Clean up bwhc startup

bbmri/modules/dnpm-compose-bwhc.yml

@@ -4,21 +4,20 @@ services:
   dnpm-frontend:
     depends_on: [ dnpm-backend ]
     build:
-      context: ../../dnpm/origin
+      context: ../../minimal/modules
-      dockerfile: Frontend.Dockerfile
+      dockerfile: dnpm-frontend.Dockerfile
-      network: host
       args:
         NUXT_HOST: 0.0.0.0
         NUXT_PORT: 3000
-        BACKEND_PROTOCOL: ${DNPM_BMHC_BACKEND_PROTOCOL}
+        BACKEND_PROTOCOL: http
-        BACKEND_HOSTNAME: ${DNPM_BWHC_BACKEND_HOSTNAME}
+        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_PROTOCOL: http
-        BACKEND_HOSTNAME: ${DNPM_BWHC_BACKEND_HOSTNAME}
+        BACKEND_HOSTNAME: dnpm-backend
         BACKEND_PORT: 9000
         no_proxy: dnpm-backend
     labels:
@@ -29,13 +28,11 @@ services:
 
   dnpm-backend:
     build:
-      context: ../../dnpm/origin
+      context: ../../minimal/modules
-      dockerfile: Backend.Dockerfile
+      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/

bbmri/modules/dnpm-setup.sh

@@ -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

ccp/modules/dnpm-compose-bwhc.yml

@@ -4,21 +4,20 @@ services:
   dnpm-frontend:
     depends_on: [ dnpm-backend ]
     build:
-      context: ../../dnpm/origin
+      context: ../../minimal/modules
-      dockerfile: Frontend.Dockerfile
+      dockerfile: dnpm-frontend.Dockerfile
-      network: host
       args:
         NUXT_HOST: 0.0.0.0
         NUXT_PORT: 3000
-        BACKEND_PROTOCOL: ${DNPM_BMHC_BACKEND_PROTOCOL}
+        BACKEND_PROTOCOL: http
-        BACKEND_HOSTNAME: ${DNPM_BWHC_BACKEND_HOSTNAME}
+        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_PROTOCOL: http
-        BACKEND_HOSTNAME: ${DNPM_BWHC_BACKEND_HOSTNAME}
+        BACKEND_HOSTNAME: dnpm-backend
         BACKEND_PORT: 9000
         no_proxy: dnpm-backend
     labels:
@@ -29,13 +28,11 @@ services:
 
   dnpm-backend:
     build:
-      context: ../../dnpm/origin
+      context: ../../minimal/modules
-      dockerfile: Backend.Dockerfile
+      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/

ccp/modules/dnpm-setup.sh

@@ -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

dnpm/dnpm-compose-beamconnect.yml

@@ -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

dnpm/dnpm-compose-bwhc.yml

@@ -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:

dnpm/dnpm-setup.sh

@@ -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
-}

dnpm/origin/logback.xml

@@ -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>

dnpm/vars

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

minimal/modules/dnpm-compose-bwhc.yml

@@ -4,21 +4,20 @@ services:
   dnpm-frontend:
     depends_on: [ dnpm-backend ]
     build:
-      context: ../../dnpm/origin
+      context: ../../minimal/modules
-      dockerfile: Frontend.Dockerfile
+      dockerfile: dnpm-frontend.Dockerfile
-      network: host
       args:
         NUXT_HOST: 0.0.0.0
         NUXT_PORT: 3000
-        BACKEND_PROTOCOL: ${DNPM_BMHC_BACKEND_PROTOCOL}
+        BACKEND_PROTOCOL: http
-        BACKEND_HOSTNAME: ${DNPM_BWHC_BACKEND_HOSTNAME}
+        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_PROTOCOL: http
-        BACKEND_HOSTNAME: ${DNPM_BWHC_BACKEND_HOSTNAME}
+        BACKEND_HOSTNAME: dnpm-backend
         BACKEND_PORT: 9000
         no_proxy: dnpm-backend
     labels:
@@ -29,13 +28,11 @@ services:
 
   dnpm-backend:
     build:
-      context: ../../dnpm/origin
+      context: ../../minimal/modules
-      dockerfile: Backend.Dockerfile
+      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/

minimal/modules/dnpm-setup.sh

@@ -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