Some more adjustments for the new deployment

2022-01-08 09:46:45 +01:00 · 2022-01-08 09:46:45 +01:00 · 3709c0dbf7
parent ca7e3a641a
commit 3709c0dbf7
5 changed files with 85 additions and 46 deletions
--- a/c4/docker-compose.yml
+++ b/c4/docker-compose.yml
@ -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"
--- a/dktk/docker-compose.yml
+++ b/dktk/docker-compose.yml
@ -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"
--- a/install-bridgehead.sh
+++ b/install-bridgehead.sh
@ -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 ..."
--- a/start-bridgehead.sh
+++ b/start-bridgehead.sh
@ -3,7 +3,7 @@

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

--- a/uninstall-bridgehead.sh
+++ b/uninstall-bridgehead.sh
@ -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