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Make C4 and Dktk work

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root
2022-01-21 09:32:21 +01:00
parent 7357870670
commit 31525571e1
8 changed files with 409 additions and 176 deletions
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197
c4/docker-compose.yml
View File

@ -20,181 +20,136 @@ secrets:
file: ../internal-configuration/proxy.xml
services:
traefik:
container_name: bridgehead_traefik
image: traefik:2.4
command:
- --api.insecure=true
- --entrypoints.web.address=:80
- --entrypoints.web-secure.address=:443
- --providers.docker=true
environment:
http_proxy: ""
HTTP_PROXY: ""
https_proxy: ""
HTTPS_PROXY: ""
ports:
- 80:80
- 443:443
- 8080:8080
volumes:
- /var/run/docker.sock:/var/run/docker.sock:ro
landing:
container_name: bridgehead_landingpage
image: nginx:stable
volumes:
- ../landing/:/usr/share/nginx/html
labels:
- "traefik.enable=true"
- "traefik.http.routers.landing.rule=PathPrefix(`/`)"
- "traefik.http.services.landing.loadbalancer.server.port=80"
connector:
container_name: bridgehead_c4_connector
image: "samply/share-client:c4-7"
image: docker.verbis.dkfz.de/ccp/connector:3
environment:
SITE: ${SITE}
SITEID: ${SITEID}
CENTRAL_SEARCH: ${CCP_CENTRALSEARCH_URL}
DECENTRAL_SEARCH: ${CCP_DECENTRALSEARCH_URL}
MDR_URL: ${CCP_MDR_URL}
MONITOR_URL: ${CCP_MONITOR_URL}
SHARE_URL: "${PROTOCOL}://${HOST}:${PORT}"
ID_MANAGER_URL: ${ID_MANAGER_URL}
PROJECTPSEUDONYMISATION_URL: ${PROJECTPSEUDONYMISATION_URL}
PATIENTLIST_URL: ${PATIENTLIST_URL}
STORE_URL: ${LDM_URL}
STORE_URL: http://bridgehead_c4_store:8080
LDM_URL: http://bridgehead_c4_store:8080
POSTGRES_HOST: ${CONNECTOR_DB_HOST}
POSTGRES_PORT: ${CONNECTOR_POSTGRES_PORT}
POSTGRES_DB: ${CONNECTOR_POSTGRES_DB}
POSTGRES_USER: ${CONNECTOR_POSTGRES_USER}
POSTGRES_PASS: ${CONNECTOR_POSTGRES_PASS}
HTTP_PROXY: ${HTTP_PROXY_URL}
HTTPS_PROXY: ${HTTP_PROXY_URL}
HTTP_PROXY_USERNAME: ${HTTP_PROXY_USER}
HTTP_PROXY_PASSWORD: ${HTTP_PROXY_PASSWORD}
HTTPS_PROXY_URL: ${HTTPS_PROXY_URL}
HTTPS_PROXY_USERNAME: ${HTTPS_PROXY_USER}
HTTPS_PROXY_PASSWORD: ${HTTPS_PROXY_PASSWORD}
NO_PROXY: ${NO_PROXY}
TZ: Europe/Berlin
POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
NNGM_PASSWORD: ${NNGM_PASSWORD}
NNGM_MAINZELLISTE_APIKEY: ${NNGM_MAINZELLISTE_APIKEY}
volumes:
- "connector_logs:/usr/local/tomcat/logs"
labels:
- "traefik.enable=true"
- "traefik.http.routers.c4_connector.rule=PathPrefix(`/c4-connector`)"
- "traefik.http.services.c4_connector.loadbalancer.server.port=8080"
depends_on:
- connector_db
ports:
- "8080:8080"
restart: always
networks:
- "samply"
- "connector-db"
env_file:
###TODO: Move into Image
- internal.env
connector_db:
container_name: bridgehead_c4_connector_db
image: postgres:10.17
environment:
POSTGRES_HOST: ${CONNECTOR_DB_HOST}
POSTGRES_DB: ${CONNECTOR_POSTGRES_DB}
POSTGRES_USER: ${CONNECTOR_POSTGRES_USER}
POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
TZ: Europe/Berlin
volumes:
- "connector_db_data:/var/lib/postgresql/data"
restart: always
networks:
- "connector-db"
ports:
- "8088:5432"
env_file:
###TODO: Move into Image
- internal.env
idmanager:
container_name: bridgehead_c4_idmanager
image: docker.verbis.dkfz.de/pseudonymisierung/magicpl:0.2.0-RC23
container_name: bridgehead_idmanager
image: docker.verbis.dkfz.de/ccp/idmanager:deploy-c4
environment:
MAGICPL_MAINZELLISTE_URL: ${MAGICPL_MAINZELLISTE_URL}
TOMCAT_REVERSEPROXY_FQDN: ${HOST}/id-manager
MAGICPL_MAINZELLISTE_API_KEY: ${MAGICPL_MAINZELLISTE_API_KEY}
MAGICPL_API_KEY: ${MAGICPL_API_KEY}
MAGICPL_API_KEY_CONNECTOR: ${MAGICPL_API_KEY_CONNECTOR}
MAGICPL_PASSPHRASE: ${MAGICPL_PASSPHRASE}
MAGICPL_MAINZELLISTE_CENTRAL_URL: ${MAGICPL_MAINZELLISTE_CENTRAL_URL}
MAGICPL_MAINZELLISTE_CENTRAL_API_KEY: ${MAGICPL_MAINZELLISTE_CENTRAL_API_KEY}
MAGICPL_CENTRAL_URL: ${MAGICPL_CENTRAL_URL}
MAGICPL_CENTRAL_API_KEY: ${MAGICPL_CENTRAL_API_KEY}
MAGICPL_OIDC_PROVIDER: ${MAGICPL_OIDC_PROVIDER}
MAGICPL_OIDC_CLIENT_ID: ${MAGICPL_OIDC_CLIENT_ID}
MAGICPL_OIDC_CLIENT_SECRET: ${MAGICPL_OIDC_CLIENT_SECRET}
MAGICPL_SITE: ${SITEID}
MAGICPL_LOG_LEVEL: info
TZ: Europe/Berlin
volumes:
- "idmanager_logs:/usr/local/tomcat/logs"
secrets:
- magicpl.docker.xml
- dktk_bridgehead_info.docker.xml
- proxy.docker.xml
depends_on:
- patientlist
ports:
- "8085:8080"
networks:
- "samply"
patientlist:
container_name: bridgehead_c4_patientlist
image: medicalinformatics/mainzelliste:develop
environment:
ML_DB_DRIVER: org.postgresql.Driver
ML_DB_TYPE: postgresql
ML_DB_HOST: ${ML_DB_HOST}
ML_DB_PORT: ${ML_DB_PORT}
ML_DB_NAME: ${ML_DB_NAME}
ML_DB_USER: ${ML_DB_USER}
ML_DB_PASS: ${ML_DB_PASS}
ML_API_KEY: ${ML_API_KEY}
ML_LOG_LEVEL: warning
ML_SITE: ${SITEID}
TZ: Europe/Berlin
labels:
- "traefik.http.routers.idmanager.rule=PathPrefix(`/id-manager`)"
- "traefik.http.middlewares.idmanager_strip.stripprefix.prefixes=/id-mana\
ger"
- "traefik.http.routers.idmanager.middlewares=idmanager_strip"
- "traefik.http.services.idmanager.loadbalancer.server.port=8080"
env_file:
- ../site-config/patientlist.env
volumes:
- "patientlist_logs:/usr/local/tomcat/logs"
secrets:
- mainzelliste.docker.conf
- centralSearchPublicKey
depends_on:
- patientlist_db
ports:
- "8086:8080"
networks:
- "samply"
patientlist_db:
container_name: bridgehead_c4_patientlist_db
image: postgres:13.1-alpine
environment:
POSTGRES_DB: ${ML_DB_NAME}
POSTGRES_USER: ${ML_DB_USER}
POSTGRES_PASSWORD: ${ML_DB_PASS}
TZ: Europe/Berlin
volumes:
- "patientlist_db_data:/var/lib/postgresql/data"
networks:
- "samply"
###TODO: Move into Image
- internal.env
store:
container_name: bridgehead_c4_store
image: docker.verbis.dkfz.de/ccp/samply.store:release-5.1.2
environment:
MDR_URL: ${CCP_MDR_URL}
MDR_NAMESPACE: ${MDR_NAMESPACE}
MDR_VALIDATION: ${MDR_VALIDATION}
POSTGRES_HOST: ${STORE_POSTGRES_HOST}
POSTGRES_PORT: ${STORE_POSTGRES_PORT}
POSTGRES_DB: ${STORE_POSTGRES_DB}
POSTGRES_USER: ${STORE_POSTGRES_USER}
POSTGRES_PASSWORD: ${STORE_POSTGRES_PASS}
POSTGRES_HOST: bridgehead_c4_store_db
POSTGRES_PORT: 5432
POSTGRES_DB: samplystore
POSTGRES_USER: samplystore
POSTGRES_PASSWORD: samplystore
TZ: Europe/Berlin
volumes:
- "store_logs:/usr/local/tomcat/logs"
labels:
- "traefik.enable=true"
- "traefik.http.routers.store_c4.rule=PathPrefix(`/c4-loc\
aldatamanagement`)"
depends_on:
- store_db
ports:
- "8083:8080"
restart: always
networks:
- "samply"
env_file:
###TODO: Move into Image
- internal.env
store_db:
container_name: bridgehead_c4_store_db
image: postgres:9.5-alpine
command: postgres -c datestyle='iso, dmy'
environment:
POSTGRES_PORT: ${STORE_POSTGRES_PORT}
POSTGRES_DB: ${STORE_POSTGRES_DB}
POSTGRES_USER: ${STORE_POSTGRES_USER}
POSTGRES_PASSWORD: ${STORE_POSTGRES_PASS}
TZ: Europe/Berlin
POSTGRES_PORT: 5432
POSTGRES_DB: samplystore
POSTGRES_USER: samplystore
POSTGRES_PASSWORD: samplystore
volumes:
- "store_db_data:/var/lib/postgresql/data"
restart: always
networks:
- "samply"
ports:
- "8084:5432"
networks:
samply:
driver: "bridge"
connector-db:
driver: "bridge"
env_file:
###TODO: Move into Image
- internal.env

18
c4/internal.env
View File

@ -1,14 +1,17 @@
SITE=bridgehead_test
SITEID=BRIDGEHEAD_TEST
TOMCAT_REVERSEPROXY_FQDN=${HOST}/c4-connector
DEPLOYMENT_CONTEXT=c4-connector
CONNECTOR_SHARE_URL="http://${HOST}:8080"
CONNECTOR_ENABLE_METRICS=false
CONNECTOR_MONITOR_INTERVAL=
CONNECTOR_UPDATE_SERVER=
CONNECTOR_POSTGRES_PORT=5432
CONNECTOR_POSTGRES_DB=samply.connector
CONNECTOR_POSTGRES_USER=samply.connector
POSTGRES_PORT=5432
POSTGRES_DB=samply.connector
POSTGRES_USER=samply.connector
HTTP_PROXY_HOST=${PROXY_URL}
HTTP_PROXY_USER=
@ -22,9 +25,12 @@ http_proxy=${PROXY_URL}
https_proxy=${PROXY_URL}
CCP_CENTRALSEARCH_URL=https://centralsearch-test.dktk.dkfz.de/
CENTRAL_SEARCH=https://centralsearch-test.dktk.dkfz.de/
CCP_DECENTRALSEARCH_URL=https://decentralsearch-test.ccp-it.dktk.dkfz.de/
DECENTRAL_SEARCH=https://decentralsearch-test.ccp-it.dktk.dkfz.de/
CCP_MDR_URL=https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr
MDR_URL=https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr
CCP_MONITOR_URL=
MONITOR_OPTOUT=
@ -44,4 +50,8 @@ ML_DB_USER=mainzelliste
CENTRAL_CONTROL_NUMBER_GENERATPR_URL=http://e260-serv-03/central/api
GLOBAL_ID=DKTK
MAINZELLISTE_URL=https://patientlist-test.ccpit.dktk.dkfz.de/mainzelliste
MAINZELLISTE_URL=https://patientlist-test.ccpit.dktk.dkfz.de/mainzelliste
NNGM_URL=https://test.anforderung.nngm.de/trial/nNGMv09/import-fb
NNGM_PROFILE=http://uk-koeln.de/fhir/StructureDefinition/Patient/nNGM/pseudonymisiert
NNGM_MAINZELLISTE_URL=https://test.verbis.dkfz.de/mpl