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https://github.com/samply/bridgehead.git
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Compare commits
2 Commits
test/expor
...
refactor/l
Author | SHA1 | Date | |
---|---|---|---|
104fd05ce3 | |||
f3a14adf62 |
1
.github/CODEOWNERS
vendored
1
.github/CODEOWNERS
vendored
@ -1 +0,0 @@
|
||||
* @samply/bridgehead-developers
|
@ -76,7 +76,7 @@ The following URLs need to be accessible (prefix with `https://`):
|
||||
* git.verbis.dkfz.de
|
||||
* To fetch docker images
|
||||
* docker.verbis.dkfz.de
|
||||
* Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/setup/allow-list/))
|
||||
* Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/all))
|
||||
* hub.docker.com
|
||||
* registry-1.docker.io
|
||||
* production.cloudflare.docker.com
|
||||
@ -154,7 +154,7 @@ Pay special attention to:
|
||||
Clone the bridgehead repository:
|
||||
```shell
|
||||
sudo mkdir -p /srv/docker/
|
||||
sudo git clone -b main https://github.com/samply/bridgehead.git /srv/docker/bridgehead
|
||||
sudo git clone https://github.com/samply/bridgehead.git /srv/docker/bridgehead
|
||||
```
|
||||
|
||||
Then, run the installation script:
|
||||
@ -254,8 +254,6 @@ sh bridgehead uninstall
|
||||
|
||||
## Site-specific configuration
|
||||
|
||||
[How to Change Config Access Token](docs/update-access-token.md)
|
||||
|
||||
### HTTPS Access
|
||||
|
||||
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).
|
||||
|
@ -4,7 +4,7 @@ version: "3.7"
|
||||
|
||||
services:
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
container_name: bridgehead-bbmri-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-bbmri-blaze:8080"
|
||||
|
@ -10,10 +10,6 @@ if [ "${ENABLE_ERIC}" == "true" ]; then
|
||||
export ERIC_BROKER_ID=broker.bbmri.samply.de
|
||||
export ERIC_ROOT_CERT=eric
|
||||
;;
|
||||
"acceptance")
|
||||
export ERIC_BROKER_ID=broker-acc.bbmri-acc.samply.de
|
||||
export ERIC_ROOT_CERT=eric.acc
|
||||
;;
|
||||
"test")
|
||||
export ERIC_BROKER_ID=broker-test.bbmri-test.samply.de
|
||||
export ERIC_ROOT_CERT=eric.test
|
||||
|
@ -1,20 +0,0 @@
|
||||
-----BEGIN CERTIFICATE-----
|
||||
MIIDNTCCAh2gAwIBAgIUE/wu6FmI+KSMOalI65b+lI3HI4cwDQYJKoZIhvcNAQEL
|
||||
BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwOTE2MTUyMzU0WhcNMzQw
|
||||
OTE0MTUyNDI0WjAWMRQwEgYDVQQDEwtCcm9rZXItUm9vdDCCASIwDQYJKoZIhvcN
|
||||
AQEBBQADggEPADCCAQoCggEBAOt1I1FQt2bI4Nnjtg8JBYid29cBIkDT4MMb45Jr
|
||||
ays24y4R3WO7VJK9UjNduSq/A1jlA0W0A/szDf8Ojq6bBtg+uL92PTDjYH1QXwX0
|
||||
c7eMo2tvvyyrs/cb2/ovDBQ1lpibcxVmVAv042ASmil3SdqKKXpv3ATnF9I7V4cv
|
||||
fwB56FChaGIov5EK+9JOMjTx6oMlBEgUFR6qq/lSqM9my0HYwUFbX2W+nT9EKEIP
|
||||
9UP1eyfRZR3E/+oticnm/cS20BGCbjoYrNgLthXKyaASuhGoElKs8EZ3h9MiI+u0
|
||||
DpR0KpePhAkMLugBrgYWqkMwwD1684LfC4YVQrsLwzo5OW8CAwEAAaN7MHkwDgYD
|
||||
VR0PAQH/BAQDAgEGMA8GA1UdEwEB/wQFMAMBAf8wHQYDVR0OBBYEFPbXs3g3lMjH
|
||||
1JMe0a5aVbN7lB92MB8GA1UdIwQYMBaAFPbXs3g3lMjH1JMe0a5aVbN7lB92MBYG
|
||||
A1UdEQQPMA2CC0Jyb2tlci1Sb290MA0GCSqGSIb3DQEBCwUAA4IBAQBM5RsXb2HN
|
||||
FpC1mYfocXAn20Zu4d603qmc/IqkiOWbp36pWo+jk1AxejyRS9hEpQalgSnvcRPQ
|
||||
1hPEhGU+wvI0WWVi/01iNjVbXmJNPQEouXQWAT17dyp9vqQkPw8LNzpSV/qdPgbT
|
||||
Z9o3sZrjUsSLsK7A7Q5ky4ePkiJBaMsHeAD+wqGwpiJ4D2Xhp8e1v36TWM0qt2EA
|
||||
gySx9isx/jeGGPBmDqYB9BCal5lrihPN56jd+5pCkyXeZqKWiiXFJKXwcwxctYZc
|
||||
ADHIiTLLPXE8LHTUJAO51it1NAZ1S24aMzax4eWDXcWO7/ybbx5pkYkMd6EqlKHd
|
||||
8riQJIhY4huX
|
||||
-----END CERTIFICATE-----
|
52
bridgehead
52
bridgehead
@ -53,47 +53,17 @@ case "$PROJECT" in
|
||||
;;
|
||||
esac
|
||||
|
||||
# Loads config variables and runs the projects setup script
|
||||
loadVars() {
|
||||
# Load variables from /etc/bridgehead and /srv/docker/bridgehead
|
||||
set -a
|
||||
# Source the project specific config file
|
||||
source /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "/etc/bridgehead/$PROJECT.conf not found"
|
||||
# Source the project specific local config file if present
|
||||
# This file is ignored by git as oposed to the regular config file as it contains private site information like etl auth data
|
||||
if [ -e /etc/bridgehead/$PROJECT.local.conf ]; then
|
||||
log INFO "Applying /etc/bridgehead/$PROJECT.local.conf"
|
||||
source /etc/bridgehead/$PROJECT.local.conf || fail_and_report 1 "Found /etc/bridgehead/$PROJECT.local.conf but failed to import"
|
||||
fi
|
||||
# Set execution environment on main default to prod else test
|
||||
if [[ -z "${ENVIRONMENT+x}" ]]; then
|
||||
if [ "$(git rev-parse --abbrev-ref HEAD)" == "main" ]; then
|
||||
ENVIRONMENT="production"
|
||||
else
|
||||
ENVIRONMENT="test" # we have acceptance environment in BBMRI ERIC and it would be more appropriate to default to that one in case the data they have in BH is real, but I'm gonna leave it as is for backward compatibility
|
||||
fi
|
||||
fi
|
||||
# Source the versions of the images components
|
||||
case "$ENVIRONMENT" in
|
||||
"production")
|
||||
source ./versions/prod
|
||||
;;
|
||||
"test")
|
||||
source ./versions/test
|
||||
;;
|
||||
"acceptance")
|
||||
source ./versions/acceptance
|
||||
;;
|
||||
*)
|
||||
report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
|
||||
source ./versions/prod
|
||||
;;
|
||||
esac
|
||||
fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
|
||||
setHostname
|
||||
optimizeBlazeMemoryUsage
|
||||
# Run project specific setup if it exists
|
||||
# This will ususally modiy the `OVERRIDE` to include all the compose files that the project depends on
|
||||
# This is also where projects specify which modules to load
|
||||
[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
|
||||
set +a
|
||||
|
||||
@ -109,6 +79,26 @@ loadVars() {
|
||||
fi
|
||||
detectCompose
|
||||
setupProxy
|
||||
|
||||
# Set some project-independent default values
|
||||
: ${ENVIRONMENT:=production}
|
||||
export ENVIRONMENT
|
||||
|
||||
case "$ENVIRONMENT" in
|
||||
"production")
|
||||
export FOCUS_TAG=main
|
||||
export BEAM_TAG=main
|
||||
;;
|
||||
"test")
|
||||
export FOCUS_TAG=develop
|
||||
export BEAM_TAG=develop
|
||||
;;
|
||||
*)
|
||||
report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
|
||||
export FOCUS_TAG=main
|
||||
export BEAM_TAG=main
|
||||
;;
|
||||
esac
|
||||
}
|
||||
|
||||
case "$ACTION" in
|
||||
|
@ -2,14 +2,13 @@ version: "3.7"
|
||||
|
||||
services:
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
container_name: bridgehead-cce-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-cce-blaze:8080"
|
||||
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
|
||||
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
|
||||
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
|
||||
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
|
||||
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
|
||||
ENFORCE_REFERENTIAL_INTEGRITY: "false"
|
||||
volumes:
|
||||
- "blaze-data:/app/data"
|
||||
@ -32,10 +31,6 @@ services:
|
||||
BEAM_PROXY_URL: http://beam-proxy:8081
|
||||
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
|
||||
EPSILON: 0.28
|
||||
QUERIES_TO_CACHE: '/queries_to_cache.conf'
|
||||
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
|
||||
volumes:
|
||||
- /srv/docker/bridgehead/cce/queries_to_cache.conf:/queries_to_cache.conf:ro
|
||||
depends_on:
|
||||
- "beam-proxy"
|
||||
- "blaze"
|
||||
|
@ -1,2 +0,0 @@
|
||||
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
|
||||
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
|
@ -2,7 +2,7 @@ version: "3.7"
|
||||
|
||||
services:
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
container_name: bridgehead-ccp-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-ccp-blaze:8080"
|
||||
@ -11,6 +11,7 @@ services:
|
||||
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
|
||||
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
|
||||
ENFORCE_REFERENTIAL_INTEGRITY: "false"
|
||||
LOG_LEVEL: ${LOG_LEVEL_BLAZE:-WARN}
|
||||
volumes:
|
||||
- "blaze-data:/app/data"
|
||||
labels:
|
||||
@ -34,8 +35,9 @@ services:
|
||||
EPSILON: 0.28
|
||||
QUERIES_TO_CACHE: '/queries_to_cache.conf'
|
||||
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
|
||||
RUST_LOG: ${LOG_LEVEL_FOCUS:-WARN}
|
||||
volumes:
|
||||
- /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf:ro
|
||||
- /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf
|
||||
depends_on:
|
||||
- "beam-proxy"
|
||||
- "blaze"
|
||||
@ -51,6 +53,7 @@ services:
|
||||
ALL_PROXY: http://forward_proxy:3128
|
||||
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
|
||||
ROOTCERT_FILE: /conf/root.crt.pem
|
||||
RUST_LOG: ${LOG_LEVEL_FOCUS:-WARN}
|
||||
secrets:
|
||||
- proxy.pem
|
||||
depends_on:
|
||||
|
@ -2,7 +2,7 @@ version: "3.7"
|
||||
|
||||
services:
|
||||
blaze-secondary:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
container_name: bridgehead-ccp-blaze-secondary
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"
|
||||
@ -10,6 +10,7 @@ services:
|
||||
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
|
||||
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
|
||||
ENFORCE_REFERENTIAL_INTEGRITY: "false"
|
||||
LOG_LEVEL: ${LOG_LEVEL_BLAZE:-WARN}
|
||||
volumes:
|
||||
- "blaze-secondary-data:/app/data"
|
||||
labels:
|
||||
|
@ -10,6 +10,7 @@ services:
|
||||
DISABLE_AUTH: "true" # https://rocker-project.org/images/versioned/rstudio.html#how-to-use
|
||||
HTTP_RELATIVE_PATH: "/rstudio"
|
||||
ALL_PROXY: "http://forward_proxy:3128" # https://rocker-project.org/use/networking.html
|
||||
LOG_LEVEL: ${LOG_LEVEL_RSTUDIO:-WARN}
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.rstudio_ccp.rule=PathPrefix(`/rstudio`)"
|
||||
@ -54,6 +55,7 @@ services:
|
||||
BEAM_APP_ID: token-manager.${PROXY_ID}
|
||||
BEAM_SECRET: ${TOKEN_MANAGER_SECRET}
|
||||
BEAM_DATASHIELD_PROXY: request-manager
|
||||
LOG_LEVEL: ${LOG_LEVEL_OPAL:-WARN}
|
||||
volumes:
|
||||
- "/var/cache/bridgehead/ccp/opal-metadata-db:/srv" # Opal metadata
|
||||
secrets:
|
||||
@ -75,6 +77,8 @@ services:
|
||||
image: docker.verbis.dkfz.de/ccp/dktk-rserver # datashield/rock-base + dsCCPhos
|
||||
tmpfs:
|
||||
- /srv
|
||||
environment:
|
||||
LOG_LEVEL: ${LOG_LEVEL_OPAL:-WARN}
|
||||
|
||||
beam-connect:
|
||||
image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
|
||||
@ -87,6 +91,7 @@ services:
|
||||
DISCOVERY_URL: "./map/central.json"
|
||||
LOCAL_TARGETS_FILE: "./map/local.json"
|
||||
NO_AUTH: "true"
|
||||
RUST_LOG: ${LOG_LEVEL_BEAMCONNECT:-WARN}
|
||||
secrets:
|
||||
- opal-cert.pem
|
||||
depends_on:
|
||||
|
@ -13,11 +13,11 @@ services:
|
||||
PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
|
||||
APP_ID: dnpm-connect.${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: beam-proxy,dnpm-backend,host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
|
||||
RUST_LOG: ${RUST_LOG:-info}
|
||||
RUST_LOG: ${LOG_LEVEL_BEAMCONNECTDNPM:-WARN}
|
||||
NO_AUTH: "true"
|
||||
TLS_CA_CERTIFICATES_DIR: ./conf/trusted-ca-certs
|
||||
extra_hosts:
|
||||
@ -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
|
||||
- /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
|
||||
|
@ -2,11 +2,10 @@ version: "3.7"
|
||||
|
||||
services:
|
||||
exporter:
|
||||
image: docker.verbis.dkfz.de/ccp/dktk-exporter:test
|
||||
image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest
|
||||
container_name: bridgehead-ccp-exporter
|
||||
environment:
|
||||
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
|
||||
LOG_LEVEL: "INFO"
|
||||
EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh
|
||||
CROSS_ORIGINS: "https://${HOST}"
|
||||
EXPORTER_DB_USER: "exporter"
|
||||
@ -16,6 +15,7 @@ services:
|
||||
SITE: "${SITE_ID}"
|
||||
HTTP_SERVLET_REQUEST_SCHEME: "https"
|
||||
OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
|
||||
LOG_LEVEL: ${LOG_LEVEL_EXPORTER:-WARN}
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)"
|
||||
@ -42,7 +42,6 @@ services:
|
||||
container_name: bridgehead-ccp-reporter
|
||||
environment:
|
||||
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC"
|
||||
LOG_LEVEL: "INFO"
|
||||
CROSS_ORIGINS: "https://${HOST}"
|
||||
HTTP_RELATIVE_PATH: "/ccp-reporter"
|
||||
SITE: "${SITE_ID}"
|
||||
@ -50,6 +49,7 @@ services:
|
||||
EXPORTER_URL: "http://exporter:8092"
|
||||
LOG_FHIR_VALIDATION: "false"
|
||||
HTTP_SERVLET_REQUEST_SCHEME: "https"
|
||||
LOG_LEVEL: ${LOG_LEVEL_REPORTER:-WARN}
|
||||
|
||||
# In this initial development state of the bridgehead, we are trying to have so many volumes as possible.
|
||||
# However, in the first executions in the CCP sites, this volume seems to be very important. A report is
|
||||
@ -69,4 +69,4 @@ services:
|
||||
focus:
|
||||
environment:
|
||||
EXPORTER_URL: "http://exporter:8092"
|
||||
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
|
||||
AUTH_HEADER: "${EXPORTER_API_KEY}"
|
||||
|
@ -14,6 +14,7 @@ services:
|
||||
MAGICPL_CONNECTOR_APIKEY: ${IDMANAGER_READ_APIKEY}
|
||||
MAGICPL_CENTRAL_PATIENTLIST_APIKEY: ${IDMANAGER_CENTRAL_PATIENTLIST_APIKEY}
|
||||
MAGICPL_CONTROLNUMBERGENERATOR_APIKEY: ${IDMANAGER_CONTROLNUMBERGENERATOR_APIKEY}
|
||||
ML_LOG_LEVEL: ${LOG_LEVEL_IDMANAGER:-WARN}
|
||||
depends_on:
|
||||
- patientlist
|
||||
- traefik-forward-auth
|
||||
@ -44,6 +45,8 @@ services:
|
||||
- ML_UPLOAD_API_KEY=${IDMANAGER_UPLOAD_APIKEY}
|
||||
# Add Variables from /etc/patientlist-id-generators.env
|
||||
- PATIENTLIST_SEEDS_TRANSFORMED
|
||||
- ML_LOG_LEVEL=${LOG_LEVEL_PATIENTLIST:-WARN}
|
||||
#TODO confirm LOG_LEVEL
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.patientlist.rule=PathPrefix(`/patientlist`)"
|
||||
@ -102,11 +105,11 @@ 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: ${SITE_NAME}
|
||||
|
||||
volumes:
|
||||
patientlist-db-data:
|
||||
|
@ -25,6 +25,7 @@ services:
|
||||
OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
|
||||
OIDC_REALM: "${OIDC_REALM}"
|
||||
OIDC_URL: "${OIDC_URL}"
|
||||
LOG_LEVEL: ${LOG_LEVEL_MTBA:-WARN}
|
||||
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
|
@ -12,6 +12,8 @@ services:
|
||||
CTS_API_KEY: ${NNGM_CTS_APIKEY}
|
||||
CRYPT_KEY: ${NNGM_CRYPTKEY}
|
||||
#CTS_MAGICPL_SITE: ${SITE_ID}TODO
|
||||
LOG_LEVEL: ${LOG_LEVEL_NNGM:-WARN}
|
||||
restart: always
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"
|
||||
|
@ -3,13 +3,15 @@ version: "3.7"
|
||||
services:
|
||||
obds2fhir-rest:
|
||||
container_name: bridgehead-obds2fhir-rest
|
||||
image: docker.verbis.dkfz.de/samply/obds2fhir-rest:main
|
||||
image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main
|
||||
environment:
|
||||
IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
|
||||
MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
|
||||
SALT: ${LOCAL_SALT}
|
||||
KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false}
|
||||
MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
|
||||
LOG_LEVEL: ${LOG_LEVEL_REPORTER:-WARN}
|
||||
restart: always
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"
|
||||
|
@ -17,10 +17,10 @@ services:
|
||||
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
|
||||
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}"
|
||||
HTTP_RELATIVE_PATH: "/ccp-teiler"
|
||||
LOG_LEVEL: ${LOG_LEVEL_TEILER:-WARN}
|
||||
|
||||
teiler-dashboard:
|
||||
#image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
|
||||
image: samply/teiler-dashboard:develop
|
||||
image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop
|
||||
container_name: bridgehead-teiler-dashboard
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
@ -32,7 +32,6 @@ services:
|
||||
environment:
|
||||
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
|
||||
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
|
||||
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
|
||||
OIDC_URL: "${OIDC_URL}"
|
||||
OIDC_REALM: "${OIDC_REALM}"
|
||||
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
|
||||
@ -43,11 +42,13 @@ services:
|
||||
TEILER_PROJECT: "${PROJECT}"
|
||||
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
|
||||
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
|
||||
TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
|
||||
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
|
||||
TEILER_USER: "${OIDC_USER_GROUP}"
|
||||
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
|
||||
REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb"
|
||||
EXPORTER_DEFAULT_TEMPLATE_ID: "ccp"
|
||||
LOG_LEVEL: ${LOG_LEVEL_TEILER:-WARN}
|
||||
|
||||
|
||||
teiler-backend:
|
||||
@ -61,7 +62,6 @@ services:
|
||||
- "traefik.http.middlewares.teiler_backend_ccp_strip.stripprefix.prefixes=/ccp-teiler-backend"
|
||||
- "traefik.http.routers.teiler_backend_ccp.middlewares=teiler_backend_ccp_strip"
|
||||
environment:
|
||||
LOG_LEVEL: "INFO"
|
||||
APPLICATION_PORT: "8085"
|
||||
APPLICATION_ADDRESS: "${HOST}"
|
||||
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
|
||||
@ -70,10 +70,11 @@ services:
|
||||
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
|
||||
TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
|
||||
TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
|
||||
CENTRAX_URL: "${CENTRAXX_URL}"
|
||||
HTTP_PROXY: "http://forward_proxy:3128"
|
||||
ENABLE_MTBA: "${ENABLE_MTBA}"
|
||||
ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
|
||||
IDMANAGER_UPLOAD_APIKEY: "${IDMANAGER_UPLOAD_APIKEY}" # Only used to check if the ID Manager is active
|
||||
LOG_LEVEL: ${LOG_LEVEL_TEILER:-WARN}
|
||||
secrets:
|
||||
- ccp.conf
|
||||
|
||||
|
@ -1,2 +1,2 @@
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
10
ccp/vars
10
ccp/vars
@ -29,12 +29,4 @@ done
|
||||
idManagementSetup
|
||||
mtbaSetup
|
||||
obds2fhirRestSetup
|
||||
blazeSecondarySetup
|
||||
|
||||
for module in modules/*.sh
|
||||
do
|
||||
log DEBUG "sourcing $module"
|
||||
source $module
|
||||
done
|
||||
|
||||
transfairSetup
|
||||
blazeSecondarySetup
|
@ -2,7 +2,7 @@ version: "3.7"
|
||||
|
||||
services:
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
container_name: bridgehead-dhki-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-dhki-blaze:8080"
|
||||
@ -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
|
||||
- /srv/docker/bridgehead/dhki/queries_to_cache.conf:/queries_to_cache.conf
|
||||
depends_on:
|
||||
- "beam-proxy"
|
||||
- "blaze"
|
||||
|
10
dhki/vars
10
dhki/vars
@ -17,12 +17,4 @@ do
|
||||
done
|
||||
|
||||
idManagementSetup
|
||||
obds2fhirRestSetup
|
||||
|
||||
for module in modules/*.sh
|
||||
do
|
||||
log DEBUG "sourcing $module"
|
||||
source $module
|
||||
done
|
||||
|
||||
transfairSetup
|
||||
obds2fhirRestSetup
|
@ -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
|
||||
```
|
@ -2,14 +2,13 @@ version: "3.7"
|
||||
|
||||
services:
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||
container_name: bridgehead-itcc-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-itcc-blaze:8080"
|
||||
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
|
||||
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
|
||||
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
|
||||
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
|
||||
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
|
||||
ENFORCE_REFERENTIAL_INTEGRITY: "false"
|
||||
volumes:
|
||||
- "blaze-data:/app/data"
|
||||
@ -32,10 +31,6 @@ services:
|
||||
BEAM_PROXY_URL: http://beam-proxy:8081
|
||||
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
|
||||
EPSILON: 0.28
|
||||
QUERIES_TO_CACHE: '/queries_to_cache.conf'
|
||||
ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
|
||||
volumes:
|
||||
- /srv/docker/bridgehead/itcc/queries_to_cache.conf:/queries_to_cache.conf:ro
|
||||
depends_on:
|
||||
- "beam-proxy"
|
||||
- "blaze"
|
||||
|
@ -1,2 +0,0 @@
|
||||
bGlicmFyeSBSZXRyaWV2ZQp1c2luZyBGSElSIHZlcnNpb24gJzQuMC4wJwppbmNsdWRlIEZISVJIZWxwZXJzIHZlcnNpb24gJzQuMC4wJwpjb2Rlc3lzdGVtIFNhbXBsZU1hdGVyaWFsVHlwZTogJ2h0dHBzOi8vZmhpci5iYm1yaS5kZS9Db2RlU3lzdGVtL1NhbXBsZU1hdGVyaWFsVHlwZScKCmNvZGVzeXN0ZW0gbG9pbmM6ICdodHRwOi8vbG9pbmMub3JnJwoKY29udGV4dCBQYXRpZW50CkRLVEtfU1RSQVRfR0VOREVSX1NUUkFUSUZJRVIKICBES1RLX1NUUkFUX0RJQUdOT1NJU19TVFJBVElGSUVSCiAgSVRDQ19TVFJBVF9BR0VfQ0xBU1NfU1RSQVRJRklFUgogIERLVEtfU1RSQVRfREVGX0lOX0lOSVRJQUxfUE9QVUxBVElPTgp0cnVl
|
||||
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
|
@ -6,7 +6,7 @@ services:
|
||||
replicas: 0 #deactivate landing page
|
||||
|
||||
blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||
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: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist}
|
||||
restart: always
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)"
|
||||
|
@ -31,7 +31,6 @@ services:
|
||||
environment:
|
||||
DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}"
|
||||
TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend"
|
||||
TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard"
|
||||
OIDC_URL: "${OIDC_URL}"
|
||||
OIDC_REALM: "${OIDC_REALM}"
|
||||
OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}"
|
||||
@ -42,6 +41,7 @@ services:
|
||||
TEILER_PROJECT: "${PROJECT}"
|
||||
EXPORTER_API_KEY: "${EXPORTER_API_KEY}"
|
||||
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
|
||||
TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard"
|
||||
TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler"
|
||||
TEILER_USER: "${OIDC_USER_GROUP}"
|
||||
TEILER_ADMIN: "${OIDC_ADMIN_GROUP}"
|
||||
@ -69,6 +69,7 @@ services:
|
||||
TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler"
|
||||
TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de"
|
||||
TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en"
|
||||
CENTRAX_URL: "${CENTRAXX_URL}"
|
||||
HTTP_PROXY: "http://forward_proxy:3128"
|
||||
ENABLE_MTBA: "${ENABLE_MTBA}"
|
||||
ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}"
|
||||
|
@ -116,7 +116,7 @@ assertVarsNotEmpty() {
|
||||
MISSING_VARS=""
|
||||
|
||||
for VAR in $@; do
|
||||
if [ -z "${!VAR}" ]; then
|
||||
if [ -z "${!VAR}" ]; then
|
||||
MISSING_VARS+="$VAR "
|
||||
fi
|
||||
done
|
||||
@ -313,82 +313,15 @@ function sync_secrets() {
|
||||
-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 OIDC_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
|
||||
-e SECRET_DEFINITIONS=$secret_sync_args \
|
||||
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
|
||||
|
||||
set -a # Export variables as environment variables
|
||||
source /var/cache/bridgehead/secrets/oidc
|
||||
source /var/cache/bridgehead/secrets/*
|
||||
set +a # Export variables in the regular way
|
||||
}
|
||||
|
||||
function secret_sync_gitlab_token() {
|
||||
# Map the origin of the git repository /etc/bridgehead to the prefix recognized by Secret Sync
|
||||
local gitlab
|
||||
case "$(git -C /etc/bridgehead remote get-url origin)" in
|
||||
*git.verbis.dkfz.de*) gitlab=verbis;;
|
||||
*gitlab.bbmri-eric.eu*) gitlab=bbmri;;
|
||||
*)
|
||||
log "WARN" "Not running Secret Sync because the git repository /etc/bridgehead has unknown origin"
|
||||
return
|
||||
;;
|
||||
esac
|
||||
|
||||
if [ "$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
|
||||
|
||||
# Create a temporary directory for Secret Sync that is valid per boot
|
||||
secret_sync_tempdir="/tmp/bridgehead/secret-sync.boot-$(cat /proc/sys/kernel/random/boot_id)"
|
||||
mkdir -p $secret_sync_tempdir
|
||||
|
||||
# Use Secret Sync to validate the GitLab token in $secret_sync_tempdir/cache.
|
||||
# If it is missing or expired, Secret Sync will create a new token and write it to the file.
|
||||
# The git credential helper reads the token from the file during git pull.
|
||||
log "INFO" "Running Secret Sync for the GitLab token (gitlab=$gitlab)"
|
||||
docker pull docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest # make sure we have the latest image
|
||||
docker run --rm \
|
||||
-v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
|
||||
-v $root_crt_file:/run/secrets/root.crt.pem:ro \
|
||||
-v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
|
||||
-v $secret_sync_tempdir:/secret-sync/ \
|
||||
-e CACHE_PATH=/secret-sync/gitlab-token \
|
||||
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
|
||||
-e NO_PROXY=localhost,127.0.0.1 \
|
||||
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
|
||||
-e PROXY_ID=$proxy_id \
|
||||
-e BROKER_URL=$broker_url \
|
||||
-e GITLAB_PROJECT_ACCESS_TOKEN_PROVIDER=secret-sync-central.central-secret-sync.$broker_id \
|
||||
-e SECRET_DEFINITIONS=GitLabProjectAccessToken:BRIDGEHEAD_CONFIG_REPO_TOKEN:$gitlab \
|
||||
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
|
||||
if [ $? -eq 0 ]; then
|
||||
log "INFO" "Secret Sync was successful"
|
||||
# In the past we used to hardcode tokens into the repository URL. We have to remove those now for the git credential helper to become effective.
|
||||
CLEAN_REPO="$(git -C /etc/bridgehead remote get-url origin | sed -E 's|https://[^@]+@|https://|')"
|
||||
git -C /etc/bridgehead remote set-url origin "$CLEAN_REPO"
|
||||
# Set the git credential helper
|
||||
git -C /etc/bridgehead config credential.helper /srv/docker/bridgehead/lib/gitlab-token-helper.sh
|
||||
else
|
||||
log "WARN" "Secret Sync failed"
|
||||
# Remove the git credential helper
|
||||
git -C /etc/bridgehead config --unset credential.helper
|
||||
fi
|
||||
|
||||
# In the past the git credential helper was also set for /srv/docker/bridgehead but never used.
|
||||
# Let's remove it to avoid confusion. This line can be removed at some point the future when we
|
||||
# believe that it was removed on all/most production servers.
|
||||
git -C /srv/docker/bridgehead config --unset credential.helper
|
||||
}
|
||||
|
||||
capitalize_first_letter() {
|
||||
input="$1"
|
||||
capitalized="$(tr '[:lower:]' '[:upper:]' <<< ${input:0:1})${input:1}"
|
||||
|
@ -1,11 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
[ "$1" = "get" ] || exit
|
||||
|
||||
source "/tmp/bridgehead/secret-sync.boot-$(cat /proc/sys/kernel/random/boot_id)/gitlab-token"
|
||||
|
||||
# Any non-empty username works, only the token matters
|
||||
cat << EOF
|
||||
username=bk
|
||||
password=$BRIDGEHEAD_CONFIG_REPO_TOKEN
|
||||
EOF
|
41
lib/gitpassword.sh
Executable file
41
lib/gitpassword.sh
Executable file
@ -0,0 +1,41 @@
|
||||
#!/bin/bash
|
||||
|
||||
if [ "$1" != "get" ]; then
|
||||
echo "Usage: $0 get"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
baseDir() {
|
||||
# see https://stackoverflow.com/questions/59895
|
||||
SOURCE=${BASH_SOURCE[0]}
|
||||
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
|
||||
DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
|
||||
SOURCE=$(readlink "$SOURCE")
|
||||
[[ $SOURCE != /* ]] && SOURCE=$DIR/$SOURCE # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
|
||||
done
|
||||
DIR=$( cd -P "$( dirname "$SOURCE" )/.." >/dev/null 2>&1 && pwd )
|
||||
echo $DIR
|
||||
}
|
||||
|
||||
BASE=$(baseDir)
|
||||
cd $BASE
|
||||
|
||||
source lib/functions.sh
|
||||
|
||||
assertVarsNotEmpty SITE_ID || fail_and_report 1 "gitpassword.sh failed: SITE_ID is empty."
|
||||
|
||||
PARAMS="$(cat)"
|
||||
GITHOST=$(echo "$PARAMS" | grep "^host=" | sed 's/host=\(.*\)/\1/g')
|
||||
|
||||
fetchVarsFromVault GIT_PASSWORD
|
||||
|
||||
if [ -z "${GIT_PASSWORD}" ]; then
|
||||
fail_and_report 1 "gitpassword.sh failed: Git password not found."
|
||||
fi
|
||||
|
||||
cat <<EOF
|
||||
protocol=https
|
||||
host=$GITHOST
|
||||
username=bk-${SITE_ID}
|
||||
password=${GIT_PASSWORD}
|
||||
EOF
|
@ -41,14 +41,6 @@ if [ ! -z "$NNGM_CTS_APIKEY" ] && [ -z "$NNGM_AUTH" ]; then
|
||||
add_basic_auth_user "nngm" $generated_passwd "NNGM_AUTH" $PROJECT
|
||||
fi
|
||||
|
||||
if [ -z "$TRANSFAIR_AUTH" ]; then
|
||||
if [[ -n "$TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
|
||||
log "INFO" "Now generating basic auth user for transfair API (see adduser in bridgehead for more information). "
|
||||
generated_passwd="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 32)"
|
||||
add_basic_auth_user "transfair" $generated_passwd "TRANSFAIR_AUTH" $PROJECT
|
||||
fi
|
||||
fi
|
||||
|
||||
log "INFO" "Registering system units for bridgehead and bridgehead-update"
|
||||
cp -v \
|
||||
lib/systemd/bridgehead\@.service \
|
||||
|
@ -19,7 +19,7 @@ fi
|
||||
|
||||
hc_send log "Checking for bridgehead updates ..."
|
||||
|
||||
CONFFILE=/etc/bridgehead/$PROJECT.conf
|
||||
CONFFILE=/etc/bridgehead/$1.conf
|
||||
|
||||
if [ ! -e $CONFFILE ]; then
|
||||
fail_and_report 1 "Configuration file $CONFFILE not found."
|
||||
@ -33,7 +33,7 @@ export SITE_ID
|
||||
checkOwner /srv/docker/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /srv/docker/bridgehead"
|
||||
checkOwner /etc/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /etc/bridgehead"
|
||||
|
||||
secret_sync_gitlab_token
|
||||
CREDHELPER="/srv/docker/bridgehead/lib/gitpassword.sh"
|
||||
|
||||
CHANGES=""
|
||||
|
||||
@ -45,6 +45,10 @@ for DIR in /etc/bridgehead $(pwd); do
|
||||
if [ -n "$OUT" ]; then
|
||||
report_error log "The working directory $DIR is modified. Changed files: $OUT"
|
||||
fi
|
||||
if [ "$(git -C $DIR config --get credential.helper)" != "$CREDHELPER" ]; then
|
||||
log "INFO" "Configuring repo to use bridgehead git credential helper."
|
||||
git -C $DIR config credential.helper "$CREDHELPER"
|
||||
fi
|
||||
old_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
|
||||
if [ -z "$HTTPS_PROXY_FULL_URL" ]; then
|
||||
log "INFO" "Git is using no proxy!"
|
||||
@ -54,8 +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: ${SITE_ID}TODO
|
||||
restart: always
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"
|
||||
|
@ -1,17 +0,0 @@
|
||||
version: "3.7"
|
||||
|
||||
services:
|
||||
ssh-tunnel:
|
||||
image: docker.verbis.dkfz.de/cache/samply/ssh-tunnel
|
||||
container_name: bridgehead-ccp-ssh-tunnel
|
||||
environment:
|
||||
SSH_TUNNEL_USERNAME: "${SSH_TUNNEL_USERNAME}"
|
||||
SSH_TUNNEL_HOST: "${SSH_TUNNEL_HOST}"
|
||||
SSH_TUNNEL_PORT: "${SSH_TUNNEL_PORT:-22}"
|
||||
volumes:
|
||||
- "/etc/bridgehead/ssh-tunnel.conf:/ssh-tunnel.conf:ro"
|
||||
secrets:
|
||||
- privkey
|
||||
secrets:
|
||||
privkey:
|
||||
file: /etc/bridgehead/pki/ssh-tunnel.priv.pem
|
@ -1,6 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
if [ -n "$ENABLE_SSH_TUNNEL" ]; then
|
||||
log INFO "SSH Tunnel setup detected -- will start SSH Tunnel."
|
||||
OVERRIDE+=" -f ./modules/ssh-tunnel-compose.yml"
|
||||
fi
|
@ -1,19 +0,0 @@
|
||||
# SSH Tunnel Module
|
||||
|
||||
This module enables SSH tunneling capabilities for the Bridgehead installation.
|
||||
The primary use case for this is to connect bridgehead components that are hosted externally due to security concerns.
|
||||
To connect the new components to the locally running bridgehead infra one is supposed to write a docker-compose.override.yml changing the urls to point to the corresponding forwarded port of the ssh-tunnel container.
|
||||
|
||||
## Configuration Variables
|
||||
|
||||
- `ENABLE_SSH_TUNNEL`: Required to enable the module
|
||||
- `SSH_TUNNEL_USERNAME`: Username for SSH connection
|
||||
- `SSH_TUNNEL_HOST`: Target host for SSH tunnel
|
||||
- `SSH_TUNNEL_PORT`: SSH port (defaults to 22)
|
||||
|
||||
## Configuration Files
|
||||
|
||||
The module requires the following files to be present:
|
||||
|
||||
- `/etc/bridgehead/ssh-tunnel.conf`: SSH tunnel configuration file. Detailed information can be found [here](https://github.com/samply/ssh-tunnel?tab=readme-ov-file#configuration).
|
||||
- `/etc/bridgehead/pki/ssh-tunnel.priv.pem`: The SSH private key used to connect to the `SSH_TUNNEL_HOST`. **Passphrases for the key are not supported!**
|
@ -1,86 +0,0 @@
|
||||
|
||||
services:
|
||||
transfair:
|
||||
image: docker.verbis.dkfz.de/cache/samply/transfair:latest
|
||||
container_name: bridgehead-transfair
|
||||
environment:
|
||||
# NOTE: Those 3 variables need only to be passed if their set, otherwise transfair will complain about empty url values
|
||||
- TTP_URL
|
||||
- TTP_ML_API_KEY
|
||||
- TTP_GW_SOURCE
|
||||
- TTP_GW_EPIX_DOMAIN
|
||||
- TTP_GW_GPAS_DOMAIN
|
||||
- TTP_TYPE
|
||||
- TTP_AUTH
|
||||
- PROJECT_ID_SYSTEM
|
||||
- FHIR_REQUEST_URL=${FHIR_REQUEST_URL}
|
||||
- FHIR_INPUT_URL=${FHIR_INPUT_URL}
|
||||
- FHIR_OUTPUT_URL=${FHIR_OUTPUT_URL:-http://blaze:8080}
|
||||
- FHIR_REQUEST_CREDENTIALS=${FHIR_REQUEST_CREDENTIALS}
|
||||
- FHIR_INPUT_CREDENTIALS=${FHIR_INPUT_CREDENTIALS}
|
||||
- FHIR_OUTPUT_CREDENTIALS=${FHIR_OUTPUT_CREDENTIALS}
|
||||
- EXCHANGE_ID_SYSTEM=${EXCHANGE_ID_SYSTEM:-SESSION_ID}
|
||||
- DATABASE_URL=sqlite://transfair/data_requests.sql?mode=rwc
|
||||
- RUST_LOG=${RUST_LOG:-info}
|
||||
- TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs
|
||||
- TLS_DISABLE=${TRANSFAIR_TLS_DISABLE:-false}
|
||||
- NO_PROXY=${TRANSFAIR_NO_PROXIES}
|
||||
- ALL_PROXY=http://forward_proxy:3128
|
||||
volumes:
|
||||
- /var/cache/bridgehead/${PROJECT}/transfair:/transfair
|
||||
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.middlewares.transfair-strip.stripprefix.prefixes=/transfair"
|
||||
- "traefik.http.routers.transfair.middlewares=transfair-strip,transfair-auth"
|
||||
- "traefik.http.routers.transfair.rule=PathPrefix(`/transfair`)"
|
||||
- "traefik.http.services.transfair.loadbalancer.server.port=8080"
|
||||
- "traefik.http.routers.transfair.tls=true"
|
||||
|
||||
traefik:
|
||||
labels:
|
||||
- "traefik.http.middlewares.transfair-auth.basicauth.users=${TRANSFAIR_AUTH}"
|
||||
|
||||
transfair-input-blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||
container_name: bridgehead-transfair-input-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-transfair-input-blaze:8080"
|
||||
JAVA_TOOL_OPTIONS: "-Xmx1024m"
|
||||
DB_BLOCK_CACHE_SIZE: 1024
|
||||
CQL_EXPR_CACHE_SIZE: 8
|
||||
ENFORCE_REFERENTIAL_INTEGRITY: "false"
|
||||
volumes:
|
||||
- "transfair-input-blaze-data:/app/data"
|
||||
profiles: ["transfair-input-blaze"]
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.transfair-input-blaze.rule=PathPrefix(`/data-delivery`)"
|
||||
- "traefik.http.middlewares.transfair-input-strip.stripprefix.prefixes=/data-delivery"
|
||||
- "traefik.http.services.transfair-input-blaze.loadbalancer.server.port=8080"
|
||||
- "traefik.http.routers.transfair-input-blaze.middlewares=transfair-input-strip,transfair-auth"
|
||||
- "traefik.http.routers.transfair-input-blaze.tls=true"
|
||||
|
||||
transfair-request-blaze:
|
||||
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
|
||||
container_name: bridgehead-transfair-request-blaze
|
||||
environment:
|
||||
BASE_URL: "http://bridgehead-transfair-request-blaze:8080"
|
||||
JAVA_TOOL_OPTIONS: "-Xmx1024m"
|
||||
DB_BLOCK_CACHE_SIZE: 1024
|
||||
CQL_EXPR_CACHE_SIZE: 8
|
||||
ENFORCE_REFERENTIAL_INTEGRITY: "false"
|
||||
volumes:
|
||||
- "transfair-request-blaze-data:/app/data"
|
||||
profiles: ["transfair-request-blaze"]
|
||||
labels:
|
||||
- "traefik.enable=true"
|
||||
- "traefik.http.routers.transfair-request-blaze.rule=PathPrefix(`/data-requests`)"
|
||||
- "traefik.http.middlewares.transfair-request-strip.stripprefix.prefixes=/data-requests"
|
||||
- "traefik.http.services.transfair-request-blaze.loadbalancer.server.port=8080"
|
||||
- "traefik.http.routers.transfair-request-blaze.middlewares=transfair-request-strip,transfair-auth"
|
||||
- "traefik.http.routers.transfair-request-blaze.tls=true"
|
||||
|
||||
volumes:
|
||||
transfair-input-blaze-data:
|
||||
transfair-request-blaze-data:
|
@ -1,35 +0,0 @@
|
||||
#!/bin/bash -e
|
||||
|
||||
function transfairSetup() {
|
||||
if [[ -n "$TTP_URL" || -n "$EXCHANGE_ID_SYSTEM" ]]; then
|
||||
echo "Starting transfair."
|
||||
OVERRIDE+=" -f ./modules/transfair-compose.yml"
|
||||
if [ -n "$FHIR_INPUT_URL" ]; then
|
||||
log INFO "TransFAIR input fhir store set to external $FHIR_INPUT_URL"
|
||||
else
|
||||
log INFO "TransFAIR input fhir store not set writing to internal blaze"
|
||||
FHIR_INPUT_URL="http://transfair-input-blaze:8080"
|
||||
OVERRIDE+=" --profile transfair-input-blaze"
|
||||
fi
|
||||
if [ -n "$FHIR_REQUEST_URL" ]; then
|
||||
log INFO "TransFAIR request fhir store set to external $FHIR_REQUEST_URL"
|
||||
else
|
||||
log INFO "TransFAIR request fhir store not set writing to internal blaze"
|
||||
FHIR_REQUEST_URL="http://transfair-request-blaze:8080"
|
||||
OVERRIDE+=" --profile transfair-request-blaze"
|
||||
fi
|
||||
if [ -n "$TTP_GW_SOURCE" ]; then
|
||||
log INFO "TransFAIR configured with greifswald as ttp"
|
||||
TTP_TYPE="greifswald"
|
||||
elif [ -n "$TTP_ML_API_KEY" ]; then
|
||||
log INFO "TransFAIR configured with mainzelliste as ttp"
|
||||
TTP_TYPE="mainzelliste"
|
||||
else
|
||||
log INFO "TransFAIR configured without ttp"
|
||||
fi
|
||||
TRANSFAIR_NO_PROXIES="transfair-input-blaze,blaze,transfair-requests-blaze"
|
||||
if [ -n "${TRANSFAIR_NO_PROXY}" ]; then
|
||||
TRANSFAIR_NO_PROXIES+=",${TRANSFAIR_NO_PROXY}"
|
||||
fi
|
||||
fi
|
||||
}
|
@ -1,3 +0,0 @@
|
||||
FOCUS_TAG=develop
|
||||
BEAM_TAG=develop
|
||||
BLAZE_TAG=main
|
@ -1,3 +0,0 @@
|
||||
FOCUS_TAG=main
|
||||
BEAM_TAG=main
|
||||
BLAZE_TAG=0.32
|
@ -1,3 +0,0 @@
|
||||
FOCUS_TAG=develop
|
||||
BEAM_TAG=develop
|
||||
BLAZE_TAG=main
|
Reference in New Issue
Block a user