mirror of
https://github.com/samply/bridgehead.git
synced 2025-06-16 21:50:14 +02:00
Compare commits
1 Commits
ovis
...
bugfix/tes
| Author | SHA1 | Date | |
|---|---|---|---|
| da069b7473 |
@ -154,7 +154,7 @@ Pay special attention to:
|
|||||||
Clone the bridgehead repository:
|
Clone the bridgehead repository:
|
||||||
```shell
|
```shell
|
||||||
sudo mkdir -p /srv/docker/
|
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:
|
Then, run the installation script:
|
||||||
|
|||||||
@ -2,7 +2,7 @@ version: "3.7"
|
|||||||
|
|
||||||
services:
|
services:
|
||||||
blaze:
|
blaze:
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.31
|
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
||||||
container_name: bridgehead-ccp-blaze
|
container_name: bridgehead-ccp-blaze
|
||||||
environment:
|
environment:
|
||||||
BASE_URL: "http://bridgehead-ccp-blaze:8080"
|
BASE_URL: "http://bridgehead-ccp-blaze:8080"
|
||||||
|
|||||||
@ -13,7 +13,7 @@ services:
|
|||||||
PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
|
PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
|
||||||
APP_ID: dnpm-connect.${PROXY_ID}
|
APP_ID: dnpm-connect.${PROXY_ID}
|
||||||
DISCOVERY_URL: "./conf/central_targets.json"
|
DISCOVERY_URL: "./conf/central_targets.json"
|
||||||
LOCAL_TARGETS_FILE: "/conf/connect_targets.json"
|
LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
|
||||||
HTTP_PROXY: "http://forward_proxy:3128"
|
HTTP_PROXY: "http://forward_proxy:3128"
|
||||||
HTTPS_PROXY: "http://forward_proxy:3128"
|
HTTPS_PROXY: "http://forward_proxy:3128"
|
||||||
NO_PROXY: beam-proxy,dnpm-backend,host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
|
NO_PROXY: beam-proxy,dnpm-backend,host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
|
||||||
@ -25,7 +25,7 @@ services:
|
|||||||
volumes:
|
volumes:
|
||||||
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
|
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
|
||||||
- /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json: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:
|
labels:
|
||||||
- "traefik.enable=true"
|
- "traefik.enable=true"
|
||||||
- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"
|
- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"
|
||||||
|
|||||||
@ -1,99 +1,34 @@
|
|||||||
version: "3.7"
|
version: "3.7"
|
||||||
|
|
||||||
services:
|
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://${HOST}/auth/
|
|
||||||
labels:
|
|
||||||
- "traefik.enable=true"
|
|
||||||
- "traefik.http.routers.dnpm-frontend.rule=PathPrefix(`/`)"
|
|
||||||
- "traefik.http.services.dnpm-frontend.loadbalancer.server.port=3000"
|
|
||||||
- "traefik.http.routers.dnpm-frontend.tls=true"
|
|
||||||
|
|
||||||
dnpm-backend:
|
dnpm-backend:
|
||||||
|
image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
|
||||||
container_name: bridgehead-dnpm-backend
|
container_name: bridgehead-dnpm-backend
|
||||||
image: ghcr.io/dnpm-dip/backend:latest
|
|
||||||
environment:
|
environment:
|
||||||
- LOCAL_SITE=${ZPM_SITE}:${SITE_NAME} # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
|
- ZPM_SITE=${ZPM_SITE}
|
||||||
- RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
|
- N_RANDOM_FILES=${DNPM_SYNTH_NUM}
|
||||||
- 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
|
|
||||||
volumes:
|
volumes:
|
||||||
- /etc/bridgehead/dnpm/config:/dnpm_config
|
- /etc/bridgehead/dnpm:/bwhc_config:ro
|
||||||
- /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
|
- ${DNPM_DATA_DIR}:/bwhc_data
|
||||||
depends_on:
|
|
||||||
dnpm-authup:
|
|
||||||
condition: service_healthy
|
|
||||||
labels:
|
labels:
|
||||||
- "traefik.enable=true"
|
- "traefik.enable=true"
|
||||||
- "traefik.http.services.dnpm-backend.loadbalancer.server.port=9000"
|
- "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
|
||||||
# expose everything
|
- "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
|
||||||
- "traefik.http.routers.dnpm-backend.rule=PathPrefix(`/api`)"
|
- "traefik.http.routers.bwhc-backend.tls=true"
|
||||||
- "traefik.http.routers.dnpm-backend.tls=true"
|
|
||||||
- "traefik.http.routers.dnpm-backend.service=dnpm-backend"
|
|
||||||
# except ETL
|
|
||||||
- "traefik.http.routers.dnpm-backend-etl.rule=PathRegexp(`^/api(/.*)?etl(/.*)?$`)"
|
|
||||||
- "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(/.*)?$`)"
|
|
||||||
- "traefik.http.routers.dnpm-backend-peer.tls=true"
|
|
||||||
- "traefik.http.routers.dnpm-backend-peer.service=dnpm-backend"
|
|
||||||
- "traefik.http.routers.dnpm-backend-peer.middlewares=dnpm-backend-peer"
|
|
||||||
# this effectively denies all requests
|
|
||||||
# this is okay, because requests from peers don't go through Traefik
|
|
||||||
- "traefik.http.middlewares.dnpm-backend-peer.ipWhiteList.sourceRange=0.0.0.0/32"
|
|
||||||
|
|
||||||
landing:
|
dnpm-frontend:
|
||||||
|
image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
|
||||||
|
container_name: bridgehead-dnpm-frontend
|
||||||
|
links:
|
||||||
|
- dnpm-backend
|
||||||
|
environment:
|
||||||
|
- NUXT_HOST=0.0.0.0
|
||||||
|
- NUXT_PORT=8080
|
||||||
|
- BACKEND_PROTOCOL=https
|
||||||
|
- BACKEND_HOSTNAME=$HOST
|
||||||
|
- BACKEND_PORT=443
|
||||||
labels:
|
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
|
#!/bin/bash
|
||||||
|
|
||||||
if [ -n "${ENABLE_DNPM_NODE}" ]; then
|
if [ -n "${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 ./$PROJECT/modules/dnpm-node-compose.yml"
|
OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
|
||||||
|
|
||||||
# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
|
# 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 "${ZPM_SITE+x}" ]; then
|
if [ -z "${ZPM_SITE+x}" ]; then
|
||||||
log ERROR "Mandatory variable ZPM_SITE not defined!"
|
log ERROR "Mandatory variable ZPM_SITE not defined!"
|
||||||
exit 1
|
exit 1
|
||||||
fi
|
fi
|
||||||
mkdir -p /var/cache/bridgehead/dnpm/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/dnpm/'. Please run sudo './bridgehead install $PROJECT' again to fix the permissions."
|
if [ -z "${DNPM_DATA_DIR+x}" ]; then
|
||||||
DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:--1}
|
log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
|
||||||
DNPM_MYSQL_ROOT_PASSWORD="$(generate_simple_password 'dnpm mysql')"
|
exit 1
|
||||||
DNPM_AUTHUP_SECRET="$(generate_simple_password 'dnpm authup')"
|
fi
|
||||||
|
DNPM_SYNTH_NUM=${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
|
fi
|
||||||
|
|||||||
@ -1,112 +0,0 @@
|
|||||||
version: '3.7'
|
|
||||||
|
|
||||||
services:
|
|
||||||
|
|
||||||
ovis-traefik-forward-auth:
|
|
||||||
image: quay.io/oauth2-proxy/oauth2-proxy:latest
|
|
||||||
environment:
|
|
||||||
- http_proxy=${http_proxy:-http://forward_proxy:3128}
|
|
||||||
- https_proxy=${https_proxy:-http://forward_proxy:3128}
|
|
||||||
- OAUTH2_PROXY_PROVIDER=oidc
|
|
||||||
- OAUTH2_PROXY_SKIP_PROVIDER_BUTTON=true
|
|
||||||
- OAUTH2_PROXY_OIDC_ISSUER_URL=${OAUTH_ISSUER_URL}
|
|
||||||
- OAUTH2_PROXY_CLIENT_ID=${OAUTH_CLIENT_ID}
|
|
||||||
- OAUTH2_PROXY_CLIENT_SECRET=${OAUTH_CLIENT_SECRET}
|
|
||||||
- OAUTH2_PROXY_COOKIE_SECRET=${AUTHENTICATION_SECRET}
|
|
||||||
- OAUTH2_PROXY_COOKIE_DOMAINS=.${HOST:-localhost}
|
|
||||||
- OAUTH2_PROXY_COOKIE_REFRESH=4m
|
|
||||||
- OAUTH2_PROXY_COOKIE_EXPIRE=24h
|
|
||||||
- OAUTH2_PROXY_HTTP_ADDRESS=:4180
|
|
||||||
- OAUTH2_PROXY_REVERSE_PROXY=true
|
|
||||||
- OAUTH2_PROXY_WHITELIST_DOMAINS=.${HOST:-localhost}
|
|
||||||
- OAUTH2_PROXY_UPSTREAMS=static://202
|
|
||||||
- OAUTH2_PROXY_EMAIL_DOMAINS=*
|
|
||||||
#- OAUTH2_PROXY_ALLOWED_GROUPS=app-ovis
|
|
||||||
#- OAUTH2_PROXY_ERRORS_TO_INFO_LOG=true
|
|
||||||
- OAUTH2_PROXY_CODE_CHALLENGE_METHOD=S256
|
|
||||||
# For some reason, login.verbis.dkfz.de does not have a "groups" scope but this comes automatically through a
|
|
||||||
# scope called microprofile-jwt. Remove the following line once we have a "groups" scope.
|
|
||||||
- OAUTH2_PROXY_SCOPE=openid profile email
|
|
||||||
# Pass Authorization Header and some user information to spot
|
|
||||||
- OAUTH2_PROXY_SET_AUTHORIZATION_HEADER=true
|
|
||||||
- OAUTH2_PROXY_SET_XAUTHREQUEST=true
|
|
||||||
labels:
|
|
||||||
- "traefik.enable=true"
|
|
||||||
- "traefik.http.middlewares.ovis-traefik-forward-auth.forwardauth.address=http://ovis-traefik-forward-auth:4180"
|
|
||||||
- "traefik.http.middlewares.ovis-traefik-forward-auth.forwardauth.authResponseHeaders=Authorization, X-Forwarded-User, X-Auth-Request-User, X-Auth-Request-Email"
|
|
||||||
- "traefik.http.services.ovis-traefik-forward-auth.loadbalancer.server.port=4180"
|
|
||||||
- "traefik.http.routers.oauth2.rule=Host(`${HOST:-localhost}`) && PathPrefix(`/oauth2-ovis/`)"
|
|
||||||
- "traefik.http.routers.oauth2.tls=true"
|
|
||||||
|
|
||||||
fhir-transformer:
|
|
||||||
image: docker.verbis.dkfz.de/ovis/adt-mon-gql-fhir-transformer:latest
|
|
||||||
restart: on-failure
|
|
||||||
environment:
|
|
||||||
- FHIR_SERVER_URL=${FHIR_SERVER_URL:-http://bridgehead-ccp-blaze:8080/fhir}
|
|
||||||
- FHIR_USERNAME=${FHIR_USERNAME}
|
|
||||||
- FHIR_PASSWORD=${FHIR_PASSWORD}
|
|
||||||
volumes:
|
|
||||||
- /var/cache/bridgehead/ccp/ovis/shared_data:/app/output
|
|
||||||
|
|
||||||
mongo:
|
|
||||||
image: mongo:${MONGO_VER:-latest}
|
|
||||||
restart: always
|
|
||||||
command: mongod
|
|
||||||
- /var/cache/bridgehead/ccp/ovis/mongo/init/init.js:/docker-entrypoint-initdb.d/init.js
|
|
||||||
|
|
||||||
backend:
|
|
||||||
image: docker.verbis.dkfz.de/ovis/adt-mon-gql-backend:latest
|
|
||||||
restart: always
|
|
||||||
user: root
|
|
||||||
working_dir: /app
|
|
||||||
environment:
|
|
||||||
- APOLLO_PORT=${APOLLO_PORT:-4001}
|
|
||||||
- CREDOS_PORT=${CREDOS_PORT:-4000}
|
|
||||||
- MONGO_VER=latest
|
|
||||||
- CORS_ORIGIN=*
|
|
||||||
- DB=${DB:-onc_test}
|
|
||||||
- ADRESS=${ADRESS:-mongodb://mongo:27017}
|
|
||||||
depends_on:
|
|
||||||
- mongo
|
|
||||||
- fhir-transformer
|
|
||||||
healthcheck:
|
|
||||||
test: ["CMD", "curl", "-f", "http://localhost:${APOLLO_PORT:-4001}/health"]
|
|
||||||
interval: 5s
|
|
||||||
timeout: 3s
|
|
||||||
retries: 5
|
|
||||||
start_period: 10s
|
|
||||||
entrypoint: >
|
|
||||||
sh -c "
|
|
||||||
# First run the initialization process
|
|
||||||
while [ ! -f /shared/omock.json ]; do
|
|
||||||
echo 'Waiting for omock.json...'
|
|
||||||
sleep 5
|
|
||||||
done;
|
|
||||||
mkdir -p ./prep &&
|
|
||||||
cp /shared/omock.json ./prep/omock.json &&
|
|
||||||
node ./mgDB/prep/preprocessor.mjs &&
|
|
||||||
echo 'Processing complete' &&
|
|
||||||
exec node --watch index.js"
|
|
||||||
labels:
|
|
||||||
- "traefik.enable=true"
|
|
||||||
- "traefik.http.routers.ovis-backend.rule=Host(`${HOST:-localhost}`) && PathPrefix(`/graphql`)"
|
|
||||||
- "traefik.http.routers.ovis-backend.tls=true"
|
|
||||||
- "traefik.http.services.ovis-backend.loadbalancer.server.port=${APOLLO_PORT:-4001}"
|
|
||||||
volumes:
|
|
||||||
- /var/cache/bridgehead/ccp/ovis/shared_data:/shared
|
|
||||||
|
|
||||||
frontend:
|
|
||||||
image: docker.verbis.dkfz.de/ovis/adt-mon-gql-frontend:latest
|
|
||||||
restart: always
|
|
||||||
environment:
|
|
||||||
- PUBLIC_GRAPHQL_URL=https://${HOST:-localhost}/graphql
|
|
||||||
depends_on:
|
|
||||||
backend:
|
|
||||||
condition: service_healthy
|
|
||||||
working_dir: /app
|
|
||||||
labels:
|
|
||||||
- "traefik.enable=true"
|
|
||||||
- "traefik.http.routers.ovis-frontend.tls=true"
|
|
||||||
- "traefik.http.routers.ovis-frontend.rule=Host(`${HOST:-localhost}`)"
|
|
||||||
- "traefik.http.routers.ovis-frontend.middlewares=traefik-forward-auth"
|
|
||||||
- "traefik.http.services.ovis-frontend.loadbalancer.server.port=5173"
|
|
||||||
@ -1,108 +0,0 @@
|
|||||||
#!/bin/bash -e
|
|
||||||
|
|
||||||
if [ -n "$ENABLE_OVIS" ];then
|
|
||||||
# Setup MongoDB initialization directory if it doesn't exist
|
|
||||||
mkdir -p "/var/cache/bridgehead/ccp/ovis/mongo/init"
|
|
||||||
|
|
||||||
# Generate MongoDB initialization script directly
|
|
||||||
cat > "/var/cache/bridgehead/ccp/ovis/mongo/init/init.js" << 'EOF'
|
|
||||||
db = db.getSiblingDB("test_credos");
|
|
||||||
db.createCollection("user");
|
|
||||||
db.user.insertMany([{
|
|
||||||
"_id": "OVIS-Root",
|
|
||||||
"createdAt": new Date(),
|
|
||||||
"createdBy": "system",
|
|
||||||
"role": "super-admin",
|
|
||||||
"status": "active",
|
|
||||||
"pseudonymization": false,
|
|
||||||
"darkMode": false,
|
|
||||||
"colorTheme": "CCCMunich",
|
|
||||||
"language": "de",
|
|
||||||
}]);
|
|
||||||
|
|
||||||
db = db.getSiblingDB("onc_test");
|
|
||||||
db.createCollection("user");
|
|
||||||
db.user.insertMany([{
|
|
||||||
"_id": "OVIS-Root",
|
|
||||||
"createdAt": new Date(),
|
|
||||||
"createdBy": "system",
|
|
||||||
"role": "super-admin",
|
|
||||||
"status": "active",
|
|
||||||
"pseudonymization": false,
|
|
||||||
"darkMode": false,
|
|
||||||
"colorTheme": "CCCMunich",
|
|
||||||
"language": "de",
|
|
||||||
}]);
|
|
||||||
|
|
||||||
db.ops.insertMany([
|
|
||||||
{"OPSC_4":"1-40","OPS_Gruppen_Text":"Biopsie ohne Inzision an Nervensystem und endokrinen Organen "},
|
|
||||||
{"OPSC_4":"1-44","OPS_Gruppen_Text":"Biopsie ohne Inzision an den Verdauungsorganen"},
|
|
||||||
{"OPSC_4":"1-40","OPS_Gruppen_Text":"Biopsie ohne Inzision an anderen Organen und Geweben"},
|
|
||||||
{"OPSC_4":"1-50","OPS_Gruppen_Text":"Biopsie an Haut, Mamma, Knochen und Muskeln durch Inzision"},
|
|
||||||
{"OPSC_4":"1-51","OPS_Gruppen_Text":"Biopsie an Nervengewebe, Hypophyse, Corpus pineale durch Inzision und Trepanation von Schädelknochen "},
|
|
||||||
{"OPSC_4":"1-55","OPS_Gruppen_Text":"Biopsie an anderen Verdauungsorganen, Zwerchfell und (Retro-)Peritoneum durch Inzision "},
|
|
||||||
{"OPSC_4":"1-56","OPS_Gruppen_Text":"Biopsie an Harnwegen und männlichen Geschlechtsorgannen durch Inzision"},
|
|
||||||
{"OPSC_4":"1-58","OPS_Gruppen_Text":"Biopsie an anderen Organen durch Inzision "},
|
|
||||||
{"OPSC_4":"1-63","OPS_Gruppen_Text":"Diagnostische Endoskopie des oberen Verdauungstraktes"},
|
|
||||||
{"OPSC_4":"1-65","OPS_Gruppen_Text":"Diagnostische Endoskopie des unteren Verdauungstraktes"},
|
|
||||||
{"OPSC_4":"1-69","OPS_Gruppen_Text":"Diagnostische Endoskopie durch Inzision und intraoperativ "},
|
|
||||||
{"OPSC_4":"5-01","OPS_Gruppen_Text":"Inzision (Trepanation) und Exzision an Schädel, Gehirn und Hirnhäuten"},
|
|
||||||
{"OPSC_4":"5-02","OPS_Gruppen_Text":"Andere Operationen an Schädel, Gehirn und Hirnhäuten"},
|
|
||||||
{"OPSC_4":"5-03","OPS_Gruppen_Text":"Operationen an Rückenmark, Rückenmarkhäuten und Spinalkanal"},
|
|
||||||
{"OPSC_4":"5-05","OPS_Gruppen_Text":"Andere Operationen an Nerven und Nervenganglien "},
|
|
||||||
{"OPSC_4":"5-06","OPS_Gruppen_Text":"Operationen an Schilddrüse und Nebenschilddrüse "},
|
|
||||||
{"OPSC_4":"5-07","OPS_Gruppen_Text":"Operationen an anderen endokrinen Drüsen "},
|
|
||||||
{"OPSC_4":"5-20","OPS_Gruppen_Text":"Andere Operationen an Mittel- und Innenohr "},
|
|
||||||
{"OPSC_4":"5-25","OPS_Gruppen_Text":"Operationen an der Zunge "},
|
|
||||||
{"OPSC_4":"5-31","OPS_Gruppen_Text":"Andere Larynxoperationen und Operationen an der Trachea "},
|
|
||||||
{"OPSC_4":"5-32","OPS_Gruppen_Text":"Exzision und Resektion an Lunge und Bronchus "},
|
|
||||||
{"OPSC_4":"5-33","OPS_Gruppen_Text":"Andere Operationen an Lunge und Bronchus"},
|
|
||||||
{"OPSC_4":"5-34","OPS_Gruppen_Text":"Operationen an Brustwand, Pleura, Mediastinum und Zwerchfell "},
|
|
||||||
{"OPSC_4":"5-37","OPS_Gruppen_Text":"Rhythmuschirurgie und andere Operationen an Herz und Perikard"},
|
|
||||||
{"OPSC_4":"5-38","OPS_Gruppen_Text":"Inzision, Exzision und Verschluß von Blutgefäßen "},
|
|
||||||
{"OPSC_4":"5-39","OPS_Gruppen_Text":"Andere Operationen an Blutgefäßen "},
|
|
||||||
{"OPSC_4":"5-40","OPS_Gruppen_Text":"Operationen am Lymphgewebe "},
|
|
||||||
{"OPSC_4":"5-41","OPS_Gruppen_Text":"Operationen an Milz und Knochenmark "},
|
|
||||||
{"OPSC_4":"5-42","OPS_Gruppen_Text":"Operationen am Ösophagus "},
|
|
||||||
{"OPSC_4":"5-43","OPS_Gruppen_Text":"Inzision, Exzision und Resektion am Magen "},
|
|
||||||
{"OPSC_4":"5-44","OPS_Gruppen_Text":"Erweiterte Magenresektion und andere Operationen am Magen "},
|
|
||||||
{"OPSC_4":"5-45","OPS_Gruppen_Text":"Inzision, Exzision, Resektion und Anastomose an Dünn- und Dickdarm "},
|
|
||||||
{"OPSC_4":"5-46","OPS_Gruppen_Text":"Andere Operationen an Dünn- und Dickdarm "},
|
|
||||||
{"OPSC_4":"5-47","OPS_Gruppen_Text":"Operationen an der Appendix "},
|
|
||||||
{"OPSC_4":"5-48","OPS_Gruppen_Text":"Operationen am Rektum "},
|
|
||||||
{"OPSC_4":"5-49","OPS_Gruppen_Text":"Operationen am Anus "},
|
|
||||||
{"OPSC_4":"5-50","OPS_Gruppen_Text":"Operationen an der Leber "},
|
|
||||||
{"OPSC_4":"5-51","OPS_Gruppen_Text":"Operationen an Gallenblase und Gallenwegen "},
|
|
||||||
{"OPSC_4":"5-52","OPS_Gruppen_Text":"Operationen am Pankreas "},
|
|
||||||
{"OPSC_4":"5-53","OPS_Gruppen_Text":"Verschluß abdominaler Hernien "},
|
|
||||||
{"OPSC_4":"5-54","OPS_Gruppen_Text":"Andere Operationen in der Bauchregion "},
|
|
||||||
{"OPSC_4":"5-55","OPS_Gruppen_Text":"Operationen an der Niere "},
|
|
||||||
{"OPSC_4":"5-56","OPS_Gruppen_Text":"Operationen am Ureter "},
|
|
||||||
{"OPSC_4":"5-57","OPS_Gruppen_Text":"Operationen an der Harnblase "},
|
|
||||||
{"OPSC_4":"5-59","OPS_Gruppen_Text":"Andere Operationen an den Harnorganen "},
|
|
||||||
{"OPSC_4":"5-60","OPS_Gruppen_Text":"Operationen an Prostata und Vesiculae seminales "},
|
|
||||||
{"OPSC_4":"5-61","OPS_Gruppen_Text":"Operationen an Skrotum und Tunica vaginalis testis"},
|
|
||||||
{"OPSC_4":"5-62","OPS_Gruppen_Text":"Operationen am Hoden "},
|
|
||||||
{"OPSC_4":"5-65","OPS_Gruppen_Text":"Operationen am Ovar "},
|
|
||||||
{"OPSC_4":"5-68","OPS_Gruppen_Text":"Inzision, Exzision und Exstirpation des Uterus "},
|
|
||||||
{"OPSC_4":"5-70","OPS_Gruppen_Text":"Operationen an Vagina und Douglasraum "},
|
|
||||||
{"OPSC_4":"5-71","OPS_Gruppen_Text":"Operationen an der Vulva "},
|
|
||||||
{"OPSC_4":"5-85","OPS_Gruppen_Text":"Operationen an Muskeln, Sehnen, Faszien und Schleimbeuteln"},
|
|
||||||
{"OPSC_4":"5-87","OPS_Gruppen_Text":"Exzision und Resektion der Mamma "},
|
|
||||||
{"OPSC_4":"5-89","OPS_Gruppen_Text":"Operationen an Haut und Unterhaut "},
|
|
||||||
{"OPSC_4":"5-90","OPS_Gruppen_Text":"Operative Wiederherstellung und Rekonstruktion von Haut und Unterhaut"},
|
|
||||||
{"OPSC_4":"5-91","OPS_Gruppen_Text":"Andere Operationen an Haut und Unterhaut "},
|
|
||||||
{"OPSC_4":"5-93","OPS_Gruppen_Text":"Angaben zum Transplantat und zu verwendeten Materialien"},
|
|
||||||
{"OPSC_4":"5-98","OPS_Gruppen_Text":"Spezielle Operationstechniken und Operationen bei speziellen Versorgungssituationen "},
|
|
||||||
{"OPSC_4":"8-13","OPS_Gruppen_Text":"Manipulation am Harntrakt"},
|
|
||||||
{"OPSC_4":"8-14","OPS_Gruppen_Text":"Therapeutische Kathedirisierung, Aspiration, Punktion und Spülung "},
|
|
||||||
{"OPSC_4":"8-15","OPS_Gruppen_Text":"Therapeutische Aspiration und Entleerung durch Punktion "},
|
|
||||||
{"OPSC_4":"8-17","OPS_Gruppen_Text":"Spülung (Lavage) "},
|
|
||||||
{"OPSC_4":"8-19","OPS_Gruppen_Text":"Verbände "},
|
|
||||||
{"OPSC_4":"8-77","OPS_Gruppen_Text":"Maßnahmen im Rahmen der Reanimation "},
|
|
||||||
{"OPSC_4":"8-92","OPS_Gruppen_Text":"Neurologisches Monitoring "},
|
|
||||||
])
|
|
||||||
EOF
|
|
||||||
|
|
||||||
OVERRIDE+=" -f ./$PROJECT/modules/ovis-compose.yml"
|
|
||||||
fi
|
|
||||||
10
dhki/vars
10
dhki/vars
@ -17,12 +17,4 @@ do
|
|||||||
done
|
done
|
||||||
|
|
||||||
idManagementSetup
|
idManagementSetup
|
||||||
obds2fhirRestSetup
|
obds2fhirRestSetup
|
||||||
|
|
||||||
for module in modules/*.sh
|
|
||||||
do
|
|
||||||
log DEBUG "sourcing $module"
|
|
||||||
source $module
|
|
||||||
done
|
|
||||||
|
|
||||||
transfairSetup
|
|
||||||
@ -16,7 +16,7 @@ services:
|
|||||||
- --entrypoints.web.http.redirections.entrypoint.scheme=https
|
- --entrypoints.web.http.redirections.entrypoint.scheme=https
|
||||||
labels:
|
labels:
|
||||||
- "traefik.enable=true"
|
- "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.entrypoints=websecure"
|
||||||
- "traefik.http.routers.dashboard.service=api@internal"
|
- "traefik.http.routers.dashboard.service=api@internal"
|
||||||
- "traefik.http.routers.dashboard.tls=true"
|
- "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}
|
PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
|
||||||
APP_ID: dnpm-connect.${DNPM_PROXY_ID}
|
APP_ID: dnpm-connect.${DNPM_PROXY_ID}
|
||||||
DISCOVERY_URL: "./conf/central_targets.json"
|
DISCOVERY_URL: "./conf/central_targets.json"
|
||||||
LOCAL_TARGETS_FILE: "/conf/connect_targets.json"
|
LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
|
||||||
HTTP_PROXY: http://forward_proxy:3128
|
HTTP_PROXY: http://forward_proxy:3128
|
||||||
HTTPS_PROXY: http://forward_proxy:3128
|
HTTPS_PROXY: http://forward_proxy:3128
|
||||||
NO_PROXY: dnpm-beam-proxy,dnpm-backend, host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
|
NO_PROXY: dnpm-beam-proxy,dnpm-backend, host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
|
||||||
@ -41,7 +41,7 @@ services:
|
|||||||
volumes:
|
volumes:
|
||||||
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
|
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
|
||||||
- /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json: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:
|
labels:
|
||||||
- "traefik.enable=true"
|
- "traefik.enable=true"
|
||||||
- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"
|
- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"
|
||||||
|
|||||||
@ -1,99 +1,34 @@
|
|||||||
version: "3.7"
|
version: "3.7"
|
||||||
|
|
||||||
services:
|
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://${HOST}/auth/
|
|
||||||
labels:
|
|
||||||
- "traefik.enable=true"
|
|
||||||
- "traefik.http.routers.dnpm-frontend.rule=PathPrefix(`/`)"
|
|
||||||
- "traefik.http.services.dnpm-frontend.loadbalancer.server.port=3000"
|
|
||||||
- "traefik.http.routers.dnpm-frontend.tls=true"
|
|
||||||
|
|
||||||
dnpm-backend:
|
dnpm-backend:
|
||||||
|
image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
|
||||||
container_name: bridgehead-dnpm-backend
|
container_name: bridgehead-dnpm-backend
|
||||||
image: ghcr.io/dnpm-dip/backend:latest
|
|
||||||
environment:
|
environment:
|
||||||
- LOCAL_SITE=${ZPM_SITE}:${SITE_NAME} # Format: {Site-ID}:{Site-name}, e.g. UKT:Tübingen
|
- ZPM_SITE=${ZPM_SITE}
|
||||||
- RD_RANDOM_DATA=${DNPM_SYNTH_NUM:--1}
|
- N_RANDOM_FILES=${DNPM_SYNTH_NUM}
|
||||||
- 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
|
|
||||||
volumes:
|
volumes:
|
||||||
- /etc/bridgehead/dnpm/config:/dnpm_config
|
- /etc/bridgehead/dnpm:/bwhc_config:ro
|
||||||
- /var/cache/bridgehead/dnpm/backend-data:/dnpm_data
|
- ${DNPM_DATA_DIR}:/bwhc_data
|
||||||
depends_on:
|
|
||||||
dnpm-authup:
|
|
||||||
condition: service_healthy
|
|
||||||
labels:
|
labels:
|
||||||
- "traefik.enable=true"
|
- "traefik.enable=true"
|
||||||
- "traefik.http.services.dnpm-backend.loadbalancer.server.port=9000"
|
- "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
|
||||||
# expose everything
|
- "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
|
||||||
- "traefik.http.routers.dnpm-backend.rule=PathPrefix(`/api`)"
|
- "traefik.http.routers.bwhc-backend.tls=true"
|
||||||
- "traefik.http.routers.dnpm-backend.tls=true"
|
|
||||||
- "traefik.http.routers.dnpm-backend.service=dnpm-backend"
|
|
||||||
# except ETL
|
|
||||||
- "traefik.http.routers.dnpm-backend-etl.rule=PathRegexp(`^/api(/.*)?etl(/.*)?$`)"
|
|
||||||
- "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(/.*)?$`)"
|
|
||||||
- "traefik.http.routers.dnpm-backend-peer.tls=true"
|
|
||||||
- "traefik.http.routers.dnpm-backend-peer.service=dnpm-backend"
|
|
||||||
- "traefik.http.routers.dnpm-backend-peer.middlewares=dnpm-backend-peer"
|
|
||||||
# this effectively denies all requests
|
|
||||||
# this is okay, because requests from peers don't go through Traefik
|
|
||||||
- "traefik.http.middlewares.dnpm-backend-peer.ipWhiteList.sourceRange=0.0.0.0/32"
|
|
||||||
|
|
||||||
landing:
|
dnpm-frontend:
|
||||||
|
image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
|
||||||
|
container_name: bridgehead-dnpm-frontend
|
||||||
|
links:
|
||||||
|
- dnpm-backend
|
||||||
|
environment:
|
||||||
|
- NUXT_HOST=0.0.0.0
|
||||||
|
- NUXT_PORT=8080
|
||||||
|
- BACKEND_PROTOCOL=https
|
||||||
|
- BACKEND_HOSTNAME=$HOST
|
||||||
|
- BACKEND_PORT=443
|
||||||
labels:
|
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
|
#!/bin/bash
|
||||||
|
|
||||||
if [ -n "${ENABLE_DNPM_NODE}" ]; then
|
if [ -n "${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 ./$PROJECT/modules/dnpm-node-compose.yml"
|
OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml"
|
||||||
|
|
||||||
# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.conf
|
# 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 "${ZPM_SITE+x}" ]; then
|
if [ -z "${ZPM_SITE+x}" ]; then
|
||||||
log ERROR "Mandatory variable ZPM_SITE not defined!"
|
log ERROR "Mandatory variable ZPM_SITE not defined!"
|
||||||
exit 1
|
exit 1
|
||||||
fi
|
fi
|
||||||
mkdir -p /var/cache/bridgehead/dnpm/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/dnpm/'. Please run sudo './bridgehead install $PROJECT' again to fix the permissions."
|
if [ -z "${DNPM_DATA_DIR+x}" ]; then
|
||||||
DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:--1}
|
log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
|
||||||
DNPM_MYSQL_ROOT_PASSWORD="$(generate_simple_password 'dnpm mysql')"
|
exit 1
|
||||||
DNPM_AUTHUP_SECRET="$(generate_simple_password 'dnpm authup')"
|
fi
|
||||||
|
DNPM_SYNTH_NUM=${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
|
fi
|
||||||
|
|||||||
@ -1,51 +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
|
|
||||||
- INSTITUTE_TTP_URL
|
|
||||||
- INSTITUTE_TTP_API_KEY
|
|
||||||
- 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}
|
|
||||||
volumes:
|
|
||||||
- /var/cache/bridgehead/${PROJECT}/transfair:/transfair
|
|
||||||
|
|
||||||
transfair-input-blaze:
|
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
|
||||||
container_name: bridgehead-transfair-input-blaze
|
|
||||||
environment:
|
|
||||||
BASE_URL: "http://bridgehead-transfair-input-blaze:8080"
|
|
||||||
JAVA_TOOL_OPTIONS: "-Xmx1024m"
|
|
||||||
DB_BLOCK_CACHE_SIZE: 1024
|
|
||||||
CQL_EXPR_CACHE_SIZE: 8
|
|
||||||
ENFORCE_REFERENTIAL_INTEGRITY: "false"
|
|
||||||
volumes:
|
|
||||||
- "transfair-input-blaze-data:/app/data"
|
|
||||||
profiles: ["transfair-input-blaze"]
|
|
||||||
|
|
||||||
transfair-request-blaze:
|
|
||||||
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
|
|
||||||
container_name: bridgehead-transfair-requests-blaze
|
|
||||||
environment:
|
|
||||||
BASE_URL: "http://bridgehead-transfair-requests-blaze:8080"
|
|
||||||
JAVA_TOOL_OPTIONS: "-Xmx1024m"
|
|
||||||
DB_BLOCK_CACHE_SIZE: 1024
|
|
||||||
CQL_EXPR_CACHE_SIZE: 8
|
|
||||||
ENFORCE_REFERENTIAL_INTEGRITY: "false"
|
|
||||||
volumes:
|
|
||||||
- "transfair-request-blaze-data:/app/data"
|
|
||||||
profiles: ["transfair-request-blaze"]
|
|
||||||
|
|
||||||
volumes:
|
|
||||||
transfair-input-blaze-data:
|
|
||||||
transfair-request-blaze-data:
|
|
||||||
@ -1,22 +0,0 @@
|
|||||||
#!/bin/bash -e
|
|
||||||
|
|
||||||
function transfairSetup() {
|
|
||||||
if [[ -n "$INSTITUTE_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-requests-blaze:8080"
|
|
||||||
OVERRIDE+=" --profile transfair-request-blaze"
|
|
||||||
fi
|
|
||||||
fi
|
|
||||||
}
|
|
||||||
Reference in New Issue
Block a user