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8 Commits

Author SHA1 Message Date
p.delpy@dkfz-heidelberg.de
95f4d4eb0c feat: add pscc - fix rebase issues 2025-08-12 13:56:28 +02:00
djuarezgf
ada3226044 Replace hardcoded image: ...:develop references with version variables (#335)
* added: Teiler Dashboard Version

* added: MTBA Version

* added: beam proxy tag version
2025-07-30 11:21:10 +02:00
Paul-Christian Volkmer
a2e7330cee docs: Add ghcr.io to URL list (#321) 2025-07-25 10:58:56 +02:00
Jan
9c8d0ee8f5 fix(dnpm): fix env subsitution (#333) 2025-07-25 10:58:07 +02:00
djuarezgf
fcad7104f0 mtba: fallback to keycloak test server pending migration 2025-07-23 09:53:14 +02:00
djuarezgf
7e13e251f8 feat: migrate PSP to Authentik (#329) 2025-07-22 11:34:49 +02:00
Jan
2cfdc3ac3e feat(dnpm): allow setting custom dnpm image tag (#326) 2025-07-07 15:36:14 +02:00
djuarezgf
43b24c2a62 Fixed: Authentik URL for Opal (#328)
* Fixed: Authentik URL for Opal

* Removed: Unnecessary OIDC config in CCE and BBMRI

* KR with basic auth instead of OIDC
2025-07-07 15:35:54 +02:00
29 changed files with 256 additions and 130 deletions

View File

@@ -85,6 +85,8 @@ The following URLs need to be accessible (prefix with `https://`):
* hub.docker.com
* registry-1.docker.io
* production.cloudflare.docker.com
* GitHub Container Registry - (for use of DNPM:DIP)
* ghcr.io
* To report bridgeheads operational status
* healthchecks.verbis.dkfz.de
* only for DKTK/CCP
@@ -95,7 +97,7 @@ The following URLs need to be accessible (prefix with `https://`):
* only for German Biobank Node
* broker.bbmri.de
> 📝 This URL list is subject to change. Instead of the individual names, we highly recommend whitelisting wildcard domains: *.dkfz.de, github.com, *.docker.com, *.docker.io, *.samply.de, *.bbmri.de.
> 📝 This URL list is subject to change. Instead of the individual names, we highly recommend whitelisting wildcard domains: *.dkfz.de, github.com, *.docker.com, *.docker.io, *.ghcr.io, *.samply.de, *.bbmri.de.
> 📝 Ubuntu's pre-installed uncomplicated firewall (ufw) is known to conflict with Docker, more info [here](https://github.com/chaifeng/ufw-docker).

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@@ -19,7 +19,7 @@ services:
HTTP_RELATIVE_PATH: "/bbmri-teiler"
teiler-dashboard:
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:${TEILER_DASHBOARD_TAG}
container_name: bridgehead-teiler-dashboard
labels:
- "traefik.enable=true"
@@ -32,9 +32,6 @@ services:
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "/bbmri-teiler-backend"
TEILER_DASHBOARD_URL: "/bbmri-teiler-dashboard"
OIDC_URL: "${OIDC_URL}"
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
@@ -42,8 +39,6 @@ services:
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
TEILER_ORCHESTRATOR_URL: "/bbmri-teiler"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/bbmri-teiler"
TEILER_USER: "${OIDC_USER_GROUP}"
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
REPORTER_DEFAULT_TEMPLATE_ID: "bbmri-qb"
EXPORTER_DEFAULT_TEMPLATE_ID: "bbmri"

View File

@@ -35,6 +35,9 @@ case "$PROJECT" in
cce)
#nothing extra to do
;;
pscc)
#nothing extra to do
;;
itcc)
#nothing extra to do
;;

View File

@@ -19,7 +19,7 @@ services:
HTTP_RELATIVE_PATH: "/cce-teiler"
teiler-dashboard:
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:${TEILER_DASHBOARD_TAG}
container_name: bridgehead-teiler-dashboard
labels:
- "traefik.enable=true"
@@ -32,9 +32,6 @@ services:
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "/cce-teiler-backend"
TEILER_DASHBOARD_URL: "/cce-teiler-dashboard"
OIDC_URL: "${OIDC_URL}"
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
@@ -42,8 +39,6 @@ services:
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
TEILER_ORCHESTRATOR_URL: "/cce-teiler"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/cce-teiler"
TEILER_USER: "${OIDC_USER_GROUP}"
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
REPORTER_DEFAULT_TEMPLATE_ID: "cce-qb"
EXPORTER_DEFAULT_TEMPLATE_ID: "cce"

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@@ -25,7 +25,7 @@ services:
APP_CONTEXT_PATH: "/opal"
OPAL_PRIVATE_KEY: "/run/secrets/opal-key.pem"
OPAL_CERTIFICATE: "/run/secrets/opal-cert.pem"
OIDC_URL: "${OIDC_URL}"
OIDC_URL: "${OIDC_PRIVATE_URL}"
OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"

View File

@@ -43,7 +43,7 @@ services:
- "traefik.http.routers.dnpm-auth.tls=true"
dnpm-portal:
image: ghcr.io/dnpm-dip/portal:latest
image: ghcr.io/dnpm-dip/portal:${DNPM_IMAGE_TAG:-latest}
container_name: bridgehead-dnpm-portal
environment:
- NUXT_API_URL=http://dnpm-backend:9000/
@@ -58,7 +58,7 @@ services:
dnpm-backend:
container_name: bridgehead-dnpm-backend
image: ghcr.io/dnpm-dip/backend:latest
image: ghcr.io/dnpm-dip/backend:${DNPM_IMAGE_TAG:-latest}
environment:
- LOCAL_SITE=${ZPM_SITE}:${SITE_NAME} # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
- RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}

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@@ -14,6 +14,7 @@ services:
MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_READ_APIKEY}
MAGICPL_CENTRAL_PATIENTLIST_APIKEY: ${IDMANAGER_CENTRAL_PATIENTLIST_APIKEY}
MAGICPL_CONTROLNUMBERGENERATOR_APIKEY: ${IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY}
MAGICPL_OIDC_PROVIDER: ${OIDC_PRIVATE_URL}
depends_on:
- patientlist
- traefik-forward-auth
@@ -71,12 +72,14 @@ services:
- https_proxy=http://forward_proxy:3128
- OAUTH2_PROXY_PROVIDER=oidc
- OAUTH2_PROXY_SKIP_PROVIDER_BUTTON=true
- OAUTH2_PROXY_OIDC_ISSUER_URL=https://login.verbis.dkfz.de/realms/master
- OAUTH2_PROXY_CLIENT_ID=bridgehead-${SITE_ID}
- OAUTH2_PROXY_CLIENT_SECRET=${IDMANAGER_AUTH_CLIENT_SECRET}
- OAUTH2_PROXY_OIDC_ISSUER_URL=${OIDC_PRIVATE_URL}
- OAUTH2_PROXY_CLIENT_ID=${OIDC_PRIVATE_CLIENT_ID}
- OAUTH2_PROXY_CLIENT_SECRET=${OIDC_CLIENT_SECRET}
- OAUTH2_PROXY_COOKIE_SECRET=${IDMANAGER_AUTH_COOKIE_SECRET}
- OAUTH2_PROXY_COOKIE_NAME=_BRIDGEHEAD_oauth2_idm
- OAUTH2_PROXY_COOKIE_DOMAINS=.${HOST}
- OAUTH2_PROXY_COOKIE_REFRESH=4m
- OAUTH2_PROXY_COOKIE_EXPIRE=24h
- OAUTH2_PROXY_HTTP_ADDRESS=:4180
- OAUTH2_PROXY_REVERSE_PROXY=true
- OAUTH2_PROXY_WHITELIST_DOMAINS=.${HOST}
@@ -87,8 +90,8 @@ services:
- OAUTH2_PROXY_SET_AUTHORIZATION_HEADER=true
- OAUTH2_PROXY_SET_XAUTHREQUEST=true
# Keycloak has an expiration time of 60s therefore oauth2-proxy needs to refresh after that
- OAUTH2_PROXY_COOKIE_REFRESH=60s
- OAUTH2_PROXY_ALLOWED_GROUPS=DKTK-CCP-PPSN
- OAUTH2_PROXY_ALLOWED_GROUPS=${OIDC_PSP_GROUP}
- OAUTH2_PROXY_OIDC_GROUPS_CLAIM=${OIDC_GROUP_CLAIM}
- OAUTH2_PROXY_PROXY_PREFIX=/oauth2-idm
labels:
- "traefik.enable=true"

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@@ -14,6 +14,8 @@ function idManagementSetup() {
# Ensure old ids are working !!!
export IDMANAGEMENT_FRIENDLY_ID=$(legacyIdMapping "$SITE_ID")
add_private_oidc_redirect_url "/oauth2-idm/callback"
fi
}

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@@ -2,7 +2,7 @@ version: "3.7"
services:
mtba:
image: docker.verbis.dkfz.de/cache/samply/mtba:develop
image: docker.verbis.dkfz.de/cache/samply/mtba:${MTBA_TAG}
container_name: bridgehead-mtba
environment:
BLAZE_STORE_URL: http://blaze:8080
@@ -22,8 +22,14 @@ services:
HTTP_RELATIVE_PATH: "/mtba"
OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
OIDC_URL: "${OIDC_URL}"
# TODO: Add following variables after moving to Authentik:
#OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
#OIDC_URL: "${OIDC_URL}"
# TODO: Remove following variables after moving to Authentik:
# Please add KECLOAK_CLIENT_SECRET in ccp.conf
OIDC_CLIENT_SECRET: "${KEYCLOAK_CLIENT_SECRET}"
OIDC_URL: "https://login.verbis.dkfz.de/realms/test-realm-01"
OIDC_ADMIN_URL: "https://login.verbis.dkfz.de/admin/realms/test-realm-01"
labels:
- "traefik.enable=true"

View File

@@ -19,7 +19,7 @@ services:
HTTP_RELATIVE_PATH: "/ccp-teiler"
teiler-dashboard:
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:${TEILER_DASHBOARD_TAG}
container_name: bridgehead-teiler-dashboard
labels:
- "traefik.enable=true"

View File

@@ -10,9 +10,11 @@ BROKER_URL_FOR_PREREQ=$BROKER_URL
OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"
OIDC_PSP_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_PSP"
OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
OIDC_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PUBLIC_CLIENT_ID}/"
OIDC_PRIVATE_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PRIVATE_CLIENT_ID}/"
OIDC_GROUP_CLAIM="groups"
for module in $PROJECT/modules/*.sh

View File

@@ -39,7 +39,7 @@ services:
- "blaze"
beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
container_name: bridgehead-beam-proxy
environment:
BROKER_URL: ${BROKER_URL}

View File

@@ -40,7 +40,7 @@ services:
- "blaze"
beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
container_name: bridgehead-beam-proxy
environment:
BROKER_URL: ${BROKER_URL}

View File

@@ -1,9 +1,10 @@
version: "3.7"
services:
exporter:
image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
container_name: bridgehead-ccp-exporter
container_name: bridgehead-kr-exporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO"
@@ -12,39 +13,51 @@ services:
EXPORTER_DB_USER: "exporter"
EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
HTTP_RELATIVE_PATH: "/ccp-exporter"
HTTP_RELATIVE_PATH: "/kr-exporter"
SITE: "${SITE_ID}"
HTTP_SERVLET_REQUEST_SCHEME: "https"
OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
labels:
- "traefik.enable=true"
- "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
- "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092"
- "traefik.http.routers.exporter_ccp.tls=true"
- "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
- "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
- "traefik.http.routers.exporter_kr.rule=PathPrefix(`/kr-exporter`)"
- "traefik.http.services.exporter_kr.loadbalancer.server.port=8092"
- "traefik.http.routers.exporter_kr.tls=true"
- "traefik.http.middlewares.exporter_kr_strip.stripprefix.prefixes=/kr-exporter"
- "traefik.http.routers.exporter_kr.middlewares=exporter_kr_strip"
# Main router
- "traefik.http.routers.exporter_kr.priority=20"
# API router
- "traefik.http.routers.exporter_kr_api.middlewares=exporter_kr_strip,exporter_auth"
- "traefik.http.routers.exporter_kr_api.rule=PathRegexp(`/kr-exporter/.+`)"
- "traefik.http.routers.exporter_kr_api.tls=true"
- "traefik.http.routers.exporter_kr_api.priority=25"
# Shared middlewares
- "traefik.http.middlewares.exporter_auth.basicauth.users=${EXPORTER_USER}"
volumes:
- "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
- "/var/cache/bridgehead/kr/exporter-files:/app/exporter-files/output"
exporter-db:
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
container_name: bridgehead-ccp-exporter-db
container_name: bridgehead-kr-exporter-db
environment:
POSTGRES_USER: "exporter"
POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
POSTGRES_DB: "exporter"
volumes:
# Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
- "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data"
- "/var/cache/bridgehead/kr/exporter-db:/var/lib/postgresql/data"
reporter:
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
container_name: bridgehead-ccp-reporter
container_name: bridgehead-kr-reporter
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO"
CROSS_ORIGINS: "https://${HOST}"
HTTP_RELATIVE_PATH: "/ccp-reporter"
HTTP_RELATIVE_PATH: "/kr-reporter"
SITE: "${SITE_ID}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
EXPORTER_URL: "http://exporter:8092"
@@ -52,16 +65,23 @@ services:
HTTP_SERVLET_REQUEST_SCHEME: "https"
# In this initial development state of the bridgehead, we are trying to have so many volumes as possible.
# However, in the first executions in the CCP sites, this volume seems to be very important. A report is
# However, in the first executions in the kr sites, this volume seems to be very important. A report is
# a process that can take several hours, because it depends on the exporter.
# There is a risk that the bridgehead restarts, losing the already created export.
volumes:
- "/var/cache/bridgehead/ccp/reporter-files:/app/reports"
- "/var/cache/bridgehead/kr/reporter-files:/app/reports"
labels:
- "traefik.enable=true"
- "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)"
- "traefik.http.services.reporter_ccp.loadbalancer.server.port=8095"
- "traefik.http.routers.reporter_ccp.tls=true"
- "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter"
- "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip"
- "traefik.http.routers.reporter_kr.rule=PathPrefix(`/kr-reporter`)"
- "traefik.http.services.reporter_kr.loadbalancer.server.port=8095"
- "traefik.http.routers.reporter_kr.tls=true"
- "traefik.http.middlewares.reporter_kr_strip.stripprefix.prefixes=/kr-reporter"
- "traefik.http.routers.reporter_kr.middlewares=reporter_kr_strip"
- "traefik.http.routers.reporter_kr.priority=20"
- "traefik.http.routers.reporter_kr_api.middlewares=reporter_kr_strip,exporter_auth"
- "traefik.http.routers.reporter_kr_api.rule=PathRegexp(`/kr-reporter/.+`)"
- "traefik.http.routers.reporter_kr_api.tls=true"
- "traefik.http.routers.reporter_kr_api.priority=25"

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@@ -1,15 +0,0 @@
# Exporter and Reporter
## Exporter
The exporter is a REST API that exports the data of the different databases of the bridgehead in a set of tables.
It can accept different output formats as CSV, Excel, JSON or XML. It can also export data into Opal.
## Exporter-DB
It is a database to save queries for its execution in the exporter.
The exporter manages also the different executions of the same query in through the database.
## Reporter
This component is a plugin of the exporter that allows to create more complex Excel reports described in templates.
It is compatible with different template engines as Groovy, Thymeleaf,...
It is perfect to generate a document as our traditional CCP quality report.

View File

@@ -7,73 +7,58 @@ services:
container_name: bridgehead-teiler-orchestrator
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_orchestrator_ccp.rule=PathPrefix(`/ccp-teiler`)"
- "traefik.http.services.teiler_orchestrator_ccp.loadbalancer.server.port=9000"
- "traefik.http.routers.teiler_orchestrator_ccp.tls=true"
- "traefik.http.middlewares.teiler_orchestrator_ccp_strip.stripprefix.prefixes=/ccp-teiler"
- "traefik.http.routers.teiler_orchestrator_ccp.middlewares=teiler_orchestrator_ccp_strip"
- "traefik.http.routers.teiler_orchestrator_kr.rule=PathPrefix(`/kr-teiler`)"
- "traefik.http.services.teiler_orchestrator_kr.loadbalancer.server.port=9000"
- "traefik.http.routers.teiler_orchestrator_kr.tls=true"
- "traefik.http.middlewares.teiler_orchestrator_kr_strip.stripprefix.prefixes=/kr-teiler"
- "traefik.http.routers.teiler_orchestrator_kr.middlewares=teiler_orchestrator_kr_strip"
environment:
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
TEILER_BACKEND_URL: "/kr-teiler-backend"
TEILER_DASHBOARD_URL: "/kr-teiler-dashboard"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
HTTP_RELATIVE_PATH: "/ccp-teiler"
HTTP_RELATIVE_PATH: "/kr-teiler"
teiler-dashboard:
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:${TEILER_DASHBOARD_TAG}
container_name: bridgehead-teiler-dashboard
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_dashboard_ccp.rule=PathPrefix(`/ccp-teiler-dashboard`)"
- "traefik.http.services.teiler_dashboard_ccp.loadbalancer.server.port=80"
- "traefik.http.routers.teiler_dashboard_ccp.tls=true"
- "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard"
- "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
- "traefik.http.routers.teiler_dashboard_kr.rule=PathPrefix(`/kr-teiler-dashboard`)"
- "traefik.http.services.teiler_dashboard_kr.loadbalancer.server.port=80"
- "traefik.http.routers.teiler_dashboard_kr.tls=true"
- "traefik.http.middlewares.teiler_dashboard_kr_strip.stripprefix.prefixes=/kr-teiler-dashboard"
- "traefik.http.routers.teiler_dashboard_kr.middlewares=teiler_dashboard_kr_strip"
environment:
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
OIDC_URL: "${OIDC_URL}"
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}"
TEILER_BACKEND_URL: "/kr-teiler-backend"
TEILER_DASHBOARD_URL: "/kr-teiler-dashboard"
TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
TEILER_PROJECT: "${PROJECT}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
TEILER_USER: "${OIDC_USER_GROUP}"
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
TEILER_ORCHESTRATOR_URL: "/kr-teiler"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/kr-teiler"
REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
teiler-backend:
image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest
image: docker.verbis.dkfz.de/ccp/kr-teiler-backend:latest
container_name: bridgehead-teiler-backend
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_backend_ccp.rule=PathPrefix(`/ccp-teiler-backend`)"
- "traefik.http.services.teiler_backend_ccp.loadbalancer.server.port=8085"
- "traefik.http.routers.teiler_backend_ccp.tls=true"
- "traefik.http.middlewares.teiler_backend_ccp_strip.stripprefix.prefixes=/ccp-teiler-backend"
- "traefik.http.routers.teiler_backend_ccp.middlewares=teiler_backend_ccp_strip"
- "traefik.http.routers.teiler_backend_kr.rule=PathPrefix(`/kr-teiler-backend`)"
- "traefik.http.services.teiler_backend_kr.loadbalancer.server.port=8085"
- "traefik.http.routers.teiler_backend_kr.tls=true"
- "traefik.http.middlewares.teiler_backend_kr_strip.stripprefix.prefixes=/kr-teiler-backend"
- "traefik.http.routers.teiler_backend_kr.middlewares=teiler_backend_kr_strip"
environment:
LOG_LEVEL: "INFO"
APPLICATION_PORT: "8085"
APPLICATION_ADDRESS: "${HOST}"
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
CONFIG_ENV_VAR_PATH: "/run/secrets/ccp.conf"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/kr-teiler"
TEILER_ORCHESTRATOR_URL: "/kr-teiler"
TEILER_DASHBOARD_DE_URL: "/kr-teiler-dashboard/de"
TEILER_DASHBOARD_EN_URL: "/kr-teiler-dashboard/en"
HTTP_PROXY: "http://forward_proxy:3128"
ENABLE_MTBA: "${ENABLE_MTBA}"
ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
secrets:
- ccp.conf
secrets:
ccp.conf:
file: /etc/bridgehead/ccp.conf

View File

@@ -3,7 +3,6 @@
if [ "$ENABLE_TEILER" == true ];then
log INFO "Teiler setup detected -- will start Teiler services."
OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
TEILER_DEFAULT_LANGUAGE=DE
TEILER_DEFAULT_LANGUAGE=EN
TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,}
add_public_oidc_redirect_url "/ccp-teiler/*"
fi

View File

@@ -1,19 +0,0 @@
# Teiler
This module orchestrates the different microfrontends of the bridgehead as a single page application.
## Teiler Orchestrator
Single SPA component that consists on the root HTML site of the single page application and a javascript code that
gets the information about the microfrontend calling the teiler backend and is responsible for registering them. With the
resulting mapping, it can initialize, mount and unmount the required microfrontends on the fly.
The microfrontends run independently in different containers and can be based on different frameworks (Angular, Vue, React,...)
This microfrontends can run as single alone but need an extension with Single-SPA (https://single-spa.js.org/docs/ecosystem).
There are also available three templates (Angular, Vue, React) to be directly extended to be used directly in the teiler.
## Teiler Dashboard
It consists on the main dashboard and a set of embedded services.
### Login
user and password in ccp.local.conf
## Teiler Backend
In this component, the microfrontends are configured.

View File

@@ -55,6 +55,9 @@ case "$PROJECT" in
cce)
site_configuration_repository_middle="git.verbis.dkfz.de/cce-sites/"
;;
pscc)
site_configuration_repository_middle="git.verbis.dkfz.de/pscc-sites/"
;;
itcc)
site_configuration_repository_middle="git.verbis.dkfz.de/itcc-sites/"
;;

View File

@@ -59,3 +59,4 @@ services:
PROJECT: ${PROJECT}
SITE_NAME: ${SITE_NAME}
ENVIRONMENT: ${ENVIRONMENT}
profiles: [deactivated]

View File

@@ -43,7 +43,7 @@ services:
- "traefik.http.routers.dnpm-auth.tls=true"
dnpm-portal:
image: ghcr.io/dnpm-dip/portal:latest
image: ghcr.io/dnpm-dip/portal:${DNPM_IMAGE_TAG:-latest}
container_name: bridgehead-dnpm-portal
environment:
- NUXT_API_URL=http://dnpm-backend:9000/
@@ -58,7 +58,7 @@ services:
dnpm-backend:
container_name: bridgehead-dnpm-backend
image: ghcr.io/dnpm-dip/backend:latest
image: ghcr.io/dnpm-dip/backend:${DNPM_IMAGE_TAG:-latest}
environment:
- LOCAL_SITE=${ZPM_SITE}:${SITE_NAME} # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
- RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}

65
pscc/docker-compose.yml Normal file
View File

@@ -0,0 +1,65 @@
version: "3.7"
services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-pscc-blaze
environment:
BASE_URL: "http://bridgehead-pscc-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"
labels:
- "traefik.enable=true"
- "traefik.http.routers.blaze_pscc.rule=PathPrefix(`/pscc-localdatamanagement`)"
- "traefik.http.middlewares.pscc_b_strip.stripprefix.prefixes=/pscc-localdatamanagement"
- "traefik.http.services.blaze_pscc.loadbalancer.server.port=8080"
- "traefik.http.routers.blaze_pscc.middlewares=pscc_b_strip,auth"
- "traefik.http.routers.blaze_pscc.tls=true"
focus:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
container_name: bridgehead-focus
environment:
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
BEAM_APP_ID_LONG: focus.${PROXY_ID}
PROXY_ID: ${PROXY_ID}
BLAZE_URL: "http://bridgehead-pscc-blaze:8080/fhir/"
BEAM_PROXY_URL: http://beam-proxy:8081
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
EPSILON: 0.28
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
depends_on:
- "beam-proxy"
- "blaze"
beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
container_name: bridgehead-beam-proxy
environment:
BROKER_URL: ${BROKER_URL}
PROXY_ID: ${PROXY_ID}
APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
PRIVKEY_FILE: /run/secrets/proxy.pem
ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
ROOTCERT_FILE: /conf/root.crt.pem
secrets:
- proxy.pem
depends_on:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/pscc/root.crt.pem:/conf/root.crt.pem:ro
volumes:
blaze-data:
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

View File

@@ -0,0 +1,34 @@
version: "3.7"
services:
landing:
container_name: lens_federated-search
image: docker.verbis.dkfz.de/dashboard/pscc-explorer
labels:
- "traefik.enable=true"
- "traefik.http.routers.landing.rule=PathPrefix(`/`)"
- "traefik.http.services.landing.loadbalancer.server.port=5173"
- "traefik.http.routers.landing.middlewares=auth"
- "traefik.http.routers.landing.tls=true"
# spot:
# image: docker.verbis.dkfz.de/ccp-private/central-spot
# environment:
# BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
# BEAM_URL: http://beam-proxy:8081
# BEAM_PROXY_ID: ${SITE_ID}
# BEAM_BROKER_ID: ${BROKER_ID}
# BEAM_APP_ID: "focus"
# PROJECT_METADATA: "cce_supervisors"
# depends_on:
# - "beam-proxy"
# labels:
# - "traefik.enable=true"
# - "traefik.http.services.spot.loadbalancer.server.port=8080"
# - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
# - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
# - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
# - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
# - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
# - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
# - "traefik.http.routers.spot.tls=true"
# - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"

View File

@@ -0,0 +1,5 @@
#!/bin/bash
if [ -n "$ENABLE_LENS" ];then
OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
fi

20
pscc/root.crt.pem Normal file
View File

@@ -0,0 +1,20 @@
-----BEGIN CERTIFICATE-----
MIIDNTCCAh2gAwIBAgIUW34NEb7bl0+Ywx+I1VKtY5vpAOowDQYJKoZIhvcNAQEL
BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwMTIyMTMzNzEzWhcNMzQw
MTE5MTMzNzQzWjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
AQEBBQADggEPADCCAQoCggEBAL5UegLXTlq3XRRj8LyFs3aF0tpRPVoW9RXp5kFI
TnBvyO6qjNbMDT/xK+4iDtEX4QQUvsxAKxfXbe9i1jpdwjgH7JHaSGm2IjAiKLqO
OXQQtguWwfNmmp96Ql13ArLj458YH08xMO/w2NFWGwB/hfARa4z/T0afFuc/tKJf
XbGCG9xzJ9tmcG45QN8NChGhVvaTweNdVxGWlpHxmi0Mn8OM9CEuB7nPtTTiBuiu
pRC2zVVmNjVp4ktkAqL7IHOz+/F5nhiz6tOika9oD3376Xj055lPznLcTQn2+4d7
K7ZrBopCFxIQPjkgmYRLfPejbpdUjK1UVJw7hbWkqWqH7JMCAwEAAaN7MHkwDgYD
VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFGjvRcaIP4HM
poIguUAK9YL2n7fbMB8GA1UdIwQYMBaAFGjvRcaIP4HMpoIguUAK9YL2n7fbMBYG
A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQCbzycJSaDm
AXXNJqQ88djrKs5MDXS8RIjS/cu2ayuLaYDe+BzVmUXNA0Vt9nZGdaz63SLLcjpU
fNSxBfKbwmf7s30AK8Cnfj9q4W/BlBeVizUHQsg1+RQpDIdMrRQrwkXv8mfLw+w5
3oaXNW6W/8KpBp/H8TBZ6myl6jCbeR3T8EMXBwipMGop/1zkbF01i98Xpqmhx2+l
n+80ofPsSspOo5XmgCZym8CD/m/oFHmjcvOfpOCvDh4PZ+i37pmbSlCYoMpla3u/
7MJMP5lugfLBYNDN2p+V4KbHP/cApCDT5UWLOeAWjgiZQtHH5ilDeYqEc1oPjyJt
Rtup0MTxSJtN
-----END CERTIFICATE-----

14
pscc/vars Normal file
View File

@@ -0,0 +1,14 @@
BROKER_ID=test-no-real-data.broker.samply.de
BROKER_URL=https://${BROKER_ID}
PROXY_ID=${SITE_ID}.${BROKER_ID}
FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
SUPPORT_EMAIL=denis.koether@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"
source $module
done

View File

@@ -1,4 +1,6 @@
FOCUS_TAG=develop
BEAM_TAG=develop
BLAZE_TAG=main
POSTGRES_TAG=15.13-alpine
POSTGRES_TAG=15.13-alpine
TEILER_DASHBOARD_TAG=develop
MTBA_TAG=develop

View File

@@ -1,4 +1,6 @@
FOCUS_TAG=main
BEAM_TAG=main
BLAZE_TAG=0.32
POSTGRES_TAG=15.13-alpine
POSTGRES_TAG=15.13-alpine
TEILER_DASHBOARD_TAG=main
MTBA_TAG=main

View File

@@ -1,4 +1,6 @@
FOCUS_TAG=develop
BEAM_TAG=develop
BLAZE_TAG=main
POSTGRES_TAG=15.13-alpine
POSTGRES_TAG=15.13-alpine
TEILER_DASHBOARD_TAG=develop
MTBA_TAG=develop