Merge branch 'version-1' into martinsFixes

This commit is contained in:
Patrick Skowronek 2022-05-10 09:16:47 +02:00
commit d092d28980
7 changed files with 33 additions and 24 deletions

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@ -44,7 +44,7 @@ The Bridgehead has two primary components:
* The **Blaze Store**. This is a highly responsive FHIR data store, which you will need to fill with your data via an ETL chain. * The **Blaze Store**. This is a highly responsive FHIR data store, which you will need to fill with your data via an ETL chain.
* The **Connector**. This is the communication portal to the Sample Locator, with specially designed features that make it possible to run it behind a corporate firewall without making any compromises on security. * The **Connector**. This is the communication portal to the Sample Locator, with specially designed features that make it possible to run it behind a corporate firewall without making any compromises on security.
#### CPP(DKTK/C4) #### CCP(DKTK/C4)
TODO: TODO:
@ -79,6 +79,7 @@ For running your bridgehead we recommend the follwing Hardware:
Before starting the installation process, please ensure that following software is available on your system: Before starting the installation process, please ensure that following software is available on your system:
//Remove
#### [Git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git) #### [Git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)
To check that you have a working git installation, please run To check that you have a working git installation, please run
@ -90,6 +91,8 @@ rm -rf Hello-World;
``` ```
If you see the output "Hello World!" your installation should be working. If you see the output "Hello World!" your installation should be working.
//Just install docker-compose und docker with version
#### [Docker](https://docs.docker.com/get-docker/) #### [Docker](https://docs.docker.com/get-docker/)
To check your docker installation, you can try to execute dockers "Hello World" Image. The command is: To check your docker installation, you can try to execute dockers "Hello World" Image. The command is:
@ -149,10 +152,15 @@ sudo git clone https://github.com/samply/bridgehead.git /srv/docker/bridgehead;
When using the systemd services we you need to create a bridgehead user for security reasons. This should be done after clone the repository. Since not all linux distros support ```adduser```, we provide a action for the systemcall ```useradd```. When using the systemd services we you need to create a bridgehead user for security reasons. This should be done after clone the repository. Since not all linux distros support ```adduser```, we provide a action for the systemcall ```useradd```.
//
``` shell ``` shell
adduser --no-create-home --disabled-login --ingroup docker --gecos "" bridgehead adduser --no-create-home --disabled-login --ingroup docker --gecos "" bridgehead
```
``` shell
useradd -M -g docker -N -s /sbin/nologin bridgehead useradd -M -g docker -N -s /sbin/nologin bridgehead
chown bridghead /srv/docker/bridgehead/ -R chown bridgehead /srv/docker/bridgehead/ -R
``` ```
@ -216,7 +224,7 @@ To make the configuration effective, you need to tell systemd to reload the conf
``` shell ``` shell
sudo systemctl daemon-reload; sudo systemctl daemon-reload;
sudo systemctl bridgehead@cpp.service; sudo systemctl bridgehead@ccp.service;
``` ```
### DKTK/C4 ### DKTK/C4

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@ -3,7 +3,7 @@ version: "3.7"
services: services:
traefik: traefik:
container_name: bridgehead-traefik container_name: bridgehead-traefik
image: traefik:2.4 image: traefik:latest
command: command:
- --entrypoints.web.address=:80 - --entrypoints.web.address=:80
- --entrypoints.websecure.address=:443 - --entrypoints.websecure.address=:443
@ -60,20 +60,20 @@ services:
- "blaze-data:/app/data" - "blaze-data:/app/data"
labels: labels:
- "traefik.enable=true" - "traefik.enable=true"
- "traefik.http.middlewares.cpp-auth.basicauth.users=${bc_auth_users}" - "traefik.http.middlewares.ccp-auth.basicauth.users=${bc_auth_users}"
- "traefik.http.routers.blaze_ccp.rule=PathPrefix(`/ccp-localdatamanagement`)" - "traefik.http.routers.blaze_ccp.rule=PathPrefix(`/ccp-localdatamanagement`)"
- "traefik.http.middlewares.ccp_b_strip.stripprefix.prefixes=/ccp-localdatamanagement" - "traefik.http.middlewares.ccp_b_strip.stripprefix.prefixes=/ccp-localdatamanagement"
- "traefik.http.services.blaze_ccp.loadbalancer.server.port=8080" - "traefik.http.services.blaze_ccp.loadbalancer.server.port=8080"
- "traefik.http.routers.blaze_ccp.middlewares=ccp_b_strip,cpp-auth" - "traefik.http.routers.blaze_ccp.middlewares=ccp_b_strip,ccp-auth"
- "traefik.http.routers.blaze_ccp.tls=true" - "traefik.http.routers.blaze_ccp.tls=true"
ccp-search-share: ccp-search-share:
image: "ghcr.io/samply/dktk-fed-search-share:main" image: "samply/dktk-fed-search-share"
container_name: bridgehead-ccp-share container_name: bridgehead-ccp-share
environment: environment:
APP_BASE_URL: "http://dktk-fed-search-share:8080" APP_BASE_URL: "http://dktk-fed-search-share:8080"
APP_BROKER_BASEURL: "https://dktk-fed-search.verbis.dkfz.de/broker/rest/searchbroker" APP_BROKER_BASEURL: "https://dktk-fed-search.verbis.dkfz.de/broker/rest/searchbroker"
APP_BROKER_MAIL: ${CCP_MAIL} APP_BROKER_MAIL: ${CCP_SEARCHBROKER_USERNAME}
APP_STORE_BASEURL: "http://bridgehead-ccp-blaze:8080/fhir" APP_STORE_BASEURL: "http://bridgehead-ccp-blaze:8080/fhir"
SPRING_DATASOURCE_URL: "jdbc:postgresql://bridgehead-ccp-share-db:5432/dktk-fed-search-share" SPRING_DATASOURCE_URL: "jdbc:postgresql://bridgehead-ccp-share-db:5432/dktk-fed-search-share"
JAVA_TOOL_OPTIONS: "-Xmx1g" JAVA_TOOL_OPTIONS: "-Xmx1g"
@ -86,7 +86,7 @@ services:
- blaze - blaze
labels: labels:
- "traefik.enable=true" - "traefik.enable=true"
- "traefik.http.routers.dktk-fed-search.rule=PathPrefix(`/cpp-connector`)" - "traefik.http.routers.dktk-fed-search.rule=PathPrefix(`/ccp-connector`)"
- "traefik.http.services.dktk-fed-search.loadbalancer.server.port=8080" - "traefik.http.services.dktk-fed-search.loadbalancer.server.port=8080"
ccp-search-share-db: ccp-search-share-db:

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@ -1,4 +1,4 @@
version: '3.4' version: '3.7'
volumes: volumes:
gbn-connector-logs: gbn-connector-logs:
@ -8,7 +8,7 @@ volumes:
services: services:
traefik: traefik:
container_name: bridgehead-traefik container_name: bridgehead-traefik
image: traefik:2.4 image: traefik:2
command: command:
- --entrypoints.web.address=:80 - --entrypoints.web.address=:80
- --entrypoints.websecure.address=:443 - --entrypoints.websecure.address=:443
@ -65,11 +65,11 @@ services:
- "blaze-data:/app/data" - "blaze-data:/app/data"
labels: labels:
- "traefik.enable=true" - "traefik.enable=true"
- "traefik.http.middlewares.cpp-auth.basicauth.users=${bc_auth_users}" - "traefik.http.middlewares.ccp-auth.basicauth.users=${bc_auth_users}"
- "traefik.http.routers.blaze_ccp.rule=PathPrefix(`/ccp-localdatamanagement`)" - "traefik.http.routers.blaze_ccp.rule=PathPrefix(`/ccp-localdatamanagement`)"
- "traefik.http.middlewares.ccp_b_strip.stripprefix.prefixes=/ccp-localdatamanagement" - "traefik.http.middlewares.ccp_b_strip.stripprefix.prefixes=/ccp-localdatamanagement"
- "traefik.http.services.blaze_ccp.loadbalancer.server.port=8080" - "traefik.http.services.blaze_ccp.loadbalancer.server.port=8080"
- "traefik.http.routers.blaze_ccp.middlewares=ccp_b_strip,cpp-auth" - "traefik.http.routers.blaze_ccp.middlewares=ccp_b_strip,ccp-auth"
- "traefik.http.routers.blaze_ccp.tls=true" - "traefik.http.routers.blaze_ccp.tls=true"
gbn-connector: gbn-connector:

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@ -1,14 +1,15 @@
#!/bin/bash -e #!/bin/bash -e
source lib/functions.sh
echo "This script add's a user with password to the bridghead" log "This script add's a user with password to the bridghead"
if [ $# -eq 0 ]; then if [ $# -eq 0 ]; then
echo "No arguments provided, please provide the project name" log "No arguments provided, please provide the project name"
exit 1 exit 1
fi fi
if [ ! -f /etc/systemd/system/bridgehead@$1.service.d/override.conf ]; then if [ ! -f /etc/systemd/system/bridgehead@$1.service.d/override.conf ]; then
echo "Please create a Service first, with setup-bridgehead-units.sh" log "Please create a Service first, with setup-bridgehead-units.sh"
exit exit
fi fi

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@ -40,7 +40,7 @@ then
" "
LOCAL_SERVICES+=" <tr> LOCAL_SERVICES+=" <tr>
<td>CCP</td> <td>CCP</td>
<td><a href=\"https://${HOST}/cpp-localdatamanagement/fhir/\">Blaze</a></td> <td><a href=\"https://${HOST}/ccp-localdatamanagement/fhir/\">Blaze</a></td>
</tr> </tr>
" "
fi fi

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@ -3,12 +3,12 @@
source lib/functions.sh source lib/functions.sh
if [ $# -eq 0 ]; then if [ $# -eq 0 ]; then
echo "Please provide a Project as argument" log "Please provide a Project as argument"
exit 1 exit 1
fi fi
if [ $1 != "ccp" ] && [ $1 != "nngm" ] && [ $1 != "gbn" ]; then if [ $1 != "ccp" ] && [ $1 != "nngm" ] && [ $1 != "gbn" ]; then
echo "Please provide a supported project like ccp, gbn or nngm" log "Please provide a supported project like ccp, gbn or nngm"
exit 1 exit 1
fi fi
@ -16,7 +16,7 @@ export project=$1
#checkRequirements // not needed when uninstalling #checkRequirements // not needed when uninstalling
echo "Stopping systemd services and removing bridgehead ..." log "Stopping systemd services and removing bridgehead ..."
systemctl disable --now bridgehead@${project}.service bridgehead-update@${project}.timer bridgehead-update@${project}.service systemctl disable --now bridgehead@${project}.service bridgehead-update@${project}.timer bridgehead-update@${project}.service

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@ -5,12 +5,12 @@ source lib/functions.sh
exitIfNotRoot exitIfNotRoot
if [ $# -eq 0 ]; then if [ $# -eq 0 ]; then
echo "Please provide a Project as argument" log "Please provide a Project as argument"
exit 1 exit 1
fi fi
if [ $1 != "ccp" ] && [ $1 != "nngm" ] && [ $1 != "gbn" ]; then if [ $1 != "ccp" ] && [ $1 != "nngm" ] && [ $1 != "gbn" ]; then
echo "Please provide a supported project like ccp, gbn or nngm" log "Please provide a supported project like ccp, gbn or nngm"
exit 1 exit 1
fi fi
@ -30,9 +30,9 @@ systemctl daemon-reload
echo echo
if ! systemctl is-active --quiet bridgehead@"${project}"; then if ! systemctl is-active --quiet bridgehead@"${project}"; then
echo "Enabling autostart of bridgehead@${project}.service" log "Enabling autostart of bridgehead@${project}.service"
systemctl enable bridgehead@"${project}" systemctl enable bridgehead@"${project}"
echo "Enabling nightly updates for bridgehead@${project}.service ..." log "Enabling nightly updates for bridgehead@${project}.service ..."
systemctl enable --now bridgehead-update@"${project}".timer systemctl enable --now bridgehead-update@"${project}".timer
fi fi