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Merge branch 'develop' into feature/add-pscc

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This commit is contained in:
p.delpy@dkfz-heidelberg.de
2025-07-24 16:39:28 +02:00
parent a53f9caa92 fcad7104f0
commit 771cbcf0b8
15 changed files with 111 additions and 124 deletions
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5
bbmri/modules/teiler-compose.yml
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@@ -32,9 +32,6 @@ services:
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}" DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "/bbmri-teiler-backend" TEILER_BACKEND_URL: "/bbmri-teiler-backend"
TEILER_DASHBOARD_URL: "/bbmri-teiler-dashboard" 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} ${OPERATOR_LAST_NAME}" TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}" TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}" TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
@@ -42,8 +39,6 @@ services:
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
TEILER_ORCHESTRATOR_URL: "/bbmri-teiler" TEILER_ORCHESTRATOR_URL: "/bbmri-teiler"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/bbmri-teiler" TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/bbmri-teiler"
TEILER_USER: "${OIDC_USER_GROUP}"
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
REPORTER_DEFAULT_TEMPLATE_ID: "bbmri-qb" REPORTER_DEFAULT_TEMPLATE_ID: "bbmri-qb"
EXPORTER_DEFAULT_TEMPLATE_ID: "bbmri" EXPORTER_DEFAULT_TEMPLATE_ID: "bbmri"

5
cce/modules/teiler-compose.yml
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@@ -32,9 +32,6 @@ services:
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}" DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
TEILER_BACKEND_URL: "/cce-teiler-backend" TEILER_BACKEND_URL: "/cce-teiler-backend"
TEILER_DASHBOARD_URL: "/cce-teiler-dashboard" 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} ${OPERATOR_LAST_NAME}" TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}" TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}" TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
@@ -42,8 +39,6 @@ services:
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
TEILER_ORCHESTRATOR_URL: "/cce-teiler" TEILER_ORCHESTRATOR_URL: "/cce-teiler"
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/cce-teiler" TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/cce-teiler"
TEILER_USER: "${OIDC_USER_GROUP}"
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
REPORTER_DEFAULT_TEMPLATE_ID: "cce-qb" REPORTER_DEFAULT_TEMPLATE_ID: "cce-qb"
EXPORTER_DEFAULT_TEMPLATE_ID: "cce" EXPORTER_DEFAULT_TEMPLATE_ID: "cce"

2
ccp/modules/datashield-compose.yml
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@@ -25,7 +25,7 @@ services:
APP_CONTEXT_PATH: "/opal" APP_CONTEXT_PATH: "/opal"
OPAL_PRIVATE_KEY: "/run/secrets/opal-key.pem" OPAL_PRIVATE_KEY: "/run/secrets/opal-key.pem"
OPAL_CERTIFICATE: "/run/secrets/opal-cert.pem" OPAL_CERTIFICATE: "/run/secrets/opal-cert.pem"
OIDC_URL: "${OIDC_URL}" OIDC_URL: "${OIDC_PRIVATE_URL}"
OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}" OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}" OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}" OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"

4
ccp/modules/dnpm-node-compose.yml
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@@ -43,7 +43,7 @@ services:
- "traefik.http.routers.dnpm-auth.tls=true" - "traefik.http.routers.dnpm-auth.tls=true"
dnpm-portal: dnpm-portal:
image: ghcr.io/dnpm-dip/portal:latest image: ghcr.io/dnpm-dip/portal:{DNPM_IMAGE_TAG:-latest}
container_name: bridgehead-dnpm-portal container_name: bridgehead-dnpm-portal
environment: environment:
- NUXT_API_URL=http://dnpm-backend:9000/ - NUXT_API_URL=http://dnpm-backend:9000/
@@ -58,7 +58,7 @@ services:
dnpm-backend: dnpm-backend:
container_name: bridgehead-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: environment:
- LOCAL_SITE=${ZPM_SITE}:${SITE_NAME} # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen - LOCAL_SITE=${ZPM_SITE}:${SITE_NAME} # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
- RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1} - RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}

13
ccp/modules/id-management-compose.yml
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@@ -14,6 +14,7 @@ services:
MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_READ_APIKEY} MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_READ_APIKEY}
MAGICPL_CENTRAL_PATIENTLIST_APIKEY: ${IDMANAGER_CENTRAL_PATIENTLIST_APIKEY} MAGICPL_CENTRAL_PATIENTLIST_APIKEY: ${IDMANAGER_CENTRAL_PATIENTLIST_APIKEY}
MAGICPL_CONTROLNUMBERGENERATOR_APIKEY: ${IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY} MAGICPL_CONTROLNUMBERGENERATOR_APIKEY: ${IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY}
MAGICPL_OIDC_PROVIDER: ${OIDC_PRIVATE_URL}
depends_on: depends_on:
- patientlist - patientlist
- traefik-forward-auth - traefik-forward-auth
@@ -71,12 +72,14 @@ services:
- https_proxy=http://forward_proxy:3128 - https_proxy=http://forward_proxy:3128
- OAUTH2_PROXY_PROVIDER=oidc - OAUTH2_PROXY_PROVIDER=oidc
- OAUTH2_PROXY_SKIP_PROVIDER_BUTTON=true - OAUTH2_PROXY_SKIP_PROVIDER_BUTTON=true
- OAUTH2_PROXY_OIDC_ISSUER_URL=https://login.verbis.dkfz.de/realms/master - OAUTH2_PROXY_OIDC_ISSUER_URL=${OIDC_PRIVATE_URL}
- OAUTH2_PROXY_CLIENT_ID=bridgehead-${SITE_ID} - OAUTH2_PROXY_CLIENT_ID=${OIDC_PRIVATE_CLIENT_ID}
- OAUTH2_PROXY_CLIENT_SECRET=${IDMANAGER_AUTH_CLIENT_SECRET} - OAUTH2_PROXY_CLIENT_SECRET=${OIDC_CLIENT_SECRET}
- OAUTH2_PROXY_COOKIE_SECRET=${IDMANAGER_AUTH_COOKIE_SECRET} - OAUTH2_PROXY_COOKIE_SECRET=${IDMANAGER_AUTH_COOKIE_SECRET}
- OAUTH2_PROXY_COOKIE_NAME=_BRIDGEHEAD_oauth2_idm - OAUTH2_PROXY_COOKIE_NAME=_BRIDGEHEAD_oauth2_idm
- OAUTH2_PROXY_COOKIE_DOMAINS=.${HOST} - OAUTH2_PROXY_COOKIE_DOMAINS=.${HOST}
- OAUTH2_PROXY_COOKIE_REFRESH=4m
- OAUTH2_PROXY_COOKIE_EXPIRE=24h
- OAUTH2_PROXY_HTTP_ADDRESS=:4180 - OAUTH2_PROXY_HTTP_ADDRESS=:4180
- OAUTH2_PROXY_REVERSE_PROXY=true - OAUTH2_PROXY_REVERSE_PROXY=true
- OAUTH2_PROXY_WHITELIST_DOMAINS=.${HOST} - OAUTH2_PROXY_WHITELIST_DOMAINS=.${HOST}
@@ -87,8 +90,8 @@ services:
- OAUTH2_PROXY_SET_AUTHORIZATION_HEADER=true - OAUTH2_PROXY_SET_AUTHORIZATION_HEADER=true
- OAUTH2_PROXY_SET_XAUTHREQUEST=true - OAUTH2_PROXY_SET_XAUTHREQUEST=true
# Keycloak has an expiration time of 60s therefore oauth2-proxy needs to refresh after that # Keycloak has an expiration time of 60s therefore oauth2-proxy needs to refresh after that
- OAUTH2_PROXY_COOKIE_REFRESH=60s - OAUTH2_PROXY_ALLOWED_GROUPS=${OIDC_PSP_GROUP}
- OAUTH2_PROXY_ALLOWED_GROUPS=DKTK-CCP-PPSN - OAUTH2_PROXY_OIDC_GROUPS_CLAIM=${OIDC_GROUP_CLAIM}
- OAUTH2_PROXY_PROXY_PREFIX=/oauth2-idm - OAUTH2_PROXY_PROXY_PREFIX=/oauth2-idm
labels: labels:
- "traefik.enable=true" - "traefik.enable=true"

2
ccp/modules/id-management-setup.sh
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@@ -14,6 +14,8 @@ function idManagementSetup() {
# Ensure old ids are working !!! # Ensure old ids are working !!!
export IDMANAGEMENT_FRIENDLY_ID=$(legacyIdMapping "$SITE_ID") export IDMANAGEMENT_FRIENDLY_ID=$(legacyIdMapping "$SITE_ID")
add_private_oidc_redirect_url "/oauth2-idm/callback"
fi fi
} }

10
ccp/modules/mtba-compose.yml
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@@ -22,8 +22,14 @@ services:
HTTP_RELATIVE_PATH: "/mtba" HTTP_RELATIVE_PATH: "/mtba"
OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}" OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}" OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}" # TODO: Add following variables after moving to Authentik:
OIDC_URL: "${OIDC_URL}" #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: labels:
- "traefik.enable=true" - "traefik.enable=true"

4
ccp/vars
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@@ -10,9 +10,11 @@ BROKER_URL_FOR_PREREQ=$BROKER_URL
OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})" OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter" OIDC_ADMIN_GROUP="DKTK_CCP_$(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_PRIVATE_CLIENT_ID=${SITE_ID}-private
OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
OIDC_URL="https://login.verbis.dkfz.de/realms/test-realm-01" OIDC_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PUBLIC_CLIENT_ID}/"
OIDC_PRIVATE_URL="https://sso.verbis.dkfz.de/application/o/${OIDC_PRIVATE_CLIENT_ID}/"
OIDC_GROUP_CLAIM="groups" OIDC_GROUP_CLAIM="groups"
for module in $PROJECT/modules/*.sh for module in $PROJECT/modules/*.sh

58
kr/modules/exporter-compose.yml
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@@ -1,9 +1,10 @@
version: "3.7" version: "3.7"
services: services:
exporter: exporter:
image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
container_name: bridgehead-ccp-exporter container_name: bridgehead-kr-exporter
environment: environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC" JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO" LOG_LEVEL: "INFO"
@@ -12,39 +13,51 @@ services:
EXPORTER_DB_USER: "exporter" EXPORTER_DB_USER: "exporter"
EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter" EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter"
HTTP_RELATIVE_PATH: "/ccp-exporter" HTTP_RELATIVE_PATH: "/kr-exporter"
SITE: "${SITE_ID}" SITE: "${SITE_ID}"
HTTP_SERVLET_REQUEST_SCHEME: "https" HTTP_SERVLET_REQUEST_SCHEME: "https"
OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}" OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
labels: labels:
- "traefik.enable=true" - "traefik.enable=true"
- "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)" - "traefik.http.routers.exporter_kr.rule=PathPrefix(`/kr-exporter`)"
- "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092" - "traefik.http.services.exporter_kr.loadbalancer.server.port=8092"
- "traefik.http.routers.exporter_ccp.tls=true" - "traefik.http.routers.exporter_kr.tls=true"
- "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter" - "traefik.http.middlewares.exporter_kr_strip.stripprefix.prefixes=/kr-exporter"
- "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip" - "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=${EXPORTER_USER}"
volumes: volumes:
- "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output" - "/var/cache/bridgehead/kr/exporter-files:/app/exporter-files/output"
exporter-db: exporter-db:
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG} image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
container_name: bridgehead-ccp-exporter-db container_name: bridgehead-kr-exporter-db
environment: environment:
POSTGRES_USER: "exporter" POSTGRES_USER: "exporter"
POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh
POSTGRES_DB: "exporter" POSTGRES_DB: "exporter"
volumes: volumes:
# Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer. # Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer.
- "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data" - "/var/cache/bridgehead/kr/exporter-db:/var/lib/postgresql/data"
reporter: reporter:
image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest
container_name: bridgehead-ccp-reporter container_name: bridgehead-kr-reporter
environment: environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC" JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
LOG_LEVEL: "INFO" LOG_LEVEL: "INFO"
CROSS_ORIGINS: "https://${HOST}" CROSS_ORIGINS: "https://${HOST}"
HTTP_RELATIVE_PATH: "/ccp-reporter" HTTP_RELATIVE_PATH: "/kr-reporter"
SITE: "${SITE_ID}" SITE: "${SITE_ID}"
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
EXPORTER_URL: "http://exporter:8092" EXPORTER_URL: "http://exporter:8092"
@@ -52,16 +65,23 @@ services:
HTTP_SERVLET_REQUEST_SCHEME: "https" HTTP_SERVLET_REQUEST_SCHEME: "https"
# In this initial development state of the bridgehead, we are trying to have so many volumes as possible. # 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. # 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. # There is a risk that the bridgehead restarts, losing the already created export.
volumes: volumes:
- "/var/cache/bridgehead/ccp/reporter-files:/app/reports" - "/var/cache/bridgehead/kr/reporter-files:/app/reports"
labels: labels:
- "traefik.enable=true" - "traefik.enable=true"
- "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)" - "traefik.http.routers.reporter_kr.rule=PathPrefix(`/kr-reporter`)"
- "traefik.http.services.reporter_ccp.loadbalancer.server.port=8095" - "traefik.http.services.reporter_kr.loadbalancer.server.port=8095"
- "traefik.http.routers.reporter_ccp.tls=true" - "traefik.http.routers.reporter_kr.tls=true"
- "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter" - "traefik.http.middlewares.reporter_kr_strip.stripprefix.prefixes=/kr-reporter"
- "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip" - "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"

15
kr/modules/exporter.md
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.

69
kr/modules/teiler-compose.yml
View File

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

3
kr/modules/teiler-setup.sh
View File

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

19
kr/modules/teiler.md
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.

22
lib/functions.sh
View File

@@ -301,19 +301,33 @@ function sync_secrets() {
if [[ $secret_sync_args == "" ]]; then if [[ $secret_sync_args == "" ]]; then
return return
fi fi
if [ "$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." 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 touch /var/cache/bridgehead/secrets/oidc
docker run --rm \ docker run --rm \
-v /var/cache/bridgehead/secrets/oidc:/usr/local/cache \ -v /var/cache/bridgehead/secrets/oidc:/usr/local/cache \
-v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \ -v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
-v /srv/docker/bridgehead/$PROJECT/root.crt.pem:/run/secrets/root.crt.pem:ro \ -v $root_crt_file:/run/secrets/root.crt.pem:ro \
-v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \ -v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \ -e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
-e NO_PROXY=localhost,127.0.0.1 \ -e NO_PROXY=localhost,127.0.0.1 \
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \ -e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
-e PROXY_ID=$PROXY_ID \ -e PROXY_ID=$proxy_id \
-e BROKER_URL=$BROKER_URL \ -e BROKER_URL=$broker_url \
-e OIDC_PROVIDER=secret-sync-central.central-secret-sync.$BROKER_ID \ -e OIDC_PROVIDER=secret-sync-central.test-secret-sync.$broker_id \
-e SECRET_DEFINITIONS=$secret_sync_args \ -e SECRET_DEFINITIONS=$secret_sync_args \
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest

4
minimal/modules/dnpm-node-compose.yml
View File

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