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mirror of https://github.com/pcvolkmer/mv64e-etl-processor synced 2025-09-13 09:02:50 +00:00

46 Commits

Author SHA1 Message Date
Jakub Lidke
4bd6117ba8 fix: remove policyRule at consent resource 2025-09-05 16:00:11 +02:00
Jakub Lidke
ace5637ed8 test: added failing test 2025-09-05 15:58:31 +02:00
Jakub Lidke
88857cf201 refactor: cleanup GicsConsentService.java constant. 2025-09-05 14:59:12 +02:00
Jakub Lidke
db89d84353 fix: Setze in der Broad Consent Resource das MII Broad Consent Profil und die Consent Policy, falls diese fehlen sollten. Die von gICS einzeln gelieferte Consent Provisions werden in einer Ressource zusammengefasst. 2025-09-05 14:55:58 +02:00
3d9d84438d refactor: several changes related to code style and readability (#152)
* refactor: extract provision code extraction
* refactor: catch exceptions by type without later type check
* refactor: further code cleanup
* chore: log error with error level, not debug level
2025-09-04 12:47:56 +02:00
10b5bedac3 Merge branch '0.11.x'
# Conflicts:
#	build.gradle.kts
2025-09-03 22:03:52 +02:00
96f22a6744 feat: mark older request with unknown state (#150) 2025-09-03 21:30:36 +02:00
6dfec5c341 fix: add status badge for 'NO_CONSENT' (#149) 2025-09-03 21:18:28 +02:00
c38c0c6197 build: prepare for v0.12 development (#147) 2025-09-02 10:40:30 +02:00
4602032bcf chore: bump version 2025-09-01 13:33:29 +02:00
9cc9f130df chore: add custom banner file (#146) 2025-09-01 13:31:08 +02:00
b92fbae2c5 chore: update dependencies (#145) 2025-09-01 13:25:51 +02:00
5704282a1c docs: some additions to README.md (#143) 2025-08-28 19:37:57 +02:00
ba21d029d1 fix: add missing requestId to KafkaMtbFileSender (#142) 2025-08-27 15:07:43 +02:00
b7aa187293 fix: do not set unexpected config values (#141) 2025-08-26 09:16:07 +02:00
8402462c3b chore: use apache image including SSL config (#140)
The main purpose is to abandon bitnami kafka image.

The examples now include localhost certs and keys for development
purposes only.
More advanced support for SSL connections to kafka will be
available in later versions.
2025-08-25 12:43:32 +02:00
d3e6aa5821 fix: mime type representation in kafka header (#139) 2025-08-25 12:13:44 +02:00
eed0972018 docs: update README.md and add current changes (#137) 2025-08-21 15:51:36 +02:00
jlidke
3b66f42eb2 feat: configuration of genomDe test submission via 'app.genomDeTestSubmission' = 'true', is implemented, now. (#136)
Co-authored-by: Paul-Christian Volkmer <code@pcvolkmer.de>
2025-08-20 10:47:38 +02:00
c40fd7f816 feat: do not default to test submissions (#135) 2025-08-18 13:25:34 +02:00
1759729931 fix: add /mtb path alias for /mtbfile (#134) 2025-08-18 12:51:22 +02:00
jlidke
7f80224eac 132 fix consent check (#133) 2025-08-18 12:30:19 +02:00
3eb1c79cec feat: check consent for DNPM 2.1 requests (#126)
Co-authored-by: Jakub Lidke <jakub.lidke@uni-marburg.de>
2025-08-15 12:37:42 +02:00
jlidke
be513f305a 108 anonym id mtb v2 (#131) 2025-08-14 10:33:55 +02:00
2e88157893 refactor: remove obsolete bwHC data model V1.0 (#129) 2025-08-12 23:11:50 +02:00
bf898e5c25 docs: cleanup README file (#127) 2025-07-23 23:18:19 +02:00
e5693736d8 refactor: simple code cleanups (#125) 2025-07-23 22:45:04 +02:00
jlidke
dfc9de78ce 119 add transaction (#124) 2025-07-23 22:11:47 +02:00
jlidke
199511e567 63 check consent status (#120)
Co-authored-by: Paul-Christian Volkmer <code@pcvolkmer.de>
2025-07-22 20:02:15 +02:00
1319be8b3f chore: update dependencies (#122) 2025-07-20 12:04:38 +02:00
1a5737189c chore: update mtb data model example file (#123) 2025-07-20 11:57:53 +02:00
7543785116 chore: update to Spring Boot 3.5.3 (#116) 2025-06-26 01:14:07 +02:00
858189aa59 chore: data model changes (#117)
See: 3234082af1
2025-06-26 01:08:30 +02:00
17f4dc3512 chore: update to Spring Boot 3.5.0 (#115) 2025-06-08 20:02:16 +02:00
1dd601e8db chore: update dnpm mtb dto library (#113) 2025-05-30 22:36:38 +02:00
b748603c06 chore: update Spring Boot (#112) 2025-05-24 09:46:20 +02:00
b939b2bf57 chore: update Spring Boot (#111) 2025-04-26 11:18:40 +02:00
c6b37fda69 feat: support multiple request content types (#109) 2025-04-06 22:17:46 +02:00
8e3de6a220 feat: add pseudonymization for patient IDs (#107) 2025-04-06 14:42:09 +02:00
c5c553f817 refactor: move CustomMediaType into types.kt (#105) 2025-04-06 13:43:58 +02:00
7d97365aea feat: add endpoint for DNPM-Datamodel V2 using content negotiation (#104)
This simply adds an REST endpoint without proper implementation. The goal is to accept DNPM V2 JSON data.
2025-04-06 13:36:30 +02:00
48b1e62e22 feat: remove obsolete config params (#101) 2025-04-04 17:31:50 +02:00
66cc818755 feat: remove SSL-CA-Location config (#99) 2025-04-04 17:06:09 +02:00
9d4786fae3 refactor: update use of deprecated methods (#96) 2025-04-04 16:39:47 +02:00
b78dc3519b refactor: replace deprecated MockBean annotations (#95) 2025-04-04 16:13:07 +02:00
46015c5b66 chore: update to Spring Boot 3.4 2025-04-04 15:33:49 +02:00
78 changed files with 10705 additions and 1989 deletions

2
.gitignore vendored
View File

@@ -39,3 +39,5 @@ out/
.vscode/ .vscode/
/dev/gpas* /dev/gpas*
/deploy/.env /deploy/.env
/dev/gICS*
/dev/gPAS*

354
README.md
View File

@@ -1,12 +1,15 @@
# ETL-Processor for DNPM:DIP [![Run Tests](https://github.com/pcvolkmer/etl-processor/actions/workflows/test.yml/badge.svg)](https://github.com/pcvolkmer/etl-processor/actions/workflows/test.yml) # ETL-Processor 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)
Diese Anwendung versendet ein bwHC-MTB-File im bwHC-Datenmodell 1.0 an DNPM:DIP und pseudonymisiert die Patienten-ID. 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.
## Einordnung innerhalb einer DNPM-ETL-Strecke ## Einordnung innerhalb einer DNPM-ETL-Strecke
Diese Anwendung erlaubt das Entgegennehmen von HTTP/REST-Anfragen aus dem Onkostar-Plugin **[onkostar-plugin-dnpmexport](https://github.com/CCC-MF/onkostar-plugin-dnpmexport)**. Diese Anwendung erlaubt das Entgegennehmen von HTTP/REST-Anfragen aus dem Onkostar-Plugin
**[mv64e-onkostar-plugin-export](https://github.com/pcvolkmer/mv64e-onkostar-plugin-export)**.
Der Inhalt einer Anfrage, wenn ein bwHC-MTBFile, wird pseudonymisiert und auf Duplikate geprüft. Der Inhalt einer Anfrage, wenn ein MTB-File, wird pseudonymisiert und auf Duplikate geprüft.
Duplikate werden verworfen, Änderungen werden weitergeleitet. Duplikate werden verworfen, Änderungen werden weitergeleitet.
Löschanfragen werden immer als Löschanfrage an DNPM:DIP weitergeleitet. Löschanfragen werden immer als Löschanfrage an DNPM:DIP weitergeleitet.
@@ -15,16 +18,48 @@ Zudem ist eine minimalistische Weboberfläche integriert, die einen Einblick in
![Modell DNPM-ETL-Strecke](docs/etl.png) ![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 ### 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. `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 ### 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 | | HTTP-Request | URL | Consent-Status im Datensatz | Bemerkung |
|--------------|-----------------------------------------|-----------------------------|---------------------------------------------------------------------------------| |--------------|-----------------------------------------|-----------------------------|---------------------------------------------------------------------------------|
@@ -32,34 +67,20 @@ Ein HTTP Request kann, angenommen die Installation erfolgte auf dem Host `dnpm.e
| `POST` | `https://dnpm.example.com/mtb` | `REJECT` | Die Anwendung sendet einen Lösch-Request für die im Datensatz angegebene Pat-ID | | `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` | | `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 ### Datenübermittlung mit Apache Kafka
Anfragen werden, wenn nicht als Duplikat behandelt, nach der Pseudonymisierung an Apache Kafka übergeben. Anfragen werden, wenn nicht als Duplikat behandelt, nach der Pseudonymisierung an Apache Kafka
Eine Antwort wird dabei ebenfalls mithilfe von Apache Kafka übermittelt und nach der Entgegennahme verarbeitet. 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 Siehe hierzu auch: https://github.com/CCC-MF/kafka-to-bwhc
## Konfiguration ## 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 ### Pseudonymisierung der Patienten-ID
Wenn eine URI zu einer gPAS-Instanz (Version >= 2023.1.0) angegeben ist, wird diese verwendet. Wenn eine URI zu einer gPAS-Instanz (Version >= 2023.1.0) angegeben ist, wird diese verwendet.
@@ -68,40 +89,93 @@ Ist diese nicht gesetzt. wird intern eine Anonymisierung der Patienten-ID vorgen
* `APP_PSEUDONYMIZE_PREFIX`: Standortbezogenes Präfix - `UNKNOWN`, wenn nicht gesetzt * `APP_PSEUDONYMIZE_PREFIX`: Standortbezogenes Präfix - `UNKNOWN`, wenn nicht gesetzt
* `APP_PSEUDONYMIZE_GENERATOR`: `BUILDIN` oder `GPAS` - `BUILDIN`, wenn nicht gesetzt * `APP_PSEUDONYMIZE_GENERATOR`: `BUILDIN` oder `GPAS` - `BUILDIN`, wenn nicht gesetzt
**Hinweise**: **Hinweis**
* Der alte Konfigurationsparameter `APP_PSEUDONYMIZER` mit den Werten `GPAS` oder `BUILDIN` sollte nicht mehr verwendet Die Pseudonymisierung erfolgt im ETL-Prozessor nur für die Patienten-ID.
werden. Andere IDs werden mithilfe des standortbezogenen Präfixes (erneut) anonymisiert, um für den
* Die Pseudonymisierung erfolgt im ETL-Prozessor nur für die Patienten-ID. aktuellen Kontext nicht
Andere IDs werden mithilfe des standortbezogenen Präfixes (erneut) anonymisiert, um für den aktuellen Kontext nicht vergleichbare IDs bereitzustellen.
vergleichbare IDs bereitzustellen.
#### Eingebaute Anonymisierung #### Eingebaute Anonymisierung
Wurde keine oder die Verwendung der eingebauten Anonymisierung konfiguriert, so wird für die Patienten-ID der Wurde keine oder die Verwendung der eingebauten Anonymisierung konfiguriert, so wird für die
entsprechende SHA-256-Hash gebildet und Base64-codiert - hier ohne endende "=" - zuzüglich des konfigurierten Präfixes Patienten-ID der entsprechende SHA-256-Hash gebildet und Base64-codiert - hier ohne endende
als Patienten-Pseudonym verwendet. "=" - zuzüglich des konfigurierten Präfixes als Patienten-Pseudonym verwendet.
#### Pseudonymisierung mit gPAS #### Pseudonymisierung mit gPAS
Wurde die Verwendung von gPAS konfiguriert, so sind weitere Angaben zu konfigurieren. Wurde die Verwendung von gPAS konfiguriert, so sind weitere Angaben zu konfigurieren.
* `APP_PSEUDONYMIZE_GPAS_URI`: URI der gPAS-Instanz inklusive Endpoint (z.B. `http://localhost:8080/ttp-fhir/fhir/gpas/$$pseudonymizeAllowCreate`) Ab Version 2025.1 (Multi-Pseudonym Support)
* `APP_PSEUDONYMIZE_GPAS_TARGET`: gPas Domänenname
* `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_USERNAME`: gPas Basic-Auth Benutzername * `APP_PSEUDONYMIZE_GPAS_USERNAME`: gPas Basic-Auth Benutzername
* `APP_PSEUDONYMIZE_GPAS_PASSWORD`: gPas Basic-Auth Passwort * `APP_PSEUDONYMIZE_GPAS_PASSWORD`: gPas Basic-Auth Passwort
* ~~`APP_PSEUDONYMIZE_GPAS_SSLCALOCATION`~~: **Veraltet** - Root Zertifikat für gPas, falls es dediziert hinzugefügt werden muss. * `APP_PSEUDONYMIZE_GPAS_PID_DOMAIN`: gPas Domänenname für Patienten ID
**Wird in nach Version 0.10 entfernt** * `APP_PSEUDONYMIZE_GPAS_GENOM_DE_TAN_DOMAIN`: gPas Multi-Pseudonym-Domäne für genomDE Vorgangsnummern (
Clinical data node)
Der Konfigurationsparameter `APP_PSEUDONYMIZE_GPAS_SSLCALOCATION` sollte nicht mehr verwendet werden und wird nach ### (Externe) Consent-Services
Version 0.10 entfernt.
Stattdessen sollte das Root Zertifikat wie unter [_Integration eines eigenen Root CA Consent-Services können konfiguriert werden.
Zertifikats_](#integration-eines-eigenen-root-ca-zertifikats) beschrieben eingebunden 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.
### Anmeldung mit einem Passwort ### Anmeldung mit einem Passwort
Ein initialer Administrator-Account kann optional konfiguriert werden und sorgt dafür, dass bestimmte Bereiche nur nach Ein initialer Administrator-Account kann optional konfiguriert werden und sorgt dafür, dass
einem erfolgreichen Login erreichbar sind. bestimmte Bereiche nur nach einem erfolgreichen Login erreichbar sind.
* `APP_SECURITY_ADMIN_USER`: Muss angegeben werden zur Aktivierung der Zugriffsbeschränkung. * `APP_SECURITY_ADMIN_USER`: Muss angegeben werden zur Aktivierung der Zugriffsbeschränkung.
* `APP_SECURITY_ADMIN_PASSWORD`: Das Passwort für den Administrator (Empfohlen). * `APP_SECURITY_ADMIN_PASSWORD`: Das Passwort für den Administrator (Empfohlen).
@@ -114,27 +188,34 @@ Hier Beispiele für das Beispielpasswort `very-secret`:
* `{bcrypt}$2y$05$CCkfsMr/wbTleMyjVIK8g.Aa3RCvrvoLXVAsL.f6KeouS88vXD9b6` * `{bcrypt}$2y$05$CCkfsMr/wbTleMyjVIK8g.Aa3RCvrvoLXVAsL.f6KeouS88vXD9b6`
* `{sha256}9a34717f0646b5e9cfcba70055de62edb026ff4f68671ba3db96aa29297d2df5f1a037d58c745657` * `{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. angezeigt.
#### Weitere (nicht administrative) Nutzer mit OpenID Connect #### 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. zu delegieren.
Ein Admin-Benutzer muss dabei konfiguriert sein. Ein Admin-Benutzer muss dabei konfiguriert sein.
* `APP_SECURITY_ENABLE_OIDC`: Aktiviert die Nutzung von OpenID Connect. Damit sind weitere Parameter erforderlich * `APP_SECURITY_ENABLE_OIDC`: Aktiviert die Nutzung von OpenID Connect. Damit sind weitere Parameter
* `SPRING_SECURITY_OAUTH2_CLIENT_REGISTRATION_CUSTOM_CLIENT_NAME`: Name. Wird beim zusätzlichen Loginbutton angezeigt. 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_ID`: Client-ID
* `SPRING_SECURITY_OAUTH2_CLIENT_REGISTRATION_CUSTOM_CLIENT_SECRET`: Client-Secret * `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, * `SPRING_SECURITY_OAUTH2_CLIENT_PROVIDER_CUSTOM_ISSUER_URI`: Die URI des Providers,
z.B. `https://auth.example.com/realm/example` 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. enthält.
Oft verwendet: `preferred_username` 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`. und dem konfigurierten `CLIENT_NAME`.
![Login mit OpenID Connect](docs/login.png) ![Login mit OpenID Connect](docs/login.png)
@@ -145,62 +226,75 @@ zu finden.
#### Rollenbasierte Berechtigungen #### Rollenbasierte Berechtigungen
Wird OpenID Connect verwendet, gibt es eine rollenbasierte Berechtigungszuweisung. 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`. Mögliche Werte sind `user` oder `guest`. Standardwert ist `user`.
Benutzer mit der Rolle "Gast" sehen nur die Inhalte, die auch nicht angemeldete Benutzer sehen. 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. einzelne Benutzer als vollwertige Nutzer zuzulassen.
![Rollenverwaltung](docs/userroles.png) ![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. Sie bekommen dabei wieder die Standardrolle zugewiesen.
#### Auswirkungen auf den dargestellten Inhalt #### Auswirkungen auf den dargestellten Inhalt
Nur Administratoren haben Zugriff auf den Konfigurationsbereich, nur angemeldete Benutzer können die anonymisierte oder Nur Administratoren haben Zugriff auf den Konfigurationsbereich, nur angemeldete Benutzer können die
anonymisierte oder
pseudonymisierte Patienten-ID sowie den Qualitätsbericht von DNPM:DIP einsehen. pseudonymisierte Patienten-ID sowie den Qualitätsbericht von DNPM:DIP einsehen.
Wurde kein Administrator-Account konfiguriert, sind diese Inhalte generell nicht verfügbar. Wurde kein Administrator-Account konfiguriert, sind diese Inhalte generell nicht verfügbar.
### Tokenbasierte Authentifizierung für MTBFile-Endpunkt ### 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. 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. zur Nutzung des MTB-File-Endpunkts eine HTTP-Basic-Authentifizierung voraussetzen.
![Tokenverwaltung](docs/tokens.png) ![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 *
*[mv64e-onkostar-plugin-export](https://github.com/pcvolkmer/mv64e-onkostar-plugin-export)** wie folgt
konfiguriert werden:
``` ```
https://testonkostar:MTg1NTL...NGU4@etl.example.com/mtbfile 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. Alternativ kann eine Authentifizierung über Benutzername/Passwort oder OIDC erfolgen.
### Transformation von Werten ### Transformation von Werten
In Onkostar kann es vorkommen, dass ein Wert eines Merkmalskatalogs an einem Standort angepasst wurde und dadurch nicht dem Wert entspricht, In Onkostar kann es vorkommen, dass ein Wert eines Merkmalskatalogs an einem Standort angepasst
wurde und dadurch nicht dem Wert entspricht,
der von DNPM:DIP akzeptiert wird. der 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 Diese Anwendung bietet daher die Möglichkeit, eine Transformation vorzunehmen. Hierzu muss der "Pfad"
welcher Wert wie ersetzt werden soll. innerhalb des JSON-MTB-Files angegeben werden und welcher Wert wie ersetzt werden soll.
Hier ein Beispiel für die erste (Index 0 - weitere dann mit 1,2, ...) Transformationsregel: Hier ein Beispiel für die erste (Index 0 - weitere dann mit 1,2, ...) Transformationsregel:
* `APP_TRANSFORMATIONS_0_PATH`: Pfad zum Wert in der JSON-MTB-Datei. Beispiel: `diagnoses[*].icd10.version` für **alle** Diagnosen * `APP_TRANSFORMATIONS_0_PATH`: Pfad zum Wert in der JSON-MTB-Datei. Beispiel:
* `APP_TRANSFORMATIONS_0_FROM`: Angabe des Werts, der ersetzt werden soll. Andere Werte bleiben dabei unverändert. `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. * `APP_TRANSFORMATIONS_0_TO`: Angabe des neuen Werts.
### Mögliche Endpunkte zur Datenübermittlung ### Mögliche Endpunkte zur Datenübermittlung
@@ -212,56 +306,61 @@ Werden sowohl REST als auch Kafka-Endpunkt konfiguriert, wird nur der REST-Endpu
#### REST #### REST
Folgende Umgebungsvariablen müssen gesetzt sein, damit ein bwHC-MTB-File an DNPM:DIP gesendet wird: Folgende Umgebungsvariablen müssen gesetzt sein, damit ein MTB-File an DNPM:DIP gesendet wird:
* `APP_REST_URI`: URI der zu benutzenden API der Backend-Instanz. Zum Beispiel: * `APP_REST_URI`: URI der zu benutzenden API der Backend-Instanz. Zum Beispiel `http://localhost:9000/api`
* `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_USERNAME`: Basic-Auth-Benutzername für den REST-Endpunkt
* `APP_REST_PASSWORD`: Basic-Auth-Passwort 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 #### Kafka-Topics
Folgende Umgebungsvariablen müssen gesetzt sein, damit ein bwHC-MTB-File an ein Kafka-Topic übermittelt wird: Folgende Umgebungsvariablen müssen gesetzt sein, damit ein MTB-File an ein Kafka-Topic
übermittelt wird:
* `APP_KAFKA_OUTPUT_TOPIC`: Zu verwendendes Topic zum Versenden von Anfragen. * `APP_KAFKA_OUTPUT_TOPIC`: Zu verwendendes Topic zum Versenden von Anfragen.
Ersetzt ~~`APP_KAFKA_TOPIC`~~, **welches nach Version 0.10 entfernt wird**. * `APP_KAFKA_OUTPUT_RESPONSE_TOPIC`: Topic mit Antworten über den Erfolg des Versendens.
* `APP_KAFKA_OUTPUT_RESPONSE_TOPIC`: Topic mit Antworten über den Erfolg des Versendens. Standardwert: `APP_KAFKA_TOPIC` mit Anhang "_response". 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 "_
* `APP_KAFKA_GROUP_ID`: Kafka GroupID des Consumers. Standardwert: `APP_KAFKA_TOPIC` mit Anhang "_group". group".
* `APP_KAFKA_SERVERS`: Zu verwendende Kafka-Bootstrap-Server als kommagetrennte Liste * `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. 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. 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 ##### Retention Time
Generell werden in Apache Kafka alle Records entsprechend der Konfiguration vorgehalten. 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. 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. Durch eine entsprechende Konfiguration des Topics kann dies verhindert werden.
Beispiel - auszuführen innerhalb des Kafka-Containers: Löschen alter Records nach einem Tag 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 kafka-configs.sh --bootstrap-server localhost:9092 --alter --topic test --add-config retention.ms=86400000
``` ```
##### Key based Retention ##### Key based Retention
Möchten Sie hingegen immer nur die letzte Meldung für einen Patienten und eine Erkrankung in Apache Kafka vorhalten, 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. 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
* `retention.ms`: Möglichst kurze Zeit in der alte Records noch erhalten bleiben, z.B. 10 Sekunden 10000 10000
* `cleanup.policy`: Löschen alter Records und Beibehalten des letzten Records zu einem Key [delete,compact] * `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. Beispiele für ein Topic `test`, hier bitte an die verwendeten Topics anpassen.
@@ -270,32 +369,28 @@ 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] 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 Da als Key eines Records die (pseudonymisierte) Patienten-ID verwendet wird, stehen mit obiger
der Kafka-Topics nach 10 Sekunden nur noch der jeweils letzte Eintrag für den entsprechenden Key zur Verfügung. Konfiguration
der Kafka-Topics nach 10 Sekunden nur noch der jeweils letzte Eintrag für den entsprechenden Key zur
Verfügung.
Da der Key sowohl für die Records in Richtung DNPM:DIP, als auch für die Rückantwort identisch aufgebaut ist, lassen sich so Da der Key sowohl für die Records in Richtung DNPM:DIP, als auch für die Rückantwort identisch
auch im Falle eines Consent-Widerspruchs die enthaltenen Daten als auch die Offenlegung durch Verifikationsdaten in der 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. 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. 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 ### Antworten und Statusauswertung
Anfragen an das bwHC-Backend aus Versionen bis 0.9.x wurden wie folgt behandelt: Seit Version 0.10 wird die Issue-Liste der Antwort verwendet und die darion enthaltene höchste
Severity-Stufe als Ergebnis verwendet.
| 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 | | Höchste Severity | Status |
|------------------|-----------| |------------------|-----------|
@@ -305,9 +400,10 @@ Ab Version 0.10 wird die Issue-Liste der Antwort verwendet und die darion enthal
## Docker-Images ## 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 ### Images lokal bauen
```bash ```bash
./gradlew bootBuildImage ./gradlew bootBuildImage
@@ -315,20 +411,25 @@ Diese Anwendung ist auch als Docker-Image verfügbar: https://github.com/pcvolkm
### Integration eines eigenen Root CA Zertifikats ### 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. Hier bietet es sich an, das Root CA Zertifikat in das Image zu integrieren.
#### Integration beim Bauen des Images #### 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 #### Integration zur Laufzeit
Hier muss die Umgebungsvariable `SERVICE_BINDING_ROOT` z.B. auf den Wert `/bindings` gesetzt sein. 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 und der
Datei [`bindings/ca-certificates/type`](bindings/ca-certificates/type) als Docker-Volume eingebunden werden.
Beispiel für Docker-Compose: Beispiel für Docker-Compose:
@@ -343,12 +444,14 @@ Beispiel für Docker-Compose:
``` ```
## Deployment ## Deployment
*Ausführen als Docker Container:* *Ausführen als Docker Container:*
```bash ```bash
cd ./deploy cd ./deploy
cp env-sample.env .env cp env-sample.env .env
``` ```
Wenn gewünscht, Änderungen in der `.env` vornehmen. Wenn gewünscht, Änderungen in der `.env` vornehmen.
```bash ```bash
@@ -357,15 +460,19 @@ docker compose up -d
### Einfaches Beispiel für ein eigenes Docker-Compose-File ### 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. auf Docker-Compose mit der gestartet werden kann.
### Betrieb hinter einem Reverse-Proxy ### 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 Dabei werden, je nachdem welche Header durch den Reverse-Proxy gesendet werden auch Protokoll, Host
automatisch erkannt und verwendet werden. Dadurch ist z.B. eine abweichende Angabe des Pfads problemlos möglich. 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): #### Beispiel *Traefik* (mit Docker-Labels):
@@ -401,13 +508,17 @@ Das folgende Beispiel zeigt die Konfiguration einer _location_ in einer nginx-Ko
## Entwicklungssetup ## 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. 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 Zur Nutzung von Apache Kafka muss dazu ein Eintrag im hosts-File vorgenommen werden und der Hostname
IP-Adresse verweisen. Ohne diese Einstellung ist eine Nutzung von Apache Kafka außerhalb der Docker-Umgebung nicht möglich. `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: Anwendung mit gestartet:
``` ```
@@ -419,4 +530,5 @@ Die Datei `application-dev.yml` enthält hierzu die Konfiguration für das Profi
Beim Ausführen der Integrationstests wird eine Testdatenbank in einem Docker-Container gestartet. Beim Ausführen der Integrationstests wird eine Testdatenbank in einem Docker-Container gestartet.
Siehe hier auch die Klasse `AbstractTestcontainerTest` unter `src/integrationTest`. 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.

View File

@@ -5,25 +5,24 @@ import org.springframework.boot.gradle.tasks.bundling.BootBuildImage
plugins { plugins {
war war
id("org.springframework.boot") version "3.3.10" id("org.springframework.boot") version "3.5.5"
id("io.spring.dependency-management") version "1.1.7" id("io.spring.dependency-management") version "1.1.7"
kotlin("jvm") version "1.9.25" kotlin("jvm") version "2.2.10"
kotlin("plugin.spring") version "1.9.25" kotlin("plugin.spring") version "2.2.10"
jacoco jacoco
} }
group = "dev.dnpm" group = "dev.dnpm"
version = "0.10.0" version = "0.12.0-SNAPSHOT"
var versions = mapOf( var versions = mapOf(
"bwhc-dto-java" to "0.4.0", "mtb-dto" to "0.1.0-SNAPSHOT",
"hapi-fhir" to "7.6.0", "hapi-fhir" to "8.4.0",
"commons-compress" to "1.26.2", "mockito-kotlin" to "6.0.0",
"mockito-kotlin" to "5.4.0", "archunit" to "1.4.1",
"archunit" to "1.3.0",
// Webjars // Webjars
"webjars-locator" to "0.52", "webjars-locator" to "0.52",
"echarts" to "5.4.3", "echarts" to "6.0.0",
"htmx.org" to "1.9.12" "htmx.org" to "1.9.12"
) )
@@ -49,9 +48,18 @@ configurations {
compileOnly { compileOnly {
extendsFrom(configurations.annotationProcessor.get()) extendsFrom(configurations.annotationProcessor.get())
} }
all {
resolutionStrategy {
cacheChangingModulesFor(5, "minutes")
}
}
} }
repositories { repositories {
maven {
url = uri("https://git.dnpm.dev/api/packages/public-snapshots/maven")
}
maven { maven {
url = uri("https://git.dnpm.dev/api/packages/public/maven") url = uri("https://git.dnpm.dev/api/packages/public/maven")
} }
@@ -72,7 +80,7 @@ dependencies {
implementation("org.flywaydb:flyway-mysql") implementation("org.flywaydb:flyway-mysql")
implementation("commons-codec:commons-codec") implementation("commons-codec:commons-codec")
implementation("io.projectreactor.kotlin:reactor-kotlin-extensions") implementation("io.projectreactor.kotlin:reactor-kotlin-extensions")
implementation("de.ukw.ccc:bwhc-dto-java:${versions["bwhc-dto-java"]}") implementation("dev.pcvolkmer.mv64e:mtb-dto:${versions["mtb-dto"]}") { isChanging = true }
implementation("ca.uhn.hapi.fhir:hapi-fhir-base:${versions["hapi-fhir"]}") implementation("ca.uhn.hapi.fhir:hapi-fhir-base:${versions["hapi-fhir"]}")
implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${versions["hapi-fhir"]}") implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${versions["hapi-fhir"]}")
implementation("org.apache.httpcomponents.client5:httpclient5") implementation("org.apache.httpcomponents.client5:httpclient5")
@@ -80,6 +88,8 @@ dependencies {
implementation("org.webjars:webjars-locator:${versions["webjars-locator"]}") implementation("org.webjars:webjars-locator:${versions["webjars-locator"]}")
implementation("org.webjars.npm:echarts:${versions["echarts"]}") implementation("org.webjars.npm:echarts:${versions["echarts"]}")
implementation("org.webjars.npm:htmx.org:${versions["htmx.org"]}") implementation("org.webjars.npm:htmx.org:${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.mariadb.jdbc:mariadb-java-client")
runtimeOnly("org.postgresql:postgresql") runtimeOnly("org.postgresql:postgresql")
@@ -99,10 +109,10 @@ dependencies {
integrationTestImplementation("org.testcontainers:junit-jupiter") integrationTestImplementation("org.testcontainers:junit-jupiter")
integrationTestImplementation("org.testcontainers:postgresql") integrationTestImplementation("org.testcontainers:postgresql")
integrationTestImplementation("com.tngtech.archunit:archunit:${versions["archunit"]}") integrationTestImplementation("com.tngtech.archunit:archunit:${versions["archunit"]}")
integrationTestImplementation("net.sourceforge.htmlunit:htmlunit") integrationTestImplementation("org.htmlunit:htmlunit")
integrationTestImplementation("org.springframework:spring-webflux") integrationTestImplementation("org.springframework:spring-webflux")
// Override dependency version from org.testcontainers:junit-jupiter - CVE-2024-26308, CVE-2024-25710 // Fix for CVE-2024-25710
integrationTestImplementation("org.apache.commons:commons-compress:${versions["commons-compress"]}") integrationTestImplementation("org.apache.commons:commons-compress:1.26.0")
} }
tasks.withType<KotlinCompile> { tasks.withType<KotlinCompile> {
@@ -119,8 +129,9 @@ tasks.withType<Test> {
} }
} }
task<Test>("integrationTest") { tasks.register<Test>("integrationTest") {
description = "Runs integration tests" description = "Runs integration tests"
group = "verification"
testClassesDirs = sourceSets["integrationTest"].output.classesDirs testClassesDirs = sourceSets["integrationTest"].output.classesDirs
classpath = sourceSets["integrationTest"].runtimeClasspath classpath = sourceSets["integrationTest"].runtimeClasspath
@@ -145,7 +156,7 @@ tasks.jacocoTestReport {
} }
tasks.named<BootBuildImage>("bootBuildImage") { tasks.named<BootBuildImage>("bootBuildImage") {
imageName.set("ghcr.io/pcvolkmer/etl-processor") imageName.set("ghcr.io/pcvolkmer/mv64e-etl-processor")
// Binding for CA Certs // Binding for CA Certs
bindings.set(listOf( bindings.set(listOf(
@@ -155,8 +166,8 @@ tasks.named<BootBuildImage>("bootBuildImage") {
environment.set(environment.get() + mapOf( environment.set(environment.get() + mapOf(
// Enable this line to embed CA Certs into image on build time // Enable this line to embed CA Certs into image on build time
//"BP_EMBED_CERTS" to "true", //"BP_EMBED_CERTS" to "true",
"BP_OCI_SOURCE" to "https://github.com/pcvolkmer/etl-processor", "BP_OCI_SOURCE" to "https://github.com/pcvolkmer/mv64e-etl-processor",
"BP_OCI_LICENSES" to "AGPLv3", "BP_OCI_LICENSES" to "AGPLv3",
"BP_OCI_DESCRIPTION" to "ETL Processor for bwHC MTB files" "BP_OCI_DESCRIPTION" to "ETL Processor for MV § 64e and DNPM:DIP"
)) ))
} }

View File

@@ -1,21 +1,121 @@
services: services:
kafka: kafka:
image: bitnami/kafka image: apache/kafka
hostname: kafka hostname: kafka
ports: ports:
- "9092:9092" - "9092:9092"
- "9094:9094" - "9094:9094"
environment: environment:
ALLOW_PLAINTEXT_LISTENER: "yes" ALLOW_PLAINTEXT_LISTENER: "yes"
KAFKA_CFG_NODE_ID: "0" KAFKA_NODE_ID: "0"
KAFKA_CFG_PROCESS_ROLES: "controller,broker" KAFKA_KRAFT_CLUSTER_ID: "mv64e-etl-processor-dev"
KAFKA_CFG_LISTENERS: PLAINTEXT://:9092,CONTROLLER://:9093,EXTERNAL://:9094 KAFKA_CONTROLLER_QUORUM_VOTERS: 0@kafka:9093
KAFKA_CFG_ADVERTISED_LISTENERS: PLAINTEXT://kafka:9092,EXTERNAL://localhost:9094 KAFKA_PROCESS_ROLES: "controller,broker"
KAFKA_CFG_LISTENER_SECURITY_PROTOCOL_MAP: CONTROLLER:PLAINTEXT,EXTERNAL:PLAINTEXT,PLAINTEXT:PLAINTEXT KAFKA_CONTROLLER_LISTENER_NAMES: CONTROLLER
KAFKA_CFG_INTER_BROKER_LISTENER_NAME: PLAINTEXT KAFKA_INTER_BROKER_LISTENER_NAME: PLAINTEXT
KAFKA_CFG_AUTO_CREATE_TOPICS_ENABLE: true KAFKA_OFFSETS_TOPIC_REPLICATION_FACTOR: "1"
KAFKA_CFG_CONTROLLER_QUORUM_VOTERS: 0@kafka:9093 KAFKA_TRANSACTION_STATE_LOG_REPLICATION_FACTOR: "1"
KAFKA_CFG_CONTROLLER_LISTENER_NAMES: CONTROLLER KAFKA_TRANSACTION_STATE_LOG_MIN_ISR: "1"
KAFKA_GROUP_INITIAL_REBALANCE_DELAY_MS: "0"
KAFKA_AUTO_CREATE_TOPICS_ENABLE: "true"
# Without SSL
KAFKA_LISTENERS: PLAINTEXT://:9092,CONTROLLER://:9093,EXTERNAL://:9094
KAFKA_ADVERTISED_LISTENERS: PLAINTEXT://kafka:9092,EXTERNAL://localhost:9094
KAFKA_LISTENER_SECURITY_PROTOCOL_MAP: CONTROLLER:PLAINTEXT,EXTERNAL:PLAINTEXT,PLAINTEXT:PLAINTEXT
# Using SSL
# KAFKA_LISTENERS: PLAINTEXT://:9092,CONTROLLER://:9093,EXTERNAL://:9094
# KAFKA_ADVERTISED_LISTENERS: PLAINTEXT://kafka:9092,EXTERNAL://localhost:9094
# KAFKA_LISTENER_SECURITY_PROTOCOL_MAP: CONTROLLER:PLAINTEXT,EXTERNAL:SSL,PLAINTEXT:PLAINTEXT
# KAFKA_SSL_KEYSTORE_TYPE: "PEM"
# KAFKA_SSL_KEYSTORE_CERTIFICATE_CHAIN: -----BEGIN CERTIFICATE-----
# MIIDCzCCAfOgAwIBAgIUaXNh4PahaKeLUaab2rUPSVESx28wDQYJKoZIhvcNAQEL
# BQAwFTETMBEGA1UEAwwKRXhhbXBsZSBDQTAeFw0yNTA4MjExODEyMTFaFw0zNTA4
# MTkxODEyMTFaMBUxEzARBgNVBAMMCkV4YW1wbGUgQ0EwggEiMA0GCSqGSIb3DQEB
# AQUAA4IBDwAwggEKAoIBAQCsqalqVOLFglVbX9oSHU91ebyL1kPyb/2N90UGQIcD
# UAjzKxxysId1Vdvtbbwgli6UgfPwlzFP2Wlw51h496yL4QU/9tNV956UJ1RoS/fG
# qBAEHctqavfMI27UQmIzw4pGMkGzEQxRMc6a9pdabBhbMMTJsjtmOv2YMYHj1HHK
# Dr7wTBTt2l0eRyCR0kZ8XGIMWhYowPa4EMpC7+4e5Nf/7LSJZWLLy9jXPpazsjkJ
# jEmDNlFfx2tZiq0Wz2Xj1pZSDLbcuIX4IHcLfMvagibfrCMX/h6+WuW42sWPRuBW
# wB6cHGlXs+K/gBBWxtD7sOTacO5hbHFsfaJOhSEIGoIpAgMBAAGjUzBRMB0GA1Ud
# DgQWBBT2S/C2++ECY+CSuN5KKql0umfbTDAfBgNVHSMEGDAWgBT2S/C2++ECY+CS
# uN5KKql0umfbTDAPBgNVHRMBAf8EBTADAQH/MA0GCSqGSIb3DQEBCwUAA4IBAQBj
# H4DdwqrOHg7sVsqiwDsZfTharpUDCYeG5XhrJQlnA9eKwyofTb929W/fjOwBdDtg
# 9THT/omR0lA8/UyHtezMT6nMsCn4HG2mXvx6ghgvA3jrFTEY7R80dHkboLMTV3u4
# RYgC9S3BJPcbJYpM0cXzkp2T0F4FxWZlfqefuedHuX3zcCxpgVD56qQb2a131TX7
# O3UDJfVg8a65IFtehndqILgLVrf7w6+pbmDAlCg5RKrt2USEYyZXYdyTryJbdtn4
# BCLp0avYtSYVUGwgH0oUCpkjQRwMg1003TTz8SNnmE7mAXHYljyYejnjL8vBHfch
# 8tTDVXQn08BT9H3jZTnF
# -----END CERTIFICATE-----
# -----BEGIN CERTIFICATE-----
# MIIC+TCCAeGgAwIBAgIUUoCwz8GS6xQ3mmI7RUUYSNPIOi4wDQYJKoZIhvcNAQEL
# BQAwFTETMBEGA1UEAwwKRXhhbXBsZSBDQTAeFw0yNTA4MjExODE0NDhaFw0zNTA4
# MTkxODE0NDhaMBQxEjAQBgNVBAMMCWxvY2FsaG9zdDCCASIwDQYJKoZIhvcNAQEB
# BQADggEPADCCAQoCggEBAL9PW99MhhBwdEmTHyZgfnhfTrxZPrNU6z1UdV8b82Lk
# 3p75o8eCKa9iOd7DDQlo75hQBhhX0+Xc3mucrstx5p8TYFMbypif8ojWh3LM++P8
# tz3ezQZlq86ycyKpm8dqlA03b227tFDfiYTev2eD2HN40BU7yDAYhhqd/QW8+MV2
# jkcRGv5cE21GZxWmPUpkVN+bNoBC8H90WmkST90LfeYF+wZnlsAJZH6AQzR1GnGD
# ICE5evMhC78hvRnpgeA310SyxssZEigkePL5lTZOBPY2IuzBqL05agyVTiVq4Xd6
# y3xOqXoxxOhZu06yd3nymorqeTgbF1fW8wQF0u3KsFECAwEAAaNCMEAwHQYDVR0O
# BBYEFHk9jMWRAAt2YsBSxUcOQVoWayoHMB8GA1UdIwQYMBaAFPZL8Lb74QJj4JK4
# 3koqqXS6Z9tMMA0GCSqGSIb3DQEBCwUAA4IBAQBqabAA9INONDaLHqs9i9YQHm/g
# AnB7xRl/RFbERKKCTSMZUYM8oEaaH0W2ENoPMc/7xOB/R8a7Rm62PTr6syxwhZrY
# 5NtGKJOD+rh90/5l83tulf93KqOJtGkiv6NBDvCNrITcA+UKRk/z4GcFi2YjWAl4
# wvY44lzTasMKSpjUQ5N0VNANcW3nVuEgPQ8rrr0NOK/5j4guPjsXDsixa47gqblA
# 5xGfBKeVmEXdPbzawZfP4hPIw7DpX2m8Y0erswF1ZxkIV73V3TDsFSLcqSKSzZr6
# mtj8COlV9Us7zqaJbV5eOl7GN1T9orZJwZmX1Z46gCkkSLYDP/dqtl2j9JgN
# -----END CERTIFICATE-----
# KAFKA_SSL_KEYSTORE_KEY: -----BEGIN PRIVATE KEY-----
# MIIEvQIBADANBgkqhkiG9w0BAQEFAASCBKcwggSjAgEAAoIBAQC/T1vfTIYQcHRJ
# kx8mYH54X068WT6zVOs9VHVfG/Ni5N6e+aPHgimvYjneww0JaO+YUAYYV9Pl3N5r
# nK7LceafE2BTG8qYn/KI1odyzPvj/Lc93s0GZavOsnMiqZvHapQNN29tu7RQ34mE
# 3r9ng9hzeNAVO8gwGIYanf0FvPjFdo5HERr+XBNtRmcVpj1KZFTfmzaAQvB/dFpp
# Ek/dC33mBfsGZ5bACWR+gEM0dRpxgyAhOXrzIQu/Ib0Z6YHgN9dEssbLGRIoJHjy
# +ZU2TgT2NiLswai9OWoMlU4lauF3est8Tql6McToWbtOsnd58pqK6nk4GxdX1vME
# BdLtyrBRAgMBAAECggEAC1wXfPlqxoQe65WAVoOJTvV90+JKvlRPCZu/wm+C8r7b
# Vz5Ekt6wQflHrWoQlpv0CivKSNzCONZ2IJazrGHti0mXwSeXzptEyApRDaiNVnrV
# mKdnrjcQThw7iPXgSaWS9/vwMmhgayLy5ABkBi4GhsjINlKP7wctw1vZP+N6NCNd
# Ql3taStvDKmG0SfJHF6/2o/XBpof3IJEL7ghbzyTTbWWaO34J1mJ8A+AmjGhj9GE
# Dp3XuOrO9W7MVd1nfZDtGBS8qf80AwROyodZZRma9vZuWJZ5aQFi2CnUEtU1T+Uv
# tW+F6tg2FOMr8M0Fb79wGIDwSF8u/QcTvwhEzZAfiQKBgQDioOofnE1oB1DOMnqZ
# SOFjs+vsirvS6G3lo27+HkE3TgvCHR4sk1305AiXtjmPu8iaUCo9qn18MtduY2RS
# CcKMOG/FxhmDyP5I29DhJRhvERIpJd0kcSDQOgtaoVPC1XzIlyTqte6nGX9kAnA/
# x/OOXrZ0hjhMNDcZzf2NasPYJQKBgQDYGqTobkVBk+eekNWklnTh41/649rUIgTu
# JStArtY2hgaEInYcGa2e7cEj7nIHA0iGy3EJ2yvwoUIyxtoXVcGohu2IrzlhS33T
# R4jA7nE2/yHZrEMEJovuSU0eMw7rgvEtL79Q0RToYnTY1EU6X/BBoFfiiEeNMHKz
# zjDOOQ6ZvQKBgGCWChIc0FSkwYiPtPZ9PCn89XCjk/cIPkYfiF9fT5Ydeh9pv4Fp
# 8SI8yXi3HgMnGhDCV65eagqztGMEky3voO2X4/MbQaaL0+wDWxuJbsdvNBk7XOt6
# F20HP+2JUiR4Ti1DVWV+0k5/LG7YJzTXp/KmZQZ2aan4mv8xbn2F4h/NAoGAI4ou
# OLN53FEQtHkpSYoc6tFUBZTXdi+qE+g09sxKGmlsROrN9c0bSpnbO6eJRTH7CYAH
# tRFAZrB+jI87ar8FvEuEYQhALYoWxVpsWR5drCfFT2EPHG2icavIbQEEoSLFuyKx
# Gf9oqtcWVFqEkBcbEg/mpDC5Y7TmCEAOsrubdRkCgYEAl7B+EzIdG0rabGoti09q
# QXfyiTjR7nQYkhpLxMCeNlCpQ8Y15XSa8bm1UIGYqj/ZBpeBNhrj64IHoub5Vd43
# tzbb8yNgoLUd16TU1VvyccCMGQVPIF8RkDsAtEawV2eoXbHAstN99xbC8jsLNZRQ
# fcfgTiQaXRJmlVx6jfbfZd4=
# -----END PRIVATE KEY-----
# #KAFKA_SSL_KEYSTORE_CREDENTIALS: example
# KAFKA_SSL_KEY_CREDENTIALS: example
# KAFKA_SSL_TRUSTSTORE_TYPE: "PEM"
# KAFKA_SSL_TRUSTSTORE_CERTIFICATES: -----BEGIN CERTIFICATE-----
# MIIDCzCCAfOgAwIBAgIUaXNh4PahaKeLUaab2rUPSVESx28wDQYJKoZIhvcNAQEL
# BQAwFTETMBEGA1UEAwwKRXhhbXBsZSBDQTAeFw0yNTA4MjExODEyMTFaFw0zNTA4
# MTkxODEyMTFaMBUxEzARBgNVBAMMCkV4YW1wbGUgQ0EwggEiMA0GCSqGSIb3DQEB
# AQUAA4IBDwAwggEKAoIBAQCsqalqVOLFglVbX9oSHU91ebyL1kPyb/2N90UGQIcD
# UAjzKxxysId1Vdvtbbwgli6UgfPwlzFP2Wlw51h496yL4QU/9tNV956UJ1RoS/fG
# qBAEHctqavfMI27UQmIzw4pGMkGzEQxRMc6a9pdabBhbMMTJsjtmOv2YMYHj1HHK
# Dr7wTBTt2l0eRyCR0kZ8XGIMWhYowPa4EMpC7+4e5Nf/7LSJZWLLy9jXPpazsjkJ
# jEmDNlFfx2tZiq0Wz2Xj1pZSDLbcuIX4IHcLfMvagibfrCMX/h6+WuW42sWPRuBW
# wB6cHGlXs+K/gBBWxtD7sOTacO5hbHFsfaJOhSEIGoIpAgMBAAGjUzBRMB0GA1Ud
# DgQWBBT2S/C2++ECY+CSuN5KKql0umfbTDAfBgNVHSMEGDAWgBT2S/C2++ECY+CS
# uN5KKql0umfbTDAPBgNVHRMBAf8EBTADAQH/MA0GCSqGSIb3DQEBCwUAA4IBAQBj
# H4DdwqrOHg7sVsqiwDsZfTharpUDCYeG5XhrJQlnA9eKwyofTb929W/fjOwBdDtg
# 9THT/omR0lA8/UyHtezMT6nMsCn4HG2mXvx6ghgvA3jrFTEY7R80dHkboLMTV3u4
# RYgC9S3BJPcbJYpM0cXzkp2T0F4FxWZlfqefuedHuX3zcCxpgVD56qQb2a131TX7
# O3UDJfVg8a65IFtehndqILgLVrf7w6+pbmDAlCg5RKrt2USEYyZXYdyTryJbdtn4
# BCLp0avYtSYVUGwgH0oUCpkjQRwMg1003TTz8SNnmE7mAXHYljyYejnjL8vBHfch
# 8tTDVXQn08BT9H3jZTnF
# -----END CERTIFICATE-----
# KAFKA_SSL_CLIENT_AUTH: none
###
## Use AKHQ as Kafka web frontend ## Use AKHQ as Kafka web frontend
akhq: akhq:
@@ -53,4 +153,4 @@ services:
# environment: # environment:
# POSTGRES_DB: dev # POSTGRES_DB: dev
# POSTGRES_USER: dev # POSTGRES_USER: dev
# POSTGRES_PASSWORD: dev # POSTGRES_PASSWORD: dev

View File

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

View File

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

View File

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

View File

@@ -20,15 +20,18 @@
package dev.dnpm.etl.processor.config package dev.dnpm.etl.processor.config
import com.fasterxml.jackson.databind.ObjectMapper 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.input.KafkaInputListener
import dev.dnpm.etl.processor.monitoring.RequestRepository import dev.dnpm.etl.processor.monitoring.RequestRepository
import dev.dnpm.etl.processor.output.KafkaMtbFileSender import dev.dnpm.etl.processor.output.KafkaMtbFileSender
import dev.dnpm.etl.processor.output.RestMtbFileSender import dev.dnpm.etl.processor.output.RestMtbFileSender
import dev.dnpm.etl.processor.pseudonym.AnonymizingGenerator import dev.dnpm.etl.processor.pseudonym.AnonymizingGenerator
import dev.dnpm.etl.processor.pseudonym.GpasPseudonymGenerator 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.TokenRepository
import dev.dnpm.etl.processor.security.TokenService import dev.dnpm.etl.processor.security.TokenService
import dev.dnpm.etl.processor.services.RequestProcessor
import org.assertj.core.api.Assertions.assertThat import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.Nested import org.junit.jupiter.api.Nested
import org.junit.jupiter.api.Test import org.junit.jupiter.api.Test
@@ -36,24 +39,26 @@ import org.junit.jupiter.api.assertThrows
import org.springframework.beans.factory.NoSuchBeanDefinitionException import org.springframework.beans.factory.NoSuchBeanDefinitionException
import org.springframework.boot.autoconfigure.kafka.KafkaAutoConfiguration import org.springframework.boot.autoconfigure.kafka.KafkaAutoConfiguration
import org.springframework.boot.test.context.SpringBootTest import org.springframework.boot.test.context.SpringBootTest
import org.springframework.boot.test.mock.mockito.MockBean
import org.springframework.boot.test.mock.mockito.MockBeans
import org.springframework.context.ApplicationContext import org.springframework.context.ApplicationContext
import org.springframework.retry.support.RetryTemplate import org.springframework.retry.support.RetryTemplate
import org.springframework.security.crypto.password.PasswordEncoder import org.springframework.security.crypto.password.PasswordEncoder
import org.springframework.security.provisioning.InMemoryUserDetailsManager import org.springframework.security.provisioning.InMemoryUserDetailsManager
import org.springframework.test.context.ContextConfiguration import org.springframework.test.context.ContextConfiguration
import org.springframework.test.context.TestPropertySource import org.springframework.test.context.TestPropertySource
import org.springframework.test.context.bean.override.mockito.MockitoBean
@SpringBootTest @SpringBootTest
@ContextConfiguration(classes = [ @ContextConfiguration(
AppConfiguration::class, classes = [
AppSecurityConfiguration::class, AppConfiguration::class,
KafkaAutoConfiguration::class, AppSecurityConfiguration::class,
AppKafkaConfiguration::class, KafkaAutoConfiguration::class,
AppRestConfiguration::class AppKafkaConfiguration::class,
]) AppRestConfiguration::class,
@MockBean(ObjectMapper::class) ConsentEvaluator::class
]
)
@MockitoBean(types = [ObjectMapper::class])
@TestPropertySource( @TestPropertySource(
properties = [ properties = [
"app.pseudonymize.generator=BUILDIN", "app.pseudonymize.generator=BUILDIN",
@@ -86,7 +91,7 @@ class AppConfigurationTest {
"app.kafka.group-id=test" "app.kafka.group-id=test"
] ]
) )
@MockBean(RequestRepository::class) @MockitoBean(types = [RequestRepository::class])
inner class AppConfigurationKafkaTest(private val context: ApplicationContext) { inner class AppConfigurationKafkaTest(private val context: ApplicationContext) {
@Test @Test
@@ -145,7 +150,7 @@ class AppConfigurationTest {
"app.kafka.group-id=test" "app.kafka.group-id=test"
] ]
) )
@MockBean(RequestProcessor::class) @MockitoBean(types = [RequestProcessor::class])
inner class AppConfigurationUsingKafkaInputTest(private val context: ApplicationContext) { inner class AppConfigurationUsingKafkaInputTest(private val context: ApplicationContext) {
@Test @Test
@@ -181,40 +186,7 @@ class AppConfigurationTest {
@Nested @Nested
@TestPropertySource( @TestPropertySource(
properties = [ properties = [
"app.pseudonymize.generator=", "app.pseudonymize.generator=buildin"
"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) { inner class AppConfigurationPseudonymizeGeneratorBuildinTest(private val context: ApplicationContext) {
@@ -229,8 +201,7 @@ class AppConfigurationTest {
@Nested @Nested
@TestPropertySource( @TestPropertySource(
properties = [ properties = [
"app.pseudonymize.generator=gpas", "app.pseudonymize.generator=gpas"
"app.pseudonymizer=",
] ]
) )
inner class AppConfigurationPseudonymizeGeneratorGpasTest(private val context: ApplicationContext) { inner class AppConfigurationPseudonymizeGeneratorGpasTest(private val context: ApplicationContext) {
@@ -248,11 +219,13 @@ class AppConfigurationTest {
"app.security.enable-tokens=true" "app.security.enable-tokens=true"
] ]
) )
@MockBeans(value = [ @MockitoBean(
MockBean(InMemoryUserDetailsManager::class), types = [
MockBean(PasswordEncoder::class), InMemoryUserDetailsManager::class,
MockBean(TokenRepository::class) PasswordEncoder::class,
]) TokenRepository::class
]
)
inner class AppConfigurationTokenEnabledTest(private val context: ApplicationContext) { inner class AppConfigurationTokenEnabledTest(private val context: ApplicationContext) {
@Test @Test
@@ -263,11 +236,13 @@ class AppConfigurationTest {
} }
@Nested @Nested
@MockBeans(value = [ @MockitoBean(
MockBean(InMemoryUserDetailsManager::class), types = [
MockBean(PasswordEncoder::class), InMemoryUserDetailsManager::class,
MockBean(TokenRepository::class) PasswordEncoder::class,
]) TokenRepository::class
]
)
inner class AppConfigurationTokenDisabledTest(private val context: ApplicationContext) { inner class AppConfigurationTokenDisabledTest(private val context: ApplicationContext) {
@Test @Test
@@ -305,4 +280,30 @@ 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
}
}
}

View File

@@ -20,44 +20,47 @@
package dev.dnpm.etl.processor.input package dev.dnpm.etl.processor.input
import com.fasterxml.jackson.databind.ObjectMapper 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.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.TokenRepository
import dev.dnpm.etl.processor.security.UserRoleRepository import dev.dnpm.etl.processor.security.UserRoleRepository
import dev.dnpm.etl.processor.services.RequestProcessor import dev.dnpm.etl.processor.services.RequestProcessor
import dev.pcvolkmer.mv64e.mtb.*
import org.junit.jupiter.api.BeforeEach import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Nested import org.junit.jupiter.api.Nested
import org.junit.jupiter.api.Test import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith import org.junit.jupiter.api.extension.ExtendWith
import org.mockito.junit.jupiter.MockitoExtension import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.any import org.mockito.kotlin.*
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.beans.factory.annotation.Autowired
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest 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.http.MediaType
import org.springframework.security.oauth2.client.registration.ClientRegistrationRepository 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.anonymous
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user
import org.springframework.test.context.ContextConfiguration import org.springframework.test.context.ContextConfiguration
import org.springframework.test.context.TestPropertySource 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.context.junit.jupiter.SpringExtension
import org.springframework.test.web.servlet.MockMvc import org.springframework.test.web.servlet.MockMvc
import org.springframework.test.web.servlet.delete import org.springframework.test.web.servlet.delete
import org.springframework.test.web.servlet.post import org.springframework.test.web.servlet.post
import java.time.Instant
import java.util.*
@WebMvcTest(controllers = [MtbFileRestController::class]) @WebMvcTest(controllers = [MtbFileRestController::class])
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class]) @ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
@ContextConfiguration( @ContextConfiguration(
classes = [ classes = [
MtbFileRestController::class, MtbFileRestController::class,
AppSecurityConfiguration::class AppSecurityConfiguration::class,
MtbFileConsentService::class
] ]
) )
@MockBean(TokenRepository::class, RequestProcessor::class) @MockitoBean(types = [TokenRepository::class, RequestProcessor::class, ConsentEvaluator::class])
@TestPropertySource( @TestPropertySource(
properties = [ properties = [
"app.pseudonymize.generator=BUILDIN", "app.pseudonymize.generator=BUILDIN",
@@ -68,17 +71,23 @@ import org.springframework.test.web.servlet.post
) )
class MtbFileRestControllerTest { class MtbFileRestControllerTest {
private lateinit var mockMvc: MockMvc lateinit var mockMvc: MockMvc
lateinit var requestProcessor: RequestProcessor
private lateinit var requestProcessor: RequestProcessor lateinit var consentEvaluator: ConsentEvaluator
@BeforeEach @BeforeEach
fun setup( fun setup(
@Autowired mockMvc: MockMvc, @Autowired mockMvc: MockMvc,
@Autowired requestProcessor: RequestProcessor @Autowired requestProcessor: RequestProcessor,
@Autowired consentEvaluator: ConsentEvaluator
) { ) {
this.mockMvc = mockMvc this.mockMvc = mockMvc
this.requestProcessor = requestProcessor this.requestProcessor = requestProcessor
this.consentEvaluator = consentEvaluator
doAnswer {
ConsentEvaluation(TtpConsentStatus.BROAD_CONSENT_GIVEN, true)
}.whenever(consentEvaluator).check(any())
} }
@Test @Test
@@ -91,7 +100,7 @@ class MtbFileRestControllerTest {
status { isAccepted() } status { isAccepted() }
} }
verify(requestProcessor, times(1)).processMtbFile(any()) verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
} }
@Test @Test
@@ -104,7 +113,7 @@ class MtbFileRestControllerTest {
status { isAccepted() } status { isAccepted() }
} }
verify(requestProcessor, times(1)).processMtbFile(any()) verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
} }
@Test @Test
@@ -117,7 +126,7 @@ class MtbFileRestControllerTest {
status { isUnauthorized() } status { isUnauthorized() }
} }
verify(requestProcessor, never()).processMtbFile(any()) verify(requestProcessor, never()).processMtbFile(any<Mtb>())
} }
@Test @Test
@@ -130,7 +139,7 @@ class MtbFileRestControllerTest {
status { isForbidden() } status { isForbidden() }
} }
verify(requestProcessor, never()).processMtbFile(any()) verify(requestProcessor, never()).processMtbFile(any<Mtb>())
} }
@Test @Test
@@ -141,7 +150,7 @@ class MtbFileRestControllerTest {
status { isAccepted() } status { isAccepted() }
} }
verify(requestProcessor, times(1)).processDeletion(anyValueClass()) verify(requestProcessor, times(1)).processDeletion(anyValueClass(), eq(TtpConsentStatus.UNKNOWN_CHECK_FILE))
} }
@Test @Test
@@ -152,11 +161,11 @@ class MtbFileRestControllerTest {
status { isUnauthorized() } status { isUnauthorized() }
} }
verify(requestProcessor, never()).processDeletion(anyValueClass()) verify(requestProcessor, never()).processDeletion(anyValueClass(), any())
} }
@Nested @Nested
@MockBean(UserRoleRepository::class, ClientRegistrationRepository::class) @MockitoBean(types = [UserRoleRepository::class, ClientRegistrationRepository::class])
@TestPropertySource( @TestPropertySource(
properties = [ properties = [
"app.pseudonymize.generator=BUILDIN", "app.pseudonymize.generator=BUILDIN",
@@ -177,7 +186,7 @@ class MtbFileRestControllerTest {
status { isAccepted() } status { isAccepted() }
} }
verify(requestProcessor, times(1)).processMtbFile(any()) verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
} }
@Test @Test
@@ -190,33 +199,26 @@ class MtbFileRestControllerTest {
status { isAccepted() } status { isAccepted() }
} }
verify(requestProcessor, times(1)).processMtbFile(any()) verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
} }
} }
companion object { companion object {
val mtbFile: MtbFile = MtbFile.builder() val mtbFile = Mtb.builder()
.withPatient( .patient(
Patient.builder() Patient.builder()
.withId("PID") .id("PID")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build() .build()
) )
.withConsent( .episodesOfCare(
Consent.builder() listOf(
.withId("1") MtbEpisodeOfCare.builder()
.withStatus(Consent.Status.ACTIVE) .id("1")
.withPatient("PID") .patient(Reference.builder().id("PID").build())
.build() .period(PeriodDate.builder().start(Date.from(Instant.parse("2023-08-08T02:00:00.00Z"))).build())
) .build()
.withEpisode( )
Episode.builder()
.withId("1")
.withPatient("PID")
.withPeriod(PeriodStart("2023-08-08"))
.build()
) )
.build() .build()

View File

@@ -27,8 +27,8 @@ import org.junit.jupiter.api.extension.ExtendWith
import org.springframework.beans.factory.annotation.Autowired import org.springframework.beans.factory.annotation.Autowired
import org.springframework.boot.test.autoconfigure.data.jdbc.DataJdbcTest import org.springframework.boot.test.autoconfigure.data.jdbc.DataJdbcTest
import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase 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.TestPropertySource
import org.springframework.test.context.bean.override.mockito.MockitoBean
import org.springframework.test.context.junit.jupiter.SpringExtension import org.springframework.test.context.junit.jupiter.SpringExtension
import org.springframework.transaction.annotation.Transactional import org.springframework.transaction.annotation.Transactional
import org.testcontainers.junit.jupiter.Testcontainers import org.testcontainers.junit.jupiter.Testcontainers
@@ -39,7 +39,7 @@ import java.time.Instant
@DataJdbcTest @DataJdbcTest
@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE) @AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE)
@Transactional @Transactional
@MockBean(MtbFileSender::class) @MockitoBean(types = [MtbFileSender::class])
@TestPropertySource( @TestPropertySource(
properties = [ properties = [
"app.pseudonymize.generator=buildin", "app.pseudonymize.generator=buildin",

View File

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

View File

@@ -31,8 +31,8 @@ import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith import org.junit.jupiter.api.extension.ExtendWith
import org.springframework.beans.factory.annotation.Autowired import org.springframework.beans.factory.annotation.Autowired
import org.springframework.boot.test.context.SpringBootTest import org.springframework.boot.test.context.SpringBootTest
import org.springframework.boot.test.mock.mockito.MockBean
import org.springframework.test.context.TestPropertySource 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.context.junit.jupiter.SpringExtension
import org.springframework.transaction.annotation.Transactional import org.springframework.transaction.annotation.Transactional
import org.testcontainers.junit.jupiter.Testcontainers import org.testcontainers.junit.jupiter.Testcontainers
@@ -42,7 +42,7 @@ import java.time.Instant
@ExtendWith(SpringExtension::class) @ExtendWith(SpringExtension::class)
@SpringBootTest @SpringBootTest
@Transactional @Transactional
@MockBean(MtbFileSender::class) @MockitoBean(types = [MtbFileSender::class])
@TestPropertySource( @TestPropertySource(
properties = [ properties = [
"app.pseudonymize.generator=buildin", "app.pseudonymize.generator=buildin",

View File

@@ -19,21 +19,22 @@
package dev.dnpm.etl.processor.web 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.AppConfiguration
import dev.dnpm.etl.processor.config.AppSecurityConfiguration import dev.dnpm.etl.processor.config.AppSecurityConfiguration
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult 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.GPasConnectionCheckService
import dev.dnpm.etl.processor.monitoring.RestConnectionCheckService import dev.dnpm.etl.processor.monitoring.RestConnectionCheckService
import dev.dnpm.etl.processor.output.MtbFileSender import dev.dnpm.etl.processor.output.MtbFileSender
import dev.dnpm.etl.processor.pseudonym.Generator import dev.dnpm.etl.processor.pseudonym.Generator
import dev.dnpm.etl.processor.security.Role import dev.dnpm.etl.processor.security.Role
import dev.dnpm.etl.processor.services.RequestProcessor
import dev.dnpm.etl.processor.security.TokenService import dev.dnpm.etl.processor.security.TokenService
import dev.dnpm.etl.processor.services.TransformationService
import dev.dnpm.etl.processor.security.UserRoleService import dev.dnpm.etl.processor.security.UserRoleService
import dev.dnpm.etl.processor.services.RequestProcessor
import dev.dnpm.etl.processor.services.TransformationService
import org.assertj.core.api.Assertions.assertThat import org.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.BeforeEach
import org.junit.jupiter.api.Nested import org.junit.jupiter.api.Nested
import org.junit.jupiter.api.Test import org.junit.jupiter.api.Test
@@ -46,7 +47,6 @@ import org.mockito.kotlin.verify
import org.mockito.kotlin.whenever import org.mockito.kotlin.whenever
import org.springframework.beans.factory.annotation.Autowired import org.springframework.beans.factory.annotation.Autowired
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest 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.HttpHeaders
import org.springframework.http.MediaType import org.springframework.http.MediaType
import org.springframework.http.MediaType.TEXT_EVENT_STREAM import org.springframework.http.MediaType.TEXT_EVENT_STREAM
@@ -55,6 +55,7 @@ import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequ
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user
import org.springframework.test.context.ContextConfiguration import org.springframework.test.context.ContextConfiguration
import org.springframework.test.context.TestPropertySource 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.context.junit.jupiter.SpringExtension
import org.springframework.test.web.reactive.server.WebTestClient import org.springframework.test.web.reactive.server.WebTestClient
import org.springframework.test.web.servlet.* import org.springframework.test.web.servlet.*
@@ -81,14 +82,17 @@ abstract class MockSink : Sinks.Many<Boolean>
"app.pseudonymize.generator=BUILDIN" "app.pseudonymize.generator=BUILDIN"
] ]
) )
@MockBean(name = "configsUpdateProducer", classes = [MockSink::class]) @MockitoBean(name = "configsUpdateProducer", types = [MockSink::class])
@MockBean( @MockitoBean(
Generator::class, types = [
MtbFileSender::class, Generator::class,
RequestProcessor::class, MtbFileSender::class,
TransformationService::class, RequestProcessor::class,
GPasConnectionCheckService::class, TransformationService::class,
RestConnectionCheckService::class, GPasConnectionCheckService::class,
RestConnectionCheckService::class,
GIcsConnectionCheckService::class
]
) )
class ConfigControllerTest { class ConfigControllerTest {
@@ -143,8 +147,10 @@ class ConfigControllerTest {
"app.security.admin-user=admin" "app.security.admin-user=admin"
] ]
) )
@MockBean( @MockitoBean(
TokenService::class types = [
TokenService::class
]
) )
inner class WithTokensEnabled { inner class WithTokensEnabled {
private lateinit var tokenService: TokenService private lateinit var tokenService: TokenService
@@ -178,7 +184,13 @@ class ConfigControllerTest {
@Test @Test
fun testShouldNotSaveTokenWithExstingName() { fun testShouldNotSaveTokenWithExstingName() {
whenever(tokenService.addToken(anyString())).thenReturn(Result.failure(RuntimeException("Testfailure"))) whenever(tokenService.addToken(anyString())).thenReturn(
Result.failure(
RuntimeException(
"Testfailure"
)
)
)
mockMvc.post("/configs/tokens") { mockMvc.post("/configs/tokens") {
with(user("admin").roles("ADMIN")) with(user("admin").roles("ADMIN"))
@@ -252,8 +264,10 @@ class ConfigControllerTest {
"app.security.admin-password={noop}very-secret" "app.security.admin-password={noop}very-secret"
] ]
) )
@MockBean( @MockitoBean(
UserRoleService::class types = [
UserRoleService::class
]
) )
inner class WithUserRolesEnabled { inner class WithUserRolesEnabled {
private lateinit var userRoleService: UserRoleService private lateinit var userRoleService: UserRoleService
@@ -297,7 +311,10 @@ class ConfigControllerTest {
val idCaptor = argumentCaptor<Long>() val idCaptor = argumentCaptor<Long>()
val roleCaptor = argumentCaptor<Role>() 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(idCaptor.firstValue).isEqualTo(42)
assertThat(roleCaptor.firstValue).isEqualTo(Role.ADMIN) assertThat(roleCaptor.firstValue).isEqualTo(Role.ADMIN)
@@ -335,23 +352,26 @@ class ConfigControllerTest {
@BeforeEach @BeforeEach
fun setup( fun setup(
applicationContext: WebApplicationContext, applicationContext: WebApplicationContext
) { ) {
this.webClient = MockMvcWebTestClient this.webClient = MockMvcWebTestClient
.bindToApplicationContext(applicationContext).build() .bindToApplicationContext(applicationContext).build()
} }
@Test @Test
fun testShouldRequestSSE() { fun testShouldRequestGPasSSE() {
val expectedEvent = ConnectionCheckResult.GPasConnectionCheckResult(true, Instant.now(), Instant.now()) val expectedEvent =
ConnectionCheckResult.GPasConnectionCheckResult(true, Instant.now(), Instant.now())
connectionCheckUpdateProducer.tryEmitNext(expectedEvent) connectionCheckUpdateProducer.tryEmitNext(expectedEvent)
connectionCheckUpdateProducer.emitComplete { _, _ -> true } connectionCheckUpdateProducer.emitComplete { _, _ -> true }
val result = webClient.get().uri("http://localhost/configs/events").accept(TEXT_EVENT_STREAM).exchange() val result =
.expectStatus().isOk() webClient.get().uri("http://localhost/configs/events").accept(TEXT_EVENT_STREAM)
.expectHeader().contentType(TEXT_EVENT_STREAM) .exchange()
.returnResult(ConnectionCheckResult.GPasConnectionCheckResult::class.java) .expectStatus().isOk()
.expectHeader().contentType(TEXT_EVENT_STREAM)
.returnResult(ConnectionCheckResult.GPasConnectionCheckResult::class.java)
StepVerifier.create(result.responseBody) StepVerifier.create(result.responseBody)
.expectNext(expectedEvent) .expectNext(expectedEvent)

View File

@@ -19,8 +19,6 @@
package dev.dnpm.etl.processor.web 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.*
import dev.dnpm.etl.processor.config.AppConfiguration import dev.dnpm.etl.processor.config.AppConfiguration
import dev.dnpm.etl.processor.config.AppSecurityConfiguration import dev.dnpm.etl.processor.config.AppSecurityConfiguration
@@ -30,6 +28,8 @@ import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.monitoring.RequestType import dev.dnpm.etl.processor.monitoring.RequestType
import dev.dnpm.etl.processor.services.RequestService import dev.dnpm.etl.processor.services.RequestService
import org.assertj.core.api.Assertions.assertThat 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.BeforeEach
import org.junit.jupiter.api.Nested import org.junit.jupiter.api.Nested
import org.junit.jupiter.api.Test import org.junit.jupiter.api.Test
@@ -40,13 +40,13 @@ import org.mockito.kotlin.any
import org.mockito.kotlin.whenever import org.mockito.kotlin.whenever
import org.springframework.beans.factory.annotation.Autowired import org.springframework.beans.factory.annotation.Autowired
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest 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.Page
import org.springframework.data.domain.PageImpl import org.springframework.data.domain.PageImpl
import org.springframework.data.domain.Pageable import org.springframework.data.domain.Pageable
import org.springframework.security.test.context.support.WithMockUser import org.springframework.security.test.context.support.WithMockUser
import org.springframework.test.context.ContextConfiguration import org.springframework.test.context.ContextConfiguration
import org.springframework.test.context.TestPropertySource 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.context.junit.jupiter.SpringExtension
import org.springframework.test.web.servlet.MockMvc import org.springframework.test.web.servlet.MockMvc
import org.springframework.test.web.servlet.get import org.springframework.test.web.servlet.get
@@ -71,8 +71,8 @@ import java.util.*
"app.security.admin-password={noop}very-secret" "app.security.admin-password={noop}very-secret"
] ]
) )
@MockBean( @MockitoBean(
RequestService::class types = [RequestService::class]
) )
class HomeControllerTest { class HomeControllerTest {
@@ -282,6 +282,30 @@ class HomeControllerTest {
assertThat(page.querySelectorAll("tbody tr")).isEmpty() assertThat(page.querySelectorAll("tbody tr")).isEmpty()
assertThat(page.querySelectorAll("div.notification.info")).hasSize(1) assertThat(page.querySelectorAll("div.notification.info")).hasSize(1)
} }
@Test
@WithMockUser(username = "admin", roles = ["ADMIN"])
fun testShouldShowNoConsentStatusBadge() {
whenever(requestService.findRequestByPatientId(anyValueClass(), any<Pageable>())).thenReturn(
PageImpl(
listOf(
Request(
1L,
randomRequestId(),
PatientPseudonym("PSEUDO1"),
PatientId("PATIENT1"),
Fingerprint("ashdkasdh"),
RequestType.MTB_FILE,
RequestStatus.NO_CONSENT
)
)
)
)
val page = webClient.getPage<HtmlPage>("http://localhost/patient/PSEUDO1")
assertThat(page.querySelectorAll("tbody tr")).hasSize(1)
assertThat(page.querySelectorAll("tbody tr > td > small").first().textContent).isEqualTo("NO_CONSENT")
}
} }
} }

View File

@@ -19,21 +19,21 @@
package dev.dnpm.etl.processor.web 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.AppConfiguration
import dev.dnpm.etl.processor.config.AppSecurityConfiguration import dev.dnpm.etl.processor.config.AppSecurityConfiguration
import dev.dnpm.etl.processor.security.TokenService import dev.dnpm.etl.processor.security.TokenService
import org.assertj.core.api.Assertions.assertThat 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.BeforeEach
import org.junit.jupiter.api.Test import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith import org.junit.jupiter.api.extension.ExtendWith
import org.mockito.junit.jupiter.MockitoExtension import org.mockito.junit.jupiter.MockitoExtension
import org.springframework.beans.factory.annotation.Autowired import org.springframework.beans.factory.annotation.Autowired
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest 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.ContextConfiguration
import org.springframework.test.context.TestPropertySource 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.context.junit.jupiter.SpringExtension
import org.springframework.test.web.servlet.MockMvc import org.springframework.test.web.servlet.MockMvc
import org.springframework.test.web.servlet.get import org.springframework.test.web.servlet.get
@@ -56,8 +56,8 @@ import org.springframework.test.web.servlet.htmlunit.MockMvcWebClientBuilder
"app.security.enable-tokens=true" "app.security.enable-tokens=true"
] ]
) )
@MockBean( @MockitoBean(
TokenService::class, types = [TokenService::class]
) )
class LoginControllerTest { class LoginControllerTest {

View File

@@ -19,9 +19,9 @@
package dev.dnpm.etl.processor.web package dev.dnpm.etl.processor.web
import com.gargoylesoftware.htmlunit.WebClient
import dev.dnpm.etl.processor.config.AppConfiguration import dev.dnpm.etl.processor.config.AppConfiguration
import dev.dnpm.etl.processor.config.AppSecurityConfiguration import dev.dnpm.etl.processor.config.AppSecurityConfiguration
import org.htmlunit.WebClient
import org.junit.jupiter.api.BeforeEach import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Test import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith import org.junit.jupiter.api.extension.ExtendWith

View File

@@ -41,10 +41,10 @@ import org.mockito.kotlin.doAnswer
import org.mockito.kotlin.whenever import org.mockito.kotlin.whenever
import org.springframework.beans.factory.annotation.Autowired import org.springframework.beans.factory.annotation.Autowired
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest 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.http.MediaType.TEXT_EVENT_STREAM
import org.springframework.test.context.ContextConfiguration import org.springframework.test.context.ContextConfiguration
import org.springframework.test.context.TestPropertySource 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.context.junit.jupiter.SpringExtension
import org.springframework.test.web.reactive.server.WebTestClient import org.springframework.test.web.reactive.server.WebTestClient
import org.springframework.test.web.servlet.MockMvc import org.springframework.test.web.servlet.MockMvc
@@ -74,8 +74,8 @@ import java.time.temporal.ChronoUnit
"app.security.admin-password={noop}very-secret" "app.security.admin-password={noop}very-secret"
] ]
) )
@MockBean( @MockitoBean(
RequestService::class types = [RequestService::class]
) )
class StatisticsRestControllerTest { class StatisticsRestControllerTest {

View File

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

View File

@@ -0,0 +1,339 @@
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;
private final String BROAD_CONSENT_PROFILE_URI = "https://www.medizininformatik-initiative.de/fhir/modul-consent/StructureDefinition/mii-pr-consent-einwilligung";
private final String BROAD_CONSENT_POLICY = "urn:oid:2.16.840.1.113883.3.1937.777.24.2.1791";
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) {
Bundle gIcsResultBundle = currentConsentForPersonAndTemplate(patientId, consentDomain, requestDate);
if (ConsentDomain.BROAD_CONSENT == consentDomain) {
return convertGicsResultToMiiBroadConsent(gIcsResultBundle);
}
return gIcsResultBundle;
}
protected Bundle convertGicsResultToMiiBroadConsent(Bundle gIcsResultBundle) {
if (gIcsResultBundle == null
|| gIcsResultBundle.getEntry().isEmpty()
|| !(gIcsResultBundle.getEntry().getFirst().getResource() instanceof Consent))
return gIcsResultBundle;
Bundle.BundleEntryComponent bundleEntryComponent = gIcsResultBundle.getEntry().getFirst();
var consentAsOne = (Consent) bundleEntryComponent.getResource();
if (consentAsOne.getPolicy().stream().noneMatch(p -> p.getUri().equals(BROAD_CONSENT_POLICY))) {
consentAsOne.addPolicy(new Consent.ConsentPolicyComponent().setUri(BROAD_CONSENT_POLICY));
}
if (consentAsOne.getMeta().getProfile().stream().noneMatch(p -> p.getValue().equals(BROAD_CONSENT_PROFILE_URI))) {
consentAsOne.getMeta().addProfile(BROAD_CONSENT_PROFILE_URI);
}
consentAsOne.setPolicyRule(null);
gIcsResultBundle.getEntry().stream().skip(1).forEach(c -> consentAsOne.getProvision().addProvision(((Consent) c.getResource()).getProvision().getProvisionFirstRep()));
gIcsResultBundle.getEntry().clear();
gIcsResultBundle.addEntry(bundleEntryComponent);
return gIcsResultBundle;
}
}

View File

@@ -0,0 +1,27 @@
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);
}

View File

@@ -0,0 +1,31 @@
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();
}
}

View File

@@ -0,0 +1,38 @@
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
}

View File

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

View File

@@ -21,8 +21,11 @@ package dev.dnpm.etl.processor.pseudonym;
import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.IParser; import ca.uhn.fhir.parser.IParser;
import dev.dnpm.etl.processor.config.AppFhirConfig;
import dev.dnpm.etl.processor.config.GPasConfigProperties; import dev.dnpm.etl.processor.config.GPasConfigProperties;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.StringUtils; 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.Identifier;
import org.hl7.fhir.r4.model.Parameters; import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent; import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
@@ -32,42 +35,78 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import org.springframework.http.*; import org.springframework.http.*;
import org.springframework.retry.support.RetryTemplate; 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.RestTemplate; import org.springframework.web.client.RestTemplate;
import java.net.URI;
import java.net.URISyntaxException;
public class GpasPseudonymGenerator implements Generator { public class GpasPseudonymGenerator implements Generator {
private final static FhirContext r4Context = FhirContext.forR4(); private final FhirContext r4Context;
private final String gPasUrl; private final String gPasUrl;
private final String psnTargetDomain;
private final HttpHeaders httpHeader; private final HttpHeaders httpHeader;
private final RetryTemplate retryTemplate; private final RetryTemplate retryTemplate;
private final Logger log = LoggerFactory.getLogger(GpasPseudonymGenerator.class); private final Logger log = LoggerFactory.getLogger(GpasPseudonymGenerator.class);
private final RestTemplate restTemplate; private final RestTemplate restTemplate;
private final @NotNull String genomDeTanDomain;
private final @NotNull String pidPsnDomain;
protected static final String CREATE_OR_GET_PSN = "$pseudonymizeAllowCreate";
protected static final String CREATE_MULTI_DOMAIN_PSN = "$pseudonymize-secondary";
private static final String SINGLE_PSN_PART_NAME = "pseudonym";
private static final String MULTI_PSN_PART_NAME = "value";
public GpasPseudonymGenerator(GPasConfigProperties gpasCfg, RetryTemplate retryTemplate, RestTemplate restTemplate) { public GpasPseudonymGenerator(GPasConfigProperties gpasCfg, RetryTemplate retryTemplate,
RestTemplate restTemplate, AppFhirConfig appFhirConfig) {
this.retryTemplate = retryTemplate; this.retryTemplate = retryTemplate;
this.restTemplate = restTemplate; this.restTemplate = restTemplate;
this.gPasUrl = gpasCfg.getUri(); this.gPasUrl = gpasCfg.getUri();
this.psnTargetDomain = gpasCfg.getTarget(); this.pidPsnDomain = gpasCfg.getPatientDomain();
this.genomDeTanDomain = gpasCfg.getGenomDeTanDomain();
this.r4Context = appFhirConfig.fhirContext();
httpHeader = getHttpHeaders(gpasCfg.getUsername(), gpasCfg.getPassword()); httpHeader = getHttpHeaders(gpasCfg.getUsername(), gpasCfg.getPassword());
log.debug(String.format("%s has been initialized", this.getClass().getName())); log.debug("{} has been initialized", this.getClass().getName());
} }
@Override @Override
public String generate(String id) { public String generate(String id) {
var gPasRequestBody = getGpasRequestBody(id); return generate(id, PsnDomainType.SINGLE_PSN_DOMAIN);
var responseEntity = getGpasPseudonym(gPasRequestBody); }
var gPasPseudonymResult = (Parameters) r4Context.newJsonParser()
.parseResource(responseEntity.getBody());
return unwrapPseudonym(gPasPseudonymResult); @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, CREATE_OR_GET_PSN);
final 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, CREATE_MULTI_DOMAIN_PSN);
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));
} }
@NotNull @NotNull
public static String unwrapPseudonym(Parameters gPasPseudonymResult) { public static String unwrapPseudonym(Parameters gPasPseudonymResult, String targetPartName) {
final var parameters = gPasPseudonymResult.getParameter().stream().findFirst(); final var parameters = gPasPseudonymResult.getParameter().stream().findFirst();
if (parameters.isEmpty()) { if (parameters.isEmpty()) {
@@ -75,9 +114,9 @@ public class GpasPseudonymGenerator implements Generator {
} }
final var identifier = (Identifier) parameters.get().getPart().stream() final var identifier = (Identifier) parameters.get().getPart().stream()
.filter(a -> a.getName().equals("pseudonym")) .filter(a -> a.getName().equals(targetPartName))
.findFirst() .findFirst()
.orElseGet(ParametersParameterComponent::new).getValue(); .orElseGet(ParametersParameterComponent::new).getValue();
// pseudonym // pseudonym
return sanitizeValue(identifier.getValue()); return sanitizeValue(identifier.getValue());
@@ -97,42 +136,79 @@ public class GpasPseudonymGenerator implements Generator {
return psnValue.replaceAll(forbiddenCharsRegex, "_"); return psnValue.replaceAll(forbiddenCharsRegex, "_");
} }
@NotNull @NotNull
protected ResponseEntity<String> getGpasPseudonym(String gPasRequestBody) { protected ResponseEntity<String> getGpasPseudonym(String gPasRequestBody, String apiEndpoint) {
HttpEntity<String> requestEntity = new HttpEntity<>(gPasRequestBody, this.httpHeader); HttpEntity<String> requestEntity = new HttpEntity<>(gPasRequestBody, this.httpHeader);
ResponseEntity<String> responseEntity;
try { try {
responseEntity = retryTemplate.execute( var targetUrl = buildRequestUrl(apiEndpoint);
ctx -> restTemplate.exchange(gPasUrl, HttpMethod.POST, requestEntity, ResponseEntity<String> responseEntity = retryTemplate.execute(
String.class)); ctx -> restTemplate.exchange(targetUrl, HttpMethod.POST, requestEntity,
String.class));
if (responseEntity.getStatusCode().is2xxSuccessful()) { if (responseEntity.getStatusCode().is2xxSuccessful()) {
log.debug("API request succeeded. Response: {}", responseEntity.getStatusCode()); log.debug("API request succeeded. Response: {}", responseEntity.getStatusCode());
} else { return responseEntity;
log.warn("API request unsuccessful. Response: {}", requestEntity.getBody());
throw new PseudonymRequestFailed("API request unsuccessful gPas unsuccessful.");
} }
} catch (BadRequest e) {
return responseEntity; String msg = "gPas or request configuration is incorrect. Please check both."
} catch (Exception unexpected) { + e.getMessage();
throw new PseudonymRequestFailed( log.error(msg);
"API request due unexpected error unsuccessful gPas unsuccessful.", unexpected); throw new PseudonymRequestFailed(msg, e);
} catch (Unauthorized e) {
var msg = "gPas access credentials are invalid check your configuration. msg: '%s"
.formatted(e.getMessage());
log.error(msg);
throw new PseudonymRequestFailed(msg, e);
} }
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 String getGpasRequestBody(String id) { protected URI buildRequestUrl(String apiEndpoint) throws URISyntaxException {
var requestParameters = new Parameters(); 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();
requestParameters.addParameter().setName("target") requestParameters.addParameter().setName("target")
.setValue(new StringType().setValue(psnTargetDomain)); .setValue(new StringType().setValue(targetDomain));
requestParameters.addParameter().setName("original") requestParameters.addParameter().setName("original")
.setValue(new StringType().setValue(id)); .setValue(new StringType().setValue(id));
final IParser iParser = r4Context.newJsonParser(); final IParser iParser = r4Context.newJsonParser();
return iParser.encodeResourceToString(requestParameters); 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 @NotNull
protected HttpHeaders getHttpHeaders(String gPasUserName, String gPasPassword) { protected HttpHeaders getHttpHeaders(String gPasUserName, String gPasPassword) {
var headers = new HttpHeaders(); var headers = new HttpHeaders();

View File

@@ -0,0 +1,12 @@
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
}

View File

@@ -1,7 +1,7 @@
/* /*
* This file is part of ETL-Processor * This file is part of ETL-Processor
* *
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors * Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* *
* This program is free software: you can redistribute it and/or modify * This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published * it under the terms of the GNU Affero General Public License as published
@@ -21,19 +21,13 @@ package dev.dnpm.etl.processor.config
import dev.dnpm.etl.processor.security.Role import dev.dnpm.etl.processor.security.Role
import org.springframework.boot.context.properties.ConfigurationProperties import org.springframework.boot.context.properties.ConfigurationProperties
import org.springframework.boot.context.properties.DeprecatedConfigurationProperty
@ConfigurationProperties(AppConfigProperties.NAME) @ConfigurationProperties(AppConfigProperties.NAME)
data class AppConfigProperties( data class AppConfigProperties(
var bwhcUri: String?,
@get:DeprecatedConfigurationProperty(
reason = "Deprecated in favor of 'app.pseudonymize.generator'",
replacement = "app.pseudonymize.generator"
)
var pseudonymizer: PseudonymGenerator = PseudonymGenerator.BUILDIN,
var transformations: List<TransformationProperties> = listOf(), var transformations: List<TransformationProperties> = listOf(),
var maxRetryAttempts: Int = 3, var maxRetryAttempts: Int = 3,
var duplicationDetection: Boolean = true var duplicationDetection: Boolean = true,
var genomDeTestSubmission: Boolean = false
) { ) {
companion object { companion object {
const val NAME = "app" const val NAME = "app"
@@ -53,25 +47,87 @@ data class PseudonymizeConfigProperties(
@ConfigurationProperties(GPasConfigProperties.NAME) @ConfigurationProperties(GPasConfigProperties.NAME)
data class GPasConfigProperties( data class GPasConfigProperties(
val uri: String?, val uri: String?,
val target: String = "etl-processor", val patientDomain: String = "etl-processor",
val genomDeTanDomain: String = "ccdn",
val username: String?, val username: String?,
val password: String?, val password: String?,
@get:DeprecatedConfigurationProperty(
reason = "Deprecated in favor of including Root CA"
)
val sslCaLocation: String?
) { ) {
companion object { companion object {
const val NAME = "app.pseudonymize.gpas" 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) @ConfigurationProperties(RestTargetProperties.NAME)
data class RestTargetProperties( data class RestTargetProperties(
val uri: String?, val uri: String?,
val username: String?, val username: String?,
val password: String?, val password: String?
val isBwhc: Boolean = false,
) { ) {
companion object { companion object {
const val NAME = "app.rest" const val NAME = "app.rest"
@@ -82,18 +138,8 @@ data class RestTargetProperties(
data class KafkaProperties( data class KafkaProperties(
val inputTopic: String?, val inputTopic: String?,
val outputTopic: String = "etl-processor", val outputTopic: String = "etl-processor",
@get:DeprecatedConfigurationProperty(
reason = "Deprecated",
replacement = "outputTopic"
)
val topic: String = outputTopic,
val outputResponseTopic: String = "${outputTopic}_response", val outputResponseTopic: String = "${outputTopic}_response",
@get:DeprecatedConfigurationProperty( val groupId: String = "${outputTopic}_group",
reason = "Deprecated",
replacement = "outputResponseTopic"
)
val responseTopic: String = outputResponseTopic,
val groupId: String = "${topic}_group",
val servers: String = "" val servers: String = ""
) { ) {
companion object { companion object {
@@ -119,8 +165,13 @@ enum class PseudonymGenerator {
GPAS GPAS
} }
enum class ConsentService {
NONE,
GICS
}
data class TransformationProperties( data class TransformationProperties(
val path: String, val path: String,
val from: String, val from: String,
val to: String val to: String
) )

View File

@@ -1,7 +1,7 @@
/* /*
* This file is part of ETL-Processor * This file is part of ETL-Processor
* *
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors * Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* *
* This program is free software: you can redistribute it and/or modify * This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published * it under the terms of the GNU Affero General Public License as published
@@ -20,32 +20,29 @@
package dev.dnpm.etl.processor.config package dev.dnpm.etl.processor.config
import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult import dev.dnpm.etl.processor.consent.MtbFileConsentService
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService import dev.dnpm.etl.processor.consent.GicsConsentService
import dev.dnpm.etl.processor.monitoring.GPasConnectionCheckService import dev.dnpm.etl.processor.consent.IConsentService
import dev.dnpm.etl.processor.monitoring.ReportService import dev.dnpm.etl.processor.monitoring.*
import dev.dnpm.etl.processor.pseudonym.AnonymizingGenerator import dev.dnpm.etl.processor.pseudonym.AnonymizingGenerator
import dev.dnpm.etl.processor.pseudonym.Generator import dev.dnpm.etl.processor.pseudonym.Generator
import dev.dnpm.etl.processor.pseudonym.GpasPseudonymGenerator import dev.dnpm.etl.processor.pseudonym.GpasPseudonymGenerator
import dev.dnpm.etl.processor.pseudonym.PseudonymizeService import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
import dev.dnpm.etl.processor.security.TokenRepository import dev.dnpm.etl.processor.security.TokenRepository
import dev.dnpm.etl.processor.security.TokenService 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.Transformation
import dev.dnpm.etl.processor.services.TransformationService 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.slf4j.LoggerFactory
import org.springframework.boot.autoconfigure.condition.AnyNestedCondition
import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty
import org.springframework.boot.context.properties.EnableConfigurationProperties import org.springframework.boot.context.properties.EnableConfigurationProperties
import org.springframework.context.annotation.Bean import org.springframework.context.annotation.Bean
import org.springframework.context.annotation.Conditional
import org.springframework.context.annotation.Configuration import org.springframework.context.annotation.Configuration
import org.springframework.context.annotation.ConfigurationCondition
import org.springframework.data.jdbc.repository.config.AbstractJdbcConfiguration import org.springframework.data.jdbc.repository.config.AbstractJdbcConfiguration
import org.springframework.http.client.HttpComponentsClientHttpRequestFactory
import org.springframework.retry.RetryCallback import org.springframework.retry.RetryCallback
import org.springframework.retry.RetryContext import org.springframework.retry.RetryContext
import org.springframework.retry.RetryListener import org.springframework.retry.RetryListener
@@ -58,13 +55,6 @@ import org.springframework.security.provisioning.InMemoryUserDetailsManager
import org.springframework.web.client.HttpClientErrorException import org.springframework.web.client.HttpClientErrorException
import org.springframework.web.client.RestTemplate import org.springframework.web.client.RestTemplate
import reactor.core.publisher.Sinks 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.Duration.Companion.seconds
import kotlin.time.toJavaDuration import kotlin.time.toJavaDuration
@@ -74,7 +64,9 @@ import kotlin.time.toJavaDuration
value = [ value = [
AppConfigProperties::class, AppConfigProperties::class,
PseudonymizeConfigProperties::class, PseudonymizeConfigProperties::class,
GPasConfigProperties::class GPasConfigProperties::class,
ConsentConfigProperties::class,
GIcsConfigProperties::class
] ]
) )
@EnableScheduling @EnableScheduling
@@ -87,113 +79,31 @@ class AppConfiguration {
return RestTemplate() return RestTemplate()
} }
@Bean
fun appFhirConfig(): AppFhirConfig {
return AppFhirConfig()
}
@ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "GPAS") @ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "GPAS")
@Bean @Bean
fun gpasPseudonymGenerator(configProperties: GPasConfigProperties, retryTemplate: RetryTemplate, restTemplate: RestTemplate): Generator { fun gpasPseudonymGenerator(
try { configProperties: GPasConfigProperties,
if (!configProperties.sslCaLocation.isNullOrBlank()) { retryTemplate: RetryTemplate,
return GpasPseudonymGenerator( restTemplate: RestTemplate,
configProperties, appFhirConfig: AppFhirConfig
retryTemplate, ): Generator {
createCustomGpasRestTemplate(configProperties) logger.info("Selected 'GpasPseudonym Generator'")
) return GpasPseudonymGenerator(configProperties, retryTemplate, restTemplate, appFhirConfig)
}
} catch (e: Exception) {
throw RuntimeException(e)
}
return GpasPseudonymGenerator(configProperties, retryTemplate, restTemplate)
} }
@ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "BUILDIN", matchIfMissing = true) @ConditionalOnProperty(
value = ["app.pseudonymize.generator"],
havingValue = "BUILDIN",
matchIfMissing = true
)
@Bean @Bean
fun buildinPseudonymGenerator(): Generator { fun buildinPseudonymGenerator(): Generator {
return AnonymizingGenerator() logger.info("Selected 'BUILDIN Pseudonym Generator'")
}
@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() return AnonymizingGenerator()
} }
@@ -206,17 +116,21 @@ class AppConfiguration {
} }
@Bean @Bean
fun reportService(objectMapper: ObjectMapper): ReportService { fun reportService(): ReportService {
return ReportService(objectMapper) return ReportService(getObjectMapper())
}
@Bean
fun getObjectMapper(): ObjectMapper {
return JacksonConfig().objectMapper()
} }
@Bean @Bean
fun transformationService( fun transformationService(
objectMapper: ObjectMapper,
configProperties: AppConfigProperties configProperties: AppConfigProperties
): TransformationService { ): TransformationService {
logger.info("Apply ${configProperties.transformations.size} transformation rules") logger.info("Apply ${configProperties.transformations.size} transformation rules")
return TransformationService(objectMapper, configProperties.transformations.map { return TransformationService(getObjectMapper(), configProperties.transformations.map {
Transformation.of(it.path) from it.from to it.to Transformation.of(it.path) from it.from to it.to
}) })
} }
@@ -235,7 +149,11 @@ class AppConfiguration {
callback: RetryCallback<T, E>, callback: RetryCallback<T, E>,
throwable: Throwable throwable: Throwable
) { ) {
logger.warn("Error occured: {}. Retrying {}", throwable.message, context.retryCount) logger.warn(
"Error occured: {}. Retrying {}",
throwable.message,
context.retryCount
)
} }
}) })
.build() .build()
@@ -243,7 +161,11 @@ class AppConfiguration {
@ConditionalOnProperty(value = ["app.security.enable-tokens"], havingValue = "true") @ConditionalOnProperty(value = ["app.security.enable-tokens"], havingValue = "true")
@Bean @Bean
fun tokenService(userDetailsManager: InMemoryUserDetailsManager, passwordEncoder: PasswordEncoder, tokenRepository: TokenRepository): TokenService { fun tokenService(
userDetailsManager: InMemoryUserDetailsManager,
passwordEncoder: PasswordEncoder,
tokenRepository: TokenRepository
): TokenService {
return TokenService(userDetailsManager, passwordEncoder, tokenRepository) return TokenService(userDetailsManager, passwordEncoder, tokenRepository)
} }
@@ -264,7 +186,11 @@ class AppConfiguration {
gPasConfigProperties: GPasConfigProperties, gPasConfigProperties: GPasConfigProperties,
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult> connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
): ConnectionCheckService { ): ConnectionCheckService {
return GPasConnectionCheckService(restTemplate, gPasConfigProperties, connectionCheckUpdateProducer) return GPasConnectionCheckService(
restTemplate,
gPasConfigProperties,
connectionCheckUpdateProducer
)
} }
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS") @ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS")
@@ -275,12 +201,81 @@ class AppConfiguration {
gPasConfigProperties: GPasConfigProperties, gPasConfigProperties: GPasConfigProperties,
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult> connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
): ConnectionCheckService { ): ConnectionCheckService {
return GPasConnectionCheckService(restTemplate, gPasConfigProperties, connectionCheckUpdateProducer) return GPasConnectionCheckService(
restTemplate,
gPasConfigProperties,
connectionCheckUpdateProducer
)
} }
@Bean @Bean
fun jdbcConfiguration(): AbstractJdbcConfiguration { fun jdbcConfiguration(): AbstractJdbcConfiguration {
return AppJdbcConfiguration() 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
}
}

View File

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

View File

@@ -1,7 +1,7 @@
/* /*
* This file is part of ETL-Processor * This file is part of ETL-Processor
* *
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors * Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* *
* This program is free software: you can redistribute it and/or modify * This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published * it under the terms of the GNU Affero General Public License as published
@@ -20,6 +20,7 @@
package dev.dnpm.etl.processor.config package dev.dnpm.etl.processor.config
import com.fasterxml.jackson.databind.ObjectMapper 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.input.KafkaInputListener
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
@@ -71,7 +72,7 @@ class AppKafkaConfiguration {
kafkaProperties: KafkaProperties, kafkaProperties: KafkaProperties,
kafkaResponseProcessor: KafkaResponseProcessor kafkaResponseProcessor: KafkaResponseProcessor
): KafkaMessageListenerContainer<String, String> { ): KafkaMessageListenerContainer<String, String> {
val containerProperties = ContainerProperties(kafkaProperties.responseTopic) val containerProperties = ContainerProperties(kafkaProperties.outputResponseTopic)
containerProperties.messageListener = kafkaResponseProcessor containerProperties.messageListener = kafkaResponseProcessor
return KafkaMessageListenerContainer(consumerFactory, containerProperties) return KafkaMessageListenerContainer(consumerFactory, containerProperties)
} }
@@ -100,9 +101,10 @@ class AppKafkaConfiguration {
@ConditionalOnProperty(value = ["app.kafka.input-topic"]) @ConditionalOnProperty(value = ["app.kafka.input-topic"])
fun kafkaInputListener( fun kafkaInputListener(
requestProcessor: RequestProcessor, requestProcessor: RequestProcessor,
objectMapper: ObjectMapper objectMapper: ObjectMapper,
consentEvaluator: ConsentEvaluator
): KafkaInputListener { ): KafkaInputListener {
return KafkaInputListener(requestProcessor, objectMapper) return KafkaInputListener(requestProcessor, consentEvaluator, objectMapper)
} }
@Bean @Bean
@@ -113,4 +115,4 @@ class AppKafkaConfiguration {
return KafkaConnectionCheckService(consumerFactory.createConsumer(), connectionCheckUpdateProducer) return KafkaConnectionCheckService(consumerFactory.createConsumer(), connectionCheckUpdateProducer)
} }
} }

View File

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

View File

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

View File

@@ -0,0 +1,18 @@
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
}
}

View File

@@ -0,0 +1,15 @@
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)
}
}

View File

@@ -0,0 +1,12 @@
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())
}
}

View File

@@ -0,0 +1,27 @@
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()
)
}

View File

@@ -0,0 +1,66 @@
/*
* 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
}
}

View File

@@ -1,7 +1,7 @@
/* /*
* This file is part of ETL-Processor * This file is part of ETL-Processor
* *
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors * Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* *
* This program is free software: you can redistribute it and/or modify * This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published * it under the terms of the GNU Affero General Public License as published
@@ -20,32 +20,56 @@
package dev.dnpm.etl.processor.input package dev.dnpm.etl.processor.input
import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.Consent import dev.dnpm.etl.processor.CustomMediaType
import de.ukw.ccc.bwhc.dto.MtbFile
import dev.dnpm.etl.processor.PatientId import dev.dnpm.etl.processor.PatientId
import dev.dnpm.etl.processor.RequestId 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.dnpm.etl.processor.services.RequestProcessor
import dev.pcvolkmer.mv64e.mtb.Mtb
import org.apache.kafka.clients.consumer.ConsumerRecord import org.apache.kafka.clients.consumer.ConsumerRecord
import org.slf4j.LoggerFactory import org.slf4j.LoggerFactory
import org.springframework.http.MediaType
import org.springframework.kafka.listener.MessageListener import org.springframework.kafka.listener.MessageListener
import java.nio.charset.Charset
class KafkaInputListener( class KafkaInputListener(
private val requestProcessor: RequestProcessor, private val requestProcessor: RequestProcessor,
private val consentEvaluator: ConsentEvaluator,
private val objectMapper: ObjectMapper private val objectMapper: ObjectMapper
) : MessageListener<String, String> { ) : MessageListener<String, String> {
private val logger = LoggerFactory.getLogger(KafkaInputListener::class.java) private val logger = LoggerFactory.getLogger(KafkaInputListener::class.java)
override fun onMessage(data: ConsumerRecord<String, String>) { override fun onMessage(record: ConsumerRecord<String, String>) {
val mtbFile = objectMapper.readValue(data.value(), MtbFile::class.java) 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()?.toString(Charset.forName("UTF-8"))
}
private fun handleDnpmV2Message(record: ConsumerRecord<String, String>) {
val mtbFile = objectMapper.readValue(record.value(), Mtb::class.java)
val patientId = PatientId(mtbFile.patient.id) val patientId = PatientId(mtbFile.patient.id)
val firstRequestIdHeader = data.headers().headers("requestId")?.firstOrNull() val firstRequestIdHeader = record.headers().headers("requestId")?.firstOrNull()
val requestId = if (null != firstRequestIdHeader) { val requestId = if (null != firstRequestIdHeader) {
RequestId(String(firstRequestIdHeader.value())) RequestId(String(firstRequestIdHeader.value()))
} else { } else {
RequestId("") RequestId("")
} }
if (mtbFile.consent.status == Consent.Status.ACTIVE) { if (consentEvaluator.check(mtbFile).hasConsent()) {
logger.debug("Accepted MTB File for processing") logger.debug("Accepted MTB File for processing")
if (requestId.isBlank()) { if (requestId.isBlank()) {
requestProcessor.processMtbFile(mtbFile) requestProcessor.processMtbFile(mtbFile)
@@ -55,10 +79,15 @@ class KafkaInputListener(
} else { } else {
logger.debug("Accepted MTB File and process deletion") logger.debug("Accepted MTB File and process deletion")
if (requestId.isBlank()) { if (requestId.isBlank()) {
requestProcessor.processDeletion(patientId) requestProcessor.processDeletion(patientId, TtpConsentStatus.UNKNOWN_CHECK_FILE)
} else { } else {
requestProcessor.processDeletion(patientId, requestId) requestProcessor.processDeletion(
patientId,
requestId,
TtpConsentStatus.UNKNOWN_CHECK_FILE
)
} }
} }
} }
}
}

View File

@@ -19,11 +19,14 @@
package dev.dnpm.etl.processor.input package dev.dnpm.etl.processor.input
import de.ukw.ccc.bwhc.dto.Consent import dev.dnpm.etl.processor.CustomMediaType
import de.ukw.ccc.bwhc.dto.MtbFile
import dev.dnpm.etl.processor.PatientId 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.dnpm.etl.processor.services.RequestProcessor
import dev.pcvolkmer.mv64e.mtb.Mtb
import org.slf4j.LoggerFactory import org.slf4j.LoggerFactory
import org.springframework.http.MediaType
import org.springframework.http.ResponseEntity import org.springframework.http.ResponseEntity
import org.springframework.web.bind.annotation.* import org.springframework.web.bind.annotation.*
@@ -31,8 +34,8 @@ import org.springframework.web.bind.annotation.*
@RequestMapping(path = ["mtbfile", "mtb"]) @RequestMapping(path = ["mtbfile", "mtb"])
class MtbFileRestController( class MtbFileRestController(
private val requestProcessor: RequestProcessor, private val requestProcessor: RequestProcessor,
private val consentEvaluator: ConsentEvaluator
) { ) {
private val logger = LoggerFactory.getLogger(MtbFileRestController::class.java) private val logger = LoggerFactory.getLogger(MtbFileRestController::class.java)
@GetMapping @GetMapping
@@ -40,15 +43,16 @@ class MtbFileRestController(
return ResponseEntity.ok("Test") return ResponseEntity.ok("Test")
} }
@PostMapping @PostMapping(consumes = [MediaType.APPLICATION_JSON_VALUE, CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE])
fun mtbFile(@RequestBody mtbFile: MtbFile): ResponseEntity<Unit> { fun mtbFile(@RequestBody mtbFile: Mtb): ResponseEntity<Unit> {
if (mtbFile.consent.status == Consent.Status.ACTIVE) { val consentEvaluation = consentEvaluator.check(mtbFile)
logger.debug("Accepted MTB File for processing") if (consentEvaluation.hasConsent()) {
logger.debug("Accepted MTB File (DNPM V2) for processing")
requestProcessor.processMtbFile(mtbFile) requestProcessor.processMtbFile(mtbFile)
} else { } else {
logger.debug("Accepted MTB File and process deletion") logger.debug("Accepted MTB File (DNPM V2) and process deletion")
val patientId = PatientId(mtbFile.patient.id) val patientId = PatientId(mtbFile.patient.id)
requestProcessor.processDeletion(patientId) requestProcessor.processDeletion(patientId, consentEvaluation.getStatus())
} }
return ResponseEntity.accepted().build() return ResponseEntity.accepted().build()
} }
@@ -56,8 +60,8 @@ class MtbFileRestController(
@DeleteMapping(path = ["{patientId}"]) @DeleteMapping(path = ["{patientId}"])
fun deleteData(@PathVariable patientId: String): ResponseEntity<Unit> { fun deleteData(@PathVariable patientId: String): ResponseEntity<Unit> {
logger.debug("Accepted patient ID to process deletion") logger.debug("Accepted patient ID to process deletion")
requestProcessor.processDeletion(PatientId(patientId)) requestProcessor.processDeletion(PatientId(patientId), TtpConsentStatus.UNKNOWN_CHECK_FILE)
return ResponseEntity.accepted().build() return ResponseEntity.accepted().build()
} }
} }

View File

@@ -20,6 +20,7 @@
package dev.dnpm.etl.processor.monitoring 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.GPasConfigProperties
import dev.dnpm.etl.processor.config.RestTargetProperties import dev.dnpm.etl.processor.config.RestTargetProperties
import jakarta.annotation.PostConstruct import jakarta.annotation.PostConstruct
@@ -68,6 +69,12 @@ sealed class ConnectionCheckResult {
override val timestamp: Instant, override val timestamp: Instant,
override val lastChange: Instant override val lastChange: Instant
) : ConnectionCheckResult() ) : ConnectionCheckResult()
data class GIcsConnectionCheckResult(
override val available: Boolean,
override val timestamp: Instant,
override val lastChange: Instant
) : ConnectionCheckResult()
} }
class KafkaConnectionCheckService( class KafkaConnectionCheckService(
@@ -121,15 +128,11 @@ class RestConnectionCheckService(
fun check() { fun check() {
result = try { result = try {
val available = restTemplate.getForEntity( val available = restTemplate.getForEntity(
if (restTargetProperties.isBwhc) { UriComponentsBuilder.fromUriString(restTargetProperties.uri.toString())
UriComponentsBuilder.fromUriString(restTargetProperties.uri.toString()).path("").toUriString() .pathSegment("mtb")
} else { .pathSegment("kaplan-meier")
UriComponentsBuilder.fromUriString(restTargetProperties.uri.toString()) .pathSegment("config")
.pathSegment("mtb") .toUriString(),
.pathSegment("kaplan-meier")
.pathSegment("config")
.toUriString()
},
String::class.java String::class.java
).statusCode == HttpStatus.OK ).statusCode == HttpStatus.OK
@@ -207,4 +210,57 @@ class GPasConnectionCheckService(
override fun connectionAvailable(): ConnectionCheckResult.GPasConnectionCheckResult { override fun connectionAvailable(): ConnectionCheckResult.GPasConnectionCheckResult {
return this.result 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
}
}

View File

@@ -30,6 +30,7 @@ import org.springframework.data.relational.core.mapping.Table
import org.springframework.data.repository.CrudRepository import org.springframework.data.repository.CrudRepository
import org.springframework.data.repository.PagingAndSortingRepository import org.springframework.data.repository.PagingAndSortingRepository
import java.time.Instant import java.time.Instant
import java.time.temporal.ChronoUnit
import java.util.* import java.util.*
@Table("request") @Table("request")
@@ -65,6 +66,12 @@ data class Request(
processedAt: Instant processedAt: Instant
) : ) :
this(null, uuid, patientPseudonym, pid, fingerprint, type, status, processedAt) this(null, uuid, patientPseudonym, pid, fingerprint, type, status, processedAt)
fun isPendingUnknown(): Boolean {
return this.status == RequestStatus.UNKNOWN && this.processedAt.isBefore(
Instant.now().minus(10, ChronoUnit.MINUTES)
)
}
} }
@JvmRecord @JvmRecord
@@ -90,19 +97,23 @@ interface RequestRepository : CrudRepository<Request, Long>, PagingAndSortingRep
@Query("SELECT count(*) AS count, status FROM request WHERE type = 'MTB_FILE' GROUP BY status ORDER BY status, count DESC;") @Query("SELECT count(*) AS count, status FROM request WHERE type = 'MTB_FILE' GROUP BY status ORDER BY status, count DESC;")
fun countStates(): List<CountedState> fun countStates(): List<CountedState>
@Query("SELECT count(*) AS count, status FROM (" + @Query(
"SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " + "SELECT count(*) AS count, status FROM (" +
"WHERE type = 'MTB_FILE' AND status NOT IN ('DUPLICATION') " + "SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " +
") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;") "WHERE type = 'MTB_FILE' AND status NOT IN ('DUPLICATION') " +
") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;"
)
fun findPatientUniqueStates(): List<CountedState> fun findPatientUniqueStates(): List<CountedState>
@Query("SELECT count(*) AS count, status FROM request WHERE type = 'DELETE' GROUP BY status ORDER BY status, count DESC;") @Query("SELECT count(*) AS count, status FROM request WHERE type = 'DELETE' GROUP BY status ORDER BY status, count DESC;")
fun countDeleteStates(): List<CountedState> fun countDeleteStates(): List<CountedState>
@Query("SELECT count(*) AS count, status FROM (" + @Query(
"SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " + "SELECT count(*) AS count, status FROM (" +
"WHERE type = 'DELETE'" + "SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " +
") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;") "WHERE type = 'DELETE'" +
") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;"
)
fun findPatientUniqueDeleteStates(): List<CountedState> fun findPatientUniqueDeleteStates(): List<CountedState>
} }

View File

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

View File

@@ -1,7 +1,7 @@
/* /*
* This file is part of ETL-Processor * This file is part of ETL-Processor
* *
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors * Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* *
* This program is free software: you can redistribute it and/or modify * This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published * it under the terms of the GNU Affero General Public License as published
@@ -20,11 +20,12 @@
package dev.dnpm.etl.processor.output package dev.dnpm.etl.processor.output
import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.Consent import dev.dnpm.etl.processor.CustomMediaType
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.config.KafkaProperties
import dev.dnpm.etl.processor.monitoring.RequestStatus 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.slf4j.LoggerFactory
import org.springframework.kafka.core.KafkaTemplate import org.springframework.kafka.core.KafkaTemplate
import org.springframework.retry.support.RetryTemplate import org.springframework.retry.support.RetryTemplate
@@ -38,14 +39,25 @@ class KafkaMtbFileSender(
private val logger = LoggerFactory.getLogger(KafkaMtbFileSender::class.java) private val logger = LoggerFactory.getLogger(KafkaMtbFileSender::class.java)
override fun send(request: MtbFileSender.MtbFileRequest): MtbFileSender.Response { override fun <T> send(request: MtbFileRequest<T>): MtbFileSender.Response {
return try { return try {
return retryTemplate.execute<MtbFileSender.Response, Exception> { return retryTemplate.execute<MtbFileSender.Response, Exception> {
val result = kafkaTemplate.send( val record =
kafkaProperties.topic, ProducerRecord(
key(request), kafkaProperties.outputTopic,
objectMapper.writeValueAsString(Data(request.requestId, request.mtbFile)) key(request),
) objectMapper.writeValueAsString(request),
)
record.headers().add("requestId", request.requestId.value.toByteArray())
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) { if (result.get() != null) {
logger.debug("Sent file via KafkaMtbFileSender") logger.debug("Sent file via KafkaMtbFileSender")
MtbFileSender.Response(RequestStatus.UNKNOWN) MtbFileSender.Response(RequestStatus.UNKNOWN)
@@ -59,24 +71,26 @@ class KafkaMtbFileSender(
} }
} }
override fun send(request: MtbFileSender.DeleteRequest): MtbFileSender.Response { override fun send(request: DeleteRequest): MtbFileSender.Response {
val dummyMtbFile = MtbFile.builder() val dummyMtbFile = Mtb.builder()
.withConsent( .metadata(MvhMetadata())
Consent.builder()
.withPatient(request.patientId.value)
.withStatus(Consent.Status.REJECTED)
.build()
)
.build() .build()
return try { return try {
return retryTemplate.execute<MtbFileSender.Response, Exception> { return retryTemplate.execute<MtbFileSender.Response, Exception> {
val result = kafkaTemplate.send( val record =
kafkaProperties.topic, ProducerRecord(
key(request), kafkaProperties.outputTopic,
objectMapper.writeValueAsString(Data(request.requestId, dummyMtbFile)) key(request),
) objectMapper.writeValueAsString(
DnpmV2MtbFileRequest(
request.requestId,
dummyMtbFile
)
)
)
record.headers().add("requestId", request.requestId.value.toByteArray())
val result = kafkaTemplate.send(record)
if (result.get() != null) { if (result.get() != null) {
logger.debug("Sent deletion request via KafkaMtbFileSender") logger.debug("Sent deletion request via KafkaMtbFileSender")
MtbFileSender.Response(RequestStatus.UNKNOWN) MtbFileSender.Response(RequestStatus.UNKNOWN)
@@ -91,16 +105,14 @@ class KafkaMtbFileSender(
} }
override fun endpoint(): String { override fun endpoint(): String {
return "${this.kafkaProperties.servers} (${this.kafkaProperties.topic}/${this.kafkaProperties.responseTopic})" return "${this.kafkaProperties.servers} (${this.kafkaProperties.outputTopic}/${this.kafkaProperties.outputResponseTopic})"
} }
private fun key(request: MtbFileSender.MtbFileRequest): String { private fun key(request: MtbRequest): String {
return "{\"pid\": \"${request.mtbFile.patient.id}\"}" return when (request) {
is DnpmV2MtbFileRequest -> "{\"pid\": \"${request.content.patient.id}\"}"
is DeleteRequest -> "{\"pid\": \"${request.patientId.value}\"}"
else -> throw IllegalArgumentException("Unsupported request type: ${request::class.simpleName}")
}
} }
}
private fun key(request: MtbFileSender.DeleteRequest): String {
return "{\"pid\": \"${request.patientId.value}\"}"
}
data class Data(val requestId: RequestId, val content: MtbFile)
}

View File

@@ -19,25 +19,17 @@
package dev.dnpm.etl.processor.output 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 dev.dnpm.etl.processor.monitoring.RequestStatus
import org.springframework.http.HttpStatusCode import org.springframework.http.HttpStatusCode
interface MtbFileSender { interface MtbFileSender {
fun send(request: MtbFileRequest): Response fun <T> send(request: MtbFileRequest<T>): Response
fun send(request: DeleteRequest): Response fun send(request: DeleteRequest): Response
fun endpoint(): String fun endpoint(): String
data class Response(val status: RequestStatus, val body: 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 { fun Int.asRequestStatus(): RequestStatus {
@@ -51,4 +43,4 @@ fun Int.asRequestStatus(): RequestStatus {
fun HttpStatusCode.asRequestStatus(): RequestStatus { fun HttpStatusCode.asRequestStatus(): RequestStatus {
return this.value().asRequestStatus() return this.value().asRequestStatus()
} }

View File

@@ -0,0 +1,49 @@
/*
* 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

View File

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

View File

@@ -1,7 +1,7 @@
/* /*
* This file is part of ETL-Processor * This file is part of ETL-Processor
* *
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors * Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* *
* This program is free software: you can redistribute it and/or modify * This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published * it under the terms of the GNU Affero General Public License as published
@@ -19,10 +19,11 @@
package dev.dnpm.etl.processor.output package dev.dnpm.etl.processor.output
import dev.dnpm.etl.processor.config.RestTargetProperties import dev.dnpm.etl.processor.CustomMediaType
import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.PatientPseudonym 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.ReportService
import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.monitoring.asRequestStatus import dev.dnpm.etl.processor.monitoring.asRequestStatus
import org.slf4j.LoggerFactory import org.slf4j.LoggerFactory
import org.springframework.http.HttpEntity import org.springframework.http.HttpEntity
@@ -46,11 +47,11 @@ abstract class RestMtbFileSender(
abstract fun deleteUrl(patientId: PatientPseudonym): String abstract fun deleteUrl(patientId: PatientPseudonym): String
override fun send(request: MtbFileSender.MtbFileRequest): MtbFileSender.Response { override fun <T> send(request: MtbFileRequest<T>): MtbFileSender.Response {
try { try {
return retryTemplate.execute<MtbFileSender.Response, Exception> { return retryTemplate.execute<MtbFileSender.Response, Exception> {
val headers = getHttpHeaders() val headers = getHttpHeaders(request)
val entityReq = HttpEntity(request.mtbFile, headers) val entityReq = HttpEntity(request.content, headers)
val response = restTemplate.postForEntity( val response = restTemplate.postForEntity(
sendUrl(), sendUrl(),
entityReq, entityReq,
@@ -76,10 +77,10 @@ abstract class RestMtbFileSender(
return MtbFileSender.Response(RequestStatus.ERROR, "Sonstiger Fehler bei der Übertragung") return MtbFileSender.Response(RequestStatus.ERROR, "Sonstiger Fehler bei der Übertragung")
} }
override fun send(request: MtbFileSender.DeleteRequest): MtbFileSender.Response { override fun send(request: DeleteRequest): MtbFileSender.Response {
try { try {
return retryTemplate.execute<MtbFileSender.Response, Exception> { return retryTemplate.execute<MtbFileSender.Response, Exception> {
val headers = getHttpHeaders() val headers = getHttpHeaders(request)
val entityReq = HttpEntity(null, headers) val entityReq = HttpEntity(null, headers)
restTemplate.delete( restTemplate.delete(
deleteUrl(request.patientId), deleteUrl(request.patientId),
@@ -102,11 +103,14 @@ abstract class RestMtbFileSender(
return this.restTargetProperties.uri.orEmpty() return this.restTargetProperties.uri.orEmpty()
} }
private fun getHttpHeaders(): HttpHeaders { private fun getHttpHeaders(request: MtbRequest): HttpHeaders {
val username = restTargetProperties.username val username = restTargetProperties.username
val password = restTargetProperties.password val password = restTargetProperties.password
val headers = HttpHeaders() val headers = HttpHeaders()
headers.contentType = MediaType.APPLICATION_JSON headers.contentType = when (request) {
is DnpmV2MtbFileRequest -> CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON
else -> MediaType.APPLICATION_JSON
}
if (username.isNullOrBlank() || password.isNullOrBlank()) { if (username.isNullOrBlank() || password.isNullOrBlank()) {
return headers return headers
@@ -116,4 +120,4 @@ abstract class RestMtbFileSender(
return headers return headers
} }
} }

View File

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

View File

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

View File

@@ -19,54 +19,96 @@
package dev.dnpm.etl.processor.pseudonym package dev.dnpm.etl.processor.pseudonym
import de.ukw.ccc.bwhc.dto.MtbFile
import dev.dnpm.etl.processor.PatientId 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 import org.apache.commons.codec.digest.DigestUtils
/** Replaces patient ID with generated patient pseudonym /** Replaces patient ID with generated patient pseudonym
* *
* @param pseudonymizeService The pseudonymizeService to be used * @since 0.11.0
* *
* @param pseudonymizeService The pseudonymizeService to be used
* @return The MTB file containing patient pseudonymes * @return The MTB file containing patient pseudonymes
*/ */
infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) { infix fun Mtb.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
val patientPseudonym = pseudonymizeService.patientPseudonym(PatientId(this.patient.id)).value val patientPseudonym = pseudonymizeService.patientPseudonym(PatientId(this.patient.id)).value
this.episode?.patient = patientPseudonym this.episodesOfCare?.forEach { it.patient.id = patientPseudonym }
this.carePlans?.forEach { it.patient = patientPseudonym } this.carePlans?.forEach {
this.patient.id = patientPseudonym it.patient.id = patientPseudonym
this.claims?.forEach { it.patient = patientPseudonym } it.rebiopsyRequests?.forEach { it.patient.id = patientPseudonym }
this.consent?.patient = patientPseudonym it.histologyReevaluationRequests?.forEach { it.patient.id = patientPseudonym }
this.claimResponses?.forEach { it.patient = patientPseudonym } it.medicationRecommendations.forEach { it.patient.id = patientPseudonym }
this.diagnoses?.forEach { it.patient = patientPseudonym } it.studyEnrollmentRecommendations?.forEach { it.patient.id = patientPseudonym }
this.ecogStatus?.forEach { it.patient = patientPseudonym } it.procedureRecommendations?.forEach { it.patient.id = patientPseudonym }
this.familyMemberDiagnoses?.forEach { it.patient = patientPseudonym } it.geneticCounselingRecommendation.patient.id = patientPseudonym
this.geneticCounsellingRequests?.forEach { it.patient = patientPseudonym } }
this.histologyReevaluationRequests?.forEach { it.patient = patientPseudonym } this.diagnoses?.forEach { it.patient.id = patientPseudonym }
this.histologyReports?.forEach { this.guidelineTherapies?.forEach { it.patient.id = patientPseudonym }
it.patient = patientPseudonym this.guidelineProcedures?.forEach { it.patient.id = patientPseudonym }
it.tumorMorphology?.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.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/$patientPseudonym")
}
} }
this.lastGuidelineTherapies?.forEach { it.patient = patientPseudonym }
this.molecularPathologyFindings?.forEach { it.patient = patientPseudonym }
this.molecularTherapies?.forEach { molecularTherapy -> molecularTherapy.history.forEach { it.patient = patientPseudonym } }
this.ngsReports?.forEach { it.patient = patientPseudonym }
this.previousGuidelineTherapies?.forEach { it.patient = patientPseudonym }
this.rebiopsyRequests?.forEach { it.patient = patientPseudonym }
this.recommendations?.forEach { it.patient = patientPseudonym }
this.responses?.forEach { it.patient = patientPseudonym }
this.studyInclusionRequests?.forEach { it.patient = patientPseudonym }
this.specimens?.forEach { it.patient = patientPseudonym }
} }
/** /**
* Creates new hash of content IDs with given prefix except for patient IDs * Creates new hash of content IDs with given prefix except for patient IDs
* *
* @param pseudonymizeService The pseudonymizeService to be used * @since 0.11.0
* *
* @param pseudonymizeService The pseudonymizeService to be used
* @return The MTB file containing rehashed content IDs * @return The MTB file containing rehashed content IDs
*/ */
infix fun MtbFile.anonymizeContentWith(pseudonymizeService: PseudonymizeService) { infix fun Mtb.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
val prefix = pseudonymizeService.prefix() val prefix = pseudonymizeService.prefix()
fun anonymize(id: String): String { fun anonymize(id: String): String {
@@ -74,153 +116,199 @@ infix fun MtbFile.anonymizeContentWith(pseudonymizeService: PseudonymizeService)
return "$prefix$hash" return "$prefix$hash"
} }
this.episode?.apply { this.episodesOfCare?.forEach {
id = id?.let { it?.apply { id = id?.let(::anonymize) }
anonymize(it) it.diagnoses?.forEach { it ->
it?.id = it.id?.let(::anonymize)
} }
} }
this.carePlans?.onEach { carePlan -> this.carePlans?.onEach { carePlan ->
carePlan?.apply { carePlan?.apply {
id = id?.let { anonymize(it) } id = id?.let { anonymize(it) }
diagnosis = diagnosis?.let { anonymize(it) }
geneticCounsellingRequest = geneticCounsellingRequest?.let { anonymize(it) } diagnoses?.forEach { it -> it?.id = it.id?.let(::anonymize) }
rebiopsyRequests = rebiopsyRequests.map { it?.let { anonymize(it) } } geneticCounselingRecommendation?.apply {
recommendations = recommendations.map { it?.let { anonymize(it) } } id = geneticCounselingRecommendation.id?.let(::anonymize)
studyInclusionRequests = studyInclusionRequests.map { it?.let { anonymize(it) } }
}
}
this.claims?.onEach { claim ->
claim?.apply {
id = id?.let { anonymize(it) }
therapy = therapy?.let { anonymize(it) }
}
}
this.claimResponses?.onEach { claimResponse ->
claimResponse?.apply {
id = id?.let { anonymize(it) }
claim = claim?.let { anonymize(it) }
}
}
this.consent?.apply {
id = id?.let { anonymize(it) }
}
this.diagnoses?.onEach { diagnosis ->
diagnosis?.apply {
id = id?.let { anonymize(it) }
histologyResults = histologyResults?.map { it?.let { anonymize(it) } }
}
}
this.ecogStatus?.onEach { ecogStatus ->
ecogStatus?.apply {
id = id?.let { anonymize(it) }
}
}
this.familyMemberDiagnoses?.onEach { familyMemberDiagnosis ->
familyMemberDiagnosis?.apply {
id = id?.let { anonymize(it) }
}
}
this.geneticCounsellingRequests?.onEach { geneticCounsellingRequest ->
geneticCounsellingRequest?.apply {
id = id?.let { anonymize(it) }
}
}
this.histologyReevaluationRequests?.onEach { histologyReevaluationRequest ->
histologyReevaluationRequest?.apply {
id = id?.let { anonymize(it) }
specimen = specimen?.let { anonymize(it) }
}
}
this.histologyReports?.onEach { histologyReport ->
histologyReport?.apply {
id = id?.let { anonymize(it) }
specimen = specimen?.let { anonymize(it) }
tumorMorphology?.apply {
id = id?.let { anonymize(it) }
specimen = specimen?.let { anonymize(it) }
} }
tumorCellContent?.apply { rebiopsyRequests?.forEach { it ->
id = id?.let { anonymize(it) } it.id = it.id?.let(::anonymize)
specimen = specimen?.let { anonymize(it) } it.tumorEntity?.id = it.tumorEntity?.id?.let(::anonymize)
} }
} histologyReevaluationRequests?.forEach { it ->
} it.id = it?.id?.let(::anonymize)
this.lastGuidelineTherapies?.onEach { lastGuidelineTherapy -> it.specimen?.id = it.specimen?.id?.let(::anonymize)
lastGuidelineTherapy?.apply { }
id = id?.let { anonymize(it) }
diagnosis = diagnosis?.let { anonymize(it) } medicationRecommendations?.forEach { it ->
} it.id = it?.id?.let(::anonymize)
} it.supportingVariants?.forEach { it ->
this.molecularPathologyFindings?.onEach { molecularPathologyFinding -> it.variant?.id = it.variant?.id?.let(::anonymize)
molecularPathologyFinding?.apply { }
id = id?.let { anonymize(it) } it.reason?.id = it.reason?.id?.let(::anonymize)
specimen = specimen?.let { anonymize(it) } }
} reason?.id = reason?.id?.let(::anonymize)
} studyEnrollmentRecommendations?.forEach { it ->
this.molecularTherapies?.onEach { molecularTherapy -> it?.reason?.id = it.reason?.id?.let(::anonymize)
molecularTherapy?.apply { }
history?.onEach { history ->
history?.apply { procedureRecommendations?.forEach { it ->
id = id?.let { anonymize(it) }
basedOn = basedOn?.let { anonymize(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)
studyEnrollmentRecommendations?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.supportingVariants.forEach { it ->
it.variant?.id = it?.variant?.id?.let(::anonymize)
}
responses?.forEach { it ->
it.id = it?.id?.let(::anonymize)
it.id = it?.id?.let(::anonymize)
}
} }
} }
} }
} }
this.ngsReports?.onEach { ngsReport ->
ngsReport?.apply {
id = id?.let { anonymize(it) } this.responses?.forEach { it ->
specimen = specimen?.let { anonymize(it) }
tumorCellContent?.apply { it?.id = it.id?.let(::anonymize)
id = id?.let { anonymize(it) } it?.therapy?.id = it.therapy?.id?.let(::anonymize)
specimen = specimen?.let { anonymize(it) }
}
simpleVariants?.onEach { simpleVariant ->
simpleVariant?.apply {
id = id?.let { anonymize(it) }
}
}
}
} }
this.previousGuidelineTherapies?.onEach { previousGuidelineTherapy ->
previousGuidelineTherapy?.apply { this.diagnoses?.forEach { it ->
id = id?.let { anonymize(it) }
diagnosis = diagnosis?.let { anonymize(it) } it.id = it?.id?.let(::anonymize)
medication.forEach { medication -> it.histology?.forEach { it -> it.id = it?.id?.let(::anonymize) }
medication?.apply {
id = id?.let { anonymize(it) }
}
}
}
} }
this.rebiopsyRequests?.onEach { rebiopsyRequest ->
rebiopsyRequest?.apply { this.ngsReports?.forEach { it ->
id = id?.let { anonymize(it) } it.id = it?.id?.let(::anonymize)
specimen = specimen?.let { anonymize(it) } 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 ->
this.recommendations?.onEach { recommendation -> it?.id = it.id?.let(::anonymize)
recommendation?.apply { it?.transcriptId?.value = it.transcriptId?.value?.let(::anonymize)
id = id?.let { anonymize(it) }
diagnosis = diagnosis?.let { anonymize(it) }
ngsReport = ngsReport?.let { anonymize(it) }
} }
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.responses?.onEach { response ->
response?.apply { this.histologyReports?.forEach { it ->
id = id?.let { anonymize(it) } it.id = it?.id?.let(::anonymize)
therapy = therapy?.let { anonymize(it) } 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)
} }
} }
this.studyInclusionRequests?.onEach { studyInclusionRequest -> }
studyInclusionRequest?.apply {
id = id?.let { anonymize(it) } fun Mtb.ensureMetaDataIsInitialized() {
reason = reason?.let { anonymize(it) } // init metadata if necessary
} if (this.metadata == null) {
val mvhMetadata = MvhMetadata.builder().build()
this.metadata = mvhMetadata
} }
this.specimens?.onEach { specimen -> if (this.metadata.researchConsents == null) {
specimen?.apply { this.metadata.researchConsents = mutableListOf()
id = id?.let { anonymize(it) }
}
} }
} 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))
}

View File

@@ -0,0 +1,276 @@
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()
val provisionCode = getProvisionCode(provisionComponent)
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 getProvisionCode(provisionComponent: ProvisionComponent): String? {
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
}
}
return provisionCode
}
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().any { code ->
targetCode.equals(code.code) && targetSystem.equals(code.system)
}
}.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.any { code ->
researchAllowedPolicySystem.equals(code.getSystem()) && (researchAllowedPolicyOid.equals(
code.getCode()
))
}
}
fun isRequestDateInRange(requestDate: Date?, provPeriod: Period): Boolean {
val isRequestDateAfterOrEqualStart = provPeriod.start.compareTo(requestDate)
val isRequestDateBeforeOrEqualEnd = provPeriod.end.compareTo(requestDate)
return isRequestDateAfterOrEqualStart <= 0 && isRequestDateBeforeOrEqualEnd >= 0
}
}

View File

@@ -1,7 +1,7 @@
/* /*
* This file is part of ETL-Processor * This file is part of ETL-Processor
* *
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors * Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* *
* This program is free software: you can redistribute it and/or modify * This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published * it under the terms of the GNU Affero General Public License as published
@@ -20,19 +20,28 @@
package dev.dnpm.etl.processor.services package dev.dnpm.etl.processor.services
import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.MtbFile
import dev.dnpm.etl.processor.* import dev.dnpm.etl.processor.*
import dev.dnpm.etl.processor.config.AppConfigProperties 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.Report
import dev.dnpm.etl.processor.monitoring.Request import dev.dnpm.etl.processor.monitoring.Request
import dev.dnpm.etl.processor.monitoring.RequestStatus import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.monitoring.RequestType import dev.dnpm.etl.processor.monitoring.RequestType
import 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.output.MtbFileSender
import dev.dnpm.etl.processor.pseudonym.PseudonymizeService 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.anonymizeContentWith
import dev.dnpm.etl.processor.pseudonym.pseudonymizeWith 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.binary.Base32
import org.apache.commons.codec.digest.DigestUtils import org.apache.commons.codec.digest.DigestUtils
import org.slf4j.Logger
import org.slf4j.LoggerFactory
import org.springframework.context.ApplicationEventPublisher import org.springframework.context.ApplicationEventPublisher
import org.springframework.stereotype.Service import org.springframework.stereotype.Service
import java.time.Instant import java.time.Instant
@@ -46,40 +55,63 @@ class RequestProcessor(
private val requestService: RequestService, private val requestService: RequestService,
private val objectMapper: ObjectMapper, private val objectMapper: ObjectMapper,
private val applicationEventPublisher: ApplicationEventPublisher, private val applicationEventPublisher: ApplicationEventPublisher,
private val appConfigProperties: AppConfigProperties private val appConfigProperties: AppConfigProperties,
private val consentProcessor: ConsentProcessor?
) { ) {
fun processMtbFile(mtbFile: MtbFile) { private var logger: Logger = LoggerFactory.getLogger("RequestProcessor")
fun processMtbFile(mtbFile: Mtb) {
processMtbFile(mtbFile, randomRequestId()) processMtbFile(mtbFile, randomRequestId())
} }
fun processMtbFile(mtbFile: MtbFile, requestId: RequestId) {
val pid = PatientId(mtbFile.patient.id)
mtbFile pseudonymizeWith pseudonymizeService fun processMtbFile(mtbFile: Mtb, requestId: RequestId) {
mtbFile anonymizeContentWith pseudonymizeService val pid = PatientId(extractPatientIdentifier(mtbFile))
val request = MtbFileSender.MtbFileRequest(requestId, transformationService.transform(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
)
)
}
}
val patientPseudonym = PatientPseudonym(request.mtbFile.patient.id) 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
}
private fun <T> saveAndSend(request: MtbFileRequest<T>, pid: PatientId) {
requestService.save( requestService.save(
Request( Request(
requestId, request.requestId,
patientPseudonym, request.patientPseudonym(),
pid, pid,
fingerprint(request.mtbFile), fingerprint(request),
RequestType.MTB_FILE, RequestType.MTB_FILE,
RequestStatus.UNKNOWN RequestStatus.UNKNOWN
) )
) )
if (appConfigProperties.duplicationDetection && isDuplication(mtbFile)) { if (appConfigProperties.duplicationDetection && isDuplication(request)) {
applicationEventPublisher.publishEvent( applicationEventPublisher.publishEvent(
ResponseEvent( ResponseEvent(
requestId, request.requestId, Instant.now(), RequestStatus.DUPLICATION
Instant.now(),
RequestStatus.DUPLICATION
) )
) )
return return
@@ -89,7 +121,7 @@ class RequestProcessor(
applicationEventPublisher.publishEvent( applicationEventPublisher.publishEvent(
ResponseEvent( ResponseEvent(
requestId, request.requestId,
Instant.now(), Instant.now(),
responseStatus.status, responseStatus.status,
when (responseStatus.status) { when (responseStatus.status) {
@@ -100,26 +132,38 @@ class RequestProcessor(
) )
} }
private fun isDuplication(pseudonymizedMtbFile: MtbFile): Boolean { private fun <T> isDuplication(pseudonymizedMtbFileRequest: MtbFileRequest<T>): Boolean {
val patientPseudonym = PatientPseudonym(pseudonymizedMtbFile.patient.id) val patientPseudonym = when (pseudonymizedMtbFileRequest) {
is DnpmV2MtbFileRequest -> PatientPseudonym(pseudonymizedMtbFileRequest.content.patient.id)
}
val lastMtbFileRequestForPatient = val lastMtbFileRequestForPatient =
requestService.lastMtbFileRequestForPatientPseudonym(patientPseudonym) requestService.lastMtbFileRequestForPatientPseudonym(patientPseudonym)
val isLastRequestDeletion = requestService.isLastRequestWithKnownStatusDeletion(patientPseudonym) val isLastRequestDeletion =
requestService.isLastRequestWithKnownStatusDeletion(patientPseudonym)
return null != lastMtbFileRequestForPatient return null != lastMtbFileRequestForPatient && !isLastRequestDeletion && lastMtbFileRequestForPatient.fingerprint == fingerprint(
&& !isLastRequestDeletion pseudonymizedMtbFileRequest
&& lastMtbFileRequestForPatient.fingerprint == fingerprint(pseudonymizedMtbFile) )
} }
fun processDeletion(patientId: PatientId) { fun processDeletion(patientId: PatientId, isConsented: TtpConsentStatus) {
processDeletion(patientId, randomRequestId()) processDeletion(patientId, randomRequestId(), isConsented)
} }
fun processDeletion(patientId: PatientId, requestId: RequestId) { fun processDeletion(patientId: PatientId, requestId: RequestId, isConsented: TtpConsentStatus) {
try { try {
val patientPseudonym = pseudonymizeService.patientPseudonym(patientId) 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( requestService.save(
Request( Request(
requestId, requestId,
@@ -127,25 +171,22 @@ class RequestProcessor(
patientId, patientId,
fingerprint(patientPseudonym.value), fingerprint(patientPseudonym.value),
RequestType.DELETE, RequestType.DELETE,
RequestStatus.UNKNOWN requestStatus
) )
) )
val responseStatus = sender.send(MtbFileSender.DeleteRequest(requestId, patientPseudonym)) val responseStatus = sender.send(DeleteRequest(requestId, patientPseudonym))
applicationEventPublisher.publishEvent( applicationEventPublisher.publishEvent(
ResponseEvent( ResponseEvent(
requestId, requestId, Instant.now(), responseStatus.status, when (responseStatus.status) {
Instant.now(),
responseStatus.status,
when (responseStatus.status) {
RequestStatus.WARNING, RequestStatus.ERROR -> Optional.of(responseStatus.body) RequestStatus.WARNING, RequestStatus.ERROR -> Optional.of(responseStatus.body)
else -> Optional.empty() else -> Optional.empty()
} }
) )
) )
} catch (e: Exception) { } catch (_: Exception) {
requestService.save( requestService.save(
Request( Request(
uuid = requestId, uuid = requestId,
@@ -160,16 +201,18 @@ class RequestProcessor(
} }
} }
private fun fingerprint(mtbFile: MtbFile): Fingerprint { private fun <T> fingerprint(request: MtbFileRequest<T>): Fingerprint {
return fingerprint(objectMapper.writeValueAsString(mtbFile)) return when (request) {
is DnpmV2MtbFileRequest -> fingerprint(objectMapper.writeValueAsString(request.content))
}
} }
private fun fingerprint(s: String): Fingerprint { private fun fingerprint(s: String): Fingerprint {
return Fingerprint( return Fingerprint(
Base32().encodeAsString(DigestUtils.sha256(s)) Base32().encodeAsString(DigestUtils.sha256(s)).replace("=", "").lowercase()
.replace("=", "")
.lowercase()
) )
} }
} }
private fun extractPatientIdentifier(mtbFile: Mtb): String = mtbFile.patient.id

View File

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

View File

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

View File

@@ -1,7 +1,7 @@
/* /*
* This file is part of ETL-Processor * This file is part of ETL-Processor
* *
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors * Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* *
* This program is free software: you can redistribute it and/or modify * This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published * it under the terms of the GNU Affero General Public License as published
@@ -19,6 +19,7 @@
package dev.dnpm.etl.processor package dev.dnpm.etl.processor
import org.springframework.http.MediaType
import java.util.* import java.util.*
class Fingerprint(val value: String) { class Fingerprint(val value: String) {
@@ -46,4 +47,17 @@ value class PatientId(val value: String)
@JvmInline @JvmInline
value class PatientPseudonym(val value: String) value class PatientPseudonym(val value: String)
fun emptyPatientPseudonym() = PatientPseudonym("") 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"
}

View File

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

View File

@@ -18,13 +18,107 @@ spring:
issuer-uri: https://dnpm.dev/auth/realms/intern issuer-uri: https://dnpm.dev/auth/realms/intern
user-name-attribute: name user-name-attribute: name
# kafka:
# security:
# protocol: "SSL"
# ssl:
# key-store-type: "PEM"
# key-store-certificate-chain: -----BEGIN CERTIFICATE-----
# MIIDCzCCAfOgAwIBAgIUaXNh4PahaKeLUaab2rUPSVESx28wDQYJKoZIhvcNAQEL
# BQAwFTETMBEGA1UEAwwKRXhhbXBsZSBDQTAeFw0yNTA4MjExODEyMTFaFw0zNTA4
# MTkxODEyMTFaMBUxEzARBgNVBAMMCkV4YW1wbGUgQ0EwggEiMA0GCSqGSIb3DQEB
# AQUAA4IBDwAwggEKAoIBAQCsqalqVOLFglVbX9oSHU91ebyL1kPyb/2N90UGQIcD
# UAjzKxxysId1Vdvtbbwgli6UgfPwlzFP2Wlw51h496yL4QU/9tNV956UJ1RoS/fG
# qBAEHctqavfMI27UQmIzw4pGMkGzEQxRMc6a9pdabBhbMMTJsjtmOv2YMYHj1HHK
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# DgQWBBT2S/C2++ECY+CSuN5KKql0umfbTDAfBgNVHSMEGDAWgBT2S/C2++ECY+CS
# uN5KKql0umfbTDAPBgNVHRMBAf8EBTADAQH/MA0GCSqGSIb3DQEBCwUAA4IBAQBj
# H4DdwqrOHg7sVsqiwDsZfTharpUDCYeG5XhrJQlnA9eKwyofTb929W/fjOwBdDtg
# 9THT/omR0lA8/UyHtezMT6nMsCn4HG2mXvx6ghgvA3jrFTEY7R80dHkboLMTV3u4
# RYgC9S3BJPcbJYpM0cXzkp2T0F4FxWZlfqefuedHuX3zcCxpgVD56qQb2a131TX7
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# BCLp0avYtSYVUGwgH0oUCpkjQRwMg1003TTz8SNnmE7mAXHYljyYejnjL8vBHfch
# 8tTDVXQn08BT9H3jZTnF
# -----END CERTIFICATE-----
# -----BEGIN CERTIFICATE-----
# MIIC+TCCAeGgAwIBAgIUUoCwz8GS6xQ3mmI7RUUYSNPIOi4wDQYJKoZIhvcNAQEL
# BQAwFTETMBEGA1UEAwwKRXhhbXBsZSBDQTAeFw0yNTA4MjExODE0NDhaFw0zNTA4
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# -----END CERTIFICATE-----
# ### For dev/testing purposes only!
# key-store-key: -----BEGIN PRIVATE KEY-----
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# R4jA7nE2/yHZrEMEJovuSU0eMw7rgvEtL79Q0RToYnTY1EU6X/BBoFfiiEeNMHKz
# zjDOOQ6ZvQKBgGCWChIc0FSkwYiPtPZ9PCn89XCjk/cIPkYfiF9fT5Ydeh9pv4Fp
# 8SI8yXi3HgMnGhDCV65eagqztGMEky3voO2X4/MbQaaL0+wDWxuJbsdvNBk7XOt6
# F20HP+2JUiR4Ti1DVWV+0k5/LG7YJzTXp/KmZQZ2aan4mv8xbn2F4h/NAoGAI4ou
# OLN53FEQtHkpSYoc6tFUBZTXdi+qE+g09sxKGmlsROrN9c0bSpnbO6eJRTH7CYAH
# tRFAZrB+jI87ar8FvEuEYQhALYoWxVpsWR5drCfFT2EPHG2icavIbQEEoSLFuyKx
# Gf9oqtcWVFqEkBcbEg/mpDC5Y7TmCEAOsrubdRkCgYEAl7B+EzIdG0rabGoti09q
# QXfyiTjR7nQYkhpLxMCeNlCpQ8Y15XSa8bm1UIGYqj/ZBpeBNhrj64IHoub5Vd43
# tzbb8yNgoLUd16TU1VvyccCMGQVPIF8RkDsAtEawV2eoXbHAstN99xbC8jsLNZRQ
# fcfgTiQaXRJmlVx6jfbfZd4=
# -----END PRIVATE KEY-----
# trust-store-type: "PEM"
# trust-store-certificates: -----BEGIN CERTIFICATE-----
# MIIDCzCCAfOgAwIBAgIUaXNh4PahaKeLUaab2rUPSVESx28wDQYJKoZIhvcNAQEL
# BQAwFTETMBEGA1UEAwwKRXhhbXBsZSBDQTAeFw0yNTA4MjExODEyMTFaFw0zNTA4
# MTkxODEyMTFaMBUxEzARBgNVBAMMCkV4YW1wbGUgQ0EwggEiMA0GCSqGSIb3DQEB
# AQUAA4IBDwAwggEKAoIBAQCsqalqVOLFglVbX9oSHU91ebyL1kPyb/2N90UGQIcD
# UAjzKxxysId1Vdvtbbwgli6UgfPwlzFP2Wlw51h496yL4QU/9tNV956UJ1RoS/fG
# qBAEHctqavfMI27UQmIzw4pGMkGzEQxRMc6a9pdabBhbMMTJsjtmOv2YMYHj1HHK
# Dr7wTBTt2l0eRyCR0kZ8XGIMWhYowPa4EMpC7+4e5Nf/7LSJZWLLy9jXPpazsjkJ
# jEmDNlFfx2tZiq0Wz2Xj1pZSDLbcuIX4IHcLfMvagibfrCMX/h6+WuW42sWPRuBW
# wB6cHGlXs+K/gBBWxtD7sOTacO5hbHFsfaJOhSEIGoIpAgMBAAGjUzBRMB0GA1Ud
# DgQWBBT2S/C2++ECY+CSuN5KKql0umfbTDAfBgNVHSMEGDAWgBT2S/C2++ECY+CS
# uN5KKql0umfbTDAPBgNVHRMBAf8EBTADAQH/MA0GCSqGSIb3DQEBCwUAA4IBAQBj
# H4DdwqrOHg7sVsqiwDsZfTharpUDCYeG5XhrJQlnA9eKwyofTb929W/fjOwBdDtg
# 9THT/omR0lA8/UyHtezMT6nMsCn4HG2mXvx6ghgvA3jrFTEY7R80dHkboLMTV3u4
# RYgC9S3BJPcbJYpM0cXzkp2T0F4FxWZlfqefuedHuX3zcCxpgVD56qQb2a131TX7
# O3UDJfVg8a65IFtehndqILgLVrf7w6+pbmDAlCg5RKrt2USEYyZXYdyTryJbdtn4
# BCLp0avYtSYVUGwgH0oUCpkjQRwMg1003TTz8SNnmE7mAXHYljyYejnjL8vBHfch
# 8tTDVXQn08BT9H3jZTnF
# -----END CERTIFICATE-----
app: app:
rest: rest:
uri: http://localhost:9000/bwhc/etl/api uri: http://localhost/api
#kafka: #kafka:
# topic: test
# response-topic: test_response
# servers: localhost:9094 # servers: localhost:9094
# group-id: "test1234"
# input-topic: test_input
# output-topic: test_output
# output-response-topic: test_response
security: security:
admin-user: admin admin-user: admin
admin-password: "{noop}very-secret" admin-password: "{noop}very-secret"

View File

@@ -16,6 +16,5 @@ spring:
content: content:
enabled: true enabled: true
paths: /**/*.js,/**/*.css,/**/*.svg,/**/*.jpeg paths: /**/*.js,/**/*.css,/**/*.svg,/**/*.jpeg
server: server:
forward-headers-strategy: framework forward-headers-strategy: framework

View File

@@ -0,0 +1,7 @@
__ _ _ _ _
_ __ _____ __/ /_ | || | ___ ___| |_| | _ __ _ __ ___ ___ ___ ___ ___ ___ _ __
| '_ ` _ \ \ / / '_ \| || |_ / _ \_____ / _ \ __| |_____| '_ \| '__/ _ \ / __/ _ \/ __/ __|/ _ \| '__|
| | | | | \ V /| (_) |__ _| __/_____| __/ |_| |_____| |_) | | | (_) | (_| __/\__ \__ \ (_) | |
|_| |_| |_|\_/ \___/ |_| \___| \___|\__|_| | .__/|_| \___/ \___\___||___/___/\___/|_|
|_|
:: mv64e-etl-processor :: ${application.formatted-version}

View File

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

View File

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

View File

@@ -52,8 +52,10 @@
<td th:if="${request.status.value.contains('success')}" class="bg-green"><small>[[ ${request.status} ]]</small></td> <td th:if="${request.status.value.contains('success')}" class="bg-green"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value.contains('warning')}" class="bg-yellow"><small>[[ ${request.status} ]]</small></td> <td th:if="${request.status.value.contains('warning')}" class="bg-yellow"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value.contains('error')}" class="bg-red"><small>[[ ${request.status} ]]</small></td> <td th:if="${request.status.value.contains('error')}" class="bg-red"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value == 'unknown'}" class="bg-gray"><small>[[ ${request.status} ]]</small></td> <td th:if="${request.status.value == 'unknown' and not request.isPendingUnknown()}" class="bg-gray"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value == 'unknown' and request.isPendingUnknown()}" class="bg-yellow"><small>⏰ [[ ${request.status} ]] ⏰</small></td>
<td th:if="${request.status.value == 'duplication'}" class="bg-gray"><small>[[ ${request.status} ]]</small></td> <td th:if="${request.status.value == 'duplication'}" class="bg-gray"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value == 'no-consent'}" class="bg-blue"><small>[[ ${request.status} ]]</small></td>
<td th:style="${request.type.value == 'delete'} ? 'color: red;'"><small>[[ ${request.type} ]]</small></td> <td th:style="${request.type.value == 'delete'} ? 'color: red;'"><small>[[ ${request.type} ]]</small></td>
<td th:if="not ${request.report}">[[ ${request.uuid} ]]</td> <td th:if="not ${request.report}">[[ ${request.uuid} ]]</td>
<td th:if="${request.report}"> <td th:if="${request.report}">
@@ -100,4 +102,4 @@
}); });
</script> </script>
</body> </body>
</html> </html>

View File

@@ -0,0 +1,185 @@
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.assertj.core.api.Assertions.fail;
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
);
}
@Test
public void convertGicsResultToMiiBroadConsent() {
fail("todo: implement Test gicsConsentService.convertGicsResultToMiiBroadConsent");
}
}

View File

@@ -0,0 +1,287 @@
/*
* 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()
}
}
}
}

View File

@@ -17,4 +17,15 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>. * along with this program. If not, see <https://www.gnu.org/licenses/>.
*/ */
package dev.dnpm.etl.processor 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)
}

View File

@@ -1,7 +1,7 @@
/* /*
* This file is part of ETL-Processor * This file is part of ETL-Processor
* *
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors * Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* *
* This program is free software: you can redistribute it and/or modify * This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published * it under the terms of the GNU Affero General Public License as published
@@ -20,10 +20,12 @@
package dev.dnpm.etl.processor.input package dev.dnpm.etl.processor.input
import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.Consent import dev.dnpm.etl.processor.CustomMediaType
import de.ukw.ccc.bwhc.dto.MtbFile import dev.dnpm.etl.processor.consent.ConsentEvaluation
import de.ukw.ccc.bwhc.dto.Patient import dev.dnpm.etl.processor.consent.ConsentEvaluator
import dev.dnpm.etl.processor.consent.TtpConsentStatus
import dev.dnpm.etl.processor.services.RequestProcessor import dev.dnpm.etl.processor.services.RequestProcessor
import dev.pcvolkmer.mv64e.mtb.*
import org.apache.kafka.clients.consumer.ConsumerRecord import org.apache.kafka.clients.consumer.ConsumerRecord
import org.apache.kafka.common.header.internals.RecordHeader import org.apache.kafka.common.header.internals.RecordHeader
import org.apache.kafka.common.header.internals.RecordHeaders import org.apache.kafka.common.header.internals.RecordHeaders
@@ -33,80 +35,268 @@ import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith import org.junit.jupiter.api.extension.ExtendWith
import org.mockito.Mock import org.mockito.Mock
import org.mockito.junit.jupiter.MockitoExtension import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.any import org.mockito.kotlin.*
import org.mockito.kotlin.anyValueClass
import org.mockito.kotlin.times
import org.mockito.kotlin.verify
import java.util.* import java.util.*
@ExtendWith(MockitoExtension::class) @ExtendWith(MockitoExtension::class)
class KafkaInputListenerTest { class KafkaInputListenerTest {
private lateinit var requestProcessor: RequestProcessor private lateinit var requestProcessor: RequestProcessor
private lateinit var consentEvaluator: ConsentEvaluator
private lateinit var objectMapper: ObjectMapper private lateinit var objectMapper: ObjectMapper
private lateinit var kafkaInputListener: KafkaInputListener private lateinit var kafkaInputListener: KafkaInputListener
@BeforeEach @BeforeEach
fun setup( fun setup(
@Mock requestProcessor: RequestProcessor @Mock requestProcessor: RequestProcessor,
@Mock consentEvaluator: ConsentEvaluator,
) { ) {
this.requestProcessor = requestProcessor this.requestProcessor = requestProcessor
this.consentEvaluator = consentEvaluator
this.objectMapper = ObjectMapper() this.objectMapper = ObjectMapper()
this.kafkaInputListener = KafkaInputListener(requestProcessor, objectMapper) this.kafkaInputListener = KafkaInputListener(requestProcessor, consentEvaluator, objectMapper)
} }
@Test @Test
fun shouldProcessMtbFileRequest() { fun shouldProcessMtbFileRequest() {
val mtbFile = MtbFile.builder() whenever(consentEvaluator.check(any())).thenReturn(
.withPatient(Patient.builder().withId("DUMMY_12345678").build()) ConsentEvaluation(
.withConsent(Consent.builder().withStatus(Consent.Status.ACTIVE).build()) 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()
)
.build() .build()
kafkaInputListener.onMessage(ConsumerRecord("testtopic", 0, 0, "", this.objectMapper.writeValueAsString(mtbFile))) kafkaInputListener.onMessage(
ConsumerRecord(
"testtopic",
0,
0,
"",
this.objectMapper.writeValueAsString(mtbFile)
)
)
verify(requestProcessor, times(1)).processMtbFile(any()) verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
} }
@Test @Test
fun shouldProcessDeleteRequest() { fun shouldProcessDeleteRequest() {
val mtbFile = MtbFile.builder() whenever(consentEvaluator.check(any())).thenReturn(
.withPatient(Patient.builder().withId("DUMMY_12345678").build()) ConsentEvaluation(
.withConsent(Consent.builder().withStatus(Consent.Status.REJECTED).build()) 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()
)
.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()) verify(requestProcessor, times(1)).processDeletion(
anyValueClass(),
eq(TtpConsentStatus.UNKNOWN_CHECK_FILE)
)
} }
@Test @Test
fun shouldProcessMtbFileRequestWithExistingRequestId() { fun shouldProcessMtbFileRequestWithExistingRequestId() {
val mtbFile = MtbFile.builder() whenever(consentEvaluator.check(any())).thenReturn(
.withPatient(Patient.builder().withId("DUMMY_12345678").build()) ConsentEvaluation(
.withConsent(Consent.builder().withStatus(Consent.Status.ACTIVE).build()) 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()
)
.build() .build()
val headers = RecordHeaders(listOf(RecordHeader("requestId", UUID.randomUUID().toString().toByteArray()))) val headers = RecordHeaders(listOf(RecordHeader("requestId", UUID.randomUUID().toString().toByteArray())))
kafkaInputListener.onMessage( 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(), anyValueClass()) verify(requestProcessor, times(1)).processMtbFile(any<Mtb>(), anyValueClass())
} }
@Test @Test
fun shouldProcessDeleteRequestWithExistingRequestId() { fun shouldProcessDeleteRequestWithExistingRequestId() {
val mtbFile = MtbFile.builder() whenever(consentEvaluator.check(any())).thenReturn(
.withPatient(Patient.builder().withId("DUMMY_12345678").build()) ConsentEvaluation(
.withConsent(Consent.builder().withStatus(Consent.Status.REJECTED).build()) 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()
)
.build() .build()
val headers = RecordHeaders(listOf(RecordHeader("requestId", UUID.randomUUID().toString().toByteArray()))) val headers = RecordHeaders(listOf(RecordHeader("requestId", UUID.randomUUID().toString().toByteArray())))
kafkaInputListener.onMessage( 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)).processDeletion(
anyValueClass(), anyValueClass(), eq(
TtpConsentStatus.UNKNOWN_CHECK_FILE
)
) )
verify(requestProcessor, times(1)).processDeletion(anyValueClass(), anyValueClass())
} }
} @Test
fun shouldProcessDnpmV2Request() {
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()
)
.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(1)).processDeletion(
anyValueClass(), anyValueClass(), eq(
TtpConsentStatus.UNKNOWN_CHECK_FILE
)
)
}
}

View File

@@ -20,23 +20,34 @@
package dev.dnpm.etl.processor.input package dev.dnpm.etl.processor.input
import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.* 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 dev.dnpm.etl.processor.services.RequestProcessor import dev.dnpm.etl.processor.services.RequestProcessor
import dev.pcvolkmer.mv64e.mtb.*
import org.junit.jupiter.api.BeforeEach import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Nested import org.junit.jupiter.api.Nested
import org.junit.jupiter.api.Test import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith 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.Mock
import org.mockito.Mockito.times import org.mockito.Mockito.times
import org.mockito.Mockito.verify import org.mockito.Mockito.verify
import org.mockito.junit.jupiter.MockitoExtension import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.any import org.mockito.kotlin.any
import org.mockito.kotlin.anyValueClass import org.mockito.kotlin.anyValueClass
import org.springframework.http.MediaType import org.mockito.kotlin.whenever
import org.springframework.core.io.ClassPathResource
import org.springframework.test.web.servlet.MockMvc import org.springframework.test.web.servlet.MockMvc
import org.springframework.test.web.servlet.delete import org.springframework.test.web.servlet.delete
import org.springframework.test.web.servlet.post import org.springframework.test.web.servlet.post
import org.springframework.test.web.servlet.setup.MockMvcBuilders import org.springframework.test.web.servlet.setup.MockMvcBuilders
import java.time.Instant
import java.util.*
@ExtendWith(MockitoExtension::class) @ExtendWith(MockitoExtension::class)
class MtbFileRestControllerTest { class MtbFileRestControllerTest {
@@ -44,47 +55,78 @@ class MtbFileRestControllerTest {
private val objectMapper = ObjectMapper() private val objectMapper = ObjectMapper()
@Nested @Nested
inner class BwhcRequests { inner class RequestsForDnpmDataModel21 {
private lateinit var mockMvc: MockMvc private lateinit var mockMvc: MockMvc
private lateinit var requestProcessor: RequestProcessor private lateinit var requestProcessor: RequestProcessor
private lateinit var consentEvaluator: ConsentEvaluator
@BeforeEach @BeforeEach
fun setup( fun setup(
@Mock requestProcessor: RequestProcessor @Mock requestProcessor: RequestProcessor,
@Mock consentEvaluator: ConsentEvaluator
) { ) {
this.requestProcessor = requestProcessor this.requestProcessor = requestProcessor
val controller = MtbFileRestController(requestProcessor) this.consentEvaluator = consentEvaluator
val controller = MtbFileRestController(
requestProcessor,
consentEvaluator
)
this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build() this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build()
} }
@Test @Test
fun shouldProcessPostRequest() { fun shouldRespondPostRequest() {
mockMvc.post("/mtbfile") { whenever(consentEvaluator.check(any())).thenReturn(
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Consent.Status.ACTIVE)) ConsentEvaluation(
contentType = MediaType.APPLICATION_JSON 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 { }.andExpect {
status { status {
isAccepted() isAccepted()
} }
} }
verify(requestProcessor, times(1)).processMtbFile(any()) verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
} }
@Test @ParameterizedTest
fun shouldProcessPostRequestWithRejectedConsent() { @ArgumentsSource(Dnpm21MtbFile::class)
fun shouldProcessPostRequest(mtb: Mtb, broadConsent: TtpConsentStatus, shouldProcess: String) {
whenever(consentEvaluator.check(any<Mtb>())).thenReturn(
ConsentEvaluation(
broadConsent,
shouldProcess == "process"
)
)
mockMvc.post("/mtbfile") { mockMvc.post("/mtbfile") {
content = objectMapper.writeValueAsString(bwhcMtbFileContent(Consent.Status.REJECTED)) content = objectMapper.writeValueAsString(mtb)
contentType = MediaType.APPLICATION_JSON contentType = CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON
}.andExpect { }.andExpect {
status { status {
isAccepted() isAccepted()
} }
} }
verify(requestProcessor, times(1)).processDeletion(anyValueClass()) if (shouldProcess == "process") {
verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
} else {
verify(requestProcessor, times(1)).processDeletion(
anyValueClass(),
org.mockito.kotlin.eq(broadConsent)
)
}
} }
@Test @Test
@@ -95,89 +137,90 @@ class MtbFileRestControllerTest {
} }
} }
verify(requestProcessor, times(1)).processDeletion(anyValueClass()) verify(requestProcessor, times(1)).processDeletion(
} anyValueClass(),
} org.mockito.kotlin.eq(TtpConsentStatus.UNKNOWN_CHECK_FILE)
@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 bwhcMtbFileContent(consentStatus: Consent.Status) = MtbFile.builder()
.withPatient(
Patient.builder()
.withId("TEST_12345678")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
) )
.withConsent( verify(consentEvaluator, times(0)).check(any<Mtb>())
Consent.builder() }
.withId("1") }
.withStatus(consentStatus) }
.withPatient("TEST_12345678")
.build() class Dnpm21MtbFile : ArgProvider(
) // No Metadata and no broad consent => delete
.withEpisode( Arguments.of(
Episode.builder() buildMtb(null),
.withId("1") TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED,
.withPatient("TEST_12345678") "delete"
.withPeriod(PeriodStart("2023-08-08")) ),
.build() // No Metadata and broad consent given => process
) Arguments.of(
.build() 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"
)
) {
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())
.build()
)
)
.build()
}
} }
} }

View File

@@ -1,7 +1,7 @@
/* /*
* This file is part of ETL-Processor * This file is part of ETL-Processor
* *
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors * Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* *
* This program is free software: you can redistribute it and/or modify * This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published * it under the terms of the GNU Affero General Public License as published
@@ -20,18 +20,20 @@
package dev.dnpm.etl.processor.output package dev.dnpm.etl.processor.output
import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.* import dev.dnpm.etl.processor.CustomMediaType
import dev.dnpm.etl.processor.PatientPseudonym import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.RequestId import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.config.KafkaProperties import dev.dnpm.etl.processor.config.KafkaProperties
import dev.dnpm.etl.processor.monitoring.RequestStatus 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.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Nested
import org.junit.jupiter.api.Test import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith import org.junit.jupiter.api.extension.ExtendWith
import org.junit.jupiter.params.ParameterizedTest import org.junit.jupiter.params.ParameterizedTest
import org.junit.jupiter.params.provider.MethodSource import org.junit.jupiter.params.provider.MethodSource
import org.mockito.ArgumentMatchers.anyString
import org.mockito.Mock import org.mockito.Mock
import org.mockito.junit.jupiter.MockitoExtension import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.* import org.mockito.kotlin.*
@@ -39,184 +41,191 @@ import org.springframework.kafka.core.KafkaTemplate
import org.springframework.kafka.support.SendResult import org.springframework.kafka.support.SendResult
import org.springframework.retry.policy.SimpleRetryPolicy import org.springframework.retry.policy.SimpleRetryPolicy
import org.springframework.retry.support.RetryTemplateBuilder import org.springframework.retry.support.RetryTemplateBuilder
import java.time.Instant
import java.util.*
import java.util.concurrent.CompletableFuture.completedFuture import java.util.concurrent.CompletableFuture.completedFuture
import java.util.concurrent.ExecutionException import java.util.concurrent.ExecutionException
@ExtendWith(MockitoExtension::class) @ExtendWith(MockitoExtension::class)
class KafkaMtbFileSenderTest { class KafkaMtbFileSenderTest {
private lateinit var kafkaTemplate: KafkaTemplate<String, String> @Nested
inner class BwhcV1Record {
private lateinit var kafkaMtbFileSender: KafkaMtbFileSender private lateinit var kafkaTemplate: KafkaTemplate<String, String>
private lateinit var objectMapper: ObjectMapper private lateinit var kafkaMtbFileSender: KafkaMtbFileSender
@BeforeEach private lateinit var objectMapper: ObjectMapper
fun setup(
@Mock kafkaTemplate: KafkaTemplate<String, String>
) {
val kafkaProperties = KafkaProperties("testtopic")
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
this.objectMapper = ObjectMapper() @BeforeEach
this.kafkaTemplate = kafkaTemplate fun setup(
@Mock kafkaTemplate: KafkaTemplate<String, String>
) {
val kafkaProperties = KafkaProperties("testtopic")
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
this.kafkaMtbFileSender = KafkaMtbFileSender(kafkaTemplate, kafkaProperties, retryTemplate, objectMapper) this.objectMapper = ObjectMapper()
} this.kafkaTemplate = kafkaTemplate
@ParameterizedTest this.kafkaMtbFileSender = KafkaMtbFileSender(kafkaTemplate, kafkaProperties, retryTemplate, objectMapper)
@MethodSource("requestWithResponseSource")
fun shouldSendMtbFileRequestAndReturnExpectedState(testData: TestData) {
doAnswer {
if (null != testData.exception) {
throw testData.exception
}
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
val response = kafkaMtbFileSender.send(MtbFileSender.MtbFileRequest(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 shouldSendMtbFileRequestWithCorrectKeyAndBody() {
doAnswer {
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
kafkaMtbFileSender.send(MtbFileSender.MtbFileRequest(TEST_REQUEST_ID, mtbFile(Consent.Status.ACTIVE)))
val captor = argumentCaptor<String>()
verify(kafkaTemplate, times(1)).send(anyString(), captor.capture(), captor.capture())
assertThat(captor.firstValue).isNotNull
assertThat(captor.firstValue).isEqualTo("{\"pid\": \"PID\"}")
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("requestWithResponseSource")
fun shouldRetryOnMtbFileKafkaSendError(testData: TestData) {
val kafkaProperties = KafkaProperties("testtopic")
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
this.kafkaMtbFileSender = KafkaMtbFileSender(this.kafkaTemplate, kafkaProperties, retryTemplate, this.objectMapper)
doAnswer {
if (null != testData.exception) {
throw testData.exception
}
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString())
kafkaMtbFileSender.send(MtbFileSender.MtbFileRequest(TEST_REQUEST_ID, mtbFile(Consent.Status.ACTIVE)))
val expectedCount = when (testData.exception) {
// OK - No Retry
null -> times(1)
// Request failed - Retry max 3 times
else -> times(3)
} }
verify(kafkaTemplate, expectedCount).send(anyString(), anyString(), anyString()) @ParameterizedTest
} @MethodSource("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>>())
@ParameterizedTest val response = kafkaMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
@MethodSource("requestWithResponseSource") assertThat(response.status).isEqualTo(testData.requestStatus)
fun shouldRetryOnDeleteKafkaSendError(testData: TestData) { }
val kafkaProperties = KafkaProperties("testtopic")
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build() @ParameterizedTest
this.kafkaMtbFileSender = KafkaMtbFileSender(this.kafkaTemplate, kafkaProperties, retryTemplate, this.objectMapper) @MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
fun shouldRetryOnDeleteKafkaSendError(testData: TestData) {
doAnswer { val kafkaProperties = KafkaProperties("testtopic")
if (null != testData.exception) { val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
throw testData.exception this.kafkaMtbFileSender = KafkaMtbFileSender(this.kafkaTemplate, kafkaProperties, retryTemplate, this.objectMapper)
}
completedFuture(SendResult<String, String>(null, null)) doAnswer {
}.whenever(kafkaTemplate).send(anyString(), anyString(), anyString()) if (null != testData.exception) {
throw testData.exception
kafkaMtbFileSender.send(MtbFileSender.DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM)) }
completedFuture(SendResult<String, String>(null, null))
val expectedCount = when (testData.exception) { }.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
// OK - No Retry
null -> times(1) kafkaMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
// Request failed - Retry max 3 times
else -> times(3) val expectedCount = when (testData.exception) {
// OK - No Retry
null -> times(1)
// Request failed - Retry max 3 times
else -> times(3)
}
verify(kafkaTemplate, expectedCount).send(any<ProducerRecord<String, String>>())
}
}
@Nested
inner class DnpmV2Record {
private lateinit var kafkaTemplate: KafkaTemplate<String, String>
private lateinit var kafkaMtbFileSender: KafkaMtbFileSender
private lateinit var objectMapper: ObjectMapper
@BeforeEach
fun setup(
@Mock kafkaTemplate: KafkaTemplate<String, String>
) {
val kafkaProperties = KafkaProperties("testtopic")
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
this.objectMapper = ObjectMapper()
this.kafkaTemplate = kafkaTemplate
this.kafkaMtbFileSender = KafkaMtbFileSender(kafkaTemplate, kafkaProperties, retryTemplate, objectMapper)
}
@ParameterizedTest
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
fun shouldSendMtbFileRequestAndReturnExpectedState(testData: TestData) {
doAnswer {
if (null != testData.exception) {
throw testData.exception
}
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
val response = kafkaMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile()))
assertThat(response.status).isEqualTo(testData.requestStatus)
}
@Test
fun shouldSendMtbFileRequestWithCorrectKeyAndHeaderAndBody() {
doAnswer {
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
kafkaMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile()))
val captor = argumentCaptor<ProducerRecord<String, String>>()
verify(kafkaTemplate, times(1)).send(captor.capture())
assertThat(captor.firstValue.key()).isNotNull
assertThat(captor.firstValue.key()).isEqualTo("{\"pid\": \"PID\"}")
assertThat(captor.firstValue.headers().headers("contentType")).isNotNull
assertThat(captor.firstValue.headers().headers("contentType")?.firstOrNull()?.value()).isEqualTo(CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE.toByteArray())
assertThat(captor.firstValue.headers().headers("requestId")).isNotNull
assertThat(captor.firstValue.headers().headers("requestId")?.firstOrNull()?.value()).isEqualTo(TEST_REQUEST_ID.value.toByteArray())
assertThat(captor.firstValue.value()).isNotNull
assertThat(captor.firstValue.value()).isEqualTo(objectMapper.writeValueAsString(dnmpV2kafkaRecordData(TEST_REQUEST_ID)))
}
@ParameterizedTest
@MethodSource("dev.dnpm.etl.processor.output.KafkaMtbFileSenderTest#requestWithResponseSource")
fun shouldRetryOnMtbFileKafkaSendError(testData: TestData) {
val kafkaProperties = KafkaProperties("testtopic")
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
this.kafkaMtbFileSender = KafkaMtbFileSender(this.kafkaTemplate, kafkaProperties, retryTemplate, this.objectMapper)
doAnswer {
if (null != testData.exception) {
throw testData.exception
}
completedFuture(SendResult<String, String>(null, null))
}.whenever(kafkaTemplate).send(any<ProducerRecord<String, String>>())
kafkaMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile()))
val expectedCount = when (testData.exception) {
// OK - No Retry
null -> times(1)
// Request failed - Retry max 3 times
else -> times(3)
}
verify(kafkaTemplate, expectedCount).send(any<ProducerRecord<String, String>>())
} }
verify(kafkaTemplate, expectedCount).send(anyString(), anyString(), anyString())
} }
companion object { companion object {
val TEST_REQUEST_ID = RequestId("TestId") val TEST_REQUEST_ID = RequestId("TestId")
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID") val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID")
fun mtbFile(consentStatus: Consent.Status): MtbFile { fun dnpmV2MtbFile(): Mtb {
return if (consentStatus == Consent.Status.ACTIVE) { return Mtb().apply {
MtbFile.builder() this.patient = dev.pcvolkmer.mv64e.mtb.Patient().apply {
.withPatient( this.id = "PID"
Patient.builder() this.birthDate = Date.from(Instant.now())
.withId("PID") this.gender = GenderCoding().apply {
.withBirthDate("2000-08-08") this.code = GenderCodingCode.MALE
.withGender(Patient.Gender.MALE) }
.build() }
) this.episodesOfCare = listOf(
.withConsent( MtbEpisodeOfCare().apply {
Consent.builder() this.id = "1"
.withId("1") this.patient = Reference().apply {
.withStatus(consentStatus) this.id = "PID"
.withPatient("PID") }
.build() this.period = PeriodDate().apply {
) this.start = Date.from(Instant.now())
.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 kafkaRecordData(requestId: RequestId, consentStatus: Consent.Status): KafkaMtbFileSender.Data { fun dnmpV2kafkaRecordData(requestId: RequestId): MtbRequest {
return KafkaMtbFileSender.Data(requestId, mtbFile(consentStatus)) return DnpmV2MtbFileRequest(requestId, dnpmV2MtbFile())
} }
data class TestData(val requestStatus: RequestStatus, val exception: Throwable? = null) data class TestData(val requestStatus: RequestStatus, val exception: Throwable? = null)
@@ -231,4 +240,4 @@ class KafkaMtbFileSenderTest {
} }
} }
} }

View File

@@ -1,312 +0,0 @@
/*
* This file is part of ETL-Processor
*
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
package dev.dnpm.etl.processor.output
import com.fasterxml.jackson.databind.ObjectMapper
import com.fasterxml.jackson.module.kotlin.KotlinModule
import de.ukw.ccc.bwhc.dto.*
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.config.RestTargetProperties
import dev.dnpm.etl.processor.monitoring.ReportService
import dev.dnpm.etl.processor.monitoring.RequestStatus
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.params.ParameterizedTest
import org.junit.jupiter.params.provider.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" }
]
}
"""
}
}
}
}

View File

@@ -21,7 +21,7 @@ package dev.dnpm.etl.processor.output
import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import com.fasterxml.jackson.module.kotlin.KotlinModule import com.fasterxml.jackson.module.kotlin.KotlinModule
import de.ukw.ccc.bwhc.dto.* import dev.dnpm.etl.processor.CustomMediaType
import dev.dnpm.etl.processor.PatientPseudonym import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.RequestId import dev.dnpm.etl.processor.RequestId
import dev.dnpm.etl.processor.config.AppConfigProperties import dev.dnpm.etl.processor.config.AppConfigProperties
@@ -29,136 +29,136 @@ import dev.dnpm.etl.processor.config.AppConfiguration
import dev.dnpm.etl.processor.config.RestTargetProperties import dev.dnpm.etl.processor.config.RestTargetProperties
import dev.dnpm.etl.processor.monitoring.ReportService import dev.dnpm.etl.processor.monitoring.ReportService
import dev.dnpm.etl.processor.monitoring.RequestStatus import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.output.RestBwhcMtbFileSenderTest.Companion import dev.pcvolkmer.mv64e.mtb.*
import org.assertj.core.api.Assertions.assertThat import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Nested
import org.junit.jupiter.params.ParameterizedTest import org.junit.jupiter.params.ParameterizedTest
import org.junit.jupiter.params.provider.MethodSource import org.junit.jupiter.params.provider.MethodSource
import org.springframework.http.HttpHeaders
import org.springframework.http.HttpMethod import org.springframework.http.HttpMethod
import org.springframework.http.HttpStatus import org.springframework.http.HttpStatus
import org.springframework.http.MediaType
import org.springframework.retry.backoff.NoBackOffPolicy import org.springframework.retry.backoff.NoBackOffPolicy
import org.springframework.retry.policy.SimpleRetryPolicy import org.springframework.retry.policy.SimpleRetryPolicy
import org.springframework.retry.support.RetryTemplateBuilder import org.springframework.retry.support.RetryTemplateBuilder
import org.springframework.test.web.client.ExpectedCount import org.springframework.test.web.client.ExpectedCount
import org.springframework.test.web.client.MockRestServiceServer import org.springframework.test.web.client.MockRestServiceServer
import org.springframework.test.web.client.match.MockRestRequestMatchers.method import org.springframework.test.web.client.match.MockRestRequestMatchers.*
import org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo
import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus
import org.springframework.web.client.RestTemplate import org.springframework.web.client.RestTemplate
import java.time.Instant
import java.util.*
class RestDipMtbFileSenderTest { class RestDipMtbFileSenderTest {
private lateinit var mockRestServiceServer: MockRestServiceServer @Nested
inner class DnpmV2ContentRequest {
private lateinit var restMtbFileSender: RestMtbFileSender private lateinit var mockRestServiceServer: MockRestServiceServer
private var reportService = ReportService(ObjectMapper().registerModule(KotlinModule.Builder().build())) private lateinit var restMtbFileSender: RestMtbFileSender
@BeforeEach private var reportService = ReportService(ObjectMapper().registerModule(KotlinModule.Builder().build()))
fun setup() {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null, false)
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate) @BeforeEach
fun setup() {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null)
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
this.restMtbFileSender = RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService) this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
}
@ParameterizedTest this.restMtbFileSender = RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
@MethodSource("deleteRequestWithResponseSource")
fun shouldReturnExpectedResponseForDelete(requestWithResponse: RequestWithResponse) {
this.mockRestServiceServer
.expect(method(HttpMethod.DELETE))
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient/${TEST_PATIENT_PSEUDONYM.value}"))
.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(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/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 @ParameterizedTest
.expect(expectedCount, method(HttpMethod.POST)) @MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#mtbFileRequestWithResponseSource")
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient-record")) fun shouldReturnExpectedResponseForDnpmV2MtbFilePost(requestWithResponse: RequestWithResponse) {
.andRespond { this.mockRestServiceServer
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it) .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(MtbFileSender.MtbFileRequest(TEST_REQUEST_ID, mtbFile)) val response = restMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile()))
assertThat(response.status).isEqualTo(requestWithResponse.response.status) assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body) 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, false)
val retryTemplate = AppConfiguration().retryTemplate(AppConfigProperties("http://localhost:9000"))
retryTemplate.setBackOffPolicy(NoBackOffPolicy())
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.restMtbFileSender =
RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
val expectedCount = when (requestWithResponse.httpStatus) {
// OK - No Retry
HttpStatus.OK, HttpStatus.CREATED, HttpStatus.UNPROCESSABLE_ENTITY, HttpStatus.BAD_REQUEST -> ExpectedCount.max(
1
)
// Request failed - Retry max 3 times
else -> ExpectedCount.max(3)
} }
this.mockRestServiceServer }
.expect(expectedCount, method(HttpMethod.DELETE))
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient/${TEST_PATIENT_PSEUDONYM.value}")) @Nested
.andRespond { inner class DeleteRequest {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
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")
fun shouldReturnExpectedResponseForDelete(requestWithResponse: RequestWithResponse) {
this.mockRestServiceServer
.expect(method(HttpMethod.DELETE))
.andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient/${TEST_PATIENT_PSEUDONYM.value}"))
.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
@ParameterizedTest
@MethodSource("dev.dnpm.etl.processor.output.RestDipMtbFileSenderTest#deleteRequestWithResponseSource")
fun shouldRetryOnDeleteHttpRequestError(requestWithResponse: RequestWithResponse) {
val restTemplate = RestTemplate()
val restTargetProperties = RestTargetProperties("http://localhost:9000/api", null, null)
val retryTemplate = AppConfiguration().retryTemplate(AppConfigProperties())
retryTemplate.setBackOffPolicy(NoBackOffPolicy())
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
this.restMtbFileSender =
RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
val expectedCount = when (requestWithResponse.httpStatus) {
// OK - No Retry
HttpStatus.OK, HttpStatus.CREATED, HttpStatus.UNPROCESSABLE_ENTITY, HttpStatus.BAD_REQUEST -> ExpectedCount.max(
1
)
// Request failed - Retry max 3 times
else -> ExpectedCount.max(3)
} }
val response = restMtbFileSender.send(MtbFileSender.DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM)) this.mockRestServiceServer
assertThat(response.status).isEqualTo(requestWithResponse.response.status) .expect(expectedCount, method(HttpMethod.DELETE))
assertThat(response.body).isEqualTo(requestWithResponse.response.body) .andExpect(requestTo("http://localhost:9000/api/mtb/etl/patient/${TEST_PATIENT_PSEUDONYM.value}"))
.andRespond {
withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it)
}
val response = restMtbFileSender.send(DeleteRequest(TEST_REQUEST_ID, TEST_PATIENT_PSEUDONYM))
assertThat(response.status).isEqualTo(requestWithResponse.response.status)
assertThat(response.body).isEqualTo(requestWithResponse.response.body)
}
} }
companion object { companion object {
@@ -171,29 +171,28 @@ class RestDipMtbFileSenderTest {
val TEST_REQUEST_ID = RequestId("TestId") val TEST_REQUEST_ID = RequestId("TestId")
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID") val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID")
val mtbFile: MtbFile = MtbFile.builder() fun dnpmV2MtbFile(): Mtb {
.withPatient( return Mtb().apply {
Patient.builder() this.patient = dev.pcvolkmer.mv64e.mtb.Patient().apply {
.withId("PID") this.id = "PID"
.withBirthDate("2000-08-08") this.birthDate = Date.from(Instant.now())
.withGender(Patient.Gender.MALE) this.gender = GenderCoding().apply {
.build() this.code = GenderCodingCode.MALE
) }
.withConsent( }
Consent.builder() this.episodesOfCare = listOf(
.withId("1") MtbEpisodeOfCare().apply {
.withStatus(Consent.Status.ACTIVE) this.id = "1"
.withPatient("PID") this.patient = Reference().apply {
.build() this.id = "PID"
) }
.withEpisode( this.period = PeriodDate().apply {
Episode.builder() this.start = Date.from(Instant.now())
.withId("1") }
.withPatient("PID") }
.withPeriod(PeriodStart("2023-08-08")) )
.build() }
) }
.build()
private const val ERROR_RESPONSE_BODY = "Sonstiger Fehler bei der Übertragung" private const val ERROR_RESPONSE_BODY = "Sonstiger Fehler bei der Übertragung"
@@ -311,4 +310,4 @@ class RestDipMtbFileSenderTest {
} }
} }

View File

@@ -1,7 +1,7 @@
/* /*
* This file is part of ETL-Processor * This file is part of ETL-Processor
* *
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors * Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
* *
* This program is free software: you can redistribute it and/or modify * This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published * it under the terms of the GNU Affero General Public License as published
@@ -19,9 +19,18 @@
package dev.dnpm.etl.processor.pseudonym package dev.dnpm.etl.processor.pseudonym
import ca.uhn.fhir.context.FhirContext
import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.* 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 org.assertj.core.api.Assertions.assertThat 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.Test
import org.junit.jupiter.api.assertThrows import org.junit.jupiter.api.assertThrows
import org.junit.jupiter.api.extension.ExtendWith import org.junit.jupiter.api.extension.ExtendWith
@@ -31,168 +40,161 @@ import org.mockito.kotlin.anyValueClass
import org.mockito.kotlin.doAnswer import org.mockito.kotlin.doAnswer
import org.mockito.kotlin.whenever import org.mockito.kotlin.whenever
import org.springframework.core.io.ClassPathResource import org.springframework.core.io.ClassPathResource
import java.time.Instant
const val FAKE_MTB_FILE_PATH = "fake_MTBFile.json" import java.util.*
const val CLEAN_PATIENT_ID = "5dad2f0b-49c6-47d8-a952-7b9e9e0f7549"
@ExtendWith(MockitoExtension::class) @ExtendWith(MockitoExtension::class)
class ExtensionsTest { class ExtensionsTest {
fun getObjectMapper(): ObjectMapper {
private fun fakeMtbFile(): MtbFile { return JacksonConfig().objectMapper()
val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
return ObjectMapper().readValue(mtbFile, MtbFile::class.java)
} }
private fun MtbFile.serialized(): String { @Nested
return ObjectMapper().writeValueAsString(this) inner class UsingDnpmV2Datamodel {
}
@Test val FAKE_MTB_FILE_PATH = "mv64e-mtb-fake-patient.json"
fun shouldNotContainCleanPatientId(@Mock pseudonymizeService: PseudonymizeService) { val CLEAN_PATIENT_ID = "644bae7a-56f6-4ee8-b02f-c532e65af5b1"
doAnswer {
it.arguments[0]
"PSEUDO-ID"
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
val mtbFile = fakeMtbFile() private fun fakeMtbFile(): Mtb {
val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
mtbFile.pseudonymizeWith(pseudonymizeService) return getObjectMapper().readValue(mtbFile, Mtb::class.java)
assertThat(mtbFile.patient.id).isEqualTo("PSEUDO-ID")
assertThat(mtbFile.serialized()).doesNotContain(CLEAN_PATIENT_ID)
}
@Test
fun shouldNotContainAnyUuidAfterRehashingOfIds(@Mock pseudonymizeService: PseudonymizeService) {
doAnswer {
it.arguments[0]
"PSEUDO-ID"
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
doAnswer {
"TESTDOMAIN"
}.whenever(pseudonymizeService).prefix()
val mtbFile = fakeMtbFile()
mtbFile.pseudonymizeWith(pseudonymizeService)
mtbFile.anonymizeContentWith(pseudonymizeService)
val pattern = "\"[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}\"".toRegex().toPattern()
val matcher = pattern.matcher(mtbFile.serialized())
assertThrows<IllegalStateException> {
matcher.find()
matcher.group()
}.also {
assertThat(it.message).isEqualTo("No match found")
} }
private fun Mtb.serialized(): String {
return getObjectMapper().writeValueAsString(this)
}
@Test
fun shouldNotContainCleanPatientId(@Mock pseudonymizeService: PseudonymizeService) {
doAnswer {
it.arguments[0]
"PSEUDO-ID"
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
val mtbFile = fakeMtbFile()
mtbFile.ensureMetaDataIsInitialized()
addConsentData(mtbFile)
mtbFile.pseudonymizeWith(pseudonymizeService)
assertThat(mtbFile.patient.id).isEqualTo("PSEUDO-ID")
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 {
it.arguments[0]
"PSEUDO-ID"
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
doAnswer {
"TESTDOMAIN"
}.whenever(pseudonymizeService).prefix()
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 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")
}
}
} }
}
@Test
fun shouldRehashIdsWithPrefix(@Mock pseudonymizeService: PseudonymizeService) {
doAnswer {
it.arguments[0]
"PSEUDO-ID"
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
doAnswer {
"TESTDOMAIN"
}.whenever(pseudonymizeService).prefix()
val mtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.withId("1")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.withConsent(
Consent.builder()
.withId("1")
.withStatus(Consent.Status.ACTIVE)
.withPatient("123")
.build()
)
.withEpisode(
Episode.builder()
.withId("1")
.withPatient("1")
.withPeriod(PeriodStart("2023-08-08"))
.build()
)
.build()
mtbFile.pseudonymizeWith(pseudonymizeService)
mtbFile.anonymizeContentWith(pseudonymizeService)
assertThat(mtbFile.episode.id)
// TESTDOMAIN<sha256(TESTDOMAIN-1)[0-41]>
.isEqualTo("TESTDOMAIN44e20a53bbbf9f3ae39626d05df7014dcd77d6098")
}
@Test
fun shouldNotThrowExceptionOnNullValues(@Mock pseudonymizeService: PseudonymizeService) {
doAnswer {
it.arguments[0]
"PSEUDO-ID"
}.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
doAnswer {
"TESTDOMAIN"
}.whenever(pseudonymizeService).prefix()
val mtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
.withId("1")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build()
)
.withConsent(
Consent.builder()
.withId("1")
.withStatus(Consent.Status.ACTIVE)
.withPatient("123")
.build()
)
.withEpisode(
Episode.builder()
.withId("1")
.withPatient("1")
.withPeriod(PeriodStart("2023-08-08"))
.build()
)
.withClaims(null)
.withDiagnoses(null)
.withCarePlans(null)
.withClaimResponses(null)
.withEcogStatus(null)
.withFamilyMemberDiagnoses(null)
.withGeneticCounsellingRequests(null)
.withHistologyReevaluationRequests(null)
.withHistologyReports(null)
.withLastGuidelineTherapies(null)
.withMolecularPathologyFindings(null)
.withMolecularTherapies(null)
.withNgsReports(null)
.withPreviousGuidelineTherapies(null)
.withRebiopsyRequests(null)
.withRecommendations(null)
.withResponses(null)
.withStudyInclusionRequests(null)
.withSpecimens(null)
.build()
mtbFile.pseudonymizeWith(pseudonymizeService)
mtbFile.anonymizeContentWith(pseudonymizeService)
assertThat(mtbFile.episode.id).isNotNull()
}
}

View File

@@ -19,8 +19,8 @@
package dev.dnpm.etl.processor.pseudonym package dev.dnpm.etl.processor.pseudonym
import de.ukw.ccc.bwhc.dto.*
import dev.dnpm.etl.processor.config.PseudonymizeConfigProperties import dev.dnpm.etl.processor.config.PseudonymizeConfigProperties
import dev.pcvolkmer.mv64e.mtb.*
import org.assertj.core.api.Assertions.assertThat import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.Test import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith import org.junit.jupiter.api.extension.ExtendWith
@@ -29,31 +29,26 @@ import org.mockito.Mock
import org.mockito.junit.jupiter.MockitoExtension import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.doAnswer import org.mockito.kotlin.doAnswer
import org.mockito.kotlin.whenever import org.mockito.kotlin.whenever
import java.time.Instant
import java.util.*
@ExtendWith(MockitoExtension::class) @ExtendWith(MockitoExtension::class)
class PseudonymizeServiceTest { class PseudonymizeServiceTest {
private val mtbFile = MtbFile.builder() private val mtbFile = Mtb.builder()
.withPatient( .patient(
Patient.builder() Patient.builder()
.withId("123") .id("123")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build() .build()
) )
.withConsent( .episodesOfCare(
Consent.builder() listOf(
.withId("1") MtbEpisodeOfCare.builder()
.withStatus(Consent.Status.ACTIVE) .id("1")
.withPatient("123") .patient(Reference.builder().id("123").build())
.build() .period(PeriodDate.builder().start(Date.from(Instant.parse("2021-01-01T00:00:00.00Z"))).build())
) .build()
.withEpisode( )
Episode.builder()
.withId("1")
.withPatient("123")
.withPeriod(PeriodStart("2023-08-08"))
.build()
) )
.build() .build()
@@ -71,8 +66,8 @@ class PseudonymizeServiceTest {
} }
@Test @Test
fun sanitizeFileName(@Mock generator: GpasPseudonymGenerator) { fun sanitizeFileName() {
val result= GpasPseudonymGenerator.sanitizeValue("l://a\\bs;1*2?3>") val result = GpasPseudonymGenerator.sanitizeValue("l://a\\bs;1*2?3>")
assertThat(result).isEqualTo("l___a_bs_1_2_3_") assertThat(result).isEqualTo("l___a_bs_1_2_3_")
} }
@@ -90,4 +85,16 @@ class PseudonymizeServiceTest {
assertThat(mtbFile.patient.id).isEqualTo("UNKNOWN_123") 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
}
}
}

View File

@@ -0,0 +1,232 @@
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).isNotEmpty
}
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)
}
}
}

View File

@@ -20,15 +20,21 @@
package dev.dnpm.etl.processor.services package dev.dnpm.etl.processor.services
import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import de.ukw.ccc.bwhc.dto.* import dev.dnpm.etl.processor.Fingerprint
import dev.dnpm.etl.processor.* import dev.dnpm.etl.processor.PatientId
import dev.dnpm.etl.processor.PatientPseudonym
import dev.dnpm.etl.processor.config.AppConfigProperties 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.Request
import dev.dnpm.etl.processor.monitoring.RequestStatus import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.monitoring.RequestType import dev.dnpm.etl.processor.monitoring.RequestType
import 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.MtbFileSender
import dev.dnpm.etl.processor.output.RestMtbFileSender import dev.dnpm.etl.processor.output.RestMtbFileSender
import dev.dnpm.etl.processor.pseudonym.PseudonymizeService 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.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Test import org.junit.jupiter.api.Test
@@ -42,6 +48,7 @@ import org.mockito.kotlin.argumentCaptor
import org.mockito.kotlin.whenever import org.mockito.kotlin.whenever
import org.springframework.context.ApplicationEventPublisher import org.springframework.context.ApplicationEventPublisher
import java.time.Instant import java.time.Instant
import java.util.*
@ExtendWith(MockitoExtension::class) @ExtendWith(MockitoExtension::class)
@@ -53,7 +60,7 @@ class RequestProcessorTest {
private lateinit var requestService: RequestService private lateinit var requestService: RequestService
private lateinit var applicationEventPublisher: ApplicationEventPublisher private lateinit var applicationEventPublisher: ApplicationEventPublisher
private lateinit var appConfigProperties: AppConfigProperties private lateinit var appConfigProperties: AppConfigProperties
private lateinit var consentProcessor: ConsentProcessor
private lateinit var requestProcessor: RequestProcessor private lateinit var requestProcessor: RequestProcessor
@BeforeEach @BeforeEach
@@ -62,14 +69,16 @@ class RequestProcessorTest {
@Mock transformationService: TransformationService, @Mock transformationService: TransformationService,
@Mock sender: RestMtbFileSender, @Mock sender: RestMtbFileSender,
@Mock requestService: RequestService, @Mock requestService: RequestService,
@Mock applicationEventPublisher: ApplicationEventPublisher @Mock applicationEventPublisher: ApplicationEventPublisher,
@Mock consentProcessor: ConsentProcessor
) { ) {
this.pseudonymizeService = pseudonymizeService this.pseudonymizeService = pseudonymizeService
this.transformationService = transformationService this.transformationService = transformationService
this.sender = sender this.sender = sender
this.requestService = requestService this.requestService = requestService
this.applicationEventPublisher = applicationEventPublisher this.applicationEventPublisher = applicationEventPublisher
this.appConfigProperties = AppConfigProperties(null) this.appConfigProperties = AppConfigProperties()
this.consentProcessor = consentProcessor
val objectMapper = ObjectMapper() val objectMapper = ObjectMapper()
@@ -80,7 +89,8 @@ class RequestProcessorTest {
requestService, requestService,
objectMapper, objectMapper,
applicationEventPublisher, applicationEventPublisher,
appConfigProperties appConfigProperties,
consentProcessor
) )
} }
@@ -92,7 +102,7 @@ class RequestProcessorTest {
randomRequestId(), randomRequestId(),
PatientPseudonym("TEST_12345678901"), PatientPseudonym("TEST_12345678901"),
PatientId("P1"), PatientId("P1"),
Fingerprint("zdlzv5s5ydmd4ktw2v5piohegc4jcyrm6j66bq6tv2uxuerndmga"), Fingerprint("6vkiti5bk6ikwifpajpt7cygmd3dvw54d6lwfhzlynb3pqtzferq"),
RequestType.MTB_FILE, RequestType.MTB_FILE,
RequestStatus.SUCCESS, RequestStatus.SUCCESS,
Instant.parse("2023-08-08T02:00:00Z") Instant.parse("2023-08-08T02:00:00Z")
@@ -109,29 +119,24 @@ class RequestProcessorTest {
doAnswer { doAnswer {
it.arguments[0] it.arguments[0]
}.whenever(transformationService).transform(any()) }.whenever(transformationService).transform(any<Mtb>())
val mtbFile = MtbFile.builder() whenever(consentProcessor.consentGatedCheckAndTryEmbedding(any())).thenReturn(true)
.withPatient(
val mtbFile = Mtb.builder()
.patient(
Patient.builder() Patient.builder()
.withId("1") .id("123")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build() .build()
) )
.withConsent( .episodesOfCare(
Consent.builder() listOf(
.withId("1") MtbEpisodeOfCare.builder()
.withStatus(Consent.Status.ACTIVE) .id("1")
.withPatient("123") .patient(Reference.builder().id("123").build())
.build() .period(PeriodDate.builder().start(Date.from(Instant.parse("2023-08-08T02:00:00.00Z"))).build())
) .build()
.withEpisode( )
Episode.builder()
.withId("1")
.withPatient("1")
.withPeriod(PeriodStart("2023-08-08"))
.build()
) )
.build() .build()
@@ -151,7 +156,7 @@ class RequestProcessorTest {
randomRequestId(), randomRequestId(),
PatientPseudonym("TEST_12345678901"), PatientPseudonym("TEST_12345678901"),
PatientId("P1"), PatientId("P1"),
Fingerprint("zdlzv5s5ydmd4ktw2v5piohegc4jcyrm6j66bq6tv2uxuerndmga"), Fingerprint("4gcjwtjjtcczybsljxepdfpkaeusvd7g3vogfqpmphyffyzfx7dq"),
RequestType.MTB_FILE, RequestType.MTB_FILE,
RequestStatus.SUCCESS, RequestStatus.SUCCESS,
Instant.parse("2023-08-08T02:00:00Z") Instant.parse("2023-08-08T02:00:00Z")
@@ -168,29 +173,24 @@ class RequestProcessorTest {
doAnswer { doAnswer {
it.arguments[0] it.arguments[0]
}.whenever(transformationService).transform(any()) }.whenever(transformationService).transform(any<Mtb>())
val mtbFile = MtbFile.builder() whenever(consentProcessor.consentGatedCheckAndTryEmbedding(any())).thenReturn(true)
.withPatient(
val mtbFile = Mtb.builder()
.patient(
Patient.builder() Patient.builder()
.withId("1") .id("123")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build() .build()
) )
.withConsent( .episodesOfCare(
Consent.builder() listOf(
.withId("1") MtbEpisodeOfCare.builder()
.withStatus(Consent.Status.ACTIVE) .id("1")
.withPatient("123") .patient(Reference.builder().id("123").build())
.build() .period(PeriodDate.builder().start(Date.from(Instant.parse("2021-01-01T00:00:00.00Z"))).build())
) .build()
.withEpisode( )
Episode.builder()
.withId("1")
.withPatient("1")
.withPeriod(PeriodStart("2023-08-08"))
.build()
) )
.build() .build()
@@ -223,7 +223,7 @@ class RequestProcessorTest {
doAnswer { doAnswer {
MtbFileSender.Response(status = RequestStatus.SUCCESS) MtbFileSender.Response(status = RequestStatus.SUCCESS)
}.whenever(sender).send(any<MtbFileSender.MtbFileRequest>()) }.whenever(sender).send(any<DnpmV2MtbFileRequest>())
doAnswer { doAnswer {
it.arguments[0] as String it.arguments[0] as String
@@ -231,29 +231,24 @@ class RequestProcessorTest {
doAnswer { doAnswer {
it.arguments[0] it.arguments[0]
}.whenever(transformationService).transform(any()) }.whenever(transformationService).transform(any<Mtb>())
val mtbFile = MtbFile.builder() whenever(consentProcessor.consentGatedCheckAndTryEmbedding(any())).thenReturn(true)
.withPatient(
val mtbFile = Mtb.builder()
.patient(
Patient.builder() Patient.builder()
.withId("1") .id("123")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build() .build()
) )
.withConsent( .episodesOfCare(
Consent.builder() listOf(
.withId("1") MtbEpisodeOfCare.builder()
.withStatus(Consent.Status.ACTIVE) .id("1")
.withPatient("123") .patient(Reference.builder().id("123").build())
.build() .period(PeriodDate.builder().start(Date.from(Instant.parse("2021-01-01T00:00:00.00Z"))).build())
) .build()
.withEpisode( )
Episode.builder()
.withId("1")
.withPatient("1")
.withPeriod(PeriodStart("2023-08-08"))
.build()
) )
.build() .build()
@@ -286,7 +281,7 @@ class RequestProcessorTest {
doAnswer { doAnswer {
MtbFileSender.Response(status = RequestStatus.ERROR) MtbFileSender.Response(status = RequestStatus.ERROR)
}.whenever(sender).send(any<MtbFileSender.MtbFileRequest>()) }.whenever(sender).send(any<DnpmV2MtbFileRequest>())
doAnswer { doAnswer {
it.arguments[0] as String it.arguments[0] as String
@@ -294,29 +289,36 @@ class RequestProcessorTest {
doAnswer { doAnswer {
it.arguments[0] it.arguments[0]
}.whenever(transformationService).transform(any()) }.whenever(transformationService).transform(any<Mtb>())
val mtbFile = MtbFile.builder() whenever(consentProcessor.consentGatedCheckAndTryEmbedding(any())).thenReturn(true)
.withPatient(
val mtbFile = Mtb.builder()
.patient(
Patient.builder() Patient.builder()
.withId("1") .id("123")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build() .build()
) )
.withConsent( .metadata(
Consent.builder() MvhMetadata
.withId("1") .builder()
.withStatus(Consent.Status.ACTIVE) .modelProjectConsent(
.withPatient("123") ModelProjectConsent
.builder()
.provisions(
listOf(Provision.builder().type(ConsentProvision.PERMIT).purpose(ModelProjectConsentPurpose.SEQUENCING).build())
).build()
)
.build() .build()
) )
.withEpisode( .episodesOfCare(
Episode.builder() listOf(
.withId("1") MtbEpisodeOfCare.builder()
.withPatient("1") .id("1")
.withPeriod(PeriodStart("2023-08-08")) .patient(Reference.builder().id("123").build())
.build() .period(PeriodDate.builder().start(Date.from(Instant.parse("2021-01-01T00:00:00.00Z"))).build())
.build()
)
) )
.build() .build()
@@ -336,9 +338,12 @@ class RequestProcessorTest {
doAnswer { doAnswer {
MtbFileSender.Response(status = RequestStatus.UNKNOWN) MtbFileSender.Response(status = RequestStatus.UNKNOWN)
}.whenever(sender).send(any<MtbFileSender.DeleteRequest>()) }.whenever(sender).send(any<DeleteRequest>())
this.requestProcessor.processDeletion(TEST_PATIENT_ID) this.requestProcessor.processDeletion(
TEST_PATIENT_ID,
isConsented = TtpConsentStatus.UNKNOWN_CHECK_FILE
)
val requestCaptor = argumentCaptor<Request>() val requestCaptor = argumentCaptor<Request>()
verify(requestService, times(1)).save(requestCaptor.capture()) verify(requestService, times(1)).save(requestCaptor.capture())
@@ -354,9 +359,12 @@ class RequestProcessorTest {
doAnswer { doAnswer {
MtbFileSender.Response(status = RequestStatus.SUCCESS) MtbFileSender.Response(status = RequestStatus.SUCCESS)
}.whenever(sender).send(any<MtbFileSender.DeleteRequest>()) }.whenever(sender).send(any<DeleteRequest>())
this.requestProcessor.processDeletion(TEST_PATIENT_ID) this.requestProcessor.processDeletion(
TEST_PATIENT_ID,
isConsented = TtpConsentStatus.UNKNOWN_CHECK_FILE
)
val eventCaptor = argumentCaptor<ResponseEvent>() val eventCaptor = argumentCaptor<ResponseEvent>()
verify(applicationEventPublisher, times(1)).publishEvent(eventCaptor.capture()) verify(applicationEventPublisher, times(1)).publishEvent(eventCaptor.capture())
@@ -372,9 +380,12 @@ class RequestProcessorTest {
doAnswer { doAnswer {
MtbFileSender.Response(status = RequestStatus.ERROR) MtbFileSender.Response(status = RequestStatus.ERROR)
}.whenever(sender).send(any<MtbFileSender.DeleteRequest>()) }.whenever(sender).send(any<DeleteRequest>())
this.requestProcessor.processDeletion(TEST_PATIENT_ID) this.requestProcessor.processDeletion(
TEST_PATIENT_ID,
isConsented = TtpConsentStatus.UNKNOWN_CHECK_FILE
)
val eventCaptor = argumentCaptor<ResponseEvent>() val eventCaptor = argumentCaptor<ResponseEvent>()
verify(applicationEventPublisher, times(1)).publishEvent(eventCaptor.capture()) verify(applicationEventPublisher, times(1)).publishEvent(eventCaptor.capture())
@@ -386,7 +397,10 @@ class RequestProcessorTest {
fun testShouldSendDeleteRequestWithPseudonymErrorAndSaveErrorRequestStatus() { fun testShouldSendDeleteRequestWithPseudonymErrorAndSaveErrorRequestStatus() {
doThrow(RuntimeException()).whenever(pseudonymizeService).patientPseudonym(anyValueClass()) doThrow(RuntimeException()).whenever(pseudonymizeService).patientPseudonym(anyValueClass())
this.requestProcessor.processDeletion(TEST_PATIENT_ID) this.requestProcessor.processDeletion(
TEST_PATIENT_ID,
isConsented = TtpConsentStatus.UNKNOWN_CHECK_FILE
)
val requestCaptor = argumentCaptor<Request>() val requestCaptor = argumentCaptor<Request>()
verify(requestService, times(1)).save(requestCaptor.capture()) verify(requestService, times(1)).save(requestCaptor.capture())
@@ -404,33 +418,28 @@ class RequestProcessorTest {
doAnswer { doAnswer {
it.arguments[0] it.arguments[0]
}.whenever(transformationService).transform(any()) }.whenever(transformationService).transform(any<Mtb>())
doAnswer { doAnswer {
MtbFileSender.Response(status = RequestStatus.SUCCESS) MtbFileSender.Response(status = RequestStatus.SUCCESS)
}.whenever(sender).send(any<MtbFileSender.MtbFileRequest>()) }.whenever(sender).send(any<DnpmV2MtbFileRequest>())
val mtbFile = MtbFile.builder() whenever(consentProcessor.consentGatedCheckAndTryEmbedding(any())).thenReturn(true)
.withPatient(
val mtbFile = Mtb.builder()
.patient(
Patient.builder() Patient.builder()
.withId("1") .id("123")
.withBirthDate("2000-08-08")
.withGender(Patient.Gender.MALE)
.build() .build()
) )
.withConsent( .episodesOfCare(
Consent.builder() listOf(
.withId("1") MtbEpisodeOfCare.builder()
.withStatus(Consent.Status.ACTIVE) .id("1")
.withPatient("123") .patient(Reference.builder().id("123").build())
.build() .period(PeriodDate.builder().start(Date.from(Instant.parse("2021-01-01T00:00:00.00Z"))).build())
) .build()
.withEpisode( )
Episode.builder()
.withId("1")
.withPatient("1")
.withPeriod(PeriodStart("2023-08-08"))
.build()
) )
.build() .build()
@@ -446,4 +455,4 @@ class RequestProcessorTest {
val TEST_PATIENT_ID = PatientId("TEST_12345678901") val TEST_PATIENT_ID = PatientId("TEST_12345678901")
} }
} }

View File

@@ -19,14 +19,14 @@
package dev.dnpm.etl.processor.services package dev.dnpm.etl.processor.services
import com.fasterxml.jackson.databind.ObjectMapper import dev.dnpm.etl.processor.config.JacksonConfig
import de.ukw.ccc.bwhc.dto.Consent import dev.pcvolkmer.mv64e.mtb.*
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.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Test import org.junit.jupiter.api.Test
import org.hl7.fhir.instance.model.api.IBaseResource
import java.time.Instant
import java.util.Date
class TransformationServiceTest { class TransformationServiceTest {
@@ -35,61 +35,92 @@ class TransformationServiceTest {
@BeforeEach @BeforeEach
fun setup() { fun setup() {
this.service = TransformationService( this.service = TransformationService(
ObjectMapper(), listOf( JacksonConfig().objectMapper(), listOf(
Transformation.of("consent.status") from Consent.Status.ACTIVE to Consent.Status.REJECTED, Transformation.of("diagnoses[*].code.version") from "2013" to "2014",
Transformation.of("diagnoses[*].icd10.version") from "2013" to "2014",
) )
) )
} }
@Test @Test
fun shouldTransformMtbFile() { fun shouldTransformMtbFile() {
val mtbFile = MtbFile.builder().withDiagnoses( val mtbFile = Mtb.builder().diagnoses(
listOf( listOf(
Diagnosis.builder().withId("1234").withIcd10(Icd10("F79.9").also { MtbDiagnosis.builder().id("1234").code(Coding.builder().code("F79.9").version("2013").build()).build()
it.version = "2013"
}).build()
) )
).build() ).build()
val actual = this.service.transform(mtbFile) val actual = this.service.transform(mtbFile)
assertThat(actual).isNotNull assertThat(actual).isNotNull
assertThat(actual.diagnoses[0].icd10.version).isEqualTo("2014") assertThat(actual.diagnoses[0].code.version).isEqualTo("2014")
} }
@Test @Test
fun shouldOnlyTransformGivenValues() { fun shouldOnlyTransformGivenValues() {
val mtbFile = MtbFile.builder().withDiagnoses( val mtbFile = Mtb.builder().diagnoses(
listOf( listOf(
Diagnosis.builder().withId("1234").withIcd10(Icd10("F79.9").also { MtbDiagnosis.builder().id("1234").code(Coding.builder().code("F79.9").version("2013").build()).build(),
it.version = "2013" MtbDiagnosis.builder().id("1234").code(Coding.builder().code("F79.8").version("2019").build()).build()
}).build(),
Diagnosis.builder().withId("5678").withIcd10(Icd10("F79.8").also {
it.version = "2019"
}).build()
) )
).build() ).build()
val actual = this.service.transform(mtbFile) val actual = this.service.transform(mtbFile)
assertThat(actual).isNotNull assertThat(actual).isNotNull
assertThat(actual.diagnoses[0].icd10.code).isEqualTo("F79.9") assertThat(actual.diagnoses[0].code.code).isEqualTo("F79.9")
assertThat(actual.diagnoses[0].icd10.version).isEqualTo("2014") assertThat(actual.diagnoses[0].code.version).isEqualTo("2014")
assertThat(actual.diagnoses[1].icd10.code).isEqualTo("F79.8") assertThat(actual.diagnoses[1].code.code).isEqualTo("F79.8")
assertThat(actual.diagnoses[1].icd10.version).isEqualTo("2019") assertThat(actual.diagnoses[1].code.version).isEqualTo("2019")
} }
@Test @Test
fun shouldTransformMtbFileWithConsentEnum() { fun shouldTransformConsentValues() {
val mtbFile = MtbFile.builder().withConsent( val mtbFile = Mtb.builder().diagnoses(
Consent("123", "456", Consent.Status.ACTIVE) 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()
)
).build() ).build()
val actual = this.service.transform(mtbFile) val actual = this.service.transform(mtbFile)
assertThat(actual.consent).isNotNull assertThat(actual).isNotNull
assertThat(actual.consent.status).isEqualTo(Consent.Status.REJECTED) 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
}
}

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

View File

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

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