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dnpm-etl-r
...
feature/op
Author | SHA1 | Date | |
---|---|---|---|
d9208c4be2 |
@ -254,8 +254,6 @@ sh bridgehead uninstall
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## Site-specific configuration
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[How to Change Config Access Token](docs/update-access-token.md)
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|
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### HTTPS Access
|
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|
||||
Even within your internal network, the Bridgehead enforces HTTPS for all services. During the installation, a self-signed, long-lived certificate was created for you. To increase security, you can simply replace the files under `/etc/bridgehead/traefik-tls` with ones from established certification authorities such as [Let's Encrypt](https://letsencrypt.org) or [DFN-AAI](https://www.aai.dfn.de).
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|
@ -4,7 +4,7 @@ version: "3.7"
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||||
services:
|
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blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
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image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
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container_name: bridgehead-bbmri-blaze
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environment:
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BASE_URL: "http://bridgehead-bbmri-blaze:8080"
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|
@ -2,7 +2,7 @@ version: "3.7"
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services:
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blaze:
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image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
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image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
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container_name: bridgehead-cce-blaze
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environment:
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BASE_URL: "http://bridgehead-cce-blaze:8080"
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|
@ -2,7 +2,7 @@ version: "3.7"
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services:
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blaze:
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image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
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image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
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container_name: bridgehead-ccp-blaze
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environment:
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BASE_URL: "http://bridgehead-ccp-blaze:8080"
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|
@ -2,7 +2,7 @@ version: "3.7"
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services:
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blaze-secondary:
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image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
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image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
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container_name: bridgehead-ccp-blaze-secondary
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environment:
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BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"
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|
@ -22,7 +22,7 @@ services:
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opal:
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container_name: bridgehead-opal
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image: docker.verbis.dkfz.de/ccp/dktk-opal:latest
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image: docker.verbis.dkfz.de/ccp/dktk-opal:test
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labels:
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- "traefik.enable=true"
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- "traefik.http.routers.opal_ccp.rule=PathPrefix(`/opal`)"
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|
@ -13,7 +13,7 @@ services:
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PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
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APP_ID: dnpm-connect.${PROXY_ID}
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DISCOVERY_URL: "./conf/central_targets.json"
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LOCAL_TARGETS_FILE: "/conf/connect_targets.json"
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LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
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HTTP_PROXY: "http://forward_proxy:3128"
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HTTPS_PROXY: "http://forward_proxy:3128"
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NO_PROXY: beam-proxy,dnpm-backend,host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
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@ -25,7 +25,7 @@ services:
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volumes:
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- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
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- /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
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- /srv/docker/bridgehead/minimal/modules/dnpm-central-targets.json:/conf/central_targets.json:ro
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- /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
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labels:
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- "traefik.enable=true"
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- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"
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|
@ -1,103 +1,34 @@
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version: "3.7"
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services:
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dnpm-mysql:
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image: mysql:9
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healthcheck:
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test: [ "CMD", "mysqladmin" ,"ping", "-h", "localhost" ]
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interval: 3s
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timeout: 5s
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retries: 5
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environment:
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MYSQL_ROOT_HOST: "%"
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MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
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volumes:
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- /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
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dnpm-authup:
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image: authup/authup:latest
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container_name: bridgehead-dnpm-authup
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volumes:
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- /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
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depends_on:
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dnpm-mysql:
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condition: service_healthy
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command: server/core start
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environment:
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- PUBLIC_URL=https://${HOST}/auth/
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- AUTHORIZE_REDIRECT_URL=https://${HOST}
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- ROBOT_ADMIN_ENABLED=true
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- ROBOT_ADMIN_SECRET=${DNPM_AUTHUP_SECRET}
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- ROBOT_ADMIN_SECRET_RESET=true
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- DB_TYPE=mysql
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- DB_HOST=dnpm-mysql
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- DB_USERNAME=root
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- DB_PASSWORD=${DNPM_MYSQL_ROOT_PASSWORD}
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- DB_DATABASE=auth
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labels:
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- "traefik.enable=true"
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- "traefik.http.middlewares.authup-strip.stripprefix.prefixes=/auth"
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- "traefik.http.routers.dnpm-auth.middlewares=authup-strip"
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- "traefik.http.routers.dnpm-auth.rule=PathPrefix(`/auth`)"
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- "traefik.http.services.dnpm-auth.loadbalancer.server.port=3000"
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- "traefik.http.routers.dnpm-auth.tls=true"
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dnpm-portal:
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image: ghcr.io/dnpm-dip/portal:latest
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container_name: bridgehead-dnpm-portal
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environment:
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- NUXT_API_URL=http://dnpm-backend:9000/
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- NUXT_PUBLIC_API_URL=https://${HOST}/api/
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- NUXT_AUTHUP_URL=http://dnpm-authup:3000/
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- NUXT_PUBLIC_AUTHUP_URL=https://${HOST}/auth/
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labels:
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- "traefik.enable=true"
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- "traefik.http.routers.dnpm-frontend.rule=PathPrefix(`/`)"
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- "traefik.http.services.dnpm-frontend.loadbalancer.server.port=3000"
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- "traefik.http.routers.dnpm-frontend.tls=true"
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dnpm-backend:
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image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
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container_name: bridgehead-dnpm-backend
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image: ghcr.io/dnpm-dip/backend:latest
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environment:
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- LOCAL_SITE=${ZPM_SITE}:${SITE_NAME} # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
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- RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
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- MTB_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
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- HATEOAS_HOST=https://${HOST}
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- CONNECTOR_TYPE=broker
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- AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
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- ZPM_SITE=${ZPM_SITE}
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- N_RANDOM_FILES=${DNPM_SYNTH_NUM}
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volumes:
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- /etc/bridgehead/dnpm/config:/dnpm_config
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- /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
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depends_on:
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dnpm-authup:
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condition: service_healthy
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- /etc/bridgehead/dnpm:/bwhc_config:ro
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- ${DNPM_DATA_DIR}:/bwhc_data
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labels:
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- "traefik.enable=true"
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- "traefik.http.services.dnpm-backend.loadbalancer.server.port=9000"
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# expose everything
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- "traefik.http.routers.dnpm-backend.rule=PathPrefix(`/api`)"
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- "traefik.http.routers.dnpm-backend.tls=true"
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- "traefik.http.routers.dnpm-backend.service=dnpm-backend"
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# except ETL
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- "traefik.http.routers.dnpm-backend-etl.rule=PathRegexp(`^/api(/.*)?etl(/.*)?$`)"
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- "traefik.http.routers.dnpm-backend-etl.tls=true"
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- "traefik.http.routers.dnpm-backend-etl.service=dnpm-backend"
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# TODO: add to minimal and document
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- "traefik.http.middlewares.rewrite-mtbfile.replacepathregex.regex=^(.*)/MTBFile$"
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- "traefik.http.middlewares.rewrite-mtbfile.replacepathregex.replacement=$1"
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- "traefik.http.routers.dnpm-backend-etl.middlewares=rewrite-mtbfile"
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# this needs an ETL processor with support for basic auth
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- "traefik.http.routers.dnpm-backend-etl.middlewares=auth"
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# except peer-to-peer
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- "traefik.http.routers.dnpm-backend-peer.rule=PathRegexp(`^/api(/.*)?/peer2peer(/.*)?$`)"
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- "traefik.http.routers.dnpm-backend-peer.tls=true"
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- "traefik.http.routers.dnpm-backend-peer.service=dnpm-backend"
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- "traefik.http.routers.dnpm-backend-peer.middlewares=dnpm-backend-peer"
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# this effectively denies all requests
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# this is okay, because requests from peers don't go through Traefik
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- "traefik.http.middlewares.dnpm-backend-peer.ipWhiteList.sourceRange=0.0.0.0/32"
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- "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
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- "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
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- "traefik.http.routers.bwhc-backend.tls=true"
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landing:
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dnpm-frontend:
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image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
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container_name: bridgehead-dnpm-frontend
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links:
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- dnpm-backend
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environment:
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- NUXT_HOST=0.0.0.0
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- NUXT_PORT=8080
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- BACKEND_PROTOCOL=https
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- BACKEND_HOSTNAME=$HOST
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- BACKEND_PORT=443
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labels:
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- "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"
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- "traefik.enable=true"
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- "traefik.http.routers.bwhc-frontend.rule=PathPrefix(`/`)"
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- "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080"
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- "traefik.http.routers.bwhc-frontend.tls=true"
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|
@ -1,16 +1,28 @@
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#!/bin/bash
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if [ -n "${ENABLE_DNPM_NODE}" ]; then
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log INFO "DNPM setup detected -- will start DNPM:DIP node."
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log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
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OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
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# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
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DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
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if [ -z "${ZPM_SITE+x}" ]; then
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log ERROR "Mandatory variable ZPM_SITE not defined!"
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exit 1
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fi
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mkdir -p /var/cache/bridgehead/dnpm/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/dnpm/'. Please run sudo './bridgehead install $PROJECT' again to fix the permissions."
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DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:--1}
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DNPM_MYSQL_ROOT_PASSWORD="$(generate_simple_password 'dnpm mysql')"
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DNPM_AUTHUP_SECRET="$(generate_simple_password 'dnpm authup')"
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if [ -z "${DNPM_DATA_DIR+x}" ]; then
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log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
|
||||
exit 1
|
||||
fi
|
||||
DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
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if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
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echo "Override of landing page url already in place"
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else
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||||
echo "Adding override of landing page url"
|
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if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
|
||||
echo -e ' landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
|
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else
|
||||
echo -e 'version: "3.7"\nservices:\n landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
|
||||
fi
|
||||
fi
|
||||
fi
|
||||
|
@ -69,4 +69,4 @@ services:
|
||||
focus:
|
||||
environment:
|
||||
EXPORTER_URL: "http://exporter:8092"
|
||||
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
|
||||
AUTH_HEADER: "${EXPORTER_API_KEY}"
|
||||
|
@ -102,11 +102,11 @@ services:
|
||||
condition: service_healthy
|
||||
|
||||
ccp-patient-project-identificator:
|
||||
image: docker.verbis.dkfz.de/cache/samply/ccp-patient-project-identificator
|
||||
image: samply/ccp-patient-project-identificator
|
||||
container_name: bridgehead-ccp-patient-project-identificator
|
||||
environment:
|
||||
MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
|
||||
SITE_NAME: ${IDMANAGEMENT_FRIENDLY_ID}
|
||||
SITE_NAME: ${SITE_NAME}
|
||||
|
||||
volumes:
|
||||
patientlist-db-data:
|
||||
|
@ -12,6 +12,7 @@ services:
|
||||
CTS_API_KEY: ${NNGM_CTS_APIKEY}
|
||||
CRYPT_KEY: ${NNGM_CRYPTKEY}
|
||||
#CTS_MAGICPL_SITE: ${SITE_ID}TODO
|
||||
restart: always
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"
|
||||
|
@ -10,6 +10,7 @@ services:
|
||||
SALT: ${LOCAL_SALT}
|
||||
KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
|
||||
MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
|
||||
restart: always
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"
|
||||
|
@ -2,7 +2,7 @@ version: "3.7"
|
||||
|
||||
services:
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
container_name: bridgehead-dhki-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-dhki-blaze:8080"
|
||||
|
@ -1,42 +0,0 @@
|
||||
## How to Change Config Access Token
|
||||
|
||||
### 1. Generate a New Access Token
|
||||
|
||||
1. Go to your Git configuration repository provider, it might be either [git.verbis.dkfz.de](https://git.verbis.dkfz.de) or [gitlab.bbmri-eric.eu](https://gitlab.bbmri-eric.eu).
|
||||
2. Navigate to the configuration repository for your site.
|
||||
3. Go to **Settings → Access Tokens** to check if your Access Token is valid or expired.
|
||||
- **If expired**, create a new Access Token.
|
||||
4. Configure the new Access Token with the following settings:
|
||||
- **Expiration date**: One year from today, minus one day.
|
||||
- **Role**: Developer.
|
||||
- **Scope**: Only `read_repository`.
|
||||
5. Save the newly generated Access Token in a secure location.
|
||||
|
||||
---
|
||||
|
||||
### 2. Replace the Old Access Token
|
||||
|
||||
1. Navigate to `/etc/bridgehead` in your system.
|
||||
2. Run the following command to retrieve the current Git remote URL:
|
||||
```bash
|
||||
git remote get-url origin
|
||||
```
|
||||
Example output:
|
||||
```
|
||||
https://name40dkfz-heidelberg.de:<old_access_token>@git.verbis.dkfz.de/bbmri-bridgehead-configs/test.git
|
||||
```
|
||||
3. Replace `<old_access_token>` with your new Access Token in the URL.
|
||||
4. Set the updated URL using the following command:
|
||||
```bash
|
||||
git remote set-url origin https://name40dkfz-heidelberg.de:<new_access_token>@git.verbis.dkfz.de/bbmri-bridgehead-configs/test.git
|
||||
|
||||
```
|
||||
|
||||
5. Start the Bridgehead update service by running:
|
||||
```bash
|
||||
systemctl start bridgehead-update@<project>
|
||||
```
|
||||
6. View the output to ensure the update process is successful:
|
||||
```bash
|
||||
journalctl -u bridgehead-update@<project> -f
|
||||
```
|
@ -2,7 +2,7 @@ version: "3.7"
|
||||
|
||||
services:
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
container_name: bridgehead-itcc-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-itcc-blaze:8080"
|
||||
|
@ -6,7 +6,7 @@ services:
|
||||
replicas: 0 #deactivate landing page
|
||||
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
container_name: bridgehead-kr-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-kr-blaze:8080"
|
||||
|
@ -10,6 +10,7 @@ services:
|
||||
SALT: ${LOCAL_SALT}
|
||||
KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
|
||||
MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
|
||||
restart: always
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"
|
||||
|
@ -58,8 +58,7 @@ for DIR in /etc/bridgehead $(pwd); do
|
||||
OUT=$(retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR fetch 2>&1 && retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR pull 2>&1)
|
||||
fi
|
||||
if [ $? -ne 0 ]; then
|
||||
OUT_SAN=$(echo $OUT | sed -E 's|://[^:]+:[^@]+@|://credentials@|g')
|
||||
report_error log "Unable to update git $DIR: $OUT_SAN"
|
||||
report_error log "Unable to update git $DIR: $OUT"
|
||||
fi
|
||||
|
||||
new_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
|
||||
|
@ -16,7 +16,7 @@ services:
|
||||
- --entrypoints.web.http.redirections.entrypoint.scheme=https
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.dashboard.rule=PathPrefix(`/dashboard/`)"
|
||||
- "traefik.http.routers.dashboard.rule=PathPrefix(`/api`) || PathPrefix(`/dashboard/`)"
|
||||
- "traefik.http.routers.dashboard.entrypoints=websecure"
|
||||
- "traefik.http.routers.dashboard.service=api@internal"
|
||||
- "traefik.http.routers.dashboard.tls=true"
|
||||
|
@ -1,142 +0,0 @@
|
||||
{
|
||||
"sites": [
|
||||
{
|
||||
"id": "UKFR",
|
||||
"name": "Freiburg",
|
||||
"virtualhost": "ukfr.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKHD",
|
||||
"name": "Heidelberg",
|
||||
"virtualhost": "ukhd.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKT",
|
||||
"name": "Tübingen",
|
||||
"virtualhost": "ukt.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKU",
|
||||
"name": "Ulm",
|
||||
"virtualhost": "uku.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UM",
|
||||
"name": "Mainz",
|
||||
"virtualhost": "um.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKMR",
|
||||
"name": "Marburg",
|
||||
"virtualhost": "ukmr.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKE",
|
||||
"name": "Hamburg",
|
||||
"virtualhost": "uke.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKA",
|
||||
"name": "Aachen",
|
||||
"virtualhost": "uka.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "Charite",
|
||||
"name": "Berlin",
|
||||
"virtualhost": "charite.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.berlin-test.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "MRI",
|
||||
"name": "Muenchen-tum",
|
||||
"virtualhost": "mri.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.muenchen-tum.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "KUM",
|
||||
"name": "Muenchen-lmu",
|
||||
"virtualhost": "kum.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.muenchen-lmu.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "MHH",
|
||||
"name": "Hannover",
|
||||
"virtualhost": "mhh.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.hannover.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKDD",
|
||||
"name": "dresden-dnpm",
|
||||
"virtualhost": "ukdd.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dresden-dnpm.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKB",
|
||||
"name": "Bonn",
|
||||
"virtualhost": "ukb.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.bonn-dnpm.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKD",
|
||||
"name": "Duesseldorf",
|
||||
"virtualhost": "ukd.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.duesseldorf-dnpm.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKK",
|
||||
"name": "Koeln",
|
||||
"virtualhost": "ukk.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UME",
|
||||
"name": "Essen",
|
||||
"virtualhost": "ume.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.essen.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKM",
|
||||
"name": "Muenster",
|
||||
"virtualhost": "ukm.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.muenster-dnpm.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKF",
|
||||
"name": "Frankfurt",
|
||||
"virtualhost": "ukf.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.frankfurt.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UMG",
|
||||
"name": "Goettingen",
|
||||
"virtualhost": "umg.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.goettingen.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKW",
|
||||
"name": "Würzburg",
|
||||
"virtualhost": "ukw.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.wuerzburg-dnpm.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "UKSH",
|
||||
"name": "Schleswig-Holstein",
|
||||
"virtualhost": "uksh.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.uksh-dnpm.broker.ccp-it.dktk.dkfz.de"
|
||||
},
|
||||
{
|
||||
"id": "TKT",
|
||||
"name": "Test",
|
||||
"virtualhost": "tkt.dnpm.de",
|
||||
"beamconnect": "dnpm-connect.tobias-develop.broker.ccp-it.dktk.dkfz.de"
|
||||
}
|
||||
]
|
||||
}
|
@ -29,7 +29,7 @@ services:
|
||||
PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
|
||||
APP_ID: dnpm-connect.${DNPM_PROXY_ID}
|
||||
DISCOVERY_URL: "./conf/central_targets.json"
|
||||
LOCAL_TARGETS_FILE: "/conf/connect_targets.json"
|
||||
LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
|
||||
HTTP_PROXY: http://forward_proxy:3128
|
||||
HTTPS_PROXY: http://forward_proxy:3128
|
||||
NO_PROXY: dnpm-beam-proxy,dnpm-backend, host.docker.internal${DNPM_ADDITIONAL_NO_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
|
||||
- /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"
|
||||
|
@ -1,99 +1,34 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
dnpm-mysql:
|
||||
image: mysql:9
|
||||
healthcheck:
|
||||
test: [ "CMD", "mysqladmin" ,"ping", "-h", "localhost" ]
|
||||
interval: 3s
|
||||
timeout: 5s
|
||||
retries: 5
|
||||
environment:
|
||||
MYSQL_ROOT_HOST: "%"
|
||||
MYSQL_ROOT_PASSWORD: ${DNPM_MYSQL_ROOT_PASSWORD}
|
||||
volumes:
|
||||
- /var/cache/bridgehead/dnpm/mysql:/var/lib/mysql
|
||||
|
||||
dnpm-authup:
|
||||
image: authup/authup:latest
|
||||
container_name: bridgehead-dnpm-authup
|
||||
volumes:
|
||||
- /var/cache/bridgehead/dnpm/authup:/usr/src/app/writable
|
||||
depends_on:
|
||||
dnpm-mysql:
|
||||
condition: service_healthy
|
||||
command: server/core start
|
||||
environment:
|
||||
- PUBLIC_URL=https://${HOST}/auth/
|
||||
- AUTHORIZE_REDIRECT_URL=https://${HOST}
|
||||
- ROBOT_ADMIN_ENABLED=true
|
||||
- ROBOT_ADMIN_SECRET=${DNPM_AUTHUP_SECRET}
|
||||
- ROBOT_ADMIN_SECRET_RESET=true
|
||||
- DB_TYPE=mysql
|
||||
- DB_HOST=dnpm-mysql
|
||||
- DB_USERNAME=root
|
||||
- DB_PASSWORD=${DNPM_MYSQL_ROOT_PASSWORD}
|
||||
- DB_DATABASE=auth
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.middlewares.authup-strip.stripprefix.prefixes=/auth/"
|
||||
- "traefik.http.routers.dnpm-auth.middlewares=authup-strip"
|
||||
- "traefik.http.routers.dnpm-auth.rule=PathPrefix(`/auth`)"
|
||||
- "traefik.http.services.dnpm-auth.loadbalancer.server.port=3000"
|
||||
- "traefik.http.routers.dnpm-auth.tls=true"
|
||||
|
||||
dnpm-portal:
|
||||
image: ghcr.io/dnpm-dip/portal:latest
|
||||
container_name: bridgehead-dnpm-portal
|
||||
environment:
|
||||
- NUXT_API_URL=http://dnpm-backend:9000/
|
||||
- NUXT_PUBLIC_API_URL=https://${HOST}/api/
|
||||
- NUXT_AUTHUP_URL=http://dnpm-authup:3000/
|
||||
- NUXT_PUBLIC_AUTHUP_URL=https://${HOST}/auth/
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.dnpm-frontend.rule=PathPrefix(`/`)"
|
||||
- "traefik.http.services.dnpm-frontend.loadbalancer.server.port=3000"
|
||||
- "traefik.http.routers.dnpm-frontend.tls=true"
|
||||
|
||||
dnpm-backend:
|
||||
image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
|
||||
container_name: bridgehead-dnpm-backend
|
||||
image: ghcr.io/dnpm-dip/backend:latest
|
||||
environment:
|
||||
- LOCAL_SITE=${ZPM_SITE}:${SITE_NAME} # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
|
||||
- RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
|
||||
- MTB_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
|
||||
- HATEOAS_HOST=https://${HOST}
|
||||
- CONNECTOR_TYPE=broker
|
||||
- AUTHUP_URL=robot://system:${DNPM_AUTHUP_SECRET}@http://dnpm-authup:3000
|
||||
- ZPM_SITE=${ZPM_SITE}
|
||||
- N_RANDOM_FILES=${DNPM_SYNTH_NUM}
|
||||
volumes:
|
||||
- /etc/bridgehead/dnpm/config:/dnpm_config
|
||||
- /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
|
||||
depends_on:
|
||||
dnpm-authup:
|
||||
condition: service_healthy
|
||||
- /etc/bridgehead/dnpm:/bwhc_config:ro
|
||||
- ${DNPM_DATA_DIR}:/bwhc_data
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.services.dnpm-backend.loadbalancer.server.port=9000"
|
||||
# expose everything
|
||||
- "traefik.http.routers.dnpm-backend.rule=PathPrefix(`/api`)"
|
||||
- "traefik.http.routers.dnpm-backend.tls=true"
|
||||
- "traefik.http.routers.dnpm-backend.service=dnpm-backend"
|
||||
# except ETL
|
||||
- "traefik.http.routers.dnpm-backend-etl.rule=PathRegexp(`^/api(/.*)?etl(/.*)?$`)"
|
||||
- "traefik.http.routers.dnpm-backend-etl.tls=true"
|
||||
- "traefik.http.routers.dnpm-backend-etl.service=dnpm-backend"
|
||||
# this needs an ETL processor with support for basic auth
|
||||
- "traefik.http.routers.dnpm-backend-etl.middlewares=auth"
|
||||
# except peer-to-peer
|
||||
- "traefik.http.routers.dnpm-backend-peer.rule=PathRegexp(`^/api(/.*)?/peer2peer(/.*)?$`)"
|
||||
- "traefik.http.routers.dnpm-backend-peer.tls=true"
|
||||
- "traefik.http.routers.dnpm-backend-peer.service=dnpm-backend"
|
||||
- "traefik.http.routers.dnpm-backend-peer.middlewares=dnpm-backend-peer"
|
||||
# this effectively denies all requests
|
||||
# this is okay, because requests from peers don't go through Traefik
|
||||
- "traefik.http.middlewares.dnpm-backend-peer.ipWhiteList.sourceRange=0.0.0.0/32"
|
||||
- "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
|
||||
- "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
|
||||
- "traefik.http.routers.bwhc-backend.tls=true"
|
||||
|
||||
landing:
|
||||
dnpm-frontend:
|
||||
image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
|
||||
container_name: bridgehead-dnpm-frontend
|
||||
links:
|
||||
- dnpm-backend
|
||||
environment:
|
||||
- NUXT_HOST=0.0.0.0
|
||||
- NUXT_PORT=8080
|
||||
- BACKEND_PROTOCOL=https
|
||||
- BACKEND_HOSTNAME=$HOST
|
||||
- BACKEND_PORT=443
|
||||
labels:
|
||||
- "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.bwhc-frontend.rule=PathPrefix(`/`)"
|
||||
- "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080"
|
||||
- "traefik.http.routers.bwhc-frontend.tls=true"
|
||||
|
@ -1,16 +1,28 @@
|
||||
#!/bin/bash
|
||||
|
||||
if [ -n "${ENABLE_DNPM_NODE}" ]; then
|
||||
log INFO "DNPM setup detected -- will start DNPM:DIP node."
|
||||
log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node."
|
||||
OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
|
||||
|
||||
# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
|
||||
DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
|
||||
if [ -z "${ZPM_SITE+x}" ]; then
|
||||
log ERROR "Mandatory variable ZPM_SITE not defined!"
|
||||
exit 1
|
||||
fi
|
||||
mkdir -p /var/cache/bridgehead/dnpm/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/dnpm/'. Please run sudo './bridgehead install $PROJECT' again to fix the permissions."
|
||||
DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:--1}
|
||||
DNPM_MYSQL_ROOT_PASSWORD="$(generate_simple_password 'dnpm mysql')"
|
||||
DNPM_AUTHUP_SECRET="$(generate_simple_password 'dnpm authup')"
|
||||
if [ -z "${DNPM_DATA_DIR+x}" ]; then
|
||||
log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
|
||||
exit 1
|
||||
fi
|
||||
DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
|
||||
if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
|
||||
echo "Override of landing page url already in place"
|
||||
else
|
||||
echo "Adding override of landing page url"
|
||||
if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
|
||||
echo -e ' landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
|
||||
else
|
||||
echo -e 'version: "3.7"\nservices:\n landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
|
||||
fi
|
||||
fi
|
||||
fi
|
||||
|
@ -11,6 +11,7 @@ services:
|
||||
CTS_API_KEY: ${NNGM_CTS_APIKEY}
|
||||
CRYPT_KEY: ${NNGM_CRYPTKEY}
|
||||
#CTS_MAGICPL_SITE: ${SITE_ID}TODO
|
||||
restart: always
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"
|
||||
|
Reference in New Issue
Block a user