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Some more adjustments for the new deployment

This commit is contained in:
root 2022-01-08 09:46:45 +01:00
parent ca7e3a641a
commit 3709c0dbf7
5 changed files with 85 additions and 46 deletions
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67
c4/docker-compose.yml
View File

@ -1,12 +1,12 @@
version: "3.7"
volumes:
connector_db_data: null
connector_logs: null
patientlist_db_data: null
patientlist_logs: null
idmanager_logs: null
store_db_data: null
store_logs: null
connector_db_data:
connector_logs:
patientlist_db_data:
patientlist_logs:
idmanager_logs:
store_db_data:
store_logs:
secrets:
mainzelliste.docker.conf:
file: ../internal-configuration/mainzelliste.conf
@ -36,16 +36,18 @@ services:
PATIENTLIST_URL: ${PATIENTLIST_URL}
STORE_URL: ${LDM_URL}
POSTGRES_HOST: ${CONNECTOR_DB_HOST}
POSTGRES_PORT: ${CONNECTOR_DB_PORT}
POSTGRES_PORT: ${CONNECTOR_POSTGRES_PORT}
POSTGRES_DB: ${CONNECTOR_POSTGRES_DB}
POSTGRES_USER: ${CONNECTOR_POSTGRES_USER}
POSTGRES_PASS: ${CONNECTOR_POSTGRES_PASS}
HTTP_PROXY_URL: ${HTTP_PROXY_URL}
HTTP_PROXY_USERNAME: ${HTTP_PROXY_USERNAME}
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_USERNAME}
HTTPS_PROXY_USERNAME: ${HTTPS_PROXY_USER}
HTTPS_PROXY_PASSWORD: ${HTTPS_PROXY_PASSWORD}
NO_PROXY: ${NO_PROXY}
TZ: Europe/Berlin
volumes:
- "connector_logs:/usr/local/tomcat/logs"
@ -54,12 +56,15 @@ services:
ports:
- "8080:8080"
restart: always
networks:
- "samply"
- "connector-db"
connector_db:
container_name: bridgehead_connector_db
image: postgres:10.17
environment:
POSTGRES_HOST: ${CONNECTOR_POSTGRES_HOST}
POSTGRES_HOST: ${CONNECTOR_DB_HOST}
POSTGRES_DB: ${CONNECTOR_POSTGRES_DB}
POSTGRES_USER: ${CONNECTOR_POSTGRES_USER}
POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
@ -67,10 +72,14 @@ services:
volumes:
- "connector_db_data:/var/lib/postgresql/data"
restart: always
networks:
- "connector-db"
ports:
- "8088:5432"
idmanager:
container_name: bridgehead_idmanager
container_name: bridgehead-idmanager
image: docker.verbis.dkfz.de/pseudonymisierung/magicpl:0.2.0-RC23
environment:
MAGICPL_MAINZELLISTE_URL: ${MAGICPL_MAINZELLISTE_URL}
@ -98,9 +107,11 @@ services:
- patientlist
ports:
- "8085:8080"
networks:
- "samply"
patientlist:
container_name: bridgehead_patientlist
container_name: bridgehead-patientlist
image: medicalinformatics/mainzelliste:develop
environment:
ML_DB_DRIVER: org.postgresql.Driver
@ -115,7 +126,7 @@ services:
ML_SITE: adt
TZ: Europe/Berlin
env_file:
- ./site-config/patientlist.env
- ../site-config/patientlist.env
volumes:
- "patientlist_logs:/usr/local/tomcat/logs"
secrets:
@ -125,21 +136,24 @@ services:
- patientlist_db
ports:
- "8086:8080"
networks:
- "samply"
patientlist_db:
container_name: bridgehead_patientlist_db
image: postgres:13.1-alpine
environment:
POSTGRES_HOST: ${ML_DB_HOST}
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"
store:
container_name: bridgehead_store
container_name: bridgeheadstore
image: docker.verbis.dkfz.de/ccp/samply.store:release-5.1.2
environment:
MDR_URL: ${CCP_MDR_URL}
@ -158,13 +172,14 @@ services:
ports:
- "8083:8080"
restart: always
networks:
- "samply"
store_db:
container_name: bridgehead_store_db
image: postgres:10.17
image: postgres:9.5-alpine
command: postgres -c datestyle='iso, dmy'
environment:
POSTGRES_HOST: ${STORE_POSTGRES_HOST}
POSTGRES_PORT: ${STORE_POSTGRES_PORT}
POSTGRES_DB: ${STORE_POSTGRES_DB}
POSTGRES_USER: ${STORE_POSTGRES_USER}
@ -173,3 +188,13 @@ services:
volumes:
- "store_db_data:/var/lib/postgresql/data"
restart: always
networks:
- "samply"
ports:
- "8084:5432"
networks:
samply:
driver: "bridge"
connector-db:
driver: "bridge"

57
dktk/docker-compose.yml
View File

@ -1,12 +1,12 @@
version: "3.7"
volumes:
connector_db_data: null
connector_logs: null
patientlist_db_data: null
patientlist_logs: null
idmanager_logs: null
store_db_data: null
store_logs: null
connector_db_data:
connector_logs:
patientlist_db_data:
patientlist_logs:
idmanager_logs:
store_db_data:
store_logs:
secrets:
mainzelliste.docker.conf:
file: ../internal-configuration/mainzelliste.conf
@ -21,8 +21,8 @@ secrets:
services:
connector:
container_name: bridgehead_c4_connector
image: "samply/share-client:c4-7"
container_name: bridgehead_dktk_connector
image: "samply/share-client:dktk-7"
environment:
SITE: ${SITE}
SITEID: ${SITEID}
@ -36,16 +36,17 @@ services:
PATIENTLIST_URL: ${PATIENTLIST_URL}
STORE_URL: ${LDM_URL}
POSTGRES_HOST: ${CONNECTOR_DB_HOST}
POSTGRES_PORT: ${CONNECTOR_DB_PORT}
POSTGRES_PORT: ${CONNECTOR_POSTGRES_PORT}
POSTGRES_DB: ${CONNECTOR_POSTGRES_DB}
POSTGRES_USER: ${CONNECTOR_POSTGRES_USER}
POSTGRES_PASS: ${CONNECTOR_POSTGRES_PASS}
HTTP_PROXY_URL: ${HTTP_PROXY_URL}
HTTP_PROXY_USERNAME: ${HTTP_PROXY_USERNAME}
HTTP_PROXY_USERNAME: ${HTTP_PROXY_USER}
HTTP_PROXY_PASSWORD: ${HTTP_PROXY_PASSWORD}
HTTPS_PROXY_URL: ${HTTPS_PROXY_URL}
HTTPS_PROXY_USERNAME: ${HTTPS_PROXY_USERNAME}
HTTPS_PROXY_USERNAME: ${HTTPS_PROXY_USER}
HTTPS_PROXY_PASSWORD: ${HTTPS_PROXY_PASSWORD}
NO_PROXY: ${NO_PROXY}
TZ: Europe/Berlin
volumes:
- "connector_logs:/usr/local/tomcat/logs"
@ -54,12 +55,15 @@ services:
ports:
- "8080:8080"
restart: always
networks:
- "samply"
- "connector-db"
connector_db:
container_name: bridgehead_connector_db
image: postgres:10.17
environment:
POSTGRES_HOST: ${CONNECTOR_POSTGRES_HOST}
POSTGRES_HOST: ${CONNECTOR_DB_HOST}
POSTGRES_DB: ${CONNECTOR_POSTGRES_DB}
POSTGRES_USER: ${CONNECTOR_POSTGRES_USER}
POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
@ -67,10 +71,12 @@ services:
volumes:
- "connector_db_data:/var/lib/postgresql/data"
restart: always
networks:
- "connector-db"
idmanager:
container_name: bridgehead_idmanager
container_name: bridgehead-idmanager
image: docker.verbis.dkfz.de/pseudonymisierung/magicpl:0.2.0-RC23
environment:
MAGICPL_MAINZELLISTE_URL: ${MAGICPL_MAINZELLISTE_URL}
@ -98,9 +104,11 @@ services:
- patientlist
ports:
- "8085:8080"
networks:
- "samply"
patientlist:
container_name: bridgehead_patientlist
container_name: bridgehead-patientlist
image: medicalinformatics/mainzelliste:develop
environment:
ML_DB_DRIVER: org.postgresql.Driver
@ -115,7 +123,7 @@ services:
ML_SITE: adt
TZ: Europe/Berlin
env_file:
- ./site-config/patientlist.env
- ../site-config/patientlist.env
volumes:
- "patientlist_logs:/usr/local/tomcat/logs"
secrets:
@ -125,15 +133,24 @@ services:
- patientlist_db
ports:
- "8086:8080"
networks:
- "samply"
patientlist_db:
container_name: bridgehead_patientlist_db
image: postgres:13.1-alpine
environment:
POSTGRES_HOST: ${ML_DB_HOST}
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"
- "patientlist_db_data:/var/lib/postgresql/data"
networks:
- "samply"
networks:
samply:
driver: "bridge"
connector-db:
driver: "bridge"

4
install-bridgehead.sh
View File

@ -9,14 +9,12 @@ source site.conf
echo "Installing bridgehead"
if ! grep -E 'BRIDGEHEAD_PATH=' /etc/environment; then
if [ -z "$BRIDGEHEAD_PATH" ] ; then
echo "BRIDGEHEAD_PATH=${PWD}" >> /etc/environment
echo "Please reboot the system to properly set the enviroment"
exit
fi
sed -i -e "s|\BRIDGEHEAD_PATH=.*|\BRIDGEHEAD_PATH=${PWD}|" environment
cd /etc/systemd/system/
echo "Installing bridgehead\@.service in systemd ..."

2
start-bridgehead.sh
View File

@ -3,7 +3,7 @@
if ! ./prerequisites.sh; then
echo "Prerequisites failed, exiting"
exiting
exit
fi
source site.conf

1
uninstall-bridgehead.sh
View File

@ -8,7 +8,6 @@ systemctl stop bridgehead-update@"${project}".service
sed -i -e "s|BRIDGEHEAD_PATH=.*||" /etc/environment
cd /etc/systemd/system/
rm bridgehead\@.service
rm bridgehead-update\@.timer