Manges changes and moving vars to the correct file

This commit is contained in:
root 2022-01-19 10:52:25 +01:00
parent 42d69cef4e
commit 7357870670
8 changed files with 181 additions and 66 deletions

47
c4/internal.env Normal file
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@ -0,0 +1,47 @@
SITE=bridgehead_test
SITEID=BRIDGEHEAD_TEST
CONNECTOR_SHARE_URL="http://${HOST}:8080"
CONNECTOR_ENABLE_METRICS=false
CONNECTOR_MONITOR_INTERVAL=
CONNECTOR_UPDATE_SERVER=
CONNECTOR_POSTGRES_PORT=5432
CONNECTOR_POSTGRES_DB=samply.connector
CONNECTOR_POSTGRES_USER=samply.connector
HTTP_PROXY_HOST=${PROXY_URL}
HTTP_PROXY_USER=
HTTP_PROXY_PASSWORD=
HTTPS_PROXY_HOST=${PROXY_URL}
HTTPS_PROXY_USER=
HTTPS_PROXY_PASSWORD=
HTTP_PROXY=${PROXY_URL}
HTTPS_PROXY=${PROXY_URL}
http_proxy=${PROXY_URL}
https_proxy=${PROXY_URL}
CCP_CENTRALSEARCH_URL=https://centralsearch-test.dktk.dkfz.de/
CCP_DECENTRALSEARCH_URL=https://decentralsearch-test.ccp-it.dktk.dkfz.de/
CCP_MDR_URL=https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr
CCP_MONITOR_URL=
MONITOR_OPTOUT=
## nNGM
#NNGM_URL=http://bridgeheadstore:8080
#NNGM_PROFILE=http://uk-koeln.de/fhir/StructureDefinition/Patient/nNGM/pseudonymisiert
#NNGM_MAINZELLISTE_URL=https://test.verbis.dkfz.de/mpl
##MDR
MDR_NAMESPACE=adt,dktk,marker
#MDR_MAP=
MDR_VALIDATION=false
ML_DB_NAME=mainzelliste
ML_DB_PORT=5432
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

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@ -24,30 +24,9 @@ services:
container_name: bridgehead_dktk_connector
image: "samply/share-client:dktk-7"
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: ${STORE_URL}
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_URL: ${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
volumes:
- "connector_logs:/usr/local/tomcat/logs"
depends_on:
@ -55,6 +34,9 @@ services:
ports:
- "8080:8080"
restart: always
env_file:
###TODO: Move into Image
- internal.env
networks:
- "samply"
- "connector-db"
@ -64,20 +46,20 @@ services:
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
env_file:
###TODO: Move into Image
- internal.env
networks:
- "connector-db"
idmanager:
container_name: bridgehead_dktk_idmanager
image: docker.verbis.dkfz.de/pseudonymisierung/magicpl:0.2.0-RC23
image: docker.verbis.dkfz.de/pseudonymisierung/magicpl:release-0.2.0
environment:
MAGICPL_MAINZELLISTE_URL: ${MAGICPL_MAINZELLISTE_URL}
MAGICPL_MAINZELLISTE_API_KEY: ${MAGICPL_MAINZELLISTE_API_KEY}
@ -91,8 +73,7 @@ services:
MAGICPL_OIDC_PROVIDER: ${MAGICPL_OIDC_PROVIDER}
MAGICPL_OIDC_CLIENT_ID: ${MAGICPL_OIDC_CLIENT_ID}
MAGICPL_OIDC_CLIENT_SECRET: ${MAGICPL_OIDC_CLIENT_SECRET}
MAGICPL_SITE: adt
MAGICPL_LOG_LEVEL: info
TZ: Europe/Berlin
volumes:
- "idmanager_logs:/usr/local/tomcat/logs"
@ -102,6 +83,9 @@ services:
- proxy.docker.xml
depends_on:
- patientlist
env_file:
###TODO: Move into Image
- internal.env
ports:
- "8085:8080"
networks:
@ -111,19 +95,12 @@ services:
container_name: bridgehead_dktk_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_HOST: bridgehead_dktk_patientlist_db
ML_DB_PASS: ${ML_DB_PASS}
ML_API_KEY: ${ML_API_KEY}
ML_LOG_LEVEL: warning
ML_SITE: adt
TZ: Europe/Berlin
env_file:
- ../site-config/patientlist.env
- internal.env
volumes:
- "patientlist_logs:/usr/local/tomcat/logs"
secrets:
@ -140,12 +117,12 @@ services:
container_name: bridgehead_dktk_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"
env_file:
###TODO: Move into Image
- internal.env
networks:
- "samply"

56
dktk/internal.env Normal file
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@ -0,0 +1,56 @@
SITE=bridgehead_dktk_test
SITEID=BRIDGEHEAD_DKTK_TEST
CONNECTOR_SHARE_URL="http://${HOST}:8080"
CONNECTOR_ENABLE_METRICS=false
CONNECTOR_MONITOR_INTERVAL=
CONNECTOR_UPDATE_SERVER=
POSTGRES_PORT=5432
POSTGRES_DB=samply.connector
POSTGRES_USER=samply.connector
HTTP_PROXY_HOST=${PROXY_URL}
HTTP_PROXY_USER=
HTTP_PROXY_PASSWORD=
HTTPS_PROXY_HOST=${PROXY_URL}
HTTPS_PROXY_USER=
HTTPS_PROXY_PASSWORD=
HTTP_PROXY=${PROXY_URL}
HTTPS_PROXY=${PROXY_URL}
http_proxy=${PROXY_URL}
https_proxy=${PROXY_URL}
CCP_CENTRALSEARCH_URL=https://centralsearch-test.dktk.dkfz.de/
CCP_DECENTRALSEARCH_URL=https://decentralsearch-test.ccp-it.dktk.dkfz.de/
CCP_MDR_URL=https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr
CCP_MONITOR_URL=
MONITOR_OPTOUT=
## nNGM
#NNGM_URL=http://bridgeheadstore:8080
#NNGM_PROFILE=http://uk-koeln.de/fhir/StructureDefinition/Patient/nNGM/pseudonymisiert
#NNGM_MAINZELLISTE_URL=https://test.verbis.dkfz.de/mpl
##MDR
MDR_NAMESPACE=adt,dktk,marker
#MDR_MAP=
MDR_VALIDATION=false
ML_DB_NAME=samply.connector
ML_DB_PORT=5432
ML_DB_USER=samply.connector
CENTRAL_CONTROL_NUMBER_GENERATPR_URL=http://e260-serv-03/central/api
GLOBAL_ID=DKTK
MAINZELLISTE_URL=https://patientlist-test.ccpit.dktk.dkfz.de/mainzelliste
ML_DB_DRIVER=org.postgresql.Driver
ML_DB_TYPE=postgresql
ML_LOG_LEVEL=warning
ML_SITE=BRIDGEHEAD_DKTK_TEST
TZ=Europe/Berlin
MAGICPL_SITE=adt
MAGICPL_LOG_LEVEL=info

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@ -1,6 +1,17 @@
version: '3.4'
services:
networks:
samply:
driver: "bridge"
connector-db:
driver: "bridge"
volumes:
store-db-data:
name: "store-db-data"
connector-db-data:
name: "connector-db-data"
services:
store:
container_name: "bridgehead_gbn_blaze_store"
image: "samply/blaze:0.15"
@ -20,12 +31,12 @@ services:
image: "samply/share-client:gbn-7"
environment:
POSTGRES_HOST: "bridgehead_gbn_connector_db"
POSTGRES_DB: "samply.connector"
POSTGRES_USER: "samply"
POSTGRES_PASS: ${CONNECTOR_POSTGRES_PASS}
STORE_URL: "http://bridgehead_store:8080/fhir"
QUERY_LANGUAGE: "CQL"
MDR_URL: "https://mdr.germanbiobanknode.de/v3/api/mdr"
POSTGRES_PORT: 5432
STORE_URL: "http://bridgehead_gbn_blaze_store:8080/fhir"
env_file:
###TODO: Move into Image
- internal.env
networks:
- "samply"
- "connector-db"
@ -39,23 +50,13 @@ services:
container_name: "bridgehead_gbn_connector_db"
image: "postgres:10.17"
environment:
POSTGRES_USER: "samply"
POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
POSTGRES_DB: "samply.connector"
POSTGRES_PORT: 5432
networks:
- "connector-db"
volumes:
- "connector-db-data:/var/lib/postgresql/data"
restart: "always"
networks:
samply:
driver: "bridge"
connector-db:
driver: "bridge"
volumes:
store-db-data:
name: "store-db-data"
connector-db-data:
name: "connector-db-data"
env_file:
###TODO: Move into Image
- internal.env

26
gbn/internal.env Normal file
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@ -0,0 +1,26 @@
POSTGRES_DB=samply.connector
POSTGRES_USER=samply
QUERY_LANGUAGE=CQL
CONNECTOR_SHARE_URL="http://${HOST}:8080"
MDR_URL="https://mdr.germanbiobanknode.de/v3/api/mdr"
MONITOR_URL=https://ccpit.dktk.dkfz.de/dktk.monitor/rest/info
no_proxy=bridgehead_gbn_connector,bridgehead_gbn_blaze_store,bridgehead_gbn_connector_db
CONNECTOR_MONITOR_INTERVAL=
CONNECTOR_UPDATE_SERVER=
feature_BBMRI_DIRECTORY_SYNC=false
feature_DKTK_CENTRAL_SEARCH=false
feature_NNGM_CTS=false
LOG_LEVEL=info
HTTP_PROXY_HOST=${PROXY_URL}
HTTP_PROXY_USER=
HTTP_PROXY_PASSWORD=
HTTPS_PROXY_HOST=${PROXY_URL}
HTTPS_PROXY_USER=
HTTPS_PROXY_PASSWORD=
HTTP_PROXY=${PROXY_URL}
HTTPS_PROXY=${PROXY_URL}
http_proxy=${PROXY_URL}
https_proxy=${PROXY_URL}
CONNECTOR_ENABLE_METRICS=false

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@ -11,7 +11,7 @@ if ! ./lib/prerequisites.sh; then
fi
source site.conf
log -e "\nInstalling systemd units ..."
echo -e "\nInstalling systemd units ..."
cp -v \
lib/systemd/bridgehead\@.service \
lib/systemd/bridgehead-update\@.service \
@ -23,12 +23,12 @@ systemctl daemon-reload
echo
if ! systemctl is-active --quiet bridgehead@"${project}"; then
log "Enabling autostart of bridgehead@${project}.service"
echo "Enabling autostart of bridgehead@${project}.service"
systemctl enable bridgehead@"${project}"
log "Enabling nightly updates for bridgehead@${project}.service ..."
echo "Enabling nightly updates for bridgehead@${project}.service ..."
systemctl enable --now bridgehead-update@"${project}".timer
fi
log -e "\nDone - now start your bridgehead by running\n\tsystemctl start bridgehead@${project}.service\nor by rebooting your machine."
echo -e "\nDone - now start your bridgehead by running\n\tsystemctl start bridgehead@${project}.service\nor by rebooting your machine."
# TODO: Configuration of the different modules

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@ -4,9 +4,17 @@
##Setting Network properties
export HOSTIP=$(MSYS_NO_PATHCONV=1 docker run --rm --add-host=host.docker.internal:host-gateway ubuntu cat /etc/hosts | grep 'host.docker.internal' | awk '{print $1}');
export HOST=
export PROXY_URL=
export site_name=
### Write the Project you want to start with the brigdehead
##Exmaple project=gbn
project=c4
project=
###secrets
## Connector Password
export CONNECTOR_POSTGRES_PASS=
##ID-Manager
#This needs to be set if the project is either c4 or dktk
export

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@ -3,7 +3,7 @@ service="bridgehead"
source lib/functions.sh
if ! ./prerequisites.sh; then
if ! lib/prerequisites.sh; then
log "Prerequisites failed, exiting"
exit
fi