
import de.ukw.ccc.bwhc.dto.MtbFile
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.Mtb
import dev.pcvolkmer.mv64e.mtb.MvhMetadata
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
@@ -40,24 +38,14 @@ class KafkaMtbFileSender(
private val logger = LoggerFactory.getLogger(KafkaMtbFileSender::class.java)
override fun <T> send(request: MtbFileRequest<T>): MtbFileSender.Response {
override fun send(request: MtbFileSender.MtbFileRequest): MtbFileSender.Response {
return try {
return retryTemplate.execute<MtbFileSender.Response, Exception> {
val record =
ProducerRecord(
kafkaProperties.outputTopic,
val result = kafkaTemplate.send(
kafkaProperties.topic,
key(request),
objectMapper.writeValueAsString(request)
objectMapper.writeValueAsString(Data(request.requestId, request.mtbFile))
)
when (request) {
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)
@@ -71,27 +59,24 @@ class KafkaMtbFileSender(
}
}
override fun send(request: DeleteRequest): MtbFileSender.Response {
val dummyMtbFile = Mtb.builder()
.metadata(MvhMetadata())
override fun send(request: MtbFileSender.DeleteRequest): MtbFileSender.Response {
val dummyMtbFile = MtbFile.builder()
.withConsent(
Consent.builder()
.withPatient(request.patientId.value)
.withStatus(Consent.Status.REJECTED)
.build()
)
.build()
return try {
return retryTemplate.execute<MtbFileSender.Response, Exception> {
val record =
ProducerRecord(
kafkaProperties.outputTopic,
val result = kafkaTemplate.send(
kafkaProperties.topic,
key(request),
// Always use old BwhcV1FileRequest with Consent REJECT
objectMapper.writeValueAsString(
DnpmV2MtbFileRequest(
request.requestId,
dummyMtbFile
)
)
objectMapper.writeValueAsString(Data(request.requestId, dummyMtbFile))
)
val result = kafkaTemplate.send(record)
if (result.get() != null) {
logger.debug("Sent deletion request via KafkaMtbFileSender")
MtbFileSender.Response(RequestStatus.UNKNOWN)
@@ -106,14 +91,16 @@ class KafkaMtbFileSender(
}
override fun endpoint(): String {
return "${this.kafkaProperties.servers} (${this.kafkaProperties.outputTopic}/${this.kafkaProperties.outputResponseTopic})"
return "${this.kafkaProperties.servers} (${this.kafkaProperties.topic}/${this.kafkaProperties.responseTopic})"
}
private fun key(request: MtbRequest): String {
return when (request) {
is DnpmV2MtbFileRequest -> "{\"pid\": \"${request.content.patient.id}\"}"
is DeleteRequest -> "{\"pid\": \"${request.patientId.value}\"}"
else -> throw IllegalArgumentException("Unsupported request type: ${request::class.simpleName}")
private fun key(request: MtbFileSender.MtbFileRequest): String {
return "{\"pid\": \"${request.mtbFile.patient.id}\"}"
}
private fun key(request: MtbFileSender.DeleteRequest): String {
return "{\"pid\": \"${request.patientId.value}\"}"
}
data class Data(val requestId: RequestId, val content: MtbFile)
}

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

@@ -19,17 +19,25 @@
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.dnpm.etl.processor.monitoring.RequestStatus
import org.springframework.http.HttpStatusCode
interface MtbFileSender {
fun <T> send(request: MtbFileRequest<T>): Response
fun send(request: MtbFileRequest): Response
fun send(request: DeleteRequest): Response
fun endpoint(): String
data class Response(val status: RequestStatus, val body: String = "")
data class MtbFileRequest(val requestId: RequestId, val mtbFile: MtbFile)
data class DeleteRequest(val requestId: RequestId, val patientId: PatientPseudonym)
}
fun Int.asRequestStatus(): RequestStatus {

49
src/main/kotlin/dev/dnpm/etl/processor/output/MtbRequest.kt
View File

@@ -1,49 +0,0 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.output
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.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 DnpmV2MtbFileRequest(
override val requestId: RequestId,
override val content: Mtb
) : MtbFileRequest<Mtb> {
override fun patientPseudonym(): PatientPseudonym {
return PatientPseudonym(content.patient.id)
}
}
data class DeleteRequest(
override val requestId: RequestId,
val patientId: PatientPseudonym
) : MtbRequest

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

@@ -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()
}
}

24
src/main/kotlin/dev/dnpm/etl/processor/output/RestMtbFileSender.kt
View File

@@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
@@ -19,11 +19,10 @@
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.PatientPseudonym
import dev.dnpm.etl.processor.monitoring.ReportService
import dev.dnpm.etl.processor.monitoring.asRequestStatus
import org.slf4j.LoggerFactory
import org.springframework.http.HttpEntity
@@ -47,11 +46,11 @@ abstract class RestMtbFileSender(
abstract fun deleteUrl(patientId: PatientPseudonym): String
override fun <T> send(request: MtbFileRequest<T>): MtbFileSender.Response {
override fun send(request: MtbFileSender.MtbFileRequest): MtbFileSender.Response {
try {
return retryTemplate.execute<MtbFileSender.Response, Exception> {
val headers = getHttpHeaders(request)
val entityReq = HttpEntity(request.content, headers)
val headers = getHttpHeaders()
val entityReq = HttpEntity(request.mtbFile, headers)
val response = restTemplate.postForEntity(
sendUrl(),
entityReq,
@@ -77,10 +76,10 @@ abstract class RestMtbFileSender(
return MtbFileSender.Response(RequestStatus.ERROR, "Sonstiger Fehler bei der Übertragung")
}
override fun send(request: DeleteRequest): MtbFileSender.Response {
override fun send(request: MtbFileSender.DeleteRequest): MtbFileSender.Response {
try {
return retryTemplate.execute<MtbFileSender.Response, Exception> {
val headers = getHttpHeaders(request)
val headers = getHttpHeaders()
val entityReq = HttpEntity(null, headers)
restTemplate.delete(
deleteUrl(request.patientId),
@@ -103,14 +102,11 @@ abstract class RestMtbFileSender(
return this.restTargetProperties.uri.orEmpty()
}
private fun getHttpHeaders(request: MtbRequest): HttpHeaders {
private fun getHttpHeaders(): HttpHeaders {
val username = restTargetProperties.username
val password = restTargetProperties.password
val headers = HttpHeaders()
headers.contentType = when (request) {
is DnpmV2MtbFileRequest -> CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON
else -> MediaType.APPLICATION_JSON
}
headers.contentType = MediaType.APPLICATION_JSON
if (username.isNullOrBlank() || password.isNullOrBlank()) {
return headers

15
src/main/kotlin/dev/dnpm/etl/processor/pseudonym/AnonymizingGenerator.kt
View File

@@ -21,12 +21,9 @@ package dev.dnpm.etl.processor.pseudonym
import org.apache.commons.codec.binary.Base32
import org.apache.commons.codec.digest.DigestUtils
import java.security.SecureRandom
class AnonymizingGenerator : Generator {
companion object fun getSecureRandom() : SecureRandom {
return SecureRandom()
}
override fun generate(id: String): String {
return Base32().encodeAsString(DigestUtils.sha256(id))
@@ -34,14 +31,4 @@ class AnonymizingGenerator : Generator {
.lowercase()
}
@OptIn(ExperimentalStdlibApi::class)
override fun generateGenomDeTan(id: String?): String {
val bytes = ByteArray(64 / 2)
getSecureRandom().nextBytes(bytes)
return bytes.joinToString("") { "%02x".format(it) }
}
}

4
src/main/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeService.kt
View File

@@ -35,10 +35,6 @@ class PseudonymizeService(
}
}
fun genomDeTan(patientId: PatientId): String {
return generator.generateGenomDeTan(patientId.value)
}
fun prefix(): String {
return configProperties.prefix
}

396
src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
View File

@@ -19,96 +19,54 @@
package dev.dnpm.etl.processor.pseudonym
import de.ukw.ccc.bwhc.dto.MtbFile
import dev.dnpm.etl.processor.PatientId
import dev.pcvolkmer.mv64e.mtb.ModelProjectConsent
import dev.pcvolkmer.mv64e.mtb.Mtb
import dev.pcvolkmer.mv64e.mtb.MvhMetadata
import org.apache.commons.codec.digest.DigestUtils
/** Replaces patient ID with generated patient pseudonym
*
* @since 0.11.0
*
* @param pseudonymizeService The pseudonymizeService to be used
*
* @return The MTB file containing patient pseudonymes
*/
infix fun Mtb.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
infix fun MtbFile.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.episode?.patient = patientPseudonym
this.carePlans?.forEach { it.patient = 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.familyMemberHistories?.forEach { it.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 {
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
}
this.msiFindings?.forEach { it -> it.patient.id = patientPseudonym }
this.metadata?.researchConsents?.forEach { it ->
val entry = it ?: return@forEach
if (entry.contains("patient")) {
// here we expect only a patient reference any other data like display
// need to be removed, since may contain unsecure data
entry.remove("patient")
entry["patient"] = mapOf("reference" to "Patient/$patientPseudonym")
}
it.patient = patientPseudonym
it.tumorMorphology?.patient = patientPseudonym
}
this.lastGuidelineTherapies?.forEach { it.patient = patientPseudonym }
this.molecularPathologyFindings?.forEach { it.patient = patientPseudonym }
this.molecularTherapies?.forEach { molecularTherapy -> molecularTherapy.history.forEach { it.patient = patientPseudonym } }
this.ngsReports?.forEach { it.patient = patientPseudonym }
this.previousGuidelineTherapies?.forEach { it.patient = patientPseudonym }
this.rebiopsyRequests?.forEach { it.patient = patientPseudonym }
this.recommendations?.forEach { it.patient = patientPseudonym }
this.responses?.forEach { it.patient = patientPseudonym }
this.studyInclusionRequests?.forEach { it.patient = patientPseudonym }
this.specimens?.forEach { it.patient = patientPseudonym }
}
/**
* Creates new hash of content IDs with given prefix except for patient IDs
*
* @since 0.11.0
*
* @param pseudonymizeService The pseudonymizeService to be used
*
* @return The MTB file containing rehashed content IDs
*/
infix fun Mtb.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
infix fun MtbFile.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
val prefix = pseudonymizeService.prefix()
fun anonymize(id: String): String {
@@ -116,199 +74,153 @@ infix fun Mtb.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
return "$prefix$hash"
}
this.episodesOfCare?.forEach {
it?.apply { id = id?.let(::anonymize) }
it.diagnoses?.forEach { it ->
it?.id = it.id?.let(::anonymize)
this.episode?.apply {
id = id?.let {
anonymize(it)
}
}
this.carePlans?.onEach { carePlan ->
carePlan?.apply {
id = id?.let { anonymize(it) }
diagnoses?.forEach { it -> it?.id = it.id?.let(::anonymize) }
geneticCounselingRecommendation?.apply {
id = geneticCounselingRecommendation.id?.let(::anonymize)
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) } }
}
rebiopsyRequests?.forEach { it ->
it.id = it.id?.let(::anonymize)
it.tumorEntity?.id = it.tumorEntity?.id?.let(::anonymize)
}
histologyReevaluationRequests?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.specimen?.id = it.specimen?.id?.let(::anonymize)
this.claims?.onEach { claim ->
claim?.apply {
id = id?.let { anonymize(it) }
therapy = therapy?.let { anonymize(it) }
}
medicationRecommendations?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.supportingVariants?.forEach { it ->
it.variant?.id = it.variant?.id?.let(::anonymize)
}
it.reason?.id = it.reason?.id?.let(::anonymize)
this.claimResponses?.onEach { claimResponse ->
claimResponse?.apply {
id = id?.let { anonymize(it) }
claim = claim?.let { anonymize(it) }
}
reason?.id = reason?.id?.let(::anonymize)
studyEnrollmentRecommendations?.forEach { it ->
it?.reason?.id = it.reason?.id?.let(::anonymize)
}
procedureRecommendations?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.supportingVariants?.forEach { it ->
it.variant?.id = it.variant?.id?.let(::anonymize)
this.consent?.apply {
id = id?.let { anonymize(it) }
}
it.reason?.id = it.reason?.id?.let(::anonymize)
studyEnrollmentRecommendations?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.supportingVariants.forEach { it ->
it.variant?.id = it?.variant?.id?.let(::anonymize)
this.diagnoses?.onEach { diagnosis ->
diagnosis?.apply {
id = id?.let { anonymize(it) }
histologyResults = histologyResults?.map { it?.let { anonymize(it) } }
}
responses?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.id = it?.id?.let(::anonymize)
}
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) }
}
this.responses?.forEach { it ->
it?.id = it.id?.let(::anonymize)
it?.therapy?.id = it.therapy?.id?.let(::anonymize)
}
this.diagnoses?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.histology?.forEach { it -> it.id = it?.id?.let(::anonymize) }
}
this.ngsReports?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.results?.tumorCellContent?.id = it.results.tumorCellContent?.id?.let(::anonymize)
it.results?.tumorCellContent?.specimen?.id =
it.results?.tumorCellContent?.specimen?.id?.let(::anonymize)
it.results?.rnaFusions?.forEach { it ->
it?.id = it.id?.let(::anonymize)
}
it.results?.simpleVariants?.forEach { it ->
it?.id = it.id?.let(::anonymize)
it?.transcriptId?.value = it.transcriptId?.value?.let(::anonymize)
}
it.results?.tmb?.id = it.results?.tmb?.id?.let(::anonymize)
it.results?.tmb?.specimen?.id = it.results?.tmb?.specimen?.id?.let(::anonymize)
it.results?.brcaness?.id = it.results?.brcaness?.id?.let(::anonymize)
it.results?.brcaness?.specimen?.id = it.results?.brcaness?.specimen?.id?.let(::anonymize)
it.results?.copyNumberVariants?.forEach { it -> it?.id = it.id?.let(::anonymize) }
it.results?.hrdScore?.id = it.results?.hrdScore?.id?.let(::anonymize)
it.results?.hrdScore?.specimen?.id = it.results?.hrdScore?.specimen?.id?.let(::anonymize)
it.results?.rnaSeqs?.forEach { it -> it?.id = it.id?.let(::anonymize) }
it.results?.dnaFusions?.forEach { it -> it?.id = it.id?.let(::anonymize) }
it.specimen?.id = it?.specimen?.id?.let(::anonymize)
}
this.histologyReports?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.results?.tumorCellContent?.id = it.results?.tumorCellContent?.id?.let(::anonymize)
it.results?.tumorCellContent?.specimen?.id =
it.results?.tumorCellContent?.specimen?.id?.let(::anonymize)
it.results?.tumorMorphology?.id = it.results?.tumorMorphology?.id?.let(::anonymize)
it.results?.tumorMorphology?.specimen?.id =
it.results?.tumorMorphology?.specimen?.id?.let(::anonymize)
it.specimen?.id = it.specimen?.id?.let(::anonymize)
}
this.claimResponses?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.claim?.id = it.claim?.id?.let(::anonymize)
}
this.claims?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.recommendation?.id = it.recommendation?.id?.let(::anonymize)
}
this.familyMemberHistories?.forEach { it -> it.id = it?.id?.let(::anonymize) }
this.guidelineProcedures?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.reason?.id = it.reason?.id?.let(::anonymize)
it.basedOn?.id = it.basedOn?.id?.let(::anonymize)
}
this.guidelineTherapies?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.reason?.id = it.reason?.id?.let(::anonymize)
it.basedOn?.id = it.basedOn?.id?.let(::anonymize)
}
this.ihcReports?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.specimen?.id = it.specimen?.id?.let(::anonymize)
it.results.proteinExpression.forEach { it -> it?.id = it.id.let(::anonymize) }
}
this.msiFindings?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.specimen?.id = it.specimen?.id?.let(::anonymize)
}
this.performanceStatus?.forEach { it -> it.id = it?.id?.let(::anonymize) }
this.priorDiagnosticReports?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.specimen?.id = it.specimen?.id?.let(::anonymize)
}
this.specimens?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.diagnosis?.id = it.diagnosis?.id?.let(::anonymize)
}
this.systemicTherapies?.forEach { it ->
it.history?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.reason?.id = it.reason?.id?.let(::anonymize)
it.basedOn?.id = it.basedOn?.id?.let(::anonymize)
}
simpleVariants?.onEach { simpleVariant ->
simpleVariant?.apply {
id = id?.let { anonymize(it) }
}
}
fun Mtb.ensureMetaDataIsInitialized() {
// init metadata if necessary
if (this.metadata == null) {
val mvhMetadata = MvhMetadata.builder().build()
this.metadata = mvhMetadata
}
if (this.metadata.researchConsents == null) {
this.metadata.researchConsents = mutableListOf()
}
if (this.metadata.modelProjectConsent == null) {
this.metadata.modelProjectConsent = ModelProjectConsent()
this.metadata.modelProjectConsent.provisions = mutableListOf()
} else if (this.metadata.modelProjectConsent.provisions != null) {
// make sure list can be changed
this.metadata.modelProjectConsent.provisions =
this.metadata.modelProjectConsent.provisions.toMutableList()
}
}
infix fun Mtb.addGenomDeTan(pseudonymizeService: PseudonymizeService) {
this.metadata.transferTan = pseudonymizeService.genomDeTan(PatientId(this.patient.id))
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) }
}
}
}

273
src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt
View File

@@ -1,273 +0,0 @@
package dev.dnpm.etl.processor.services
import ca.uhn.fhir.context.FhirContext
import com.fasterxml.jackson.core.JsonProcessingException
import com.fasterxml.jackson.core.type.TypeReference
import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.config.AppConfigProperties
import dev.dnpm.etl.processor.config.GIcsConfigProperties
import dev.dnpm.etl.processor.consent.ConsentDomain
import dev.dnpm.etl.processor.consent.IConsentService
import dev.dnpm.etl.processor.consent.MtbFileConsentService
import dev.dnpm.etl.processor.pseudonym.ensureMetaDataIsInitialized
import dev.pcvolkmer.mv64e.mtb.*
import org.apache.commons.lang3.NotImplementedException
import org.hl7.fhir.r4.model.*
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent
import org.hl7.fhir.r4.model.Coding
import org.hl7.fhir.r4.model.Consent.ConsentState
import org.hl7.fhir.r4.model.Consent.ProvisionComponent
import org.slf4j.Logger
import org.slf4j.LoggerFactory
import org.springframework.stereotype.Service
import java.io.IOException
import java.time.Clock
import java.time.Instant
import java.util.*
@Service
class ConsentProcessor(
private val appConfigProperties: AppConfigProperties,
private val gIcsConfigProperties: GIcsConfigProperties,
private val objectMapper: ObjectMapper,
private val fhirContext: FhirContext,
private val consentService: IConsentService
) {
private var logger: Logger = LoggerFactory.getLogger("ConsentProcessor")
/**
* In case an instance of {@link ICheckConsent} is active, consent will be embedded and checked.
*
* Logic:
* * <c>true</c> IF consent check is disabled.
* * <c>true</c> IF broad consent (BC) has been given.
* * <c>true</c> BC has been asked AND declined but genomDe consent has been consented.
* * ELSE <c>false</c> is returned.
*
* @param mtbFile File v2 (will be enriched with consent data)
* @return true if consent is given
*
*/
fun consentGatedCheckAndTryEmbedding(mtbFile: Mtb): Boolean {
if (consentService is MtbFileConsentService) {
// consent check is disabled
return true
}
mtbFile.ensureMetaDataIsInitialized()
val personIdentifierValue = mtbFile.patient.id
val requestDate = Date.from(Instant.now(Clock.systemUTC()))
// 1. Broad consent Entry exists?
// 1.1. -> yes and research consent is given -> send mtb file
// 1.2. -> no -> return status error - consent has not been asked
// 2. -> Broad consent found but rejected -> is GenomDe consent provision 'sequencing' given?
// 2.1 -> yes -> send mtb file
// 2.2 -> no -> warn/info no consent given
/*
* broad consent
*/
val broadConsent = consentService.getConsent(
personIdentifierValue, requestDate, ConsentDomain.BROAD_CONSENT
)
val broadConsentHasBeenAsked = broadConsent.entry.isNotEmpty()
// fast exit - if patient has not been asked, we can skip and exit
if (!broadConsentHasBeenAsked) return false
val genomeDeConsent = consentService.getConsent(
personIdentifierValue, requestDate, ConsentDomain.MODELLVORHABEN_64E
)
addGenomeDbProvisions(mtbFile, genomeDeConsent)
if (genomeDeConsent.entry.isNotEmpty()) setGenomDeSubmissionType(mtbFile)
embedBroadConsentResources(mtbFile, broadConsent)
val broadConsentStatus = getProvisionTypeByPolicyCode(
broadConsent, requestDate, ConsentDomain.BROAD_CONSENT
)
val genomDeSequencingStatus = getProvisionTypeByPolicyCode(
genomeDeConsent, requestDate, ConsentDomain.MODELLVORHABEN_64E
)
if (Consent.ConsentProvisionType.NULL == broadConsentStatus) {
// bc not asked
return false
}
if (Consent.ConsentProvisionType.PERMIT == broadConsentStatus || Consent.ConsentProvisionType.PERMIT == genomDeSequencingStatus) return true
return false
}
fun embedBroadConsentResources(mtbFile: Mtb, broadConsent: Bundle) {
for (entry in broadConsent.entry) {
val resource = entry.resource
if (resource is Consent) {
// since jackson convertValue does not work here,
// we need another step to back to string, before we convert to object map
val asJsonString = fhirContext.newJsonParser().encodeResourceToString(resource)
try {
val mapOfJson: HashMap<String?, Any?>? =
objectMapper.readValue<HashMap<String?, Any?>?>(
asJsonString, object : TypeReference<HashMap<String?, Any?>?>() {})
mtbFile.metadata.researchConsents.add(mapOfJson)
} catch (e: JsonProcessingException) {
throw RuntimeException(e)
}
}
}
}
fun addGenomeDbProvisions(mtbFile: Mtb, consentGnomeDe: Bundle) {
for (entry in consentGnomeDe.entry) {
val resource = entry.resource
if (resource !is Consent) {
continue
}
// We expect only one provision in collection, therefore get first or none
val provisions = resource.provision.provision
if (provisions.isEmpty()) {
continue
}
val provisionComponent: ProvisionComponent = provisions.first()
var provisionCode: String? = null
if (provisionComponent.code != null && provisionComponent.code.isNotEmpty()) {
val codableConcept: CodeableConcept = provisionComponent.code.first()
if (codableConcept.coding != null && codableConcept.coding.isNotEmpty()) {
provisionCode = codableConcept.coding.first().code
}
}
if (provisionCode != null) {
try {
val modelProjectConsentPurpose =
ModelProjectConsentPurpose.forValue(provisionCode)
if (ModelProjectConsentPurpose.SEQUENCING == modelProjectConsentPurpose) {
// CONVENTION: wrapping date is date of SEQUENCING consent
mtbFile.metadata.modelProjectConsent.date = resource.dateTime
}
val provision = Provision.builder()
.type(ConsentProvision.valueOf(provisionComponent.type.name))
.date(provisionComponent.period.start)
.purpose(modelProjectConsentPurpose).build()
mtbFile.metadata.modelProjectConsent.provisions.add(provision)
} catch (ioe: IOException) {
logger.error(
"Provision code '$provisionCode' is unknown and cannot be mapped.",
ioe.toString()
)
}
}
if (mtbFile.metadata.modelProjectConsent.provisions.isNotEmpty()) {
mtbFile.metadata.modelProjectConsent.version =
gIcsConfigProperties.genomeDeConsentVersion
}
}
}
private fun setGenomDeSubmissionType(mtbFile: Mtb) {
if (appConfigProperties.genomDeTestSubmission) {
mtbFile.metadata.type = MvhSubmissionType.TEST
logger.info("genomeDe submission mit TEST")
} else {
mtbFile.metadata.type = when (mtbFile.metadata.type) {
null -> MvhSubmissionType.INITIAL
else -> mtbFile.metadata.type
}
}
}
/**
* @param consentBundle consent resource
* @param requestDate date which must be within validation period of provision
* @return type of provision, will be [org.hl7.fhir.r4.model.Consent.ConsentProvisionType.NULL] if none is found.
*/
fun getProvisionTypeByPolicyCode(
consentBundle: Bundle, requestDate: Date?, consentDomain: ConsentDomain
): Consent.ConsentProvisionType {
val code: String?
val system: String?
if (ConsentDomain.BROAD_CONSENT == consentDomain) {
code = gIcsConfigProperties.broadConsentPolicyCode
system = gIcsConfigProperties.broadConsentPolicySystem
} else if (ConsentDomain.MODELLVORHABEN_64E == consentDomain) {
code = gIcsConfigProperties.genomeDePolicyCode
system = gIcsConfigProperties.genomeDePolicySystem
} else {
throw NotImplementedException("unknown consent domain " + consentDomain.name)
}
val provisionTypeByPolicyCode = getProvisionTypeByPolicyCode(
consentBundle, code, system, requestDate
)
return provisionTypeByPolicyCode
}
/**
* @param consentBundle consent resource
* @param targetCode policyRule and provision code value
* @param targetSystem policyRule and provision system value
* @param requestDate date which must be within validation period of provision
* @return type of provision, will be [org.hl7.fhir.r4.model.Consent.ConsentProvisionType.NULL] if none is found.
*/
fun getProvisionTypeByPolicyCode(
consentBundle: Bundle, targetCode: String?, targetSystem: String?, requestDate: Date?
): Consent.ConsentProvisionType {
val entriesOfInterest = consentBundle.entry.filter { entry ->
val isConsentResource =
entry.resource.isResource && entry.resource.resourceType == ResourceType.Consent
val consentIsActive = (entry.resource as Consent).status == ConsentState.ACTIVE
isConsentResource && consentIsActive && checkCoding(
targetCode, targetSystem, (entry.resource as Consent).policyRule.coding
) && isRequestDateInRange(requestDate, (entry.resource as Consent).provision.period)
}.map { entry: BundleEntryComponent ->
val consent = (entry.getResource() as Consent)
consent.provision.provision.filter { subProvision ->
isRequestDateInRange(requestDate, subProvision.period)
// search coding entries of current provision for code and system
subProvision.code.map { c -> c.coding }.flatten().firstOrNull { code ->
targetCode.equals(code.code) && targetSystem.equals(code.system)
} != null
}.map { subProvision ->
subProvision
}
}.flatten()
if (entriesOfInterest.isNotEmpty()) {
return entriesOfInterest.first().type
}
return Consent.ConsentProvisionType.NULL
}
fun checkCoding(
researchAllowedPolicyOid: String?,
researchAllowedPolicySystem: String?,
policyRules: Collection<Coding>
): Boolean {
return policyRules.find { code ->
researchAllowedPolicySystem.equals(code.getSystem()) && (researchAllowedPolicyOid.equals(
code.getCode()
))
} != null
}
fun isRequestDateInRange(requestDate: Date?, provPeriod: Period): Boolean {
val isRequestDateAfterOrEqualStart = provPeriod.start.compareTo(requestDate)
val isRequestDateBeforeOrEqualEnd = provPeriod.end.compareTo(requestDate)
return isRequestDateAfterOrEqualStart <= 0 && isRequestDateBeforeOrEqualEnd >= 0
}
}

119
src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
View File

@@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
@@ -20,28 +20,19 @@
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.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.DeleteRequest
import dev.dnpm.etl.processor.output.DnpmV2MtbFileRequest
import dev.dnpm.etl.processor.output.MtbFileRequest
import dev.dnpm.etl.processor.output.MtbFileSender
import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
import dev.dnpm.etl.processor.pseudonym.addGenomDeTan
import dev.dnpm.etl.processor.pseudonym.anonymizeContentWith
import dev.dnpm.etl.processor.pseudonym.pseudonymizeWith
import dev.pcvolkmer.mv64e.mtb.ConsentProvision
import dev.pcvolkmer.mv64e.mtb.ModelProjectConsentPurpose
import dev.pcvolkmer.mv64e.mtb.Mtb
import org.apache.commons.codec.binary.Base32
import org.apache.commons.codec.digest.DigestUtils
import org.slf4j.Logger
import org.slf4j.LoggerFactory
import org.springframework.context.ApplicationEventPublisher
import org.springframework.stereotype.Service
import java.time.Instant
@@ -55,63 +46,40 @@ class RequestProcessor(
private val requestService: RequestService,
private val objectMapper: ObjectMapper,
private val applicationEventPublisher: ApplicationEventPublisher,
private val appConfigProperties: AppConfigProperties,
private val consentProcessor: ConsentProcessor?
private val appConfigProperties: AppConfigProperties
) {
private var logger: Logger = LoggerFactory.getLogger("RequestProcessor")
fun processMtbFile(mtbFile: Mtb) {
fun processMtbFile(mtbFile: MtbFile) {
processMtbFile(mtbFile, randomRequestId())
}
fun processMtbFile(mtbFile: MtbFile, requestId: RequestId) {
val pid = PatientId(mtbFile.patient.id)
fun processMtbFile(mtbFile: Mtb, requestId: RequestId) {
val pid = PatientId(extractPatientIdentifier(mtbFile))
val isConsentOk =
consentProcessor != null && consentProcessor.consentGatedCheckAndTryEmbedding(mtbFile) || consentProcessor == null
if (isConsentOk) {
if (isGenomDeConsented(mtbFile)) {
mtbFile addGenomDeTan pseudonymizeService
}
mtbFile pseudonymizeWith pseudonymizeService
mtbFile anonymizeContentWith pseudonymizeService
val request = DnpmV2MtbFileRequest(requestId, transformationService.transform(mtbFile))
saveAndSend(request, pid)
} else {
logger.warn("consent check failed file will not be processed further!")
applicationEventPublisher.publishEvent(
ResponseEvent(
requestId, Instant.now(), RequestStatus.NO_CONSENT
)
)
}
}
private fun isGenomDeConsented(mtbFile: Mtb): Boolean {
val isModelProjectConsented = mtbFile.metadata?.modelProjectConsent?.provisions?.any { p ->
p.purpose == ModelProjectConsentPurpose.SEQUENCING && p.type == ConsentProvision.PERMIT
} == true
return isModelProjectConsented
}
val request = MtbFileSender.MtbFileRequest(requestId, transformationService.transform(mtbFile))
val patientPseudonym = PatientPseudonym(request.mtbFile.patient.id)
private fun <T> saveAndSend(request: MtbFileRequest<T>, pid: PatientId) {
requestService.save(
Request(
request.requestId,
request.patientPseudonym(),
requestId,
patientPseudonym,
pid,
fingerprint(request),
fingerprint(request.mtbFile),
RequestType.MTB_FILE,
RequestStatus.UNKNOWN
)
)
if (appConfigProperties.duplicationDetection && isDuplication(request)) {
if (appConfigProperties.duplicationDetection && isDuplication(mtbFile)) {
applicationEventPublisher.publishEvent(
ResponseEvent(
request.requestId, Instant.now(), RequestStatus.DUPLICATION
requestId,
Instant.now(),
RequestStatus.DUPLICATION
)
)
return
@@ -121,7 +89,7 @@ class RequestProcessor(
applicationEventPublisher.publishEvent(
ResponseEvent(
request.requestId,
requestId,
Instant.now(),
responseStatus.status,
when (responseStatus.status) {
@@ -132,38 +100,26 @@ class RequestProcessor(
)
}
private fun <T> isDuplication(pseudonymizedMtbFileRequest: MtbFileRequest<T>): Boolean {
val patientPseudonym = when (pseudonymizedMtbFileRequest) {
is DnpmV2MtbFileRequest -> PatientPseudonym(pseudonymizedMtbFileRequest.content.patient.id)
}
private fun isDuplication(pseudonymizedMtbFile: MtbFile): Boolean {
val patientPseudonym = PatientPseudonym(pseudonymizedMtbFile.patient.id)
val lastMtbFileRequestForPatient =
requestService.lastMtbFileRequestForPatientPseudonym(patientPseudonym)
val isLastRequestDeletion =
requestService.isLastRequestWithKnownStatusDeletion(patientPseudonym)
val isLastRequestDeletion = requestService.isLastRequestWithKnownStatusDeletion(patientPseudonym)
return null != lastMtbFileRequestForPatient && !isLastRequestDeletion && lastMtbFileRequestForPatient.fingerprint == fingerprint(
pseudonymizedMtbFileRequest
)
return null != lastMtbFileRequestForPatient
&& !isLastRequestDeletion
&& lastMtbFileRequestForPatient.fingerprint == fingerprint(pseudonymizedMtbFile)
}
fun processDeletion(patientId: PatientId, isConsented: TtpConsentStatus) {
processDeletion(patientId, randomRequestId(), isConsented)
fun processDeletion(patientId: PatientId) {
processDeletion(patientId, randomRequestId())
}
fun processDeletion(patientId: PatientId, requestId: RequestId, isConsented: TtpConsentStatus) {
fun processDeletion(patientId: PatientId, requestId: RequestId) {
try {
val patientPseudonym = pseudonymizeService.patientPseudonym(patientId)
val requestStatus: RequestStatus = when (isConsented) {
TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED, TtpConsentStatus.BROAD_CONSENT_MISSING, TtpConsentStatus.BROAD_CONSENT_REJECTED -> RequestStatus.NO_CONSENT
TtpConsentStatus.FAILED_TO_ASK -> RequestStatus.ERROR
TtpConsentStatus.BROAD_CONSENT_GIVEN, TtpConsentStatus.UNKNOWN_CHECK_FILE -> RequestStatus.UNKNOWN
TtpConsentStatus.GENOM_DE_CONSENT_SEQUENCING_PERMIT, TtpConsentStatus.GENOM_DE_CONSENT_MISSING, TtpConsentStatus.GENOM_DE_SEQUENCING_REJECTED -> {
throw RuntimeException("processDelete should never deal with '" + isConsented.name + "' consent status. This is a bug and need to be fixed!")
}
}
requestService.save(
Request(
requestId,
@@ -171,22 +127,25 @@ class RequestProcessor(
patientId,
fingerprint(patientPseudonym.value),
RequestType.DELETE,
requestStatus
RequestStatus.UNKNOWN
)
)
val responseStatus = sender.send(DeleteRequest(requestId, patientPseudonym))
val responseStatus = sender.send(MtbFileSender.DeleteRequest(requestId, patientPseudonym))
applicationEventPublisher.publishEvent(
ResponseEvent(
requestId, Instant.now(), responseStatus.status, when (responseStatus.status) {
requestId,
Instant.now(),
responseStatus.status,
when (responseStatus.status) {
RequestStatus.WARNING, RequestStatus.ERROR -> Optional.of(responseStatus.body)
else -> Optional.empty()
}
)
)
} catch (_: Exception) {
} catch (e: Exception) {
requestService.save(
Request(
uuid = requestId,
@@ -201,18 +160,16 @@ class RequestProcessor(
}
}
private fun <T> fingerprint(request: MtbFileRequest<T>): Fingerprint {
return when (request) {
is DnpmV2MtbFileRequest -> fingerprint(objectMapper.writeValueAsString(request.content))
}
private fun fingerprint(mtbFile: MtbFile): Fingerprint {
return fingerprint(objectMapper.writeValueAsString(mtbFile))
}
private fun fingerprint(s: String): Fingerprint {
return Fingerprint(
Base32().encodeAsString(DigestUtils.sha256(s)).replace("=", "").lowercase()
Base32().encodeAsString(DigestUtils.sha256(s))
.replace("=", "")
.lowercase()
)
}
}
private fun extractPatientIdentifier(mtbFile: Mtb): String = mtbFile.patient.id

6
src/main/kotlin/dev/dnpm/etl/processor/services/ResponseProcessor.kt
View File

@@ -70,12 +70,6 @@ class ResponseProcessor(
)
}
RequestStatus.NO_CONSENT -> {
it.report = Report(
"Einwilligung Status fehlt, widerrufen oder ungeklärt."
)
}
else -> {
logger.error("Cannot process response: Unknown response!")
return@ifPresentOrElse

14
src/main/kotlin/dev/dnpm/etl/processor/services/TransformationService.kt
View File

@@ -22,17 +22,11 @@ package dev.dnpm.etl.processor.services
import com.fasterxml.jackson.databind.ObjectMapper
import com.jayway.jsonpath.JsonPath
import com.jayway.jsonpath.PathNotFoundException
import dev.pcvolkmer.mv64e.mtb.Mtb
import de.ukw.ccc.bwhc.dto.MtbFile
class TransformationService(private val objectMapper: ObjectMapper, private val transformations: List<Transformation>) {
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
fun transform(mtbFile: MtbFile): MtbFile {
var json = objectMapper.writeValueAsString(mtbFile)
transformations.forEach { transformation ->
val jsonPath = JsonPath.parse(json)
@@ -54,7 +48,7 @@ class TransformationService(private val objectMapper: ObjectMapper, private val
json = jsonPath.jsonString()
}
return json
return objectMapper.readValue(json, MtbFile::class.java)
}
fun getTransformations(): List<Transformation> {

16
src/main/kotlin/dev/dnpm/etl/processor/types.kt
View File

@@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
@@ -19,7 +19,6 @@
package dev.dnpm.etl.processor
import org.springframework.http.MediaType
import java.util.*
class Fingerprint(val value: String) {
@@ -48,16 +47,3 @@ value class PatientId(val value: String)
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"
}

28
src/main/kotlin/dev/dnpm/etl/processor/web/ConfigController.kt
View File

@@ -19,7 +19,10 @@
package dev.dnpm.etl.processor.web
import dev.dnpm.etl.processor.monitoring.*
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
import dev.dnpm.etl.processor.monitoring.GPasConnectionCheckService
import dev.dnpm.etl.processor.monitoring.OutputConnectionCheckService
import dev.dnpm.etl.processor.output.MtbFileSender
import dev.dnpm.etl.processor.pseudonym.Generator
import dev.dnpm.etl.processor.security.Role
@@ -58,15 +61,11 @@ class ConfigController(
val gPasConnectionAvailable =
connectionCheckServices.filterIsInstance<GPasConnectionCheckService>().firstOrNull()?.connectionAvailable()
val gIcsConnectionAvailable =
connectionCheckServices.filterIsInstance<GIcsConnectionCheckService>().firstOrNull()?.connectionAvailable()
model.addAttribute("pseudonymGenerator", pseudonymGenerator.javaClass.simpleName)
model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName)
model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint())
model.addAttribute("outputConnectionAvailable", outputConnectionAvailable)
model.addAttribute("gPasConnectionAvailable", gPasConnectionAvailable)
model.addAttribute("gIcsConnectionAvailable", gIcsConnectionAvailable)
model.addAttribute("tokensEnabled", tokenService != null)
if (tokenService != null) {
model.addAttribute("tokens", tokenService.findAll())
@@ -120,24 +119,6 @@ class ConfigController(
return "configs/gPasConnectionAvailable"
}
@GetMapping(params = ["gIcsConnectionAvailable"])
fun gIcsConnectionAvailable(model: Model): String {
val gIcsConnectionAvailable =
connectionCheckServices.filterIsInstance<GIcsConnectionCheckService>().firstOrNull()?.connectionAvailable()
model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName)
model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint())
model.addAttribute("gIcsConnectionAvailable", gIcsConnectionAvailable)
if (tokenService != null) {
model.addAttribute("tokensEnabled", true)
model.addAttribute("tokens", tokenService.findAll())
} else {
model.addAttribute("tokens", listOf<Token>())
}
return "configs/gIcsConnectionAvailable"
}
@PostMapping(path = ["tokens"])
fun addToken(@ModelAttribute("name") name: String, model: Model): String {
if (tokenService == null) {
@@ -209,7 +190,6 @@ class ConfigController(
is ConnectionCheckResult.KafkaConnectionCheckResult -> "output-connection-check"
is ConnectionCheckResult.RestConnectionCheckResult -> "output-connection-check"
is ConnectionCheckResult.GPasConnectionCheckResult -> "gpas-connection-check"
is ConnectionCheckResult.GIcsConnectionCheckResult -> "gics-connection-check"
}
ServerSentEvent.builder<Any>()

2
src/main/resources/application-dev.yml
View File

@@ -20,7 +20,7 @@ spring:
app:
rest:
uri: http://localhost/api
uri: http://localhost:9000/bwhc/etl/api
#kafka:
# topic: test
# response-topic: test_response

3
src/main/resources/application.yml
View File

@@ -16,7 +16,6 @@ spring:
content:
enabled: true
paths: /**/*.js,/**/*.css,/**/*.svg,/**/*.jpeg
app:
isGenomDeTestSubmission: true
server:
forward-headers-strategy: framework

5
src/main/resources/templates/configs.html
View File

@@ -49,11 +49,6 @@
</div>
</section>
<section hx-ext="sse" th:sse-connect="@{/configs/events}">
<div th:insert="~{configs/gIcsConnectionAvailable.html}" th:hx-get="@{/configs?gIcsConnectionAvailable}" hx-trigger="sse:gics-connection-check">
</div>
</section>
<section hx-ext="sse" th:sse-connect="@{/configs/events}">
<div th:insert="~{configs/outputConnectionAvailable.html}" th:hx-get="@{/configs?outputConnectionAvailable}" hx-trigger="sse:output-connection-check">
</div>

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

@@ -1,24 +0,0 @@
<th:block th:if="${gIcsConnectionAvailable == null}">
<h2><span>🟦</span> gICS nicht konfiguriert - Einwilligung wird über Dateiinhalt geprüft</h2>
</th:block>
<th:block th:if="${gIcsConnectionAvailable != null}">
<h2><span th:if="${gIcsConnectionAvailable.available}">✅</span><span th:if="${not(gIcsConnectionAvailable.available)}">⚡</span> Verbindung zu gICS</h2>
<div>
Stand: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(gIcsConnectionAvailable.timestamp)}" th:text="${#temporals.formatISO(gIcsConnectionAvailable.timestamp)}"></time>
&nbsp;|&nbsp;
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>

181
src/test/java/dev/dnpm/etl/processor/consent/GicsConsentServiceTest.java
View File

@@ -1,181 +0,0 @@
package dev.dnpm.etl.processor.consent;
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 org.hl7.fhir.r4.model.*;
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.ParametersParameterComponent;
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.retry.support.RetryTemplate;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.TestPropertySource;
import org.springframework.test.web.client.MockRestServiceServer;
import org.springframework.web.client.RestTemplate;
import java.time.Instant;
import java.util.Date;
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.withServerError;
import static org.springframework.test.web.client.response.MockRestResponseCreators.withSuccess;
@ContextConfiguration(classes = {AppConfiguration.class, ObjectMapper.class})
@TestPropertySource(properties = {
"app.consent.service=gics",
"app.consent.gics.uri=http://localhost:8090/ttp-fhir/fhir/gics"
})
@RestClientTest
class GicsConsentServiceTest {
static final String GICS_BASE_URI = "http://localhost:8090/ttp-fhir/fhir/gics";
MockRestServiceServer mockRestServiceServer;
AppFhirConfig appFhirConfig;
GIcsConfigProperties gIcsConfigProperties;
GicsConsentService gicsConsentService;
@BeforeEach
void setUp(
@Autowired AppFhirConfig appFhirConfig,
@Autowired GIcsConfigProperties gIcsConfigProperties
) {
this.appFhirConfig = appFhirConfig;
this.gIcsConfigProperties = gIcsConfigProperties;
var restTemplate = new RestTemplate();
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate);
this.gicsConsentService = new GicsConsentService(
this.gIcsConfigProperties,
RetryTemplate.builder().maxAttempts(1).build(),
restTemplate,
this.appFhirConfig
);
}
@Test
void shouldReturnTtpBroadConsentStatus() {
final Parameters consentedResponse = 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(consentedResponse),
MediaType.APPLICATION_JSON
)
);
var consentStatus = gicsConsentService.getTtpBroadConsentStatus("123456");
assertThat(consentStatus).isEqualTo(TtpConsentStatus.BROAD_CONSENT_GIVEN);
}
@Test
void shouldReturnRevokedConsent() {
final Parameters revokedResponse = 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(revokedResponse),
MediaType.APPLICATION_JSON)
);
var consentStatus = gicsConsentService.getTtpBroadConsentStatus("123456");
assertThat(consentStatus).isEqualTo(TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED);
}
@Test
void shouldReturnInvalidParameterResponse() {
final OperationOutcome responseWithErrorOutcome = 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(responseWithErrorOutcome),
MediaType.APPLICATION_JSON
)
);
var consentStatus = gicsConsentService.getTtpBroadConsentStatus("123456");
assertThat(consentStatus).isEqualTo(TtpConsentStatus.FAILED_TO_ASK);
}
@Test
void shouldReturnRequestError() {
mockRestServiceServer
.expect(
requestTo(GICS_BASE_URI + GicsConsentService.IS_CONSENTED_ENDPOINT)
)
.andRespond(
withServerError()
);
var consentStatus = gicsConsentService.getTtpBroadConsentStatus("123456");
assertThat(consentStatus).isEqualTo(TtpConsentStatus.FAILED_TO_ASK);
}
@Test
void buildRequestParameterCurrentPolicyStatesForPersonTest() {
String pid = "12345678";
var result = gicsConsentService
.buildRequestParameterCurrentPolicyStatesForPerson(
pid,
Date.from(Instant.now()),
ConsentDomain.MODELLVORHABEN_64E
);
assertThat(result.getParameter())
.as("should contain 3 parameter resources")
.hasSize(3);
assertThat(((StringType) result.getParameter("domain").getValue()).getValue())
.isEqualTo(
gIcsConfigProperties.getGenomDeConsentDomainName()
);
assertThat(((Identifier) result.getParameter("personIdentifier").getValue()).getValue())
.isEqualTo(
pid
);
}
}

287
src/test/kotlin/dev/dnpm/etl/processor/consent/Dnpm21BasedConsentEvaluatorTest.kt
View File

@@ -1,287 +0,0 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.consent
import dev.dnpm.etl.processor.ArgProvider
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.api.extension.ExtendWith
import org.junit.jupiter.params.ParameterizedTest
import org.junit.jupiter.params.provider.Arguments
import org.junit.jupiter.params.provider.ArgumentsSource
import org.mockito.ArgumentMatchers.anyString
import org.mockito.Mock
import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.whenever
import java.time.Instant
import java.util.*
@ExtendWith(MockitoExtension::class)
class Dnpm21BasedConsentEvaluatorTest {
@Nested
inner class WithGicsConsentEnabled {
lateinit var consentService: GicsConsentService
lateinit var consentEvaluator: ConsentEvaluator
@BeforeEach
fun setUp(
@Mock consentService: GicsConsentService
) {
this.consentService = consentService
this.consentEvaluator = ConsentEvaluator(consentService)
}
@ParameterizedTest
@ArgumentsSource(WithGicsMtbFileProvider::class)
fun test(
mtbFile: Mtb,
ttpConsentStatus: TtpConsentStatus,
expectedConsentEvaluation: ConsentEvaluation
) {
whenever(consentService.getTtpBroadConsentStatus(anyString())).thenReturn(
ttpConsentStatus
)
assertThat(consentEvaluator.check(mtbFile)).isEqualTo(expectedConsentEvaluation)
}
}
@Nested
inner class WithFileConsentOnly {
lateinit var consentService: MtbFileConsentService
lateinit var consentEvaluator: ConsentEvaluator
@BeforeEach
fun setUp() {
this.consentService = MtbFileConsentService()
this.consentEvaluator = ConsentEvaluator(consentService)
}
@ParameterizedTest
@ArgumentsSource(MtbFileProvider::class)
fun test(mtbFile: Mtb, expectedConsentEvaluation: ConsentEvaluation) {
assertThat(consentEvaluator.check(mtbFile)).isEqualTo(expectedConsentEvaluation)
}
}
// Util classes
class WithGicsMtbFileProvider : ArgProvider(
// Has file ModelProjectConsent and broad consent => consent given
Arguments.of(
buildMtb(ConsentProvision.PERMIT),
TtpConsentStatus.BROAD_CONSENT_GIVEN,
ConsentEvaluation(TtpConsentStatus.BROAD_CONSENT_GIVEN, true)
),
// Has file ModelProjectConsent and broad consent missing => no consent given
Arguments.of(
buildMtb(ConsentProvision.PERMIT),
TtpConsentStatus.BROAD_CONSENT_MISSING,
ConsentEvaluation(TtpConsentStatus.BROAD_CONSENT_MISSING, false)
),
// Has file ModelProjectConsent and broad consent missing or rejected => no consent given
Arguments.of(
buildMtb(ConsentProvision.PERMIT),
TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED,
ConsentEvaluation(TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED, false)
),
// Has file ModelProjectConsent and MV consent => consent given
Arguments.of(
buildMtb(ConsentProvision.PERMIT),
TtpConsentStatus.GENOM_DE_CONSENT_SEQUENCING_PERMIT,
ConsentEvaluation(TtpConsentStatus.GENOM_DE_CONSENT_SEQUENCING_PERMIT, true)
),
// Has file ModelProjectConsent and MV consent rejected => no consent given
Arguments.of(
buildMtb(ConsentProvision.PERMIT),
TtpConsentStatus.GENOM_DE_SEQUENCING_REJECTED,
ConsentEvaluation(TtpConsentStatus.GENOM_DE_SEQUENCING_REJECTED, false)
),
// Has file ModelProjectConsent and MV consent missing => no consent given
Arguments.of(
buildMtb(ConsentProvision.PERMIT),
TtpConsentStatus.GENOM_DE_CONSENT_MISSING,
ConsentEvaluation(TtpConsentStatus.GENOM_DE_CONSENT_MISSING, false)
),
// Has file ModelProjectConsent and no broad consent result => consent given
Arguments.of(
buildMtb(ConsentProvision.PERMIT),
TtpConsentStatus.UNKNOWN_CHECK_FILE,
ConsentEvaluation(TtpConsentStatus.UNKNOWN_CHECK_FILE, true)
),
// Has file ModelProjectConsent and failed to ask => no consent given
Arguments.of(
buildMtb(ConsentProvision.PERMIT),
TtpConsentStatus.FAILED_TO_ASK,
ConsentEvaluation(TtpConsentStatus.FAILED_TO_ASK, false)
),
// File ModelProjectConsent rejected and broad consent => consent given
Arguments.of(
buildMtb(ConsentProvision.DENY),
TtpConsentStatus.BROAD_CONSENT_GIVEN,
ConsentEvaluation(TtpConsentStatus.BROAD_CONSENT_GIVEN, true)
),
// File ModelProjectConsent rejected and broad consent missing => no consent given
Arguments.of(
buildMtb(ConsentProvision.DENY),
TtpConsentStatus.BROAD_CONSENT_MISSING,
ConsentEvaluation(TtpConsentStatus.BROAD_CONSENT_MISSING, false)
),
// File ModelProjectConsent rejected and broad consent missing or rejected => no consent given
Arguments.of(
buildMtb(ConsentProvision.DENY),
TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED,
ConsentEvaluation(TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED, false)
),
// File ModelProjectConsent rejected and MV consent => consent given
Arguments.of(
buildMtb(ConsentProvision.DENY),
TtpConsentStatus.GENOM_DE_CONSENT_SEQUENCING_PERMIT,
ConsentEvaluation(TtpConsentStatus.GENOM_DE_CONSENT_SEQUENCING_PERMIT, true)
),
// File ModelProjectConsent rejected and MV consent rejected => no consent given
Arguments.of(
buildMtb(ConsentProvision.DENY),
TtpConsentStatus.GENOM_DE_SEQUENCING_REJECTED,
ConsentEvaluation(TtpConsentStatus.GENOM_DE_SEQUENCING_REJECTED, false)
),
// File ModelProjectConsent rejected and MV consent missing => no consent given
Arguments.of(
buildMtb(ConsentProvision.DENY),
TtpConsentStatus.GENOM_DE_CONSENT_MISSING,
ConsentEvaluation(TtpConsentStatus.GENOM_DE_CONSENT_MISSING, false)
),
// File ModelProjectConsent rejected and no broad consent result => no consent given
Arguments.of(
buildMtb(ConsentProvision.DENY),
TtpConsentStatus.UNKNOWN_CHECK_FILE,
ConsentEvaluation(TtpConsentStatus.UNKNOWN_CHECK_FILE, false)
),
// File ModelProjectConsent rejected and failed to ask => no consent given
Arguments.of(
buildMtb(ConsentProvision.DENY),
TtpConsentStatus.FAILED_TO_ASK,
ConsentEvaluation(TtpConsentStatus.FAILED_TO_ASK, false)
)
) {
companion object {
fun buildMtb(consentProvision: ConsentProvision): Mtb {
return Mtb.builder()
.patient(
Patient.builder().id("TEST_12345678")
.birthDate(Date.from(Instant.parse("2000-08-08T12:34:56Z"))).gender(
GenderCoding.builder().code(GenderCodingCode.MALE).build()
).build()
)
.metadata(
MvhMetadata.builder().modelProjectConsent(
ModelProjectConsent.builder().provisions(
listOf(
Provision.builder().date(Date()).type(consentProvision)
.purpose(ModelProjectConsentPurpose.SEQUENCING).build()
)
).build()
).build()
)
.episodesOfCare(
listOf(
MtbEpisodeOfCare.builder().id("1")
.patient(Reference.builder().id("TEST_12345678").build())
.build()
)
)
.build()
}
}
}
class MtbFileProvider : ArgProvider(
// Has file consent => consent given
Arguments.of(
buildMtb(ConsentProvision.PERMIT),
ConsentEvaluation(TtpConsentStatus.UNKNOWN_CHECK_FILE, true)
),
// File consent rejected => no consent given
Arguments.of(
buildMtb(ConsentProvision.DENY),
ConsentEvaluation(TtpConsentStatus.UNKNOWN_CHECK_FILE, false)
),
// policy REIDENTIFICATION has no effect on ConsentEvaluation
Arguments.of(
buildMtb(ModelProjectConsentPurpose.REIDENTIFICATION, ConsentProvision.DENY),
ConsentEvaluation(TtpConsentStatus.UNKNOWN_CHECK_FILE, false)
), Arguments.of(
buildMtb(ModelProjectConsentPurpose.REIDENTIFICATION, ConsentProvision.PERMIT),
ConsentEvaluation(TtpConsentStatus.UNKNOWN_CHECK_FILE, false)
),
// policy CASE_IDENTIFICATION has no effect on ConsentEvaluation
Arguments.of(
buildMtb(ModelProjectConsentPurpose.CASE_IDENTIFICATION, ConsentProvision.DENY),
ConsentEvaluation(TtpConsentStatus.UNKNOWN_CHECK_FILE, false)
), Arguments.of(
buildMtb(ModelProjectConsentPurpose.CASE_IDENTIFICATION, ConsentProvision.PERMIT),
ConsentEvaluation(TtpConsentStatus.UNKNOWN_CHECK_FILE, false)
)
) {
companion object {
fun buildMtb(consentProvision: ConsentProvision): Mtb {
return buildMtb(ModelProjectConsentPurpose.SEQUENCING, consentProvision)
}
fun buildMtb(
policy: ModelProjectConsentPurpose,
consentProvision: ConsentProvision
): Mtb {
return Mtb.builder()
.patient(
Patient.builder().id("TEST_12345678")
.birthDate(Date.from(Instant.parse("2000-08-08T12:34:56Z"))).gender(
GenderCoding.builder().code(GenderCodingCode.MALE).build()
).build()
)
.metadata(
MvhMetadata.builder().modelProjectConsent(
ModelProjectConsent.builder().provisions(
listOf(
Provision.builder().date(Date()).type(consentProvision)
.purpose(policy).build()
)
).build()
).build()
)
.episodesOfCare(
listOf(
MtbEpisodeOfCare.builder().id("1")
.patient(Reference.builder().id("TEST_12345678").build())
.build()
)
)
.build()
}
}
}
}

11
src/test/kotlin/dev/dnpm/etl/processor/helpers.kt
View File

@@ -18,14 +18,3 @@
*/
package dev.dnpm.etl.processor
import org.junit.jupiter.api.extension.ExtensionContext
import org.junit.jupiter.params.provider.Arguments
import org.junit.jupiter.params.provider.ArgumentsProvider
import java.util.stream.Stream
open class ArgProvider(vararg val data: Arguments) : ArgumentsProvider {
override fun provideArguments(
context: ExtensionContext?
): Stream<out Arguments> = Stream.of(*data)
}

243
src/test/kotlin/dev/dnpm/etl/processor/input/KafkaInputListenerTest.kt
View File

@@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 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
@@ -20,12 +20,10 @@
package dev.dnpm.etl.processor.input
import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.CustomMediaType
import dev.dnpm.etl.processor.consent.ConsentEvaluation
import dev.dnpm.etl.processor.consent.ConsentEvaluator
import dev.dnpm.etl.processor.consent.TtpConsentStatus
import de.ukw.ccc.bwhc.dto.Consent
import de.ukw.ccc.bwhc.dto.MtbFile
import de.ukw.ccc.bwhc.dto.Patient
import dev.dnpm.etl.processor.services.RequestProcessor
import dev.pcvolkmer.mv64e.mtb.*
import org.apache.kafka.clients.consumer.ConsumerRecord
import org.apache.kafka.common.header.internals.RecordHeader
import org.apache.kafka.common.header.internals.RecordHeaders
@@ -35,261 +33,80 @@ import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith
import org.mockito.Mock
import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.*
import org.mockito.kotlin.any
import org.mockito.kotlin.anyValueClass
import org.mockito.kotlin.times
import org.mockito.kotlin.verify
import java.util.*
@ExtendWith(MockitoExtension::class)
class KafkaInputListenerTest {
private lateinit var requestProcessor: RequestProcessor
private lateinit var consentEvaluator: ConsentEvaluator
private lateinit var objectMapper: ObjectMapper
private lateinit var kafkaInputListener: KafkaInputListener
@BeforeEach
fun setup(
@Mock requestProcessor: RequestProcessor,
@Mock consentEvaluator: ConsentEvaluator,
@Mock requestProcessor: RequestProcessor
) {
this.requestProcessor = requestProcessor
this.consentEvaluator = consentEvaluator
this.objectMapper = ObjectMapper()
this.kafkaInputListener = KafkaInputListener(requestProcessor, consentEvaluator, objectMapper)
this.kafkaInputListener = KafkaInputListener(requestProcessor, objectMapper)
}
@Test
fun shouldProcessMtbFileRequest() {
whenever(consentEvaluator.check(any())).thenReturn(
ConsentEvaluation(
TtpConsentStatus.BROAD_CONSENT_GIVEN,
true
)
)
val mtbFile = Mtb.builder()
.patient(Patient.builder().id("DUMMY_12345678").build())
.metadata(
MvhMetadata
.builder()
.modelProjectConsent(
ModelProjectConsent
.builder()
.provisions(
listOf(
Provision.builder().type(ConsentProvision.PERMIT)
.purpose(ModelProjectConsentPurpose.SEQUENCING).build()
)
).build()
)
.build()
)
val mtbFile = MtbFile.builder()
.withPatient(Patient.builder().withId("DUMMY_12345678").build())
.withConsent(Consent.builder().withStatus(Consent.Status.ACTIVE).build())
.build()
kafkaInputListener.onMessage(
ConsumerRecord(
"testtopic",
0,
0,
"",
this.objectMapper.writeValueAsString(mtbFile)
)
)
kafkaInputListener.onMessage(ConsumerRecord("testtopic", 0, 0, "", this.objectMapper.writeValueAsString(mtbFile)))
verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
verify(requestProcessor, times(1)).processMtbFile(any())
}
@Test
fun shouldProcessDeleteRequest() {
whenever(consentEvaluator.check(any())).thenReturn(
ConsentEvaluation(
TtpConsentStatus.BROAD_CONSENT_GIVEN,
false
)
)
val mtbFile = Mtb.builder()
.patient(Patient.builder().id("DUMMY_12345678").build())
.metadata(
MvhMetadata
.builder()
.modelProjectConsent(
ModelProjectConsent
.builder()
.provisions(
listOf(
Provision.builder().type(ConsentProvision.DENY)
.purpose(ModelProjectConsentPurpose.SEQUENCING).build()
)
).build()
)
.build()
)
val mtbFile = MtbFile.builder()
.withPatient(Patient.builder().withId("DUMMY_12345678").build())
.withConsent(Consent.builder().withStatus(Consent.Status.REJECTED).build())
.build()
kafkaInputListener.onMessage(
ConsumerRecord(
"testtopic",
0,
0,
"",
this.objectMapper.writeValueAsString(mtbFile)
)
)
kafkaInputListener.onMessage(ConsumerRecord("testtopic", 0, 0, "", this.objectMapper.writeValueAsString(mtbFile)))
verify(requestProcessor, times(1)).processDeletion(
anyValueClass(),
eq(TtpConsentStatus.UNKNOWN_CHECK_FILE)
)
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
}
@Test
fun shouldProcessMtbFileRequestWithExistingRequestId() {
whenever(consentEvaluator.check(any())).thenReturn(
ConsentEvaluation(
TtpConsentStatus.BROAD_CONSENT_GIVEN,
true
)
)
val mtbFile = Mtb.builder()
.patient(Patient.builder().id("DUMMY_12345678").build())
.metadata(
MvhMetadata
.builder()
.modelProjectConsent(
ModelProjectConsent
.builder()
.provisions(
listOf(
Provision.builder().type(ConsentProvision.PERMIT)
.purpose(ModelProjectConsentPurpose.SEQUENCING).build()
)
).build()
)
.build()
)
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()
)
ConsumerRecord("testtopic", 0, 0, -1L, TimestampType.NO_TIMESTAMP_TYPE, -1, -1, "", this.objectMapper.writeValueAsString(mtbFile), headers, Optional.empty())
)
verify(requestProcessor, times(1)).processMtbFile(any<Mtb>(), anyValueClass())
verify(requestProcessor, times(1)).processMtbFile(any(), anyValueClass())
}
@Test
fun shouldProcessDeleteRequestWithExistingRequestId() {
whenever(consentEvaluator.check(any())).thenReturn(
ConsentEvaluation(
TtpConsentStatus.BROAD_CONSENT_GIVEN,
false
)
)
val mtbFile = Mtb.builder()
.patient(Patient.builder().id("DUMMY_12345678").build())
.metadata(
MvhMetadata
.builder()
.modelProjectConsent(
ModelProjectConsent
.builder()
.provisions(
listOf(
Provision.builder().type(ConsentProvision.DENY)
.purpose(ModelProjectConsentPurpose.SEQUENCING).build()
)
).build()
)
.build()
)
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 = Mtb.builder()
.patient(Patient.builder().id("DUMMY_12345678").build())
.metadata(
MvhMetadata
.builder()
.modelProjectConsent(
ModelProjectConsent
.builder()
.provisions(
listOf(
Provision.builder().type(ConsentProvision.DENY)
.purpose(ModelProjectConsentPurpose.SEQUENCING).build()
)
).build()
)
.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
)
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())
}
}

235
src/test/kotlin/dev/dnpm/etl/processor/input/MtbFileRestControllerTest.kt
View File

@@ -20,34 +20,23 @@
package dev.dnpm.etl.processor.input
import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.ArgProvider
import dev.dnpm.etl.processor.CustomMediaType
import dev.dnpm.etl.processor.consent.ConsentEvaluation
import dev.dnpm.etl.processor.consent.ConsentEvaluator
import dev.dnpm.etl.processor.consent.TtpConsentStatus
import de.ukw.ccc.bwhc.dto.*
import dev.dnpm.etl.processor.services.RequestProcessor
import dev.pcvolkmer.mv64e.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.Arguments
import org.junit.jupiter.params.provider.ArgumentsSource
import org.mockito.Mock
import org.mockito.Mockito.times
import org.mockito.Mockito.verify
import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.any
import org.mockito.kotlin.anyValueClass
import org.mockito.kotlin.whenever
import org.springframework.core.io.ClassPathResource
import org.springframework.http.MediaType
import org.springframework.test.web.servlet.MockMvc
import org.springframework.test.web.servlet.delete
import org.springframework.test.web.servlet.post
import org.springframework.test.web.servlet.setup.MockMvcBuilders
import java.time.Instant
import java.util.*
@ExtendWith(MockitoExtension::class)
class MtbFileRestControllerTest {
@@ -55,78 +44,47 @@ class MtbFileRestControllerTest {
private val objectMapper = ObjectMapper()
@Nested
inner class RequestsForDnpmDataModel21 {
inner class BwhcRequests {
private lateinit var mockMvc: MockMvc
private lateinit var requestProcessor: RequestProcessor
private lateinit var consentEvaluator: ConsentEvaluator
@BeforeEach
fun setup(
@Mock requestProcessor: RequestProcessor,
@Mock consentEvaluator: ConsentEvaluator
@Mock requestProcessor: RequestProcessor
) {
this.requestProcessor = requestProcessor
this.consentEvaluator = consentEvaluator
val controller = MtbFileRestController(
requestProcessor,
consentEvaluator
)
val controller = MtbFileRestController(requestProcessor)
this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build()
}
@Test
fun shouldRespondPostRequest() {
whenever(consentEvaluator.check(any())).thenReturn(
ConsentEvaluation(
TtpConsentStatus.BROAD_CONSENT_GIVEN,
true
)
)
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>())
}
@ParameterizedTest
@ArgumentsSource(Dnpm21MtbFile::class)
fun shouldProcessPostRequest(mtb: Mtb, broadConsent: TtpConsentStatus, shouldProcess: String) {
whenever(consentEvaluator.check(any<Mtb>())).thenReturn(
ConsentEvaluation(
broadConsent,
shouldProcess == "process"
)
)
fun shouldProcessPostRequest() {
mockMvc.post("/mtbfile") {
content = objectMapper.writeValueAsString(mtb)
contentType = CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Consent.Status.ACTIVE))
contentType = MediaType.APPLICATION_JSON
}.andExpect {
status {
isAccepted()
}
}
if (shouldProcess == "process") {
verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
} else {
verify(requestProcessor, times(1)).processDeletion(
anyValueClass(),
org.mockito.kotlin.eq(broadConsent)
)
verify(requestProcessor, times(1)).processMtbFile(any())
}
@Test
fun shouldProcessPostRequestWithRejectedConsent() {
mockMvc.post("/mtbfile") {
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Consent.Status.REJECTED))
contentType = MediaType.APPLICATION_JSON
}.andExpect {
status {
isAccepted()
}
}
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
}
@Test
@@ -137,90 +95,89 @@ class MtbFileRestControllerTest {
}
}
verify(requestProcessor, times(1)).processDeletion(
anyValueClass(),
org.mockito.kotlin.eq(TtpConsentStatus.UNKNOWN_CHECK_FILE)
)
verify(consentEvaluator, times(0)).check(any<Mtb>())
}
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
}
}
class Dnpm21MtbFile : ArgProvider(
// No Metadata and no broad consent => delete
Arguments.of(
buildMtb(null),
TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED,
"delete"
),
// No Metadata and broad consent given => process
Arguments.of(
buildMtb(null),
TtpConsentStatus.BROAD_CONSENT_GIVEN,
"process"
),
// No model project consent and no broad consent => delete
Arguments.of(
buildMtb(MvhMetadata.builder().modelProjectConsent(ModelProjectConsent.builder().build()).build()),
TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED,
"delete"
),
// No model project consent and broad consent given => process
Arguments.of(
buildMtb(MvhMetadata.builder().modelProjectConsent(ModelProjectConsent.builder().build()).build()),
TtpConsentStatus.BROAD_CONSENT_GIVEN,
"process"
),
// Model project consent given and no broad consent => process
Arguments.of(
buildMtb(
MvhMetadata.builder().modelProjectConsent(
ModelProjectConsent.builder().provisions(
listOf(
Provision.builder().date(Date()).type(ConsentProvision.PERMIT)
.purpose(ModelProjectConsentPurpose.SEQUENCING).build()
)
).build()
).build()
),
TtpConsentStatus.UNKNOWN_CHECK_FILE,
"process"
),
// Model project consent given and broad consent given => process
Arguments.of(
buildMtb(
MvhMetadata.builder().modelProjectConsent(
ModelProjectConsent.builder().provisions(
listOf(
Provision.builder().date(Date()).type(ConsentProvision.PERMIT)
.purpose(ModelProjectConsentPurpose.SEQUENCING).build()
)
).build()
).build()
),
TtpConsentStatus.BROAD_CONSENT_GIVEN,
"process"
)
@Nested
inner class BwhcRequestsWithAlias {
private lateinit var mockMvc: MockMvc
private lateinit var requestProcessor: RequestProcessor
@BeforeEach
fun setup(
@Mock requestProcessor: RequestProcessor
) {
this.requestProcessor = requestProcessor
val controller = MtbFileRestController(requestProcessor)
this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build()
}
@Test
fun shouldProcessPostRequest() {
mockMvc.post("/mtb") {
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Consent.Status.ACTIVE))
contentType = MediaType.APPLICATION_JSON
}.andExpect {
status {
isAccepted()
}
}
verify(requestProcessor, times(1)).processMtbFile(any())
}
@Test
fun shouldProcessPostRequestWithRejectedConsent() {
mockMvc.post("/mtb") {
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Consent.Status.REJECTED))
contentType = MediaType.APPLICATION_JSON
}.andExpect {
status {
isAccepted()
}
}
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
}
@Test
fun shouldProcessDeleteRequest() {
mockMvc.delete("/mtb/TEST_12345678").andExpect {
status {
isAccepted()
}
}
verify(requestProcessor, times(1)).processDeletion(anyValueClass())
}
}
companion object {
fun buildMtb(metadata: MvhMetadata?): Mtb {
return Mtb.builder()
.patient(
Patient.builder().id("TEST_12345678")
.birthDate(Date.from(Instant.parse("2000-08-08T12:34:56Z"))).gender(
GenderCoding.builder().code(GenderCodingCode.MALE).build()
).build()
)
.metadata(metadata)
.episodesOfCare(
listOf(
MtbEpisodeOfCare.builder().id("1")
.patient(Reference.builder().id("TEST_12345678").build())
fun bwhcMtbFileContent(consentStatus: Consent.Status) = MtbFile.builder()
.withPatient(
Patient.builder()
.withId("TEST_12345678")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.withConsent(
Consent.builder()
.withId("1")
.withStatus(consentStatus)
.withPatient("TEST_12345678")
.build()
)
.withEpisode(
Episode.builder()
.withId("1")
.withPatient("TEST_12345678")
.withPeriod(PeriodStart("2023-08-08"))
.build()
)
.build()
}
}
}

221
src/test/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSenderTest.kt
View File

@@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 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
@@ -20,20 +20,18 @@
package dev.dnpm.etl.processor.output
import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.CustomMediaType
import de.ukw.ccc.bwhc.dto.*
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.*
@@ -41,17 +39,12 @@ 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 {
@Nested
inner class BwhcV1Record {
private lateinit var kafkaTemplate: KafkaTemplate<String, String>
private lateinit var kafkaMtbFileSender: KafkaMtbFileSender
@@ -72,103 +65,67 @@ class KafkaMtbFileSenderTest {
}
@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)
}
@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")
@MethodSource("requestWithResponseSource")
fun shouldSendMtbFileRequestAndReturnExpectedState(testData: TestData) {
doAnswer {
if (null != testData.exception) {
throw testData.exception
}
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
val response = kafkaMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile()))
val response = kafkaMtbFileSender.send(MtbFileSender.MtbFileRequest(TEST_REQUEST_ID, 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(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
assertThat(response.status).isEqualTo(testData.requestStatus)
}
@Test
fun shouldSendMtbFileRequestWithCorrectKeyAndHeaderAndBody() {
fun shouldSendMtbFileRequestWithCorrectKeyAndBody() {
doAnswer {
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
kafkaMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile()))
kafkaMtbFileSender.send(MtbFileSender.MtbFileRequest(TEST_REQUEST_ID, mtbFile(Consent.Status.ACTIVE)))
val captor = argumentCaptor<ProducerRecord<String, String>>()
verify(kafkaTemplate, times(1)).send(captor.capture())
assertThat(captor.firstValue.key()).isNotNull
assertThat(captor.firstValue.key()).isEqualTo("{\"pid\": \"PID\"}")
assertThat(captor.firstValue.headers().headers("contentType")).isNotNull
assertThat(captor.firstValue.headers().headers("contentType")?.firstOrNull()?.value()).isEqualTo(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)))
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(TEST_REQUEST_ID, Consent.Status.ACTIVE)))
}
@Test
fun shouldSendDeleteRequestWithCorrectKeyAndBody() {
doAnswer {
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
kafkaMtbFileSender.send(MtbFileSender.DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
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(TEST_REQUEST_ID, Consent.Status.REJECTED)))
}
@ParameterizedTest
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
@MethodSource("requestWithResponseSource")
fun shouldRetryOnMtbFileKafkaSendError(testData: TestData) {
val kafkaProperties = KafkaProperties("testtopic")
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
@@ -179,9 +136,9 @@ class KafkaMtbFileSenderTest {
throw testData.exception
}
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
kafkaMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile()))
kafkaMtbFileSender.send(MtbFileSender.MtbFileRequest(TEST_REQUEST_ID, mtbFile(Consent.Status.ACTIVE)))
val expectedCount = when (testData.exception) {
// OK - No Retry
@@ -190,40 +147,76 @@ class KafkaMtbFileSenderTest {
else -> times(3)
}
verify(kafkaTemplate, expectedCount).send(any<ProducerRecord<String, String>>())
verify(kafkaTemplate, expectedCount).send(anyString(), anyString(), anyString())
}
@ParameterizedTest
@MethodSource("requestWithResponseSource")
fun shouldRetryOnDeleteKafkaSendError(testData: TestData) {
val kafkaProperties = KafkaProperties("testtopic")
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
this.kafkaMtbFileSender = KafkaMtbFileSender(this.kafkaTemplate, kafkaProperties, retryTemplate, this.objectMapper)
doAnswer {
if (null != testData.exception) {
throw testData.exception
}
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
kafkaMtbFileSender.send(MtbFileSender.DeleteRequest(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(anyString(), anyString(), anyString())
}
companion object {
val TEST_REQUEST_ID = RequestId("TestId")
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID")
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 mtbFile(consentStatus: Consent.Status): MtbFile {
return if (consentStatus == Consent.Status.ACTIVE) {
MtbFile.builder()
.withPatient(
Patient.builder()
.withId("PID")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
}
.withConsent(
Consent.builder()
.withId("1")
.withStatus(consentStatus)
.withPatient("PID")
.build()
)
.withEpisode(
Episode.builder()
.withId("1")
.withPatient("PID")
.withPeriod(PeriodStart("2023-08-08"))
.build()
)
} else {
MtbFile.builder()
.withConsent(
Consent.builder()
.withStatus(consentStatus)
.withPatient("PID")
.build()
)
}.build()
}
fun dnmpV2kafkaRecordData(requestId: RequestId): MtbRequest {
return DnpmV2MtbFileRequest(requestId, dnpmV2MtbFile())
fun kafkaRecordData(requestId: RequestId, consentStatus: Consent.Status): KafkaMtbFileSender.Data {
return KafkaMtbFileSender.Data(requestId, mtbFile(consentStatus))
}
data class TestData(val requestStatus: RequestStatus, val exception: Throwable? = null)

312
src/test/kotlin/dev/dnpm/etl/processor/output/RestBwhcMtbFileSenderTest.kt Normal file
View File

@@ -0,0 +1,312 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.output
import com.fasterxml.jackson.databind.ObjectMapper
import com.fasterxml.jackson.module.kotlin.KotlinModule
import de.ukw.ccc.bwhc.dto.*
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.config.RestTargetProperties
import dev.dnpm.etl.processor.monitoring.ReportService
import dev.dnpm.etl.processor.monitoring.RequestStatus
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.params.ParameterizedTest
import org.junit.jupiter.params.provider.Arguments
import org.junit.jupiter.params.provider.MethodSource
import org.springframework.http.HttpMethod
import org.springframework.http.HttpStatus
import org.springframework.retry.policy.SimpleRetryPolicy
import org.springframework.retry.support.RetryTemplateBuilder
import org.springframework.test.web.client.ExpectedCount
import org.springframework.test.web.client.MockRestServiceServer
import org.springframework.test.web.client.match.MockRestRequestMatchers.method
import org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo
import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus
import org.springframework.web.client.RestTemplate
class RestBwhcMtbFileSenderTest {
private lateinit var mockRestServiceServer: MockRestServiceServer
private lateinit var restMtbFileSender: RestMtbFileSender
private var reportService = ReportService(ObjectMapper().registerModule(KotlinModule.Builder().build()))
@BeforeEach
fun setup() {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile", null, null)
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.restMtbFileSender =
RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
}
@ParameterizedTest
@MethodSource("deleteRequestWithResponseSource")
fun shouldReturnExpectedResponseForDelete(requestWithResponse: RequestWithResponse) {
this.mockRestServiceServer
.expect(method(HttpMethod.DELETE))
.andExpect(requestTo("http://localhost:9000/mtbfile/Patient/${TEST_PATIENT_PSEUDONYM.value}"))
.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(MtbFileSender.DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
@ParameterizedTest
@MethodSource("mtbFileRequestWithResponseSource")
fun shouldReturnExpectedResponseForMtbFilePost(requestWithResponse: RequestWithResponse) {
this.mockRestServiceServer
.expect(method(HttpMethod.POST))
.andExpect(requestTo("http://localhost:9000/mtbfile/MTBFile"))
.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(MtbFileSender.MtbFileRequest(TEST_REQUEST_ID, mtbFile))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
@ParameterizedTest
@MethodSource("mtbFileRequestWithResponseSource")
fun shouldRetryOnMtbFileHttpRequestError(requestWithResponse: RequestWithResponse) {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile", null, null)
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.restMtbFileSender =
RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
val expectedCount = when (requestWithResponse.httpStatus) {
// OK - No Retry
HttpStatus.OK, HttpStatus.CREATED -> ExpectedCount.max(1)
// Request failed - Retry max 3 times
else -> ExpectedCount.max(3)
}
this.mockRestServiceServer
.expect(expectedCount, method(HttpMethod.POST))
.andExpect(requestTo("http://localhost:9000/mtbfile/MTBFile"))
.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(MtbFileSender.MtbFileRequest(TEST_REQUEST_ID, mtbFile))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
@ParameterizedTest
@MethodSource("deleteRequestWithResponseSource")
fun shouldRetryOnDeleteHttpRequestError(requestWithResponse: RequestWithResponse) {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/mtbfile", null, null)
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.restMtbFileSender =
RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
val expectedCount = when (requestWithResponse.httpStatus) {
// OK - No Retry
HttpStatus.OK, HttpStatus.CREATED -> ExpectedCount.max(1)
// Request failed - Retry max 3 times
else -> ExpectedCount.max(3)
}
this.mockRestServiceServer
.expect(expectedCount, method(HttpMethod.DELETE))
.andExpect(requestTo("http://localhost:9000/mtbfile/Patient/${TEST_PATIENT_PSEUDONYM.value}"))
.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(MtbFileSender.DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
companion object {
data class RequestWithResponse(
val httpStatus: HttpStatus,
val body: String,
val response: MtbFileSender.Response
)
val TEST_REQUEST_ID = RequestId("TestId")
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID")
val mtbFile: MtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.withId("PID")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.withConsent(
Consent.builder()
.withId("1")
.withStatus(Consent.Status.ACTIVE)
.withPatient("PID")
.build()
)
.withEpisode(
Episode.builder()
.withId("1")
.withPatient("PID")
.withPeriod(PeriodStart("2023-08-08"))
.build()
)
.build()
private const val ERROR_RESPONSE_BODY = "Sonstiger Fehler bei der Übertragung"
/**
* Synthetic http responses with related request status
* Also see: https://ibmi-intra.cs.uni-tuebingen.de/display/ZPM/bwHC+REST+API
*/
@JvmStatic
fun mtbFileRequestWithResponseSource(): Set<RequestWithResponse> {
return setOf(
RequestWithResponse(
HttpStatus.OK,
responseBodyWithMaxSeverity(ReportService.Severity.INFO),
MtbFileSender.Response(
RequestStatus.SUCCESS,
responseBodyWithMaxSeverity(ReportService.Severity.INFO)
)
),
RequestWithResponse(
HttpStatus.CREATED,
responseBodyWithMaxSeverity(ReportService.Severity.WARNING),
MtbFileSender.Response(
RequestStatus.WARNING,
responseBodyWithMaxSeverity(ReportService.Severity.WARNING)
)
),
RequestWithResponse(
HttpStatus.BAD_REQUEST,
responseBodyWithMaxSeverity(ReportService.Severity.ERROR),
MtbFileSender.Response(RequestStatus.ERROR, responseBodyWithMaxSeverity(ReportService.Severity.ERROR))
),
RequestWithResponse(
HttpStatus.UNPROCESSABLE_ENTITY,
responseBodyWithMaxSeverity(ReportService.Severity.FATAL),
MtbFileSender.Response(
RequestStatus.ERROR,
responseBodyWithMaxSeverity(ReportService.Severity.FATAL)
)
),
// Some more errors not mentioned in documentation
RequestWithResponse(
HttpStatus.NOT_FOUND,
ERROR_RESPONSE_BODY,
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
),
RequestWithResponse(
HttpStatus.INTERNAL_SERVER_ERROR,
ERROR_RESPONSE_BODY,
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
)
)
}
/**
* Synthetic http responses with related request status
* Also see: https://ibmi-intra.cs.uni-tuebingen.de/display/ZPM/bwHC+REST+API
*/
@JvmStatic
fun deleteRequestWithResponseSource(): Set<RequestWithResponse> {
return setOf(
RequestWithResponse(HttpStatus.OK, "", MtbFileSender.Response(RequestStatus.SUCCESS)),
// Some more errors not mentioned in documentation
RequestWithResponse(
HttpStatus.NOT_FOUND,
"what????",
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
),
RequestWithResponse(
HttpStatus.INTERNAL_SERVER_ERROR,
"what????",
MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
)
)
}
fun responseBodyWithMaxSeverity(severity: ReportService.Severity): String {
return when (severity) {
ReportService.Severity.INFO -> """
{
"patient": "PID",
"issues": [
{ "severity": "info", "message": "Info Message" }
]
}
"""
ReportService.Severity.WARNING -> """
{
"patient": "PID",
"issues": [
{ "severity": "info", "message": "Info Message" },
{ "severity": "warning", "message": "Warning Message" }
]
}
"""
ReportService.Severity.ERROR -> """
{
"patient": "PID",
"issues": [
{ "severity": "info", "message": "Info Message" },
{ "severity": "warning", "message": "Warning Message" },
{ "severity": "error", "message": "Error Message" }
]
}
"""
ReportService.Severity.FATAL -> """
{
"patient": "PID",
"issues": [
{ "severity": "info", "message": "Info Message" },
{ "severity": "warning", "message": "Warning Message" },
{ "severity": "error", "message": "Error Message" },
{ "severity": "fatal", "message": "Fatal Message" }
]
}
"""
}
}
}
}

161
src/test/kotlin/dev/dnpm/etl/processor/output/RestDipMtbFileSenderTest.kt
View File

@@ -21,7 +21,7 @@ package dev.dnpm.etl.processor.output
import com.fasterxml.jackson.databind.ObjectMapper
import com.fasterxml.jackson.module.kotlin.KotlinModule
import dev.dnpm.etl.processor.CustomMediaType
import de.ukw.ccc.bwhc.dto.*
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.config.AppConfigProperties
@@ -29,32 +29,25 @@ 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 dev.dnpm.etl.processor.output.RestBwhcMtbFileSenderTest.Companion
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.match.MockRestRequestMatchers.method
import org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo
import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus
import org.springframework.web.client.RestTemplate
import java.time.Instant
import java.util.*
class RestDipMtbFileSenderTest {
@Nested
inner class DnpmV2ContentRequest {
private lateinit var mockRestServiceServer: MockRestServiceServer
private lateinit var restMtbFileSender: RestMtbFileSender
@@ -64,7 +57,7 @@ class RestDipMtbFileSenderTest {
@BeforeEach
fun setup() {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null)
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false)
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
@@ -73,46 +66,7 @@ class RestDipMtbFileSenderTest {
}
@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)
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")
@MethodSource("deleteRequestWithResponseSource")
fun shouldReturnExpectedResponseForDelete(requestWithResponse: RequestWithResponse) {
this.mockRestServiceServer
.expect(method(HttpMethod.DELETE))
@@ -121,17 +75,65 @@ class RestDipMtbFileSenderTest {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
val response = restMtbFileSender.send(MtbFileSender.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")
@MethodSource("mtbFileRequestWithResponseSource")
fun shouldReturnExpectedResponseForMtbFilePost(requestWithResponse: RequestWithResponse) {
this.mockRestServiceServer
.expect(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(MtbFileSender.MtbFileRequest(TEST_REQUEST_ID, mtbFile))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
@ParameterizedTest
@MethodSource("mtbFileRequestWithResponseSource")
fun shouldRetryOnMtbFileHttpRequestError(requestWithResponse: RequestWithResponse) {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/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(MtbFileSender.MtbFileRequest(TEST_REQUEST_ID, mtbFile))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
@ParameterizedTest
@MethodSource("deleteRequestWithResponseSource")
fun shouldRetryOnDeleteHttpRequestError(requestWithResponse: RequestWithResponse) {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null)
val retryTemplate = AppConfiguration().retryTemplate(AppConfigProperties())
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)
@@ -154,13 +156,11 @@ class RestDipMtbFileSenderTest {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
val response = restMtbFileSender.send(MtbFileSender.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,
@@ -171,28 +171,29 @@ class RestDipMtbFileSenderTest {
val TEST_REQUEST_ID = RequestId("TestId")
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID")
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())
}
}
val mtbFile: MtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.withId("PID")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
}
}
.withConsent(
Consent.builder()
.withId("1")
.withStatus(Consent.Status.ACTIVE)
.withPatient("PID")
.build()
)
.withEpisode(
Episode.builder()
.withId("1")
.withPatient("PID")
.withPeriod(PeriodStart("2023-08-08"))
.build()
)
.build()
private const val ERROR_RESPONSE_BODY = "Sonstiger Fehler bei der Übertragung"

242
src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt
View File

@@ -1,7 +1,7 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
@@ -19,18 +19,9 @@
package dev.dnpm.etl.processor.pseudonym
import ca.uhn.fhir.context.FhirContext
import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.config.AppConfigProperties
import dev.dnpm.etl.processor.config.GIcsConfigProperties
import dev.dnpm.etl.processor.config.JacksonConfig
import dev.dnpm.etl.processor.consent.MtbFileConsentService
import dev.dnpm.etl.processor.services.ConsentProcessor
import dev.dnpm.etl.processor.services.ConsentProcessorTest
import dev.pcvolkmer.mv64e.mtb.*
import de.ukw.ccc.bwhc.dto.*
import org.assertj.core.api.Assertions.assertThat
import org.hl7.fhir.r4.model.Bundle
import org.junit.jupiter.api.Nested
import org.junit.jupiter.api.Test
import org.junit.jupiter.api.assertThrows
import org.junit.jupiter.api.extension.ExtendWith
@@ -40,28 +31,20 @@ import org.mockito.kotlin.anyValueClass
import org.mockito.kotlin.doAnswer
import org.mockito.kotlin.whenever
import org.springframework.core.io.ClassPathResource
import java.time.Instant
import java.util.*
const val FAKE_MTB_FILE_PATH = "fake_MTBFile.json"
const val CLEAN_PATIENT_ID = "5dad2f0b-49c6-47d8-a952-7b9e9e0f7549"
@ExtendWith(MockitoExtension::class)
class ExtensionsTest {
fun getObjectMapper(): ObjectMapper {
return JacksonConfig().objectMapper()
}
@Nested
inner class UsingDnpmV2Datamodel {
val FAKE_MTB_FILE_PATH = "mv64e-mtb-fake-patient.json"
val CLEAN_PATIENT_ID = "644bae7a-56f6-4ee8-b02f-c532e65af5b1"
private fun fakeMtbFile(): Mtb {
private fun fakeMtbFile(): MtbFile {
val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
return getObjectMapper().readValue(mtbFile, Mtb::class.java)
return ObjectMapper().readValue(mtbFile, MtbFile::class.java)
}
private fun Mtb.serialized(): String {
return getObjectMapper().writeValueAsString(this)
private fun MtbFile.serialized(): String {
return ObjectMapper().writeValueAsString(this)
}
@Test
@@ -72,8 +55,6 @@ class ExtensionsTest {
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
val mtbFile = fakeMtbFile()
mtbFile.ensureMetaDataIsInitialized()
addConsentData(mtbFile)
mtbFile.pseudonymizeWith(pseudonymizeService)
@@ -81,64 +62,6 @@ class ExtensionsTest {
assertThat(mtbFile.serialized()).doesNotContain(CLEAN_PATIENT_ID)
}
private fun addConsentData(mtbFile: Mtb) {
val gIcsConfigProperties = GIcsConfigProperties("", "", "")
val appConfigProperties = AppConfigProperties(emptyList())
val bundle = Bundle()
val dummyConsent = ConsentProcessorTest.getDummyGenomDeConsent()
dummyConsent.patient.reference = "Patient/$CLEAN_PATIENT_ID"
bundle.addEntry().resource = dummyConsent
ConsentProcessor(
appConfigProperties,
gIcsConfigProperties,
JacksonConfig().objectMapper(),
FhirContext.forR4(),
MtbFileConsentService()
).embedBroadConsentResources(mtbFile, bundle)
}
@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
}
@Test
fun shouldNotContainAnyUuidAfterRehashingOfIds(@Mock pseudonymizeService: PseudonymizeService) {
doAnswer {
@@ -152,49 +75,124 @@ class ExtensionsTest {
val mtbFile = fakeMtbFile()
/**
* replace hex values with random long, so our test does not match false positives
*/
mtbFile.ngsReports.forEach { report ->
report.results.simpleVariants.forEach { simpleVariant ->
simpleVariant.externalIds.forEach { extIdValue ->
extIdValue.value =
Math.random().toLong().toString()
}
}
}
mtbFile.ngsReports.forEach { report ->
report.results.rnaFusions.forEach { simpleVariant ->
simpleVariant.externalIds.forEach { extIdValue ->
extIdValue.value =
Math.random().toLong().toString()
}
simpleVariant.fusionPartner3Prime?.transcriptId?.value =
Math.random().toLong().toString()
simpleVariant.fusionPartner5Prime?.transcriptId?.value =
Math.random().toLong().toString()
simpleVariant.externalIds?.forEach { it ->
it?.value = Math.random().toLong().toString()
}
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)
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 input = mtbFile.serialized()
val matcher = pattern.matcher(input)
assertThrows<IllegalStateException> {
matcher.find()
val posSt = "check at pos: " + matcher.start().toString() + ", " + matcher.end()
println(posSt + " with " + matcher.group())
}.also {
assertThat(it.message).isEqualTo("No match found")
}
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()
}
}

43
src/test/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeServiceTest.kt
View File

@@ -19,8 +19,8 @@
package dev.dnpm.etl.processor.pseudonym
import de.ukw.ccc.bwhc.dto.*
import dev.dnpm.etl.processor.config.PseudonymizeConfigProperties
import dev.pcvolkmer.mv64e.mtb.*
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith
@@ -29,26 +29,31 @@ import org.mockito.Mock
import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.doAnswer
import org.mockito.kotlin.whenever
import java.time.Instant
import java.util.*
@ExtendWith(MockitoExtension::class)
class PseudonymizeServiceTest {
private val mtbFile = Mtb.builder()
.patient(
private val mtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.id("123")
.withId("123")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.episodesOfCare(
listOf(
MtbEpisodeOfCare.builder()
.id("1")
.patient(Reference.builder().id("123").build())
.period(PeriodDate.builder().start(Date.from(Instant.parse("2021-01-01T00:00:00.00Z"))).build())
.withConsent(
Consent.builder()
.withId("1")
.withStatus(Consent.Status.ACTIVE)
.withPatient("123")
.build()
)
.withEpisode(
Episode.builder()
.withId("1")
.withPatient("123")
.withPeriod(PeriodStart("2023-08-08"))
.build()
)
.build()
@@ -66,7 +71,7 @@ class PseudonymizeServiceTest {
}
@Test
fun sanitizeFileName() {
fun sanitizeFileName(@Mock generator: GpasPseudonymGenerator) {
val result= GpasPseudonymGenerator.sanitizeValue("l://a\\bs;1*2?3>")
assertThat(result).isEqualTo("l___a_bs_1_2_3_")
@@ -85,16 +90,4 @@ class PseudonymizeServiceTest {
assertThat(mtbFile.patient.id).isEqualTo("UNKNOWN_123")
}
@Test
fun shouldReturnDifferentValues() {
val ag = AnonymizingGenerator()
val tans = HashSet<String>()
(1..1000).forEach { i ->
val tan = ag.generateGenomDeTan("12345")
assertThat(tan).hasSize(64)
assertThat(tans.add(tan)).`as`("never the same result!").isTrue
}
}
}

232
src/test/kotlin/dev/dnpm/etl/processor/services/ConsentProcessorTest.kt
View File

@@ -1,232 +0,0 @@
package dev.dnpm.etl.processor.services
import ca.uhn.fhir.context.FhirContext
import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.config.AppConfigProperties
import dev.dnpm.etl.processor.config.GIcsConfigProperties
import dev.dnpm.etl.processor.config.JacksonConfig
import dev.dnpm.etl.processor.consent.ConsentDomain
import dev.dnpm.etl.processor.consent.GicsConsentService
import dev.pcvolkmer.mv64e.mtb.Mtb
import dev.pcvolkmer.mv64e.mtb.MvhSubmissionType
import dev.pcvolkmer.mv64e.mtb.Patient
import org.assertj.core.api.Assertions.assertThat
import org.hl7.fhir.r4.model.Bundle
import org.hl7.fhir.r4.model.CodeableConcept
import org.hl7.fhir.r4.model.Coding
import org.hl7.fhir.r4.model.Consent
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith
import org.junit.jupiter.params.ParameterizedTest
import org.junit.jupiter.params.provider.CsvSource
import org.junit.jupiter.params.provider.ValueSource
import org.mockito.Mock
import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.any
import org.mockito.kotlin.doAnswer
import org.mockito.kotlin.eq
import org.mockito.kotlin.whenever
import org.springframework.core.io.ClassPathResource
import java.io.IOException
import java.io.InputStream
import java.time.Instant
import java.time.OffsetDateTime
import java.util.*
@ExtendWith(MockitoExtension::class)
class ConsentProcessorTest {
private lateinit var appConfigProperties: AppConfigProperties
private lateinit var gicsConsentService: GicsConsentService
private lateinit var objectMapper: ObjectMapper
private lateinit var gIcsConfigProperties: GIcsConfigProperties
private lateinit var fhirContext: FhirContext
private lateinit var consentProcessor: ConsentProcessor
@BeforeEach
fun setups(
@Mock gicsConsentService: GicsConsentService,
) {
this.gIcsConfigProperties = GIcsConfigProperties("https://gics.example.com")
val jacksonConfig = JacksonConfig()
this.objectMapper = jacksonConfig.objectMapper()
this.fhirContext = JacksonConfig.fhirContext()
this.gicsConsentService = gicsConsentService
this.appConfigProperties = AppConfigProperties(emptyList())
this.consentProcessor =
ConsentProcessor(
appConfigProperties,
gIcsConfigProperties,
objectMapper,
fhirContext,
gicsConsentService
)
}
@Test
fun consentOk() {
assertThat(consentProcessor.toString()).isNotNull
// prep gICS response
doAnswer { getDummyBroadConsentBundle() }.whenever(gicsConsentService)
.getConsent(any(), any(), eq(ConsentDomain.BROAD_CONSENT))
doAnswer { Bundle() }.whenever(gicsConsentService)
.getConsent(any(), any(), eq(ConsentDomain.MODELLVORHABEN_64E))
val inputMtb = Mtb.builder()
.patient(Patient.builder().id("d611d429-5003-11f0-a144-661e92ac9503").build()).build()
val checkResult = consentProcessor.consentGatedCheckAndTryEmbedding(inputMtb)
assertThat(checkResult).isTrue
assertThat(inputMtb.metadata.researchConsents).hasSize(26)
}
companion object {
fun getDummyGenomDeConsent(): Consent {
val consent = Consent()
consent.id = "consent 1 id"
consent.patient.reference = "Patient/1234-pat1"
consent.provision.setType(
Consent.ConsentProvisionType.fromCode(
"deny"
)
)
consent.provision.period.start =
Date.from(Instant.parse("2025-08-15T00:00:00.00Z"))
consent.provision.period.end =
Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
val addProvision1 = consent.provision.addProvision()
addProvision1.setType(Consent.ConsentProvisionType.fromCode("permit"))
addProvision1.period.start = Date.from(Instant.parse("2025-08-15T00:00:00.00Z"))
addProvision1.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
addProvision1.code.addLast(
CodeableConcept(
Coding(
"https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
"Teilnahme",
"Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
)
)
)
val addProvision2 = consent.provision.addProvision()
addProvision2.setType(Consent.ConsentProvisionType.fromCode("deny"))
addProvision2.period.start = Date.from(Instant.parse("2025-08-15T00:00:00.00Z"))
addProvision2.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
addProvision2.code.addLast(
CodeableConcept(
Coding(
"https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
"Rekontaktierung",
"Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
)
)
)
return consent
}
}
@ParameterizedTest
@CsvSource(
"2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2025-08-15T00:00:00+02:00,PERMIT,expect permit",
"2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2025-08-15T00:00:00+02:00,PERMIT,expect permit date is exactly on start",
"2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2055-08-15T00:00:00+02:00,PERMIT,expect permit date is exactly on end",
"2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2021-08-15T00:00:00+02:00,NULL,date is before start",
"2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2060-08-15T00:00:00+02:00,NULL,date is after end",
"2.16.840.1.113883.3.1937.777.24.5.3.27,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2025-08-15T00:00:00+02:00,DENY,provision is denied",
"unknownCode,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2025-08-15T00:00:00+02:00,NULL,code does not exist - therefore expect NULL",
"2.16.840.1.113883.3.1937.777.24.5.3.8,XXXX,2025-08-15T00:00:00+02:00,NULL,system not found - therefore expect NULL",
)
fun getProvisionTypeByPolicyCode(
code: String?, system: String?, timeStamp: String, expected: String?,
desc: String?
) {
val testData = getDummyBroadConsentBundle()
val requestDate = Date.from(OffsetDateTime.parse(timeStamp).toInstant())
val result: Consent.ConsentProvisionType =
consentProcessor.getProvisionTypeByPolicyCode(testData, code, system, requestDate)
assertThat(result).isNotNull()
assertThat(result).`as`(desc)
.isEqualTo(Consent.ConsentProvisionType.valueOf(expected!!))
}
@Test
fun getProvisionTypeOnEmptyConsent(
) {
val emptyResources = Bundle().addEntry(Bundle.BundleEntryComponent().setResource(Consent()))
val requestDate = Date.from(OffsetDateTime.parse("2025-08-15T00:00:00+02:00").toInstant())
val result: Consent.ConsentProvisionType =
consentProcessor.getProvisionTypeByPolicyCode(
emptyResources,
"anyCode",
"anySystem",
requestDate
)
assertThat(result).isNotNull()
assertThat(result).`as`("empty consent resource - expect NULL")
.isEqualTo(Consent.ConsentProvisionType.NULL)
}
fun getDummyBroadConsentBundle(): Bundle {
val bundle: InputStream?
try {
bundle = ClassPathResource(
"fake_broadConsent_gics_response_permit.json"
).getInputStream()
} catch (e: IOException) {
throw RuntimeException(e)
}
return FhirContext.forR4().newJsonParser()
.parseResource<Bundle>(Bundle::class.java, bundle)
}
@ParameterizedTest
@ValueSource(booleans = [true, false])
fun mvSubmissionTypeIsSet(isTestSubmission: Boolean) {
appConfigProperties.genomDeTestSubmission = isTestSubmission
val fixture =
ConsentProcessor(
appConfigProperties,
gIcsConfigProperties,
objectMapper,
fhirContext,
gicsConsentService
)
doAnswer { getDummyBroadConsentBundle() }.whenever(gicsConsentService)
.getConsent(any(), any(), eq(ConsentDomain.BROAD_CONSENT))
doAnswer {
Bundle().addEntry(
Bundle.BundleEntryComponent().setResource(getDummyGenomDeConsent())
)
}.whenever(gicsConsentService)
.getConsent(any(), any(), eq(ConsentDomain.MODELLVORHABEN_64E))
val inputMtb = Mtb.builder()
.patient(Patient.builder().id("d611d429-5003-11f0-a144-661e92ac9503").build()).build()
val checkResult = fixture.consentGatedCheckAndTryEmbedding(inputMtb)
assertThat(checkResult).isNotNull
if (isTestSubmission)
assertThat(inputMtb.metadata.type).isEqualTo(MvhSubmissionType.TEST)
else {
assertThat(inputMtb.metadata.type).isEqualTo(MvhSubmissionType.INITIAL)
}
}
}

213
src/test/kotlin/dev/dnpm/etl/processor/services/RequestProcessorTest.kt
View File

@@ -20,21 +20,15 @@
package dev.dnpm.etl.processor.services
import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.Fingerprint
import dev.dnpm.etl.processor.PatientId
import dev.dnpm.etl.processor.PatientPseudonym
import de.ukw.ccc.bwhc.dto.*
import dev.dnpm.etl.processor.*
import dev.dnpm.etl.processor.config.AppConfigProperties
import dev.dnpm.etl.processor.consent.TtpConsentStatus
import dev.dnpm.etl.processor.monitoring.Request
import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.monitoring.RequestType
import dev.dnpm.etl.processor.output.DeleteRequest
import dev.dnpm.etl.processor.output.DnpmV2MtbFileRequest
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 dev.pcvolkmer.mv64e.mtb.*
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Test
@@ -48,7 +42,6 @@ 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)
@@ -60,7 +53,7 @@ class RequestProcessorTest {
private lateinit var requestService: RequestService
private lateinit var applicationEventPublisher: ApplicationEventPublisher
private lateinit var appConfigProperties: AppConfigProperties
private lateinit var consentProcessor: ConsentProcessor
private lateinit var requestProcessor: RequestProcessor
@BeforeEach
@@ -69,16 +62,14 @@ class RequestProcessorTest {
@Mock transformationService: TransformationService,
@Mock sender: RestMtbFileSender,
@Mock requestService: RequestService,
@Mock applicationEventPublisher: ApplicationEventPublisher,
@Mock consentProcessor: ConsentProcessor
@Mock applicationEventPublisher: ApplicationEventPublisher
) {
this.pseudonymizeService = pseudonymizeService
this.transformationService = transformationService
this.sender = sender
this.requestService = requestService
this.applicationEventPublisher = applicationEventPublisher
this.appConfigProperties = AppConfigProperties()
this.consentProcessor = consentProcessor
this.appConfigProperties = AppConfigProperties(null)
val objectMapper = ObjectMapper()
@@ -89,8 +80,7 @@ class RequestProcessorTest {
requestService,
objectMapper,
applicationEventPublisher,
appConfigProperties,
consentProcessor
appConfigProperties
)
}
@@ -102,7 +92,7 @@ class RequestProcessorTest {
randomRequestId(),
PatientPseudonym("TEST_12345678901"),
PatientId("P1"),
Fingerprint("6vkiti5bk6ikwifpajpt7cygmd3dvw54d6lwfhzlynb3pqtzferq"),
Fingerprint("zdlzv5s5ydmd4ktw2v5piohegc4jcyrm6j66bq6tv2uxuerndmga"),
RequestType.MTB_FILE,
RequestStatus.SUCCESS,
Instant.parse("2023-08-08T02:00:00Z")
@@ -119,24 +109,29 @@ class RequestProcessorTest {
doAnswer {
it.arguments[0]
}.whenever(transformationService).transform(any<Mtb>())
}.whenever(transformationService).transform(any())
whenever(consentProcessor.consentGatedCheckAndTryEmbedding(any())).thenReturn(true)
val mtbFile = Mtb.builder()
.patient(
val mtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.id("123")
.withId("1")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.episodesOfCare(
listOf(
MtbEpisodeOfCare.builder()
.id("1")
.patient(Reference.builder().id("123").build())
.period(PeriodDate.builder().start(Date.from(Instant.parse("2023-08-08T02:00:00.00Z"))).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()
@@ -156,7 +151,7 @@ class RequestProcessorTest {
randomRequestId(),
PatientPseudonym("TEST_12345678901"),
PatientId("P1"),
Fingerprint("4gcjwtjjtcczybsljxepdfpkaeusvd7g3vogfqpmphyffyzfx7dq"),
Fingerprint("zdlzv5s5ydmd4ktw2v5piohegc4jcyrm6j66bq6tv2uxuerndmga"),
RequestType.MTB_FILE,
RequestStatus.SUCCESS,
Instant.parse("2023-08-08T02:00:00Z")
@@ -173,24 +168,29 @@ class RequestProcessorTest {
doAnswer {
it.arguments[0]
}.whenever(transformationService).transform(any<Mtb>())
}.whenever(transformationService).transform(any())
whenever(consentProcessor.consentGatedCheckAndTryEmbedding(any())).thenReturn(true)
val mtbFile = Mtb.builder()
.patient(
val mtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.id("123")
.withId("1")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.episodesOfCare(
listOf(
MtbEpisodeOfCare.builder()
.id("1")
.patient(Reference.builder().id("123").build())
.period(PeriodDate.builder().start(Date.from(Instant.parse("2021-01-01T00:00:00.00Z"))).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()
@@ -223,7 +223,7 @@ class RequestProcessorTest {
doAnswer {
MtbFileSender.Response(status = RequestStatus.SUCCESS)
}.whenever(sender).send(any<DnpmV2MtbFileRequest>())
}.whenever(sender).send(any<MtbFileSender.MtbFileRequest>())
doAnswer {
it.arguments[0] as String
@@ -231,24 +231,29 @@ class RequestProcessorTest {
doAnswer {
it.arguments[0]
}.whenever(transformationService).transform(any<Mtb>())
}.whenever(transformationService).transform(any())
whenever(consentProcessor.consentGatedCheckAndTryEmbedding(any())).thenReturn(true)
val mtbFile = Mtb.builder()
.patient(
val mtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.id("123")
.withId("1")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.episodesOfCare(
listOf(
MtbEpisodeOfCare.builder()
.id("1")
.patient(Reference.builder().id("123").build())
.period(PeriodDate.builder().start(Date.from(Instant.parse("2021-01-01T00:00:00.00Z"))).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()
@@ -281,7 +286,7 @@ class RequestProcessorTest {
doAnswer {
MtbFileSender.Response(status = RequestStatus.ERROR)
}.whenever(sender).send(any<DnpmV2MtbFileRequest>())
}.whenever(sender).send(any<MtbFileSender.MtbFileRequest>())
doAnswer {
it.arguments[0] as String
@@ -289,37 +294,30 @@ class RequestProcessorTest {
doAnswer {
it.arguments[0]
}.whenever(transformationService).transform(any<Mtb>())
}.whenever(transformationService).transform(any())
whenever(consentProcessor.consentGatedCheckAndTryEmbedding(any())).thenReturn(true)
val mtbFile = Mtb.builder()
.patient(
val mtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.id("123")
.withId("1")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.metadata(
MvhMetadata
.builder()
.modelProjectConsent(
ModelProjectConsent
.builder()
.provisions(
listOf(Provision.builder().type(ConsentProvision.PERMIT).purpose(ModelProjectConsentPurpose.SEQUENCING).build())
).build()
)
.withConsent(
Consent.builder()
.withId("1")
.withStatus(Consent.Status.ACTIVE)
.withPatient("123")
.build()
)
.episodesOfCare(
listOf(
MtbEpisodeOfCare.builder()
.id("1")
.patient(Reference.builder().id("123").build())
.period(PeriodDate.builder().start(Date.from(Instant.parse("2021-01-01T00:00:00.00Z"))).build())
.withEpisode(
Episode.builder()
.withId("1")
.withPatient("1")
.withPeriod(PeriodStart("2023-08-08"))
.build()
)
)
.build()
this.requestProcessor.processMtbFile(mtbFile)
@@ -338,12 +336,9 @@ class RequestProcessorTest {
doAnswer {
MtbFileSender.Response(status = RequestStatus.UNKNOWN)
}.whenever(sender).send(any<DeleteRequest>())
}.whenever(sender).send(any<MtbFileSender.DeleteRequest>())
this.requestProcessor.processDeletion(
TEST_PATIENT_ID,
isConsented = TtpConsentStatus.UNKNOWN_CHECK_FILE
)
this.requestProcessor.processDeletion(TEST_PATIENT_ID)
val requestCaptor = argumentCaptor<Request>()
verify(requestService, times(1)).save(requestCaptor.capture())
@@ -359,12 +354,9 @@ class RequestProcessorTest {
doAnswer {
MtbFileSender.Response(status = RequestStatus.SUCCESS)
}.whenever(sender).send(any<DeleteRequest>())
}.whenever(sender).send(any<MtbFileSender.DeleteRequest>())
this.requestProcessor.processDeletion(
TEST_PATIENT_ID,
isConsented = TtpConsentStatus.UNKNOWN_CHECK_FILE
)
this.requestProcessor.processDeletion(TEST_PATIENT_ID)
val eventCaptor = argumentCaptor<ResponseEvent>()
verify(applicationEventPublisher, times(1)).publishEvent(eventCaptor.capture())
@@ -380,12 +372,9 @@ class RequestProcessorTest {
doAnswer {
MtbFileSender.Response(status = RequestStatus.ERROR)
}.whenever(sender).send(any<DeleteRequest>())
}.whenever(sender).send(any<MtbFileSender.DeleteRequest>())
this.requestProcessor.processDeletion(
TEST_PATIENT_ID,
isConsented = TtpConsentStatus.UNKNOWN_CHECK_FILE
)
this.requestProcessor.processDeletion(TEST_PATIENT_ID)
val eventCaptor = argumentCaptor<ResponseEvent>()
verify(applicationEventPublisher, times(1)).publishEvent(eventCaptor.capture())
@@ -397,10 +386,7 @@ class RequestProcessorTest {
fun testShouldSendDeleteRequestWithPseudonymErrorAndSaveErrorRequestStatus() {
doThrow(RuntimeException()).whenever(pseudonymizeService).patientPseudonym(anyValueClass())
this.requestProcessor.processDeletion(
TEST_PATIENT_ID,
isConsented = TtpConsentStatus.UNKNOWN_CHECK_FILE
)
this.requestProcessor.processDeletion(TEST_PATIENT_ID)
val requestCaptor = argumentCaptor<Request>()
verify(requestService, times(1)).save(requestCaptor.capture())
@@ -418,28 +404,33 @@ class RequestProcessorTest {
doAnswer {
it.arguments[0]
}.whenever(transformationService).transform(any<Mtb>())
}.whenever(transformationService).transform(any())
doAnswer {
MtbFileSender.Response(status = RequestStatus.SUCCESS)
}.whenever(sender).send(any<DnpmV2MtbFileRequest>())
}.whenever(sender).send(any<MtbFileSender.MtbFileRequest>())
whenever(consentProcessor.consentGatedCheckAndTryEmbedding(any())).thenReturn(true)
val mtbFile = Mtb.builder()
.patient(
val mtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.id("123")
.withId("1")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.episodesOfCare(
listOf(
MtbEpisodeOfCare.builder()
.id("1")
.patient(Reference.builder().id("123").build())
.period(PeriodDate.builder().start(Date.from(Instant.parse("2021-01-01T00:00:00.00Z"))).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()

89
src/test/kotlin/dev/dnpm/etl/processor/services/TransformationServiceTest.kt
View File

@@ -19,14 +19,14 @@
package dev.dnpm.etl.processor.services
import dev.dnpm.etl.processor.config.JacksonConfig
import dev.pcvolkmer.mv64e.mtb.*
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 org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Test
import org.hl7.fhir.instance.model.api.IBaseResource
import java.time.Instant
import java.util.Date
class TransformationServiceTest {
@@ -35,92 +35,61 @@ class TransformationServiceTest {
@BeforeEach
fun setup() {
this.service = TransformationService(
JacksonConfig().objectMapper(), listOf(
Transformation.of("diagnoses[*].code.version") from "2013" to "2014",
ObjectMapper(), listOf(
Transformation.of("consent.status") from Consent.Status.ACTIVE to Consent.Status.REJECTED,
Transformation.of("diagnoses[*].icd10.version") from "2013" to "2014",
)
)
}
@Test
fun shouldTransformMtbFile() {
val mtbFile = Mtb.builder().diagnoses(
val mtbFile = MtbFile.builder().withDiagnoses(
listOf(
MtbDiagnosis.builder().id("1234").code(Coding.builder().code("F79.9").version("2013").build()).build()
Diagnosis.builder().withId("1234").withIcd10(Icd10("F79.9").also {
it.version = "2013"
}).build()
)
).build()
val actual = this.service.transform(mtbFile)
assertThat(actual).isNotNull
assertThat(actual.diagnoses[0].code.version).isEqualTo("2014")
assertThat(actual.diagnoses[0].icd10.version).isEqualTo("2014")
}
@Test
fun shouldOnlyTransformGivenValues() {
val mtbFile = Mtb.builder().diagnoses(
val mtbFile = MtbFile.builder().withDiagnoses(
listOf(
MtbDiagnosis.builder().id("1234").code(Coding.builder().code("F79.9").version("2013").build()).build(),
MtbDiagnosis.builder().id("1234").code(Coding.builder().code("F79.8").version("2019").build()).build()
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].code.code).isEqualTo("F79.9")
assertThat(actual.diagnoses[0].code.version).isEqualTo("2014")
assertThat(actual.diagnoses[1].code.code).isEqualTo("F79.8")
assertThat(actual.diagnoses[1].code.version).isEqualTo("2019")
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 shouldTransformConsentValues() {
val mtbFile = Mtb.builder().diagnoses(
listOf(
MtbDiagnosis.builder().id("1234").code(Coding.builder().code("F79.9").version("2013").build()).build(),
MtbDiagnosis.builder().id("1234").code(Coding.builder().code("F79.8").version("2019").build()).build()
)
fun shouldTransformMtbFileWithConsentEnum() {
val mtbFile = MtbFile.builder().withConsent(
Consent("123", "456", Consent.Status.ACTIVE)
).build()
val actual = this.service.transform(mtbFile)
assertThat(actual).isNotNull
assertThat(actual.diagnoses[0].code.code).isEqualTo("F79.9")
assertThat(actual.diagnoses[0].code.version).isEqualTo("2014")
assertThat(actual.diagnoses[1].code.code).isEqualTo("F79.8")
assertThat(actual.diagnoses[1].code.version).isEqualTo("2019")
}
@Test
fun shouldTransformConsent() {
val mvhMetadata = MvhMetadata.builder().transferTan("transfertan12345").build()
assertThat(mvhMetadata).isNotNull
mvhMetadata.modelProjectConsent =
ModelProjectConsent.builder().date(Date.from(Instant.parse("2025-08-15T00:00:00.00Z")))
.version("1").provisions(
listOf(
Provision.builder().type(ConsentProvision.PERMIT)
.purpose(ModelProjectConsentPurpose.SEQUENCING)
.date(Date.from(Instant.parse("2025-08-15T00:00:00.00Z"))).build(),
Provision.builder().type(ConsentProvision.PERMIT)
.purpose(ModelProjectConsentPurpose.REIDENTIFICATION)
.date(Date.from(Instant.parse("2025-08-15T00:00:00.00Z"))).build(),
Provision.builder().type(ConsentProvision.DENY)
.purpose(ModelProjectConsentPurpose.CASE_IDENTIFICATION)
.date(Date.from(Instant.parse("2025-08-15T00:00:00.00Z"))).build()
)
).build()
val consent = ConsentProcessorTest.getDummyGenomDeConsent()
mvhMetadata.researchConsents = mutableListOf()
mvhMetadata.researchConsents.add(mapOf(consent.id to consent as IBaseResource))
val mtbFile = Mtb.builder().metadata(mvhMetadata).build()
val transformed = service.transform(mtbFile)
assertThat(transformed.metadata.modelProjectConsent.date).isNotNull
assertThat(actual.consent).isNotNull
assertThat(actual.consent.status).isEqualTo(Consent.Status.REJECTED)
}
}

3101
src/test/resources/fake_broadConsent_gics_response_permit.json
View File

File diff suppressed because it is too large Load Diff

333
src/test/resources/fake_mv64e-gics-response_deny.json
View File

@@ -1,333 +0,0 @@
{
"resourceType": "Bundle",
"type": "collection",
"entry": [
{
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/24673204-50e1-11f0-a144-661e92ac9503",
"resource": {
"resourceType": "Consent",
"id": "24673204-50e1-11f0-a144-661e92ac9503",
"meta": {
"lastUpdated": "2025-06-24T11:58:27.178+02:00",
"profile": [
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
]
},
"extension": [
{
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
"extension": [
{
"url": "domain",
"valueReference": {
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
}
},
{
"url": "status",
"valueCoding": {
"system": "http://hl7.org/fhir/publication-status",
"code": "active"
}
}
]
}
],
"status": "active",
"scope": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
"code": "research"
}
]
},
"category": [
{
"coding": [
{
"system": "http://loinc.org",
"code": "59284-0"
}
]
},
{
"coding": [
{
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
"code": "policy"
}
]
}
],
"patient": {
"reference": "Patient/2466d49b-50e1-11f0-a144-661e92ac9503",
"display": "Patienten-ID 999999"
},
"dateTime": "2025-06-24T00:00:00+02:00",
"organization": [
{
"display": "GenomDE_MV"
}
],
"sourceReference": {
"reference": "QuestionnaireResponse/24670c77-50e1-11f0-a144-661e92ac9503"
},
"policyRule": {
"coding": [
{
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
"code": "Teilnahme",
"display": "Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
}
]
},
"provision": {
"type": "deny",
"period": {
"start": "2025-06-24T00:00:00+02:00",
"end": "3000-01-01T00:00:00+01:00"
},
"provision": [
{
"type": "deny",
"period": {
"start": "2025-06-24T00:00:00+02:00",
"end": "3000-01-01T00:00:00+01:00"
},
"code": [
{
"coding": [
{
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
"code": "Teilnahme",
"display": "Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
}
]
}
]
}
]
}
}
},
{
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/24673913-50e1-11f0-a144-661e92ac9503",
"resource": {
"resourceType": "Consent",
"id": "24673913-50e1-11f0-a144-661e92ac9503",
"meta": {
"lastUpdated": "2025-06-24T11:58:27.194+02:00",
"profile": [
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
]
},
"extension": [
{
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
"extension": [
{
"url": "domain",
"valueReference": {
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
}
},
{
"url": "status",
"valueCoding": {
"system": "http://hl7.org/fhir/publication-status",
"code": "active"
}
}
]
}
],
"status": "active",
"scope": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
"code": "research"
}
]
},
"category": [
{
"coding": [
{
"system": "http://loinc.org",
"code": "59284-0"
}
]
},
{
"coding": [
{
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
"code": "policy"
}
]
}
],
"patient": {
"reference": "Patient/2466d49b-50e1-11f0-a144-661e92ac9503",
"display": "Patienten-ID 999999"
},
"dateTime": "2025-06-24T00:00:00+02:00",
"organization": [
{
"display": "GenomDE_MV"
}
],
"sourceReference": {
"reference": "QuestionnaireResponse/24670c77-50e1-11f0-a144-661e92ac9503"
},
"policyRule": {
"coding": [
{
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
"code": "Fallidentifizierung",
"display": "Fallidentifizierung zum fachlichen Austausch unter Behandelnden"
}
]
},
"provision": {
"type": "deny",
"period": {
"start": "2025-06-24T00:00:00+02:00",
"end": "3000-01-01T00:00:00+01:00"
},
"provision": [
{
"type": "deny",
"period": {
"start": "2025-06-24T00:00:00+02:00",
"end": "3000-01-01T00:00:00+01:00"
},
"code": [
{
"coding": [
{
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
"code": "Fallidentifizierung",
"display": "Fallidentifizierung zum fachlichen Austausch unter Behandelnden"
}
]
}
]
}
]
}
}
},
{
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/24673da9-50e1-11f0-a144-661e92ac9503",
"resource": {
"resourceType": "Consent",
"id": "24673da9-50e1-11f0-a144-661e92ac9503",
"meta": {
"lastUpdated": "2025-06-24T11:58:27.211+02:00",
"profile": [
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
]
},
"extension": [
{
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
"extension": [
{
"url": "domain",
"valueReference": {
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
}
},
{
"url": "status",
"valueCoding": {
"system": "http://hl7.org/fhir/publication-status",
"code": "active"
}
}
]
}
],
"status": "active",
"scope": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
"code": "research"
}
]
},
"category": [
{
"coding": [
{
"system": "http://loinc.org",
"code": "59284-0"
}
]
},
{
"coding": [
{
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
"code": "policy"
}
]
}
],
"patient": {
"reference": "Patient/2466d49b-50e1-11f0-a144-661e92ac9503",
"display": "Patienten-ID 999999"
},
"dateTime": "2025-06-24T00:00:00+02:00",
"organization": [
{
"display": "GenomDE_MV"
}
],
"sourceReference": {
"reference": "QuestionnaireResponse/24670c77-50e1-11f0-a144-661e92ac9503"
},
"policyRule": {
"coding": [
{
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
"code": "Rekontaktierung",
"display": "Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
}
]
},
"provision": {
"type": "deny",
"period": {
"start": "2025-06-24T00:00:00+02:00",
"end": "3000-01-01T00:00:00+01:00"
},
"provision": [
{
"type": "deny",
"period": {
"start": "2025-06-24T00:00:00+02:00",
"end": "3000-01-01T00:00:00+01:00"
},
"code": [
{
"coding": [
{
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
"code": "Rekontaktierung",
"display": "Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
}
]
}
]
}
]
}
}
}
]
}

333
src/test/resources/fake_mv64e-gics-response_permit.json
View File

@@ -1,333 +0,0 @@
{
"resourceType": "Bundle",
"type": "collection",
"entry": [
{
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/121a8368-50e1-11f0-a144-661e92ac9503",
"resource": {
"resourceType": "Consent",
"id": "121a8368-50e1-11f0-a144-661e92ac9503",
"meta": {
"lastUpdated": "2025-06-24T11:55:42.079+02:00",
"profile": [
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
]
},
"extension": [
{
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
"extension": [
{
"url": "domain",
"valueReference": {
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
}
},
{
"url": "status",
"valueCoding": {
"system": "http://hl7.org/fhir/publication-status",
"code": "active"
}
}
]
}
],
"status": "active",
"scope": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
"code": "research"
}
]
},
"category": [
{
"coding": [
{
"system": "http://loinc.org",
"code": "59284-0"
}
]
},
{
"coding": [
{
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
"code": "policy"
}
]
}
],
"patient": {
"reference": "Patient/12194791-50e1-11f0-a144-661e92ac9503",
"display": "Patienten-ID 12345678"
},
"dateTime": "2025-06-24T00:00:00+02:00",
"organization": [
{
"display": "GenomDE_MV"
}
],
"sourceReference": {
"reference": "QuestionnaireResponse/1219ca42-50e1-11f0-a144-661e92ac9503"
},
"policyRule": {
"coding": [
{
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
"code": "Teilnahme",
"display": "Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
}
]
},
"provision": {
"type": "deny",
"period": {
"start": "2025-06-24T00:00:00+02:00",
"end": "3000-01-01T00:00:00+01:00"
},
"provision": [
{
"type": "permit",
"period": {
"start": "2025-06-24T00:00:00+02:00",
"end": "3000-01-01T00:00:00+01:00"
},
"code": [
{
"coding": [
{
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
"code": "Teilnahme",
"display": "Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
}
]
}
]
}
]
}
}
},
{
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/121aad40-50e1-11f0-a144-661e92ac9503",
"resource": {
"resourceType": "Consent",
"id": "121aad40-50e1-11f0-a144-661e92ac9503",
"meta": {
"lastUpdated": "2025-06-24T11:55:42.096+02:00",
"profile": [
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
]
},
"extension": [
{
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
"extension": [
{
"url": "domain",
"valueReference": {
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
}
},
{
"url": "status",
"valueCoding": {
"system": "http://hl7.org/fhir/publication-status",
"code": "active"
}
}
]
}
],
"status": "active",
"scope": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
"code": "research"
}
]
},
"category": [
{
"coding": [
{
"system": "http://loinc.org",
"code": "59284-0"
}
]
},
{
"coding": [
{
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
"code": "policy"
}
]
}
],
"patient": {
"reference": "Patient/12194791-50e1-11f0-a144-661e92ac9503",
"display": "Patienten-ID 12345678"
},
"dateTime": "2025-06-24T00:00:00+02:00",
"organization": [
{
"display": "GenomDE_MV"
}
],
"sourceReference": {
"reference": "QuestionnaireResponse/1219ca42-50e1-11f0-a144-661e92ac9503"
},
"policyRule": {
"coding": [
{
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
"code": "Fallidentifizierung",
"display": "Fallidentifizierung zum fachlichen Austausch unter Behandelnden"
}
]
},
"provision": {
"type": "deny",
"period": {
"start": "2025-06-24T00:00:00+02:00",
"end": "3000-01-01T00:00:00+01:00"
},
"provision": [
{
"type": "permit",
"period": {
"start": "2025-06-24T00:00:00+02:00",
"end": "3000-01-01T00:00:00+01:00"
},
"code": [
{
"coding": [
{
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
"code": "Fallidentifizierung",
"display": "Fallidentifizierung zum fachlichen Austausch unter Behandelnden"
}
]
}
]
}
]
}
}
},
{
"fullUrl": "http://127.0.0.1:8090/ttp-fhir/fhir/gics/Consent/121ac5f8-50e1-11f0-a144-661e92ac9503",
"resource": {
"resourceType": "Consent",
"id": "121ac5f8-50e1-11f0-a144-661e92ac9503",
"meta": {
"lastUpdated": "2025-06-24T11:55:42.110+02:00",
"profile": [
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
]
},
"extension": [
{
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
"extension": [
{
"url": "domain",
"valueReference": {
"reference": "ResearchStudy/ef86d80e-50e0-11f0-a144-661e92ac9503"
}
},
{
"url": "status",
"valueCoding": {
"system": "http://hl7.org/fhir/publication-status",
"code": "active"
}
}
]
}
],
"status": "active",
"scope": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/consentscope",
"code": "research"
}
]
},
"category": [
{
"coding": [
{
"system": "http://loinc.org",
"code": "59284-0"
}
]
},
{
"coding": [
{
"system": "http://fhir.de/ConsentManagement/CodeSystem/ResultType",
"code": "policy"
}
]
}
],
"patient": {
"reference": "Patient/12194791-50e1-11f0-a144-661e92ac9503",
"display": "Patienten-ID 12345678"
},
"dateTime": "2025-06-24T00:00:00+02:00",
"organization": [
{
"display": "GenomDE_MV"
}
],
"sourceReference": {
"reference": "QuestionnaireResponse/1219ca42-50e1-11f0-a144-661e92ac9503"
},
"policyRule": {
"coding": [
{
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
"code": "Rekontaktierung",
"display": "Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
}
]
},
"provision": {
"type": "deny",
"period": {
"start": "2025-06-24T00:00:00+02:00",
"end": "3000-01-01T00:00:00+01:00"
},
"provision": [
{
"type": "permit",
"period": {
"start": "2025-06-24T00:00:00+02:00",
"end": "3000-01-01T00:00:00+01:00"
},
"code": [
{
"coding": [
{
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
"code": "Rekontaktierung",
"display": "Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
}
]
}
]
}
]
}
}
}
]
}

2509
src/test/resources/mv64e-mtb-fake-patient.json
View File

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