From 3709c0dbf7602e97478729285a0b88fffe31e47b Mon Sep 17 00:00:00 2001 From: root Date: Sat, 8 Jan 2022 09:46:45 +0100 Subject: [PATCH] Some more adjustments for the new deployment --- c4/docker-compose.yml | 67 ++++++++++++++++++++++++++++------------- dktk/docker-compose.yml | 57 +++++++++++++++++++++++------------ install-bridgehead.sh | 4 +-- start-bridgehead.sh | 2 +- uninstall-bridgehead.sh | 1 - 5 files changed, 85 insertions(+), 46 deletions(-) diff --git a/c4/docker-compose.yml b/c4/docker-compose.yml index 5952c20..56259aa 100644 --- 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" \ No newline at end of file diff --git a/dktk/docker-compose.yml b/dktk/docker-compose.yml index 0bd5bde..b26c6b2 100644 --- 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: ${ML_DB_PASS} TZ: Europe/Berlin volumes: - - "patientlist_db_data:/var/lib/postgresql/data" \ No newline at end of file + - "patientlist_db_data:/var/lib/postgresql/data" + networks: + - "samply" + +networks: + samply: + driver: "bridge" + connector-db: + driver: "bridge" \ No newline at end of file diff --git a/install-bridgehead.sh b/install-bridgehead.sh index e4bf6f8..adf5b13 100755 --- a/install-bridgehead.sh +++ b/install-bridgehead.sh @@ -9,14 +9,12 @@ source site.conf echo "Installing bridgehead" -if ! grep -E 'BRIDGEHEAD_PATH=' /etc/environment; then +if [ -z "$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 ..." diff --git a/start-bridgehead.sh b/start-bridgehead.sh index 2e552b4..6634dd6 100755 --- 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 diff --git a/uninstall-bridgehead.sh b/uninstall-bridgehead.sh index 900221f..380313b 100755 --- 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