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Clean up bwhc startup

This commit is contained in:
Tobias Kussel 2023-05-16 10:56:28 +00:00
parent 187945b27e
commit 4e7f023b8a
13 changed files with 54 additions and 170 deletions
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20
bbmri/modules/dnpm-compose-bwhc.yml
View File

@ -4,21 +4,20 @@ services:
dnpm-frontend:
depends_on: [ dnpm-backend ]
build:
context: ../../dnpm/origin
dockerfile: Frontend.Dockerfile
network: host
context: ../../minimal/modules
dockerfile: dnpm-frontend.Dockerfile
args:
NUXT_HOST: 0.0.0.0
NUXT_PORT: 3000
BACKEND_PROTOCOL: ${DNPM_BMHC_BACKEND_PROTOCOL}
BACKEND_HOSTNAME: ${DNPM_BWHC_BACKEND_HOSTNAME}
BACKEND_PROTOCOL: http
BACKEND_HOSTNAME: dnpm-backend
BACKEND_PORT: 9000
DNPM_BWHC_FRONTEND_ZIP: ${DNPM_BWHC_FRONTEND_ZIP}
HTTP_PROXY: ${http_proxy}
HTTPS_PROXY: ${https_proxy}
environment:
BACKEND_PROTOCOL: ${DNPM_BMHC_BACKEND_PROTOCOL}
BACKEND_HOSTNAME: ${DNPM_BWHC_BACKEND_HOSTNAME}
BACKEND_PROTOCOL: http
BACKEND_HOSTNAME: dnpm-backend
BACKEND_PORT: 9000
no_proxy: dnpm-backend
labels:
@ -29,13 +28,11 @@ services:
dnpm-backend:
build:
context: ../../dnpm/origin
dockerfile: Backend.Dockerfile
context: ../../minimal/modules
dockerfile: dnpm-backend.Dockerfile
args:
BWHC_BASE_DIR: /bwhc-backend
DNPM_BWHC_BACKEND_ZIP: ${DNPM_BWHC_BACKEND_ZIP}
ports:
- 9000:9000
environment:
APPLICATION_SECRET: ${DNPM_APPLICATION_SECRET}
ZPM_SITE: ${ZPM_SITE}
@ -43,7 +40,6 @@ services:
# PLAY_HTTP_PORT: 9000
# PLAY_HTTP_ADDRESS: 0.0.0.0
volumes:
- ../dnpm/origin/logback.xml:/bwhc-backend/logback.xml:ro
- /etc/bridgehead/dnpm/bwhcConnectorConfig.xml:/bwhc-backend/bwhcConnectorConfig.xml:ro
- /etc/bridgehead/dnpm/production.conf:/bwhc-backend/production.conf:ro
- bwhc_data:/bwhc-backend/data/

10
bbmri/modules/dnpm-setup.sh
View File

@ -15,5 +15,15 @@ if [ -n "${ENABLE_DNPM}" ]; then
if [ -n "${ENABLE_DNPM_BWHC}" ]; then
log INFO "DNPM setup detected (with Frontend/Backend) -- will start BWHC Frontend/Backend. This is highly experimental!"
OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose-bwhc.yml"
if [ -z "${DNPM_BWHC_FRONTEND_ZIP}" ]; then
fail_and_report 1 "Variable DNPM_BWHC_FRONTEND_ZIP is not set."
fi
if [ -z "${DNPM_BWHC_BACKEND_ZIP}" ]; then
fail_and_report 1 "Variable DNPM_BWHC_BACKEND_ZIP is not set."
fi
if [ -z "${ZPM_SITE}" ]; then
fail_and_report 1 "Variable ZPM_SITE is not set."
fi
fi
fi

20
ccp/modules/dnpm-compose-bwhc.yml
View File

@ -4,21 +4,20 @@ services:
dnpm-frontend:
depends_on: [ dnpm-backend ]
build:
context: ../../dnpm/origin
dockerfile: Frontend.Dockerfile
network: host
context: ../../minimal/modules
dockerfile: dnpm-frontend.Dockerfile
args:
NUXT_HOST: 0.0.0.0
NUXT_PORT: 3000
BACKEND_PROTOCOL: ${DNPM_BMHC_BACKEND_PROTOCOL}
BACKEND_HOSTNAME: ${DNPM_BWHC_BACKEND_HOSTNAME}
BACKEND_PROTOCOL: http
BACKEND_HOSTNAME: dnpm-backend
BACKEND_PORT: 9000
DNPM_BWHC_FRONTEND_ZIP: ${DNPM_BWHC_FRONTEND_ZIP}
HTTP_PROXY: ${http_proxy}
HTTPS_PROXY: ${https_proxy}
environment:
BACKEND_PROTOCOL: ${DNPM_BMHC_BACKEND_PROTOCOL}
BACKEND_HOSTNAME: ${DNPM_BWHC_BACKEND_HOSTNAME}
BACKEND_PROTOCOL: http
BACKEND_HOSTNAME: dnpm-backend
BACKEND_PORT: 9000
no_proxy: dnpm-backend
labels:
@ -29,13 +28,11 @@ services:
dnpm-backend:
build:
context: ../../dnpm/origin
dockerfile: Backend.Dockerfile
context: ../../minimal/modules
dockerfile: dnpm-backend.Dockerfile
args:
BWHC_BASE_DIR: /bwhc-backend
DNPM_BWHC_BACKEND_ZIP: ${DNPM_BWHC_BACKEND_ZIP}
ports:
- 9000:9000
environment:
APPLICATION_SECRET: ${DNPM_APPLICATION_SECRET}
ZPM_SITE: ${ZPM_SITE}
@ -43,7 +40,6 @@ services:
# PLAY_HTTP_PORT: 9000
# PLAY_HTTP_ADDRESS: 0.0.0.0
volumes:
- ../dnpm/origin/logback.xml:/bwhc-backend/logback.xml:ro
- /etc/bridgehead/dnpm/bwhcConnectorConfig.xml:/bwhc-backend/bwhcConnectorConfig.xml:ro
- /etc/bridgehead/dnpm/production.conf:/bwhc-backend/production.conf:ro
- bwhc_data:/bwhc-backend/data/

10
ccp/modules/dnpm-setup.sh
View File

@ -12,5 +12,15 @@ if [ -n "${ENABLE_DNPM}" ]; then
if [ -n "${ENABLE_DNPM_BWHC}" ]; then
log INFO "DNPM setup detected (with Frontend/Backend) -- will start BWHC Frontend/Backend. This is highly experimental!"
OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose-bwhc.yml"
if [ -z "${DNPM_BWHC_FRONTEND_ZIP}" ]; then
fail_and_report 1 "Variable DNPM_BWHC_FRONTEND_ZIP is not set."
fi
if [ -z "${DNPM_BWHC_BACKEND_ZIP}" ]; then
fail_and_report 1 "Variable DNPM_BWHC_BACKEND_ZIP is not set."
fi
if [ -z "${ZPM_SITE}" ]; then
fail_and_report 1 "Variable ZPM_SITE is not set."
fi
fi
fi

29
dnpm/dnpm-compose-beamconnect.yml
View File

@ -1,29 +0,0 @@
version: "3.7"
services:
beam-proxy:
environment:
APP_2_ID: dnpm
APP_2_KEY: ${DNPM_BEAM_SECRET_SHORT}
dnpm-beam-connect:
depends_on: [ beam-proxy ]
image: samply/beam-connect:sites-without-auth
environment:
PROXY_URL: http://beam-proxy:8081
PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
APP_ID: dnpm.${PROXY_ID}
DISCOVERY_URL: ${DNPM_DISCOVERY_URL}
LOCAL_TARGETS_FILE: /run/secrets/connect_targets.json
HTTP_PROXY: http://forward_proxy:3128
HTTPS_PROXY: http://forward_proxy:3128
NO_PROXY: beam-proxy,dnpm-backend
RUST_LOG: ${RUST_LOG:-info}
secrets:
- connect_targets.json
ports:
- 8062:8062
secrets:
connect_targets.json:
file: /etc/bridgehead/dnpm/local_targets.json

51
dnpm/dnpm-compose-bwhc.yml
View File

@ -1,51 +0,0 @@
version: "3.7"
services:
dnpm-frontend:
depends_on: [ dnpm-backend ]
build:
context: ../dnpm/origin
dockerfile: Frontend.Dockerfile
network: host
args:
NUXT_HOST: 0.0.0.0
NUXT_PORT: 3000
BACKEND_PROTOCOL: ${DNPM_BMHC_BACKEND_PROTOCOL}
BACKEND_HOSTNAME: ${DNPM_BWHC_BACKEND_HOSTNAME}
BACKEND_PORT: 9000
DNPM_BWHC_FRONTEND_ZIP: ${DNPM_BWHC_FRONTEND_ZIP}
HTTP_PROXY: ${http_proxy}
HTTPS_PROXY: ${https_proxy}
ports:
- 3000:3000
environment:
BACKEND_PROTOCOL: ${DNPM_BMHC_BACKEND_PROTOCOL}
BACKEND_HOSTNAME: ${DNPM_BWHC_BACKEND_HOSTNAME}
BACKEND_PORT: 9000
no_proxy: dnpm-backend
dnpm-backend:
build:
context: ../dnpm/origin
dockerfile: Backend.Dockerfile
args:
BWHC_BASE_DIR: /bwhc-backend
DNPM_BWHC_BACKEND_ZIP: ${DNPM_BWHC_BACKEND_ZIP}
ports:
- 9000:9000
environment:
APPLICATION_SECRET: ${DNPM_APPLICATION_SECRET}
ZPM_SITE: ${ZPM_SITE}
noproxy: dnpm-frontend,connect
# PLAY_HTTP_PORT: 9000
# PLAY_HTTP_ADDRESS: 0.0.0.0
volumes:
- ../dnpm/origin/logback.xml:/bwhc-backend/logback.xml:ro
- /etc/bridgehead/dnpm/bwhcConnectorConfig.xml:/bwhc-backend/bwhcConnectorConfig.xml:ro
- /etc/bridgehead/dnpm/production.conf:/bwhc-backend/production.conf:ro
- bwhc_data:/bwhc-backend/data/
- bwhc_hgnc_data:/bwhc-backend/hgnc_data/
volumes:
bwhc_data:
bwhc_hgnc_data:

16
dnpm/dnpm-setup.sh
View File

@ -1,16 +0,0 @@
#!/bin/bash
function dnpmSetup() {
if [ -e /etc/bridgehead/dnpm/local_targets.json ]; then
log INFO "DNPM setup detected (Beam.Connect) -- will start Beam.Connect for DNPM."
OVERRIDE+=" -f ./dnpm/dnpm-compose-beamconnect.yml"
DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
source /srv/docker/bridgehead/dnpm/vars || fail_and_report 1 "Unable to load /srv/docker/bridgehead/dnpm/vars"
export DNPM_DISCOVERY_URL
if [ -e /etc/bridgehead/dnpm/bwhcConnectorConfig.xml ]; then
log INFO "DNPM setup detected (with Frontend/Backend) -- will start BWHC Frontend/Backend. This is highly experimental!"
OVERRIDE+=" -f ./dnpm/dnpm-compose-bwhc.yml"
fi
fi
}

37
dnpm/origin/logback.xml
View File

@ -1,37 +0,0 @@
<?xml version="1.0" encoding="utf-8"?>
<configuration scan="true">
<property name="LOG_DIR" value="./bwhc_logs/"/>
<property name="LOG_FILE" value="bwhealthcloud"/>
<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
<encoder>
<pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n</pattern>
</encoder>
</appender>
<!--
<appender name="FILE" class="ch.qos.logback.core.rolling.RollingFileAppender">
<file>${LOG_DIR}/${LOG_FILE}.log</file>
<rollingPolicy class="ch.qos.logback.core.rolling.TimeBasedRollingPolicy">
<fileNamePattern>${LOG_DIR}/${LOG_FILE}-%d{yyyy-MM-dd}.log</fileNamePattern>
<maxHistory>30</maxHistory>
<totalSizeCap>3GB</totalSizeCap>
</rollingPolicy>
<encoder>
<pattern>%d [%thread] %-5level %logger{36} - %msg%n</pattern>
</encoder>
</appender>
-->
<root level="DEBUG">
<appender-ref ref="STDOUT"/>
<!--
<appender-ref ref="FILE"/>
-->
</root>
</configuration>

1
dnpm/vars
View File

@ -1 +0,0 @@
DNPM_DISCOVERY_URL=https://dnpm.medizin.uni-tuebingen.de/sites

0
dnpm/origin/Backend.Dockerfile → minimal/modules/dnpm-backend.Dockerfile
View File

20
minimal/modules/dnpm-compose-bwhc.yml
View File

@ -4,21 +4,20 @@ services:
dnpm-frontend:
depends_on: [ dnpm-backend ]
build:
context: ../../dnpm/origin
dockerfile: Frontend.Dockerfile
network: host
context: ../../minimal/modules
dockerfile: dnpm-frontend.Dockerfile
args:
NUXT_HOST: 0.0.0.0
NUXT_PORT: 3000
BACKEND_PROTOCOL: ${DNPM_BMHC_BACKEND_PROTOCOL}
BACKEND_HOSTNAME: ${DNPM_BWHC_BACKEND_HOSTNAME}
BACKEND_PROTOCOL: http
BACKEND_HOSTNAME: dnpm-backend
BACKEND_PORT: 9000
DNPM_BWHC_FRONTEND_ZIP: ${DNPM_BWHC_FRONTEND_ZIP}
HTTP_PROXY: ${http_proxy}
HTTPS_PROXY: ${https_proxy}
environment:
BACKEND_PROTOCOL: ${DNPM_BMHC_BACKEND_PROTOCOL}
BACKEND_HOSTNAME: ${DNPM_BWHC_BACKEND_HOSTNAME}
BACKEND_PROTOCOL: http
BACKEND_HOSTNAME: dnpm-backend
BACKEND_PORT: 9000
no_proxy: dnpm-backend
labels:
@ -29,13 +28,11 @@ services:
dnpm-backend:
build:
context: ../../dnpm/origin
dockerfile: Backend.Dockerfile
context: ../../minimal/modules
dockerfile: dnpm-backend.Dockerfile
args:
BWHC_BASE_DIR: /bwhc-backend
DNPM_BWHC_BACKEND_ZIP: ${DNPM_BWHC_BACKEND_ZIP}
ports:
- 9000:9000
environment:
APPLICATION_SECRET: ${DNPM_APPLICATION_SECRET}
ZPM_SITE: ${ZPM_SITE}
@ -43,7 +40,6 @@ services:
# PLAY_HTTP_PORT: 9000
# PLAY_HTTP_ADDRESS: 0.0.0.0
volumes:
- ../dnpm/origin/logback.xml:/bwhc-backend/logback.xml:ro
- /etc/bridgehead/dnpm/bwhcConnectorConfig.xml:/bwhc-backend/bwhcConnectorConfig.xml:ro
- /etc/bridgehead/dnpm/production.conf:/bwhc-backend/production.conf:ro
- bwhc_data:/bwhc-backend/data/

0
dnpm/origin/Frontend.Dockerfile → minimal/modules/dnpm-frontend.Dockerfile
View File

10
minimal/modules/dnpm-setup.sh
View File

@ -15,5 +15,15 @@ if [ -n "${ENABLE_DNPM}" ]; then
if [ -n "${ENABLE_DNPM_BWHC}" ]; then
log INFO "DNPM setup detected (with Frontend/Backend) -- will start BWHC Frontend/Backend. This is highly experimental!"
OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose-bwhc.yml"
if [ -z "${DNPM_BWHC_FRONTEND_ZIP}" ]; then
fail_and_report 1 "Variable DNPM_BWHC_FRONTEND_ZIP is not set."
fi
if [ -z "${DNPM_BWHC_BACKEND_ZIP}" ]; then
fail_and_report 1 "Variable DNPM_BWHC_BACKEND_ZIP is not set."
fi
if [ -z "${ZPM_SITE}" ]; then
fail_and_report 1 "Variable ZPM_SITE is not set."
fi
fi
fi