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5 Commits

Author SHA1 Message Date
David Juarez
1ee2776238 Test 2025-07-08 14:14:37 +02:00
David Juarez
0ae8627df8 changed: Keycloak instead of Authentik 2025-07-08 13:40:55 +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
djuarezgf
8414604257 feat: migrate OIDC Configuration from Keycloak to Authentik (#327)
* Change: Authentik instead of Keycloak in CCP

Co-authored-by: Jan <59206115+Threated@users.noreply.github.com>

---------

Co-authored-by: Jan <59206115+Threated@users.noreply.github.com>
2025-07-04 14:26:19 +02:00
32 changed files with 183 additions and 206 deletions

View File

@@ -26,3 +26,7 @@ services:
volumes:
blaze-data:
# used in modules *-locator.yml
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

View File

@@ -26,11 +26,11 @@ services:
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/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro,Z
# secrets don't seem to allow us to specify Z
- /etc/bridgehead/pki/${SITE_ID}.priv.pem:/run/secrets/proxy.pem:ro
- /srv/docker/bridgehead/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro

View File

@@ -36,7 +36,7 @@ services:
- "traefik.http.middlewares.exporter_auth.basicauth.users=${EXPORTER_USER}"
volumes:
- "/var/cache/bridgehead/bbmri/exporter-files:/app/exporter-files/output:z"
- "/var/cache/bridgehead/bbmri/exporter-files:/app/exporter-files/output"
exporter-db:
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
@@ -47,7 +47,7 @@ services:
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/bbmri/exporter-db:/var/lib/postgresql/data:Z"
- "/var/cache/bridgehead/bbmri/exporter-db:/var/lib/postgresql/data"
reporter:
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
@@ -69,7 +69,7 @@ services:
# There is a risk that the bridgehead restarts, losing the already created export.
volumes:
- "/var/cache/bridgehead/bbmri/reporter-files:/app/reports:z"
- "/var/cache/bridgehead/bbmri/reporter-files:/app/reports"
labels:
- "traefik.enable=true"
- "traefik.http.routers.reporter_bbmri.rule=PathPrefix(`/bbmri-reporter`)"

View File

@@ -26,11 +26,11 @@ services:
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/bbmri/modules/${GBN_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro,Z
# secrets don't seem to allow us to specify Z
- /etc/bridgehead/pki/${SITE_ID}.priv.pem:/run/secrets/proxy.pem:ro
- /srv/docker/bridgehead/bbmri/modules/${GBN_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro

View File

@@ -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

@@ -35,7 +35,7 @@ services:
QUERIES_TO_CACHE: '/queries_to_cache.conf'
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
volumes:
- /srv/docker/bridgehead/cce/queries_to_cache.conf:/queries_to_cache.conf:ro,Z
- /srv/docker/bridgehead/cce/queries_to_cache.conf:/queries_to_cache.conf:ro
depends_on:
- "beam-proxy"
- "blaze"
@@ -57,10 +57,12 @@ services:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/cce/root.crt.pem:/conf/root.crt.pem:ro,Z
# secrets don't seem to allow us to specify Z
- /etc/bridgehead/pki/${SITE_ID}.priv.pem:/run/secrets/proxy.pem:ro
- /srv/docker/bridgehead/cce/root.crt.pem:/conf/root.crt.pem:ro
volumes:
blaze-data:
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

View File

@@ -37,7 +37,7 @@ services:
- "traefik.http.middlewares.exporter_auth.basicauth.users=${EXPORTER_USER}"
volumes:
- "/var/cache/bridgehead/cce/exporter-files:/app/exporter-files/output:z"
- "/var/cache/bridgehead/cce/exporter-files:/app/exporter-files/output"
exporter-db:
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
@@ -48,7 +48,7 @@ services:
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/cce/exporter-db:/var/lib/postgresql/data:Z"
- "/var/cache/bridgehead/cce/exporter-db:/var/lib/postgresql/data"
reporter:
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
@@ -70,7 +70,7 @@ services:
# There is a risk that the bridgehead restarts, losing the already created export.
volumes:
- "/var/cache/bridgehead/cce/reporter-files:/app/reports:z"
- "/var/cache/bridgehead/cce/reporter-files:/app/reports"
labels:
- "traefik.enable=true"
- "traefik.http.routers.reporter_cce.rule=PathPrefix(`/cce-reporter`)"

View File

@@ -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"

View File

@@ -35,7 +35,7 @@ services:
QUERIES_TO_CACHE: '/queries_to_cache.conf'
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
volumes:
- /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf:ro,Z
- /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf:ro
depends_on:
- "beam-proxy"
- "blaze"
@@ -57,9 +57,11 @@ services:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro,Z
# secrets don't seem to allow us to specify Z
- /etc/bridgehead/pki/${SITE_ID}.priv.pem:/run/secrets/proxy.pem:ro
- /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
volumes:
blaze-data:
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

View File

@@ -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}"
@@ -35,10 +35,10 @@ services:
BEAM_SECRET: ${TOKEN_MANAGER_SECRET}
BEAM_DATASHIELD_PROXY: request-manager
volumes:
- "/var/cache/bridgehead/ccp/opal-metadata-db:/srv:Z" # Opal metadata
# secrets don't seem to allow us to specify Z/z
- /tmp/bridgehead/opal-cert.pem:/run/secrets/opal-cert.pem:z
- /tmp/bridgehead/opal-key.pem:/run/secrets/opal-key.pem:Z
- "/var/cache/bridgehead/ccp/opal-metadata-db:/srv" # Opal metadata
secrets:
- opal-cert.pem
- opal-key.pem
opal-db:
container_name: bridgehead-opal-db
@@ -48,7 +48,7 @@ services:
POSTGRES_USER: "opal"
POSTGRES_DB: "opal"
volumes:
- "/var/cache/bridgehead/ccp/opal-db:/var/lib/postgresql/data:Z" # Opal project data (imported from exporter)
- "/var/cache/bridgehead/ccp/opal-db:/var/lib/postgresql/data" # Opal project data (imported from exporter)
opal-rserver:
container_name: bridgehead-opal-rserver
@@ -67,14 +67,20 @@ services:
DISCOVERY_URL: "./map/central.json"
LOCAL_TARGETS_FILE: "./map/local.json"
NO_AUTH: "true"
secrets:
- opal-cert.pem
depends_on:
- beam-proxy
volumes:
- /tmp/bridgehead/opal-map/:/map/:ro,Z
# secrets don't seem to allow us to specify Z/z
- /tmp/bridgehead/opal-cert.pem:/run/secrets/opal-cert.pem:z
- /tmp/bridgehead/opal-map/:/map/:ro
beam-proxy:
environment:
APP_datashield-connect_KEY: ${DATASHIELD_CONNECT_SECRET}
APP_token-manager_KEY: ${TOKEN_MANAGER_SECRET}
secrets:
opal-cert.pem:
file: /tmp/bridgehead/opal-cert.pem
opal-key.pem:
file: /tmp/bridgehead/opal-key.pem

View File

@@ -25,7 +25,7 @@ services:
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
- /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro,Z
- /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro
labels:
- "traefik.enable=true"
- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"

View File

@@ -12,13 +12,13 @@ services:
MYSQL_ROOT_HOST: "%"
MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
volumes:
- /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql:Z
- /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
dnpm-authup:
image: authup/authup:latest
container_name: bridgehead-dnpm-authup
volumes:
- /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable:Z
- /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
depends_on:
dnpm-mysql:
condition: service_healthy
@@ -43,7 +43,7 @@ services:
- "traefik.http.routers.dnpm-auth.tls=true"
dnpm-portal:
image: ghcr.io/dnpm-dip/portal:latest
image: ghcr.io/dnpm-dip/portal:{DNPM_IMAGE_TAG:-latest}
container_name: bridgehead-dnpm-portal
environment:
- NUXT_API_URL=http://dnpm-backend:9000/
@@ -58,7 +58,7 @@ services:
dnpm-backend:
container_name: bridgehead-dnpm-backend
image: ghcr.io/dnpm-dip/backend:latest
image: ghcr.io/dnpm-dip/backend:{DNPM_IMAGE_TAG:-latest}
environment:
- LOCAL_SITE=${ZPM_SITE}:${SITE_NAME} # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
- RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
@@ -68,7 +68,7 @@ services:
- AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
volumes:
- /etc/bridgehead/dnpm/config:/dnpm_config
- /var/cache/bridgehead/dnpm/backend-data:/dnpm_data:Z
- /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
depends_on:
dnpm-authup:
condition: service_healthy

View File

@@ -24,7 +24,7 @@ services:
- "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter"
- "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip"
volumes:
- "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output:z"
- "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output"
exporter-db:
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
@@ -35,7 +35,7 @@ services:
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:Z"
- "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data"
reporter:
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
@@ -57,7 +57,7 @@ services:
# There is a risk that the bridgehead restarts, losing the already created export.
volumes:
- "/var/cache/bridgehead/ccp/reporter-files:/app/reports:z"
- "/var/cache/bridgehead/ccp/reporter-files:/app/reports"
labels:
- "traefik.enable=true"
- "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)"

View File

@@ -22,8 +22,8 @@ services:
POSTGRES_PASSWORD: "${DASHBOARD_DB_PASSWORD}" # Set in dashboard-setup.sh
POSTGRES_DB: "dashboard"
volumes:
- "/var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data:Z"
- "/var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data"
focus:
environment:
POSTGRES_CONNECTION_STRING: "postgresql://dashboard:${DASHBOARD_DB_PASSWORD}@dashboard-db/dashboard"
POSTGRES_CONNECTION_STRING: "postgresql://dashboard:${DASHBOARD_DB_PASSWORD}@dashboard-db/dashboard"

View File

@@ -62,7 +62,7 @@ services:
volumes:
- "patientlist-db-data:/var/lib/postgresql/data"
# NOTE: Add backups here. This is only imported if /var/lib/bridgehead/data/patientlist/ is empty!!!
- "/tmp/bridgehead/patientlist/:/docker-entrypoint-initdb.d/:Z"
- "/tmp/bridgehead/patientlist/:/docker-entrypoint-initdb.d/"
traefik-forward-auth:
image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:latest

View File

@@ -32,8 +32,8 @@ services:
- "traefik.http.routers.mtba_ccp.tls=true"
volumes:
- /var/cache/bridgehead/ccp/mtba/input:/app/input:z
- /var/cache/bridgehead/ccp/mtba/persist:/app/persist:z
- /var/cache/bridgehead/ccp/mtba/input:/app/input
- /var/cache/bridgehead/ccp/mtba/persist:/app/persist
# TODO: Include CBioPortal in Deployment ...
# NOTE: CBioPortal can't load data while the system is running. So after import of data bridgehead needs to be restarted!

View File

@@ -12,7 +12,10 @@ OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"
OIDC_PRIVATE_CLIENT_ID=${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_URL="https://login.verbis.dkfz.de/realms/test-realm-01"
OIDC_PRIVATE_URL="https://login.verbis.dkfz.de/realms/test-realm-01"
OIDC_GROUP_CLAIM="groups"
for module in $PROJECT/modules/*.sh

View File

@@ -33,7 +33,7 @@ services:
EPSILON: 0.28
QUERIES_TO_CACHE: '/queries_to_cache.conf'
volumes:
- /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf:ro,Z
- /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf:ro
depends_on:
- "beam-proxy"
- "blaze"
@@ -55,10 +55,12 @@ services:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/dhki/root.crt.pem:/conf/root.crt.pem:ro,Z
# secrets don't seem to allow us to specify Z
- /etc/bridgehead/pki/${SITE_ID}.priv.pem:/run/secrets/proxy.pem:ro
- /srv/docker/bridgehead/dhki/root.crt.pem:/conf/root.crt.pem:ro
volumes:
blaze-data:
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

View File

@@ -35,7 +35,7 @@ services:
QUERIES_TO_CACHE: '/queries_to_cache.conf'
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
volumes:
- /srv/docker/bridgehead/itcc/queries_to_cache.conf:/queries_to_cache.conf:ro,Z
- /srv/docker/bridgehead/itcc/queries_to_cache.conf:/queries_to_cache.conf:ro
depends_on:
- "beam-proxy"
- "blaze"
@@ -51,14 +51,18 @@ services:
ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
ROOTCERT_FILE: /conf/root.crt.pem
secrets:
- proxy.pem
depends_on:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/itcc/root.crt.pem:/conf/root.crt.pem:ro,Z
# secrets don't seem to allow us to specify Z
- /etc/bridgehead/pki/${SITE_ID}.priv.pem:/run/secrets/proxy.pem:ro
- /srv/docker/bridgehead/itcc/root.crt.pem:/conf/root.crt.pem:ro
volumes:
blaze-data:
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

View File

@@ -56,10 +56,12 @@ services:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/kr/root.crt.pem:/conf/root.crt.pem:ro,Z
# secrets don't seem to allow us to specify Z
- /etc/bridgehead/pki/${SITE_ID}.priv.pem:/run/secrets/proxy.pem:ro
- /srv/docker/bridgehead/kr/root.crt.pem:/conf/root.crt.pem:ro
volumes:
blaze-data:
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

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:z"
- "/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:Z"
- "/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:z"
- "/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"

View File

@@ -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

@@ -7,70 +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: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
HTTP_RELATIVE_PATH: "/ccp-teiler"
HTTP_RELATIVE_PATH: "/kr-teiler"
teiler-dashboard:
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
container_name: bridgehead-teiler-dashboard
labels:
- "traefik.enable=true"
- "traefik.http.routers.teiler_dashboard_ccp.rule=PathPrefix(`/ccp-teiler-dashboard`)"
- "traefik.http.services.teiler_dashboard_ccp.loadbalancer.server.port=80"
- "traefik.http.routers.teiler_dashboard_ccp.tls=true"
- "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard"
- "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip"
- "traefik.http.routers.teiler_dashboard_kr.rule=PathPrefix(`/kr-teiler-dashboard`)"
- "traefik.http.services.teiler_dashboard_kr.loadbalancer.server.port=80"
- "traefik.http.routers.teiler_dashboard_kr.tls=true"
- "traefik.http.middlewares.teiler_dashboard_kr_strip.stripprefix.prefixes=/kr-teiler-dashboard"
- "traefik.http.routers.teiler_dashboard_kr.middlewares=teiler_dashboard_kr_strip"
environment:
DEFAULT_LANGUAGE: "${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}"
volumes:
# secrets don't seem to allow us to specify Z
- /etc/bridgehead/ccp.conf:/run/secrets/ccp.conf:ro

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

@@ -36,32 +36,6 @@ setupProxy() {
export HTTPS_PROXY_HOST HTTPS_PROXY_PORT HTTPS_PROXY_FULL_URL
}
checkAndSetSelinux() {
# This is needed for the systemd service to start on SELinux systems.
if ! command -v sestatus > /dev/null 2>&1; then
echo "SELinux not available; nothing to do"
return
fi
if ! sestatus | grep "SELinux status:" | grep enabled > /dev/null; then
echo "SELinux disabled; nothing to do"
return
fi
current_mode="$(sestatus | grep 'Current mode:' | tr -s ' ' | cut -d' ' -f 3)"
echo "SELinux is active and ${current_mode}, checking for labels..."
# TODO: perhaps split this into checkSelinux (without the need for root) and setSelinux (needing root)
# "stat /srv/docker/bridgehead/bridgehead --printf %C" could be used for a check that doesn't need root
exitIfNotRoot
labels_for_srv="$(semanage fcontext --list | grep -e ^/srv)"
echo "Found the following labels for /srv:"
echo "${labels_for_srv}"
if ! echo "${labels_for_srv}" | grep -e ^/srv/docker/bridgehead/bridgehead > /dev/null; then
echo "Adding a label for /srv/docker/bridgehead/bridgehead..."
semanage fcontext --add --type bin_t /srv/docker/bridgehead/bridgehead
fi
restorecon -v /srv/docker/bridgehead/bridgehead # this survives a reboot
# TODO: check if this survives updates
}
exitIfNotRoot() {
if [ "$EUID" -ne 0 ]; then
log "ERROR" "Please run as root"
@@ -327,19 +301,33 @@ function sync_secrets() {
if [[ $secret_sync_args == "" ]]; then
return
fi
if [ "$PROJECT" == "bbmri" ]; then
# If the project is BBMRI, use the BBMRI-ERIC broker and not the GBN broker
proxy_id=$ERIC_PROXY_ID
broker_url=$ERIC_BROKER_URL
broker_id=$ERIC_BROKER_ID
root_crt_file="/srv/docker/bridgehead/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem"
else
proxy_id=$PROXY_ID
broker_url=$BROKER_URL
broker_id=$BROKER_ID
root_crt_file="/srv/docker/bridgehead/$PROJECT/root.crt.pem"
fi
mkdir -p /var/cache/bridgehead/secrets/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/secrets/'. Please run sudo './bridgehead install $PROJECT' again."
touch /var/cache/bridgehead/secrets/oidc
docker run --rm \
-v /var/cache/bridgehead/secrets/oidc:/usr/local/cache \
-v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
-v /srv/docker/bridgehead/$PROJECT/root.crt.pem:/run/secrets/root.crt.pem:ro \
-v $root_crt_file:/run/secrets/root.crt.pem:ro \
-v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
-e NO_PROXY=localhost,127.0.0.1 \
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
-e PROXY_ID=$PROXY_ID \
-e BROKER_URL=$BROKER_URL \
-e OIDC_PROVIDER=secret-sync-central.central-secret-sync.$BROKER_ID \
-e PROXY_ID=$proxy_id \
-e BROKER_URL=$broker_url \
-e OIDC_PROVIDER=secret-sync-central.secret-sync.$broker_id \
-e SECRET_DEFINITIONS=$secret_sync_args \
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest

View File

@@ -3,7 +3,6 @@
source lib/functions.sh
exitIfNotRoot
checkAndSetSelinux
if [ $# -eq 0 ]; then
log "ERROR" "Please provide a Project as argument"

View File

@@ -25,12 +25,6 @@ services:
ports:
- 80:80
- 443:443
security_opt:
# allow access to the docker socket on systems with SELinux
- "label:type:container_runtime_t"
cap_add:
# Allow binding to ports <1024 without root
- NET_BIND_SERVICE
volumes:
- /etc/bridgehead/traefik-tls:/certs:ro
- ../lib/traefik-configuration/:/configuration:ro

View File

@@ -12,13 +12,13 @@ services:
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/ccp/root.crt.pem:/conf/root.crt.pem:ro,Z
# secrets don't seem to allow us to specify Z
- /etc/bridgehead/pki/${SITE_ID}.priv.pem:/run/secrets/proxy.pem:ro
- /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
dnpm-beam-connect:
depends_on: [ dnpm-beam-proxy ]
@@ -41,7 +41,7 @@ services:
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
- /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro,Z
- /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro
labels:
- "traefik.enable=true"
- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"
@@ -53,3 +53,7 @@ services:
dnpm-echo:
image: docker.verbis.dkfz.de/cache/samply/bridgehead-echo:latest
container_name: bridgehead-dnpm-echo
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

View File

@@ -12,13 +12,13 @@ services:
MYSQL_ROOT_HOST: "%"
MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
volumes:
- /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql:Z
- /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
dnpm-authup:
image: authup/authup:latest
container_name: bridgehead-dnpm-authup
volumes:
- /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable:Z
- /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
depends_on:
dnpm-mysql:
condition: service_healthy
@@ -43,7 +43,7 @@ services:
- "traefik.http.routers.dnpm-auth.tls=true"
dnpm-portal:
image: ghcr.io/dnpm-dip/portal:latest
image: ghcr.io/dnpm-dip/portal:{DNPM_IMAGE_TAG:-latest}
container_name: bridgehead-dnpm-portal
environment:
- NUXT_API_URL=http://dnpm-backend:9000/
@@ -58,7 +58,7 @@ services:
dnpm-backend:
container_name: bridgehead-dnpm-backend
image: ghcr.io/dnpm-dip/backend:latest
image: ghcr.io/dnpm-dip/backend:{DNPM_IMAGE_TAG:-latest}
environment:
- LOCAL_SITE=${ZPM_SITE}:${SITE_NAME} # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
- RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
@@ -68,7 +68,7 @@ services:
- AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
volumes:
- /etc/bridgehead/dnpm/config:/dnpm_config
- /var/cache/bridgehead/dnpm/backend-data:/dnpm_data:Z
- /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
depends_on:
dnpm-authup:
condition: service_healthy

View File

@@ -10,4 +10,8 @@ services:
SSH_TUNNEL_PORT: "${SSH_TUNNEL_PORT:-22}"
volumes:
- "/etc/bridgehead/ssh-tunnel.conf:/ssh-tunnel.conf:ro"
- "/etc/bridgehead/pki/ssh-tunnel.priv.pem:/run/secrets/privkey:ro"
secrets:
- privkey
secrets:
privkey:
file: /etc/bridgehead/pki/ssh-tunnel.priv.pem

View File

@@ -27,7 +27,7 @@ services:
- NO_PROXY=${TRANSFAIR_NO_PROXIES}
- ALL_PROXY=http://forward_proxy:3128
volumes:
- /var/cache/bridgehead/${PROJECT}/transfair:/transfair:Z
- /var/cache/bridgehead/${PROJECT}/transfair:/transfair
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
labels:
- "traefik.enable=true"