From f4134bcfca5f3f96974568c57ad5c2651990cf1a Mon Sep 17 00:00:00 2001
From: Tobias Kussel <tobias.kussel@dkfz-heidelberg.de>
Date: Wed, 17 May 2023 09:26:55 +0000
Subject: [PATCH] Remove DNPM-BwHC experiment

---
 bbmri/modules/dnpm-compose-bwhc.yml           | 50 --------------
 ...mpose-beamconnect.yml => dnpm-compose.yml} |  0
 bbmri/modules/dnpm-setup.sh                   | 18 +----
 ccp/modules/dnpm-compose-bwhc.yml             | 50 --------------
 ...mpose-beamconnect.yml => dnpm-compose.yml} |  0
 ccp/modules/dnpm-setup.sh                     | 18 +----
 minimal/modules/dnpm-backend.Dockerfile       | 66 -------------------
 minimal/modules/dnpm-compose-bwhc.yml         | 50 --------------
 ...mpose-beamconnect.yml => dnpm-compose.yml} |  0
 minimal/modules/dnpm-frontend.Dockerfile      | 42 ------------
 minimal/modules/dnpm-setup.sh                 | 18 +----
 11 files changed, 3 insertions(+), 309 deletions(-)
 delete mode 100644 bbmri/modules/dnpm-compose-bwhc.yml
 rename bbmri/modules/{dnpm-compose-beamconnect.yml => dnpm-compose.yml} (100%)
 delete mode 100644 ccp/modules/dnpm-compose-bwhc.yml
 rename ccp/modules/{dnpm-compose-beamconnect.yml => dnpm-compose.yml} (100%)
 delete mode 100644 minimal/modules/dnpm-backend.Dockerfile
 delete mode 100644 minimal/modules/dnpm-compose-bwhc.yml
 rename minimal/modules/{dnpm-compose-beamconnect.yml => dnpm-compose.yml} (100%)
 delete mode 100644 minimal/modules/dnpm-frontend.Dockerfile

diff --git a/bbmri/modules/dnpm-compose-bwhc.yml b/bbmri/modules/dnpm-compose-bwhc.yml
deleted file mode 100644
index a264728..0000000
--- a/bbmri/modules/dnpm-compose-bwhc.yml
+++ /dev/null
@@ -1,50 +0,0 @@
-version: "3.7"
-
-services:
-  dnpm-frontend:
-    depends_on: [ dnpm-backend ]
-    build:
-      context: ../../minimal/modules
-      dockerfile: dnpm-frontend.Dockerfile
-      args:
-        NUXT_HOST: 0.0.0.0
-        NUXT_PORT: 3000
-        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: http
-        BACKEND_HOSTNAME: dnpm-backend
-        BACKEND_PORT: 9000
-        no_proxy: dnpm-backend
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.dnpm-frontend.rule=PathPrefix(`/dnpm-frontend`)"
-      - "traefik.http.services.dnpm-frontend.loadbalancer.server.port=3000"
-      - "traefik.http.routers.dnpm-frontend.tls=true"
-
-  dnpm-backend:
-    build:
-      context: ../../minimal/modules
-      dockerfile: dnpm-backend.Dockerfile
-      args:
-        BWHC_BASE_DIR: /bwhc-backend
-        DNPM_BWHC_BACKEND_ZIP: ${DNPM_BWHC_BACKEND_ZIP}
-    environment:
-      APPLICATION_SECRET: ${DNPM_APPLICATION_SECRET}
-      ZPM_SITE: ${ZPM_SITE}
-      noproxy: dnpm-frontend,dnpm-beam-connect
-      # PLAY_HTTP_PORT: 9000
-      # PLAY_HTTP_ADDRESS: 0.0.0.0
-    volumes:
-      - /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:
diff --git a/bbmri/modules/dnpm-compose-beamconnect.yml b/bbmri/modules/dnpm-compose.yml
similarity index 100%
rename from bbmri/modules/dnpm-compose-beamconnect.yml
rename to bbmri/modules/dnpm-compose.yml
diff --git a/bbmri/modules/dnpm-setup.sh b/bbmri/modules/dnpm-setup.sh
index ca98542..4ece115 100644
--- a/bbmri/modules/dnpm-setup.sh
+++ b/bbmri/modules/dnpm-setup.sh
@@ -2,7 +2,7 @@
 
 if [ -n "${ENABLE_DNPM}" ]; then
 	log INFO "DNPM setup detected (Beam.Connect) -- will start Beam.Connect for DNPM."
-	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose-beamconnect.yml"
+	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
 
 	# Set variables required for Beam-Connect
 	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)"
@@ -10,20 +10,4 @@ if [ -n "${ENABLE_DNPM}" ]; then
 	DNPM_BROKER_ID="broker.dev.ccp-it.dktk.dkfz.de"
 	DNPM_BROKER_URL="https://${DNPM_BROKER_ID}"
 	DNPM_PROXY_ID="${SITE_ID}.${DNPM_BROKER_ID}"
-
-	# Optionally, start bwhc as well. This is currently only experimental
-	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
diff --git a/ccp/modules/dnpm-compose-bwhc.yml b/ccp/modules/dnpm-compose-bwhc.yml
deleted file mode 100644
index a264728..0000000
--- a/ccp/modules/dnpm-compose-bwhc.yml
+++ /dev/null
@@ -1,50 +0,0 @@
-version: "3.7"
-
-services:
-  dnpm-frontend:
-    depends_on: [ dnpm-backend ]
-    build:
-      context: ../../minimal/modules
-      dockerfile: dnpm-frontend.Dockerfile
-      args:
-        NUXT_HOST: 0.0.0.0
-        NUXT_PORT: 3000
-        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: http
-        BACKEND_HOSTNAME: dnpm-backend
-        BACKEND_PORT: 9000
-        no_proxy: dnpm-backend
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.dnpm-frontend.rule=PathPrefix(`/dnpm-frontend`)"
-      - "traefik.http.services.dnpm-frontend.loadbalancer.server.port=3000"
-      - "traefik.http.routers.dnpm-frontend.tls=true"
-
-  dnpm-backend:
-    build:
-      context: ../../minimal/modules
-      dockerfile: dnpm-backend.Dockerfile
-      args:
-        BWHC_BASE_DIR: /bwhc-backend
-        DNPM_BWHC_BACKEND_ZIP: ${DNPM_BWHC_BACKEND_ZIP}
-    environment:
-      APPLICATION_SECRET: ${DNPM_APPLICATION_SECRET}
-      ZPM_SITE: ${ZPM_SITE}
-      noproxy: dnpm-frontend,dnpm-beam-connect
-      # PLAY_HTTP_PORT: 9000
-      # PLAY_HTTP_ADDRESS: 0.0.0.0
-    volumes:
-      - /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:
diff --git a/ccp/modules/dnpm-compose-beamconnect.yml b/ccp/modules/dnpm-compose.yml
similarity index 100%
rename from ccp/modules/dnpm-compose-beamconnect.yml
rename to ccp/modules/dnpm-compose.yml
diff --git a/ccp/modules/dnpm-setup.sh b/ccp/modules/dnpm-setup.sh
index c6c2b29..c9250cb 100644
--- a/ccp/modules/dnpm-setup.sh
+++ b/ccp/modules/dnpm-setup.sh
@@ -2,25 +2,9 @@
 
 if [ -n "${ENABLE_DNPM}" ]; then
 	log INFO "DNPM setup detected (Beam.Connect) -- will start Beam.Connect for DNPM."
-	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose-beamconnect.yml"
+	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
 
 	# Set variables required for Beam-Connect
 	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="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
-
-	# Optionally, start bwhc as well. This is currently only experimental
-	if [ -n "${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
diff --git a/minimal/modules/dnpm-backend.Dockerfile b/minimal/modules/dnpm-backend.Dockerfile
deleted file mode 100644
index e37c008..0000000
--- a/minimal/modules/dnpm-backend.Dockerfile
+++ /dev/null
@@ -1,66 +0,0 @@
-FROM openjdk:11-jre AS builder
-
-ARG DNPM_BWHC_BACKEND_ZIP
-
-# Change to latest release
-ARG VERSION=broker
-
-ARG BWHC_BASE_DIR=/bwhc-backend
-
-ENV BWHC_BASE_DIR=$BWHC_BASE_DIR
-ENV BWHC_USER_DB_DIR=$BWHC_BASE_DIR/data/user-db
-ENV BWHC_DATA_ENTRY_DIR=$BWHC_BASE_DIR/data/data-entry
-ENV BWHC_QUERY_DATA_DIR=$BWHC_BASE_DIR/data/query-data
-
-ADD ${DNPM_BWHC_BACKEND_ZIP} /
-RUN unzip $(basename ${DNPM_BWHC_BACKEND_ZIP}) && rm $(basename ${DNPM_BWHC_BACKEND_ZIP})
-
-WORKDIR $BWHC_BASE_DIR
-
-# Prepare config file to use environment variables from docker
-RUN sed -i -r "s/APPLICATION_SECRET(.*)/#APPLICATION_SECRET\1/" ./config
-RUN sed -i -r "s/ZPM_SITE(.*)/#ZPM_SITE\1/" ./config
-
-# Prepare config file to use fix environment variables for this image
-RUN sed -i -r "s~BWHC_DATA_ENTRY_DIR.*~BWHC_DATA_ENTRY_DIR=$BWHC_DATA_ENTRY_DIR~" ./config
-RUN sed -i -r "s~BWHC_QUERY_DATA_DIR.*~BWHC_QUERY_DATA_DIR=$BWHC_QUERY_DATA_DIR~" ./config
-RUN sed -i -r "s~BWHC_USER_DB_DIR.*~BWHC_USER_DB_DIR=$BWHC_USER_DB_DIR~" ./config
-
-RUN ./install.sh $BWHC_BASE_DIR
-
-RUN mv bwhc-rest-api-gateway-*/  bwhc-rest-api-gateway/
-
-FROM openjdk:11-jre
-
-ARG BWHC_BASE_DIR=/bwhc-backend
-
-ENV BWHC_BASE_DIR=$BWHC_BASE_DIR
-ENV BWHC_USER_DB_DIR=$BWHC_BASE_DIR/data/user-db
-ENV BWHC_DATA_ENTRY_DIR=$BWHC_BASE_DIR/data/data-entry
-ENV BWHC_QUERY_DATA_DIR=$BWHC_BASE_DIR/data/query-data
-ENV BWHC_CONNECTOR_CONFIG=$BWHC_BASE_DIR/bwhcConnectorConfig.xml
-
-COPY --from=builder $BWHC_BASE_DIR/config $BWHC_BASE_DIR/
-COPY --from=builder $BWHC_BASE_DIR/bwhcConnectorConfig.xml $BWHC_BASE_DIR/
-COPY --from=builder $BWHC_BASE_DIR/logback.xml $BWHC_BASE_DIR/
-COPY --from=builder $BWHC_BASE_DIR/production.conf $BWHC_BASE_DIR/
-COPY --from=builder $BWHC_BASE_DIR/bwhc-rest-api-gateway/ $BWHC_BASE_DIR/bwhc-rest-api-gateway/
-
-VOLUME $BWHC_BASE_DIR/data
-VOLUME $BWHC_BASE_DIR/hgnc_data
-
-EXPOSE ${BWHC_BACKEND_PORT}
-
-WORKDIR $BWHC_BASE_DIR
-
-CMD $BWHC_BASE_DIR/bwhc-rest-api-gateway/bin/bwhc-rest-api-gateway \
-    -Dplay.http.secret.key=$APPLICATION_SECRET \
-    -Dconfig.file=$BWHC_BASE_DIR/production.conf \
-    -Dlogger.file=$BWHC_BASE_DIR/logback.xml \
-    -Dpidfile.path=/dev/null \
-    -Dbwhc.zpm.site=$ZPM_SITE \
-    -Dbwhc.data.entry.dir=$BWHC_DATA_ENTRY_DIR \
-    -Dbwhc.query.data.dir=$BWHC_QUERY_DATA_DIR \
-    -Dbwhc.user.data.dir=$BWHC_USER_DB_DIR \
-    -Dbwhc.hgnc.dir=$BWHC_HGNC_DIR \
-    -Dbwhc.connector.configFile=$BWHC_CONNECTOR_CONFIG
diff --git a/minimal/modules/dnpm-compose-bwhc.yml b/minimal/modules/dnpm-compose-bwhc.yml
deleted file mode 100644
index a264728..0000000
--- a/minimal/modules/dnpm-compose-bwhc.yml
+++ /dev/null
@@ -1,50 +0,0 @@
-version: "3.7"
-
-services:
-  dnpm-frontend:
-    depends_on: [ dnpm-backend ]
-    build:
-      context: ../../minimal/modules
-      dockerfile: dnpm-frontend.Dockerfile
-      args:
-        NUXT_HOST: 0.0.0.0
-        NUXT_PORT: 3000
-        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: http
-        BACKEND_HOSTNAME: dnpm-backend
-        BACKEND_PORT: 9000
-        no_proxy: dnpm-backend
-    labels:
-      - "traefik.enable=true"
-      - "traefik.http.routers.dnpm-frontend.rule=PathPrefix(`/dnpm-frontend`)"
-      - "traefik.http.services.dnpm-frontend.loadbalancer.server.port=3000"
-      - "traefik.http.routers.dnpm-frontend.tls=true"
-
-  dnpm-backend:
-    build:
-      context: ../../minimal/modules
-      dockerfile: dnpm-backend.Dockerfile
-      args:
-        BWHC_BASE_DIR: /bwhc-backend
-        DNPM_BWHC_BACKEND_ZIP: ${DNPM_BWHC_BACKEND_ZIP}
-    environment:
-      APPLICATION_SECRET: ${DNPM_APPLICATION_SECRET}
-      ZPM_SITE: ${ZPM_SITE}
-      noproxy: dnpm-frontend,dnpm-beam-connect
-      # PLAY_HTTP_PORT: 9000
-      # PLAY_HTTP_ADDRESS: 0.0.0.0
-    volumes:
-      - /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:
diff --git a/minimal/modules/dnpm-compose-beamconnect.yml b/minimal/modules/dnpm-compose.yml
similarity index 100%
rename from minimal/modules/dnpm-compose-beamconnect.yml
rename to minimal/modules/dnpm-compose.yml
diff --git a/minimal/modules/dnpm-frontend.Dockerfile b/minimal/modules/dnpm-frontend.Dockerfile
deleted file mode 100644
index 1d4bb30..0000000
--- a/minimal/modules/dnpm-frontend.Dockerfile
+++ /dev/null
@@ -1,42 +0,0 @@
-FROM node:10-alpine
-
-ARG DNPM_BWHC_FRONTEND_ZIP
-
-# Change to latest release
-# Required for image build using local copy of zip file
-ARG VERSION=2207
-
-# nuxt host and port to be replaced in package.json. (See 2.3 in bwHCPrototypeManual)
-# NUXT_HOST should have a value with public available IP address from within container.
-# If changing NUXT_PORT, also change exposed port.
-ARG NUXT_HOST=0.0.0.0
-ARG NUXT_PORT=3000
-
-# Backend access setup. (See 2.4 in bwHCPrototypeManual)
-ARG BACKEND_PROTOCOL=http
-ARG BACKEND_HOSTNAME=localhost
-ARG BACKEND_PORT=8080
-
-ARG HTTP_PROXY=""
-ARG HTTPS_PROXY=""
-
-ADD ${DNPM_BWHC_FRONTEND_ZIP} /
-RUN unzip $(basename ${DNPM_BWHC_FRONTEND_ZIP}) && rm $(basename ${DNPM_BWHC_FRONTEND_ZIP})
-
-WORKDIR /bwhc-frontend
-
-RUN npm install
-
-# Prepare package.json
-RUN sed -i -r "s/^(\s*)\"host\"[^,]*(,?)/\1\"host\": \"$NUXT_HOST\"\2/" ./package.json
-RUN sed -i -r "s/^(\s*)\"port\"[^,]*(,?)/\1\"port\": \"$NUXT_PORT\"\2/" ./package.json
-
-# Prepare nuxt.config.js
-RUN sed -i -r "s/^(\s*)baseUrl[^,]*(,?)/\1baseUrl: process.env.BASE_URL || '$BACKEND_PROTOCOL:\/\/$BACKEND_HOSTNAME'\2/" ./nuxt.config.js
-RUN sed -i -r "s/^(\s*)port[^,]*(,?)/\1port: process.env.port || ':$BACKEND_PORT'\2/" ./nuxt.config.js
-
-RUN npm run generate
-
-EXPOSE $NUXT_PORT
-
-CMD npm start
diff --git a/minimal/modules/dnpm-setup.sh b/minimal/modules/dnpm-setup.sh
index ca98542..4ece115 100644
--- a/minimal/modules/dnpm-setup.sh
+++ b/minimal/modules/dnpm-setup.sh
@@ -2,7 +2,7 @@
 
 if [ -n "${ENABLE_DNPM}" ]; then
 	log INFO "DNPM setup detected (Beam.Connect) -- will start Beam.Connect for DNPM."
-	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose-beamconnect.yml"
+	OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
 
 	# Set variables required for Beam-Connect
 	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)"
@@ -10,20 +10,4 @@ if [ -n "${ENABLE_DNPM}" ]; then
 	DNPM_BROKER_ID="broker.dev.ccp-it.dktk.dkfz.de"
 	DNPM_BROKER_URL="https://${DNPM_BROKER_ID}"
 	DNPM_PROXY_ID="${SITE_ID}.${DNPM_BROKER_ID}"
-
-	# Optionally, start bwhc as well. This is currently only experimental
-	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