mirror of
https://github.com/pcvolkmer/mv64e-etl-processor
synced 2025-09-13 17:02:52 +00:00
Compare commits
280 Commits
Author | SHA1 | Date | |
---|---|---|---|
3d9d84438d | |||
10b5bedac3 | |||
96f22a6744 | |||
6dfec5c341 | |||
c38c0c6197 | |||
4602032bcf | |||
9cc9f130df | |||
b92fbae2c5 | |||
5704282a1c | |||
ba21d029d1 | |||
b7aa187293 | |||
8402462c3b | |||
d3e6aa5821 | |||
eed0972018 | |||
|
3b66f42eb2 | ||
c40fd7f816 | |||
1759729931 | |||
|
7f80224eac | ||
3eb1c79cec | |||
|
be513f305a | ||
2e88157893 | |||
bf898e5c25 | |||
e5693736d8 | |||
|
dfc9de78ce | ||
|
199511e567 | ||
1319be8b3f | |||
1a5737189c | |||
7543785116 | |||
858189aa59 | |||
17f4dc3512 | |||
1dd601e8db | |||
b748603c06 | |||
b939b2bf57 | |||
c6b37fda69 | |||
8e3de6a220 | |||
c5c553f817 | |||
7d97365aea | |||
48b1e62e22 | |||
66cc818755 | |||
9d4786fae3 | |||
b78dc3519b | |||
46015c5b66 | |||
a4d0b73d2b | |||
9307fc0dad | |||
586d388e57 | |||
7ae34719fd | |||
033750eb10 | |||
befeef3153 | |||
98b971d7db | |||
56a63b276e | |||
c0ea5fcd51 | |||
d4fd54f51f | |||
d49671f0d4 | |||
84868dc22c | |||
4ad6c4bd0a | |||
9bdd8ba375 | |||
f027339425 | |||
3c5639708f | |||
639159c677 | |||
38261d6d2c | |||
47ebe46974 | |||
f347653be8 | |||
775a7df1ce | |||
f66b737f11 | |||
3a19212a78 | |||
280fbd445e | |||
91e2cf5ef1 | |||
262c54f2e5 | |||
|
b25e580113 | ||
ff27b7157d | |||
1e652a7856 | |||
74ff9f08a4 | |||
23cc2f365a | |||
53b4cf1a95 | |||
5ce13e962b | |||
3257493b6a | |||
2036077c06 | |||
8ce3aed870 | |||
998989d319 | |||
e95fa2fb12 | |||
1bcc8c13de | |||
2fc3299543 | |||
5575867632 | |||
46ba565c29 | |||
|
6cdbd35e64 | ||
|
d258d9081b | ||
eb49ba611b | |||
efa736f232 | |||
4a7030e85b | |||
464c8b8c1d | |||
3f1bb4f4e2 | |||
370ea87095 | |||
c8f6e6efc8 | |||
c949ec07e5 | |||
87658bfa58 | |||
99efd6c98a | |||
e42d11f125 | |||
6e0ec6b95a | |||
0ff56416dd | |||
3a2f6a2bb6 | |||
3eb9e68786 | |||
59403d1dba | |||
9f5ac664af | |||
5867ed9dd3 | |||
4d6d1879e6 | |||
2a34c0efc9 | |||
0ee00de5aa | |||
baeebdb9b8 | |||
8b194e7212 | |||
070100eba0 | |||
ce1489d9a1 | |||
ca1e73a0b5 | |||
041bf459ef | |||
c922e27758 | |||
4d5c0ce1fb | |||
bb0bbf5a28 | |||
1b4585d601 | |||
dad3ea80ee | |||
01446bdece | |||
43660a4dcb | |||
5320466b6c | |||
263cb02416 | |||
0b37fd7091 | |||
bdee969409 | |||
4c39920afd | |||
5e836c48b0 | |||
fb5a3c062c | |||
8fc0609aa4 | |||
a846a8765a | |||
8645becd82 | |||
011511d5ef | |||
e9839c2731 | |||
86bee9e2cf | |||
f419acb924 | |||
52171e8ebe | |||
a2124ba83d | |||
a046203339 | |||
b40d41ce8c | |||
57de96771c | |||
3bc148f7ea | |||
8e6b1ec799 | |||
8e5f5c73ec | |||
d4f984b138 | |||
24ebbf3b50 | |||
9c6bd64a7e | |||
6567aa803c | |||
e874350712 | |||
94d7b4c4f0 | |||
107429fda7 | |||
26b2f65e67 | |||
e863269a42 | |||
4ab95ef11f | |||
2244ef1b86 | |||
c3ddb387e2 | |||
ae5d8341cc | |||
40b2558943 | |||
9a6a0c6138 | |||
5985327219 | |||
06f9e8ace9 | |||
365a651918 | |||
5fcc24f915 | |||
3bd7239812 | |||
1672ad8640 | |||
710aeb1f18 | |||
06d11790b6 | |||
959f6889d4 | |||
0f5a68660d | |||
b809a2da02 | |||
effffcfc1a | |||
7b3151d227 | |||
26b415f336 | |||
bda3c30a74 | |||
8779600330 | |||
159fb46009 | |||
eabbbfbb68 | |||
4db38ef2f0 | |||
ed6d21e920 | |||
550bee5ad3 | |||
8313420de5 | |||
1651f446fe | |||
bd7dccbd87 | |||
8ae958b8c4 | |||
0f144568e3 | |||
08540e3bd7 | |||
43af1aa103 | |||
056a087065 | |||
a730ce2a53 | |||
12eb1feea6 | |||
af714f7b64 | |||
f47b0b7de4 | |||
d8ba6b67cb | |||
40b89dd4f1 | |||
e3aeee61de | |||
07e59f9b02 | |||
f751d64220 | |||
299bd56d63 | |||
a0c4d1863f | |||
fc1901211d | |||
bed91439db | |||
a8e008000e | |||
a9c771aa99 | |||
256d9d4ff0 | |||
41b87835ca | |||
3654962294 | |||
9382da7101 | |||
67ab0ef2be | |||
69d796dab4 | |||
4bfe7dc698 | |||
0aec5e4479 | |||
b1a83510a6 | |||
6806c4fd69 | |||
b2016df852 | |||
b332f3c5ff | |||
9eb65788e1 | |||
9392bcadc9 | |||
a008641192 | |||
5928d52237 | |||
1eb40b40c9 | |||
feb9f2430c | |||
200c5338ea | |||
5c15ad4518 | |||
0b6decf88d | |||
cfdf41d550 | |||
45c65d53ce | |||
4568f491f5 | |||
952ad8c0cf | |||
3e45bf8494 | |||
46ddaf10f7 | |||
408b121f26 | |||
61e5273158 | |||
50b8f7bbd4 | |||
25f286f73b | |||
50a6d66718 | |||
f5c80f6d81 | |||
7659939d3c | |||
f58d4a76cf | |||
c2dd450579 | |||
a1b62ad754 | |||
59d8744c84 | |||
d2a6ec17ea | |||
550403cc9f | |||
d3a4500568 | |||
2e4fee97a8 | |||
5355eee05c | |||
3e22000541 | |||
8c319197d0 | |||
a31d2b4bcc | |||
67d5fb4c67 | |||
329be65d1a | |||
91fe3d1c23 | |||
f4b86ce2ea | |||
19d0daa442 | |||
cc9811d11d | |||
8ce5b06823 | |||
3cc34fb30b | |||
17e04a3f89 | |||
f71a775e12 | |||
45c83e943b | |||
6dcbfde62e | |||
4cdc419478 | |||
90b529adb4 | |||
a3bc60986b | |||
f5df0b5d22 | |||
972ac745e9 | |||
358373cf70 | |||
27a62321fa | |||
30cf0fd22e | |||
531a8589db | |||
fa89a64ddd | |||
45ad5e8827 | |||
c4eb4d0fe2 | |||
4bc69a353c | |||
9d30f750f7 | |||
a1a252d5a9 | |||
568942bfe5 | |||
15f0432553 | |||
113bf2dd2e | |||
7ac151202a | |||
5d9d47c2df | |||
585468314c |
20
.github/workflows/deploy.yml
vendored
20
.github/workflows/deploy.yml
vendored
@@ -1,4 +1,4 @@
|
|||||||
name: "Run build and deploy"
|
name: 'Run build and deploy'
|
||||||
|
|
||||||
on:
|
on:
|
||||||
release:
|
release:
|
||||||
@@ -8,20 +8,20 @@ jobs:
|
|||||||
docker:
|
docker:
|
||||||
runs-on: ubuntu-latest
|
runs-on: ubuntu-latest
|
||||||
steps:
|
steps:
|
||||||
- uses: actions/checkout@v3
|
- uses: actions/checkout@v4
|
||||||
- uses: actions/setup-java@v3
|
- uses: actions/setup-java@v4
|
||||||
with:
|
with:
|
||||||
java-version: '17'
|
java-version: '21'
|
||||||
distribution: 'temurin'
|
distribution: 'temurin'
|
||||||
|
|
||||||
- name: Setup Gradle
|
- name: Setup Gradle
|
||||||
uses: gradle/gradle-build-action@v2.4.2
|
uses: gradle/actions/setup-gradle@v3
|
||||||
|
|
||||||
- name: Set up Docker Buildx
|
- name: Set up Docker Buildx
|
||||||
uses: docker/setup-buildx-action@v2
|
uses: docker/setup-buildx-action@v3
|
||||||
|
|
||||||
- name: Login to Docker Hub
|
- name: Login to Docker Hub
|
||||||
uses: docker/login-action@v2
|
uses: docker/login-action@v3
|
||||||
with:
|
with:
|
||||||
registry: ghcr.io
|
registry: ghcr.io
|
||||||
username: ${{ github.actor }}
|
username: ${{ github.actor }}
|
||||||
@@ -30,6 +30,6 @@ jobs:
|
|||||||
- name: Execute image build and push
|
- name: Execute image build and push
|
||||||
run: |
|
run: |
|
||||||
./gradlew bootBuildImage
|
./gradlew bootBuildImage
|
||||||
docker tag ghcr.io/ccc-mf/etl-processor ghcr.io/ccc-mf/etl-processor:${{ github.ref_name }}
|
docker tag ghcr.io/${{ github.repository }} ghcr.io/${{ github.repository }}:${{ github.ref_name }}
|
||||||
docker push ghcr.io/ccc-mf/etl-processor
|
docker push ghcr.io/${{ github.repository }}
|
||||||
docker push ghcr.io/ccc-mf/etl-processor:${{ github.ref_name }}
|
docker push ghcr.io/${{ github.repository }}:${{ github.ref_name }}
|
16
.github/workflows/test.yml
vendored
16
.github/workflows/test.yml
vendored
@@ -11,14 +11,14 @@ jobs:
|
|||||||
tests:
|
tests:
|
||||||
runs-on: ubuntu-latest
|
runs-on: ubuntu-latest
|
||||||
steps:
|
steps:
|
||||||
- uses: actions/checkout@v3
|
- uses: actions/checkout@v4
|
||||||
- uses: actions/setup-java@v3
|
- uses: actions/setup-java@v4
|
||||||
with:
|
with:
|
||||||
java-version: '17'
|
java-version: '21'
|
||||||
distribution: 'temurin'
|
distribution: 'temurin'
|
||||||
|
|
||||||
- name: Setup Gradle
|
- name: Setup Gradle
|
||||||
uses: gradle/gradle-build-action@v2.4.2
|
uses: gradle/actions/setup-gradle@v3
|
||||||
|
|
||||||
- name: Execute tests
|
- name: Execute tests
|
||||||
run: ./gradlew test
|
run: ./gradlew test
|
||||||
@@ -26,14 +26,14 @@ jobs:
|
|||||||
integrationTests:
|
integrationTests:
|
||||||
runs-on: ubuntu-latest
|
runs-on: ubuntu-latest
|
||||||
steps:
|
steps:
|
||||||
- uses: actions/checkout@v3
|
- uses: actions/checkout@v4
|
||||||
- uses: actions/setup-java@v3
|
- uses: actions/setup-java@v4
|
||||||
with:
|
with:
|
||||||
java-version: '17'
|
java-version: '21'
|
||||||
distribution: 'temurin'
|
distribution: 'temurin'
|
||||||
|
|
||||||
- name: Setup Gradle
|
- name: Setup Gradle
|
||||||
uses: gradle/gradle-build-action@v2.4.2
|
uses: gradle/actions/setup-gradle@v3
|
||||||
|
|
||||||
- name: Execute integration tests
|
- name: Execute integration tests
|
||||||
run: ./gradlew integrationTest
|
run: ./gradlew integrationTest
|
4
.gitignore
vendored
4
.gitignore
vendored
@@ -5,6 +5,8 @@ build/
|
|||||||
!**/src/main/**/build/
|
!**/src/main/**/build/
|
||||||
!**/src/test/**/build/
|
!**/src/test/**/build/
|
||||||
|
|
||||||
|
bindings/ca-certificates/*.pem
|
||||||
|
|
||||||
### STS ###
|
### STS ###
|
||||||
.apt_generated
|
.apt_generated
|
||||||
.classpath
|
.classpath
|
||||||
@@ -37,3 +39,5 @@ out/
|
|||||||
.vscode/
|
.vscode/
|
||||||
/dev/gpas*
|
/dev/gpas*
|
||||||
/deploy/.env
|
/deploy/.env
|
||||||
|
/dev/gICS*
|
||||||
|
/dev/gPAS*
|
||||||
|
400
README.md
400
README.md
@@ -1,28 +1,81 @@
|
|||||||
# ETL-Processor for bwHC data [](https://github.com/CCC-MF/etl-processor/actions/workflows/test.yml)
|
# ETL-Processor für das MV gem. §64e und DNPM:DIP
|
||||||
|
[](https://github.com/pcvolkmer/etl-processor/actions/workflows/test.yml)
|
||||||
|
|
||||||
Diese Anwendung versendet ein bwHC-MTB-File an das bwHC-Backend und pseudonymisiert die Patienten-ID.
|
Diese Anwendung 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 das bwHC-backend weitergeleitet.
|
Löschanfragen werden immer als Löschanfrage an DNPM:DIP weitergeleitet.
|
||||||
|
|
||||||
Zudem ist eine minimalistische Weboberfläche integriert, die einen Einblick in den aktuellen Zustand der Anwendung gewährt.
|
Zudem ist eine minimalistische Weboberfläche integriert, die einen Einblick in den aktuellen Zustand der Anwendung gewährt.
|
||||||
|
|
||||||

|

|
||||||
|
|
||||||
|
### 🔥 Wichtige Änderungen in Version 0.11
|
||||||
|
|
||||||
|
Ab Version 0.11 wird ausschließlich [DNPM:DIP](https://github.com/dnpm-dip) unterstützt.
|
||||||
|
|
||||||
|
Zudem wurde der Name des Pakets in **mv64e-etl-processor** geändert.
|
||||||
|
|
||||||
|
## Funktionsweise
|
||||||
|
|
||||||
|
### Duplikaterkennung
|
||||||
|
|
||||||
|
Die Erkennung von Duplikaten ist normalerweise immer aktiv, kann jedoch über den
|
||||||
|
Konfigurationsparameter
|
||||||
|
`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 das bwHC-Backend gesendet.
|
Anfragen werden, wenn nicht als Duplikat behandelt, nach der Pseudonymisierung direkt an DNPM:DIP
|
||||||
|
gesendet.
|
||||||
|
|
||||||
|
Ein HTTP-Request kann, angenommen die Installation erfolgte auf dem Host `dnpm.example.com` an
|
||||||
|
nachfolgende URLs gesendet werden:
|
||||||
|
|
||||||
|
| HTTP-Request | URL | Consent-Status im Datensatz | Bemerkung |
|
||||||
|
|--------------|-----------------------------------------|-----------------------------|---------------------------------------------------------------------------------|
|
||||||
|
| `POST` | `https://dnpm.example.com/mtb` | `ACTIVE` | Die Anwendung verarbeitet den eingehenden Datensatz |
|
||||||
|
| `POST` | `https://dnpm.example.com/mtb` | `REJECT` | Die Anwendung sendet einen Lösch-Request für die im Datensatz angegebene Pat-ID |
|
||||||
|
| `DELETE` | `https://dnpm.example.com/mtb/12345678` | - | Die Anwendung sendet einen Lösch-Request für Pat-ID `12345678` |
|
||||||
|
|
||||||
|
Anstelle des Pfads `/mtb` kann auch, wie in Version 0.9 und älter üblich, `/mtbfile` verwendet
|
||||||
|
werden.
|
||||||
|
|
||||||
### Datenübermittlung mit Apache Kafka
|
### 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
|
||||||
|
|
||||||
@@ -33,34 +86,101 @@ Siehe hierzu auch: https://github.com/CCC-MF/kafka-to-bwhc
|
|||||||
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.
|
||||||
Ist diese nicht gesetzt. wird intern eine Anonymisierung der Patienten-ID vorgenommen.
|
Ist diese nicht gesetzt. wird intern eine Anonymisierung der Patienten-ID vorgenommen.
|
||||||
|
|
||||||
* `APP_PSEUDONYMIZE_PREFIX`: Standortbezogenes Prefix - `UNKNOWN`, wenn nicht gesetzt
|
* `APP_PSEUDONYMIZE_PREFIX`: Standortbezogenes Präfix - `UNKNOWN`, wenn nicht gesetzt
|
||||||
* `APP_PSEUDONYMIZE_GENERATOR`: `BUILDIN` oder `GPAS` - `BUILDIN`, wenn nicht gesetzt
|
* `APP_PSEUDONYMIZE_GENERATOR`: `BUILDIN` oder `GPAS` - `BUILDIN`, wenn nicht gesetzt
|
||||||
|
|
||||||
|
**Hinweis**
|
||||||
|
|
||||||
|
Die Pseudonymisierung erfolgt im ETL-Prozessor nur für die Patienten-ID.
|
||||||
|
Andere IDs werden mithilfe des standortbezogenen Präfixes (erneut) anonymisiert, um für den
|
||||||
|
aktuellen Kontext nicht
|
||||||
|
vergleichbare IDs bereitzustellen.
|
||||||
|
|
||||||
#### Eingebaute Anonymisierung
|
#### 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 Prefixes
|
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`: Root Zertifikat für gPas, falls es dediziert hinzugefügt werden muss.
|
* `APP_PSEUDONYMIZE_GPAS_PID_DOMAIN`: gPas Domänenname für Patienten ID
|
||||||
|
* `APP_PSEUDONYMIZE_GPAS_GENOM_DE_TAN_DOMAIN`: gPas Multi-Pseudonym-Domäne für genomDE Vorgangsnummern (
|
||||||
|
Clinical data node)
|
||||||
|
|
||||||
|
### (Externe) Consent-Services
|
||||||
|
|
||||||
|
Consent-Services können konfiguriert werden.
|
||||||
|
|
||||||
|
* `APP_CONSENT_SERVICE`: Zu verwendender (externer) Consent-Service:
|
||||||
|
* `NONE`: Verwende Consent-Angaben im MTB-File v1 und ändere diese nicht. Für MTB-File v2 wird
|
||||||
|
die Prüfung übersprungen.
|
||||||
|
* `GICS`: Verwende gICS der Greiswalder Tools (siehe unten).
|
||||||
|
|
||||||
|
#### Einwilligung gICS
|
||||||
|
|
||||||
|
Ab gIcs Version 2.13.0 kann im ETL-Processor
|
||||||
|
per [REST-Schnittstelle](https://simplifier.net/guide/ttp-fhir-gateway-ig/ImplementationGuide-markdown-Einwilligungsmanagement-Operations-isConsented?version=current)
|
||||||
|
der Einwilligungsstatus abgefragt werden.
|
||||||
|
Vor der MTB-Übertragung kann der zum Sendezeitpunkt verfügbarer Einwilligungsstatus über Endpunkt
|
||||||
|
*isConsented* (MTB-File v1) und *currentPolicyStatesForPerson* (MTB-File v2) abgefragt werden.
|
||||||
|
|
||||||
|
Falls Anbindung an gICS aktiviert wurde, wird der Einwilligungsstatus der MTB Datei ignoriert.
|
||||||
|
Stattdessen werden vorhandene Einwilligungen abgefragt und in die MTB Datei eingebettet.
|
||||||
|
|
||||||
|
Es werden zwei Einwilligungsdomänen unterstützt, eine für Broad Consent und als zweites GenomDE
|
||||||
|
Modelvorhaben §64e.
|
||||||
|
|
||||||
|
##### Hinweise
|
||||||
|
|
||||||
|
1. Die aktuelle Impl. nimmt an, dass die hinterlegten Domänen der Einwilligungen ausschließlich für
|
||||||
|
die genannten Art von Einwilligungen genutzt werden. Es finde keine weitere Filterung statt. Wir
|
||||||
|
fragen pro Domäne die Schnittstelle `CurrentPolicyStatesForPerson` - siehe
|
||||||
|
auch [IG TTP-FHIR Gateway
|
||||||
|
](https://www.ths-greifswald.de/wp-content/uploads/tools/fhirgw/ig/2024-3-0/ImplementationGuide-markdown-Einwilligungsmanagement-Operations-currentPolicyStatesForPerson.html)
|
||||||
|
ab.
|
||||||
|
2. Die Einwilligung wird für den Patienten-Identifier der MTB abgerufen und anschließend durch das
|
||||||
|
DNPM Pseudonym ersetzt.
|
||||||
|
3. Abfragen von Einwilligungen über gesonderte Pseudonyme anstatt des MTB-Identifiers fehlt in der
|
||||||
|
ersten Implementierung.
|
||||||
|
4. Bei Verarbeitung von MTB Version 1.x Inhalten ist eine positive Einwilligung für die
|
||||||
|
Weiterverarbeitung notwendig. Das Fehlen einer Einwilligung löst die Löschung des Patienten im
|
||||||
|
Brückenkopf aus.
|
||||||
|
|
||||||
|
##### Konfiguration
|
||||||
|
|
||||||
|
* `APP_CONSENT_SERVICE`: Muss Wert `GICS` gesetzt sein um die Abfragen zu aktivieren. Der Wert
|
||||||
|
`NONE` deaktiviert die Abfrage in gICS.
|
||||||
|
* `APP_CONSENT_GICS_URI`: URI der gICS-Instanz (z.B. `http://localhost:8090/ttp-fhir/fhir/gics`)
|
||||||
|
* `APP_CONSENT_GICS_USERNAME`: gIcs Basic-Auth Benutzername
|
||||||
|
* `APP_CONSENT_GICS_PASSWORD`: gIcs Basic-Auth Passwort
|
||||||
|
* `APP_CONSENT_GICS_PERSONIDENTIFIERSYSTEM`: Derzeit wird nur die PID unterstützt. wenn leer wird
|
||||||
|
`https://ths-greifswald.de/fhir/gics/identifiers/Patienten-ID` angenommen
|
||||||
|
* `APP_CONSENT_GICS_BROADCONSENTDOMAINNAME`: Domäne in der gIcs Broad Consent Einwilligungen
|
||||||
|
verwaltet. Falls Wert leer, wird `MII` angenommen.
|
||||||
|
* `APP_CONSENT_GICS_GNOMDECONSENTDOMAINNAME`: Domäne in der gIcs GenomDE Modelvorhaben §64e
|
||||||
|
Einwilligungen verwaltet. Falls Wert leer, wird `GenomDE_MV` angenommen.
|
||||||
|
* `APP_CONSENT_GICS_POLICYCODE`: Die entscheidende Objekt-ID der zu prüfenden Einwilligung-Regel.
|
||||||
|
Falls leer wird `2.16.840.1.113883.3.1937.777.24.5.3.6` angenommen.
|
||||||
|
* `APP_CONSENT_GICS_POLICYSYSTEM`: Das System der Einwilligung-Regel der Objekt-IDs. Falls leer wird
|
||||||
|
`urn:oid:2.16.840.1.113883.3.1937.777.24.5.3` angenommen.
|
||||||
|
|
||||||
### 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).
|
||||||
|
|
||||||
Ein Administrator-Passwort muss inklusive des Encoding-Prefixes vorliegen.
|
Ein Administrator-Passwort muss inklusive des Encoding-Präfixes vorliegen.
|
||||||
|
|
||||||
Hier Beispiele für das Beispielpasswort `very-secret`:
|
Hier Beispiele für das Beispielpasswort `very-secret`:
|
||||||
|
|
||||||
@@ -68,28 +188,113 @@ 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
|
||||||
|
|
||||||
|
Die folgenden Konfigurationsparameter werden benötigt, um die Authentifizierung weiterer Benutzer an
|
||||||
|
einen OIDC-Provider
|
||||||
|
zu delegieren.
|
||||||
|
Ein Admin-Benutzer muss dabei konfiguriert sein.
|
||||||
|
|
||||||
|
* `APP_SECURITY_ENABLE_OIDC`: Aktiviert die Nutzung von OpenID Connect. Damit sind weitere Parameter
|
||||||
|
erforderlich
|
||||||
|
* `SPRING_SECURITY_OAUTH2_CLIENT_REGISTRATION_CUSTOM_CLIENT_NAME`: Name. Wird beim zusätzlichen
|
||||||
|
Loginbutton angezeigt.
|
||||||
|
* `SPRING_SECURITY_OAUTH2_CLIENT_REGISTRATION_CUSTOM_CLIENT_ID`: Client-ID
|
||||||
|
* `SPRING_SECURITY_OAUTH2_CLIENT_REGISTRATION_CUSTOM_CLIENT_SECRET`: Client-Secret
|
||||||
|
* `SPRING_SECURITY_OAUTH2_CLIENT_REGISTRATION_CUSTOM_CLIENT_SCOPE[0]`: Hier sollte immer `openid`
|
||||||
|
angegeben werden.
|
||||||
|
* `SPRING_SECURITY_OAUTH2_CLIENT_PROVIDER_CUSTOM_ISSUER_URI`: Die URI des Providers,
|
||||||
|
z.B. `https://auth.example.com/realm/example`
|
||||||
|
* `SPRING_SECURITY_OAUTH2_CLIENT_PROVIDER_CUSTOM_USER_NAME_ATTRIBUTE`: Name des Attributes, welches
|
||||||
|
den Benutzernamen
|
||||||
|
enthält.
|
||||||
|
Oft verwendet: `preferred_username`
|
||||||
|
|
||||||
|
Ist die Nutzung von OpenID Connect konfiguriert, erscheint ein zusätzlicher Login-Button zur Nutzung
|
||||||
|
mit OpenID Connect
|
||||||
|
und dem konfigurierten `CLIENT_NAME`.
|
||||||
|
|
||||||
|

|
||||||
|
|
||||||
|
Weitere Informationen zur Konfiguration des OIDC-Providers
|
||||||
|
sind [hier](https://docs.spring.io/spring-security/reference/servlet/oauth2/index.html#oauth2-client)
|
||||||
|
zu finden.
|
||||||
|
|
||||||
|
#### Rollenbasierte Berechtigungen
|
||||||
|
|
||||||
|
Wird OpenID Connect verwendet, gibt es eine rollenbasierte Berechtigungszuweisung.
|
||||||
|
|
||||||
|
Die Standardrolle für neue OIDC-Benutzer kann mit der Option `APP_SECURITY_DEFAULT_USER_ROLE`
|
||||||
|
festgelegt werden.
|
||||||
|
Mögliche Werte sind `user` oder `guest`. Standardwert ist `user`.
|
||||||
|
|
||||||
|
Benutzer mit der Rolle "Gast" sehen nur die Inhalte, die auch nicht angemeldete Benutzer sehen.
|
||||||
|
|
||||||
|
Hierdurch ist es möglich, einzelne Benutzer einzuschränken oder durch Änderung der Standardrolle auf
|
||||||
|
`guest` nur
|
||||||
|
einzelne Benutzer als vollwertige Nutzer zuzulassen.
|
||||||
|
|
||||||
|

|
||||||
|
|
||||||
|
Benutzer werden nach dem Entfernen oder der Änderung der vergebenen Rolle automatisch abgemeldet und
|
||||||
|
müssen sich neu anmelden.
|
||||||
|
Sie bekommen dabei wieder die Standardrolle zugewiesen.
|
||||||
|
|
||||||
#### Auswirkungen auf den dargestellten Inhalt
|
#### 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
|
||||||
pseudonymisierte Patienten-ID einsehen.
|
anonymisierte oder
|
||||||
|
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
|
||||||
|
|
||||||
|
Die Anwendung unterstützt das Erstellen und Nutzen einer tokenbasierten Authentifizierung für den
|
||||||
|
MTB-File-Endpunkt.
|
||||||
|
|
||||||
|
Dies kann mit der Umgebungsvariable `APP_SECURITY_ENABLE_TOKENS` aktiviert (`true` oder `false`)
|
||||||
|
werden
|
||||||
|
und ist als Standardeinstellung nicht aktiv.
|
||||||
|
|
||||||
|
Ist diese Einstellung aktiviert worden, ist es Administratoren möglich, Zugriffstokens für Onkostar
|
||||||
|
zu erstellen, die
|
||||||
|
zur Nutzung des MTB-File-Endpunkts eine HTTP-Basic-Authentifizierung voraussetzen.
|
||||||
|
|
||||||
|

|
||||||
|
|
||||||
|
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
|
||||||
|
```
|
||||||
|
|
||||||
|
Ist die Verwendung von Tokens aktiv, werden Anfragen ohne die Angabe der Token-Information
|
||||||
|
abgelehnt.
|
||||||
|
|
||||||
|
Alternativ kann eine Authentifizierung über Benutzername/Passwort oder OIDC erfolgen.
|
||||||
|
|
||||||
### Transformation von Werten
|
### Transformation von Werten
|
||||||
|
|
||||||
In Onkostar kann es vorkommen, dass ein Wert eines Merkmalskatalogs an einem Standort angepasst wurde und dadurch nicht dem Wert entspricht,
|
In Onkostar kann es vorkommen, dass ein Wert eines Merkmalskatalogs an einem Standort angepasst
|
||||||
der vom bwHC-Backend akzeptiert wird.
|
wurde und dadurch nicht dem Wert entspricht,
|
||||||
|
der von DNPM:DIP akzeptiert wird.
|
||||||
|
|
||||||
Diese Anwendung bietet daher die Möglichkeit, eine Transformation vorzunehmen. Hierzu muss der "Pfad" innerhalb des JSON-MTB-Files angegeben werden und
|
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
|
||||||
@@ -101,47 +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 das bwHC-Backend 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 bwHC-Backend-Instanz. z.B.: `http://localhost:9000/bwhc/etl/api`
|
* `APP_REST_URI`: URI der zu benutzenden API der Backend-Instanz. Zum Beispiel `http://localhost:9000/api`
|
||||||
|
* `APP_REST_USERNAME`: Basic-Auth-Benutzername für den REST-Endpunkt
|
||||||
|
* `APP_REST_PASSWORD`: Basic-Auth-Passwort für den REST-Endpunkt
|
||||||
|
|
||||||
#### 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_TOPIC`: Zu verwendendes Topic zum Versenden von Anfragen
|
* `APP_KAFKA_OUTPUT_TOPIC`: Zu verwendendes Topic zum Versenden von Anfragen.
|
||||||
* `APP_KAFKA_RESPONSE_TOPIC`: Topic mit Antworten über den Erfolg des Versendens. Standardwert: `APP_KAFKA_TOPIC` mit Anhang "_response".
|
* `APP_KAFKA_OUTPUT_RESPONSE_TOPIC`: Topic mit Antworten über den Erfolg des Versendens.
|
||||||
* `APP_KAFKA_GROUP_ID`: Kafka GroupID des Consumers. Standardwert: `APP_KAFKA_TOPIC` mit Anhang "_group".
|
Standardwert: `APP_KAFKA_TOPIC` mit Anhang "_response".
|
||||||
|
* `APP_KAFKA_GROUP_ID`: Kafka GroupID des Consumers. Standardwert: `APP_KAFKA_TOPIC` mit Anhang "_
|
||||||
|
group".
|
||||||
* `APP_KAFKA_SERVERS`: Zu verwendende Kafka-Bootstrap-Server als kommagetrennte Liste
|
* `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 bwHC-Backend aufbauen, wird eine Rückantwort mit Status-Code `900` erwartet, welchen es
|
Lässt sich keine Verbindung zu dem Backend aufbauen, wird eine Rückantwort mit Status-Code `900`
|
||||||
|
erwartet, welchen es
|
||||||
für HTTP nicht gibt.
|
für HTTP nicht gibt.
|
||||||
|
|
||||||
|
Wird die Umgebungsvariable `APP_KAFKA_INPUT_TOPIC` gesetzt, kann eine Nachricht auch über dieses
|
||||||
|
Kafka-Topic an den ETL-Prozessor übermittelt werden.
|
||||||
|
|
||||||
##### Retention Time
|
##### Retention Time
|
||||||
|
|
||||||
Generell werden in Apache Kafka alle Records entsprechend der Konfiguration vorgehalten.
|
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.
|
||||||
|
|
||||||
@@ -150,19 +369,39 @@ 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 und die (anonymisierte) Erkrankungs-ID verwendet wird,
|
Da als Key eines Records die (pseudonymisierte) Patienten-ID verwendet wird, stehen mit obiger
|
||||||
stehen mit obiger Konfiguration der Kafka-Topics nach 10 Sekunden nur noch der jeweils letzte Eintrag für den entsprechenden
|
Konfiguration
|
||||||
Key zur Verfügung.
|
der Kafka-Topics nach 10 Sekunden nur noch der jeweils letzte Eintrag für den entsprechenden Key zur
|
||||||
|
Verfügung.
|
||||||
|
|
||||||
Da der Key sowohl für die Records in Richtung bwHC-Backend für die Rückantwort identisch aufgebaut ist, lassen sich so
|
Da der Key sowohl für die Records in Richtung DNPM:DIP, als auch für die Rückantwort identisch
|
||||||
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.
|
||||||
|
|
||||||
|
### Antworten und Statusauswertung
|
||||||
|
|
||||||
|
Seit Version 0.10 wird die Issue-Liste der Antwort verwendet und die darion enthaltene höchste
|
||||||
|
Severity-Stufe als Ergebnis verwendet.
|
||||||
|
|
||||||
|
| Höchste Severity | Status |
|
||||||
|
|------------------|-----------|
|
||||||
|
| `info` | `SUCCESS` |
|
||||||
|
| `warning` | `WARNING` |
|
||||||
|
| `error`, `fatal` | `ERROR` |
|
||||||
|
|
||||||
## Docker-Images
|
## Docker-Images
|
||||||
|
|
||||||
Diese Anwendung ist auch als Docker-Image verfügbar: https://github.com/CCC-MF/etl-processor/pkgs/container/etl-processor
|
Diese Anwendung ist auch als Docker-Image
|
||||||
|
verfügbar: https://github.com/pcvolkmer/etl-processor/pkgs/container/etl-processor
|
||||||
|
|
||||||
### Images lokal bauen
|
### Images lokal bauen
|
||||||
|
|
||||||
@@ -170,13 +409,49 @@ Diese Anwendung ist auch als Docker-Image verfügbar: https://github.com/CCC-MF/
|
|||||||
./gradlew bootBuildImage
|
./gradlew bootBuildImage
|
||||||
```
|
```
|
||||||
|
|
||||||
|
### Integration eines eigenen Root CA Zertifikats
|
||||||
|
|
||||||
|
Wird eine eigene Root CA verwendet, die nicht offiziell signiert ist, wird es zu Problemen beim
|
||||||
|
SSL-Handshake kommen, wenn z.B. gPAS zur Generierung von Pseudonymen verwendet wird.
|
||||||
|
|
||||||
|
Hier bietet es sich an, das Root CA Zertifikat in das Image zu integrieren.
|
||||||
|
|
||||||
|
#### Integration beim Bauen des Images
|
||||||
|
|
||||||
|
Hier muss die Zeile `"BP_EMBED_CERTS" to "true"` in der Datei `build.gradle.kts` verwendet werden
|
||||||
|
und darf nicht als Kommentar verwendet werden.
|
||||||
|
|
||||||
|
Die PEM-Datei mit dem/den Root CA Zertifikat(en) muss dabei im vorbereiteten Verzeichnis [
|
||||||
|
`bindings/ca-certificates`](bindings/ca-certificates) enthalten sein.
|
||||||
|
|
||||||
|
#### Integration zur Laufzeit
|
||||||
|
|
||||||
|
Hier muss die Umgebungsvariable `SERVICE_BINDING_ROOT` z.B. auf den Wert `/bindings` gesetzt sein.
|
||||||
|
Zudem muss ein Verzeichnis `bindings/ca-certificates` - analog zum Verzeichnis
|
||||||
|
[`bindings/ca-certificates`](bindings/ca-certificates) mit einer PEM-Datei und der
|
||||||
|
Datei [`bindings/ca-certificates/type`](bindings/ca-certificates/type) als Docker-Volume eingebunden werden.
|
||||||
|
|
||||||
|
Beispiel für Docker-Compose:
|
||||||
|
|
||||||
|
```
|
||||||
|
...
|
||||||
|
environment:
|
||||||
|
SERVICE_BINDING_ROOT: /bindings
|
||||||
|
...
|
||||||
|
volumes:
|
||||||
|
- "/path/to/bindings/ca-certificates/:/bindings/ca-certificates/:ro"
|
||||||
|
...
|
||||||
|
```
|
||||||
|
|
||||||
## Deployment
|
## Deployment
|
||||||
*Ausführen als Docker Conatiner:*
|
|
||||||
|
*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
|
||||||
@@ -185,15 +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-Prefix
|
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):
|
||||||
|
|
||||||
@@ -229,13 +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:
|
||||||
|
|
||||||
```
|
```
|
||||||
@@ -246,3 +529,6 @@ 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.
|
||||||
|
5
bindings/README.md
Normal file
5
bindings/README.md
Normal file
@@ -0,0 +1,5 @@
|
|||||||
|
# Hinweis für Root CA Zertifikate
|
||||||
|
|
||||||
|
PEM-Datei(en) in das Verzeichnis `ca-certificates` ablegen.
|
||||||
|
|
||||||
|
Die Datei `type` gibt dabei an, dass hier CA Zertifikate zu finden sind.
|
1
bindings/ca-certificates/type
Normal file
1
bindings/ca-certificates/type
Normal file
@@ -0,0 +1 @@
|
|||||||
|
ca-certificates
|
100
build.gradle.kts
100
build.gradle.kts
@@ -1,27 +1,35 @@
|
|||||||
import org.gradle.api.tasks.testing.logging.TestLogEvent
|
import org.gradle.api.tasks.testing.logging.TestLogEvent
|
||||||
|
import org.jetbrains.kotlin.gradle.dsl.JvmTarget
|
||||||
import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
|
import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
|
||||||
import org.springframework.boot.gradle.tasks.bundling.BootBuildImage
|
import org.springframework.boot.gradle.tasks.bundling.BootBuildImage
|
||||||
|
|
||||||
plugins {
|
plugins {
|
||||||
war
|
war
|
||||||
id("org.springframework.boot") version "3.2.1"
|
id("org.springframework.boot") version "3.5.5"
|
||||||
id("io.spring.dependency-management") version "1.1.4"
|
id("io.spring.dependency-management") version "1.1.7"
|
||||||
kotlin("jvm") version "1.9.22"
|
kotlin("jvm") version "2.2.10"
|
||||||
kotlin("plugin.spring") version "1.9.22"
|
kotlin("plugin.spring") version "2.2.10"
|
||||||
|
jacoco
|
||||||
}
|
}
|
||||||
|
|
||||||
group = "de.ukw.ccc"
|
group = "dev.dnpm"
|
||||||
version = "0.4.0"
|
version = "0.12.0-SNAPSHOT"
|
||||||
|
|
||||||
var versions = mapOf(
|
var versions = mapOf(
|
||||||
"bwhc-dto-java" to "0.2.0",
|
"mtb-dto" to "0.1.0-SNAPSHOT",
|
||||||
"hapi-fhir" to "6.10.2",
|
"hapi-fhir" to "8.4.0",
|
||||||
"httpclient5" to "5.2.1",
|
"mockito-kotlin" to "6.0.0",
|
||||||
"mockito-kotlin" to "5.2.1"
|
"archunit" to "1.4.1",
|
||||||
|
// Webjars
|
||||||
|
"webjars-locator" to "0.52",
|
||||||
|
"echarts" to "6.0.0",
|
||||||
|
"htmx.org" to "1.9.12"
|
||||||
)
|
)
|
||||||
|
|
||||||
java {
|
java {
|
||||||
sourceCompatibility = JavaVersion.VERSION_17
|
toolchain {
|
||||||
|
languageVersion = JavaLanguageVersion.of(21)
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
sourceSets {
|
sourceSets {
|
||||||
@@ -40,9 +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")
|
||||||
}
|
}
|
||||||
@@ -55,34 +72,53 @@ dependencies {
|
|||||||
implementation("org.springframework.boot:spring-boot-starter-web")
|
implementation("org.springframework.boot:spring-boot-starter-web")
|
||||||
implementation("org.springframework.boot:spring-boot-starter-data-jdbc")
|
implementation("org.springframework.boot:spring-boot-starter-data-jdbc")
|
||||||
implementation("org.springframework.boot:spring-boot-starter-security")
|
implementation("org.springframework.boot:spring-boot-starter-security")
|
||||||
|
implementation("org.springframework.boot:spring-boot-starter-oauth2-client")
|
||||||
implementation("org.thymeleaf.extras:thymeleaf-extras-springsecurity6")
|
implementation("org.thymeleaf.extras:thymeleaf-extras-springsecurity6")
|
||||||
implementation("com.fasterxml.jackson.module:jackson-module-kotlin")
|
implementation("com.fasterxml.jackson.module:jackson-module-kotlin")
|
||||||
implementation("org.springframework.kafka:spring-kafka")
|
implementation("org.springframework.kafka:spring-kafka")
|
||||||
|
implementation("org.flywaydb:flyway-database-postgresql")
|
||||||
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:${versions["httpclient5"]}")
|
implementation("org.apache.httpcomponents.client5:httpclient5")
|
||||||
implementation("com.jayway.jsonpath:json-path")
|
implementation("com.jayway.jsonpath:json-path")
|
||||||
|
implementation("org.webjars:webjars-locator:${versions["webjars-locator"]}")
|
||||||
|
implementation("org.webjars.npm:echarts:${versions["echarts"]}")
|
||||||
|
implementation("org.webjars.npm:htmx.org:${versions["htmx.org"]}")
|
||||||
|
// 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")
|
||||||
|
|
||||||
developmentOnly("org.springframework.boot:spring-boot-devtools")
|
developmentOnly("org.springframework.boot:spring-boot-devtools")
|
||||||
developmentOnly("org.springframework.boot:spring-boot-docker-compose")
|
developmentOnly("org.springframework.boot:spring-boot-docker-compose")
|
||||||
|
|
||||||
annotationProcessor("org.springframework.boot:spring-boot-configuration-processor")
|
annotationProcessor("org.springframework.boot:spring-boot-configuration-processor")
|
||||||
|
|
||||||
providedRuntime("org.springframework.boot:spring-boot-starter-tomcat")
|
providedRuntime("org.springframework.boot:spring-boot-starter-tomcat")
|
||||||
|
|
||||||
testImplementation("org.springframework.boot:spring-boot-starter-test")
|
testImplementation("org.springframework.boot:spring-boot-starter-test")
|
||||||
|
testImplementation("org.springframework.security:spring-security-test")
|
||||||
testImplementation("io.projectreactor:reactor-test")
|
testImplementation("io.projectreactor:reactor-test")
|
||||||
testImplementation("org.mockito.kotlin:mockito-kotlin:${versions["mockito-kotlin"]}")
|
testImplementation("org.mockito.kotlin:mockito-kotlin:${versions["mockito-kotlin"]}")
|
||||||
|
|
||||||
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("org.htmlunit:htmlunit")
|
||||||
|
integrationTestImplementation("org.springframework:spring-webflux")
|
||||||
|
// Fix for CVE-2024-25710
|
||||||
|
integrationTestImplementation("org.apache.commons:commons-compress:1.26.0")
|
||||||
}
|
}
|
||||||
|
|
||||||
tasks.withType<KotlinCompile> {
|
tasks.withType<KotlinCompile> {
|
||||||
kotlinOptions {
|
compilerOptions {
|
||||||
freeCompilerArgs += "-Xjsr305=strict"
|
freeCompilerArgs.add("-Xjsr305=strict")
|
||||||
jvmTarget = "17"
|
jvmTarget.set(JvmTarget.JVM_21)
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@@ -93,8 +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
|
||||||
@@ -102,12 +139,35 @@ task<Test>("integrationTest") {
|
|||||||
shouldRunAfter("test")
|
shouldRunAfter("test")
|
||||||
}
|
}
|
||||||
|
|
||||||
|
tasks.register("allTests") {
|
||||||
|
description = "Run all tests"
|
||||||
|
group = JavaBasePlugin.VERIFICATION_GROUP
|
||||||
|
dependsOn(tasks.withType<Test>())
|
||||||
|
}
|
||||||
|
|
||||||
|
tasks.jacocoTestReport {
|
||||||
|
dependsOn("allTests")
|
||||||
|
|
||||||
|
executionData(fileTree(project.rootDir.absolutePath).include("**/build/jacoco/*.exec"))
|
||||||
|
|
||||||
|
reports {
|
||||||
|
xml.required = true
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
tasks.named<BootBuildImage>("bootBuildImage") {
|
tasks.named<BootBuildImage>("bootBuildImage") {
|
||||||
imageName.set("ghcr.io/ccc-mf/etl-processor")
|
imageName.set("ghcr.io/pcvolkmer/mv64e-etl-processor")
|
||||||
|
|
||||||
|
// Binding for CA Certs
|
||||||
|
bindings.set(listOf(
|
||||||
|
"$rootDir/bindings/ca-certificates/:/platform/bindings/ca-certificates"
|
||||||
|
))
|
||||||
|
|
||||||
environment.set(environment.get() + mapOf(
|
environment.set(environment.get() + mapOf(
|
||||||
"BP_OCI_SOURCE" to "https://github.com/CCC-MF/etl-processor",
|
// Enable this line to embed CA Certs into image on build time
|
||||||
|
//"BP_EMBED_CERTS" to "true",
|
||||||
|
"BP_OCI_SOURCE" to "https://github.com/pcvolkmer/mv64e-etl-processor",
|
||||||
"BP_OCI_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"
|
||||||
))
|
))
|
||||||
}
|
}
|
||||||
|
@@ -18,6 +18,11 @@ services:
|
|||||||
APP_KAFKA_GROUP_ID: ${DNPM_KAFKA_GROUP_ID}
|
APP_KAFKA_GROUP_ID: ${DNPM_KAFKA_GROUP_ID}
|
||||||
APP_KAFKA_RESPONSE_TOPIC: ${DNPM_KAFKA_RESPONSE_TOPIC}
|
APP_KAFKA_RESPONSE_TOPIC: ${DNPM_KAFKA_RESPONSE_TOPIC}
|
||||||
APP_REST_URI: ${DNPM_BWHC_REST_URI}
|
APP_REST_URI: ${DNPM_BWHC_REST_URI}
|
||||||
|
APP_REST_USERNAME: ${DNPM_BWHC_REST_USERNAME}
|
||||||
|
APP_REST_PASSWORD: ${DNPM_BWHC_REST_PASSWORD}
|
||||||
|
APP_REST_IS_BWHC: ${DNPM_BWHC_REST_IS_BWHC}
|
||||||
|
APP_SECURITY_ADMIN_USER: ${DNPM_ADMIN_USER}
|
||||||
|
APP_SECURITY_ADMIN_PASSWORD: ${DNPM_ADMIN_PASSWORD}
|
||||||
SPRING_DATASOURCE_URL: ${DNPM_DATASOURCE_URL}
|
SPRING_DATASOURCE_URL: ${DNPM_DATASOURCE_URL}
|
||||||
SPRING_DATASOURCE_PASSWORD: ${DNPM_MARIADB_USER_PW}
|
SPRING_DATASOURCE_PASSWORD: ${DNPM_MARIADB_USER_PW}
|
||||||
SPRING_DATASOURCE_USERNAME: ${DNPM_MARIADB_DB}
|
SPRING_DATASOURCE_USERNAME: ${DNPM_MARIADB_DB}
|
||||||
|
@@ -2,6 +2,10 @@
|
|||||||
DNPM_MONITORING_HTTP_PORT=8088
|
DNPM_MONITORING_HTTP_PORT=8088
|
||||||
DNPM_LOG_LEVEL=INFO
|
DNPM_LOG_LEVEL=INFO
|
||||||
|
|
||||||
|
# ADMIN USER CREDENTIALS
|
||||||
|
DNPM_ADMIN_USER=admin
|
||||||
|
DNPM_ADMIN_PASSWORD=
|
||||||
|
|
||||||
# GPAS or BUILDIN
|
# GPAS or BUILDIN
|
||||||
DNPM_PSEUDONYMIZE_GENERATOR=BUILDIN
|
DNPM_PSEUDONYMIZE_GENERATOR=BUILDIN
|
||||||
DNPM_APP_PSEUDONYMIZE_PREFIX=ANONYM
|
DNPM_APP_PSEUDONYMIZE_PREFIX=ANONYM
|
||||||
@@ -24,6 +28,9 @@ DNPM_DATASOURCE_URL=jdbc:mariadb://dnpm-monitor-db:3306/$DNPM_MARIADB_DB
|
|||||||
## TARGET SYSTEMS CONFIG
|
## TARGET SYSTEMS CONFIG
|
||||||
# in case of direct access to bwhc enter endpoint url here
|
# in case of direct access to bwhc enter endpoint url here
|
||||||
DNPM_BWHC_REST_URI=
|
DNPM_BWHC_REST_URI=
|
||||||
|
DNPM_BWHC_REST_USERNAME=
|
||||||
|
DNPM_BWHC_REST_PASSWORD=
|
||||||
|
DNPM_BWHC_REST_IS_BWHC=false
|
||||||
|
|
||||||
# produce mtb files to this topic - values 'false' disabling kafka processing
|
# produce mtb files to this topic - values 'false' disabling kafka processing
|
||||||
DNPM_KAFKA_TOPIC=false
|
DNPM_KAFKA_TOPIC=false
|
||||||
|
126
dev-compose.yml
126
dev-compose.yml
@@ -1,24 +1,125 @@
|
|||||||
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
|
||||||
akhq:
|
akhq:
|
||||||
image: tchiotludo/akhq:0.21.0
|
image: tchiotludo/akhq:0.25.0
|
||||||
environment:
|
environment:
|
||||||
AKHQ_CONFIGURATION: |
|
AKHQ_CONFIGURATION: |
|
||||||
akhq:
|
akhq:
|
||||||
@@ -32,6 +133,8 @@ services:
|
|||||||
ports:
|
ports:
|
||||||
- "8084:8080"
|
- "8084:8080"
|
||||||
|
|
||||||
|
|
||||||
|
## For use with MariaDB
|
||||||
mariadb:
|
mariadb:
|
||||||
image: mariadb:10
|
image: mariadb:10
|
||||||
ports:
|
ports:
|
||||||
@@ -42,6 +145,7 @@ services:
|
|||||||
MARIADB_PASSWORD: dev
|
MARIADB_PASSWORD: dev
|
||||||
MARIADB_ROOT_PASSWORD: dev
|
MARIADB_ROOT_PASSWORD: dev
|
||||||
|
|
||||||
|
## For use with Postgres
|
||||||
# postgres:
|
# postgres:
|
||||||
# image: postgres:alpine
|
# image: postgres:alpine
|
||||||
# ports:
|
# ports:
|
||||||
|
@@ -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
|
|
||||||
|
@@ -9,6 +9,8 @@ services:
|
|||||||
### ETL-Processor
|
### ETL-Processor
|
||||||
etl-processor:
|
etl-processor:
|
||||||
image: ghcr.io/ccc-mf/etl-processor:latest
|
image: ghcr.io/ccc-mf/etl-processor:latest
|
||||||
|
ports:
|
||||||
|
- 8080:8080
|
||||||
environment:
|
environment:
|
||||||
APP_REST_URI: http://bwhc-backend/bwhc/etl/api
|
APP_REST_URI: http://bwhc-backend/bwhc/etl/api
|
||||||
SPRING_DATASOURCE_URL: jdbc:postgresql://postgres/etl
|
SPRING_DATASOURCE_URL: jdbc:postgresql://postgres/etl
|
||||||
|
BIN
docs/etl.png
BIN
docs/etl.png
Binary file not shown.
Before Width: | Height: | Size: 75 KiB After Width: | Height: | Size: 115 KiB |
BIN
docs/login.png
Normal file
BIN
docs/login.png
Normal file
Binary file not shown.
After Width: | Height: | Size: 9.2 KiB |
BIN
docs/tokens.png
Normal file
BIN
docs/tokens.png
Normal file
Binary file not shown.
After Width: | Height: | Size: 30 KiB |
BIN
docs/userroles.png
Normal file
BIN
docs/userroles.png
Normal file
Binary file not shown.
After Width: | Height: | Size: 16 KiB |
2
gradle/wrapper/gradle-wrapper.properties
vendored
2
gradle/wrapper/gradle-wrapper.properties
vendored
@@ -1,6 +1,6 @@
|
|||||||
distributionBase=GRADLE_USER_HOME
|
distributionBase=GRADLE_USER_HOME
|
||||||
distributionPath=wrapper/dists
|
distributionPath=wrapper/dists
|
||||||
distributionUrl=https\://services.gradle.org/distributions/gradle-8.1.1-bin.zip
|
distributionUrl=https\://services.gradle.org/distributions/gradle-8.13-bin.zip
|
||||||
networkTimeout=10000
|
networkTimeout=10000
|
||||||
zipStoreBase=GRADLE_USER_HOME
|
zipStoreBase=GRADLE_USER_HOME
|
||||||
zipStorePath=wrapper/dists
|
zipStorePath=wrapper/dists
|
||||||
|
@@ -1 +1 @@
|
|||||||
rootProject.name = "etl-processor"
|
rootProject.name = "mv64e-etl-processor"
|
||||||
|
@@ -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
|
||||||
@@ -45,10 +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.consent.service=none"
|
||||||
]
|
]
|
||||||
)
|
)
|
||||||
class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
|
class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
|
||||||
@@ -64,14 +67,16 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
|
|||||||
@AutoConfigureMockMvc
|
@AutoConfigureMockMvc
|
||||||
@TestPropertySource(
|
@TestPropertySource(
|
||||||
properties = [
|
properties = [
|
||||||
"app.transformations[0].path=diagnoses[*].icd10.version",
|
"app.pseudonymize.generator=buildin",
|
||||||
|
"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
|
||||||
@@ -89,36 +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()
|
||||||
@@ -132,10 +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"
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
@@ -0,0 +1,73 @@
|
|||||||
|
package dev.dnpm.etl.processor
|
||||||
|
|
||||||
|
import com.tngtech.archunit.core.domain.JavaClasses
|
||||||
|
import com.tngtech.archunit.core.importer.ClassFileImporter
|
||||||
|
import com.tngtech.archunit.lang.syntax.ArchRuleDefinition.classes
|
||||||
|
import com.tngtech.archunit.lang.syntax.ArchRuleDefinition.noClasses
|
||||||
|
import org.junit.jupiter.api.BeforeEach
|
||||||
|
import org.junit.jupiter.api.Test
|
||||||
|
import org.springframework.data.repository.Repository
|
||||||
|
|
||||||
|
class EtlProcessorArchTest {
|
||||||
|
|
||||||
|
private lateinit var noTestClasses: JavaClasses
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setUp() {
|
||||||
|
this.noTestClasses = ClassFileImporter()
|
||||||
|
.withImportOption { !(it.contains("/test/") || it.contains("/integrationTest/")) }
|
||||||
|
.importPackages("dev.dnpm.etl.processor")
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun noClassesInInputPackageShouldDependOnMonitoringPackage() {
|
||||||
|
val rule = noClasses()
|
||||||
|
.that()
|
||||||
|
.resideInAPackage("..input")
|
||||||
|
.should().dependOnClassesThat()
|
||||||
|
.resideInAnyPackage("..monitoring")
|
||||||
|
|
||||||
|
rule.check(noTestClasses)
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun noClassesInInputPackageShouldDependOnRepositories() {
|
||||||
|
val rule = noClasses()
|
||||||
|
.that()
|
||||||
|
.resideInAPackage("..input")
|
||||||
|
.should().dependOnClassesThat().haveSimpleNameEndingWith("Repository")
|
||||||
|
|
||||||
|
rule.check(noTestClasses)
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun noClassesInOutputPackageShouldDependOnRepositories() {
|
||||||
|
val rule = noClasses()
|
||||||
|
.that()
|
||||||
|
.resideInAPackage("..output")
|
||||||
|
.should().dependOnClassesThat().haveSimpleNameEndingWith("Repository")
|
||||||
|
|
||||||
|
rule.check(noTestClasses)
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun noClassesInWebPackageShouldDependOnRepositories() {
|
||||||
|
val rule = noClasses()
|
||||||
|
.that()
|
||||||
|
.resideInAPackage("..web")
|
||||||
|
.should().dependOnClassesThat().haveSimpleNameEndingWith("Repository")
|
||||||
|
|
||||||
|
rule.check(noTestClasses)
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun repositoryClassNamesShouldEndWithRepository() {
|
||||||
|
val rule = classes()
|
||||||
|
.that()
|
||||||
|
.areInterfaces().and().areAssignableTo(Repository::class.java)
|
||||||
|
.should().haveSimpleNameEndingWith("Repository")
|
||||||
|
|
||||||
|
rule.check(noTestClasses)
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
@@ -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) 2024 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
|
||||||
@@ -20,9 +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.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.GpasPseudonymGenerator
|
||||||
|
import dev.dnpm.etl.processor.security.TokenRepository
|
||||||
|
import dev.dnpm.etl.processor.security.TokenService
|
||||||
|
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||||
import org.assertj.core.api.Assertions.assertThat
|
import org.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
|
||||||
@@ -30,14 +39,31 @@ 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.context.ApplicationContext
|
import org.springframework.context.ApplicationContext
|
||||||
|
import org.springframework.retry.support.RetryTemplate
|
||||||
|
import org.springframework.security.crypto.password.PasswordEncoder
|
||||||
|
import org.springframework.security.provisioning.InMemoryUserDetailsManager
|
||||||
import org.springframework.test.context.ContextConfiguration
|
import org.springframework.test.context.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 = [AppConfiguration::class, KafkaAutoConfiguration::class, AppKafkaConfiguration::class, AppRestConfiguration::class])
|
@ContextConfiguration(
|
||||||
@MockBean(ObjectMapper::class)
|
classes = [
|
||||||
|
AppConfiguration::class,
|
||||||
|
AppSecurityConfiguration::class,
|
||||||
|
KafkaAutoConfiguration::class,
|
||||||
|
AppKafkaConfiguration::class,
|
||||||
|
AppRestConfiguration::class,
|
||||||
|
ConsentEvaluator::class
|
||||||
|
]
|
||||||
|
)
|
||||||
|
@MockitoBean(types = [ObjectMapper::class])
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.pseudonymize.generator=BUILDIN",
|
||||||
|
]
|
||||||
|
)
|
||||||
class AppConfigurationTest {
|
class AppConfigurationTest {
|
||||||
|
|
||||||
@Nested
|
@Nested
|
||||||
@@ -60,12 +86,12 @@ class AppConfigurationTest {
|
|||||||
@TestPropertySource(
|
@TestPropertySource(
|
||||||
properties = [
|
properties = [
|
||||||
"app.kafka.servers=localhost:9092",
|
"app.kafka.servers=localhost:9092",
|
||||||
"app.kafka.topic=test",
|
"app.kafka.output-topic=test",
|
||||||
"app.kafka.response-topic=test-response",
|
"app.kafka.output-response-topic=test-response",
|
||||||
"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
|
||||||
@@ -81,8 +107,8 @@ class AppConfigurationTest {
|
|||||||
properties = [
|
properties = [
|
||||||
"app.rest.uri=http://localhost:9000",
|
"app.rest.uri=http://localhost:9000",
|
||||||
"app.kafka.servers=localhost:9092",
|
"app.kafka.servers=localhost:9092",
|
||||||
"app.kafka.topic=test",
|
"app.kafka.output-topic=test",
|
||||||
"app.kafka.response-topic=test-response",
|
"app.kafka.output-response-topic=test-response",
|
||||||
"app.kafka.group-id=test"
|
"app.kafka.group-id=test"
|
||||||
]
|
]
|
||||||
)
|
)
|
||||||
@@ -96,6 +122,44 @@ class AppConfigurationTest {
|
|||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.kafka.servers=localhost:9092",
|
||||||
|
"app.kafka.output-topic=test",
|
||||||
|
"app.kafka.output-response-topic=test-response",
|
||||||
|
"app.kafka.group-id=test"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
inner class AppConfigurationWithoutKafkaInputTest(private val context: ApplicationContext) {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun shouldNotUseKafkaInputListener() {
|
||||||
|
assertThrows<NoSuchBeanDefinitionException> { context.getBean(KafkaInputListener::class.java) }
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.kafka.servers=localhost:9092",
|
||||||
|
"app.kafka.input-topic=test_input",
|
||||||
|
"app.kafka.output-topic=test",
|
||||||
|
"app.kafka.output-response-topic=test-response",
|
||||||
|
"app.kafka.group-id=test"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
@MockitoBean(types = [RequestProcessor::class])
|
||||||
|
inner class AppConfigurationUsingKafkaInputTest(private val context: ApplicationContext) {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun shouldUseKafkaInputListener() {
|
||||||
|
assertThat(context.getBean(KafkaInputListener::class.java)).isNotNull
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
@Nested
|
@Nested
|
||||||
@TestPropertySource(
|
@TestPropertySource(
|
||||||
properties = [
|
properties = [
|
||||||
@@ -116,4 +180,130 @@ class AppConfigurationTest {
|
|||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
inner class AppConfigurationPseudonymizeTest {
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.pseudonymize.generator=buildin"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
inner class AppConfigurationPseudonymizeGeneratorBuildinTest(private val context: ApplicationContext) {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun shouldUseConfiguredGenerator() {
|
||||||
|
assertThat(context.getBean(AnonymizingGenerator::class.java)).isNotNull
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.pseudonymize.generator=gpas"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
inner class AppConfigurationPseudonymizeGeneratorGpasTest(private val context: ApplicationContext) {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun shouldUseConfiguredGenerator() {
|
||||||
|
assertThat(context.getBean(GpasPseudonymGenerator::class.java)).isNotNull
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.security.enable-tokens=true"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
@MockitoBean(
|
||||||
|
types = [
|
||||||
|
InMemoryUserDetailsManager::class,
|
||||||
|
PasswordEncoder::class,
|
||||||
|
TokenRepository::class
|
||||||
|
]
|
||||||
|
)
|
||||||
|
inner class AppConfigurationTokenEnabledTest(private val context: ApplicationContext) {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun checkTokenService() {
|
||||||
|
assertThat(context.getBean(TokenService::class.java)).isNotNull
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
@MockitoBean(
|
||||||
|
types = [
|
||||||
|
InMemoryUserDetailsManager::class,
|
||||||
|
PasswordEncoder::class,
|
||||||
|
TokenRepository::class
|
||||||
|
]
|
||||||
|
)
|
||||||
|
inner class AppConfigurationTokenDisabledTest(private val context: ApplicationContext) {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun checkTokenService() {
|
||||||
|
assertThrows<NoSuchBeanDefinitionException> { context.getBean(TokenService::class.java) }
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.rest.uri=http://localhost:9000",
|
||||||
|
"app.max-retry-attempts=5"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
inner class AppConfigurationRetryTest(private val context: ApplicationContext) {
|
||||||
|
|
||||||
|
private val maxRetryAttempts = 5
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun shouldUseRetryTemplateWithConfiguredMaxAttempts() {
|
||||||
|
val retryTemplate = context.getBean(RetryTemplate::class.java)
|
||||||
|
assertThat(retryTemplate).isNotNull
|
||||||
|
|
||||||
|
assertThrows<RuntimeException> {
|
||||||
|
retryTemplate.execute<Void, RuntimeException> {
|
||||||
|
assertThat(it.retryCount).isLessThan(maxRetryAttempts)
|
||||||
|
throw RuntimeException()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
@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
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
30
src/integrationTest/kotlin/dev/dnpm/etl/processor/helpers.kt
Normal file
30
src/integrationTest/kotlin/dev/dnpm/etl/processor/helpers.kt
Normal file
@@ -0,0 +1,30 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of ETL-Processor
|
||||||
|
*
|
||||||
|
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||||
|
*
|
||||||
|
* This program is free software: you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
|
* by the Free Software Foundation, either version 3 of the License, or
|
||||||
|
* (at your option) any later version.
|
||||||
|
*
|
||||||
|
* This program is distributed in the hope that it will be useful,
|
||||||
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
* GNU Affero General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU Affero General Public License
|
||||||
|
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package dev.dnpm.etl.processor
|
||||||
|
|
||||||
|
import org.mockito.ArgumentMatchers
|
||||||
|
|
||||||
|
@Suppress("UNCHECKED_CAST")
|
||||||
|
inline fun <reified T> anyValueClass(): T {
|
||||||
|
val unboxedClass = T::class.java.declaredFields.first().type
|
||||||
|
return ArgumentMatchers.any(unboxedClass as Class<T>)
|
||||||
|
?: T::class.java.getDeclaredMethod("box-impl", unboxedClass)
|
||||||
|
.invoke(null, null) as T
|
||||||
|
}
|
@@ -0,0 +1,227 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of ETL-Processor
|
||||||
|
*
|
||||||
|
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||||
|
*
|
||||||
|
* This program is free software: you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
|
* by the Free Software Foundation, either version 3 of the License, or
|
||||||
|
* (at your option) any later version.
|
||||||
|
*
|
||||||
|
* This program is distributed in the hope that it will be useful,
|
||||||
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
* GNU Affero General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU Affero General Public License
|
||||||
|
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package dev.dnpm.etl.processor.input
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
|
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||||
|
import dev.dnpm.etl.processor.consent.ConsentEvaluation
|
||||||
|
import dev.dnpm.etl.processor.consent.ConsentEvaluator
|
||||||
|
import dev.dnpm.etl.processor.consent.MtbFileConsentService
|
||||||
|
import dev.dnpm.etl.processor.consent.TtpConsentStatus
|
||||||
|
import dev.dnpm.etl.processor.security.TokenRepository
|
||||||
|
import dev.dnpm.etl.processor.security.UserRoleRepository
|
||||||
|
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||||
|
import dev.pcvolkmer.mv64e.mtb.*
|
||||||
|
import org.junit.jupiter.api.BeforeEach
|
||||||
|
import org.junit.jupiter.api.Nested
|
||||||
|
import org.junit.jupiter.api.Test
|
||||||
|
import org.junit.jupiter.api.extension.ExtendWith
|
||||||
|
import org.mockito.junit.jupiter.MockitoExtension
|
||||||
|
import org.mockito.kotlin.*
|
||||||
|
import org.springframework.beans.factory.annotation.Autowired
|
||||||
|
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
||||||
|
import org.springframework.http.MediaType
|
||||||
|
import org.springframework.security.oauth2.client.registration.ClientRegistrationRepository
|
||||||
|
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.anonymous
|
||||||
|
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user
|
||||||
|
import org.springframework.test.context.ContextConfiguration
|
||||||
|
import org.springframework.test.context.TestPropertySource
|
||||||
|
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||||
|
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||||
|
import org.springframework.test.web.servlet.MockMvc
|
||||||
|
import org.springframework.test.web.servlet.delete
|
||||||
|
import org.springframework.test.web.servlet.post
|
||||||
|
import java.time.Instant
|
||||||
|
import java.util.*
|
||||||
|
|
||||||
|
@WebMvcTest(controllers = [MtbFileRestController::class])
|
||||||
|
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
|
||||||
|
@ContextConfiguration(
|
||||||
|
classes = [
|
||||||
|
MtbFileRestController::class,
|
||||||
|
AppSecurityConfiguration::class,
|
||||||
|
MtbFileConsentService::class
|
||||||
|
]
|
||||||
|
)
|
||||||
|
@MockitoBean(types = [TokenRepository::class, RequestProcessor::class, ConsentEvaluator::class])
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.pseudonymize.generator=BUILDIN",
|
||||||
|
"app.security.admin-user=admin",
|
||||||
|
"app.security.admin-password={noop}very-secret",
|
||||||
|
"app.security.enable-tokens=true"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
class MtbFileRestControllerTest {
|
||||||
|
|
||||||
|
lateinit var mockMvc: MockMvc
|
||||||
|
lateinit var requestProcessor: RequestProcessor
|
||||||
|
lateinit var consentEvaluator: ConsentEvaluator
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setup(
|
||||||
|
@Autowired mockMvc: MockMvc,
|
||||||
|
@Autowired requestProcessor: RequestProcessor,
|
||||||
|
@Autowired consentEvaluator: ConsentEvaluator
|
||||||
|
) {
|
||||||
|
this.mockMvc = mockMvc
|
||||||
|
this.requestProcessor = requestProcessor
|
||||||
|
this.consentEvaluator = consentEvaluator
|
||||||
|
|
||||||
|
doAnswer {
|
||||||
|
ConsentEvaluation(TtpConsentStatus.BROAD_CONSENT_GIVEN, true)
|
||||||
|
}.whenever(consentEvaluator).check(any())
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldGrantPermissionToSendMtbFile() {
|
||||||
|
mockMvc.post("/mtbfile") {
|
||||||
|
with(user("onkostarserver").roles("MTBFILE"))
|
||||||
|
contentType = MediaType.APPLICATION_JSON
|
||||||
|
content = ObjectMapper().writeValueAsString(mtbFile)
|
||||||
|
}.andExpect {
|
||||||
|
status { isAccepted() }
|
||||||
|
}
|
||||||
|
|
||||||
|
verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldGrantPermissionToSendMtbFileToAdminUser() {
|
||||||
|
mockMvc.post("/mtbfile") {
|
||||||
|
with(user("onkostarserver").roles("ADMIN"))
|
||||||
|
contentType = MediaType.APPLICATION_JSON
|
||||||
|
content = ObjectMapper().writeValueAsString(mtbFile)
|
||||||
|
}.andExpect {
|
||||||
|
status { isAccepted() }
|
||||||
|
}
|
||||||
|
|
||||||
|
verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldDenyPermissionToSendMtbFile() {
|
||||||
|
mockMvc.post("/mtbfile") {
|
||||||
|
with(anonymous())
|
||||||
|
contentType = MediaType.APPLICATION_JSON
|
||||||
|
content = ObjectMapper().writeValueAsString(mtbFile)
|
||||||
|
}.andExpect {
|
||||||
|
status { isUnauthorized() }
|
||||||
|
}
|
||||||
|
|
||||||
|
verify(requestProcessor, never()).processMtbFile(any<Mtb>())
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldDenyPermissionToSendMtbFileForUser() {
|
||||||
|
mockMvc.post("/mtbfile") {
|
||||||
|
with(user("fakeuser").roles("USER"))
|
||||||
|
contentType = MediaType.APPLICATION_JSON
|
||||||
|
content = ObjectMapper().writeValueAsString(mtbFile)
|
||||||
|
}.andExpect {
|
||||||
|
status { isForbidden() }
|
||||||
|
}
|
||||||
|
|
||||||
|
verify(requestProcessor, never()).processMtbFile(any<Mtb>())
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldGrantPermissionToDeletePatientData() {
|
||||||
|
mockMvc.delete("/mtbfile/12345678") {
|
||||||
|
with(user("onkostarserver").roles("MTBFILE"))
|
||||||
|
}.andExpect {
|
||||||
|
status { isAccepted() }
|
||||||
|
}
|
||||||
|
|
||||||
|
verify(requestProcessor, times(1)).processDeletion(anyValueClass(), eq(TtpConsentStatus.UNKNOWN_CHECK_FILE))
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldDenyPermissionToDeletePatientData() {
|
||||||
|
mockMvc.delete("/mtbfile/12345678") {
|
||||||
|
with(anonymous())
|
||||||
|
}.andExpect {
|
||||||
|
status { isUnauthorized() }
|
||||||
|
}
|
||||||
|
|
||||||
|
verify(requestProcessor, never()).processDeletion(anyValueClass(), any())
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
@MockitoBean(types = [UserRoleRepository::class, ClientRegistrationRepository::class])
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.pseudonymize.generator=BUILDIN",
|
||||||
|
"app.security.admin-user=admin",
|
||||||
|
"app.security.admin-password={noop}very-secret",
|
||||||
|
"app.security.enable-tokens=true",
|
||||||
|
"app.security.enable-oidc=true"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
inner class WithOidcEnabled {
|
||||||
|
@Test
|
||||||
|
fun testShouldGrantPermissionToSendMtbFileToAdminUser() {
|
||||||
|
mockMvc.post("/mtbfile") {
|
||||||
|
with(user("onkostarserver").roles("ADMIN"))
|
||||||
|
contentType = MediaType.APPLICATION_JSON
|
||||||
|
content = ObjectMapper().writeValueAsString(mtbFile)
|
||||||
|
}.andExpect {
|
||||||
|
status { isAccepted() }
|
||||||
|
}
|
||||||
|
|
||||||
|
verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldGrantPermissionToSendMtbFileToUser() {
|
||||||
|
mockMvc.post("/mtbfile") {
|
||||||
|
with(user("onkostarserver").roles("USER"))
|
||||||
|
contentType = MediaType.APPLICATION_JSON
|
||||||
|
content = ObjectMapper().writeValueAsString(mtbFile)
|
||||||
|
}.andExpect {
|
||||||
|
status { isAccepted() }
|
||||||
|
}
|
||||||
|
|
||||||
|
verify(requestProcessor, times(1)).processMtbFile(any<Mtb>())
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
companion object {
|
||||||
|
|
||||||
|
val mtbFile = Mtb.builder()
|
||||||
|
.patient(
|
||||||
|
Patient.builder()
|
||||||
|
.id("PID")
|
||||||
|
.build()
|
||||||
|
)
|
||||||
|
.episodesOfCare(
|
||||||
|
listOf(
|
||||||
|
MtbEpisodeOfCare.builder()
|
||||||
|
.id("1")
|
||||||
|
.patient(Reference.builder().id("PID").build())
|
||||||
|
.period(PeriodDate.builder().start(Date.from(Instant.parse("2023-08-08T02:00:00.00Z"))).build())
|
||||||
|
.build()
|
||||||
|
)
|
||||||
|
)
|
||||||
|
.build()
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
@@ -0,0 +1,75 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of ETL-Processor
|
||||||
|
*
|
||||||
|
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||||
|
*
|
||||||
|
* This program is free software: you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
|
* by the Free Software Foundation, either version 3 of the License, or
|
||||||
|
* (at your option) any later version.
|
||||||
|
*
|
||||||
|
* This program is distributed in the hope that it will be useful,
|
||||||
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
* GNU Affero General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU Affero General Public License
|
||||||
|
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package dev.dnpm.etl.processor.monitoring
|
||||||
|
|
||||||
|
import dev.dnpm.etl.processor.*
|
||||||
|
import dev.dnpm.etl.processor.output.MtbFileSender
|
||||||
|
import org.junit.jupiter.api.BeforeEach
|
||||||
|
import org.junit.jupiter.api.Test
|
||||||
|
import org.junit.jupiter.api.extension.ExtendWith
|
||||||
|
import org.springframework.beans.factory.annotation.Autowired
|
||||||
|
import org.springframework.boot.test.autoconfigure.data.jdbc.DataJdbcTest
|
||||||
|
import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase
|
||||||
|
import org.springframework.test.context.TestPropertySource
|
||||||
|
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||||
|
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||||
|
import org.springframework.transaction.annotation.Transactional
|
||||||
|
import org.testcontainers.junit.jupiter.Testcontainers
|
||||||
|
import java.time.Instant
|
||||||
|
|
||||||
|
@Testcontainers
|
||||||
|
@ExtendWith(SpringExtension::class)
|
||||||
|
@DataJdbcTest
|
||||||
|
@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE)
|
||||||
|
@Transactional
|
||||||
|
@MockitoBean(types = [MtbFileSender::class])
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.pseudonymize.generator=buildin",
|
||||||
|
"app.rest.uri=http://example.com"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
class RequestRepositoryTest : AbstractTestcontainerTest() {
|
||||||
|
|
||||||
|
private lateinit var requestRepository: RequestRepository
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setUp(
|
||||||
|
@Autowired requestRepository: RequestRepository
|
||||||
|
) {
|
||||||
|
this.requestRepository = requestRepository
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun shouldSaveRequest() {
|
||||||
|
val request = Request(
|
||||||
|
randomRequestId(),
|
||||||
|
PatientPseudonym("TEST_12345678901"),
|
||||||
|
PatientId("P1"),
|
||||||
|
Fingerprint("0123456789abcdef1"),
|
||||||
|
RequestType.MTB_FILE,
|
||||||
|
RequestStatus.WARNING,
|
||||||
|
Instant.parse("2023-07-07T00:00:00Z")
|
||||||
|
)
|
||||||
|
|
||||||
|
requestRepository.save(request)
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
@@ -0,0 +1,147 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of ETL-Processor
|
||||||
|
*
|
||||||
|
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||||
|
*
|
||||||
|
* This program is free software: you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
|
* by the Free Software Foundation, either version 3 of the License, or
|
||||||
|
* (at your option) any later version.
|
||||||
|
*
|
||||||
|
* This program is distributed in the hope that it will be useful,
|
||||||
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
* GNU Affero General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU Affero General Public License
|
||||||
|
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package dev.dnpm.etl.processor.pseudonym
|
||||||
|
|
||||||
|
import dev.dnpm.etl.processor.config.AppFhirConfig
|
||||||
|
import dev.dnpm.etl.processor.config.GPasConfigProperties
|
||||||
|
import org.assertj.core.api.Assertions.assertThat
|
||||||
|
import org.junit.jupiter.api.BeforeEach
|
||||||
|
import org.junit.jupiter.api.Test
|
||||||
|
import org.junit.jupiter.api.assertThrows
|
||||||
|
import org.springframework.http.HttpHeaders
|
||||||
|
import org.springframework.http.HttpMethod
|
||||||
|
import org.springframework.http.HttpStatus
|
||||||
|
import org.springframework.retry.policy.SimpleRetryPolicy
|
||||||
|
import org.springframework.retry.support.RetryTemplateBuilder
|
||||||
|
import org.springframework.test.web.client.MockRestServiceServer
|
||||||
|
import org.springframework.test.web.client.match.MockRestRequestMatchers.method
|
||||||
|
import org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo
|
||||||
|
import org.springframework.test.web.client.response.MockRestResponseCreators.withException
|
||||||
|
import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus
|
||||||
|
import org.springframework.web.client.RestTemplate
|
||||||
|
import java.io.IOException
|
||||||
|
|
||||||
|
class GpasPseudonymGeneratorTest {
|
||||||
|
|
||||||
|
private lateinit var mockRestServiceServer: MockRestServiceServer
|
||||||
|
private lateinit var generator: GpasPseudonymGenerator
|
||||||
|
private lateinit var restTemplate: RestTemplate
|
||||||
|
private var appFhirConfig: AppFhirConfig = AppFhirConfig()
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setup() {
|
||||||
|
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
|
||||||
|
val gPasConfigProperties = GPasConfigProperties(
|
||||||
|
"https://localhost:9990/ttp-fhir/fhir/gpas",
|
||||||
|
"test", "test2",
|
||||||
|
null,
|
||||||
|
null
|
||||||
|
)
|
||||||
|
|
||||||
|
this.restTemplate = RestTemplate()
|
||||||
|
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
|
||||||
|
this.generator =
|
||||||
|
GpasPseudonymGenerator(gPasConfigProperties, retryTemplate, restTemplate, appFhirConfig)
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun shouldReturnExpectedPseudonym() {
|
||||||
|
this.mockRestServiceServer.expect {
|
||||||
|
method(HttpMethod.POST)
|
||||||
|
requestTo("https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
|
||||||
|
}.andRespond {
|
||||||
|
withStatus(HttpStatus.OK).body(
|
||||||
|
getDummyResponseBody(
|
||||||
|
"1234",
|
||||||
|
"test",
|
||||||
|
"test1234ABCDEF567890"
|
||||||
|
)
|
||||||
|
)
|
||||||
|
.createResponse(it)
|
||||||
|
}
|
||||||
|
|
||||||
|
assertThat(this.generator.generate("ID1234")).isEqualTo("test1234ABCDEF567890")
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun shouldThrowExceptionIfGpasNotAvailable() {
|
||||||
|
this.mockRestServiceServer.expect {
|
||||||
|
method(HttpMethod.POST)
|
||||||
|
requestTo("https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
|
||||||
|
}.andRespond {
|
||||||
|
withException(IOException("Simulated IO error")).createResponse(it)
|
||||||
|
}
|
||||||
|
|
||||||
|
assertThrows<PseudonymRequestFailed> { this.generator.generate("ID1234") }
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun shouldThrowExceptionIfGpasDoesNotReturn2xxResponse() {
|
||||||
|
this.mockRestServiceServer.expect {
|
||||||
|
method(HttpMethod.POST)
|
||||||
|
requestTo("https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
|
||||||
|
}.andRespond {
|
||||||
|
withStatus(HttpStatus.FOUND)
|
||||||
|
.header(
|
||||||
|
HttpHeaders.LOCATION,
|
||||||
|
"https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate"
|
||||||
|
)
|
||||||
|
.createResponse(it)
|
||||||
|
}
|
||||||
|
|
||||||
|
assertThrows<PseudonymRequestFailed> { this.generator.generate("ID1234") }
|
||||||
|
}
|
||||||
|
|
||||||
|
companion object {
|
||||||
|
|
||||||
|
fun getDummyResponseBody(original: String, target: String, pseudonym: String) = """{
|
||||||
|
"resourceType": "Parameters",
|
||||||
|
"parameter": [
|
||||||
|
{
|
||||||
|
"name": "pseudonym",
|
||||||
|
"part": [
|
||||||
|
{
|
||||||
|
"name": "original",
|
||||||
|
"valueIdentifier": {
|
||||||
|
"system": "https://ths-greifswald.de/gpas",
|
||||||
|
"value": "$original"
|
||||||
|
}
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"name": "target",
|
||||||
|
"valueIdentifier": {
|
||||||
|
"system": "https://ths-greifswald.de/gpas",
|
||||||
|
"value": "$target"
|
||||||
|
}
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"name": "pseudonym",
|
||||||
|
"valueIdentifier": {
|
||||||
|
"system": "https://ths-greifswald.de/gpas",
|
||||||
|
"value": "$pseudonym"
|
||||||
|
}
|
||||||
|
}
|
||||||
|
]
|
||||||
|
}
|
||||||
|
]
|
||||||
|
}""".trimIndent()
|
||||||
|
|
||||||
|
}
|
||||||
|
}
|
@@ -19,7 +19,7 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.services
|
package dev.dnpm.etl.processor.services
|
||||||
|
|
||||||
import dev.dnpm.etl.processor.AbstractTestcontainerTest
|
import dev.dnpm.etl.processor.*
|
||||||
import dev.dnpm.etl.processor.monitoring.Request
|
import dev.dnpm.etl.processor.monitoring.Request
|
||||||
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
|
||||||
@@ -31,21 +31,21 @@ 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
|
||||||
import java.time.Instant
|
import java.time.Instant
|
||||||
import java.util.*
|
|
||||||
|
|
||||||
@Testcontainers
|
@Testcontainers
|
||||||
@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.rest.uri=http://example.com"
|
"app.rest.uri=http://example.com"
|
||||||
]
|
]
|
||||||
)
|
)
|
||||||
@@ -65,7 +65,7 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
|
|||||||
|
|
||||||
@Test
|
@Test
|
||||||
fun shouldResultInEmptyRequestList() {
|
fun shouldResultInEmptyRequestList() {
|
||||||
val actual = requestService.allRequestsByPatientPseudonym("TEST_12345678901")
|
val actual = requestService.allRequestsByPatientPseudonym(TEST_PATIENT_PSEUDONYM)
|
||||||
|
|
||||||
assertThat(actual).isEmpty()
|
assertThat(actual).isEmpty()
|
||||||
}
|
}
|
||||||
@@ -75,33 +75,33 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
|
|||||||
this.requestRepository.saveAll(
|
this.requestRepository.saveAll(
|
||||||
listOf(
|
listOf(
|
||||||
Request(
|
Request(
|
||||||
uuid = UUID.randomUUID().toString(),
|
randomRequestId(),
|
||||||
patientId = "TEST_12345678901",
|
PatientPseudonym("TEST_12345678901"),
|
||||||
pid = "P1",
|
PatientId("P1"),
|
||||||
fingerprint = "0123456789abcdef1",
|
Fingerprint("0123456789abcdef1"),
|
||||||
type = RequestType.MTB_FILE,
|
RequestType.MTB_FILE,
|
||||||
status = RequestStatus.SUCCESS,
|
RequestStatus.SUCCESS,
|
||||||
processedAt = Instant.parse("2023-07-07T02:00:00Z")
|
Instant.parse("2023-07-07T02:00:00Z")
|
||||||
),
|
),
|
||||||
// Should be ignored - wrong patient ID -->
|
// Should be ignored - wrong patient ID -->
|
||||||
Request(
|
Request(
|
||||||
uuid = UUID.randomUUID().toString(),
|
randomRequestId(),
|
||||||
patientId = "TEST_12345678902",
|
PatientPseudonym("TEST_12345678902"),
|
||||||
pid = "P2",
|
PatientId("P2"),
|
||||||
fingerprint = "0123456789abcdef2",
|
Fingerprint("0123456789abcdef2"),
|
||||||
type = RequestType.MTB_FILE,
|
RequestType.MTB_FILE,
|
||||||
status = RequestStatus.WARNING,
|
RequestStatus.WARNING,
|
||||||
processedAt = Instant.parse("2023-08-08T00:00:00Z")
|
Instant.parse("2023-08-08T00:00:00Z")
|
||||||
),
|
),
|
||||||
// <--
|
// <--
|
||||||
Request(
|
Request(
|
||||||
uuid = UUID.randomUUID().toString(),
|
randomRequestId(),
|
||||||
patientId = "TEST_12345678901",
|
PatientPseudonym("TEST_12345678901"),
|
||||||
pid = "P2",
|
PatientId("P2"),
|
||||||
fingerprint = "0123456789abcdee1",
|
Fingerprint("0123456789abcdee1"),
|
||||||
type = RequestType.DELETE,
|
RequestType.DELETE,
|
||||||
status = RequestStatus.SUCCESS,
|
RequestStatus.SUCCESS,
|
||||||
processedAt = Instant.parse("2023-08-08T02:00:00Z")
|
Instant.parse("2023-08-08T02:00:00Z")
|
||||||
)
|
)
|
||||||
)
|
)
|
||||||
)
|
)
|
||||||
@@ -111,18 +111,18 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
|
|||||||
fun shouldResultInSortedRequestList() {
|
fun shouldResultInSortedRequestList() {
|
||||||
setupTestData()
|
setupTestData()
|
||||||
|
|
||||||
val actual = requestService.allRequestsByPatientPseudonym("TEST_12345678901")
|
val actual = requestService.allRequestsByPatientPseudonym(TEST_PATIENT_PSEUDONYM)
|
||||||
|
|
||||||
assertThat(actual).hasSize(2)
|
assertThat(actual).hasSize(2)
|
||||||
assertThat(actual[0].fingerprint).isEqualTo("0123456789abcdee1")
|
assertThat(actual[0].fingerprint).isEqualTo(Fingerprint("0123456789abcdee1"))
|
||||||
assertThat(actual[1].fingerprint).isEqualTo("0123456789abcdef1")
|
assertThat(actual[1].fingerprint).isEqualTo(Fingerprint("0123456789abcdef1"))
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
fun shouldReturnDeleteRequestAsLastRequest() {
|
fun shouldReturnDeleteRequestAsLastRequest() {
|
||||||
setupTestData()
|
setupTestData()
|
||||||
|
|
||||||
val actual = requestService.isLastRequestWithKnownStatusDeletion("TEST_12345678901")
|
val actual = requestService.isLastRequestWithKnownStatusDeletion(TEST_PATIENT_PSEUDONYM)
|
||||||
|
|
||||||
assertThat(actual).isTrue()
|
assertThat(actual).isTrue()
|
||||||
}
|
}
|
||||||
@@ -131,10 +131,14 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
|
|||||||
fun shouldReturnLastMtbFileRequest() {
|
fun shouldReturnLastMtbFileRequest() {
|
||||||
setupTestData()
|
setupTestData()
|
||||||
|
|
||||||
val actual = requestService.lastMtbFileRequestForPatientPseudonym("TEST_12345678901")
|
val actual = requestService.lastMtbFileRequestForPatientPseudonym(TEST_PATIENT_PSEUDONYM)
|
||||||
|
|
||||||
assertThat(actual).isNotNull
|
assertThat(actual).isNotNull
|
||||||
assertThat(actual?.fingerprint).isEqualTo("0123456789abcdef1")
|
assertThat(actual?.fingerprint).isEqualTo(Fingerprint("0123456789abcdef1"))
|
||||||
|
}
|
||||||
|
|
||||||
|
companion object {
|
||||||
|
val TEST_PATIENT_PSEUDONYM = PatientPseudonym("TEST_12345678901")
|
||||||
}
|
}
|
||||||
|
|
||||||
}
|
}
|
@@ -0,0 +1,383 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of ETL-Processor
|
||||||
|
*
|
||||||
|
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||||
|
*
|
||||||
|
* This program is free software: you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
|
* by the Free Software Foundation, either version 3 of the License, or
|
||||||
|
* (at your option) any later version.
|
||||||
|
*
|
||||||
|
* This program is distributed in the hope that it will be useful,
|
||||||
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
* GNU Affero General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU Affero General Public License
|
||||||
|
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package dev.dnpm.etl.processor.web
|
||||||
|
|
||||||
|
import dev.dnpm.etl.processor.config.AppConfiguration
|
||||||
|
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||||
|
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
|
||||||
|
import dev.dnpm.etl.processor.monitoring.GIcsConnectionCheckService
|
||||||
|
import dev.dnpm.etl.processor.monitoring.GPasConnectionCheckService
|
||||||
|
import dev.dnpm.etl.processor.monitoring.RestConnectionCheckService
|
||||||
|
import dev.dnpm.etl.processor.output.MtbFileSender
|
||||||
|
import dev.dnpm.etl.processor.pseudonym.Generator
|
||||||
|
import dev.dnpm.etl.processor.security.Role
|
||||||
|
import dev.dnpm.etl.processor.security.TokenService
|
||||||
|
import dev.dnpm.etl.processor.security.UserRoleService
|
||||||
|
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||||
|
import dev.dnpm.etl.processor.services.TransformationService
|
||||||
|
import org.assertj.core.api.Assertions.assertThat
|
||||||
|
import org.htmlunit.WebClient
|
||||||
|
import org.htmlunit.html.HtmlPage
|
||||||
|
import org.junit.jupiter.api.BeforeEach
|
||||||
|
import org.junit.jupiter.api.Nested
|
||||||
|
import org.junit.jupiter.api.Test
|
||||||
|
import org.junit.jupiter.api.extension.ExtendWith
|
||||||
|
import org.mockito.ArgumentMatchers.anyString
|
||||||
|
import org.mockito.junit.jupiter.MockitoExtension
|
||||||
|
import org.mockito.kotlin.argumentCaptor
|
||||||
|
import org.mockito.kotlin.times
|
||||||
|
import org.mockito.kotlin.verify
|
||||||
|
import org.mockito.kotlin.whenever
|
||||||
|
import org.springframework.beans.factory.annotation.Autowired
|
||||||
|
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
||||||
|
import org.springframework.http.HttpHeaders
|
||||||
|
import org.springframework.http.MediaType
|
||||||
|
import org.springframework.http.MediaType.TEXT_EVENT_STREAM
|
||||||
|
import org.springframework.security.test.context.support.WithMockUser
|
||||||
|
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.anonymous
|
||||||
|
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user
|
||||||
|
import org.springframework.test.context.ContextConfiguration
|
||||||
|
import org.springframework.test.context.TestPropertySource
|
||||||
|
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||||
|
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||||
|
import org.springframework.test.web.reactive.server.WebTestClient
|
||||||
|
import org.springframework.test.web.servlet.*
|
||||||
|
import org.springframework.test.web.servlet.client.MockMvcWebTestClient
|
||||||
|
import org.springframework.test.web.servlet.htmlunit.MockMvcWebClientBuilder
|
||||||
|
import org.springframework.web.context.WebApplicationContext
|
||||||
|
import reactor.core.publisher.Sinks
|
||||||
|
import reactor.test.StepVerifier
|
||||||
|
import java.time.Instant
|
||||||
|
|
||||||
|
abstract class MockSink : Sinks.Many<Boolean>
|
||||||
|
|
||||||
|
@WebMvcTest(controllers = [ConfigController::class])
|
||||||
|
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
|
||||||
|
@ContextConfiguration(
|
||||||
|
classes = [
|
||||||
|
ConfigController::class,
|
||||||
|
AppConfiguration::class,
|
||||||
|
AppSecurityConfiguration::class
|
||||||
|
]
|
||||||
|
)
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.pseudonymize.generator=BUILDIN"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
@MockitoBean(name = "configsUpdateProducer", types = [MockSink::class])
|
||||||
|
@MockitoBean(
|
||||||
|
types = [
|
||||||
|
Generator::class,
|
||||||
|
MtbFileSender::class,
|
||||||
|
RequestProcessor::class,
|
||||||
|
TransformationService::class,
|
||||||
|
GPasConnectionCheckService::class,
|
||||||
|
RestConnectionCheckService::class,
|
||||||
|
GIcsConnectionCheckService::class
|
||||||
|
]
|
||||||
|
)
|
||||||
|
class ConfigControllerTest {
|
||||||
|
|
||||||
|
private lateinit var mockMvc: MockMvc
|
||||||
|
private lateinit var webClient: WebClient
|
||||||
|
|
||||||
|
private lateinit var requestProcessor: RequestProcessor
|
||||||
|
private lateinit var connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setup(
|
||||||
|
@Autowired mockMvc: MockMvc,
|
||||||
|
@Autowired requestProcessor: RequestProcessor,
|
||||||
|
@Autowired connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||||
|
) {
|
||||||
|
this.mockMvc = mockMvc
|
||||||
|
this.webClient = MockMvcWebClientBuilder.mockMvcSetup(mockMvc).build()
|
||||||
|
this.requestProcessor = requestProcessor
|
||||||
|
this.connectionCheckUpdateProducer = connectionCheckUpdateProducer
|
||||||
|
|
||||||
|
webClient.options.isThrowExceptionOnScriptError = false
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldRequestConfigPageIfLoggedIn() {
|
||||||
|
mockMvc.get("/configs") {
|
||||||
|
with(user("admin").roles("ADMIN"))
|
||||||
|
accept(MediaType.TEXT_HTML)
|
||||||
|
}.andExpect {
|
||||||
|
status { isOk() }
|
||||||
|
view { name("configs") }
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldRedirectToLoginPageIfNotLoggedIn() {
|
||||||
|
mockMvc.get("/configs") {
|
||||||
|
with(anonymous())
|
||||||
|
accept(MediaType.TEXT_HTML)
|
||||||
|
}.andExpect {
|
||||||
|
status { isFound() }
|
||||||
|
header {
|
||||||
|
stringValues(HttpHeaders.LOCATION, "http://localhost/login")
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.security.enable-tokens=true",
|
||||||
|
"app.security.admin-user=admin"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
@MockitoBean(
|
||||||
|
types = [
|
||||||
|
TokenService::class
|
||||||
|
]
|
||||||
|
)
|
||||||
|
inner class WithTokensEnabled {
|
||||||
|
private lateinit var tokenService: TokenService
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setup(
|
||||||
|
@Autowired tokenService: TokenService
|
||||||
|
) {
|
||||||
|
webClient.options.isThrowExceptionOnScriptError = false
|
||||||
|
|
||||||
|
this.tokenService = tokenService
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldSaveNewToken() {
|
||||||
|
mockMvc.post("/configs/tokens") {
|
||||||
|
with(user("admin").roles("ADMIN"))
|
||||||
|
accept(MediaType.TEXT_HTML)
|
||||||
|
contentType = MediaType.APPLICATION_FORM_URLENCODED
|
||||||
|
content = "name=Testtoken"
|
||||||
|
}.andExpect {
|
||||||
|
status { is2xxSuccessful() }
|
||||||
|
view { name("configs/tokens") }
|
||||||
|
}
|
||||||
|
|
||||||
|
val captor = argumentCaptor<String>()
|
||||||
|
verify(tokenService, times(1)).addToken(captor.capture())
|
||||||
|
|
||||||
|
assertThat(captor.firstValue).isEqualTo("Testtoken")
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldNotSaveTokenWithExstingName() {
|
||||||
|
whenever(tokenService.addToken(anyString())).thenReturn(
|
||||||
|
Result.failure(
|
||||||
|
RuntimeException(
|
||||||
|
"Testfailure"
|
||||||
|
)
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
|
mockMvc.post("/configs/tokens") {
|
||||||
|
with(user("admin").roles("ADMIN"))
|
||||||
|
accept(MediaType.TEXT_HTML)
|
||||||
|
contentType = MediaType.APPLICATION_FORM_URLENCODED
|
||||||
|
content = "name=Testtoken"
|
||||||
|
}.andExpect {
|
||||||
|
status { is2xxSuccessful() }
|
||||||
|
view { name("configs/tokens") }
|
||||||
|
}
|
||||||
|
|
||||||
|
val captor = argumentCaptor<String>()
|
||||||
|
verify(tokenService, times(1)).addToken(captor.capture())
|
||||||
|
|
||||||
|
assertThat(captor.firstValue).isEqualTo("Testtoken")
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldDeleteToken() {
|
||||||
|
mockMvc.delete("/configs/tokens/42") {
|
||||||
|
with(user("admin").roles("ADMIN"))
|
||||||
|
accept(MediaType.TEXT_HTML)
|
||||||
|
}.andExpect {
|
||||||
|
status { is2xxSuccessful() }
|
||||||
|
view { name("configs/tokens") }
|
||||||
|
}
|
||||||
|
|
||||||
|
val captor = argumentCaptor<Long>()
|
||||||
|
verify(tokenService, times(1)).deleteToken(captor.capture())
|
||||||
|
|
||||||
|
assertThat(captor.firstValue).isEqualTo(42)
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
@WithMockUser(username = "admin", roles = ["ADMIN"])
|
||||||
|
fun testShouldRenderConfigPageWithTokens() {
|
||||||
|
val page = webClient.getPage<HtmlPage>("http://localhost/configs")
|
||||||
|
assertThat(
|
||||||
|
page.getElementById("tokens")
|
||||||
|
).isNotNull
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.security.enable-tokens=false"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
inner class WithTokensDisabled {
|
||||||
|
@BeforeEach
|
||||||
|
fun setup() {
|
||||||
|
webClient.options.isThrowExceptionOnScriptError = false
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
@WithMockUser(username = "admin", roles = ["ADMIN"])
|
||||||
|
fun testShouldRenderConfigPageWithoutTokens() {
|
||||||
|
val page = webClient.getPage<HtmlPage>("http://localhost/configs")
|
||||||
|
assertThat(
|
||||||
|
page.getElementById("tokens")
|
||||||
|
).isNull()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.security.enable-tokens=false",
|
||||||
|
"app.security.admin-user=admin",
|
||||||
|
"app.security.admin-password={noop}very-secret"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
@MockitoBean(
|
||||||
|
types = [
|
||||||
|
UserRoleService::class
|
||||||
|
]
|
||||||
|
)
|
||||||
|
inner class WithUserRolesEnabled {
|
||||||
|
private lateinit var userRoleService: UserRoleService
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setup(
|
||||||
|
@Autowired userRoleService: UserRoleService
|
||||||
|
) {
|
||||||
|
webClient.options.isThrowExceptionOnScriptError = false
|
||||||
|
|
||||||
|
this.userRoleService = userRoleService
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldDeleteUserRole() {
|
||||||
|
mockMvc.delete("/configs/userroles/42") {
|
||||||
|
with(user("admin").roles("ADMIN"))
|
||||||
|
accept(MediaType.TEXT_HTML)
|
||||||
|
}.andExpect {
|
||||||
|
status { is2xxSuccessful() }
|
||||||
|
view { name("configs/userroles") }
|
||||||
|
}
|
||||||
|
|
||||||
|
val captor = argumentCaptor<Long>()
|
||||||
|
verify(userRoleService, times(1)).deleteUserRole(captor.capture())
|
||||||
|
|
||||||
|
assertThat(captor.firstValue).isEqualTo(42)
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldUpdateUserRole() {
|
||||||
|
mockMvc.put("/configs/userroles/42") {
|
||||||
|
with(user("admin").roles("ADMIN"))
|
||||||
|
accept(MediaType.TEXT_HTML)
|
||||||
|
contentType = MediaType.APPLICATION_FORM_URLENCODED
|
||||||
|
content = "role=ADMIN"
|
||||||
|
}.andExpect {
|
||||||
|
status { is2xxSuccessful() }
|
||||||
|
view { name("configs/userroles") }
|
||||||
|
}
|
||||||
|
|
||||||
|
val idCaptor = argumentCaptor<Long>()
|
||||||
|
val roleCaptor = argumentCaptor<Role>()
|
||||||
|
verify(userRoleService, times(1)).updateUserRole(
|
||||||
|
idCaptor.capture(),
|
||||||
|
roleCaptor.capture()
|
||||||
|
)
|
||||||
|
|
||||||
|
assertThat(idCaptor.firstValue).isEqualTo(42)
|
||||||
|
assertThat(roleCaptor.firstValue).isEqualTo(Role.ADMIN)
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
@WithMockUser(username = "admin", roles = ["ADMIN"])
|
||||||
|
fun testShouldRenderConfigPageWithUserRoles() {
|
||||||
|
val page = webClient.getPage<HtmlPage>("http://localhost/configs")
|
||||||
|
assertThat(
|
||||||
|
page.getElementById("userroles")
|
||||||
|
).isNotNull
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
inner class WithUserRolesDisabled {
|
||||||
|
@BeforeEach
|
||||||
|
fun setup() {
|
||||||
|
webClient.options.isThrowExceptionOnScriptError = false
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldRenderConfigPageWithoutUserRoles() {
|
||||||
|
val page = webClient.getPage<HtmlPage>("http://localhost/configs")
|
||||||
|
assertThat(
|
||||||
|
page.getElementById("userroles")
|
||||||
|
).isNull()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
inner class SseTest {
|
||||||
|
private lateinit var webClient: WebTestClient
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setup(
|
||||||
|
applicationContext: WebApplicationContext
|
||||||
|
) {
|
||||||
|
this.webClient = MockMvcWebTestClient
|
||||||
|
.bindToApplicationContext(applicationContext).build()
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldRequestGPasSSE() {
|
||||||
|
val expectedEvent =
|
||||||
|
ConnectionCheckResult.GPasConnectionCheckResult(true, Instant.now(), Instant.now())
|
||||||
|
|
||||||
|
connectionCheckUpdateProducer.tryEmitNext(expectedEvent)
|
||||||
|
connectionCheckUpdateProducer.emitComplete { _, _ -> true }
|
||||||
|
|
||||||
|
val result =
|
||||||
|
webClient.get().uri("http://localhost/configs/events").accept(TEXT_EVENT_STREAM)
|
||||||
|
.exchange()
|
||||||
|
.expectStatus().isOk()
|
||||||
|
.expectHeader().contentType(TEXT_EVENT_STREAM)
|
||||||
|
.returnResult(ConnectionCheckResult.GPasConnectionCheckResult::class.java)
|
||||||
|
|
||||||
|
StepVerifier.create(result.responseBody)
|
||||||
|
.expectNext(expectedEvent)
|
||||||
|
.expectComplete()
|
||||||
|
.verify()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
@@ -0,0 +1,311 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of ETL-Processor
|
||||||
|
*
|
||||||
|
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||||
|
*
|
||||||
|
* This program is free software: you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
|
* by the Free Software Foundation, either version 3 of the License, or
|
||||||
|
* (at your option) any later version.
|
||||||
|
*
|
||||||
|
* This program is distributed in the hope that it will be useful,
|
||||||
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
* GNU Affero General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU Affero General Public License
|
||||||
|
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package dev.dnpm.etl.processor.web
|
||||||
|
|
||||||
|
import dev.dnpm.etl.processor.*
|
||||||
|
import dev.dnpm.etl.processor.config.AppConfiguration
|
||||||
|
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||||
|
import dev.dnpm.etl.processor.monitoring.Report
|
||||||
|
import dev.dnpm.etl.processor.monitoring.Request
|
||||||
|
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||||
|
import dev.dnpm.etl.processor.monitoring.RequestType
|
||||||
|
import dev.dnpm.etl.processor.services.RequestService
|
||||||
|
import org.assertj.core.api.Assertions.assertThat
|
||||||
|
import org.htmlunit.WebClient
|
||||||
|
import org.htmlunit.html.HtmlPage
|
||||||
|
import org.junit.jupiter.api.BeforeEach
|
||||||
|
import org.junit.jupiter.api.Nested
|
||||||
|
import org.junit.jupiter.api.Test
|
||||||
|
import org.junit.jupiter.api.assertThrows
|
||||||
|
import org.junit.jupiter.api.extension.ExtendWith
|
||||||
|
import org.mockito.junit.jupiter.MockitoExtension
|
||||||
|
import org.mockito.kotlin.any
|
||||||
|
import org.mockito.kotlin.whenever
|
||||||
|
import org.springframework.beans.factory.annotation.Autowired
|
||||||
|
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
||||||
|
import org.springframework.data.domain.Page
|
||||||
|
import org.springframework.data.domain.PageImpl
|
||||||
|
import org.springframework.data.domain.Pageable
|
||||||
|
import org.springframework.security.test.context.support.WithMockUser
|
||||||
|
import org.springframework.test.context.ContextConfiguration
|
||||||
|
import org.springframework.test.context.TestPropertySource
|
||||||
|
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||||
|
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||||
|
import org.springframework.test.web.servlet.MockMvc
|
||||||
|
import org.springframework.test.web.servlet.get
|
||||||
|
import org.springframework.test.web.servlet.htmlunit.MockMvcWebClientBuilder
|
||||||
|
import java.io.IOException
|
||||||
|
import java.time.Instant
|
||||||
|
import java.util.*
|
||||||
|
|
||||||
|
@WebMvcTest(controllers = [HomeController::class])
|
||||||
|
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
|
||||||
|
@ContextConfiguration(
|
||||||
|
classes = [
|
||||||
|
HomeController::class,
|
||||||
|
AppConfiguration::class,
|
||||||
|
AppSecurityConfiguration::class
|
||||||
|
]
|
||||||
|
)
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.pseudonymize.generator=BUILDIN",
|
||||||
|
"app.security.admin-user=admin",
|
||||||
|
"app.security.admin-password={noop}very-secret"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
@MockitoBean(
|
||||||
|
types = [RequestService::class]
|
||||||
|
)
|
||||||
|
class HomeControllerTest {
|
||||||
|
|
||||||
|
private lateinit var mockMvc: MockMvc
|
||||||
|
private lateinit var webClient: WebClient
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setup(
|
||||||
|
@Autowired mockMvc: MockMvc,
|
||||||
|
@Autowired requestService: RequestService
|
||||||
|
) {
|
||||||
|
this.mockMvc = mockMvc
|
||||||
|
this.webClient = MockMvcWebClientBuilder.mockMvcSetup(mockMvc).build()
|
||||||
|
|
||||||
|
whenever(requestService.findAll(any<Pageable>())).thenReturn(Page.empty())
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldRequestHomePage() {
|
||||||
|
mockMvc.get("/").andExpect {
|
||||||
|
status { isOk() }
|
||||||
|
view { name("index") }
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
inner class WithRequests {
|
||||||
|
|
||||||
|
private lateinit var requestService: RequestService
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setup(
|
||||||
|
@Autowired requestService: RequestService
|
||||||
|
) {
|
||||||
|
this.requestService = requestService
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldShowHomePage() {
|
||||||
|
whenever(requestService.findAll(any<Pageable>())).thenReturn(
|
||||||
|
PageImpl(
|
||||||
|
listOf(
|
||||||
|
Request(
|
||||||
|
2L,
|
||||||
|
randomRequestId(),
|
||||||
|
PatientPseudonym("PSEUDO1"),
|
||||||
|
PatientId("PATIENT1"),
|
||||||
|
Fingerprint("ashdkasdh"),
|
||||||
|
RequestType.MTB_FILE,
|
||||||
|
RequestStatus.SUCCESS
|
||||||
|
),
|
||||||
|
Request(
|
||||||
|
1L,
|
||||||
|
randomRequestId(),
|
||||||
|
PatientPseudonym("PSEUDO1"),
|
||||||
|
PatientId("PATIENT1"),
|
||||||
|
Fingerprint("asdasdasd"),
|
||||||
|
RequestType.MTB_FILE,
|
||||||
|
RequestStatus.ERROR
|
||||||
|
)
|
||||||
|
)
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
|
val page = webClient.getPage<HtmlPage>("http://localhost/")
|
||||||
|
assertThat(page.querySelectorAll("tbody tr")).hasSize(2)
|
||||||
|
assertThat(page.querySelectorAll("div.notification.info")).isEmpty()
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
@WithMockUser(username = "admin", roles = ["ADMIN"])
|
||||||
|
fun testShouldShowRequestDetails() {
|
||||||
|
val requestId = randomRequestId()
|
||||||
|
|
||||||
|
whenever(requestService.findByUuid(anyValueClass())).thenReturn(
|
||||||
|
Optional.of(
|
||||||
|
Request(
|
||||||
|
2L,
|
||||||
|
requestId,
|
||||||
|
PatientPseudonym("PSEUDO1"),
|
||||||
|
PatientId("PATIENT1"),
|
||||||
|
Fingerprint("ashdkasdh"),
|
||||||
|
RequestType.MTB_FILE,
|
||||||
|
RequestStatus.SUCCESS,
|
||||||
|
Instant.now(),
|
||||||
|
Report("Test")
|
||||||
|
)
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
|
val page = webClient.getPage<HtmlPage>("http://localhost/report/${requestId.value}")
|
||||||
|
assertThat(page.querySelectorAll("tbody tr")).hasSize(1)
|
||||||
|
assertThat(page.querySelectorAll("div.notification.info")).isEmpty()
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
@WithMockUser(username = "admin", roles = ["ADMIN"])
|
||||||
|
fun testShouldShowPatientDetails() {
|
||||||
|
whenever(requestService.findRequestByPatientId(anyValueClass(), any<Pageable>())).thenReturn(
|
||||||
|
PageImpl(
|
||||||
|
listOf(
|
||||||
|
Request(
|
||||||
|
2L,
|
||||||
|
randomRequestId(),
|
||||||
|
PatientPseudonym("PSEUDO1"),
|
||||||
|
PatientId("PATIENT1"),
|
||||||
|
Fingerprint("ashdkasdh"),
|
||||||
|
RequestType.MTB_FILE,
|
||||||
|
RequestStatus.SUCCESS
|
||||||
|
),
|
||||||
|
Request(
|
||||||
|
1L,
|
||||||
|
randomRequestId(),
|
||||||
|
PatientPseudonym("PSEUDO1"),
|
||||||
|
PatientId("PATIENT1"),
|
||||||
|
Fingerprint("asdasdasd"),
|
||||||
|
RequestType.MTB_FILE,
|
||||||
|
RequestStatus.ERROR
|
||||||
|
)
|
||||||
|
)
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
|
val page = webClient.getPage<HtmlPage>("http://localhost/patient/PSEUDO1")
|
||||||
|
assertThat(page.querySelectorAll("tbody tr")).hasSize(2)
|
||||||
|
assertThat(page.querySelectorAll("div.notification.info")).isEmpty()
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
@WithMockUser(username = "admin", roles = ["ADMIN"])
|
||||||
|
fun testShouldShowPatientPseudonym() {
|
||||||
|
whenever(requestService.findRequestByPatientId(anyValueClass(), any<Pageable>())).thenReturn(
|
||||||
|
PageImpl(
|
||||||
|
listOf(
|
||||||
|
Request(
|
||||||
|
2L,
|
||||||
|
randomRequestId(),
|
||||||
|
PatientPseudonym("PSEUDO1"),
|
||||||
|
PatientId("PATIENT1"),
|
||||||
|
Fingerprint("ashdkasdh"),
|
||||||
|
RequestType.MTB_FILE,
|
||||||
|
RequestStatus.SUCCESS
|
||||||
|
),
|
||||||
|
Request(
|
||||||
|
1L,
|
||||||
|
randomRequestId(),
|
||||||
|
PatientPseudonym("PSEUDO1"),
|
||||||
|
PatientId("PATIENT1"),
|
||||||
|
Fingerprint("asdasdasd"),
|
||||||
|
RequestType.MTB_FILE,
|
||||||
|
RequestStatus.ERROR
|
||||||
|
)
|
||||||
|
)
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
|
val page = webClient.getPage<HtmlPage>("http://localhost/patient/PSEUDO1")
|
||||||
|
assertThat(page.querySelectorAll("h2 > span")).hasSize(1)
|
||||||
|
assertThat(page.querySelectorAll("h2 > span").first().textContent).isEqualTo("PSEUDO1")
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
inner class WithoutRequests {
|
||||||
|
|
||||||
|
private lateinit var requestService: RequestService
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setup(
|
||||||
|
@Autowired requestService: RequestService
|
||||||
|
) {
|
||||||
|
this.requestService = requestService
|
||||||
|
|
||||||
|
whenever(requestService.findAll(any<Pageable>())).thenReturn(Page.empty())
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldShowHomePage() {
|
||||||
|
val page = webClient.getPage<HtmlPage>("http://localhost/")
|
||||||
|
assertThat(page.querySelectorAll("tbody tr")).isEmpty()
|
||||||
|
assertThat(page.querySelectorAll("div.notification.info")).hasSize(1)
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
@WithMockUser(username = "admin", roles = ["ADMIN"])
|
||||||
|
fun testShouldThrowNotFoundExceptionForUnknownReport() {
|
||||||
|
val requestId = randomRequestId()
|
||||||
|
|
||||||
|
whenever(requestService.findByUuid(anyValueClass())).thenReturn(
|
||||||
|
Optional.empty()
|
||||||
|
)
|
||||||
|
|
||||||
|
assertThrows<IOException> {
|
||||||
|
webClient.getPage<HtmlPage>("http://localhost/report/${requestId.value}")
|
||||||
|
}.also {
|
||||||
|
assertThat(it).hasRootCauseInstanceOf(NotFoundException::class.java)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
@WithMockUser(username = "admin", roles = ["ADMIN"])
|
||||||
|
fun testShouldShowEmptyPatientDetails() {
|
||||||
|
whenever(requestService.findRequestByPatientId(anyValueClass(), any<Pageable>())).thenReturn(Page.empty())
|
||||||
|
|
||||||
|
val page = webClient.getPage<HtmlPage>("http://localhost/patient/PSEUDO1")
|
||||||
|
assertThat(page.querySelectorAll("tbody tr")).isEmpty()
|
||||||
|
assertThat(page.querySelectorAll("div.notification.info")).hasSize(1)
|
||||||
|
}
|
||||||
|
|
||||||
|
@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")
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
@@ -0,0 +1,88 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of ETL-Processor
|
||||||
|
*
|
||||||
|
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||||
|
*
|
||||||
|
* This program is free software: you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
|
* by the Free Software Foundation, either version 3 of the License, or
|
||||||
|
* (at your option) any later version.
|
||||||
|
*
|
||||||
|
* This program is distributed in the hope that it will be useful,
|
||||||
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
* GNU Affero General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU Affero General Public License
|
||||||
|
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package dev.dnpm.etl.processor.web
|
||||||
|
|
||||||
|
import dev.dnpm.etl.processor.config.AppConfiguration
|
||||||
|
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||||
|
import dev.dnpm.etl.processor.security.TokenService
|
||||||
|
import org.assertj.core.api.Assertions.assertThat
|
||||||
|
import org.htmlunit.WebClient
|
||||||
|
import org.htmlunit.html.HtmlPage
|
||||||
|
import org.junit.jupiter.api.BeforeEach
|
||||||
|
import org.junit.jupiter.api.Test
|
||||||
|
import org.junit.jupiter.api.extension.ExtendWith
|
||||||
|
import org.mockito.junit.jupiter.MockitoExtension
|
||||||
|
import org.springframework.beans.factory.annotation.Autowired
|
||||||
|
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
||||||
|
import org.springframework.test.context.ContextConfiguration
|
||||||
|
import org.springframework.test.context.TestPropertySource
|
||||||
|
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||||
|
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||||
|
import org.springframework.test.web.servlet.MockMvc
|
||||||
|
import org.springframework.test.web.servlet.get
|
||||||
|
import org.springframework.test.web.servlet.htmlunit.MockMvcWebClientBuilder
|
||||||
|
|
||||||
|
@WebMvcTest(controllers = [LoginController::class])
|
||||||
|
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
|
||||||
|
@ContextConfiguration(
|
||||||
|
classes = [
|
||||||
|
LoginController::class,
|
||||||
|
AppConfiguration::class,
|
||||||
|
AppSecurityConfiguration::class
|
||||||
|
]
|
||||||
|
)
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.pseudonymize.generator=BUILDIN",
|
||||||
|
"app.security.admin-user=admin",
|
||||||
|
"app.security.admin-password={noop}very-secret",
|
||||||
|
"app.security.enable-tokens=true"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
@MockitoBean(
|
||||||
|
types = [TokenService::class]
|
||||||
|
)
|
||||||
|
class LoginControllerTest {
|
||||||
|
|
||||||
|
private lateinit var mockMvc: MockMvc
|
||||||
|
private lateinit var webClient: WebClient
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setup(@Autowired mockMvc: MockMvc) {
|
||||||
|
this.mockMvc = mockMvc
|
||||||
|
this.webClient = MockMvcWebClientBuilder.mockMvcSetup(mockMvc).build()
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldRequestLoginPage() {
|
||||||
|
mockMvc.get("/login").andExpect {
|
||||||
|
status { isOk() }
|
||||||
|
view { name("login") }
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldShowLoginForm() {
|
||||||
|
val page = webClient.getPage<HtmlPage>("http://localhost/login")
|
||||||
|
assertThat(
|
||||||
|
page.getElementsByTagName("main").first().firstElementChild.getAttribute("class")
|
||||||
|
).isEqualTo("login-form")
|
||||||
|
}
|
||||||
|
}
|
@@ -0,0 +1,73 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of ETL-Processor
|
||||||
|
*
|
||||||
|
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||||
|
*
|
||||||
|
* This program is free software: you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
|
* by the Free Software Foundation, either version 3 of the License, or
|
||||||
|
* (at your option) any later version.
|
||||||
|
*
|
||||||
|
* This program is distributed in the hope that it will be useful,
|
||||||
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
* GNU Affero General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU Affero General Public License
|
||||||
|
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package dev.dnpm.etl.processor.web
|
||||||
|
|
||||||
|
import dev.dnpm.etl.processor.config.AppConfiguration
|
||||||
|
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||||
|
import org.htmlunit.WebClient
|
||||||
|
import org.junit.jupiter.api.BeforeEach
|
||||||
|
import org.junit.jupiter.api.Test
|
||||||
|
import org.junit.jupiter.api.extension.ExtendWith
|
||||||
|
import org.mockito.junit.jupiter.MockitoExtension
|
||||||
|
import org.springframework.beans.factory.annotation.Autowired
|
||||||
|
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
||||||
|
import org.springframework.test.context.ContextConfiguration
|
||||||
|
import org.springframework.test.context.TestPropertySource
|
||||||
|
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||||
|
import org.springframework.test.web.servlet.MockMvc
|
||||||
|
import org.springframework.test.web.servlet.get
|
||||||
|
import org.springframework.test.web.servlet.htmlunit.MockMvcWebClientBuilder
|
||||||
|
|
||||||
|
@WebMvcTest(controllers = [StatisticsController::class])
|
||||||
|
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
|
||||||
|
@ContextConfiguration(
|
||||||
|
classes = [
|
||||||
|
StatisticsController::class,
|
||||||
|
AppConfiguration::class,
|
||||||
|
AppSecurityConfiguration::class
|
||||||
|
]
|
||||||
|
)
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.pseudonymize.generator=BUILDIN",
|
||||||
|
"app.security.admin-user=admin",
|
||||||
|
"app.security.admin-password={noop}very-secret"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
class StatisticsControllerTest {
|
||||||
|
|
||||||
|
private lateinit var mockMvc: MockMvc
|
||||||
|
private lateinit var webClient: WebClient
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setup(@Autowired mockMvc: MockMvc) {
|
||||||
|
this.mockMvc = mockMvc
|
||||||
|
this.webClient = MockMvcWebClientBuilder.mockMvcSetup(mockMvc).build()
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldRequestLoginPage() {
|
||||||
|
mockMvc.get("/statistics").andExpect {
|
||||||
|
status { isOk() }
|
||||||
|
view { name("statistics") }
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
@@ -0,0 +1,314 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of ETL-Processor
|
||||||
|
*
|
||||||
|
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||||
|
*
|
||||||
|
* This program is free software: you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
|
* by the Free Software Foundation, either version 3 of the License, or
|
||||||
|
* (at your option) any later version.
|
||||||
|
*
|
||||||
|
* This program is distributed in the hope that it will be useful,
|
||||||
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
* GNU Affero General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU Affero General Public License
|
||||||
|
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package dev.dnpm.etl.processor.web
|
||||||
|
|
||||||
|
import dev.dnpm.etl.processor.Fingerprint
|
||||||
|
import dev.dnpm.etl.processor.PatientId
|
||||||
|
import dev.dnpm.etl.processor.PatientPseudonym
|
||||||
|
import dev.dnpm.etl.processor.config.AppConfiguration
|
||||||
|
import dev.dnpm.etl.processor.config.AppSecurityConfiguration
|
||||||
|
import dev.dnpm.etl.processor.monitoring.CountedState
|
||||||
|
import dev.dnpm.etl.processor.monitoring.Request
|
||||||
|
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||||
|
import dev.dnpm.etl.processor.monitoring.RequestType
|
||||||
|
import dev.dnpm.etl.processor.randomRequestId
|
||||||
|
import dev.dnpm.etl.processor.services.RequestService
|
||||||
|
import org.hamcrest.Matchers.equalTo
|
||||||
|
import org.hamcrest.Matchers.hasSize
|
||||||
|
import org.junit.jupiter.api.BeforeEach
|
||||||
|
import org.junit.jupiter.api.Nested
|
||||||
|
import org.junit.jupiter.api.Test
|
||||||
|
import org.junit.jupiter.api.extension.ExtendWith
|
||||||
|
import org.mockito.junit.jupiter.MockitoExtension
|
||||||
|
import org.mockito.kotlin.doAnswer
|
||||||
|
import org.mockito.kotlin.whenever
|
||||||
|
import org.springframework.beans.factory.annotation.Autowired
|
||||||
|
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest
|
||||||
|
import org.springframework.http.MediaType.TEXT_EVENT_STREAM
|
||||||
|
import org.springframework.test.context.ContextConfiguration
|
||||||
|
import org.springframework.test.context.TestPropertySource
|
||||||
|
import org.springframework.test.context.bean.override.mockito.MockitoBean
|
||||||
|
import org.springframework.test.context.junit.jupiter.SpringExtension
|
||||||
|
import org.springframework.test.web.reactive.server.WebTestClient
|
||||||
|
import org.springframework.test.web.servlet.MockMvc
|
||||||
|
import org.springframework.test.web.servlet.client.MockMvcWebTestClient
|
||||||
|
import org.springframework.test.web.servlet.get
|
||||||
|
import org.springframework.web.context.WebApplicationContext
|
||||||
|
import reactor.core.publisher.Sinks
|
||||||
|
import reactor.test.StepVerifier
|
||||||
|
import java.time.Instant
|
||||||
|
import java.time.ZoneId
|
||||||
|
import java.time.temporal.ChronoUnit
|
||||||
|
|
||||||
|
|
||||||
|
@WebMvcTest(controllers = [StatisticsRestController::class])
|
||||||
|
@ExtendWith(value = [MockitoExtension::class, SpringExtension::class])
|
||||||
|
@ContextConfiguration(
|
||||||
|
classes = [
|
||||||
|
StatisticsRestController::class,
|
||||||
|
AppConfiguration::class,
|
||||||
|
AppSecurityConfiguration::class
|
||||||
|
]
|
||||||
|
)
|
||||||
|
@TestPropertySource(
|
||||||
|
properties = [
|
||||||
|
"app.pseudonymize.generator=BUILDIN",
|
||||||
|
"app.security.admin-user=admin",
|
||||||
|
"app.security.admin-password={noop}very-secret"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
@MockitoBean(
|
||||||
|
types = [RequestService::class]
|
||||||
|
)
|
||||||
|
class StatisticsRestControllerTest {
|
||||||
|
|
||||||
|
private lateinit var mockMvc: MockMvc
|
||||||
|
|
||||||
|
private lateinit var statisticsUpdateProducer: Sinks.Many<Any>
|
||||||
|
private lateinit var requestService: RequestService
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setup(
|
||||||
|
@Autowired mockMvc: MockMvc,
|
||||||
|
@Autowired statisticsUpdateProducer: Sinks.Many<Any>,
|
||||||
|
@Autowired requestService: RequestService
|
||||||
|
) {
|
||||||
|
this.mockMvc = mockMvc
|
||||||
|
this.statisticsUpdateProducer = statisticsUpdateProducer
|
||||||
|
this.requestService = requestService
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
inner class RequestStatesTest {
|
||||||
|
@Test
|
||||||
|
fun testShouldRequestStatesForMtbFiles() {
|
||||||
|
doAnswer { _ ->
|
||||||
|
listOf(
|
||||||
|
CountedState(42, RequestStatus.WARNING),
|
||||||
|
CountedState(1, RequestStatus.UNKNOWN)
|
||||||
|
)
|
||||||
|
}.whenever(requestService).countStates()
|
||||||
|
|
||||||
|
mockMvc.get("/statistics/requeststates").andExpect {
|
||||||
|
status { isOk() }.also {
|
||||||
|
jsonPath("$", hasSize<Int>(2))
|
||||||
|
jsonPath("$[0].name", equalTo(RequestStatus.WARNING.name))
|
||||||
|
jsonPath("$[0].value", equalTo(42))
|
||||||
|
jsonPath("$[1].name", equalTo(RequestStatus.UNKNOWN.name))
|
||||||
|
jsonPath("$[1].value", equalTo(1))
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldRequestStatesForDeletes() {
|
||||||
|
doAnswer { _ ->
|
||||||
|
listOf(
|
||||||
|
CountedState(42, RequestStatus.SUCCESS),
|
||||||
|
CountedState(1, RequestStatus.ERROR)
|
||||||
|
)
|
||||||
|
}.whenever(requestService).countDeleteStates()
|
||||||
|
|
||||||
|
mockMvc.get("/statistics/requeststates?delete=true").andExpect {
|
||||||
|
status { isOk() }.also {
|
||||||
|
jsonPath("$", hasSize<Int>(2))
|
||||||
|
jsonPath("$[0].name", equalTo(RequestStatus.SUCCESS.name))
|
||||||
|
jsonPath("$[0].value", equalTo(42))
|
||||||
|
jsonPath("$[1].name", equalTo(RequestStatus.ERROR.name))
|
||||||
|
jsonPath("$[1].value", equalTo(1))
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
inner class PatientRequestStatesTest {
|
||||||
|
@Test
|
||||||
|
fun testShouldRequestPatientStatesForMtbFiles() {
|
||||||
|
doAnswer { _ ->
|
||||||
|
listOf(
|
||||||
|
CountedState(42, RequestStatus.WARNING),
|
||||||
|
CountedState(1, RequestStatus.UNKNOWN)
|
||||||
|
)
|
||||||
|
}.whenever(requestService).findPatientUniqueStates()
|
||||||
|
|
||||||
|
mockMvc.get("/statistics/requestpatientstates").andExpect {
|
||||||
|
status { isOk() }.also {
|
||||||
|
jsonPath("$", hasSize<Int>(2))
|
||||||
|
jsonPath("$[0].name", equalTo(RequestStatus.WARNING.name))
|
||||||
|
jsonPath("$[0].value", equalTo(42))
|
||||||
|
jsonPath("$[1].name", equalTo(RequestStatus.UNKNOWN.name))
|
||||||
|
jsonPath("$[1].value", equalTo(1))
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldRequestPatientStatesForDeletes() {
|
||||||
|
doAnswer { _ ->
|
||||||
|
listOf(
|
||||||
|
CountedState(42, RequestStatus.SUCCESS),
|
||||||
|
CountedState(1, RequestStatus.ERROR)
|
||||||
|
)
|
||||||
|
}.whenever(requestService).findPatientUniqueDeleteStates()
|
||||||
|
|
||||||
|
mockMvc.get("/statistics/requestpatientstates?delete=true").andExpect {
|
||||||
|
status { isOk() }.also {
|
||||||
|
jsonPath("$", hasSize<Int>(2))
|
||||||
|
jsonPath("$[0].name", equalTo(RequestStatus.SUCCESS.name))
|
||||||
|
jsonPath("$[0].value", equalTo(42))
|
||||||
|
jsonPath("$[1].name", equalTo(RequestStatus.ERROR.name))
|
||||||
|
jsonPath("$[1].value", equalTo(1))
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
inner class LastMonthStatesTest {
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setup() {
|
||||||
|
val zoneId = ZoneId.of("Europe/Berlin")
|
||||||
|
doAnswer { _ ->
|
||||||
|
listOf(
|
||||||
|
Request(
|
||||||
|
1,
|
||||||
|
randomRequestId(),
|
||||||
|
PatientPseudonym("TEST_12345678901"),
|
||||||
|
PatientId("P1"),
|
||||||
|
Fingerprint("0123456789abcdef1"),
|
||||||
|
RequestType.MTB_FILE,
|
||||||
|
RequestStatus.SUCCESS,
|
||||||
|
Instant.now().atZone(zoneId).truncatedTo(ChronoUnit.DAYS).minus(2, ChronoUnit.DAYS).toInstant()
|
||||||
|
),
|
||||||
|
Request(
|
||||||
|
2,
|
||||||
|
randomRequestId(),
|
||||||
|
PatientPseudonym("TEST_12345678902"),
|
||||||
|
PatientId("P2"),
|
||||||
|
Fingerprint("0123456789abcdef2"),
|
||||||
|
RequestType.MTB_FILE,
|
||||||
|
RequestStatus.WARNING,
|
||||||
|
Instant.now().atZone(zoneId).truncatedTo(ChronoUnit.DAYS).minus(2, ChronoUnit.DAYS).toInstant()
|
||||||
|
),
|
||||||
|
Request(
|
||||||
|
3,
|
||||||
|
randomRequestId(),
|
||||||
|
PatientPseudonym("TEST_12345678901"),
|
||||||
|
PatientId("P2"),
|
||||||
|
Fingerprint("0123456789abcdee1"),
|
||||||
|
RequestType.DELETE,
|
||||||
|
RequestStatus.ERROR,
|
||||||
|
Instant.now().atZone(zoneId).truncatedTo(ChronoUnit.DAYS).minus(1, ChronoUnit.DAYS).toInstant()
|
||||||
|
),
|
||||||
|
Request(
|
||||||
|
4,
|
||||||
|
randomRequestId(),
|
||||||
|
PatientPseudonym("TEST_12345678902"),
|
||||||
|
PatientId("P2"),
|
||||||
|
Fingerprint("0123456789abcdef2"),
|
||||||
|
RequestType.MTB_FILE,
|
||||||
|
RequestStatus.DUPLICATION,
|
||||||
|
Instant.now().atZone(zoneId).truncatedTo(ChronoUnit.DAYS).minus(1, ChronoUnit.DAYS).toInstant()
|
||||||
|
),
|
||||||
|
Request(
|
||||||
|
5,
|
||||||
|
randomRequestId(),
|
||||||
|
PatientPseudonym("TEST_12345678902"),
|
||||||
|
PatientId("P2"),
|
||||||
|
Fingerprint("0123456789abcdef2"),
|
||||||
|
RequestType.DELETE,
|
||||||
|
RequestStatus.UNKNOWN,
|
||||||
|
Instant.now().atZone(zoneId).truncatedTo(ChronoUnit.DAYS).toInstant()
|
||||||
|
),
|
||||||
|
)
|
||||||
|
}.whenever(requestService).findAll()
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldRequestLastMonthForMtbFiles() {
|
||||||
|
mockMvc.get("/statistics/requestslastmonth").andExpect {
|
||||||
|
status { isOk() }.also {
|
||||||
|
jsonPath("$", hasSize<Int>(31))
|
||||||
|
}.also {
|
||||||
|
jsonPath("$[28].nameValues.error", equalTo(0))
|
||||||
|
jsonPath("$[28].nameValues.warning", equalTo(1))
|
||||||
|
jsonPath("$[28].nameValues.success", equalTo(1))
|
||||||
|
jsonPath("$[28].nameValues.duplication", equalTo(0))
|
||||||
|
jsonPath("$[28].nameValues.unknown", equalTo(0))
|
||||||
|
jsonPath("$[29].nameValues.error", equalTo(0))
|
||||||
|
jsonPath("$[29].nameValues.warning", equalTo(0))
|
||||||
|
jsonPath("$[29].nameValues.success", equalTo(0))
|
||||||
|
jsonPath("$[29].nameValues.duplication", equalTo(1))
|
||||||
|
jsonPath("$[29].nameValues.unknown", equalTo(0))
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldRequestLastMonthForDeletes() {
|
||||||
|
mockMvc.get("/statistics/requestslastmonth?delete=true").andExpect {
|
||||||
|
status { isOk() }.also {
|
||||||
|
jsonPath("$", hasSize<Int>(31))
|
||||||
|
}.also {
|
||||||
|
jsonPath("$[29].nameValues.error", equalTo(1))
|
||||||
|
jsonPath("$[29].nameValues.warning", equalTo(0))
|
||||||
|
jsonPath("$[29].nameValues.success", equalTo(0))
|
||||||
|
jsonPath("$[29].nameValues.duplication", equalTo(0))
|
||||||
|
jsonPath("$[29].nameValues.unknown", equalTo(0))
|
||||||
|
jsonPath("$[30].nameValues.error", equalTo(0))
|
||||||
|
jsonPath("$[30].nameValues.warning", equalTo(0))
|
||||||
|
jsonPath("$[30].nameValues.success", equalTo(0))
|
||||||
|
jsonPath("$[30].nameValues.duplication", equalTo(0))
|
||||||
|
jsonPath("$[30].nameValues.unknown", equalTo(1))
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Nested
|
||||||
|
inner class SseTest {
|
||||||
|
private lateinit var webClient: WebTestClient
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
fun setup(
|
||||||
|
applicationContext: WebApplicationContext,
|
||||||
|
) {
|
||||||
|
this.webClient = MockMvcWebTestClient
|
||||||
|
.bindToApplicationContext(applicationContext).build()
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
fun testShouldRequestSSE() {
|
||||||
|
statisticsUpdateProducer.emitComplete { _, _ -> true }
|
||||||
|
|
||||||
|
val result = webClient.get().uri("http://localhost/statistics/events").accept(TEXT_EVENT_STREAM).exchange()
|
||||||
|
.expectStatus().isOk()
|
||||||
|
.expectHeader().contentType(TEXT_EVENT_STREAM)
|
||||||
|
.returnResult(String::class.java)
|
||||||
|
|
||||||
|
StepVerifier.create(result.responseBody)
|
||||||
|
.expectComplete()
|
||||||
|
.verify()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
@@ -0,0 +1,13 @@
|
|||||||
|
package dev.dnpm.etl.processor.consent;
|
||||||
|
|
||||||
|
public enum ConsentDomain {
|
||||||
|
/**
|
||||||
|
* MII Broad consent
|
||||||
|
*/
|
||||||
|
BROAD_CONSENT,
|
||||||
|
|
||||||
|
/**
|
||||||
|
* GenomDe Modellvorhaben §64e
|
||||||
|
*/
|
||||||
|
MODELLVORHABEN_64E
|
||||||
|
}
|
@@ -0,0 +1,307 @@
|
|||||||
|
package dev.dnpm.etl.processor.consent;
|
||||||
|
|
||||||
|
import ca.uhn.fhir.context.FhirContext;
|
||||||
|
import ca.uhn.fhir.parser.DataFormatException;
|
||||||
|
import dev.dnpm.etl.processor.config.AppFhirConfig;
|
||||||
|
import dev.dnpm.etl.processor.config.GIcsConfigProperties;
|
||||||
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
import org.hl7.fhir.r4.model.*;
|
||||||
|
import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
|
||||||
|
import org.jetbrains.annotations.NotNull;
|
||||||
|
import org.slf4j.Logger;
|
||||||
|
import org.slf4j.LoggerFactory;
|
||||||
|
import org.springframework.http.HttpEntity;
|
||||||
|
import org.springframework.http.HttpHeaders;
|
||||||
|
import org.springframework.http.HttpMethod;
|
||||||
|
import org.springframework.http.MediaType;
|
||||||
|
import org.springframework.retry.TerminatedRetryException;
|
||||||
|
import org.springframework.retry.support.RetryTemplate;
|
||||||
|
import org.springframework.web.client.RestClientException;
|
||||||
|
import org.springframework.web.client.RestTemplate;
|
||||||
|
import org.springframework.web.util.UriComponentsBuilder;
|
||||||
|
|
||||||
|
import java.net.URI;
|
||||||
|
import java.util.Date;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Service to request Consent from remote gICS installation
|
||||||
|
*
|
||||||
|
* @since 0.11
|
||||||
|
*/
|
||||||
|
public class GicsConsentService implements IConsentService {
|
||||||
|
|
||||||
|
private final Logger log = LoggerFactory.getLogger(GicsConsentService.class);
|
||||||
|
|
||||||
|
public static final String IS_CONSENTED_ENDPOINT = "/$isConsented";
|
||||||
|
public static final String IS_POLICY_STATES_FOR_PERSON_ENDPOINT = "/$currentPolicyStatesForPerson";
|
||||||
|
|
||||||
|
private final RetryTemplate retryTemplate;
|
||||||
|
private final RestTemplate restTemplate;
|
||||||
|
private final FhirContext fhirContext;
|
||||||
|
private final GIcsConfigProperties gIcsConfigProperties;
|
||||||
|
|
||||||
|
public GicsConsentService(
|
||||||
|
GIcsConfigProperties gIcsConfigProperties,
|
||||||
|
RetryTemplate retryTemplate,
|
||||||
|
RestTemplate restTemplate,
|
||||||
|
AppFhirConfig appFhirConfig
|
||||||
|
) {
|
||||||
|
this.retryTemplate = retryTemplate;
|
||||||
|
this.restTemplate = restTemplate;
|
||||||
|
this.fhirContext = appFhirConfig.fhirContext();
|
||||||
|
this.gIcsConfigProperties = gIcsConfigProperties;
|
||||||
|
log.info("GicsConsentService initialized...");
|
||||||
|
}
|
||||||
|
|
||||||
|
protected Parameters getFhirRequestParameters(
|
||||||
|
String personIdentifierValue
|
||||||
|
) {
|
||||||
|
var result = new Parameters();
|
||||||
|
result.addParameter(
|
||||||
|
new ParametersParameterComponent()
|
||||||
|
.setName("personIdentifier")
|
||||||
|
.setValue(
|
||||||
|
new Identifier()
|
||||||
|
.setValue(personIdentifierValue)
|
||||||
|
.setSystem(this.gIcsConfigProperties.getPersonIdentifierSystem())
|
||||||
|
)
|
||||||
|
);
|
||||||
|
result.addParameter(
|
||||||
|
new ParametersParameterComponent()
|
||||||
|
.setName("domain")
|
||||||
|
.setValue(
|
||||||
|
new StringType()
|
||||||
|
.setValue(this.gIcsConfigProperties.getBroadConsentDomainName())
|
||||||
|
)
|
||||||
|
);
|
||||||
|
result.addParameter(
|
||||||
|
new ParametersParameterComponent()
|
||||||
|
.setName("policy")
|
||||||
|
.setValue(
|
||||||
|
new Coding()
|
||||||
|
.setCode(this.gIcsConfigProperties.getBroadConsentPolicyCode())
|
||||||
|
.setSystem(this.gIcsConfigProperties.getBroadConsentPolicySystem())
|
||||||
|
)
|
||||||
|
);
|
||||||
|
|
||||||
|
/*
|
||||||
|
* is mandatory parameter, but we ignore it via additional configuration parameter
|
||||||
|
* 'ignoreVersionNumber'.
|
||||||
|
*/
|
||||||
|
result.addParameter(
|
||||||
|
new ParametersParameterComponent()
|
||||||
|
.setName("version")
|
||||||
|
.setValue(new StringType().setValue("1.1")
|
||||||
|
)
|
||||||
|
);
|
||||||
|
|
||||||
|
/* add config parameter with:
|
||||||
|
* ignoreVersionNumber -> true ->> Reason is we cannot know which policy version each patient
|
||||||
|
* has possibly signed or not, therefore we are happy with any version found.
|
||||||
|
* unknownStateIsConsideredAsDecline -> true
|
||||||
|
*/
|
||||||
|
var config = new ParametersParameterComponent()
|
||||||
|
.setName("config")
|
||||||
|
.addPart(
|
||||||
|
new ParametersParameterComponent()
|
||||||
|
.setName("ignoreVersionNumber")
|
||||||
|
.setValue(new BooleanType().setValue(true))
|
||||||
|
)
|
||||||
|
.addPart(
|
||||||
|
new ParametersParameterComponent()
|
||||||
|
.setName("unknownStateIsConsideredAsDecline")
|
||||||
|
.setValue(new BooleanType().setValue(false))
|
||||||
|
);
|
||||||
|
|
||||||
|
result.addParameter(config);
|
||||||
|
|
||||||
|
return result;
|
||||||
|
}
|
||||||
|
|
||||||
|
private URI endpointUri(String endpoint) {
|
||||||
|
assert this.gIcsConfigProperties.getUri() != null;
|
||||||
|
return UriComponentsBuilder.fromUriString(this.gIcsConfigProperties.getUri()).path(endpoint).build().toUri();
|
||||||
|
}
|
||||||
|
|
||||||
|
private HttpHeaders headersWithHttpBasicAuth() {
|
||||||
|
assert this.gIcsConfigProperties.getUri() != null;
|
||||||
|
|
||||||
|
var headers = new HttpHeaders();
|
||||||
|
headers.setContentType(MediaType.APPLICATION_XML);
|
||||||
|
|
||||||
|
if (
|
||||||
|
StringUtils.isBlank(this.gIcsConfigProperties.getUsername())
|
||||||
|
|| StringUtils.isBlank(this.gIcsConfigProperties.getPassword())
|
||||||
|
) {
|
||||||
|
return headers;
|
||||||
|
}
|
||||||
|
|
||||||
|
headers.setBasicAuth(this.gIcsConfigProperties.getUsername(), this.gIcsConfigProperties.getPassword());
|
||||||
|
return headers;
|
||||||
|
}
|
||||||
|
|
||||||
|
protected String callGicsApi(Parameters parameter, String endpoint) {
|
||||||
|
var parameterAsXml = fhirContext.newXmlParser().encodeResourceToString(parameter);
|
||||||
|
HttpEntity<String> requestEntity = new HttpEntity<>(parameterAsXml, this.headersWithHttpBasicAuth());
|
||||||
|
try {
|
||||||
|
var responseEntity = retryTemplate.execute(
|
||||||
|
ctx -> restTemplate.exchange(endpointUri(endpoint), HttpMethod.POST, requestEntity, String.class)
|
||||||
|
);
|
||||||
|
|
||||||
|
if (responseEntity.getStatusCode().is2xxSuccessful()) {
|
||||||
|
return responseEntity.getBody();
|
||||||
|
} else {
|
||||||
|
var msg = String.format(
|
||||||
|
"Trusted party system reached but request failed! code: '%s' response: '%s'",
|
||||||
|
responseEntity.getStatusCode(), responseEntity.getBody());
|
||||||
|
log.error(msg);
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
} catch (RestClientException e) {
|
||||||
|
var msg = String.format("Get consents status request failed reason: '%s",
|
||||||
|
e.getMessage());
|
||||||
|
log.error(msg);
|
||||||
|
return null;
|
||||||
|
|
||||||
|
} catch (TerminatedRetryException terminatedRetryException) {
|
||||||
|
var msg = String.format(
|
||||||
|
"Get consents status process has been terminated. termination reason: '%s",
|
||||||
|
terminatedRetryException.getMessage());
|
||||||
|
log.error(msg);
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public TtpConsentStatus getTtpBroadConsentStatus(String personIdentifierValue) {
|
||||||
|
var consentStatusResponse = callGicsApi(
|
||||||
|
getFhirRequestParameters(personIdentifierValue),
|
||||||
|
GicsConsentService.IS_CONSENTED_ENDPOINT
|
||||||
|
);
|
||||||
|
return evaluateConsentResponse(consentStatusResponse);
|
||||||
|
}
|
||||||
|
|
||||||
|
protected Bundle currentConsentForPersonAndTemplate(
|
||||||
|
String personIdentifierValue,
|
||||||
|
ConsentDomain consentDomain,
|
||||||
|
Date requestDate
|
||||||
|
) {
|
||||||
|
|
||||||
|
var requestParameter = buildRequestParameterCurrentPolicyStatesForPerson(
|
||||||
|
personIdentifierValue,
|
||||||
|
requestDate,
|
||||||
|
consentDomain
|
||||||
|
);
|
||||||
|
|
||||||
|
var consentDataSerialized = callGicsApi(requestParameter,
|
||||||
|
GicsConsentService.IS_POLICY_STATES_FOR_PERSON_ENDPOINT);
|
||||||
|
|
||||||
|
if (consentDataSerialized == null) {
|
||||||
|
// error occurred - should not process further!
|
||||||
|
throw new IllegalStateException(
|
||||||
|
"consent data request failed - stopping processing! - try again or fix other problems first.");
|
||||||
|
}
|
||||||
|
var iBaseResource = fhirContext.newJsonParser()
|
||||||
|
.parseResource(consentDataSerialized);
|
||||||
|
if (iBaseResource instanceof OperationOutcome) {
|
||||||
|
// log error - very likely a configuration error
|
||||||
|
String errorMessage =
|
||||||
|
"Consent request failed! Check outcome:\n " + consentDataSerialized;
|
||||||
|
log.error(errorMessage);
|
||||||
|
throw new IllegalStateException(errorMessage);
|
||||||
|
} else if (iBaseResource instanceof Bundle bundle) {
|
||||||
|
return bundle;
|
||||||
|
} else {
|
||||||
|
String errorMessage = "Consent request failed! Unexpected response received! -> "
|
||||||
|
+ consentDataSerialized;
|
||||||
|
log.error(errorMessage);
|
||||||
|
throw new IllegalStateException(errorMessage);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@NotNull
|
||||||
|
private String getConsentDomainName(ConsentDomain targetConsentDomain) {
|
||||||
|
return switch (targetConsentDomain) {
|
||||||
|
case BROAD_CONSENT -> gIcsConfigProperties.getBroadConsentDomainName();
|
||||||
|
case MODELLVORHABEN_64E -> gIcsConfigProperties.getGenomDeConsentDomainName();
|
||||||
|
};
|
||||||
|
}
|
||||||
|
|
||||||
|
protected Parameters buildRequestParameterCurrentPolicyStatesForPerson(
|
||||||
|
String personIdentifierValue,
|
||||||
|
Date requestDate,
|
||||||
|
ConsentDomain consentDomain
|
||||||
|
) {
|
||||||
|
var requestParameter = new Parameters();
|
||||||
|
requestParameter.addParameter(
|
||||||
|
new ParametersParameterComponent()
|
||||||
|
.setName("personIdentifier")
|
||||||
|
.setValue(
|
||||||
|
new Identifier()
|
||||||
|
.setValue(personIdentifierValue)
|
||||||
|
.setSystem(this.gIcsConfigProperties.getPersonIdentifierSystem())
|
||||||
|
)
|
||||||
|
);
|
||||||
|
|
||||||
|
requestParameter.addParameter(
|
||||||
|
new ParametersParameterComponent()
|
||||||
|
.setName("domain")
|
||||||
|
.setValue(new StringType().setValue(getConsentDomainName(consentDomain)))
|
||||||
|
);
|
||||||
|
|
||||||
|
Parameters nestedConfigParameters = new Parameters();
|
||||||
|
nestedConfigParameters
|
||||||
|
.addParameter(
|
||||||
|
new ParametersParameterComponent()
|
||||||
|
.setName("idMatchingType")
|
||||||
|
.setValue(new Coding()
|
||||||
|
.setSystem("https://ths-greifswald.de/fhir/CodeSystem/gics/IdMatchingType")
|
||||||
|
.setCode("AT_LEAST_ONE")
|
||||||
|
)
|
||||||
|
)
|
||||||
|
.addParameter("ignoreVersionNumber", false)
|
||||||
|
.addParameter("unknownStateIsConsideredAsDecline", false)
|
||||||
|
.addParameter("requestDate", new DateType().setValue(requestDate));
|
||||||
|
|
||||||
|
requestParameter.addParameter(
|
||||||
|
new ParametersParameterComponent().setName("config").addPart().setResource(nestedConfigParameters)
|
||||||
|
);
|
||||||
|
|
||||||
|
return requestParameter;
|
||||||
|
}
|
||||||
|
|
||||||
|
private TtpConsentStatus evaluateConsentResponse(String consentStatusResponse) {
|
||||||
|
if (consentStatusResponse == null) {
|
||||||
|
return TtpConsentStatus.FAILED_TO_ASK;
|
||||||
|
}
|
||||||
|
try {
|
||||||
|
var response = fhirContext.newJsonParser().parseResource(consentStatusResponse);
|
||||||
|
|
||||||
|
if (response instanceof Parameters responseParameters) {
|
||||||
|
|
||||||
|
var responseValue = responseParameters.getParameter("consented").getValue();
|
||||||
|
var isConsented = responseValue.castToBoolean(responseValue);
|
||||||
|
if (!isConsented.hasValue()) {
|
||||||
|
return TtpConsentStatus.FAILED_TO_ASK;
|
||||||
|
}
|
||||||
|
if (isConsented.booleanValue()) {
|
||||||
|
return TtpConsentStatus.BROAD_CONSENT_GIVEN;
|
||||||
|
} else {
|
||||||
|
return TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED;
|
||||||
|
}
|
||||||
|
} else if (response instanceof OperationOutcome outcome) {
|
||||||
|
log.error("failed to get consent status from ttp. probably configuration error. "
|
||||||
|
+ "outcome: '{}'", fhirContext.newJsonParser().encodeToString(outcome));
|
||||||
|
|
||||||
|
}
|
||||||
|
} catch (DataFormatException dfe) {
|
||||||
|
log.error("failed to parse response to FHIR R4 resource.", dfe);
|
||||||
|
}
|
||||||
|
return TtpConsentStatus.FAILED_TO_ASK;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public Bundle getConsent(String patientId, Date requestDate, ConsentDomain consentDomain) {
|
||||||
|
return currentConsentForPersonAndTemplate(patientId, consentDomain, requestDate);
|
||||||
|
}
|
||||||
|
}
|
@@ -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);
|
||||||
|
|
||||||
|
}
|
@@ -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();
|
||||||
|
}
|
||||||
|
}
|
@@ -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
|
||||||
|
}
|
@@ -23,4 +23,6 @@ public interface Generator {
|
|||||||
|
|
||||||
String generate(String id);
|
String generate(String id);
|
||||||
|
|
||||||
|
String generateGenomDeTan(String id);
|
||||||
|
|
||||||
}
|
}
|
||||||
|
@@ -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) 2024 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
|
||||||
@@ -21,100 +21,92 @@ 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 java.io.BufferedInputStream;
|
import org.apache.commons.lang3.NotImplementedException;
|
||||||
import java.io.FileInputStream;
|
|
||||||
import java.io.IOException;
|
|
||||||
import java.net.ConnectException;
|
|
||||||
import java.security.KeyManagementException;
|
|
||||||
import java.security.KeyStore;
|
|
||||||
import java.security.KeyStoreException;
|
|
||||||
import java.security.NoSuchAlgorithmException;
|
|
||||||
import java.security.cert.CertificateException;
|
|
||||||
import java.security.cert.CertificateFactory;
|
|
||||||
import java.security.cert.X509Certificate;
|
|
||||||
import java.util.Base64;
|
|
||||||
import java.util.HashMap;
|
|
||||||
import javax.net.ssl.SSLContext;
|
|
||||||
import javax.net.ssl.TrustManagerFactory;
|
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
import org.apache.hc.client5.http.impl.classic.CloseableHttpClient;
|
import org.apache.hc.core5.net.URIBuilder;
|
||||||
import org.apache.hc.client5.http.impl.classic.HttpClients;
|
|
||||||
import org.apache.hc.client5.http.impl.io.BasicHttpClientConnectionManager;
|
|
||||||
import org.apache.hc.client5.http.socket.ConnectionSocketFactory;
|
|
||||||
import org.apache.hc.client5.http.socket.PlainConnectionSocketFactory;
|
|
||||||
import org.apache.hc.client5.http.ssl.SSLConnectionSocketFactory;
|
|
||||||
import org.apache.hc.core5.http.config.Registry;
|
|
||||||
import org.apache.hc.core5.http.config.RegistryBuilder;
|
|
||||||
import org.hl7.fhir.r4.model.Identifier;
|
import org.hl7.fhir.r4.model.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;
|
||||||
import org.hl7.fhir.r4.model.StringType;
|
import org.hl7.fhir.r4.model.StringType;
|
||||||
import org.jetbrains.annotations.NotNull;
|
import org.jetbrains.annotations.NotNull;
|
||||||
import org.jetbrains.annotations.Nullable;
|
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
import org.slf4j.LoggerFactory;
|
import org.slf4j.LoggerFactory;
|
||||||
import org.springframework.http.HttpEntity;
|
import org.springframework.http.*;
|
||||||
import org.springframework.http.HttpHeaders;
|
|
||||||
import org.springframework.http.HttpMethod;
|
|
||||||
import org.springframework.http.MediaType;
|
|
||||||
import org.springframework.http.ResponseEntity;
|
|
||||||
import org.springframework.http.client.HttpComponentsClientHttpRequestFactory;
|
|
||||||
import org.springframework.retry.RetryCallback;
|
|
||||||
import org.springframework.retry.RetryContext;
|
|
||||||
import org.springframework.retry.RetryListener;
|
|
||||||
import org.springframework.retry.RetryPolicy;
|
|
||||||
import org.springframework.retry.backoff.ExponentialBackOffPolicy;
|
|
||||||
import org.springframework.retry.policy.SimpleRetryPolicy;
|
|
||||||
import org.springframework.retry.support.RetryTemplate;
|
import org.springframework.retry.support.RetryTemplate;
|
||||||
import org.springframework.web.client.RestClientException;
|
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 = defaultTemplate();
|
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 @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";
|
||||||
|
|
||||||
private SSLContext customSslContext;
|
public GpasPseudonymGenerator(GPasConfigProperties gpasCfg, RetryTemplate retryTemplate,
|
||||||
private RestTemplate restTemplate;
|
RestTemplate restTemplate, AppFhirConfig appFhirConfig) {
|
||||||
|
this.retryTemplate = retryTemplate;
|
||||||
public GpasPseudonymGenerator(GPasConfigProperties gpasCfg) {
|
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());
|
||||||
|
|
||||||
try {
|
log.debug("{} has been initialized", this.getClass().getName());
|
||||||
if (StringUtils.isNotBlank(gpasCfg.getSslCaLocation())) {
|
|
||||||
customSslContext = getSslContext(gpasCfg.getSslCaLocation());
|
|
||||||
log.debug(String.format("%s has been initialized with SSL certificate %s",
|
|
||||||
this.getClass().getName(), gpasCfg.getSslCaLocation()));
|
|
||||||
}
|
|
||||||
} catch (IOException | KeyManagementException | KeyStoreException | CertificateException |
|
|
||||||
NoSuchAlgorithmException e) {
|
|
||||||
throw new RuntimeException(e);
|
|
||||||
}
|
|
||||||
|
|
||||||
log.debug(String.format("%s has been initialized", this.getClass().getName()));
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
@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()) {
|
||||||
@@ -122,7 +114,7 @@ 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();
|
||||||
|
|
||||||
@@ -144,43 +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;
|
|
||||||
var restTemplate = getRestTemplete();
|
|
||||||
|
|
||||||
try {
|
try {
|
||||||
responseEntity = retryTemplate.execute(
|
var targetUrl = buildRequestUrl(apiEndpoint);
|
||||||
ctx -> restTemplate.exchange(gPasUrl, HttpMethod.POST, requestEntity,
|
ResponseEntity<String> responseEntity = retryTemplate.execute(
|
||||||
|
ctx -> restTemplate.exchange(targetUrl, HttpMethod.POST, requestEntity,
|
||||||
String.class));
|
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();
|
||||||
@@ -190,99 +218,7 @@ public class GpasPseudonymGenerator implements Generator {
|
|||||||
return headers;
|
return headers;
|
||||||
}
|
}
|
||||||
|
|
||||||
String authHeader = gPasUserName + ":" + gPasPassword;
|
headers.setBasicAuth(gPasUserName, gPasPassword);
|
||||||
byte[] authHeaderBytes = authHeader.getBytes();
|
|
||||||
byte[] encodedAuthHeaderBytes = Base64.getEncoder().encode(authHeaderBytes);
|
|
||||||
String encodedAuthHeader = new String(encodedAuthHeaderBytes);
|
|
||||||
|
|
||||||
if (StringUtils.isNotBlank(gPasUserName) && StringUtils.isNotBlank(gPasPassword)) {
|
|
||||||
headers.set("Authorization", "Basic " + encodedAuthHeader);
|
|
||||||
}
|
|
||||||
|
|
||||||
return headers;
|
return headers;
|
||||||
}
|
}
|
||||||
|
|
||||||
protected RetryTemplate defaultTemplate() {
|
|
||||||
RetryTemplate retryTemplate = new RetryTemplate();
|
|
||||||
ExponentialBackOffPolicy backOffPolicy = new ExponentialBackOffPolicy();
|
|
||||||
backOffPolicy.setInitialInterval(1000);
|
|
||||||
backOffPolicy.setMultiplier(1.25);
|
|
||||||
retryTemplate.setBackOffPolicy(backOffPolicy);
|
|
||||||
HashMap<Class<? extends Throwable>, Boolean> retryableExceptions = new HashMap<>();
|
|
||||||
retryableExceptions.put(RestClientException.class, true);
|
|
||||||
retryableExceptions.put(ConnectException.class, true);
|
|
||||||
RetryPolicy retryPolicy = new SimpleRetryPolicy(3, retryableExceptions);
|
|
||||||
retryTemplate.setRetryPolicy(retryPolicy);
|
|
||||||
|
|
||||||
retryTemplate.registerListener(new RetryListener() {
|
|
||||||
@Override
|
|
||||||
public <T, E extends Throwable> void onError(RetryContext context,
|
|
||||||
RetryCallback<T, E> callback, Throwable throwable) {
|
|
||||||
log.warn("HTTP Error occurred: {}. Retrying {}", throwable.getMessage(),
|
|
||||||
context.getRetryCount());
|
|
||||||
RetryListener.super.onError(context, callback, throwable);
|
|
||||||
}
|
|
||||||
});
|
|
||||||
|
|
||||||
return retryTemplate;
|
|
||||||
}
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Read SSL root certificate and return SSLContext
|
|
||||||
*
|
|
||||||
* @param certificateLocation file location to root certificate (PEM)
|
|
||||||
* @return initialized SSLContext
|
|
||||||
* @throws IOException file cannot be read
|
|
||||||
* @throws CertificateException in case we have an invalid certificate of type X.509
|
|
||||||
* @throws KeyStoreException keystore cannot be initialized
|
|
||||||
* @throws NoSuchAlgorithmException missing trust manager algorithmus
|
|
||||||
* @throws KeyManagementException key management failed at init SSLContext
|
|
||||||
*/
|
|
||||||
@Nullable
|
|
||||||
protected SSLContext getSslContext(String certificateLocation)
|
|
||||||
throws IOException, CertificateException, KeyStoreException, KeyManagementException, NoSuchAlgorithmException {
|
|
||||||
|
|
||||||
KeyStore ks = KeyStore.getInstance(KeyStore.getDefaultType());
|
|
||||||
|
|
||||||
FileInputStream fis = new FileInputStream(certificateLocation);
|
|
||||||
X509Certificate ca = (X509Certificate) CertificateFactory.getInstance("X.509")
|
|
||||||
.generateCertificate(new BufferedInputStream(fis));
|
|
||||||
|
|
||||||
ks.load(null, null);
|
|
||||||
ks.setCertificateEntry(Integer.toString(1), ca);
|
|
||||||
|
|
||||||
TrustManagerFactory tmf = TrustManagerFactory.getInstance(
|
|
||||||
TrustManagerFactory.getDefaultAlgorithm());
|
|
||||||
tmf.init(ks);
|
|
||||||
|
|
||||||
SSLContext sslContext = SSLContext.getInstance("TLS");
|
|
||||||
sslContext.init(null, tmf.getTrustManagers(), null);
|
|
||||||
|
|
||||||
return sslContext;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected RestTemplate getRestTemplete() {
|
|
||||||
|
|
||||||
if (restTemplate != null) {
|
|
||||||
return restTemplate;
|
|
||||||
}
|
|
||||||
|
|
||||||
if (customSslContext == null) {
|
|
||||||
restTemplate = new RestTemplate();
|
|
||||||
return restTemplate;
|
|
||||||
}
|
|
||||||
final var sslsf = new SSLConnectionSocketFactory(customSslContext);
|
|
||||||
final Registry<ConnectionSocketFactory> socketFactoryRegistry = RegistryBuilder.<ConnectionSocketFactory>create()
|
|
||||||
.register("https", sslsf).register("http", new PlainConnectionSocketFactory()).build();
|
|
||||||
|
|
||||||
final BasicHttpClientConnectionManager connectionManager = new BasicHttpClientConnectionManager(
|
|
||||||
socketFactoryRegistry);
|
|
||||||
final CloseableHttpClient httpClient = HttpClients.custom()
|
|
||||||
.setConnectionManager(connectionManager).build();
|
|
||||||
|
|
||||||
final HttpComponentsClientHttpRequestFactory requestFactory = new HttpComponentsClientHttpRequestFactory(
|
|
||||||
httpClient);
|
|
||||||
restTemplate = new RestTemplate(requestFactory);
|
|
||||||
return restTemplate;
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
@@ -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
|
||||||
|
}
|
@@ -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
|
||||||
@@ -19,13 +19,15 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.config
|
package dev.dnpm.etl.processor.config
|
||||||
|
|
||||||
|
import dev.dnpm.etl.processor.security.Role
|
||||||
import org.springframework.boot.context.properties.ConfigurationProperties
|
import org.springframework.boot.context.properties.ConfigurationProperties
|
||||||
|
|
||||||
@ConfigurationProperties(AppConfigProperties.NAME)
|
@ConfigurationProperties(AppConfigProperties.NAME)
|
||||||
data class AppConfigProperties(
|
data class AppConfigProperties(
|
||||||
var bwhcUri: String?,
|
var transformations: List<TransformationProperties> = listOf(),
|
||||||
var generator: PseudonymGenerator = PseudonymGenerator.BUILDIN,
|
var maxRetryAttempts: Int = 3,
|
||||||
var transformations: List<TransformationProperties> = listOf()
|
var duplicationDetection: Boolean = true,
|
||||||
|
var genomDeTestSubmission: Boolean = false
|
||||||
) {
|
) {
|
||||||
companion object {
|
companion object {
|
||||||
const val NAME = "app"
|
const val NAME = "app"
|
||||||
@@ -34,6 +36,7 @@ data class AppConfigProperties(
|
|||||||
|
|
||||||
@ConfigurationProperties(PseudonymizeConfigProperties.NAME)
|
@ConfigurationProperties(PseudonymizeConfigProperties.NAME)
|
||||||
data class PseudonymizeConfigProperties(
|
data class PseudonymizeConfigProperties(
|
||||||
|
var generator: PseudonymGenerator = PseudonymGenerator.BUILDIN,
|
||||||
val prefix: String = "UNKNOWN",
|
val prefix: String = "UNKNOWN",
|
||||||
) {
|
) {
|
||||||
companion object {
|
companion object {
|
||||||
@@ -44,31 +47,99 @@ 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?,
|
||||||
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 password: String?
|
||||||
) {
|
) {
|
||||||
companion object {
|
companion object {
|
||||||
const val NAME = "app.rest"
|
const val NAME = "app.rest"
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@ConfigurationProperties(KafkaTargetProperties.NAME)
|
@ConfigurationProperties(KafkaProperties.NAME)
|
||||||
data class KafkaTargetProperties(
|
data class KafkaProperties(
|
||||||
val topic: String = "etl-processor",
|
val inputTopic: String?,
|
||||||
val responseTopic: String = "${topic}_response",
|
val outputTopic: String = "etl-processor",
|
||||||
val groupId: String = "${topic}_group",
|
val outputResponseTopic: String = "${outputTopic}_response",
|
||||||
|
val groupId: String = "${outputTopic}_group",
|
||||||
val servers: String = ""
|
val servers: String = ""
|
||||||
) {
|
) {
|
||||||
companion object {
|
companion object {
|
||||||
@@ -80,6 +151,9 @@ data class KafkaTargetProperties(
|
|||||||
data class SecurityConfigProperties(
|
data class SecurityConfigProperties(
|
||||||
val adminUser: String?,
|
val adminUser: String?,
|
||||||
val adminPassword: String?,
|
val adminPassword: String?,
|
||||||
|
val enableTokens: Boolean = false,
|
||||||
|
val enableOidc: Boolean = false,
|
||||||
|
val defaultNewUserRole: Role = Role.USER
|
||||||
) {
|
) {
|
||||||
companion object {
|
companion object {
|
||||||
const val NAME = "app.security"
|
const val NAME = "app.security"
|
||||||
@@ -91,6 +165,11 @@ 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,
|
||||||
|
@@ -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
|
||||||
@@ -20,22 +20,40 @@
|
|||||||
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.ReportService
|
import dev.dnpm.etl.processor.consent.MtbFileConsentService
|
||||||
|
import dev.dnpm.etl.processor.consent.GicsConsentService
|
||||||
|
import dev.dnpm.etl.processor.consent.IConsentService
|
||||||
|
import dev.dnpm.etl.processor.monitoring.*
|
||||||
import dev.dnpm.etl.processor.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.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.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.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.retry.RetryCallback
|
||||||
|
import org.springframework.retry.RetryContext
|
||||||
|
import org.springframework.retry.RetryListener
|
||||||
import org.springframework.retry.policy.SimpleRetryPolicy
|
import org.springframework.retry.policy.SimpleRetryPolicy
|
||||||
import org.springframework.retry.support.RetryTemplate
|
import org.springframework.retry.support.RetryTemplate
|
||||||
import org.springframework.retry.support.RetryTemplateBuilder
|
import org.springframework.retry.support.RetryTemplateBuilder
|
||||||
import org.springframework.scheduling.annotation.EnableScheduling
|
import org.springframework.scheduling.annotation.EnableScheduling
|
||||||
|
import org.springframework.security.crypto.password.PasswordEncoder
|
||||||
|
import org.springframework.security.provisioning.InMemoryUserDetailsManager
|
||||||
|
import org.springframework.web.client.HttpClientErrorException
|
||||||
|
import org.springframework.web.client.RestTemplate
|
||||||
import reactor.core.publisher.Sinks
|
import reactor.core.publisher.Sinks
|
||||||
import kotlin.time.Duration.Companion.seconds
|
import kotlin.time.Duration.Companion.seconds
|
||||||
import kotlin.time.toJavaDuration
|
import kotlin.time.toJavaDuration
|
||||||
@@ -46,7 +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
|
||||||
@@ -54,15 +74,36 @@ class AppConfiguration {
|
|||||||
|
|
||||||
private val logger = LoggerFactory.getLogger(AppConfiguration::class.java)
|
private val logger = LoggerFactory.getLogger(AppConfiguration::class.java)
|
||||||
|
|
||||||
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS")
|
|
||||||
@Bean
|
@Bean
|
||||||
fun gpasPseudonymGenerator(configProperties: GPasConfigProperties): Generator {
|
fun restTemplate(): RestTemplate {
|
||||||
return GpasPseudonymGenerator(configProperties)
|
return RestTemplate()
|
||||||
}
|
}
|
||||||
|
|
||||||
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "BUILDIN", matchIfMissing = true)
|
@Bean
|
||||||
|
fun appFhirConfig(): AppFhirConfig {
|
||||||
|
return AppFhirConfig()
|
||||||
|
}
|
||||||
|
|
||||||
|
@ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "GPAS")
|
||||||
|
@Bean
|
||||||
|
fun gpasPseudonymGenerator(
|
||||||
|
configProperties: GPasConfigProperties,
|
||||||
|
retryTemplate: RetryTemplate,
|
||||||
|
restTemplate: RestTemplate,
|
||||||
|
appFhirConfig: AppFhirConfig
|
||||||
|
): Generator {
|
||||||
|
logger.info("Selected 'GpasPseudonym Generator'")
|
||||||
|
return GpasPseudonymGenerator(configProperties, retryTemplate, restTemplate, appFhirConfig)
|
||||||
|
}
|
||||||
|
|
||||||
|
@ConditionalOnProperty(
|
||||||
|
value = ["app.pseudonymize.generator"],
|
||||||
|
havingValue = "BUILDIN",
|
||||||
|
matchIfMissing = true
|
||||||
|
)
|
||||||
@Bean
|
@Bean
|
||||||
fun buildinPseudonymGenerator(): Generator {
|
fun buildinPseudonymGenerator(): Generator {
|
||||||
|
logger.info("Selected 'BUILDIN Pseudonym Generator'")
|
||||||
return AnonymizingGenerator()
|
return AnonymizingGenerator()
|
||||||
}
|
}
|
||||||
|
|
||||||
@@ -75,8 +116,57 @@ 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
|
||||||
|
fun transformationService(
|
||||||
|
configProperties: AppConfigProperties
|
||||||
|
): TransformationService {
|
||||||
|
logger.info("Apply ${configProperties.transformations.size} transformation rules")
|
||||||
|
return TransformationService(getObjectMapper(), configProperties.transformations.map {
|
||||||
|
Transformation.of(it.path) from it.from to it.to
|
||||||
|
})
|
||||||
|
}
|
||||||
|
|
||||||
|
@Bean
|
||||||
|
fun retryTemplate(configProperties: AppConfigProperties): RetryTemplate {
|
||||||
|
return RetryTemplateBuilder()
|
||||||
|
.notRetryOn(IllegalArgumentException::class.java)
|
||||||
|
.notRetryOn(HttpClientErrorException.BadRequest::class.java)
|
||||||
|
.notRetryOn(HttpClientErrorException.UnprocessableEntity::class.java)
|
||||||
|
.exponentialBackoff(2.seconds.toJavaDuration(), 1.25, 5.seconds.toJavaDuration())
|
||||||
|
.customPolicy(SimpleRetryPolicy(configProperties.maxRetryAttempts))
|
||||||
|
.withListener(object : RetryListener {
|
||||||
|
override fun <T : Any, E : Throwable> onError(
|
||||||
|
context: RetryContext,
|
||||||
|
callback: RetryCallback<T, E>,
|
||||||
|
throwable: Throwable
|
||||||
|
) {
|
||||||
|
logger.warn(
|
||||||
|
"Error occured: {}. Retrying {}",
|
||||||
|
throwable.message,
|
||||||
|
context.retryCount
|
||||||
|
)
|
||||||
|
}
|
||||||
|
})
|
||||||
|
.build()
|
||||||
|
}
|
||||||
|
|
||||||
|
@ConditionalOnProperty(value = ["app.security.enable-tokens"], havingValue = "true")
|
||||||
|
@Bean
|
||||||
|
fun tokenService(
|
||||||
|
userDetailsManager: InMemoryUserDetailsManager,
|
||||||
|
passwordEncoder: PasswordEncoder,
|
||||||
|
tokenRepository: TokenRepository
|
||||||
|
): TokenService {
|
||||||
|
return TokenService(userDetailsManager, passwordEncoder, tokenRepository)
|
||||||
}
|
}
|
||||||
|
|
||||||
@Bean
|
@Bean
|
||||||
@@ -85,24 +175,107 @@ class AppConfiguration {
|
|||||||
}
|
}
|
||||||
|
|
||||||
@Bean
|
@Bean
|
||||||
fun transformationService(
|
fun connectionCheckUpdateProducer(): Sinks.Many<ConnectionCheckResult> {
|
||||||
objectMapper: ObjectMapper,
|
return Sinks.many().multicast().onBackpressureBuffer()
|
||||||
configProperties: AppConfigProperties
|
}
|
||||||
): TransformationService {
|
|
||||||
logger.info("Apply ${configProperties.transformations.size} transformation rules")
|
@ConditionalOnProperty(value = ["app.pseudonymize.generator"], havingValue = "GPAS")
|
||||||
return TransformationService(objectMapper, configProperties.transformations.map {
|
@Bean
|
||||||
Transformation.of(it.path) from it.from to it.to
|
fun gPasConnectionCheckService(
|
||||||
})
|
restTemplate: RestTemplate,
|
||||||
|
gPasConfigProperties: GPasConfigProperties,
|
||||||
|
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||||
|
): ConnectionCheckService {
|
||||||
|
return GPasConnectionCheckService(
|
||||||
|
restTemplate,
|
||||||
|
gPasConfigProperties,
|
||||||
|
connectionCheckUpdateProducer
|
||||||
|
)
|
||||||
|
}
|
||||||
|
|
||||||
|
@ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS")
|
||||||
|
@ConditionalOnMissingBean
|
||||||
|
@Bean
|
||||||
|
fun gPasConnectionCheckServiceOnDeprecatedProperty(
|
||||||
|
restTemplate: RestTemplate,
|
||||||
|
gPasConfigProperties: GPasConfigProperties,
|
||||||
|
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||||
|
): ConnectionCheckService {
|
||||||
|
return GPasConnectionCheckService(
|
||||||
|
restTemplate,
|
||||||
|
gPasConfigProperties,
|
||||||
|
connectionCheckUpdateProducer
|
||||||
|
)
|
||||||
}
|
}
|
||||||
|
|
||||||
@Bean
|
@Bean
|
||||||
fun retryTemplate(): RetryTemplate {
|
fun jdbcConfiguration(): AbstractJdbcConfiguration {
|
||||||
return RetryTemplateBuilder()
|
return AppJdbcConfiguration()
|
||||||
.notRetryOn(IllegalArgumentException::class.java)
|
}
|
||||||
.fixedBackoff(5.seconds.toJavaDuration())
|
|
||||||
.customPolicy(SimpleRetryPolicy(3))
|
@Conditional(GicsEnabledCondition::class)
|
||||||
.build()
|
@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
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
@@ -0,0 +1,16 @@
|
|||||||
|
package dev.dnpm.etl.processor.config
|
||||||
|
|
||||||
|
import ca.uhn.fhir.context.FhirContext
|
||||||
|
import org.springframework.context.annotation.Bean
|
||||||
|
import org.springframework.context.annotation.Configuration
|
||||||
|
|
||||||
|
|
||||||
|
@Configuration
|
||||||
|
class AppFhirConfig {
|
||||||
|
private val fhirCtx: FhirContext = FhirContext.forR4()
|
||||||
|
|
||||||
|
@Bean
|
||||||
|
fun fhirContext(): FhirContext {
|
||||||
|
return fhirCtx
|
||||||
|
}
|
||||||
|
}
|
@@ -0,0 +1,25 @@
|
|||||||
|
package dev.dnpm.etl.processor.config
|
||||||
|
|
||||||
|
import dev.dnpm.etl.processor.Fingerprint
|
||||||
|
import org.springframework.context.annotation.Configuration
|
||||||
|
import org.springframework.core.convert.converter.Converter
|
||||||
|
import org.springframework.data.jdbc.repository.config.AbstractJdbcConfiguration
|
||||||
|
|
||||||
|
@Configuration
|
||||||
|
class AppJdbcConfiguration : AbstractJdbcConfiguration() {
|
||||||
|
override fun userConverters(): MutableList<*> {
|
||||||
|
return mutableListOf(StringToFingerprintConverter(), FingerprintToStringConverter())
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
class StringToFingerprintConverter : Converter<String, Fingerprint> {
|
||||||
|
override fun convert(source: String): Fingerprint {
|
||||||
|
return Fingerprint(source)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
class FingerprintToStringConverter : Converter<Fingerprint, String> {
|
||||||
|
override fun convert(source: Fingerprint): String {
|
||||||
|
return source.value
|
||||||
|
}
|
||||||
|
}
|
@@ -1,7 +1,7 @@
|
|||||||
/*
|
/*
|
||||||
* This file is part of ETL-Processor
|
* 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 +20,14 @@
|
|||||||
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.monitoring.ConnectionCheckResult
|
||||||
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
|
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
|
||||||
import dev.dnpm.etl.processor.monitoring.KafkaConnectionCheckService
|
import dev.dnpm.etl.processor.monitoring.KafkaConnectionCheckService
|
||||||
import dev.dnpm.etl.processor.output.KafkaMtbFileSender
|
import dev.dnpm.etl.processor.output.KafkaMtbFileSender
|
||||||
import dev.dnpm.etl.processor.output.MtbFileSender
|
import dev.dnpm.etl.processor.output.MtbFileSender
|
||||||
|
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||||
import dev.dnpm.etl.processor.services.kafka.KafkaResponseProcessor
|
import dev.dnpm.etl.processor.services.kafka.KafkaResponseProcessor
|
||||||
import org.slf4j.LoggerFactory
|
import org.slf4j.LoggerFactory
|
||||||
import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean
|
import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean
|
||||||
@@ -38,12 +42,13 @@ import org.springframework.kafka.core.KafkaTemplate
|
|||||||
import org.springframework.kafka.listener.ContainerProperties
|
import org.springframework.kafka.listener.ContainerProperties
|
||||||
import org.springframework.kafka.listener.KafkaMessageListenerContainer
|
import org.springframework.kafka.listener.KafkaMessageListenerContainer
|
||||||
import org.springframework.retry.support.RetryTemplate
|
import org.springframework.retry.support.RetryTemplate
|
||||||
|
import reactor.core.publisher.Sinks
|
||||||
|
|
||||||
@Configuration
|
@Configuration
|
||||||
@EnableConfigurationProperties(
|
@EnableConfigurationProperties(
|
||||||
value = [KafkaTargetProperties::class]
|
value = [KafkaProperties::class]
|
||||||
)
|
)
|
||||||
@ConditionalOnProperty(value = ["app.kafka.topic", "app.kafka.servers"])
|
@ConditionalOnProperty(value = ["app.kafka.servers"])
|
||||||
@ConditionalOnMissingBean(MtbFileSender::class)
|
@ConditionalOnMissingBean(MtbFileSender::class)
|
||||||
@Order(-5)
|
@Order(-5)
|
||||||
class AppKafkaConfiguration {
|
class AppKafkaConfiguration {
|
||||||
@@ -53,21 +58,21 @@ class AppKafkaConfiguration {
|
|||||||
@Bean
|
@Bean
|
||||||
fun kafkaMtbFileSender(
|
fun kafkaMtbFileSender(
|
||||||
kafkaTemplate: KafkaTemplate<String, String>,
|
kafkaTemplate: KafkaTemplate<String, String>,
|
||||||
kafkaTargetProperties: KafkaTargetProperties,
|
kafkaProperties: KafkaProperties,
|
||||||
retryTemplate: RetryTemplate,
|
retryTemplate: RetryTemplate,
|
||||||
objectMapper: ObjectMapper
|
objectMapper: ObjectMapper
|
||||||
): MtbFileSender {
|
): MtbFileSender {
|
||||||
logger.info("Selected 'KafkaMtbFileSender'")
|
logger.info("Selected 'KafkaMtbFileSender'")
|
||||||
return KafkaMtbFileSender(kafkaTemplate, kafkaTargetProperties, retryTemplate, objectMapper)
|
return KafkaMtbFileSender(kafkaTemplate, kafkaProperties, retryTemplate, objectMapper)
|
||||||
}
|
}
|
||||||
|
|
||||||
@Bean
|
@Bean
|
||||||
fun kafkaListenerContainer(
|
fun kafkaResponseListenerContainer(
|
||||||
consumerFactory: ConsumerFactory<String, String>,
|
consumerFactory: ConsumerFactory<String, String>,
|
||||||
kafkaTargetProperties: KafkaTargetProperties,
|
kafkaProperties: KafkaProperties,
|
||||||
kafkaResponseProcessor: KafkaResponseProcessor
|
kafkaResponseProcessor: KafkaResponseProcessor
|
||||||
): KafkaMessageListenerContainer<String, String> {
|
): KafkaMessageListenerContainer<String, String> {
|
||||||
val containerProperties = ContainerProperties(kafkaTargetProperties.responseTopic)
|
val containerProperties = ContainerProperties(kafkaProperties.outputResponseTopic)
|
||||||
containerProperties.messageListener = kafkaResponseProcessor
|
containerProperties.messageListener = kafkaResponseProcessor
|
||||||
return KafkaMessageListenerContainer(consumerFactory, containerProperties)
|
return KafkaMessageListenerContainer(consumerFactory, containerProperties)
|
||||||
}
|
}
|
||||||
@@ -81,8 +86,33 @@ class AppKafkaConfiguration {
|
|||||||
}
|
}
|
||||||
|
|
||||||
@Bean
|
@Bean
|
||||||
fun connectionCheckService(consumerFactory: ConsumerFactory<String, String>): ConnectionCheckService {
|
@ConditionalOnProperty(value = ["app.kafka.input-topic"])
|
||||||
return KafkaConnectionCheckService(consumerFactory.createConsumer())
|
fun kafkaInputListenerContainer(
|
||||||
|
consumerFactory: ConsumerFactory<String, String>,
|
||||||
|
kafkaProperties: KafkaProperties,
|
||||||
|
kafkaInputListener: KafkaInputListener
|
||||||
|
): KafkaMessageListenerContainer<String, String> {
|
||||||
|
val containerProperties = ContainerProperties(kafkaProperties.inputTopic)
|
||||||
|
containerProperties.messageListener = kafkaInputListener
|
||||||
|
return KafkaMessageListenerContainer(consumerFactory, containerProperties)
|
||||||
|
}
|
||||||
|
|
||||||
|
@Bean
|
||||||
|
@ConditionalOnProperty(value = ["app.kafka.input-topic"])
|
||||||
|
fun kafkaInputListener(
|
||||||
|
requestProcessor: RequestProcessor,
|
||||||
|
objectMapper: ObjectMapper,
|
||||||
|
consentEvaluator: ConsentEvaluator
|
||||||
|
): KafkaInputListener {
|
||||||
|
return KafkaInputListener(requestProcessor, consentEvaluator, objectMapper)
|
||||||
|
}
|
||||||
|
|
||||||
|
@Bean
|
||||||
|
fun kafkaConnectionCheckService(
|
||||||
|
consumerFactory: ConsumerFactory<String, String>,
|
||||||
|
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||||
|
): ConnectionCheckService {
|
||||||
|
return KafkaConnectionCheckService(consumerFactory.createConsumer(), connectionCheckUpdateProducer)
|
||||||
}
|
}
|
||||||
|
|
||||||
}
|
}
|
@@ -1,7 +1,7 @@
|
|||||||
/*
|
/*
|
||||||
* This file is part of ETL-Processor
|
* 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 +19,12 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.config
|
package dev.dnpm.etl.processor.config
|
||||||
|
|
||||||
|
import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
|
||||||
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
|
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
|
||||||
|
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.RestMtbFileSender
|
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
|
||||||
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty
|
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty
|
||||||
@@ -32,6 +34,7 @@ import org.springframework.context.annotation.Configuration
|
|||||||
import org.springframework.core.annotation.Order
|
import org.springframework.core.annotation.Order
|
||||||
import org.springframework.retry.support.RetryTemplate
|
import org.springframework.retry.support.RetryTemplate
|
||||||
import org.springframework.web.client.RestTemplate
|
import org.springframework.web.client.RestTemplate
|
||||||
|
import reactor.core.publisher.Sinks
|
||||||
|
|
||||||
@Configuration
|
@Configuration
|
||||||
@EnableConfigurationProperties(
|
@EnableConfigurationProperties(
|
||||||
@@ -46,27 +49,24 @@ class AppRestConfiguration {
|
|||||||
|
|
||||||
private val logger = LoggerFactory.getLogger(AppRestConfiguration::class.java)
|
private val logger = LoggerFactory.getLogger(AppRestConfiguration::class.java)
|
||||||
|
|
||||||
@Bean
|
|
||||||
fun restTemplate(): RestTemplate {
|
|
||||||
return RestTemplate()
|
|
||||||
}
|
|
||||||
|
|
||||||
@Bean
|
@Bean
|
||||||
fun restMtbFileSender(
|
fun restMtbFileSender(
|
||||||
restTemplate: RestTemplate,
|
restTemplate: RestTemplate,
|
||||||
restTargetProperties: RestTargetProperties,
|
restTargetProperties: RestTargetProperties,
|
||||||
retryTemplate: RetryTemplate
|
retryTemplate: RetryTemplate,
|
||||||
|
reportService: ReportService,
|
||||||
): MtbFileSender {
|
): MtbFileSender {
|
||||||
logger.info("Selected 'RestMtbFileSender'")
|
logger.info("Selected 'RestDipMtbFileSender'")
|
||||||
return RestMtbFileSender(restTemplate, restTargetProperties, retryTemplate)
|
return RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
|
||||||
}
|
}
|
||||||
|
|
||||||
@Bean
|
@Bean
|
||||||
fun connectionCheckService(
|
fun restConnectionCheckService(
|
||||||
restTemplate: RestTemplate,
|
restTemplate: RestTemplate,
|
||||||
restTargetProperties: RestTargetProperties
|
restTargetProperties: RestTargetProperties,
|
||||||
|
connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||||
): ConnectionCheckService {
|
): ConnectionCheckService {
|
||||||
return RestConnectionCheckService(restTemplate, restTargetProperties)
|
return RestConnectionCheckService(restTemplate, restTargetProperties, connectionCheckUpdateProducer)
|
||||||
}
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
@@ -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
|
||||||
@@ -19,6 +19,9 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.config
|
package dev.dnpm.etl.processor.config
|
||||||
|
|
||||||
|
import dev.dnpm.etl.processor.security.UserRole
|
||||||
|
import dev.dnpm.etl.processor.security.UserRoleRepository
|
||||||
|
import dev.dnpm.etl.processor.security.UserRoleService
|
||||||
import org.slf4j.LoggerFactory
|
import org.slf4j.LoggerFactory
|
||||||
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
|
||||||
@@ -27,15 +30,22 @@ import org.springframework.context.annotation.Configuration
|
|||||||
import org.springframework.security.config.annotation.web.builders.HttpSecurity
|
import org.springframework.security.config.annotation.web.builders.HttpSecurity
|
||||||
import org.springframework.security.config.annotation.web.configuration.EnableWebSecurity
|
import org.springframework.security.config.annotation.web.configuration.EnableWebSecurity
|
||||||
import org.springframework.security.config.annotation.web.invoke
|
import org.springframework.security.config.annotation.web.invoke
|
||||||
|
import org.springframework.security.core.authority.SimpleGrantedAuthority
|
||||||
|
import org.springframework.security.core.authority.mapping.GrantedAuthoritiesMapper
|
||||||
|
import org.springframework.security.core.session.SessionRegistry
|
||||||
|
import org.springframework.security.core.session.SessionRegistryImpl
|
||||||
import org.springframework.security.core.userdetails.User
|
import org.springframework.security.core.userdetails.User
|
||||||
import org.springframework.security.core.userdetails.UserDetails
|
import org.springframework.security.core.userdetails.UserDetails
|
||||||
import org.springframework.security.crypto.factory.PasswordEncoderFactories
|
import org.springframework.security.crypto.factory.PasswordEncoderFactories
|
||||||
import org.springframework.security.crypto.password.PasswordEncoder
|
import org.springframework.security.crypto.password.PasswordEncoder
|
||||||
|
import org.springframework.security.oauth2.core.oidc.user.OidcUserAuthority
|
||||||
import org.springframework.security.provisioning.InMemoryUserDetailsManager
|
import org.springframework.security.provisioning.InMemoryUserDetailsManager
|
||||||
import org.springframework.security.web.SecurityFilterChain
|
import org.springframework.security.web.SecurityFilterChain
|
||||||
import java.util.*
|
import java.util.*
|
||||||
|
|
||||||
|
|
||||||
|
private const val LOGIN_PATH = "/login"
|
||||||
|
|
||||||
@Configuration
|
@Configuration
|
||||||
@EnableConfigurationProperties(
|
@EnableConfigurationProperties(
|
||||||
value = [
|
value = [
|
||||||
@@ -76,24 +86,113 @@ class AppSecurityConfiguration(
|
|||||||
}
|
}
|
||||||
|
|
||||||
@Bean
|
@Bean
|
||||||
fun filterChain(http: HttpSecurity): SecurityFilterChain {
|
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "true")
|
||||||
|
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("/mtb/**", hasAnyRole("MTBFILE", "ADMIN", "USER"))
|
||||||
|
authorize("/report/**", hasAnyRole("ADMIN", "USER"))
|
||||||
|
authorize("*.css", permitAll)
|
||||||
|
authorize("*.ico", permitAll)
|
||||||
|
authorize("*.jpeg", permitAll)
|
||||||
|
authorize("*.js", permitAll)
|
||||||
|
authorize("*.svg", permitAll)
|
||||||
|
authorize("*.css", permitAll)
|
||||||
|
authorize("/login/**", permitAll)
|
||||||
authorize(anyRequest, permitAll)
|
authorize(anyRequest, permitAll)
|
||||||
}
|
}
|
||||||
|
httpBasic {
|
||||||
|
realmName = "ETL-Processor"
|
||||||
|
}
|
||||||
formLogin {
|
formLogin {
|
||||||
loginPage = "/login"
|
loginPage = LOGIN_PATH
|
||||||
|
}
|
||||||
|
oauth2Login {
|
||||||
|
loginPage = LOGIN_PATH
|
||||||
|
}
|
||||||
|
sessionManagement {
|
||||||
|
sessionConcurrency {
|
||||||
|
maximumSessions = 1
|
||||||
|
expiredUrl = "$LOGIN_PATH?expired"
|
||||||
|
}
|
||||||
|
sessionFixation {
|
||||||
|
newSession()
|
||||||
|
}
|
||||||
}
|
}
|
||||||
csrf { disable() }
|
csrf { disable() }
|
||||||
}
|
}
|
||||||
return http.build()
|
return http.build()
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@Bean
|
||||||
|
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "true")
|
||||||
|
fun grantedAuthoritiesMapper(
|
||||||
|
userRoleRepository: UserRoleRepository,
|
||||||
|
appSecurityConfigProperties: SecurityConfigProperties
|
||||||
|
): GrantedAuthoritiesMapper {
|
||||||
|
return GrantedAuthoritiesMapper { grantedAuthority ->
|
||||||
|
grantedAuthority.filterIsInstance<OidcUserAuthority>()
|
||||||
|
.onEach {
|
||||||
|
val userRole = userRoleRepository.findByUsername(it.userInfo.preferredUsername)
|
||||||
|
if (userRole.isEmpty) {
|
||||||
|
userRoleRepository.save(
|
||||||
|
UserRole(
|
||||||
|
null,
|
||||||
|
it.userInfo.preferredUsername,
|
||||||
|
appSecurityConfigProperties.defaultNewUserRole
|
||||||
|
)
|
||||||
|
)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
.map {
|
||||||
|
val userRole = userRoleRepository.findByUsername(it.userInfo.preferredUsername)
|
||||||
|
SimpleGrantedAuthority("ROLE_${userRole.get().role.toString().uppercase()}")
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Bean
|
||||||
|
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "false", matchIfMissing = true)
|
||||||
|
fun filterChain(http: HttpSecurity, passwordEncoder: PasswordEncoder): SecurityFilterChain {
|
||||||
|
http {
|
||||||
|
authorizeHttpRequests {
|
||||||
|
authorize("/configs/**", hasRole("ADMIN"))
|
||||||
|
authorize("/mtbfile/**", hasAnyRole("MTBFILE", "ADMIN"))
|
||||||
|
authorize("/mtb/**", hasAnyRole("MTBFILE", "ADMIN"))
|
||||||
|
authorize("/report/**", hasRole("ADMIN"))
|
||||||
|
authorize(anyRequest, permitAll)
|
||||||
|
}
|
||||||
|
httpBasic {
|
||||||
|
realmName = "ETL-Processor"
|
||||||
|
}
|
||||||
|
formLogin {
|
||||||
|
loginPage = LOGIN_PATH
|
||||||
|
}
|
||||||
|
csrf { disable() }
|
||||||
|
}
|
||||||
|
return http.build()
|
||||||
|
}
|
||||||
|
|
||||||
|
@Bean
|
||||||
|
fun sessionRegistry(): SessionRegistry {
|
||||||
|
return SessionRegistryImpl()
|
||||||
|
}
|
||||||
|
|
||||||
@Bean
|
@Bean
|
||||||
fun passwordEncoder(): PasswordEncoder {
|
fun passwordEncoder(): PasswordEncoder {
|
||||||
return PasswordEncoderFactories.createDelegatingPasswordEncoder()
|
return PasswordEncoderFactories.createDelegatingPasswordEncoder()
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@Bean
|
||||||
|
@ConditionalOnProperty(value = ["app.security.enable-oidc"], havingValue = "true")
|
||||||
|
fun userRoleService(userRoleRepository: UserRoleRepository, sessionRegistry: SessionRegistry): UserRoleService {
|
||||||
|
return UserRoleService(userRoleRepository, sessionRegistry)
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@@ -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
|
||||||
|
}
|
||||||
|
}
|
@@ -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)
|
||||||
|
}
|
||||||
|
}
|
@@ -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())
|
||||||
|
}
|
||||||
|
}
|
@@ -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()
|
||||||
|
)
|
||||||
|
}
|
@@ -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
|
||||||
|
}
|
||||||
|
}
|
@@ -0,0 +1,93 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of ETL-Processor
|
||||||
|
*
|
||||||
|
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||||
|
*
|
||||||
|
* This program is free software: you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
|
* by the Free Software Foundation, either version 3 of the License, or
|
||||||
|
* (at your option) any later version.
|
||||||
|
*
|
||||||
|
* This program is distributed in the hope that it will be useful,
|
||||||
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
* GNU Affero General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU Affero General Public License
|
||||||
|
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package dev.dnpm.etl.processor.input
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
|
import dev.dnpm.etl.processor.CustomMediaType
|
||||||
|
import dev.dnpm.etl.processor.PatientId
|
||||||
|
import dev.dnpm.etl.processor.RequestId
|
||||||
|
import dev.dnpm.etl.processor.consent.ConsentEvaluator
|
||||||
|
import dev.dnpm.etl.processor.consent.TtpConsentStatus
|
||||||
|
import dev.dnpm.etl.processor.services.RequestProcessor
|
||||||
|
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||||
|
import org.apache.kafka.clients.consumer.ConsumerRecord
|
||||||
|
import org.slf4j.LoggerFactory
|
||||||
|
import org.springframework.http.MediaType
|
||||||
|
import org.springframework.kafka.listener.MessageListener
|
||||||
|
import java.nio.charset.Charset
|
||||||
|
|
||||||
|
class KafkaInputListener(
|
||||||
|
private val requestProcessor: RequestProcessor,
|
||||||
|
private val consentEvaluator: ConsentEvaluator,
|
||||||
|
private val objectMapper: ObjectMapper
|
||||||
|
) : MessageListener<String, String> {
|
||||||
|
private val logger = LoggerFactory.getLogger(KafkaInputListener::class.java)
|
||||||
|
|
||||||
|
override fun onMessage(record: ConsumerRecord<String, String>) {
|
||||||
|
when (guessMimeType(record)) {
|
||||||
|
MediaType.APPLICATION_JSON_VALUE -> handleDnpmV2Message(record)
|
||||||
|
CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE -> handleDnpmV2Message(record)
|
||||||
|
else -> {
|
||||||
|
/* ignore other messages */
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private fun guessMimeType(record: ConsumerRecord<String, String>): String? {
|
||||||
|
if (record.headers().headers("contentType").toList().isEmpty()) {
|
||||||
|
// Fallback if no contentType set (old behavior)
|
||||||
|
return MediaType.APPLICATION_JSON_VALUE
|
||||||
|
}
|
||||||
|
|
||||||
|
return record.headers().headers("contentType")?.firstOrNull()?.value()?.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 firstRequestIdHeader = record.headers().headers("requestId")?.firstOrNull()
|
||||||
|
val requestId = if (null != firstRequestIdHeader) {
|
||||||
|
RequestId(String(firstRequestIdHeader.value()))
|
||||||
|
} else {
|
||||||
|
RequestId("")
|
||||||
|
}
|
||||||
|
|
||||||
|
if (consentEvaluator.check(mtbFile).hasConsent()) {
|
||||||
|
logger.debug("Accepted MTB File for processing")
|
||||||
|
if (requestId.isBlank()) {
|
||||||
|
requestProcessor.processMtbFile(mtbFile)
|
||||||
|
} else {
|
||||||
|
requestProcessor.processMtbFile(mtbFile, requestId)
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
logger.debug("Accepted MTB File and process deletion")
|
||||||
|
if (requestId.isBlank()) {
|
||||||
|
requestProcessor.processDeletion(patientId, TtpConsentStatus.UNKNOWN_CHECK_FILE)
|
||||||
|
} else {
|
||||||
|
requestProcessor.processDeletion(
|
||||||
|
patientId,
|
||||||
|
requestId,
|
||||||
|
TtpConsentStatus.UNKNOWN_CHECK_FILE
|
||||||
|
)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
@@ -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
|
||||||
@@ -17,38 +17,50 @@
|
|||||||
* 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.web
|
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.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.*
|
||||||
|
|
||||||
@RestController
|
@RestController
|
||||||
|
@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)
|
||||||
|
|
||||||
@PostMapping(path = ["/mtbfile"])
|
@GetMapping
|
||||||
fun mtbFile(@RequestBody mtbFile: MtbFile): ResponseEntity<Void> {
|
fun info(): ResponseEntity<String> {
|
||||||
if (mtbFile.consent.status == Consent.Status.ACTIVE) {
|
return ResponseEntity.ok("Test")
|
||||||
logger.debug("Accepted MTB File for processing")
|
}
|
||||||
|
|
||||||
|
@PostMapping(consumes = [MediaType.APPLICATION_JSON_VALUE, CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE])
|
||||||
|
fun mtbFile(@RequestBody mtbFile: Mtb): ResponseEntity<Unit> {
|
||||||
|
val consentEvaluation = consentEvaluator.check(mtbFile)
|
||||||
|
if (consentEvaluation.hasConsent()) {
|
||||||
|
logger.debug("Accepted MTB File (DNPM V2) for processing")
|
||||||
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")
|
||||||
requestProcessor.processDeletion(mtbFile.patient.id)
|
val patientId = PatientId(mtbFile.patient.id)
|
||||||
|
requestProcessor.processDeletion(patientId, consentEvaluation.getStatus())
|
||||||
}
|
}
|
||||||
return ResponseEntity.accepted().build()
|
return ResponseEntity.accepted().build()
|
||||||
}
|
}
|
||||||
|
|
||||||
@DeleteMapping(path = ["/mtbfile/{patientId}"])
|
@DeleteMapping(path = ["{patientId}"])
|
||||||
fun deleteData(@PathVariable patientId: String): ResponseEntity<Void> {
|
fun deleteData(@PathVariable patientId: String): ResponseEntity<Unit> {
|
||||||
logger.debug("Accepted patient ID to process deletion")
|
logger.debug("Accepted patient ID to process deletion")
|
||||||
requestProcessor.processDeletion(patientId)
|
requestProcessor.processDeletion(PatientId(patientId), TtpConsentStatus.UNKNOWN_CHECK_FILE)
|
||||||
return ResponseEntity.accepted().build()
|
return ResponseEntity.accepted().build()
|
||||||
}
|
}
|
||||||
|
|
@@ -20,66 +20,247 @@
|
|||||||
|
|
||||||
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.RestTargetProperties
|
import dev.dnpm.etl.processor.config.RestTargetProperties
|
||||||
import jakarta.annotation.PostConstruct
|
import jakarta.annotation.PostConstruct
|
||||||
import org.apache.kafka.clients.consumer.Consumer
|
import org.apache.kafka.clients.consumer.Consumer
|
||||||
import org.apache.kafka.common.errors.TimeoutException
|
import org.apache.kafka.common.errors.TimeoutException
|
||||||
import org.springframework.http.HttpStatus
|
import org.springframework.beans.factory.annotation.Qualifier
|
||||||
|
import org.springframework.http.*
|
||||||
import org.springframework.scheduling.annotation.Scheduled
|
import org.springframework.scheduling.annotation.Scheduled
|
||||||
import org.springframework.web.client.RestTemplate
|
import org.springframework.web.client.RestTemplate
|
||||||
|
import org.springframework.web.util.UriComponentsBuilder
|
||||||
|
import reactor.core.publisher.Sinks
|
||||||
|
import java.time.Instant
|
||||||
import kotlin.time.Duration.Companion.seconds
|
import kotlin.time.Duration.Companion.seconds
|
||||||
import kotlin.time.toJavaDuration
|
import kotlin.time.toJavaDuration
|
||||||
|
|
||||||
interface ConnectionCheckService {
|
fun interface ConnectionCheckService {
|
||||||
|
|
||||||
fun connectionAvailable(): Boolean
|
fun connectionAvailable(): ConnectionCheckResult
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
interface OutputConnectionCheckService : ConnectionCheckService
|
||||||
|
|
||||||
|
sealed class ConnectionCheckResult {
|
||||||
|
|
||||||
|
abstract val available: Boolean
|
||||||
|
|
||||||
|
abstract val timestamp: Instant
|
||||||
|
|
||||||
|
abstract val lastChange: Instant
|
||||||
|
|
||||||
|
data class KafkaConnectionCheckResult(
|
||||||
|
override val available: Boolean,
|
||||||
|
override val timestamp: Instant,
|
||||||
|
override val lastChange: Instant
|
||||||
|
) : ConnectionCheckResult()
|
||||||
|
|
||||||
|
data class RestConnectionCheckResult(
|
||||||
|
override val available: Boolean,
|
||||||
|
override val timestamp: Instant,
|
||||||
|
override val lastChange: Instant
|
||||||
|
) : ConnectionCheckResult()
|
||||||
|
|
||||||
|
data class GPasConnectionCheckResult(
|
||||||
|
override val available: Boolean,
|
||||||
|
override val timestamp: Instant,
|
||||||
|
override val lastChange: Instant
|
||||||
|
) : ConnectionCheckResult()
|
||||||
|
|
||||||
|
data class GIcsConnectionCheckResult(
|
||||||
|
override val available: Boolean,
|
||||||
|
override val timestamp: Instant,
|
||||||
|
override val lastChange: Instant
|
||||||
|
) : ConnectionCheckResult()
|
||||||
|
}
|
||||||
|
|
||||||
class KafkaConnectionCheckService(
|
class KafkaConnectionCheckService(
|
||||||
private val consumer: Consumer<String, String>
|
private val consumer: Consumer<String, String>,
|
||||||
) : ConnectionCheckService {
|
@Qualifier("connectionCheckUpdateProducer")
|
||||||
|
private val connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||||
private var connectionAvailable: Boolean = false
|
) : OutputConnectionCheckService {
|
||||||
|
|
||||||
|
private var result = ConnectionCheckResult.KafkaConnectionCheckResult(false, Instant.now(), Instant.now())
|
||||||
|
|
||||||
@PostConstruct
|
@PostConstruct
|
||||||
@Scheduled(cron = "0 * * * * *")
|
@Scheduled(cron = "0 * * * * *")
|
||||||
fun check() {
|
fun check() {
|
||||||
connectionAvailable = try {
|
result = try {
|
||||||
null != consumer.listTopics(5.seconds.toJavaDuration())
|
val available = null != consumer.listTopics(5.seconds.toJavaDuration())
|
||||||
} catch (e: TimeoutException) {
|
ConnectionCheckResult.KafkaConnectionCheckResult(
|
||||||
false
|
available,
|
||||||
|
Instant.now(),
|
||||||
|
if (result.available == available) { result.lastChange } else { Instant.now() }
|
||||||
|
)
|
||||||
|
} catch (_: TimeoutException) {
|
||||||
|
ConnectionCheckResult.KafkaConnectionCheckResult(
|
||||||
|
false,
|
||||||
|
Instant.now(),
|
||||||
|
if (!result.available) { result.lastChange } else { Instant.now() }
|
||||||
|
)
|
||||||
}
|
}
|
||||||
|
connectionCheckUpdateProducer.emitNext(
|
||||||
|
result,
|
||||||
|
Sinks.EmitFailureHandler.FAIL_FAST
|
||||||
|
)
|
||||||
}
|
}
|
||||||
|
|
||||||
override fun connectionAvailable(): Boolean {
|
override fun connectionAvailable(): ConnectionCheckResult.KafkaConnectionCheckResult {
|
||||||
return this.connectionAvailable
|
return this.result
|
||||||
}
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
class RestConnectionCheckService(
|
class RestConnectionCheckService(
|
||||||
private val restTemplate: RestTemplate,
|
private val restTemplate: RestTemplate,
|
||||||
private val restTargetProperties: RestTargetProperties
|
private val restTargetProperties: RestTargetProperties,
|
||||||
) : ConnectionCheckService {
|
@Qualifier("connectionCheckUpdateProducer")
|
||||||
|
private val connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||||
|
) : OutputConnectionCheckService {
|
||||||
|
|
||||||
private var connectionAvailable: Boolean = false
|
private var result = ConnectionCheckResult.RestConnectionCheckResult(false, Instant.now(), Instant.now())
|
||||||
|
|
||||||
@PostConstruct
|
@PostConstruct
|
||||||
@Scheduled(cron = "0 * * * * *")
|
@Scheduled(cron = "0 * * * * *")
|
||||||
fun check() {
|
fun check() {
|
||||||
connectionAvailable = try {
|
result = try {
|
||||||
restTemplate.getForEntity(
|
val available = restTemplate.getForEntity(
|
||||||
restTargetProperties.uri?.replace("/etl/api", "").toString(),
|
UriComponentsBuilder.fromUriString(restTargetProperties.uri.toString())
|
||||||
|
.pathSegment("mtb")
|
||||||
|
.pathSegment("kaplan-meier")
|
||||||
|
.pathSegment("config")
|
||||||
|
.toUriString(),
|
||||||
String::class.java
|
String::class.java
|
||||||
).statusCode == HttpStatus.OK
|
).statusCode == HttpStatus.OK
|
||||||
} catch (e: Exception) {
|
|
||||||
false
|
ConnectionCheckResult.RestConnectionCheckResult(
|
||||||
|
available,
|
||||||
|
Instant.now(),
|
||||||
|
if (result.available == available) { result.lastChange } else { Instant.now() }
|
||||||
|
)
|
||||||
|
} catch (_: Exception) {
|
||||||
|
ConnectionCheckResult.RestConnectionCheckResult(
|
||||||
|
false,
|
||||||
|
Instant.now(),
|
||||||
|
if (!result.available) { result.lastChange } else { Instant.now() }
|
||||||
|
)
|
||||||
}
|
}
|
||||||
|
connectionCheckUpdateProducer.emitNext(
|
||||||
|
result,
|
||||||
|
Sinks.EmitFailureHandler.FAIL_FAST
|
||||||
|
)
|
||||||
}
|
}
|
||||||
|
|
||||||
override fun connectionAvailable(): Boolean {
|
override fun connectionAvailable(): ConnectionCheckResult.RestConnectionCheckResult {
|
||||||
return this.connectionAvailable
|
return this.result
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
class GPasConnectionCheckService(
|
||||||
|
private val restTemplate: RestTemplate,
|
||||||
|
private val gPasConfigProperties: GPasConfigProperties,
|
||||||
|
@Qualifier("connectionCheckUpdateProducer")
|
||||||
|
private val connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||||
|
) : ConnectionCheckService {
|
||||||
|
|
||||||
|
private var result = ConnectionCheckResult.GPasConnectionCheckResult(false, Instant.now(), Instant.now())
|
||||||
|
|
||||||
|
@PostConstruct
|
||||||
|
@Scheduled(cron = "0 * * * * *")
|
||||||
|
fun check() {
|
||||||
|
result = try {
|
||||||
|
val uri = UriComponentsBuilder.fromUriString(
|
||||||
|
gPasConfigProperties.uri?.replace("/\$pseudonymizeAllowCreate", "/metadata").toString()
|
||||||
|
).build().toUri()
|
||||||
|
|
||||||
|
val headers = HttpHeaders()
|
||||||
|
headers.contentType = MediaType.APPLICATION_JSON
|
||||||
|
if (!gPasConfigProperties.username.isNullOrBlank() && !gPasConfigProperties.password.isNullOrBlank()) {
|
||||||
|
headers.setBasicAuth(gPasConfigProperties.username, gPasConfigProperties.password)
|
||||||
|
}
|
||||||
|
|
||||||
|
val available = restTemplate.exchange(
|
||||||
|
uri,
|
||||||
|
HttpMethod.GET,
|
||||||
|
HttpEntity<Void>(headers),
|
||||||
|
Void::class.java
|
||||||
|
).statusCode == HttpStatus.OK
|
||||||
|
|
||||||
|
ConnectionCheckResult.GPasConnectionCheckResult(
|
||||||
|
available,
|
||||||
|
Instant.now(),
|
||||||
|
if (result.available == available) { result.lastChange } else { Instant.now() }
|
||||||
|
)
|
||||||
|
} catch (_: Exception) {
|
||||||
|
ConnectionCheckResult.GPasConnectionCheckResult(
|
||||||
|
false,
|
||||||
|
Instant.now(),
|
||||||
|
if (!result.available) { result.lastChange } else { Instant.now() }
|
||||||
|
)
|
||||||
|
}
|
||||||
|
connectionCheckUpdateProducer.emitNext(
|
||||||
|
result,
|
||||||
|
Sinks.EmitFailureHandler.FAIL_FAST
|
||||||
|
)
|
||||||
|
}
|
||||||
|
|
||||||
|
override fun connectionAvailable(): ConnectionCheckResult.GPasConnectionCheckResult {
|
||||||
|
return this.result
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
class GIcsConnectionCheckService(
|
||||||
|
private val restTemplate: RestTemplate,
|
||||||
|
private val gIcsConfigProperties: GIcsConfigProperties,
|
||||||
|
@Qualifier("connectionCheckUpdateProducer")
|
||||||
|
private val connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>
|
||||||
|
) : ConnectionCheckService {
|
||||||
|
|
||||||
|
private var result = ConnectionCheckResult.GIcsConnectionCheckResult(false, Instant.now(), Instant.now())
|
||||||
|
|
||||||
|
@PostConstruct
|
||||||
|
@Scheduled(cron = "0 * * * * *")
|
||||||
|
fun check() {
|
||||||
|
result = try {
|
||||||
|
|
||||||
|
val uri = UriComponentsBuilder.fromUriString(
|
||||||
|
gIcsConfigProperties.uri.toString()).path("/metadata").build().toUri()
|
||||||
|
|
||||||
|
val headers = HttpHeaders()
|
||||||
|
headers.contentType = MediaType.APPLICATION_JSON
|
||||||
|
if (!gIcsConfigProperties.username.isNullOrBlank() && !gIcsConfigProperties.password.isNullOrBlank()) {
|
||||||
|
headers.setBasicAuth(gIcsConfigProperties.username, gIcsConfigProperties.password)
|
||||||
|
}
|
||||||
|
|
||||||
|
val available = restTemplate.exchange(
|
||||||
|
uri,
|
||||||
|
HttpMethod.GET,
|
||||||
|
HttpEntity<Void>(headers),
|
||||||
|
Void::class.java
|
||||||
|
).statusCode == HttpStatus.OK
|
||||||
|
|
||||||
|
ConnectionCheckResult.GIcsConnectionCheckResult(
|
||||||
|
available,
|
||||||
|
Instant.now(),
|
||||||
|
if (result.available == available) { result.lastChange } else { Instant.now() }
|
||||||
|
)
|
||||||
|
} catch (_: Exception) {
|
||||||
|
ConnectionCheckResult.GIcsConnectionCheckResult(
|
||||||
|
false,
|
||||||
|
Instant.now(),
|
||||||
|
if (!result.available) { result.lastChange } else { Instant.now() }
|
||||||
|
)
|
||||||
|
}
|
||||||
|
connectionCheckUpdateProducer.emitNext(
|
||||||
|
result,
|
||||||
|
Sinks.EmitFailureHandler.FAIL_FAST
|
||||||
|
)
|
||||||
|
}
|
||||||
|
|
||||||
|
override fun connectionAvailable(): ConnectionCheckResult.GIcsConnectionCheckResult {
|
||||||
|
return this.result
|
||||||
}
|
}
|
||||||
}
|
}
|
@@ -19,11 +19,15 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.monitoring
|
package dev.dnpm.etl.processor.monitoring
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.JsonAlias
|
||||||
import com.fasterxml.jackson.annotation.JsonIgnoreProperties
|
import com.fasterxml.jackson.annotation.JsonIgnoreProperties
|
||||||
import com.fasterxml.jackson.annotation.JsonValue
|
import com.fasterxml.jackson.annotation.JsonValue
|
||||||
import com.fasterxml.jackson.core.JsonParseException
|
import com.fasterxml.jackson.core.JsonParseException
|
||||||
import com.fasterxml.jackson.databind.JsonMappingException
|
import com.fasterxml.jackson.databind.JsonMappingException
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
|
import dev.dnpm.etl.processor.monitoring.ReportService.Issue
|
||||||
|
import dev.dnpm.etl.processor.monitoring.ReportService.Severity
|
||||||
|
import java.util.Optional
|
||||||
|
|
||||||
class ReportService(
|
class ReportService(
|
||||||
private val objectMapper: ObjectMapper
|
private val objectMapper: ObjectMapper
|
||||||
@@ -54,11 +58,25 @@ class ReportService(
|
|||||||
private data class DataQualityReport(val issues: List<Issue>)
|
private data class DataQualityReport(val issues: List<Issue>)
|
||||||
|
|
||||||
@JsonIgnoreProperties(ignoreUnknown = true)
|
@JsonIgnoreProperties(ignoreUnknown = true)
|
||||||
data class Issue(val severity: Severity, val message: String)
|
data class Issue(
|
||||||
|
val severity: Severity,
|
||||||
|
@JsonAlias("details") val message: String,
|
||||||
|
val path: Optional<String> = Optional.empty()
|
||||||
|
)
|
||||||
|
|
||||||
enum class Severity(@JsonValue val value: String) {
|
enum class Severity(@JsonValue val value: String) {
|
||||||
|
FATAL("fatal"),
|
||||||
ERROR("error"),
|
ERROR("error"),
|
||||||
WARNING("warning"),
|
WARNING("warning"),
|
||||||
INFO("info")
|
INFO("info")
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
fun List<Issue>.asRequestStatus(): RequestStatus {
|
||||||
|
val severity = this.minOfOrNull { it.severity }
|
||||||
|
return when (severity) {
|
||||||
|
Severity.FATAL, Severity.ERROR -> RequestStatus.ERROR
|
||||||
|
Severity.WARNING -> RequestStatus.WARNING
|
||||||
|
else -> RequestStatus.SUCCESS
|
||||||
|
}
|
||||||
|
}
|
@@ -19,35 +19,68 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.monitoring
|
package dev.dnpm.etl.processor.monitoring
|
||||||
|
|
||||||
|
import dev.dnpm.etl.processor.*
|
||||||
import org.springframework.data.annotation.Id
|
import org.springframework.data.annotation.Id
|
||||||
|
import org.springframework.data.domain.Page
|
||||||
|
import org.springframework.data.domain.Pageable
|
||||||
import org.springframework.data.jdbc.repository.query.Query
|
import org.springframework.data.jdbc.repository.query.Query
|
||||||
|
import org.springframework.data.relational.core.mapping.Column
|
||||||
import org.springframework.data.relational.core.mapping.Embedded
|
import org.springframework.data.relational.core.mapping.Embedded
|
||||||
import org.springframework.data.relational.core.mapping.Table
|
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.*
|
||||||
|
|
||||||
typealias RequestId = UUID
|
|
||||||
|
|
||||||
@Table("request")
|
@Table("request")
|
||||||
data class Request(
|
data class Request(
|
||||||
@Id val id: Long? = null,
|
@Id val id: Long? = null,
|
||||||
val uuid: String = RequestId.randomUUID().toString(),
|
val uuid: RequestId = randomRequestId(),
|
||||||
val patientId: String,
|
val patientPseudonym: PatientPseudonym,
|
||||||
val pid: String,
|
val pid: PatientId,
|
||||||
val fingerprint: String,
|
@Column("fingerprint")
|
||||||
|
val fingerprint: Fingerprint,
|
||||||
val type: RequestType,
|
val type: RequestType,
|
||||||
var status: RequestStatus,
|
var status: RequestStatus,
|
||||||
var processedAt: Instant = Instant.now(),
|
var processedAt: Instant = Instant.now(),
|
||||||
@Embedded.Nullable var report: Report? = null
|
@Embedded.Nullable var report: Report? = null
|
||||||
)
|
) {
|
||||||
|
constructor(
|
||||||
|
uuid: RequestId,
|
||||||
|
patientPseudonym: PatientPseudonym,
|
||||||
|
pid: PatientId,
|
||||||
|
fingerprint: Fingerprint,
|
||||||
|
type: RequestType,
|
||||||
|
status: RequestStatus
|
||||||
|
) :
|
||||||
|
this(null, uuid, patientPseudonym, pid, fingerprint, type, status, Instant.now())
|
||||||
|
|
||||||
|
constructor(
|
||||||
|
uuid: RequestId,
|
||||||
|
patientPseudonym: PatientPseudonym,
|
||||||
|
pid: PatientId,
|
||||||
|
fingerprint: Fingerprint,
|
||||||
|
type: RequestType,
|
||||||
|
status: RequestStatus,
|
||||||
|
processedAt: Instant
|
||||||
|
) :
|
||||||
|
this(null, uuid, patientPseudonym, pid, fingerprint, type, status, processedAt)
|
||||||
|
|
||||||
|
fun isPendingUnknown(): Boolean {
|
||||||
|
return this.status == RequestStatus.UNKNOWN && this.processedAt.isBefore(
|
||||||
|
Instant.now().minus(10, ChronoUnit.MINUTES)
|
||||||
|
)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@JvmRecord
|
||||||
data class Report(
|
data class Report(
|
||||||
val description: String,
|
val description: String,
|
||||||
val dataQualityReport: String = ""
|
val dataQualityReport: String = ""
|
||||||
)
|
)
|
||||||
|
|
||||||
|
@JvmRecord
|
||||||
data class CountedState(
|
data class CountedState(
|
||||||
val count: Int,
|
val count: Int,
|
||||||
val status: RequestStatus,
|
val status: RequestStatus,
|
||||||
@@ -55,26 +88,32 @@ data class CountedState(
|
|||||||
|
|
||||||
interface RequestRepository : CrudRepository<Request, Long>, PagingAndSortingRepository<Request, Long> {
|
interface RequestRepository : CrudRepository<Request, Long>, PagingAndSortingRepository<Request, Long> {
|
||||||
|
|
||||||
fun findAllByPatientIdOrderByProcessedAtDesc(patientId: String): List<Request>
|
fun findAllByPatientPseudonymOrderByProcessedAtDesc(patientId: PatientPseudonym): List<Request>
|
||||||
|
|
||||||
fun findByUuidEquals(uuid: String): Optional<Request>
|
fun findByUuidEquals(uuid: RequestId): Optional<Request>
|
||||||
|
|
||||||
|
fun findRequestByPatientPseudonym(patientPseudonym: PatientPseudonym, pageable: Pageable): Page<Request>
|
||||||
|
|
||||||
@Query("SELECT count(*) AS count, status FROM request WHERE type = 'MTB_FILE' GROUP BY status ORDER BY status, count DESC;")
|
@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_id 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_id 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>
|
||||||
|
|
||||||
}
|
}
|
@@ -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")
|
||||||
}
|
}
|
@@ -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
|
||||||
@@ -20,31 +20,44 @@
|
|||||||
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.config.KafkaProperties
|
||||||
import dev.dnpm.etl.processor.config.KafkaTargetProperties
|
|
||||||
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
|
||||||
|
|
||||||
class KafkaMtbFileSender(
|
class KafkaMtbFileSender(
|
||||||
private val kafkaTemplate: KafkaTemplate<String, String>,
|
private val kafkaTemplate: KafkaTemplate<String, String>,
|
||||||
private val kafkaTargetProperties: KafkaTargetProperties,
|
private val kafkaProperties: KafkaProperties,
|
||||||
private val retryTemplate: RetryTemplate,
|
private val retryTemplate: RetryTemplate,
|
||||||
private val objectMapper: ObjectMapper
|
private val objectMapper: ObjectMapper
|
||||||
) : MtbFileSender {
|
) : MtbFileSender {
|
||||||
|
|
||||||
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 =
|
||||||
kafkaTargetProperties.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)
|
||||||
@@ -58,24 +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)
|
|
||||||
.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 =
|
||||||
kafkaTargetProperties.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)
|
||||||
@@ -90,17 +105,14 @@ class KafkaMtbFileSender(
|
|||||||
}
|
}
|
||||||
|
|
||||||
override fun endpoint(): String {
|
override fun endpoint(): String {
|
||||||
return "${this.kafkaTargetProperties.servers} (${this.kafkaTargetProperties.topic}/${this.kafkaTargetProperties.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) {
|
||||||
"\"eid\": \"${request.mtbFile.episode.id}\"}"
|
is DnpmV2MtbFileRequest -> "{\"pid\": \"${request.content.patient.id}\"}"
|
||||||
|
is DeleteRequest -> "{\"pid\": \"${request.patientId.value}\"}"
|
||||||
|
else -> throw IllegalArgumentException("Unsupported request type: ${request::class.simpleName}")
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
private fun key(request: MtbFileSender.DeleteRequest): String {
|
|
||||||
return "{\"pid\": \"${request.patientId}\"}"
|
|
||||||
}
|
|
||||||
|
|
||||||
data class Data(val requestId: String, val content: MtbFile)
|
|
||||||
}
|
}
|
@@ -19,23 +19,17 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.output
|
package dev.dnpm.etl.processor.output
|
||||||
|
|
||||||
import de.ukw.ccc.bwhc.dto.MtbFile
|
|
||||||
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: String, val mtbFile: MtbFile)
|
|
||||||
|
|
||||||
data class DeleteRequest(val requestId: String, val patientId: String)
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
fun Int.asRequestStatus(): RequestStatus {
|
fun Int.asRequestStatus(): RequestStatus {
|
||||||
|
49
src/main/kotlin/dev/dnpm/etl/processor/output/MtbRequest.kt
Normal file
49
src/main/kotlin/dev/dnpm/etl/processor/output/MtbRequest.kt
Normal 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
|
@@ -0,0 +1,55 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of ETL-Processor
|
||||||
|
*
|
||||||
|
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||||
|
*
|
||||||
|
* This program is free software: you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
|
* by the Free Software Foundation, either version 3 of the License, or
|
||||||
|
* (at your option) any later version.
|
||||||
|
*
|
||||||
|
* This program is distributed in the hope that it will be useful,
|
||||||
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
* GNU Affero General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU Affero General Public License
|
||||||
|
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package dev.dnpm.etl.processor.output
|
||||||
|
|
||||||
|
import dev.dnpm.etl.processor.PatientPseudonym
|
||||||
|
import dev.dnpm.etl.processor.config.RestTargetProperties
|
||||||
|
import dev.dnpm.etl.processor.monitoring.ReportService
|
||||||
|
import org.springframework.retry.support.RetryTemplate
|
||||||
|
import org.springframework.web.client.RestTemplate
|
||||||
|
import org.springframework.web.util.UriComponentsBuilder
|
||||||
|
|
||||||
|
class RestDipMtbFileSender(
|
||||||
|
restTemplate: RestTemplate,
|
||||||
|
private val restTargetProperties: RestTargetProperties,
|
||||||
|
retryTemplate: RetryTemplate,
|
||||||
|
reportService: ReportService
|
||||||
|
) : RestMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService) {
|
||||||
|
|
||||||
|
override fun sendUrl(): String {
|
||||||
|
return UriComponentsBuilder
|
||||||
|
.fromUriString(restTargetProperties.uri.toString())
|
||||||
|
.pathSegment("mtb")
|
||||||
|
.pathSegment("etl")
|
||||||
|
.pathSegment("patient-record")
|
||||||
|
.toUriString()
|
||||||
|
}
|
||||||
|
|
||||||
|
override fun deleteUrl(patientId: PatientPseudonym): String {
|
||||||
|
return UriComponentsBuilder
|
||||||
|
.fromUriString(restTargetProperties.uri.toString())
|
||||||
|
.pathSegment("mtb")
|
||||||
|
.pathSegment("etl")
|
||||||
|
.pathSegment("patient")
|
||||||
|
.pathSegment(patientId.value)
|
||||||
|
.toUriString()
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
@@ -1,7 +1,7 @@
|
|||||||
/*
|
/*
|
||||||
* This file is part of ETL-Processor
|
* 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
|
||||||
@@ -19,62 +19,71 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.output
|
package dev.dnpm.etl.processor.output
|
||||||
|
|
||||||
|
import dev.dnpm.etl.processor.CustomMediaType
|
||||||
|
import dev.dnpm.etl.processor.PatientPseudonym
|
||||||
import dev.dnpm.etl.processor.config.RestTargetProperties
|
import dev.dnpm.etl.processor.config.RestTargetProperties
|
||||||
|
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.monitoring.asRequestStatus
|
||||||
import org.slf4j.LoggerFactory
|
import org.slf4j.LoggerFactory
|
||||||
import org.springframework.http.HttpEntity
|
import org.springframework.http.HttpEntity
|
||||||
import org.springframework.http.HttpHeaders
|
import org.springframework.http.HttpHeaders
|
||||||
import org.springframework.http.MediaType
|
import org.springframework.http.MediaType
|
||||||
import org.springframework.retry.support.RetryTemplate
|
import org.springframework.retry.support.RetryTemplate
|
||||||
import org.springframework.web.client.RestClientException
|
import org.springframework.web.client.RestClientException
|
||||||
|
import org.springframework.web.client.RestClientResponseException
|
||||||
import org.springframework.web.client.RestTemplate
|
import org.springframework.web.client.RestTemplate
|
||||||
|
|
||||||
class RestMtbFileSender(
|
abstract class RestMtbFileSender(
|
||||||
private val restTemplate: RestTemplate,
|
private val restTemplate: RestTemplate,
|
||||||
private val restTargetProperties: RestTargetProperties,
|
private val restTargetProperties: RestTargetProperties,
|
||||||
private val retryTemplate: RetryTemplate
|
private val retryTemplate: RetryTemplate,
|
||||||
|
private val reportService: ReportService
|
||||||
) : MtbFileSender {
|
) : MtbFileSender {
|
||||||
|
|
||||||
private val logger = LoggerFactory.getLogger(RestMtbFileSender::class.java)
|
private val logger = LoggerFactory.getLogger(RestMtbFileSender::class.java)
|
||||||
|
|
||||||
override fun send(request: MtbFileSender.MtbFileRequest): MtbFileSender.Response {
|
abstract fun sendUrl(): String
|
||||||
|
|
||||||
|
abstract fun deleteUrl(patientId: PatientPseudonym): String
|
||||||
|
|
||||||
|
override fun <T> send(request: MtbFileRequest<T>): MtbFileSender.Response {
|
||||||
try {
|
try {
|
||||||
return retryTemplate.execute<MtbFileSender.Response, Exception> {
|
return retryTemplate.execute<MtbFileSender.Response, Exception> {
|
||||||
val headers = HttpHeaders()
|
val headers = getHttpHeaders(request)
|
||||||
headers.contentType = MediaType.APPLICATION_JSON
|
val entityReq = HttpEntity(request.content, headers)
|
||||||
val entityReq = HttpEntity(request.mtbFile, headers)
|
|
||||||
val response = restTemplate.postForEntity(
|
val response = restTemplate.postForEntity(
|
||||||
"${restTargetProperties.uri}/MTBFile",
|
sendUrl(),
|
||||||
entityReq,
|
entityReq,
|
||||||
String::class.java
|
String::class.java
|
||||||
)
|
)
|
||||||
if (!response.statusCode.is2xxSuccessful) {
|
if (!response.statusCode.is2xxSuccessful) {
|
||||||
logger.warn("Error sending to remote system: {}", response.body)
|
logger.warn("Error sending to remote system: {}", response.body)
|
||||||
return@execute MtbFileSender.Response(
|
return@execute MtbFileSender.Response(
|
||||||
response.statusCode.asRequestStatus(),
|
reportService.deserialize(response.body).asRequestStatus(),
|
||||||
"Status-Code: ${response.statusCode.value()}"
|
"Status-Code: ${response.statusCode.value()}"
|
||||||
)
|
)
|
||||||
}
|
}
|
||||||
logger.debug("Sent file via RestMtbFileSender")
|
logger.debug("Sent file via RestMtbFileSender")
|
||||||
return@execute MtbFileSender.Response(response.statusCode.asRequestStatus(), response.body.orEmpty())
|
return@execute MtbFileSender.Response(reportService.deserialize(response.body).asRequestStatus(), response.body.orEmpty())
|
||||||
}
|
}
|
||||||
} catch (e: IllegalArgumentException) {
|
} catch (e: IllegalArgumentException) {
|
||||||
logger.error("Not a valid URI to export to: '{}'", restTargetProperties.uri!!)
|
logger.error("Not a valid URI to export to: '{}'", restTargetProperties.uri!!)
|
||||||
} catch (e: RestClientException) {
|
} catch (e: RestClientResponseException) {
|
||||||
logger.info(restTargetProperties.uri!!.toString())
|
logger.info(restTargetProperties.uri!!.toString())
|
||||||
logger.error("Cannot send data to remote system", e)
|
logger.error("Request data not accepted by remote system", e)
|
||||||
|
return MtbFileSender.Response(reportService.deserialize(e.responseBodyAsString).asRequestStatus(), e.responseBodyAsString)
|
||||||
}
|
}
|
||||||
return MtbFileSender.Response(RequestStatus.ERROR, "Sonstiger Fehler bei der Übertragung")
|
return MtbFileSender.Response(RequestStatus.ERROR, "Sonstiger Fehler bei der Übertragung")
|
||||||
}
|
}
|
||||||
|
|
||||||
override fun send(request: MtbFileSender.DeleteRequest): MtbFileSender.Response {
|
override fun send(request: DeleteRequest): MtbFileSender.Response {
|
||||||
try {
|
try {
|
||||||
return retryTemplate.execute<MtbFileSender.Response, Exception> {
|
return retryTemplate.execute<MtbFileSender.Response, Exception> {
|
||||||
val headers = HttpHeaders()
|
val headers = getHttpHeaders(request)
|
||||||
headers.contentType = MediaType.APPLICATION_JSON
|
|
||||||
val entityReq = HttpEntity(null, headers)
|
val entityReq = HttpEntity(null, headers)
|
||||||
restTemplate.delete(
|
restTemplate.delete(
|
||||||
"${restTargetProperties.uri}/Patient/${request.patientId}",
|
deleteUrl(request.patientId),
|
||||||
entityReq,
|
entityReq,
|
||||||
String::class.java
|
String::class.java
|
||||||
)
|
)
|
||||||
@@ -94,4 +103,21 @@ class RestMtbFileSender(
|
|||||||
return this.restTargetProperties.uri.orEmpty()
|
return this.restTargetProperties.uri.orEmpty()
|
||||||
}
|
}
|
||||||
|
|
||||||
|
private fun getHttpHeaders(request: MtbRequest): HttpHeaders {
|
||||||
|
val username = restTargetProperties.username
|
||||||
|
val password = restTargetProperties.password
|
||||||
|
val headers = HttpHeaders()
|
||||||
|
headers.contentType = when (request) {
|
||||||
|
is DnpmV2MtbFileRequest -> CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON
|
||||||
|
else -> MediaType.APPLICATION_JSON
|
||||||
|
}
|
||||||
|
|
||||||
|
if (username.isNullOrBlank() || password.isNullOrBlank()) {
|
||||||
|
return headers
|
||||||
|
}
|
||||||
|
|
||||||
|
headers.setBasicAuth(username, password)
|
||||||
|
return headers
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
@@ -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) }
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
@@ -19,6 +19,8 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.pseudonym
|
package dev.dnpm.etl.processor.pseudonym
|
||||||
|
|
||||||
|
import dev.dnpm.etl.processor.PatientId
|
||||||
|
import dev.dnpm.etl.processor.PatientPseudonym
|
||||||
import dev.dnpm.etl.processor.config.PseudonymizeConfigProperties
|
import dev.dnpm.etl.processor.config.PseudonymizeConfigProperties
|
||||||
|
|
||||||
class PseudonymizeService(
|
class PseudonymizeService(
|
||||||
@@ -26,11 +28,19 @@ class PseudonymizeService(
|
|||||||
private val configProperties: PseudonymizeConfigProperties
|
private val configProperties: PseudonymizeConfigProperties
|
||||||
) {
|
) {
|
||||||
|
|
||||||
fun patientPseudonym(patientId: String): String {
|
fun patientPseudonym(patientId: PatientId): PatientPseudonym {
|
||||||
return when (generator) {
|
return when (generator) {
|
||||||
is GpasPseudonymGenerator -> generator.generate(patientId)
|
is GpasPseudonymGenerator -> PatientPseudonym(generator.generate(patientId.value))
|
||||||
else -> "${configProperties.prefix}_${generator.generate(patientId)}"
|
else -> PatientPseudonym("${configProperties.prefix}_${generator.generate(patientId.value)}")
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
fun genomDeTan(patientId: PatientId): String {
|
||||||
|
return generator.generateGenomDeTan(patientId.value)
|
||||||
|
}
|
||||||
|
|
||||||
|
fun prefix(): String {
|
||||||
|
return configProperties.prefix
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
@@ -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) 2024 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
|
||||||
@@ -19,35 +19,296 @@
|
|||||||
|
|
||||||
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.pcvolkmer.mv64e.mtb.ModelProjectConsent
|
||||||
|
import dev.pcvolkmer.mv64e.mtb.Mtb
|
||||||
|
import dev.pcvolkmer.mv64e.mtb.MvhMetadata
|
||||||
|
import org.apache.commons.codec.digest.DigestUtils
|
||||||
|
|
||||||
infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
|
/** Replaces patient ID with generated patient pseudonym
|
||||||
val patientPseudonym = pseudonymizeService.patientPseudonym(this.patient.id)
|
*
|
||||||
|
* @since 0.11.0
|
||||||
|
*
|
||||||
|
* @param pseudonymizeService The pseudonymizeService to be used
|
||||||
|
* @return The MTB file containing patient pseudonymes
|
||||||
|
*/
|
||||||
|
infix fun Mtb.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
|
||||||
|
val patientPseudonym = pseudonymizeService.patientPseudonym(PatientId(this.patient.id)).value
|
||||||
|
|
||||||
this.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 }
|
* Creates new hash of content IDs with given prefix except for patient IDs
|
||||||
this.previousGuidelineTherapies.forEach { it.patient = patientPseudonym }
|
*
|
||||||
this.rebiopsyRequests.forEach { it.patient = patientPseudonym }
|
* @since 0.11.0
|
||||||
this.recommendations.forEach { it.patient = patientPseudonym }
|
*
|
||||||
this.recommendations.forEach { it.patient = patientPseudonym }
|
* @param pseudonymizeService The pseudonymizeService to be used
|
||||||
this.responses.forEach { it.patient = patientPseudonym }
|
* @return The MTB file containing rehashed content IDs
|
||||||
this.studyInclusionRequests.forEach { it.patient = patientPseudonym }
|
*/
|
||||||
this.specimens.forEach { it.patient = patientPseudonym }
|
infix fun Mtb.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
|
||||||
|
val prefix = pseudonymizeService.prefix()
|
||||||
|
|
||||||
|
fun anonymize(id: String): String {
|
||||||
|
val hash = DigestUtils.sha256Hex("$prefix-$id").substring(0, 41).lowercase()
|
||||||
|
return "$prefix$hash"
|
||||||
|
}
|
||||||
|
|
||||||
|
this.episodesOfCare?.forEach {
|
||||||
|
it?.apply { id = id?.let(::anonymize) }
|
||||||
|
it.diagnoses?.forEach { it ->
|
||||||
|
it?.id = it.id?.let(::anonymize)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
this.carePlans?.onEach { carePlan ->
|
||||||
|
carePlan?.apply {
|
||||||
|
id = id?.let { anonymize(it) }
|
||||||
|
|
||||||
|
diagnoses?.forEach { it -> it?.id = it.id?.let(::anonymize) }
|
||||||
|
geneticCounselingRecommendation?.apply {
|
||||||
|
id = geneticCounselingRecommendation.id?.let(::anonymize)
|
||||||
|
}
|
||||||
|
rebiopsyRequests?.forEach { it ->
|
||||||
|
it.id = it.id?.let(::anonymize)
|
||||||
|
it.tumorEntity?.id = it.tumorEntity?.id?.let(::anonymize)
|
||||||
|
}
|
||||||
|
histologyReevaluationRequests?.forEach { it ->
|
||||||
|
it.id = it?.id?.let(::anonymize)
|
||||||
|
it.specimen?.id = it.specimen?.id?.let(::anonymize)
|
||||||
|
}
|
||||||
|
|
||||||
|
medicationRecommendations?.forEach { it ->
|
||||||
|
it.id = it?.id?.let(::anonymize)
|
||||||
|
it.supportingVariants?.forEach { it ->
|
||||||
|
it.variant?.id = it.variant?.id?.let(::anonymize)
|
||||||
|
}
|
||||||
|
it.reason?.id = it.reason?.id?.let(::anonymize)
|
||||||
|
}
|
||||||
|
reason?.id = reason?.id?.let(::anonymize)
|
||||||
|
studyEnrollmentRecommendations?.forEach { it ->
|
||||||
|
it?.reason?.id = it.reason?.id?.let(::anonymize)
|
||||||
|
}
|
||||||
|
|
||||||
|
procedureRecommendations?.forEach { it ->
|
||||||
|
|
||||||
|
it.id = it?.id?.let(::anonymize)
|
||||||
|
it.supportingVariants?.forEach { it ->
|
||||||
|
it.variant?.id = it.variant?.id?.let(::anonymize)
|
||||||
|
}
|
||||||
|
|
||||||
|
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.responses?.forEach { it ->
|
||||||
|
|
||||||
|
it?.id = it.id?.let(::anonymize)
|
||||||
|
it?.therapy?.id = it.therapy?.id?.let(::anonymize)
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
this.diagnoses?.forEach { it ->
|
||||||
|
|
||||||
|
it.id = it?.id?.let(::anonymize)
|
||||||
|
it.histology?.forEach { it -> it.id = it?.id?.let(::anonymize) }
|
||||||
|
}
|
||||||
|
|
||||||
|
this.ngsReports?.forEach { it ->
|
||||||
|
it.id = it?.id?.let(::anonymize)
|
||||||
|
it.results?.tumorCellContent?.id = it.results.tumorCellContent?.id?.let(::anonymize)
|
||||||
|
it.results?.tumorCellContent?.specimen?.id =
|
||||||
|
it.results?.tumorCellContent?.specimen?.id?.let(::anonymize)
|
||||||
|
it.results?.rnaFusions?.forEach { it ->
|
||||||
|
it?.id = it.id?.let(::anonymize)
|
||||||
|
}
|
||||||
|
it.results?.simpleVariants?.forEach { it ->
|
||||||
|
it?.id = it.id?.let(::anonymize)
|
||||||
|
it?.transcriptId?.value = it.transcriptId?.value?.let(::anonymize)
|
||||||
|
}
|
||||||
|
it.results?.tmb?.id = it.results?.tmb?.id?.let(::anonymize)
|
||||||
|
it.results?.tmb?.specimen?.id = it.results?.tmb?.specimen?.id?.let(::anonymize)
|
||||||
|
|
||||||
|
it.results?.brcaness?.id = it.results?.brcaness?.id?.let(::anonymize)
|
||||||
|
it.results?.brcaness?.specimen?.id = it.results?.brcaness?.specimen?.id?.let(::anonymize)
|
||||||
|
it.results?.copyNumberVariants?.forEach { it -> it?.id = it.id?.let(::anonymize) }
|
||||||
|
it.results?.hrdScore?.id = it.results?.hrdScore?.id?.let(::anonymize)
|
||||||
|
it.results?.hrdScore?.specimen?.id = it.results?.hrdScore?.specimen?.id?.let(::anonymize)
|
||||||
|
it.results?.rnaSeqs?.forEach { it -> it?.id = it.id?.let(::anonymize) }
|
||||||
|
it.results?.dnaFusions?.forEach { it -> it?.id = it.id?.let(::anonymize) }
|
||||||
|
it.specimen?.id = it?.specimen?.id?.let(::anonymize)
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
this.histologyReports?.forEach { it ->
|
||||||
|
it.id = it?.id?.let(::anonymize)
|
||||||
|
it.results?.tumorCellContent?.id = it.results?.tumorCellContent?.id?.let(::anonymize)
|
||||||
|
it.results?.tumorCellContent?.specimen?.id =
|
||||||
|
it.results?.tumorCellContent?.specimen?.id?.let(::anonymize)
|
||||||
|
|
||||||
|
it.results?.tumorMorphology?.id = it.results?.tumorMorphology?.id?.let(::anonymize)
|
||||||
|
it.results?.tumorMorphology?.specimen?.id =
|
||||||
|
it.results?.tumorMorphology?.specimen?.id?.let(::anonymize)
|
||||||
|
it.specimen?.id = it.specimen?.id?.let(::anonymize)
|
||||||
|
|
||||||
|
}
|
||||||
|
this.claimResponses?.forEach { it ->
|
||||||
|
it.id = it?.id?.let(::anonymize)
|
||||||
|
it.claim?.id = it.claim?.id?.let(::anonymize)
|
||||||
|
}
|
||||||
|
this.claims?.forEach { it ->
|
||||||
|
|
||||||
|
it.id = it?.id?.let(::anonymize)
|
||||||
|
it.recommendation?.id = it.recommendation?.id?.let(::anonymize)
|
||||||
|
|
||||||
|
}
|
||||||
|
this.familyMemberHistories?.forEach { it -> it.id = it?.id?.let(::anonymize) }
|
||||||
|
this.guidelineProcedures?.forEach { it ->
|
||||||
|
it.id = it?.id?.let(::anonymize)
|
||||||
|
it.reason?.id = it.reason?.id?.let(::anonymize)
|
||||||
|
it.basedOn?.id = it.basedOn?.id?.let(::anonymize)
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
this.guidelineTherapies?.forEach { it ->
|
||||||
|
it.id = it?.id?.let(::anonymize)
|
||||||
|
it.reason?.id = it.reason?.id?.let(::anonymize)
|
||||||
|
it.basedOn?.id = it.basedOn?.id?.let(::anonymize)
|
||||||
|
}
|
||||||
|
this.ihcReports?.forEach { it ->
|
||||||
|
it.id = it?.id?.let(::anonymize)
|
||||||
|
it.specimen?.id = it.specimen?.id?.let(::anonymize)
|
||||||
|
it.results.proteinExpression.forEach { it -> it?.id = it.id.let(::anonymize) }
|
||||||
|
}
|
||||||
|
|
||||||
|
this.msiFindings?.forEach { it ->
|
||||||
|
|
||||||
|
it.id = it?.id?.let(::anonymize)
|
||||||
|
it.specimen?.id = it.specimen?.id?.let(::anonymize)
|
||||||
|
}
|
||||||
|
|
||||||
|
this.performanceStatus?.forEach { it -> it.id = it?.id?.let(::anonymize) }
|
||||||
|
|
||||||
|
this.priorDiagnosticReports?.forEach { it ->
|
||||||
|
|
||||||
|
it.id = it?.id?.let(::anonymize)
|
||||||
|
it.specimen?.id = it.specimen?.id?.let(::anonymize)
|
||||||
|
}
|
||||||
|
|
||||||
|
this.specimens?.forEach { it ->
|
||||||
|
|
||||||
|
it.id = it?.id?.let(::anonymize)
|
||||||
|
it.diagnosis?.id = it.diagnosis?.id?.let(::anonymize)
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
this.systemicTherapies?.forEach { it ->
|
||||||
|
|
||||||
|
it.history?.forEach { it ->
|
||||||
|
|
||||||
|
it.id = it?.id?.let(::anonymize)
|
||||||
|
it.reason?.id = it.reason?.id?.let(::anonymize)
|
||||||
|
it.basedOn?.id = it.basedOn?.id?.let(::anonymize)
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
fun Mtb.ensureMetaDataIsInitialized() {
|
||||||
|
// init metadata if necessary
|
||||||
|
if (this.metadata == null) {
|
||||||
|
val mvhMetadata = MvhMetadata.builder().build()
|
||||||
|
this.metadata = mvhMetadata
|
||||||
|
}
|
||||||
|
if (this.metadata.researchConsents == null) {
|
||||||
|
this.metadata.researchConsents = mutableListOf()
|
||||||
|
}
|
||||||
|
if (this.metadata.modelProjectConsent == null) {
|
||||||
|
this.metadata.modelProjectConsent = ModelProjectConsent()
|
||||||
|
this.metadata.modelProjectConsent.provisions = mutableListOf()
|
||||||
|
} else if (this.metadata.modelProjectConsent.provisions != null) {
|
||||||
|
// make sure list can be changed
|
||||||
|
this.metadata.modelProjectConsent.provisions =
|
||||||
|
this.metadata.modelProjectConsent.provisions.toMutableList()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
infix fun Mtb.addGenomDeTan(pseudonymizeService: PseudonymizeService) {
|
||||||
|
this.metadata.transferTan = pseudonymizeService.genomDeTan(PatientId(this.patient.id))
|
||||||
}
|
}
|
@@ -0,0 +1,92 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of ETL-Processor
|
||||||
|
*
|
||||||
|
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||||
|
*
|
||||||
|
* This program is free software: you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
|
* by the Free Software Foundation, either version 3 of the License, or
|
||||||
|
* (at your option) any later version.
|
||||||
|
*
|
||||||
|
* This program is distributed in the hope that it will be useful,
|
||||||
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
* GNU Affero General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU Affero General Public License
|
||||||
|
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package dev.dnpm.etl.processor.security
|
||||||
|
|
||||||
|
import jakarta.annotation.PostConstruct
|
||||||
|
import org.springframework.data.annotation.Id
|
||||||
|
import org.springframework.data.relational.core.mapping.Table
|
||||||
|
import org.springframework.data.repository.CrudRepository
|
||||||
|
import org.springframework.data.repository.findByIdOrNull
|
||||||
|
import org.springframework.security.core.userdetails.User
|
||||||
|
import org.springframework.security.crypto.password.PasswordEncoder
|
||||||
|
import org.springframework.security.provisioning.InMemoryUserDetailsManager
|
||||||
|
import java.time.Instant
|
||||||
|
import java.util.*
|
||||||
|
|
||||||
|
class TokenService(
|
||||||
|
private val userDetailsManager: InMemoryUserDetailsManager,
|
||||||
|
private val passwordEncoder: PasswordEncoder,
|
||||||
|
private val tokenRepository: TokenRepository
|
||||||
|
) {
|
||||||
|
|
||||||
|
@PostConstruct
|
||||||
|
fun setup() {
|
||||||
|
tokenRepository.findAll().forEach {
|
||||||
|
userDetailsManager.createUser(
|
||||||
|
User.withUsername(it.username)
|
||||||
|
.password(it.password)
|
||||||
|
.roles("MTBFILE")
|
||||||
|
.build()
|
||||||
|
)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
fun addToken(name: String): Result<String> {
|
||||||
|
val username = name.lowercase().replace("""[^a-z0-9]""".toRegex(), "")
|
||||||
|
if (userDetailsManager.userExists(username)) {
|
||||||
|
return Result.failure(RuntimeException("Cannot use token name"))
|
||||||
|
}
|
||||||
|
|
||||||
|
val password = Base64.getEncoder().encodeToString(UUID.randomUUID().toString().encodeToByteArray())
|
||||||
|
val encodedPassword = passwordEncoder.encode(password).toString()
|
||||||
|
|
||||||
|
userDetailsManager.createUser(
|
||||||
|
User.withUsername(username)
|
||||||
|
.password(encodedPassword)
|
||||||
|
.roles("MTBFILE")
|
||||||
|
.build()
|
||||||
|
)
|
||||||
|
|
||||||
|
tokenRepository.save(Token(name = name, username = username, password = encodedPassword))
|
||||||
|
|
||||||
|
return Result.success("$username:$password")
|
||||||
|
}
|
||||||
|
|
||||||
|
fun deleteToken(id: Long) {
|
||||||
|
val token = tokenRepository.findByIdOrNull(id) ?: return
|
||||||
|
userDetailsManager.deleteUser(token.username)
|
||||||
|
tokenRepository.delete(token)
|
||||||
|
}
|
||||||
|
|
||||||
|
fun findAll(): List<Token> {
|
||||||
|
return tokenRepository.findAll().toList()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Table("token")
|
||||||
|
data class Token(
|
||||||
|
@Id val id: Long? = null,
|
||||||
|
val name: String,
|
||||||
|
val username: String,
|
||||||
|
val password: String,
|
||||||
|
val createdAt: Instant = Instant.now()
|
||||||
|
)
|
||||||
|
|
||||||
|
interface TokenRepository : CrudRepository<Token, Long>
|
45
src/main/kotlin/dev/dnpm/etl/processor/security/UserRole.kt
Normal file
45
src/main/kotlin/dev/dnpm/etl/processor/security/UserRole.kt
Normal file
@@ -0,0 +1,45 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of ETL-Processor
|
||||||
|
*
|
||||||
|
* Copyright (C) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||||
|
*
|
||||||
|
* This program is free software: you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
|
* by the Free Software Foundation, either version 3 of the License, or
|
||||||
|
* (at your option) any later version.
|
||||||
|
*
|
||||||
|
* This program is distributed in the hope that it will be useful,
|
||||||
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
* GNU Affero General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU Affero General Public License
|
||||||
|
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
|
package dev.dnpm.etl.processor.security
|
||||||
|
|
||||||
|
import org.springframework.data.annotation.Id
|
||||||
|
import org.springframework.data.relational.core.mapping.Table
|
||||||
|
import org.springframework.data.repository.CrudRepository
|
||||||
|
import java.util.*
|
||||||
|
|
||||||
|
@Table("user_role")
|
||||||
|
data class UserRole(
|
||||||
|
@Id val id: Long? = null,
|
||||||
|
val username: String,
|
||||||
|
var role: Role = Role.GUEST
|
||||||
|
)
|
||||||
|
|
||||||
|
enum class Role(val value: String) {
|
||||||
|
GUEST("guest"),
|
||||||
|
USER("user"),
|
||||||
|
ADMIN("admin")
|
||||||
|
}
|
||||||
|
|
||||||
|
interface UserRoleRepository : CrudRepository<UserRole, Long> {
|
||||||
|
|
||||||
|
fun findByUsername(username: String): Optional<UserRole>
|
||||||
|
|
||||||
|
}
|
@@ -0,0 +1,58 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of ETL-Processor
|
||||||
|
*
|
||||||
|
* Copyright (c) 2024 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||||
|
*
|
||||||
|
* This program is free software: you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
|
* by the Free Software Foundation, either version 3 of the License, or
|
||||||
|
* (at your option) any later version.
|
||||||
|
*
|
||||||
|
* This program is distributed in the hope that it will be useful,
|
||||||
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
* GNU Affero General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU Affero General Public License
|
||||||
|
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package dev.dnpm.etl.processor.security
|
||||||
|
|
||||||
|
import org.springframework.data.repository.findByIdOrNull
|
||||||
|
import org.springframework.security.core.session.SessionRegistry
|
||||||
|
import org.springframework.security.oauth2.core.oidc.user.OidcUser
|
||||||
|
|
||||||
|
class UserRoleService(
|
||||||
|
private val userRoleRepository: UserRoleRepository,
|
||||||
|
private val sessionRegistry: SessionRegistry
|
||||||
|
) {
|
||||||
|
fun updateUserRole(id: Long, role: Role) {
|
||||||
|
val userRole = userRoleRepository.findByIdOrNull(id) ?: return
|
||||||
|
userRole.role = role
|
||||||
|
userRoleRepository.save(userRole)
|
||||||
|
expireSessionFor(userRole.username)
|
||||||
|
}
|
||||||
|
|
||||||
|
fun deleteUserRole(id: Long) {
|
||||||
|
val userRole = userRoleRepository.findByIdOrNull(id) ?: return
|
||||||
|
userRoleRepository.delete(userRole)
|
||||||
|
expireSessionFor(userRole.username)
|
||||||
|
}
|
||||||
|
|
||||||
|
fun findAll(): List<UserRole> {
|
||||||
|
return userRoleRepository.findAll().toList()
|
||||||
|
}
|
||||||
|
|
||||||
|
private fun expireSessionFor(username: String) {
|
||||||
|
sessionRegistry.allPrincipals
|
||||||
|
.filterIsInstance<OidcUser>()
|
||||||
|
.filter { it.preferredUsername == username }
|
||||||
|
.flatMap {
|
||||||
|
sessionRegistry.getAllSessions(it, true)
|
||||||
|
}
|
||||||
|
.onEach {
|
||||||
|
it.expireNow()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
@@ -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
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
@@ -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
|
||||||
@@ -20,16 +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.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.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
|
||||||
@@ -42,34 +54,64 @@ class RequestProcessor(
|
|||||||
private val sender: MtbFileSender,
|
private val sender: MtbFileSender,
|
||||||
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 consentProcessor: ConsentProcessor?
|
||||||
) {
|
) {
|
||||||
|
|
||||||
fun processMtbFile(mtbFile: MtbFile) {
|
private var logger: Logger = LoggerFactory.getLogger("RequestProcessor")
|
||||||
val requestId = UUID.randomUUID().toString()
|
|
||||||
val pid = mtbFile.patient.id
|
|
||||||
|
|
||||||
mtbFile pseudonymizeWith pseudonymizeService
|
fun processMtbFile(mtbFile: Mtb) {
|
||||||
|
processMtbFile(mtbFile, randomRequestId())
|
||||||
|
}
|
||||||
|
|
||||||
val request = MtbFileSender.MtbFileRequest(requestId, transformationService.transform(mtbFile))
|
|
||||||
|
|
||||||
|
fun processMtbFile(mtbFile: Mtb, requestId: RequestId) {
|
||||||
|
val pid = PatientId(extractPatientIdentifier(mtbFile))
|
||||||
|
|
||||||
|
val isConsentOk =
|
||||||
|
consentProcessor != null && consentProcessor.consentGatedCheckAndTryEmbedding(mtbFile) || consentProcessor == null
|
||||||
|
if (isConsentOk) {
|
||||||
|
if (isGenomDeConsented(mtbFile)) {
|
||||||
|
mtbFile addGenomDeTan pseudonymizeService
|
||||||
|
}
|
||||||
|
mtbFile pseudonymizeWith pseudonymizeService
|
||||||
|
mtbFile anonymizeContentWith pseudonymizeService
|
||||||
|
val request = DnpmV2MtbFileRequest(requestId, transformationService.transform(mtbFile))
|
||||||
|
saveAndSend(request, pid)
|
||||||
|
} else {
|
||||||
|
logger.warn("consent check failed file will not be processed further!")
|
||||||
|
applicationEventPublisher.publishEvent(
|
||||||
|
ResponseEvent(
|
||||||
|
requestId, Instant.now(), RequestStatus.NO_CONSENT
|
||||||
|
)
|
||||||
|
)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private fun isGenomDeConsented(mtbFile: Mtb): Boolean {
|
||||||
|
val isModelProjectConsented = mtbFile.metadata?.modelProjectConsent?.provisions?.any { p ->
|
||||||
|
p.purpose == ModelProjectConsentPurpose.SEQUENCING && p.type == ConsentProvision.PERMIT
|
||||||
|
} == true
|
||||||
|
return isModelProjectConsented
|
||||||
|
}
|
||||||
|
|
||||||
|
private fun <T> saveAndSend(request: MtbFileRequest<T>, pid: PatientId) {
|
||||||
requestService.save(
|
requestService.save(
|
||||||
Request(
|
Request(
|
||||||
uuid = requestId,
|
request.requestId,
|
||||||
patientId = request.mtbFile.patient.id,
|
request.patientPseudonym(),
|
||||||
pid = pid,
|
pid,
|
||||||
fingerprint = fingerprint(request.mtbFile),
|
fingerprint(request),
|
||||||
status = RequestStatus.UNKNOWN,
|
RequestType.MTB_FILE,
|
||||||
type = RequestType.MTB_FILE
|
RequestStatus.UNKNOWN
|
||||||
)
|
)
|
||||||
)
|
)
|
||||||
|
|
||||||
if (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
|
||||||
@@ -79,65 +121,78 @@ 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) {
|
||||||
RequestStatus.WARNING -> Optional.of(responseStatus.body)
|
RequestStatus.ERROR, RequestStatus.WARNING -> Optional.of(responseStatus.body)
|
||||||
else -> Optional.empty()
|
else -> Optional.empty()
|
||||||
}
|
}
|
||||||
)
|
)
|
||||||
)
|
)
|
||||||
}
|
}
|
||||||
|
|
||||||
private fun isDuplication(pseudonymizedMtbFile: MtbFile): Boolean {
|
private fun <T> isDuplication(pseudonymizedMtbFileRequest: MtbFileRequest<T>): Boolean {
|
||||||
val lastMtbFileRequestForPatient =
|
val patientPseudonym = when (pseudonymizedMtbFileRequest) {
|
||||||
requestService.lastMtbFileRequestForPatientPseudonym(pseudonymizedMtbFile.patient.id)
|
is DnpmV2MtbFileRequest -> PatientPseudonym(pseudonymizedMtbFileRequest.content.patient.id)
|
||||||
val isLastRequestDeletion = requestService.isLastRequestWithKnownStatusDeletion(pseudonymizedMtbFile.patient.id)
|
}
|
||||||
|
|
||||||
return null != lastMtbFileRequestForPatient
|
val lastMtbFileRequestForPatient =
|
||||||
&& !isLastRequestDeletion
|
requestService.lastMtbFileRequestForPatientPseudonym(patientPseudonym)
|
||||||
&& lastMtbFileRequestForPatient.fingerprint == fingerprint(pseudonymizedMtbFile)
|
val isLastRequestDeletion =
|
||||||
|
requestService.isLastRequestWithKnownStatusDeletion(patientPseudonym)
|
||||||
|
|
||||||
|
return null != lastMtbFileRequestForPatient && !isLastRequestDeletion && lastMtbFileRequestForPatient.fingerprint == fingerprint(
|
||||||
|
pseudonymizedMtbFileRequest
|
||||||
|
)
|
||||||
}
|
}
|
||||||
|
|
||||||
fun processDeletion(patientId: String) {
|
fun processDeletion(patientId: PatientId, isConsented: TtpConsentStatus) {
|
||||||
val requestId = UUID.randomUUID().toString()
|
processDeletion(patientId, randomRequestId(), isConsented)
|
||||||
|
}
|
||||||
|
|
||||||
|
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(
|
||||||
uuid = requestId,
|
requestId,
|
||||||
patientId = patientPseudonym,
|
patientPseudonym,
|
||||||
pid = patientId,
|
patientId,
|
||||||
fingerprint = fingerprint(patientPseudonym),
|
fingerprint(patientPseudonym.value),
|
||||||
status = RequestStatus.UNKNOWN,
|
RequestType.DELETE,
|
||||||
type = RequestType.DELETE
|
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,
|
||||||
patientId = "???",
|
patientPseudonym = emptyPatientPseudonym(),
|
||||||
pid = patientId,
|
pid = patientId,
|
||||||
fingerprint = "",
|
fingerprint = Fingerprint.empty(),
|
||||||
status = RequestStatus.ERROR,
|
status = RequestStatus.ERROR,
|
||||||
type = RequestType.DELETE,
|
type = RequestType.DELETE,
|
||||||
report = Report("Fehler bei der Pseudonymisierung")
|
report = Report("Fehler bei der Pseudonymisierung")
|
||||||
@@ -146,14 +201,18 @@ class RequestProcessor(
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
private fun fingerprint(mtbFile: MtbFile): String {
|
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): String {
|
private fun fingerprint(s: String): Fingerprint {
|
||||||
return Base32().encodeAsString(DigestUtils.sha256(s))
|
return Fingerprint(
|
||||||
.replace("=", "")
|
Base32().encodeAsString(DigestUtils.sha256(s)).replace("=", "").lowercase()
|
||||||
.lowercase()
|
)
|
||||||
}
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
private fun extractPatientIdentifier(mtbFile: Mtb): String = mtbFile.patient.id
|
||||||
|
@@ -19,11 +19,13 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.services
|
package dev.dnpm.etl.processor.services
|
||||||
|
|
||||||
import dev.dnpm.etl.processor.monitoring.Request
|
import dev.dnpm.etl.processor.PatientPseudonym
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestRepository
|
import dev.dnpm.etl.processor.RequestId
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
import dev.dnpm.etl.processor.monitoring.*
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestType
|
import org.springframework.data.domain.Page
|
||||||
|
import org.springframework.data.domain.Pageable
|
||||||
import org.springframework.stereotype.Service
|
import org.springframework.stereotype.Service
|
||||||
|
import java.util.*
|
||||||
|
|
||||||
@Service
|
@Service
|
||||||
class RequestService(
|
class RequestService(
|
||||||
@@ -32,15 +34,32 @@ class RequestService(
|
|||||||
|
|
||||||
fun save(request: Request) = requestRepository.save(request)
|
fun save(request: Request) = requestRepository.save(request)
|
||||||
|
|
||||||
fun allRequestsByPatientPseudonym(patientPseudonym: String) = requestRepository
|
fun findAll(): Iterable<Request> = requestRepository.findAll()
|
||||||
.findAllByPatientIdOrderByProcessedAtDesc(patientPseudonym)
|
|
||||||
|
|
||||||
fun lastMtbFileRequestForPatientPseudonym(patientPseudonym: String) =
|
fun findAll(pageable: Pageable): Page<Request> = requestRepository.findAll(pageable)
|
||||||
|
|
||||||
|
fun findByUuid(uuid: RequestId): Optional<Request> =
|
||||||
|
requestRepository.findByUuidEquals(uuid)
|
||||||
|
|
||||||
|
fun findRequestByPatientId(patientPseudonym: PatientPseudonym, pageable: Pageable): Page<Request> = requestRepository.findRequestByPatientPseudonym(patientPseudonym, pageable)
|
||||||
|
|
||||||
|
fun allRequestsByPatientPseudonym(patientPseudonym: PatientPseudonym) = requestRepository
|
||||||
|
.findAllByPatientPseudonymOrderByProcessedAtDesc(patientPseudonym)
|
||||||
|
|
||||||
|
fun lastMtbFileRequestForPatientPseudonym(patientPseudonym: PatientPseudonym) =
|
||||||
Companion.lastMtbFileRequestForPatientPseudonym(allRequestsByPatientPseudonym(patientPseudonym))
|
Companion.lastMtbFileRequestForPatientPseudonym(allRequestsByPatientPseudonym(patientPseudonym))
|
||||||
|
|
||||||
fun isLastRequestWithKnownStatusDeletion(patientPseudonym: String) =
|
fun isLastRequestWithKnownStatusDeletion(patientPseudonym: PatientPseudonym) =
|
||||||
Companion.isLastRequestWithKnownStatusDeletion(allRequestsByPatientPseudonym(patientPseudonym))
|
Companion.isLastRequestWithKnownStatusDeletion(allRequestsByPatientPseudonym(patientPseudonym))
|
||||||
|
|
||||||
|
fun countStates(): Iterable<CountedState> = requestRepository.countStates()
|
||||||
|
|
||||||
|
fun countDeleteStates(): Iterable<CountedState> = requestRepository.countDeleteStates()
|
||||||
|
|
||||||
|
fun findPatientUniqueStates(): List<CountedState> = requestRepository.findPatientUniqueStates()
|
||||||
|
|
||||||
|
fun findPatientUniqueDeleteStates(): List<CountedState> = requestRepository.findPatientUniqueDeleteStates()
|
||||||
|
|
||||||
companion object {
|
companion object {
|
||||||
|
|
||||||
fun lastMtbFileRequestForPatientPseudonym(allRequests: List<Request>) = allRequests
|
fun lastMtbFileRequestForPatientPseudonym(allRequests: List<Request>) = allRequests
|
||||||
|
@@ -19,8 +19,8 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.services
|
package dev.dnpm.etl.processor.services
|
||||||
|
|
||||||
|
import dev.dnpm.etl.processor.RequestId
|
||||||
import dev.dnpm.etl.processor.monitoring.Report
|
import dev.dnpm.etl.processor.monitoring.Report
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestRepository
|
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||||
import org.slf4j.LoggerFactory
|
import org.slf4j.LoggerFactory
|
||||||
import org.springframework.context.event.EventListener
|
import org.springframework.context.event.EventListener
|
||||||
@@ -31,7 +31,7 @@ import java.util.*
|
|||||||
|
|
||||||
@Service
|
@Service
|
||||||
class ResponseProcessor(
|
class ResponseProcessor(
|
||||||
private val requestRepository: RequestRepository,
|
private val requestService: RequestService,
|
||||||
private val statisticsUpdateProducer: Sinks.Many<Any>
|
private val statisticsUpdateProducer: Sinks.Many<Any>
|
||||||
) {
|
) {
|
||||||
|
|
||||||
@@ -39,7 +39,7 @@ class ResponseProcessor(
|
|||||||
|
|
||||||
@EventListener(classes = [ResponseEvent::class])
|
@EventListener(classes = [ResponseEvent::class])
|
||||||
fun handleResponseEvent(event: ResponseEvent) {
|
fun handleResponseEvent(event: ResponseEvent) {
|
||||||
requestRepository.findByUuidEquals(event.requestUuid).ifPresentOrElse({
|
requestService.findByUuid(event.requestUuid).ifPresentOrElse({
|
||||||
it.processedAt = event.timestamp
|
it.processedAt = event.timestamp
|
||||||
it.status = event.status
|
it.status = event.status
|
||||||
|
|
||||||
@@ -70,13 +70,19 @@ 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
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
requestRepository.save(it)
|
requestService.save(it)
|
||||||
|
|
||||||
statisticsUpdateProducer.emitNext("", Sinks.EmitFailureHandler.FAIL_FAST)
|
statisticsUpdateProducer.emitNext("", Sinks.EmitFailureHandler.FAIL_FAST)
|
||||||
}, {
|
}, {
|
||||||
@@ -87,7 +93,7 @@ class ResponseProcessor(
|
|||||||
}
|
}
|
||||||
|
|
||||||
data class ResponseEvent(
|
data class ResponseEvent(
|
||||||
val requestUuid: String,
|
val requestUuid: RequestId,
|
||||||
val timestamp: Instant,
|
val timestamp: Instant,
|
||||||
val status: RequestStatus,
|
val status: RequestStatus,
|
||||||
val body: Optional<String> = Optional.empty()
|
val body: Optional<String> = Optional.empty()
|
||||||
|
@@ -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> {
|
||||||
|
@@ -22,6 +22,7 @@ package dev.dnpm.etl.processor.services.kafka
|
|||||||
import com.fasterxml.jackson.annotation.JsonAlias
|
import com.fasterxml.jackson.annotation.JsonAlias
|
||||||
import com.fasterxml.jackson.annotation.JsonProperty
|
import com.fasterxml.jackson.annotation.JsonProperty
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
|
import dev.dnpm.etl.processor.RequestId
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||||
import dev.dnpm.etl.processor.output.asRequestStatus
|
import dev.dnpm.etl.processor.output.asRequestStatus
|
||||||
import dev.dnpm.etl.processor.services.ResponseEvent
|
import dev.dnpm.etl.processor.services.ResponseEvent
|
||||||
@@ -47,7 +48,7 @@ class KafkaResponseProcessor(
|
|||||||
Optional.empty()
|
Optional.empty()
|
||||||
}.ifPresentOrElse({ responseBody ->
|
}.ifPresentOrElse({ responseBody ->
|
||||||
val event = ResponseEvent(
|
val event = ResponseEvent(
|
||||||
responseBody.requestId,
|
RequestId(responseBody.requestId),
|
||||||
Instant.ofEpochMilli(data.timestamp()),
|
Instant.ofEpochMilli(data.timestamp()),
|
||||||
responseBody.statusCode.asRequestStatus(),
|
responseBody.statusCode.asRequestStatus(),
|
||||||
when (responseBody.statusCode.asRequestStatus()) {
|
when (responseBody.statusCode.asRequestStatus()) {
|
||||||
|
63
src/main/kotlin/dev/dnpm/etl/processor/types.kt
Normal file
63
src/main/kotlin/dev/dnpm/etl/processor/types.kt
Normal file
@@ -0,0 +1,63 @@
|
|||||||
|
/*
|
||||||
|
* This file is part of ETL-Processor
|
||||||
|
*
|
||||||
|
* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
|
||||||
|
*
|
||||||
|
* This program is free software: you can redistribute it and/or modify
|
||||||
|
* it under the terms of the GNU Affero General Public License as published
|
||||||
|
* by the Free Software Foundation, either version 3 of the License, or
|
||||||
|
* (at your option) any later version.
|
||||||
|
*
|
||||||
|
* This program is distributed in the hope that it will be useful,
|
||||||
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
* GNU Affero General Public License for more details.
|
||||||
|
*
|
||||||
|
* You should have received a copy of the GNU Affero General Public License
|
||||||
|
* along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package dev.dnpm.etl.processor
|
||||||
|
|
||||||
|
import org.springframework.http.MediaType
|
||||||
|
import java.util.*
|
||||||
|
|
||||||
|
class Fingerprint(val value: String) {
|
||||||
|
override fun hashCode() = value.hashCode()
|
||||||
|
|
||||||
|
override fun equals(other: Any?) = other is Fingerprint && other.value == value
|
||||||
|
|
||||||
|
companion object {
|
||||||
|
fun empty() = Fingerprint("")
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@JvmInline
|
||||||
|
value class RequestId(val value: String) {
|
||||||
|
|
||||||
|
fun isBlank() = value.isBlank()
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
fun randomRequestId() = RequestId(UUID.randomUUID().toString())
|
||||||
|
|
||||||
|
@JvmInline
|
||||||
|
value class PatientId(val value: String)
|
||||||
|
|
||||||
|
@JvmInline
|
||||||
|
value class PatientPseudonym(val value: String)
|
||||||
|
|
||||||
|
fun emptyPatientPseudonym() = PatientPseudonym("")
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Custom MediaTypes
|
||||||
|
*
|
||||||
|
* @since 0.11.0
|
||||||
|
*/
|
||||||
|
object CustomMediaType {
|
||||||
|
val APPLICATION_VND_DNPM_V2_MTB_JSON = MediaType("application", "vnd.dnpm.v2.mtb+json")
|
||||||
|
const val APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE = "application/vnd.dnpm.v2.mtb+json"
|
||||||
|
|
||||||
|
val APPLICATION_VND_DNPM_V2_RD_JSON = MediaType("application", "vnd.dnpm.v2.rd+json")
|
||||||
|
const val APPLICATION_VND_DNPM_V2_RD_JSON_VALUE = "application/vnd.dnpm.v2.rd+json"
|
||||||
|
}
|
@@ -19,34 +19,203 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.web
|
package dev.dnpm.etl.processor.web
|
||||||
|
|
||||||
import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
|
import dev.dnpm.etl.processor.monitoring.*
|
||||||
import dev.dnpm.etl.processor.output.MtbFileSender
|
import dev.dnpm.etl.processor.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.UserRole
|
||||||
|
import dev.dnpm.etl.processor.security.Token
|
||||||
|
import dev.dnpm.etl.processor.security.TokenService
|
||||||
import dev.dnpm.etl.processor.services.TransformationService
|
import dev.dnpm.etl.processor.services.TransformationService
|
||||||
|
import dev.dnpm.etl.processor.security.UserRoleService
|
||||||
|
import org.springframework.beans.factory.annotation.Qualifier
|
||||||
|
import org.springframework.http.MediaType
|
||||||
|
import org.springframework.http.codec.ServerSentEvent
|
||||||
import org.springframework.stereotype.Controller
|
import org.springframework.stereotype.Controller
|
||||||
import org.springframework.ui.Model
|
import org.springframework.ui.Model
|
||||||
import org.springframework.web.bind.annotation.GetMapping
|
import org.springframework.web.bind.annotation.*
|
||||||
import org.springframework.web.bind.annotation.RequestMapping
|
import reactor.core.publisher.Flux
|
||||||
|
import reactor.core.publisher.Sinks
|
||||||
|
|
||||||
@Controller
|
@Controller
|
||||||
@RequestMapping(path = ["configs"])
|
@RequestMapping(path = ["configs"])
|
||||||
class ConfigController(
|
class ConfigController(
|
||||||
|
@Qualifier("connectionCheckUpdateProducer")
|
||||||
|
private val connectionCheckUpdateProducer: Sinks.Many<ConnectionCheckResult>,
|
||||||
private val transformationService: TransformationService,
|
private val transformationService: TransformationService,
|
||||||
private val pseudonymGenerator: Generator,
|
private val pseudonymGenerator: Generator,
|
||||||
private val mtbFileSender: MtbFileSender,
|
private val mtbFileSender: MtbFileSender,
|
||||||
private val connectionCheckService: ConnectionCheckService
|
private val connectionCheckServices: List<ConnectionCheckService>,
|
||||||
|
private val tokenService: TokenService?,
|
||||||
|
private val userRoleService: UserRoleService?
|
||||||
) {
|
) {
|
||||||
|
|
||||||
@GetMapping
|
@GetMapping
|
||||||
fun index(model: Model): String {
|
fun index(model: Model): String {
|
||||||
|
val outputConnectionAvailable =
|
||||||
|
connectionCheckServices.filterIsInstance<OutputConnectionCheckService>().firstOrNull()?.connectionAvailable()
|
||||||
|
|
||||||
|
val gPasConnectionAvailable =
|
||||||
|
connectionCheckServices.filterIsInstance<GPasConnectionCheckService>().firstOrNull()?.connectionAvailable()
|
||||||
|
|
||||||
|
val gIcsConnectionAvailable =
|
||||||
|
connectionCheckServices.filterIsInstance<GIcsConnectionCheckService>().firstOrNull()?.connectionAvailable()
|
||||||
|
|
||||||
model.addAttribute("pseudonymGenerator", pseudonymGenerator.javaClass.simpleName)
|
model.addAttribute("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("connectionAvailable", connectionCheckService.connectionAvailable())
|
model.addAttribute("outputConnectionAvailable", outputConnectionAvailable)
|
||||||
|
model.addAttribute("gPasConnectionAvailable", gPasConnectionAvailable)
|
||||||
|
model.addAttribute("gIcsConnectionAvailable", gIcsConnectionAvailable)
|
||||||
|
model.addAttribute("tokensEnabled", tokenService != null)
|
||||||
|
if (tokenService != null) {
|
||||||
|
model.addAttribute("tokens", tokenService.findAll())
|
||||||
|
} else {
|
||||||
|
model.addAttribute("tokens", emptyList<Token>())
|
||||||
|
}
|
||||||
model.addAttribute("transformations", transformationService.getTransformations())
|
model.addAttribute("transformations", transformationService.getTransformations())
|
||||||
|
if (userRoleService != null) {
|
||||||
|
model.addAttribute("userRolesEnabled", true)
|
||||||
|
model.addAttribute("userRoles", userRoleService.findAll())
|
||||||
|
} else {
|
||||||
|
model.addAttribute("userRolesEnabled", false)
|
||||||
|
model.addAttribute("userRoles", emptyList<UserRole>())
|
||||||
|
}
|
||||||
return "configs"
|
return "configs"
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@GetMapping(params = ["outputConnectionAvailable"])
|
||||||
|
fun outputConnectionAvailable(model: Model): String {
|
||||||
|
val outputConnectionAvailable =
|
||||||
|
connectionCheckServices.filterIsInstance<OutputConnectionCheckService>().first().connectionAvailable()
|
||||||
|
|
||||||
|
model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName)
|
||||||
|
model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint())
|
||||||
|
model.addAttribute("outputConnectionAvailable", outputConnectionAvailable)
|
||||||
|
if (tokenService != null) {
|
||||||
|
model.addAttribute("tokensEnabled", true)
|
||||||
|
model.addAttribute("tokens", tokenService.findAll())
|
||||||
|
} else {
|
||||||
|
model.addAttribute("tokens", listOf<Token>())
|
||||||
|
}
|
||||||
|
|
||||||
|
return "configs/outputConnectionAvailable"
|
||||||
|
}
|
||||||
|
|
||||||
|
@GetMapping(params = ["gPasConnectionAvailable"])
|
||||||
|
fun gPasConnectionAvailable(model: Model): String {
|
||||||
|
val gPasConnectionAvailable =
|
||||||
|
connectionCheckServices.filterIsInstance<GPasConnectionCheckService>().firstOrNull()?.connectionAvailable()
|
||||||
|
|
||||||
|
model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName)
|
||||||
|
model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint())
|
||||||
|
model.addAttribute("gPasConnectionAvailable", gPasConnectionAvailable)
|
||||||
|
if (tokenService != null) {
|
||||||
|
model.addAttribute("tokensEnabled", true)
|
||||||
|
model.addAttribute("tokens", tokenService.findAll())
|
||||||
|
} else {
|
||||||
|
model.addAttribute("tokens", listOf<Token>())
|
||||||
|
}
|
||||||
|
|
||||||
|
return "configs/gPasConnectionAvailable"
|
||||||
|
}
|
||||||
|
|
||||||
|
@GetMapping(params = ["gIcsConnectionAvailable"])
|
||||||
|
fun gIcsConnectionAvailable(model: Model): String {
|
||||||
|
val gIcsConnectionAvailable =
|
||||||
|
connectionCheckServices.filterIsInstance<GIcsConnectionCheckService>().firstOrNull()?.connectionAvailable()
|
||||||
|
|
||||||
|
model.addAttribute("mtbFileSender", mtbFileSender.javaClass.simpleName)
|
||||||
|
model.addAttribute("mtbFileEndpoint", mtbFileSender.endpoint())
|
||||||
|
model.addAttribute("gIcsConnectionAvailable", gIcsConnectionAvailable)
|
||||||
|
if (tokenService != null) {
|
||||||
|
model.addAttribute("tokensEnabled", true)
|
||||||
|
model.addAttribute("tokens", tokenService.findAll())
|
||||||
|
} else {
|
||||||
|
model.addAttribute("tokens", listOf<Token>())
|
||||||
|
}
|
||||||
|
|
||||||
|
return "configs/gIcsConnectionAvailable"
|
||||||
|
}
|
||||||
|
|
||||||
|
@PostMapping(path = ["tokens"])
|
||||||
|
fun addToken(@ModelAttribute("name") name: String, model: Model): String {
|
||||||
|
if (tokenService == null) {
|
||||||
|
model.addAttribute("tokensEnabled", false)
|
||||||
|
model.addAttribute("success", false)
|
||||||
|
} else {
|
||||||
|
model.addAttribute("tokensEnabled", true)
|
||||||
|
val result = tokenService.addToken(name)
|
||||||
|
result.onSuccess {
|
||||||
|
model.addAttribute("newTokenValue", it)
|
||||||
|
model.addAttribute("success", true)
|
||||||
|
}
|
||||||
|
result.onFailure {
|
||||||
|
model.addAttribute("success", false)
|
||||||
|
}
|
||||||
|
model.addAttribute("tokens", tokenService.findAll())
|
||||||
|
}
|
||||||
|
|
||||||
|
return "configs/tokens"
|
||||||
|
}
|
||||||
|
|
||||||
|
@DeleteMapping(path = ["tokens/{id}"])
|
||||||
|
fun deleteToken(@PathVariable id: Long, model: Model): String {
|
||||||
|
if (tokenService != null) {
|
||||||
|
tokenService.deleteToken(id)
|
||||||
|
|
||||||
|
model.addAttribute("tokensEnabled", true)
|
||||||
|
model.addAttribute("tokens", tokenService.findAll())
|
||||||
|
} else {
|
||||||
|
model.addAttribute("tokensEnabled", false)
|
||||||
|
model.addAttribute("tokens", listOf<Token>())
|
||||||
|
}
|
||||||
|
return "configs/tokens"
|
||||||
|
}
|
||||||
|
|
||||||
|
@DeleteMapping(path = ["userroles/{id}"])
|
||||||
|
fun deleteUserRole(@PathVariable id: Long, model: Model): String {
|
||||||
|
if (userRoleService != null) {
|
||||||
|
userRoleService.deleteUserRole(id)
|
||||||
|
|
||||||
|
model.addAttribute("userRolesEnabled", true)
|
||||||
|
model.addAttribute("userRoles", userRoleService.findAll())
|
||||||
|
} else {
|
||||||
|
model.addAttribute("userRolesEnabled", false)
|
||||||
|
model.addAttribute("userRoles", emptyList<UserRole>())
|
||||||
|
}
|
||||||
|
return "configs/userroles"
|
||||||
|
}
|
||||||
|
|
||||||
|
@PutMapping(path = ["userroles/{id}"])
|
||||||
|
fun updateUserRole(@PathVariable id: Long, @ModelAttribute("role") role: Role, model: Model): String {
|
||||||
|
if (userRoleService != null) {
|
||||||
|
userRoleService.updateUserRole(id, role)
|
||||||
|
|
||||||
|
model.addAttribute("userRolesEnabled", true)
|
||||||
|
model.addAttribute("userRoles", userRoleService.findAll())
|
||||||
|
} else {
|
||||||
|
model.addAttribute("userRolesEnabled", false)
|
||||||
|
model.addAttribute("userRoles", emptyList<UserRole>())
|
||||||
|
}
|
||||||
|
return "configs/userroles"
|
||||||
|
}
|
||||||
|
|
||||||
|
@GetMapping(path = ["events"], produces = [MediaType.TEXT_EVENT_STREAM_VALUE])
|
||||||
|
@ResponseBody
|
||||||
|
fun events(): Flux<ServerSentEvent<Any>> {
|
||||||
|
return connectionCheckUpdateProducer.asFlux().map {
|
||||||
|
val event = when (it) {
|
||||||
|
is ConnectionCheckResult.KafkaConnectionCheckResult -> "output-connection-check"
|
||||||
|
is ConnectionCheckResult.RestConnectionCheckResult -> "output-connection-check"
|
||||||
|
is ConnectionCheckResult.GPasConnectionCheckResult -> "gpas-connection-check"
|
||||||
|
is ConnectionCheckResult.GIcsConnectionCheckResult -> "gics-connection-check"
|
||||||
|
}
|
||||||
|
|
||||||
|
ServerSentEvent.builder<Any>()
|
||||||
|
.event(event).id("none").data(it)
|
||||||
|
.build()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
@@ -20,9 +20,10 @@
|
|||||||
package dev.dnpm.etl.processor.web
|
package dev.dnpm.etl.processor.web
|
||||||
|
|
||||||
import dev.dnpm.etl.processor.NotFoundException
|
import dev.dnpm.etl.processor.NotFoundException
|
||||||
|
import dev.dnpm.etl.processor.PatientPseudonym
|
||||||
|
import dev.dnpm.etl.processor.RequestId
|
||||||
import dev.dnpm.etl.processor.monitoring.ReportService
|
import dev.dnpm.etl.processor.monitoring.ReportService
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestId
|
import dev.dnpm.etl.processor.services.RequestService
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestRepository
|
|
||||||
import org.springframework.data.domain.Pageable
|
import org.springframework.data.domain.Pageable
|
||||||
import org.springframework.data.domain.Sort
|
import org.springframework.data.domain.Sort
|
||||||
import org.springframework.data.web.PageableDefault
|
import org.springframework.data.web.PageableDefault
|
||||||
@@ -35,13 +36,29 @@ import org.springframework.web.bind.annotation.RequestMapping
|
|||||||
@Controller
|
@Controller
|
||||||
@RequestMapping(path = ["/"])
|
@RequestMapping(path = ["/"])
|
||||||
class HomeController(
|
class HomeController(
|
||||||
private val requestRepository: RequestRepository,
|
private val requestService: RequestService,
|
||||||
private val reportService: ReportService
|
private val reportService: ReportService
|
||||||
) {
|
) {
|
||||||
|
|
||||||
@GetMapping
|
@GetMapping
|
||||||
fun index(@PageableDefault(page = 0, size = 20, sort = ["processedAt"], direction = Sort.Direction.DESC) pageable: Pageable, model: Model): String {
|
fun index(
|
||||||
val requests = requestRepository.findAll(pageable)
|
@PageableDefault(page = 0, size = 20, sort = ["processedAt"], direction = Sort.Direction.DESC) pageable: Pageable,
|
||||||
|
model: Model
|
||||||
|
): String {
|
||||||
|
val requests = requestService.findAll(pageable)
|
||||||
|
model.addAttribute("requests", requests)
|
||||||
|
|
||||||
|
return "index"
|
||||||
|
}
|
||||||
|
|
||||||
|
@GetMapping(path = ["patient/{patientPseudonym}"])
|
||||||
|
fun byPatient(
|
||||||
|
@PathVariable patientPseudonym: PatientPseudonym,
|
||||||
|
@PageableDefault(page = 0, size = 20, sort = ["processedAt"], direction = Sort.Direction.DESC) pageable: Pageable,
|
||||||
|
model: Model
|
||||||
|
): String {
|
||||||
|
val requests = requestService.findRequestByPatientId(patientPseudonym, pageable)
|
||||||
|
model.addAttribute("patientPseudonym", patientPseudonym.value)
|
||||||
model.addAttribute("requests", requests)
|
model.addAttribute("requests", requests)
|
||||||
|
|
||||||
return "index"
|
return "index"
|
||||||
@@ -49,7 +66,7 @@ class HomeController(
|
|||||||
|
|
||||||
@GetMapping(path = ["/report/{id}"])
|
@GetMapping(path = ["/report/{id}"])
|
||||||
fun report(@PathVariable id: RequestId, model: Model): String {
|
fun report(@PathVariable id: RequestId, model: Model): String {
|
||||||
val request = requestRepository.findByUuidEquals(id.toString()).orElse(null) ?: throw NotFoundException()
|
val request = requestService.findByUuid(id).orElse(null) ?: throw NotFoundException()
|
||||||
model.addAttribute("request", request)
|
model.addAttribute("request", request)
|
||||||
model.addAttribute("issues", reportService.deserialize(request.report?.dataQualityReport))
|
model.addAttribute("issues", reportService.deserialize(request.report?.dataQualityReport))
|
||||||
|
|
||||||
|
@@ -19,14 +19,28 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.web
|
package dev.dnpm.etl.processor.web
|
||||||
|
|
||||||
|
import dev.dnpm.etl.processor.config.SecurityConfigProperties
|
||||||
|
import org.springframework.boot.autoconfigure.security.oauth2.client.OAuth2ClientProperties
|
||||||
import org.springframework.stereotype.Controller
|
import org.springframework.stereotype.Controller
|
||||||
|
import org.springframework.ui.Model
|
||||||
import org.springframework.web.bind.annotation.GetMapping
|
import org.springframework.web.bind.annotation.GetMapping
|
||||||
|
|
||||||
@Controller
|
@Controller
|
||||||
class LoginController {
|
class LoginController(
|
||||||
|
private val securityConfigProperties: SecurityConfigProperties?,
|
||||||
|
private val oAuth2ClientProperties: OAuth2ClientProperties?
|
||||||
|
) {
|
||||||
|
|
||||||
@GetMapping(path = ["/login"])
|
@GetMapping(path = ["/login"])
|
||||||
fun login(): String {
|
fun login(model: Model): String {
|
||||||
|
if (securityConfigProperties?.enableOidc == true) {
|
||||||
|
model.addAttribute(
|
||||||
|
"oidcLogins",
|
||||||
|
oAuth2ClientProperties?.registration?.map { (key, value) -> Pair(key, value.clientName) }.orEmpty()
|
||||||
|
)
|
||||||
|
} else {
|
||||||
|
model.addAttribute("oidcLogins", emptyList<Pair<String, String>>())
|
||||||
|
}
|
||||||
return "login"
|
return "login"
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@@ -19,9 +19,10 @@
|
|||||||
|
|
||||||
package dev.dnpm.etl.processor.web
|
package dev.dnpm.etl.processor.web
|
||||||
|
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestRepository
|
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
import dev.dnpm.etl.processor.monitoring.RequestStatus
|
||||||
import dev.dnpm.etl.processor.monitoring.RequestType
|
import dev.dnpm.etl.processor.monitoring.RequestType
|
||||||
|
import dev.dnpm.etl.processor.services.RequestService
|
||||||
|
import org.springframework.beans.factory.annotation.Qualifier
|
||||||
import org.springframework.http.MediaType
|
import org.springframework.http.MediaType
|
||||||
import org.springframework.http.codec.ServerSentEvent
|
import org.springframework.http.codec.ServerSentEvent
|
||||||
import org.springframework.web.bind.annotation.GetMapping
|
import org.springframework.web.bind.annotation.GetMapping
|
||||||
@@ -38,16 +39,17 @@ import java.time.temporal.ChronoUnit
|
|||||||
@RestController
|
@RestController
|
||||||
@RequestMapping(path = ["/statistics"])
|
@RequestMapping(path = ["/statistics"])
|
||||||
class StatisticsRestController(
|
class StatisticsRestController(
|
||||||
|
@Qualifier("statisticsUpdateProducer")
|
||||||
private val statisticsUpdateProducer: Sinks.Many<Any>,
|
private val statisticsUpdateProducer: Sinks.Many<Any>,
|
||||||
private val requestRepository: RequestRepository
|
private val requestService: RequestService
|
||||||
) {
|
) {
|
||||||
|
|
||||||
@GetMapping(path = ["requeststates"])
|
@GetMapping(path = ["requeststates"])
|
||||||
fun requestStates(@RequestParam(required = false, defaultValue = "false") delete: Boolean): List<NameValue> {
|
fun requestStates(@RequestParam(required = false, defaultValue = "false") delete: Boolean): List<NameValue> {
|
||||||
val states = if (delete) {
|
val states = if (delete) {
|
||||||
requestRepository.countDeleteStates()
|
requestService.countDeleteStates()
|
||||||
} else {
|
} else {
|
||||||
requestRepository.countStates()
|
requestService.countStates()
|
||||||
}
|
}
|
||||||
|
|
||||||
return states
|
return states
|
||||||
@@ -77,7 +79,7 @@ class StatisticsRestController(
|
|||||||
}
|
}
|
||||||
|
|
||||||
val formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd").withZone(ZoneId.of("Europe/Berlin"))
|
val formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd").withZone(ZoneId.of("Europe/Berlin"))
|
||||||
val data = requestRepository.findAll()
|
val data = requestService.findAll()
|
||||||
.filter { it.type == requestType }
|
.filter { it.type == requestType }
|
||||||
.filter { it.processedAt.isAfter(Instant.now().minus(30, ChronoUnit.DAYS)) }
|
.filter { it.processedAt.isAfter(Instant.now().minus(30, ChronoUnit.DAYS)) }
|
||||||
.groupBy { formatter.format(it.processedAt) }
|
.groupBy { formatter.format(it.processedAt) }
|
||||||
@@ -113,9 +115,9 @@ class StatisticsRestController(
|
|||||||
@GetMapping(path = ["requestpatientstates"])
|
@GetMapping(path = ["requestpatientstates"])
|
||||||
fun requestPatientStates(@RequestParam(required = false, defaultValue = "false") delete: Boolean): List<NameValue> {
|
fun requestPatientStates(@RequestParam(required = false, defaultValue = "false") delete: Boolean): List<NameValue> {
|
||||||
val states = if (delete) {
|
val states = if (delete) {
|
||||||
requestRepository.findPatientUniqueDeleteStates()
|
requestService.findPatientUniqueDeleteStates()
|
||||||
} else {
|
} else {
|
||||||
requestRepository.findPatientUniqueStates()
|
requestService.findPatientUniqueStates()
|
||||||
}
|
}
|
||||||
|
|
||||||
return states.map {
|
return states.map {
|
||||||
@@ -152,6 +154,10 @@ class StatisticsRestController(
|
|||||||
.build(),
|
.build(),
|
||||||
ServerSentEvent.builder<Any>()
|
ServerSentEvent.builder<Any>()
|
||||||
.event("deleterequestpatientstates").id("none").data(this.requestPatientStates(true))
|
.event("deleterequestpatientstates").id("none").data(this.requestPatientStates(true))
|
||||||
|
.build(),
|
||||||
|
|
||||||
|
ServerSentEvent.builder<Any>()
|
||||||
|
.event("newrequest").id("none").data("newrequest")
|
||||||
.build()
|
.build()
|
||||||
)
|
)
|
||||||
)
|
)
|
||||||
|
@@ -3,17 +3,128 @@ spring:
|
|||||||
compose:
|
compose:
|
||||||
file: ./dev-compose.yml
|
file: ./dev-compose.yml
|
||||||
|
|
||||||
|
security:
|
||||||
|
oauth2:
|
||||||
|
client:
|
||||||
|
registration:
|
||||||
|
custom:
|
||||||
|
client-name: App-Dev
|
||||||
|
client-id: app-dev
|
||||||
|
client-secret: very-secret-ae3f7a-5a9f-1190
|
||||||
|
scope:
|
||||||
|
- openid
|
||||||
|
provider:
|
||||||
|
custom:
|
||||||
|
issuer-uri: https://dnpm.dev/auth/realms/intern
|
||||||
|
user-name-attribute: name
|
||||||
|
|
||||||
|
# kafka:
|
||||||
|
# security:
|
||||||
|
# protocol: "SSL"
|
||||||
|
# ssl:
|
||||||
|
# key-store-type: "PEM"
|
||||||
|
# key-store-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-----
|
||||||
|
# ### For dev/testing purposes only!
|
||||||
|
# key-store-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-----
|
||||||
|
# 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
|
# servers: localhost:9094
|
||||||
response-topic: test_response
|
# group-id: "test1234"
|
||||||
servers: localhost:9094
|
# input-topic: test_input
|
||||||
#security:
|
# output-topic: test_output
|
||||||
# admin-user: admin
|
# output-response-topic: test_response
|
||||||
# admin-password: "{noop}very-secret"
|
security:
|
||||||
|
admin-user: admin
|
||||||
|
admin-password: "{noop}very-secret"
|
||||||
|
enable-oidc: "true"
|
||||||
|
|
||||||
server:
|
server:
|
||||||
port: 8000
|
port: 8000
|
||||||
|
|
||||||
|
|
||||||
|
@@ -6,5 +6,15 @@ spring:
|
|||||||
flyway:
|
flyway:
|
||||||
locations: "classpath:db/migration/{vendor}"
|
locations: "classpath:db/migration/{vendor}"
|
||||||
|
|
||||||
|
web:
|
||||||
|
resources:
|
||||||
|
cache:
|
||||||
|
cachecontrol:
|
||||||
|
max-age: 1d
|
||||||
|
chain:
|
||||||
|
strategy:
|
||||||
|
content:
|
||||||
|
enabled: true
|
||||||
|
paths: /**/*.js,/**/*.css,/**/*.svg,/**/*.jpeg
|
||||||
server:
|
server:
|
||||||
forward-headers-strategy: framework
|
forward-headers-strategy: framework
|
7
src/main/resources/banner.txt
Normal file
7
src/main/resources/banner.txt
Normal file
@@ -0,0 +1,7 @@
|
|||||||
|
__ _ _ _ _
|
||||||
|
_ __ _____ __/ /_ | || | ___ ___| |_| | _ __ _ __ ___ ___ ___ ___ ___ ___ _ __
|
||||||
|
| '_ ` _ \ \ / / '_ \| || |_ / _ \_____ / _ \ __| |_____| '_ \| '__/ _ \ / __/ _ \/ __/ __|/ _ \| '__|
|
||||||
|
| | | | | \ V /| (_) |__ _| __/_____| __/ |_| |_____| |_) | | | (_) | (_| __/\__ \__ \ (_) | |
|
||||||
|
|_| |_| |_|\_/ \___/ |_| \___| \___|\__|_| | .__/|_| \___/ \___\___||___/___/\___/|_|
|
||||||
|
|_|
|
||||||
|
:: mv64e-etl-processor :: ${application.formatted-version}
|
@@ -0,0 +1,8 @@
|
|||||||
|
CREATE TABLE IF NOT EXISTS token
|
||||||
|
(
|
||||||
|
id int auto_increment primary key,
|
||||||
|
name varchar(255) not null,
|
||||||
|
username varchar(255) not null unique,
|
||||||
|
password varchar(255) not null,
|
||||||
|
created_at datetime default utc_timestamp() not null
|
||||||
|
);
|
@@ -0,0 +1,7 @@
|
|||||||
|
CREATE TABLE IF NOT EXISTS user_role
|
||||||
|
(
|
||||||
|
id int auto_increment primary key,
|
||||||
|
username varchar(255) not null unique,
|
||||||
|
role varchar(255) not null,
|
||||||
|
created_at datetime default utc_timestamp() not null
|
||||||
|
);
|
@@ -0,0 +1 @@
|
|||||||
|
ALTER TABLE request RENAME COLUMN patient_id TO patient_pseudonym;
|
@@ -0,0 +1,9 @@
|
|||||||
|
CREATE TABLE IF NOT EXISTS token
|
||||||
|
(
|
||||||
|
id serial,
|
||||||
|
name varchar(255) not null,
|
||||||
|
username varchar(255) not null unique,
|
||||||
|
password varchar(255) not null,
|
||||||
|
created_at timestamp with time zone default now() not null,
|
||||||
|
PRIMARY KEY (id)
|
||||||
|
);
|
@@ -0,0 +1,8 @@
|
|||||||
|
CREATE TABLE IF NOT EXISTS user_role
|
||||||
|
(
|
||||||
|
id serial,
|
||||||
|
username varchar(255) not null unique,
|
||||||
|
role varchar(255) not null,
|
||||||
|
created_at timestamp with time zone default now() not null,
|
||||||
|
PRIMARY KEY (id)
|
||||||
|
);
|
@@ -0,0 +1 @@
|
|||||||
|
ALTER TABLE request RENAME COLUMN patient_id TO patient_pseudonym;
|
45
src/main/resources/static/echarts.min.js
vendored
45
src/main/resources/static/echarts.min.js
vendored
File diff suppressed because one or more lines are too long
@@ -4,14 +4,17 @@ const dateFormat = new Intl.DateTimeFormat('de-DE', dateFormatOptions);
|
|||||||
const dateTimeFormatOptions = { year: 'numeric', month: '2-digit', day: '2-digit', hour: '2-digit', minute: 'numeric', second: 'numeric' };
|
const dateTimeFormatOptions = { year: 'numeric', month: '2-digit', day: '2-digit', hour: '2-digit', minute: 'numeric', second: 'numeric' };
|
||||||
const dateTimeFormat = new Intl.DateTimeFormat('de-DE', dateTimeFormatOptions);
|
const dateTimeFormat = new Intl.DateTimeFormat('de-DE', dateTimeFormatOptions);
|
||||||
|
|
||||||
window.addEventListener('load', () => {
|
const formatTimeElements = () => {
|
||||||
Array.from(document.getElementsByTagName('time')).forEach((timeTag) => {
|
Array.from(document.getElementsByTagName('time')).forEach((timeTag) => {
|
||||||
let date = Date.parse(timeTag.getAttribute('datetime'));
|
let date = Date.parse(timeTag.getAttribute('datetime'));
|
||||||
if (! isNaN(date)) {
|
if (! isNaN(date)) {
|
||||||
timeTag.innerText = dateTimeFormat.format(date);
|
timeTag.innerText = dateTimeFormat.format(date);
|
||||||
}
|
}
|
||||||
});
|
});
|
||||||
});
|
};
|
||||||
|
|
||||||
|
window.addEventListener('load', formatTimeElements);
|
||||||
|
window.addEventListener('htmx:afterRequest', formatTimeElements);
|
||||||
|
|
||||||
function drawPieChart(url, elemId, title, data) {
|
function drawPieChart(url, elemId, title, data) {
|
||||||
if (data) {
|
if (data) {
|
||||||
|
@@ -2,6 +2,8 @@
|
|||||||
--text: #333;
|
--text: #333;
|
||||||
--table-border: rgba(16, 24, 40, .1);
|
--table-border: rgba(16, 24, 40, .1);
|
||||||
|
|
||||||
|
--dark: brightness(.90);
|
||||||
|
|
||||||
--bg-blue: rgb(0, 74, 157);
|
--bg-blue: rgb(0, 74, 157);
|
||||||
--bg-blue-op: rgba(0, 74, 157, .35);
|
--bg-blue-op: rgba(0, 74, 157, .35);
|
||||||
|
|
||||||
@@ -20,6 +22,10 @@
|
|||||||
--bg-gray-op: rgba(112, 128, 144, .35);
|
--bg-gray-op: rgba(112, 128, 144, .35);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
* {
|
||||||
|
font-family: sans-serif;
|
||||||
|
}
|
||||||
|
|
||||||
html {
|
html {
|
||||||
background: linear-gradient(-5deg, var(--bg-blue-op), transparent 10em);
|
background: linear-gradient(-5deg, var(--bg-blue-op), transparent 10em);
|
||||||
min-height: 100vh;
|
min-height: 100vh;
|
||||||
@@ -28,7 +34,6 @@ html {
|
|||||||
|
|
||||||
body {
|
body {
|
||||||
margin: 0 0 5em 0;
|
margin: 0 0 5em 0;
|
||||||
font-family: sans-serif;
|
|
||||||
font-size: .8rem;
|
font-size: .8rem;
|
||||||
color: var(--text);
|
color: var(--text);
|
||||||
|
|
||||||
@@ -40,7 +45,7 @@ body {
|
|||||||
|
|
||||||
nav {
|
nav {
|
||||||
margin: 0 auto;
|
margin: 0 auto;
|
||||||
padding: 2em 0;
|
padding: 1em 0;
|
||||||
|
|
||||||
line-height: 1.5rem;
|
line-height: 1.5rem;
|
||||||
max-width: 1140px;
|
max-width: 1140px;
|
||||||
@@ -48,18 +53,18 @@ nav {
|
|||||||
border-bottom: 1px solid var(--table-border);
|
border-bottom: 1px solid var(--table-border);
|
||||||
}
|
}
|
||||||
|
|
||||||
nav > a.nav-home {
|
nav a.nav-home {
|
||||||
float: left;
|
float: left;
|
||||||
|
|
||||||
color: var(--text);
|
color: var(--text);
|
||||||
line-height: 1.5em;
|
line-height: 1.5em;
|
||||||
text-decoration: none;
|
text-decoration: none;
|
||||||
|
|
||||||
font-size: 1.5em;
|
font-size: 2em;
|
||||||
font-weight: bold;
|
font-weight: bold;
|
||||||
}
|
}
|
||||||
|
|
||||||
nav > a.nav-home > img {
|
nav a.nav-home > img {
|
||||||
width: 1.5em;
|
width: 1.5em;
|
||||||
vertical-align: middle;
|
vertical-align: middle;
|
||||||
}
|
}
|
||||||
@@ -80,6 +85,57 @@ nav > ul > li.login {
|
|||||||
margin: 0 0 0 1em;
|
margin: 0 0 0 1em;
|
||||||
padding: 0 0 0 2em;
|
padding: 0 0 0 2em;
|
||||||
border-left: 1px solid var(--table-border);
|
border-left: 1px solid var(--table-border);
|
||||||
|
line-height: 3.5em;
|
||||||
|
}
|
||||||
|
|
||||||
|
nav > ul > li.login a {
|
||||||
|
text-decoration: none;
|
||||||
|
text-transform: none;
|
||||||
|
padding: 1em;
|
||||||
|
}
|
||||||
|
|
||||||
|
nav .login .user-name {
|
||||||
|
font-weight: bold;
|
||||||
|
}
|
||||||
|
|
||||||
|
nav > ul > li.login > span {
|
||||||
|
display: inline-block;
|
||||||
|
margin: 0 .5em;
|
||||||
|
}
|
||||||
|
|
||||||
|
nav > ul > li.login .user-icon {
|
||||||
|
flex-direction: column;
|
||||||
|
display: inline flex;
|
||||||
|
vertical-align: middle;
|
||||||
|
inline-size: 4em;
|
||||||
|
}
|
||||||
|
|
||||||
|
nav > ul > li.login .user-icon img {
|
||||||
|
margin: 0 0 -1em 0;
|
||||||
|
width: 80%;
|
||||||
|
align-self: center;
|
||||||
|
}
|
||||||
|
|
||||||
|
nav > ul > li.login .user-icon span {
|
||||||
|
padding: 0 .6em;
|
||||||
|
color: white;
|
||||||
|
font-size: .8em;
|
||||||
|
font-weight: bold;
|
||||||
|
border-radius: 4px;
|
||||||
|
line-height: normal;
|
||||||
|
text-align: center;
|
||||||
|
}
|
||||||
|
|
||||||
|
nav > ul > li.login .user-icon span.guest {
|
||||||
|
background: darkslategray;
|
||||||
|
}
|
||||||
|
|
||||||
|
nav > ul > li.login .user-icon span.user {
|
||||||
|
background: darkgreen;
|
||||||
|
}
|
||||||
|
|
||||||
|
nav > ul > li.login .user-icon span.admin {
|
||||||
|
background: darkred;
|
||||||
}
|
}
|
||||||
|
|
||||||
nav li a {
|
nav li a {
|
||||||
@@ -89,10 +145,6 @@ nav li a {
|
|||||||
font-weight: 700;
|
font-weight: 700;
|
||||||
}
|
}
|
||||||
|
|
||||||
nav li.login a {
|
|
||||||
color: var(--bg-red);
|
|
||||||
}
|
|
||||||
|
|
||||||
nav li a:hover {
|
nav li a:hover {
|
||||||
text-decoration: underline;
|
text-decoration: underline;
|
||||||
}
|
}
|
||||||
@@ -202,19 +254,58 @@ form.samplecode-input input:focus-visible {
|
|||||||
background: none;
|
background: none;
|
||||||
}
|
}
|
||||||
|
|
||||||
.login-form form * {
|
.login-form img {
|
||||||
|
margin: 0 auto;
|
||||||
|
width: 4em;
|
||||||
|
display: block;
|
||||||
|
}
|
||||||
|
|
||||||
|
.userrole-form {
|
||||||
|
display: inline-block;
|
||||||
|
}
|
||||||
|
|
||||||
|
.userrole-form form {
|
||||||
|
margin: 0;
|
||||||
|
padding: 0;
|
||||||
|
|
||||||
|
border: none;
|
||||||
|
border-radius: 0;
|
||||||
|
background: none;
|
||||||
|
|
||||||
|
text-align: inherit;
|
||||||
|
}
|
||||||
|
|
||||||
|
.login-form form *,
|
||||||
|
.token-form form * {
|
||||||
padding: 0.5em;
|
padding: 0.5em;
|
||||||
border: 1px solid var(--table-border);
|
border: 1px solid var(--table-border);
|
||||||
border-radius: 3px;
|
border-radius: 3px;
|
||||||
}
|
}
|
||||||
|
|
||||||
.login-form button {
|
.login-form form hr,
|
||||||
|
.token-form form hr,
|
||||||
|
.userrole-form form hr {
|
||||||
|
padding: 0;
|
||||||
|
width: 100%;
|
||||||
|
}
|
||||||
|
|
||||||
|
.login-form button,
|
||||||
|
.login-form a.btn,
|
||||||
|
.token-form button {
|
||||||
margin: 1em 0;
|
margin: 1em 0;
|
||||||
background: var(--bg-blue);
|
background: var(--bg-blue);
|
||||||
color: white;
|
color: white;
|
||||||
border: none;
|
border: none;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
.userrole-form form select {
|
||||||
|
padding: 0.5em;
|
||||||
|
border: none;
|
||||||
|
border-radius: 3px;
|
||||||
|
line-height: 1.2rem;
|
||||||
|
font-size: 0.8rem;
|
||||||
|
}
|
||||||
|
|
||||||
.border {
|
.border {
|
||||||
padding: 1.5em;
|
padding: 1.5em;
|
||||||
border: 1px solid var(--table-border);
|
border: 1px solid var(--table-border);
|
||||||
@@ -237,6 +328,15 @@ table {
|
|||||||
font-family: sans-serif;
|
font-family: sans-serif;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
table.config-table td:first-child {
|
||||||
|
width: 24em;
|
||||||
|
min-width: fit-content;
|
||||||
|
}
|
||||||
|
|
||||||
|
table.config-table td > button:last-of-type {
|
||||||
|
float: right;
|
||||||
|
}
|
||||||
|
|
||||||
.border > table {
|
.border > table {
|
||||||
padding: 0;
|
padding: 0;
|
||||||
border: none;
|
border: none;
|
||||||
@@ -393,7 +493,6 @@ td.clipboard.clipped {
|
|||||||
padding: 4px 8px;
|
padding: 4px 8px;
|
||||||
|
|
||||||
line-height: 1.2rem;
|
line-height: 1.2rem;
|
||||||
vertical-align: middle;
|
|
||||||
|
|
||||||
border: 0 solid transparent;
|
border: 0 solid transparent;
|
||||||
border-radius: 3px;
|
border-radius: 3px;
|
||||||
@@ -405,38 +504,38 @@ td.clipboard.clipped {
|
|||||||
cursor: pointer;
|
cursor: pointer;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
.btn:active,
|
||||||
.btn:hover {
|
.btn:hover {
|
||||||
filter: drop-shadow(1px 2px 2px gray);
|
filter: drop-shadow(0px 1px 1px var(--bg-gray)) var(--dark);
|
||||||
}
|
}
|
||||||
|
|
||||||
.btn:active {
|
.btn:active {
|
||||||
filter: drop-shadow(1px 1px 2px gray);
|
|
||||||
translate: 0 1px;
|
translate: 0 1px;
|
||||||
}
|
}
|
||||||
|
|
||||||
.btn.btn-red {
|
.btn.btn-red {
|
||||||
background: red;
|
background: var(--bg-red);
|
||||||
color: white;
|
color: white;
|
||||||
}
|
}
|
||||||
|
|
||||||
.btn.btn-red:hover, .btn.btn-red:active {
|
|
||||||
background: darkred !important;
|
|
||||||
}
|
|
||||||
|
|
||||||
.btn.btn-blue {
|
.btn.btn-blue {
|
||||||
background: slategray;
|
background: var(--bg-blue);
|
||||||
color: white;
|
color: white;
|
||||||
}
|
}
|
||||||
|
|
||||||
.btn.btn-blue:hover, .btn.btn-blue:active {
|
|
||||||
background: darkslategray !important;
|
|
||||||
}
|
|
||||||
|
|
||||||
.btn.btn-delete:before {
|
.btn.btn-delete:before {
|
||||||
content: '\1F5D1';
|
content: '\1F5D1';
|
||||||
padding: .2rem;
|
padding: .2rem;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
button:disabled,
|
||||||
|
.btn:disabled {
|
||||||
|
background: slategray !important;
|
||||||
|
color: lightgray;
|
||||||
|
filter: none;
|
||||||
|
cursor: default;
|
||||||
|
}
|
||||||
|
|
||||||
input.inline {
|
input.inline {
|
||||||
border: none;
|
border: none;
|
||||||
font-size: 1.1rem;
|
font-size: 1.1rem;
|
||||||
@@ -472,15 +571,24 @@ input.inline:focus-visible {
|
|||||||
font-weight: bold;
|
font-weight: bold;
|
||||||
}
|
}
|
||||||
|
|
||||||
.chart {
|
.charts {
|
||||||
width: calc(100% - 2.4rem - 4px);
|
display: grid;
|
||||||
height: 320px;
|
grid-gap: 1em;
|
||||||
|
grid-template:
|
||||||
display: inline-block;
|
"a b" 28em
|
||||||
|
"c c" 28em / 1fr 1fr;
|
||||||
}
|
}
|
||||||
|
|
||||||
.chart-50pc {
|
.charts > .grid-left {
|
||||||
width: calc(50% - 2.4rem - 4px);
|
grid-area: a;
|
||||||
|
}
|
||||||
|
|
||||||
|
.charts > .grid-right {
|
||||||
|
grid-area: b;
|
||||||
|
}
|
||||||
|
|
||||||
|
.charts > .grid-full {
|
||||||
|
grid-area: c;
|
||||||
}
|
}
|
||||||
|
|
||||||
.connection-display {
|
.connection-display {
|
||||||
@@ -488,7 +596,7 @@ input.inline:focus-visible {
|
|||||||
grid-template-columns: 10em 16em 10em;
|
grid-template-columns: 10em 16em 10em;
|
||||||
place-items: center;
|
place-items: center;
|
||||||
width: fit-content;
|
width: fit-content;
|
||||||
margin: 1em 0;
|
margin: 1em auto;
|
||||||
}
|
}
|
||||||
|
|
||||||
.connection-display > * {
|
.connection-display > * {
|
||||||
@@ -514,10 +622,89 @@ input.inline:focus-visible {
|
|||||||
text-align: center;
|
text-align: center;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
.notification.info {
|
||||||
|
color: var(--bg-blue);
|
||||||
|
}
|
||||||
|
|
||||||
.notification.success {
|
.notification.success {
|
||||||
color: var(--bg-green);
|
color: var(--bg-green);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
.notification.notice {
|
||||||
|
color: var(--bg-yellow);
|
||||||
|
}
|
||||||
|
|
||||||
.notification.error {
|
.notification.error {
|
||||||
color: var(--bg-red);
|
color: var(--bg-red);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
.tab {
|
||||||
|
padding: 1em;
|
||||||
|
border: none;
|
||||||
|
border-radius: 3px 3px 0 0;
|
||||||
|
cursor: pointer;
|
||||||
|
transition: all 0.2s;
|
||||||
|
|
||||||
|
font-weight: bold;
|
||||||
|
}
|
||||||
|
|
||||||
|
.tab:hover,
|
||||||
|
.tab.active {
|
||||||
|
background: var(--bg-gray);
|
||||||
|
color: white;
|
||||||
|
}
|
||||||
|
|
||||||
|
.tabcontent {
|
||||||
|
border: 2px solid var(--bg-gray);
|
||||||
|
border-radius: 0 .5em .5em .5em;
|
||||||
|
display: none;
|
||||||
|
padding: 1em;
|
||||||
|
background: white;
|
||||||
|
}
|
||||||
|
|
||||||
|
.tabcontent.active {
|
||||||
|
display: block;
|
||||||
|
}
|
||||||
|
|
||||||
|
a.reload {
|
||||||
|
display: none;
|
||||||
|
position: absolute;
|
||||||
|
height: 1.2em;
|
||||||
|
width: 1.2em;
|
||||||
|
background: var(--bg-red);
|
||||||
|
border-radius: 50%;
|
||||||
|
|
||||||
|
color: white;
|
||||||
|
text-decoration: none;
|
||||||
|
font-size: .6em;
|
||||||
|
align-content: center;
|
||||||
|
justify-content: center;
|
||||||
|
}
|
||||||
|
|
||||||
|
.new-token {
|
||||||
|
padding: 1em;
|
||||||
|
background: var(--bg-green-op);
|
||||||
|
}
|
||||||
|
|
||||||
|
.new-token > pre {
|
||||||
|
margin: 0;
|
||||||
|
border: 1px solid var(--bg-green);
|
||||||
|
padding: .5em;
|
||||||
|
width: max-content;
|
||||||
|
display: inline-block;
|
||||||
|
}
|
||||||
|
|
||||||
|
.no-token {
|
||||||
|
padding: 1em;
|
||||||
|
background: var(--bg-red-op);
|
||||||
|
}
|
||||||
|
|
||||||
|
.issue-message {
|
||||||
|
font-family: monospace;
|
||||||
|
font-weight: bolder;
|
||||||
|
}
|
||||||
|
|
||||||
|
.issue-path {
|
||||||
|
font-family: monospace;
|
||||||
|
line-height: 1rem;
|
||||||
|
}
|
11
src/main/resources/static/user.svg
Normal file
11
src/main/resources/static/user.svg
Normal file
@@ -0,0 +1,11 @@
|
|||||||
|
<?xml version="1.0" encoding="UTF-8"?>
|
||||||
|
<!-- Created with Inkscape (http://www.inkscape.org/) -->
|
||||||
|
<svg width="24" height="24" version="1.1" viewBox="0 0 6.35 6.35" xmlns="http://www.w3.org/2000/svg">
|
||||||
|
<g transform="matrix(1.2 0 0 1.2 -108.01 -85.977)">
|
||||||
|
<rect x="90.01" y="71.647" width="5.2917" height="5.2917" rx=".96212" fill="#b3b3b3"/>
|
||||||
|
<g transform="matrix(1.6667 0 0 1.6667 -60.888 -47.952)" fill="#fff">
|
||||||
|
<circle cx="92.126" cy="72.802" r=".70556"/>
|
||||||
|
<path d="m91.068 74.598a1.0583 1.0583 0 0 1 1.0583-1.0583 1.0583 1.0583 0 0 1 1.0583 1.0583h-1.0583z"/>
|
||||||
|
</g>
|
||||||
|
</g>
|
||||||
|
</svg>
|
After Width: | Height: | Size: 588 B |
@@ -10,95 +10,121 @@
|
|||||||
<main>
|
<main>
|
||||||
<h1>Konfiguration</h1>
|
<h1>Konfiguration</h1>
|
||||||
|
|
||||||
<section>
|
<div class="tabs">
|
||||||
<h2>🔧 Allgemeine Konfiguration</h2>
|
<button class="tab active" onclick="selectTab(this, 'common');">Allgemeine Informationen</button>
|
||||||
<table>
|
<button class="tab" onclick="selectTab(this, 'security');">Sicherheit</button>
|
||||||
<thead>
|
<button class="tab" onclick="selectTab(this, 'transformation');">Transformationen</button>
|
||||||
<tr>
|
</div>
|
||||||
<th>Name</th>
|
|
||||||
<th>Wert</th>
|
<div id="common" class="tabcontent active">
|
||||||
</tr>
|
<section>
|
||||||
</thead>
|
<h2>🔧 Allgemeine Konfiguration</h2>
|
||||||
<tbody>
|
<table class="config-table">
|
||||||
|
<thead>
|
||||||
<tr>
|
<tr>
|
||||||
<td>Pseudonym erzeugt über</td>
|
<th>Name</th>
|
||||||
<td>[[ ${pseudonymGenerator} ]]</td>
|
<th>Wert</th>
|
||||||
</tr>
|
</tr>
|
||||||
|
</thead>
|
||||||
|
<tbody>
|
||||||
|
<tr>
|
||||||
|
<td>Pseudonym erzeugt über</td>
|
||||||
|
<td>[[ ${pseudonymGenerator} ]]</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td>MTBFile-Sender</td>
|
||||||
|
<td>[[ ${mtbFileSender} ]]</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td th:if="${mtbFileSender.startsWith('Rest')}">REST-Endpunkt</td>
|
||||||
|
<td th:if="${mtbFileSender.startsWith('Kafka')}">Kafka-Broker und Topics</td>
|
||||||
|
<td>[[ ${mtbFileEndpoint} ]]</td>
|
||||||
|
</tr>
|
||||||
|
</tbody>
|
||||||
|
</table>
|
||||||
|
</section>
|
||||||
|
|
||||||
|
<section hx-ext="sse" th:sse-connect="@{/configs/events}">
|
||||||
|
<div th:insert="~{configs/gPasConnectionAvailable.html}" th:hx-get="@{/configs?gPasConnectionAvailable}" hx-trigger="sse:gpas-connection-check">
|
||||||
|
</div>
|
||||||
|
</section>
|
||||||
|
|
||||||
|
<section hx-ext="sse" th:sse-connect="@{/configs/events}">
|
||||||
|
<div th:insert="~{configs/gIcsConnectionAvailable.html}" th:hx-get="@{/configs?gIcsConnectionAvailable}" hx-trigger="sse:gics-connection-check">
|
||||||
|
</div>
|
||||||
|
</section>
|
||||||
|
|
||||||
|
<section hx-ext="sse" th:sse-connect="@{/configs/events}">
|
||||||
|
<div th:insert="~{configs/outputConnectionAvailable.html}" th:hx-get="@{/configs?outputConnectionAvailable}" hx-trigger="sse:output-connection-check">
|
||||||
|
</div>
|
||||||
|
</section>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div id="security" class="tabcontent">
|
||||||
|
<section th:insert="~{configs/tokens.html}">
|
||||||
|
</section>
|
||||||
|
|
||||||
|
<section th:insert="~{configs/userroles.html}">
|
||||||
|
</section>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div id="transformation" class="tabcontent">
|
||||||
|
<section>
|
||||||
|
<h2><span th:if="${not transformations.isEmpty()}">✅</span><span th:if="${transformations.isEmpty()}">⛔</span> Transformationen</h2>
|
||||||
|
|
||||||
|
<h3>Syntax</h3>
|
||||||
|
Hier einige Beispiele zum Syntax des JSON-Path
|
||||||
|
<ul>
|
||||||
|
<li style="padding: 0.6rem 0;"><span class="bg-path">diagnoses[*].icdO3T.version</span>: Ersetze die ICD-O3T-Version in allen Diagnosen, z.B. zur Version der deutschen Übersetzung</li>
|
||||||
|
<li style="padding: 0.6rem 0;"><span class="bg-path">patient.gender</span>: Ersetze das Geschlecht des Patienten, z.B. in das von bwHC verlangte Format</li>
|
||||||
|
</ul>
|
||||||
|
|
||||||
|
<h3>Konfigurierte Transformationen</h3>
|
||||||
|
<th:block th:if="${transformations.isEmpty()}">
|
||||||
|
<p>
|
||||||
|
Keine konfigurierten Transformationen.
|
||||||
|
</p>
|
||||||
|
</th:block>
|
||||||
|
<th:block th:if="${not transformations.isEmpty()}">
|
||||||
|
<p>
|
||||||
|
Hier sehen Sie eine Übersicht der konfigurierten Transformationen.
|
||||||
|
</p>
|
||||||
|
|
||||||
|
<table class="config-table">
|
||||||
|
<thead>
|
||||||
<tr>
|
<tr>
|
||||||
<td>MTBFile-Sender</td>
|
<th>JSON-Path</th>
|
||||||
<td>[[ ${mtbFileSender} ]]</td>
|
<th>Transformation von ⇒ nach</th>
|
||||||
</tr>
|
</tr>
|
||||||
<tr>
|
</thead>
|
||||||
<td th:if="${mtbFileSender.startsWith('Rest')}">REST-Endpunkt</td>
|
<tbody>
|
||||||
<td th:if="${mtbFileSender.startsWith('Kafka')}">Kafka-Broker und Topics</td>
|
<tr th:each="transformation : ${transformations}">
|
||||||
<td>[[ ${mtbFileEndpoint} ]]</td>
|
<td>
|
||||||
|
<span class="bg-path" title="Ersetze Wert(e) an dieser Stelle im MTB-File">[[ ${transformation.path} ]]</span>
|
||||||
|
</td>
|
||||||
|
<td>
|
||||||
|
<span class="bg-from" title="Ersetze immer dann, wenn dieser Wert enthalten ist">[[ ${transformation.existingValue} ]]</span>
|
||||||
|
<strong>⇒</strong>
|
||||||
|
<span class="bg-to" title="Ersetze durch diesen Wert">[[ ${transformation.newValue} ]]</span>
|
||||||
|
</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
</section>
|
</th:block>
|
||||||
|
</section>
|
||||||
<section>
|
</div>
|
||||||
<h2><span th:if="${connectionAvailable}">✅</span><span th:if="${not(connectionAvailable)}">⚡</span> Verbindung zum bwHC-Backend</h2>
|
|
||||||
<div>
|
|
||||||
Verbindung über <code>[[ ${mtbFileSender} ]]</code>. Die Verbindung ist aktuell
|
|
||||||
<strong th:if="${connectionAvailable}" style="color: green">verfügbar.</strong>
|
|
||||||
<strong th:if="${not(connectionAvailable)}" style="color: red">nicht verfügbar.</strong>
|
|
||||||
</div>
|
|
||||||
<div class="connection-display border">
|
|
||||||
<img th:src="@{/server.png}" alt="ETL-Processor" />
|
|
||||||
<span class="connection" th:styleappend="${connectionAvailable ? 'available' : ''}"></span>
|
|
||||||
<img th:if="${mtbFileSender.startsWith('Rest')}" th:src="@{/server.png}" alt="bwHC-Backend" />
|
|
||||||
<img th:if="${mtbFileSender.startsWith('Kafka')}" th:src="@{/kafka.png}" alt="Kafka-Broker" />
|
|
||||||
<span>ETL-Processor</span>
|
|
||||||
<span></span>
|
|
||||||
<span th:if="${mtbFileSender.startsWith('Rest')}">bwHC-Backend</span>
|
|
||||||
<span th:if="${mtbFileSender.startsWith('Kafka')}">Kafka-Broker</span>
|
|
||||||
</div>
|
|
||||||
</section>
|
|
||||||
|
|
||||||
<section>
|
|
||||||
<h2><span th:if="${not transformations.isEmpty()}">✅</span><span th:if="${transformations.isEmpty()}">⛔</span> Transformationen</h2>
|
|
||||||
|
|
||||||
<h3>Syntax</h3>
|
|
||||||
Hier einige Beispiele zum Syntax des JSON-Path
|
|
||||||
<ul>
|
|
||||||
<li style="padding: 0.6rem 0;"><span class="bg-path">diagnoses[*].icdO3T.version</span>: Ersetze die ICD-O3T-Version in allen Diagnosen, z.B. zur Version der deutschen Übersetzung</li>
|
|
||||||
<li style="padding: 0.6rem 0;"><span class="bg-path">patient.gender</span>: Ersetze das Geschlecht des Patienten, z.B. in das von bwHC verlangte Format</li>
|
|
||||||
</ul>
|
|
||||||
|
|
||||||
<h3>Konfigurierte Transformationen</h3>
|
|
||||||
<th:block th:if="${transformations.isEmpty()}">
|
|
||||||
<p>
|
|
||||||
Keine konfigurierten Transformationen.
|
|
||||||
</p>
|
|
||||||
</th:block>
|
|
||||||
<th:block th:if="${not transformations.isEmpty()}">
|
|
||||||
<p>
|
|
||||||
Hier sehen Sie eine Übersicht der konfigurierten Transformationen.
|
|
||||||
</p>
|
|
||||||
|
|
||||||
<table>
|
|
||||||
<thead>
|
|
||||||
<tr>
|
|
||||||
<th>JSON-Path</th>
|
|
||||||
<th>Transformation von ⇒ nach</th>
|
|
||||||
</tr>
|
|
||||||
</thead>
|
|
||||||
<tbody>
|
|
||||||
<tr th:each="transformation : ${transformations}">
|
|
||||||
<td>
|
|
||||||
<span class="bg-path" title="Ersetze Wert(e) an dieser Stelle im MTB-File">[[ ${transformation.path} ]]</span>
|
|
||||||
</td>
|
|
||||||
<td>
|
|
||||||
<span class="bg-from" title="Ersetze immer dann, wenn dieser Wert enthalten ist">[[ ${transformation.existingValue} ]]</span>
|
|
||||||
<strong>⇒</strong>
|
|
||||||
<span class="bg-to" title="Ersetze durch diesen Wert">[[ ${transformation.newValue} ]]</span>
|
|
||||||
</td>
|
|
||||||
</tr>
|
|
||||||
</tbody>
|
|
||||||
</table>
|
|
||||||
</th:block>
|
|
||||||
</section>
|
|
||||||
</main>
|
</main>
|
||||||
|
<script th:src="@{/scripts.js}"></script>
|
||||||
|
<script th:src="@{/webjars/htmx.org/dist/htmx.min.js}"></script>
|
||||||
|
<script th:src="@{/webjars/htmx.org/dist/ext/sse.js}"></script>
|
||||||
|
<script>
|
||||||
|
function selectTab(self, elem) {
|
||||||
|
Array.from(document.getElementsByClassName('tab')).forEach(e => e.className = 'tab');
|
||||||
|
self.className = 'tab active';
|
||||||
|
|
||||||
|
Array.from(document.getElementsByClassName('tabcontent')).forEach(e => e.className = 'tabcontent');
|
||||||
|
document.getElementById(elem).className = 'tabcontent active';
|
||||||
|
}
|
||||||
|
</script>
|
||||||
</body>
|
</body>
|
||||||
</html>
|
</html>
|
@@ -0,0 +1,24 @@
|
|||||||
|
<th:block th:if="${gIcsConnectionAvailable == null}">
|
||||||
|
<h2><span>🟦</span> gICS nicht konfiguriert - Einwilligung wird über Dateiinhalt geprüft</h2>
|
||||||
|
</th:block>
|
||||||
|
<th:block th:if="${gIcsConnectionAvailable != null}">
|
||||||
|
<h2><span th:if="${gIcsConnectionAvailable.available}">✅</span><span th:if="${not(gIcsConnectionAvailable.available)}">⚡</span> Verbindung zu gICS</h2>
|
||||||
|
<div>
|
||||||
|
Stand: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(gIcsConnectionAvailable.timestamp)}" th:text="${#temporals.formatISO(gIcsConnectionAvailable.timestamp)}"></time>
|
||||||
|
|
|
||||||
|
Letzte Änderung: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(gIcsConnectionAvailable.lastChange)}" th:text="${#temporals.formatISO(gIcsConnectionAvailable.lastChange)}"></time>
|
||||||
|
</div>
|
||||||
|
<div>
|
||||||
|
<span>Die Verbindung ist aktuell</span>
|
||||||
|
<strong th:if="${gIcsConnectionAvailable.available}" style="color: green">verfügbar.</strong>
|
||||||
|
<strong th:if="${not(gIcsConnectionAvailable.available)}" style="color: red">nicht verfügbar.</strong>
|
||||||
|
</div>
|
||||||
|
<div class="connection-display border">
|
||||||
|
<img th:src="@{/server.png}" alt="ETL-Processor" />
|
||||||
|
<span class="connection" th:classappend="${gIcsConnectionAvailable.available ? 'available' : ''}"></span>
|
||||||
|
<img th:src="@{/server.png}" alt="gICS" />
|
||||||
|
<span>ETL-Processor</span>
|
||||||
|
<span></span>
|
||||||
|
<span>gICS</span>
|
||||||
|
</div>
|
||||||
|
</th:block>
|
@@ -0,0 +1,24 @@
|
|||||||
|
<th:block th:if="${gPasConnectionAvailable == null}">
|
||||||
|
<h2><span>🟦</span> gPAS nicht konfiguriert - Patienten-IDs werden intern anonymisiert</h2>
|
||||||
|
</th:block>
|
||||||
|
<th:block th:if="${gPasConnectionAvailable != null}">
|
||||||
|
<h2><span th:if="${gPasConnectionAvailable.available}">✅</span><span th:if="${not(gPasConnectionAvailable.available)}">⚡</span> Verbindung zu gPAS</h2>
|
||||||
|
<div>
|
||||||
|
Stand: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(gPasConnectionAvailable.timestamp)}" th:text="${#temporals.formatISO(gPasConnectionAvailable.timestamp)}"></time>
|
||||||
|
|
|
||||||
|
Letzte Änderung: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(gPasConnectionAvailable.lastChange)}" th:text="${#temporals.formatISO(gPasConnectionAvailable.lastChange)}"></time>
|
||||||
|
</div>
|
||||||
|
<div>
|
||||||
|
<span>Die Verbindung ist aktuell</span>
|
||||||
|
<strong th:if="${gPasConnectionAvailable.available}" style="color: green">verfügbar.</strong>
|
||||||
|
<strong th:if="${not(gPasConnectionAvailable.available)}" style="color: red">nicht verfügbar.</strong>
|
||||||
|
</div>
|
||||||
|
<div class="connection-display border">
|
||||||
|
<img th:src="@{/server.png}" alt="ETL-Processor" />
|
||||||
|
<span class="connection" th:classappend="${gPasConnectionAvailable.available ? 'available' : ''}"></span>
|
||||||
|
<img th:src="@{/server.png}" alt="gPAS" />
|
||||||
|
<span>ETL-Processor</span>
|
||||||
|
<span></span>
|
||||||
|
<span>gPAS</span>
|
||||||
|
</div>
|
||||||
|
</th:block>
|
@@ -0,0 +1,27 @@
|
|||||||
|
<th:block th:if="${outputConnectionAvailable == null}">
|
||||||
|
<h2><span>🟦</span> Keine Ausgabenkonfiguration</h2>
|
||||||
|
</th:block>
|
||||||
|
<th:block th:if="${outputConnectionAvailable != null}">
|
||||||
|
<h2><span th:if="${outputConnectionAvailable.available}">✅</span><span th:if="${not(outputConnectionAvailable.available)}">⚡</span> MTB-File Verbindung</h2>
|
||||||
|
<div>
|
||||||
|
Stand: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(outputConnectionAvailable.timestamp)}" th:text="${#temporals.formatISO(outputConnectionAvailable.timestamp)}"></time>
|
||||||
|
|
|
||||||
|
Letzte Änderung: <time style="font-weight: bold" th:datetime="${#temporals.formatISO(outputConnectionAvailable.lastChange)}" th:text="${#temporals.formatISO(outputConnectionAvailable.lastChange)}"></time>
|
||||||
|
</div>
|
||||||
|
<div>
|
||||||
|
Verbindung über <code>[[ ${mtbFileSender} ]]</code>. Die Verbindung ist aktuell
|
||||||
|
<strong th:if="${outputConnectionAvailable.available}" style="color: green">verfügbar.</strong>
|
||||||
|
<strong th:if="${not(outputConnectionAvailable.available)}" style="color: red">nicht verfügbar.</strong>
|
||||||
|
</div>
|
||||||
|
<div class="connection-display border">
|
||||||
|
<img th:src="@{/server.png}" alt="ETL-Processor" />
|
||||||
|
<span class="connection" th:classappend="${outputConnectionAvailable.available ? 'available' : ''}"></span>
|
||||||
|
<img th:if="${mtbFileSender.startsWith('Rest')}" th:src="@{/server.png}" alt="bwHC-Backend" />
|
||||||
|
<img th:if="${mtbFileSender.startsWith('Kafka')}" th:src="@{/kafka.png}" alt="Kafka-Broker" />
|
||||||
|
<span>ETL-Processor</span>
|
||||||
|
<span></span>
|
||||||
|
<span th:if="${mtbFileSender.startsWith('RestBwhc')}">bwHC-Backend</span>
|
||||||
|
<span th:if="${mtbFileSender.startsWith('RestDip')}">DNPM:DIP-Backend</span>
|
||||||
|
<span th:if="${mtbFileSender.startsWith('Kafka')}">Kafka-Broker</span>
|
||||||
|
</div>
|
||||||
|
</th:block>
|
40
src/main/resources/templates/configs/tokens.html
Normal file
40
src/main/resources/templates/configs/tokens.html
Normal file
@@ -0,0 +1,40 @@
|
|||||||
|
<div th:if="${not tokensEnabled}">
|
||||||
|
<h2><span>⛔</span> Tokens</h2>
|
||||||
|
<p>Die Verwendung von Tokens ist nicht aktiviert.</p>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div id="tokens" th:if="${tokensEnabled}">
|
||||||
|
<h2><span>✅</span> Tokens</h2>
|
||||||
|
<div class="border">
|
||||||
|
<div th:if="${tokens.isEmpty()}">Noch keine Tokens vorhanden.</div>
|
||||||
|
<table th:if="${not tokens.isEmpty()}" class="config-table">
|
||||||
|
<thead>
|
||||||
|
<tr>
|
||||||
|
<th>Name</th>
|
||||||
|
<th>Erstellt</th>
|
||||||
|
</tr>
|
||||||
|
</thead>
|
||||||
|
<tbody>
|
||||||
|
<tr th:each="token : ${tokens}">
|
||||||
|
<td>[[ ${token.name} ]]</td>
|
||||||
|
<td>
|
||||||
|
<time th:datetime="${token.createdAt}">[[ ${token.createdAt} ]]</time>
|
||||||
|
<button class="btn btn-red" th:hx-delete="@{/configs/tokens/{id}(id=${token.id})}" hx-target="#tokens">Löschen</button>
|
||||||
|
</td>
|
||||||
|
</tr>
|
||||||
|
</tbody>
|
||||||
|
</table>
|
||||||
|
<div th:if="${newTokenValue != null and success}" class="new-token">
|
||||||
|
Verwendung über HTTP-Basic. Bitte notieren, wird nicht erneut angezeigt: <pre>[[ ${newTokenValue} ]]</pre>
|
||||||
|
</div>
|
||||||
|
<div th:if="${success != null and not success}" class="no-token">
|
||||||
|
Das Token konnte nicht erzeugt werden. Versuchen Sie einen anderen Namen.
|
||||||
|
</div>
|
||||||
|
<div class="token-form">
|
||||||
|
<form th:hx-post="@{/configs/tokens}" hx-target="#tokens">
|
||||||
|
<input placeholder="Token-Name" name="name" required />
|
||||||
|
<button class="btn">Token Erstellen</button>
|
||||||
|
</form>
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
</div>
|
37
src/main/resources/templates/configs/userroles.html
Normal file
37
src/main/resources/templates/configs/userroles.html
Normal file
@@ -0,0 +1,37 @@
|
|||||||
|
<div th:if="${not userRolesEnabled}">
|
||||||
|
<h2><span>⛔</span> Benutzerberechtigungen</h2>
|
||||||
|
<p>Die Verwendung von rollenbasierten Benutzerberechtigungen ist nicht aktiviert.</p>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div id="userroles" th:if="${userRolesEnabled}">
|
||||||
|
<h2><span>✅</span> Benutzerberechtigungen</h2>
|
||||||
|
<div class="border">
|
||||||
|
<div th:if="${userRoles.isEmpty()}">Noch keine Benutzerberechtigungen vorhanden.</div>
|
||||||
|
<table th:if="${not userRoles.isEmpty()}" class="config-table">
|
||||||
|
<thead>
|
||||||
|
<tr>
|
||||||
|
<th>Benutzername</th>
|
||||||
|
<th>Rolle</th>
|
||||||
|
</tr>
|
||||||
|
</thead>
|
||||||
|
<tbody>
|
||||||
|
<tr th:each="userRole : ${userRoles}">
|
||||||
|
<td>[[ ${userRole.username} ]]</td>
|
||||||
|
<td>
|
||||||
|
<div class="userrole-form">
|
||||||
|
<form th:hx-put="@{/configs/userroles/{id}(id=${userRole.id})}" hx-target="#userroles">
|
||||||
|
<select name="role" th:disabled="${#authorization.authentication.getName() == userRole.username}">
|
||||||
|
<option th:selected="${userRole.role.value == 'guest'}" value="GUEST">Gast</option>
|
||||||
|
<option th:selected="${userRole.role.value == 'user'}" value="USER">Benutzer</option>
|
||||||
|
<option th:selected="${userRole.role.value == 'admin'}" value="ADMIN">Administrator</option>
|
||||||
|
</select>
|
||||||
|
<button class="btn btn-blue" th:disabled="${#authorization.authentication.getName() == userRole.username}">Übernehmen</button>
|
||||||
|
</form>
|
||||||
|
</div>
|
||||||
|
<button class="btn btn-red" th:hx-delete="@{/configs/userroles/{id}(id=${userRole.id})}" hx-target="#userroles" th:disabled="${#authorization.authentication.getName() == userRole.username}">Löschen</button>
|
||||||
|
</td>
|
||||||
|
</tr>
|
||||||
|
</tbody>
|
||||||
|
</table>
|
||||||
|
</div>
|
||||||
|
</div>
|
@@ -7,10 +7,12 @@
|
|||||||
<body>
|
<body>
|
||||||
<div th:fragment="nav">
|
<div th:fragment="nav">
|
||||||
<nav>
|
<nav>
|
||||||
<a class="nav-home" th:href="@{/}">
|
<span>
|
||||||
<img th:src="@{/icon.svg}" alt="Icon" />
|
<a class="nav-home" th:href="@{/}">
|
||||||
<span>ETL-Processor</span>
|
<img th:src="@{/icon.svg}" alt="Icon" />
|
||||||
</a>
|
<span>ETL-Processor</span>
|
||||||
|
</a>
|
||||||
|
</span>
|
||||||
<ul>
|
<ul>
|
||||||
<li><a th:href="@{/}">Übersicht</a></li>
|
<li><a th:href="@{/}">Übersicht</a></li>
|
||||||
<li><a th:href="@{/statistics}">Statistiken</a></li>
|
<li><a th:href="@{/statistics}">Statistiken</a></li>
|
||||||
@@ -18,10 +20,19 @@
|
|||||||
<a th:href="@{/configs}">Konfiguration</a>
|
<a th:href="@{/configs}">Konfiguration</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="login" sec:authorize="not isAuthenticated()">
|
<li class="login" sec:authorize="not isAuthenticated()">
|
||||||
<a th:href="@{/login}">Login</a>
|
<a class="btn btn-blue" th:href="@{/login}">Login</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="login" sec:authorize="isAuthenticated()">
|
<li class="login" sec:authorize="isAuthenticated()">
|
||||||
<a th:href="@{/logout}">Abmelden</a>
|
<span>
|
||||||
|
<div class="user-icon">
|
||||||
|
<img th:src="@{/user.svg}" alt="User-Image">
|
||||||
|
<span sec:authorize="hasRole('ADMIN')" class="user-role admin">Admin</span>
|
||||||
|
<span sec:authorize="hasRole('USER')" class="user-role user">User</span>
|
||||||
|
<span sec:authorize="hasRole('GUEST')" class="user-role guest">Guest</span>
|
||||||
|
</div>
|
||||||
|
<span class="user-name" sec:authentication="name">?</span>
|
||||||
|
</span>
|
||||||
|
<a class="btn btn-red" th:href="@{/logout}">Abmelden</a>
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
</nav>
|
</nav>
|
||||||
|
@@ -9,16 +9,34 @@
|
|||||||
<div th:replace="~{fragments.html :: nav}"></div>
|
<div th:replace="~{fragments.html :: nav}"></div>
|
||||||
<main>
|
<main>
|
||||||
|
|
||||||
<h1>Letzte Anfragen</h1>
|
<h1>Alle Anfragen<a id="reload-notify" class="reload" title="Neue Anfragen" th:href="@{/}">⟳</a></h1>
|
||||||
|
|
||||||
<div class="border">
|
<div>
|
||||||
<div class="page-control">
|
<h2 th:if="${patientPseudonym != null}">
|
||||||
|
Betreffend Patienten-Pseudonym <span class="monospace" th:text="${patientPseudonym}">***</span>
|
||||||
|
<a class="btn btn-blue" th:if="${patientPseudonym != null}" th:href="@{/}">Alle anzeigen</a>
|
||||||
|
</h2>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div class="border" th:if="${requests.totalElements == 0}">
|
||||||
|
<div class="notification info">Noch keine Anfragen eingegangen</div>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div class="border" th:if="${requests.totalElements > 0}">
|
||||||
|
<div th:if="${patientPseudonym == null}" class="page-control">
|
||||||
<a id="first-page-link" th:href="@{/(page=${0})}" title="Zum Anfang: Taste W" th:if="${not requests.isFirst()}">⇤</a><a th:if="${requests.isFirst()}">⇤</a>
|
<a id="first-page-link" th:href="@{/(page=${0})}" title="Zum Anfang: Taste W" th:if="${not requests.isFirst()}">⇤</a><a th:if="${requests.isFirst()}">⇤</a>
|
||||||
<a id="prev-page-link" th:href="@{/(page=${requests.getNumber() - 1})}" title="Seite zurück: Taste A" th:if="${not requests.isFirst()}">←</a><a th:if="${requests.isFirst()}">←</a>
|
<a id="prev-page-link" th:href="@{/(page=${requests.getNumber() - 1})}" title="Seite zurück: Taste A" th:if="${not requests.isFirst()}">←</a><a th:if="${requests.isFirst()}">←</a>
|
||||||
<span>Seite [[ ${requests.getNumber() + 1} ]] von [[ ${requests.getTotalPages()} ]]</span>
|
<span>Seite [[ ${requests.getNumber() + 1} ]] von [[ ${requests.getTotalPages()} ]]</span>
|
||||||
<a id="next-page-link" th:href="@{/(page=${requests.getNumber() + 1})}" title="Seite vor: Taste D" th:if="${not requests.isLast()}">→</a><a th:if="${requests.isLast()}">→</a>
|
<a id="next-page-link" th:href="@{/(page=${requests.getNumber() + 1})}" title="Seite vor: Taste D" th:if="${not requests.isLast()}">→</a><a th:if="${requests.isLast()}">→</a>
|
||||||
<a id="last-page-link" th:href="@{/(page=${requests.getTotalPages() - 1})}" title="Zum Ende: Taste S" th:if="${not requests.isLast()}">⇥</a><a th:if="${requests.isLast()}">⇥</a>
|
<a id="last-page-link" th:href="@{/(page=${requests.getTotalPages() - 1})}" title="Zum Ende: Taste S" th:if="${not requests.isLast()}">⇥</a><a th:if="${requests.isLast()}">⇥</a>
|
||||||
</div>
|
</div>
|
||||||
|
<div th:if="${patientPseudonym != null}" class="page-control">
|
||||||
|
<a id="first-page-link" th:href="@{/patient/{patientPseudonym}(patientPseudonym=${patientPseudonym},page=${0})}" title="Zum Anfang: Taste W" th:if="${not requests.isFirst()}">⇤</a><a th:if="${requests.isFirst()}">⇤</a>
|
||||||
|
<a id="prev-page-link" th:href="@{/patient/{patientPseudonym}(patientPseudonym=${patientPseudonym},page=${requests.getNumber() - 1})}" title="Seite zurück: Taste A" th:if="${not requests.isFirst()}">←</a><a th:if="${requests.isFirst()}">←</a>
|
||||||
|
<span>Seite [[ ${requests.getNumber() + 1} ]] von [[ ${requests.getTotalPages()} ]]</span>
|
||||||
|
<a id="next-page-link" th:href="@{/patient/{patientPseudonym}(patientPseudonym=${patientPseudonym},page=${requests.getNumber() + 1})}" title="Seite vor: Taste D" th:if="${not requests.isLast()}">→</a><a th:if="${requests.isLast()}">→</a>
|
||||||
|
<a id="last-page-link" th:href="@{/patient/{patientPseudonym}(patientPseudonym=${patientPseudonym},page=${requests.getTotalPages() - 1})}" title="Zum Ende: Taste S" th:if="${not requests.isLast()}">⇥</a><a th:if="${requests.isLast()}">⇥</a>
|
||||||
|
</div>
|
||||||
<table class="paged">
|
<table class="paged">
|
||||||
<thead>
|
<thead>
|
||||||
<tr>
|
<tr>
|
||||||
@@ -34,16 +52,24 @@
|
|||||||
<td th:if="${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="${request.report}">
|
||||||
<a th:href="@{/report/{id}(id=${request.uuid})}">[[ ${request.uuid} ]]</a>
|
<a th:href="@{/report/{id}(id=${request.uuid})}" sec:authorize="hasRole('USER') or hasRole('ADMIN')">[[ ${request.uuid} ]]</a>
|
||||||
|
<th:block sec:authorize="not (hasRole('USER') or hasRole('ADMIN'))">[[ ${request.uuid} ]]</th:block>
|
||||||
</td>
|
</td>
|
||||||
<td><time th:datetime="${request.processedAt}">[[ ${request.processedAt} ]]</time></td>
|
<td><time th:datetime="${request.processedAt}">[[ ${request.processedAt} ]]</time></td>
|
||||||
<td class="patient-id" sec:authorize="authenticated">[[ ${request.patientId} ]]</td>
|
<td class="patient-id" th:if="${patientPseudonym != null}" sec:authorize="hasRole('USER') or hasRole('ADMIN')">
|
||||||
<td class="patient-id" sec:authorize="not authenticated">***</td>
|
[[ ${request.patientPseudonym} ]]
|
||||||
|
</td>
|
||||||
|
<td class="patient-id" th:if="${patientPseudonym == null}" sec:authorize="hasRole('USER') or hasRole('ADMIN')">
|
||||||
|
<a th:href="@{/patient/{pid}(pid=${request.patientPseudonym})}">[[ ${request.patientPseudonym} ]]</a>
|
||||||
|
</td>
|
||||||
|
<td class="patient-id" sec:authorize="not (hasRole('USER') or hasRole('ADMIN'))">***</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
@@ -68,6 +94,12 @@
|
|||||||
}
|
}
|
||||||
};
|
};
|
||||||
});
|
});
|
||||||
|
|
||||||
|
const eventSource = new EventSource('statistics/events');
|
||||||
|
eventSource.addEventListener('newrequest', event => {
|
||||||
|
console.log(event);
|
||||||
|
document.getElementById('reload-notify').style.display = 'inline-flex';
|
||||||
|
});
|
||||||
</script>
|
</script>
|
||||||
</body>
|
</body>
|
||||||
</html>
|
</html>
|
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user