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Updated Readme and c4 docker file

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Patrick Skowronek 2021-12-27 11:16:27 +01:00
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README.md
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This repository contains all information and tools to deploy a bridgehead. If you have any questions about deploying a bridgehead, please contact us. This repository contains all information and tools to deploy a bridgehead. If you have any questions about deploying a bridgehead, please contact us.
There are some prerequisites, which need to be meet befor starting a bridgehead. There are some prerequisites, which need to be meet befor starting a bridgehead. If you runnig a Windows or Mac OS maschine you should read starting a bridgehead. If you running a Linux maschine you can do start and install a bridgehead.
## Starting
## Install
Create the dir /src/docker and clone the repository.
The first step is to copy the site.conf file. It contains some configuration and secrets for your bridgehead. The first step is to copy the site.conf file. It contains some configuration and secrets for your bridgehead.
With cp site.dev.conf site.conf you can clone the template. You need to set the project accoriding to the which bridgehead you want to start. It's either a GBN/BBMRI-ERIC, DKTK or C4 Bridgehead. With cp site.dev.conf site.conf you can clone the template. You need to set the project accoriding to the which bridgehead you want to start. It's either a GBN/BBMRI-ERIC, DKTK or C4 Bridgehead.
In this file you can put important varibales
### DKTK
### GBA/BBMRI-ERIC
### C4
The following vairbales need to be set
C4_SAMPLY_STORE_PASS
C4_CONNECTOR_POSTGRES_PASSWORD
The next step is creating a configuration for your bridghead. We can provide you a configuration git repository for bridgehead, just ask us. When you have a DKTK or C4 Bridgehead you propably need some configuration from us anyways. The next step is creating a configuration for your bridghead. We can provide you a configuration git repository for bridgehead, just ask us. When you have a DKTK or C4 Bridgehead you propably need some configuration from us anyways.
git submodule add -f https://"$git_username":"$git_access_token"@code.mitro.dkfz.de/scm/bd/"$site_name_lowercase"-config.git ./site-config git submodule add -f https://"$git_username":"$git_access_token"@code.mitro.dkfz.de/scm/bd/"$site_name_lowercase"-config.git ./site-config

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c4/docker-compose.yml
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version: "3.7" version: "3.7"
volumes: volumes:
connector_db_data: connector_db_data: null
connector_logs: connector_logs: null
patientlist_db_data: patientlist_db_data: null
patientlist_logs: patientlist_logs: null
idmanager_logs: idmanager_logs: null
store_db_data: store_db_data: null
store_logs: store_logs: null
secrets: secrets:
mainzelliste.docker.conf: mainzelliste.docker.conf:
file: ./internal-configuration/mainzelliste.conf file: ./internal-configuration/mainzelliste.conf
@ -20,7 +20,7 @@ secrets:
file: ./internal-configuration/proxy.xml file: ./internal-configuration/proxy.xml
services: services:
connector: connector:
container_name: bridgehead_c4_connector container_name: bridgehead_c4_connector
image: "samply/share-client:c4-7" image: "samply/share-client:c4-7"
environment: environment:
@ -56,7 +56,7 @@ services:
extra_hosts: extra_hosts:
- "host.docker.internal:host-gateway" - "host.docker.internal:host-gateway"
- "${HOST}:${HOSTIP}" - "${HOST}:${HOSTIP}"
connector_db: connector_db:
container_name: bridgehead_connector_db container_name: bridgehead_connector_db
image: postgres:10.17 image: postgres:10.17
@ -105,7 +105,7 @@ services:
depends_on: depends_on:
- patientlist - patientlist
store: store:
container_name: bridgehead_store container_name: bridgehead_store
image: docker.verbis.dkfz.de/ccp/samply.store:release-5.1.2 image: docker.verbis.dkfz.de/ccp/samply.store:release-5.1.2
environment: environment:

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gbn/gbn.env.dev
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GBN_CONNECTOR_POSTGRES_PASS=samply SITE=
SITEID=
TESTPROD=
project=gbn
### Bridgehead Operator
# users may see this contact data for support purposes
OPERATOR_FIRST_NAME=
OPERATOR_LAST_NAME=
OPERATOR_EMAIL=
OPERATOR_PHONE=
### Proxy configuration
## ex.: http://my-proxy-host:my-proxy-port
HTTP_PROXY_HOST=
HTTP_PROXY_USER=
HTTP_PROXY_PASSWORD=
HTTPS_PROXY_HOST=
HTTPS_PROXY_USER=
HTTPS_PROXY_PASSWORD=
HTTP_PROXY=
HTTPS_PROXY=
http_proxy=
https_proxy=
NO_PROXY=
no_proxy=
### SMTP Server
## ex.: mailhost.intern.klinik.de
# MAIL_HOST=
# MAIL_PORT=25
## ex.: no-reply@bridgehead.intern.klinik.de
# MAIL_FROM_ADDRESS=
# MAIL_FROM_NAME=Bridgehead Searchbroker
## Connector
CONNECTOR_POSTGRES_HOST=
CONNECTOR_POSTGRES_PORT=
CONNECTOR_POSTGRES_DB=
CONNECTOR_POSTGRES_USER=
CONNECTOR_SHARE_URL=
CONNECTOR_ENABLE_METRICS=
CONNECTOR_MONITOR_INTERVAL=
CONNECTOR_UPDATE_SERVER=
CONNECTOR_QUERY_LANGUAGE=
CATALINA_OPTS=
MDR_URL=
CENTRAL_SEARCH=
DECENTRAL_SEARCH=
MONITOR_URL=
MONITOR_OPTOUT=
LOG_LEVEL=
feature_BBMRI_DIRECTORY_SYNC=false
feature_DKTK_CENTRAL_SEARCH=false
feature_NNGM_CTS=false
LDM_URL=
ID_MANAGER_URL=