From 4e7f023b8a3e050c9c591145510e3ee36a2bf939 Mon Sep 17 00:00:00 2001 From: Tobias Kussel Date: Tue, 16 May 2023 10:56:28 +0000 Subject: [PATCH] Clean up bwhc startup --- bbmri/modules/dnpm-compose-bwhc.yml | 20 +++----- bbmri/modules/dnpm-setup.sh | 10 ++++ ccp/modules/dnpm-compose-bwhc.yml | 20 +++----- ccp/modules/dnpm-setup.sh | 10 ++++ dnpm/dnpm-compose-beamconnect.yml | 29 ----------- dnpm/dnpm-compose-bwhc.yml | 51 ------------------- dnpm/dnpm-setup.sh | 16 ------ dnpm/origin/logback.xml | 37 -------------- dnpm/vars | 1 - .../modules/dnpm-backend.Dockerfile | 0 minimal/modules/dnpm-compose-bwhc.yml | 20 +++----- .../modules/dnpm-frontend.Dockerfile | 0 minimal/modules/dnpm-setup.sh | 10 ++++ 13 files changed, 54 insertions(+), 170 deletions(-) delete mode 100644 dnpm/dnpm-compose-beamconnect.yml delete mode 100644 dnpm/dnpm-compose-bwhc.yml delete mode 100644 dnpm/dnpm-setup.sh delete mode 100644 dnpm/origin/logback.xml delete mode 100644 dnpm/vars rename dnpm/origin/Backend.Dockerfile => minimal/modules/dnpm-backend.Dockerfile (100%) rename dnpm/origin/Frontend.Dockerfile => minimal/modules/dnpm-frontend.Dockerfile (100%) diff --git a/bbmri/modules/dnpm-compose-bwhc.yml b/bbmri/modules/dnpm-compose-bwhc.yml index 9ba1357..a264728 100644 --- a/bbmri/modules/dnpm-compose-bwhc.yml +++ b/bbmri/modules/dnpm-compose-bwhc.yml @@ -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: ${ZPM_SITE} @@ -43,7 +40,6 @@ services: # PLAY_HTTP_PORT: 9000 # PLAY_HTTP_ADDRESS: 0.0.0.0 volumes: - - ../dnpm/origin/logback.xml:/bwhc-backend/logback.xml:ro - /etc/bridgehead/dnpm/bwhcConnectorConfig.xml:/bwhc-backend/bwhcConnectorConfig.xml:ro - /etc/bridgehead/dnpm/production.conf:/bwhc-backend/production.conf:ro - bwhc_data:/bwhc-backend/data/ diff --git a/bbmri/modules/dnpm-setup.sh b/bbmri/modules/dnpm-setup.sh index db1969a..ca98542 100644 --- a/bbmri/modules/dnpm-setup.sh +++ b/bbmri/modules/dnpm-setup.sh @@ -15,5 +15,15 @@ if [ -n "${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 diff --git a/ccp/modules/dnpm-compose-bwhc.yml b/ccp/modules/dnpm-compose-bwhc.yml index 9ba1357..a264728 100644 --- a/ccp/modules/dnpm-compose-bwhc.yml +++ b/ccp/modules/dnpm-compose-bwhc.yml @@ -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: ${ZPM_SITE} @@ -43,7 +40,6 @@ services: # PLAY_HTTP_PORT: 9000 # PLAY_HTTP_ADDRESS: 0.0.0.0 volumes: - - ../dnpm/origin/logback.xml:/bwhc-backend/logback.xml:ro - /etc/bridgehead/dnpm/bwhcConnectorConfig.xml:/bwhc-backend/bwhcConnectorConfig.xml:ro - /etc/bridgehead/dnpm/production.conf:/bwhc-backend/production.conf:ro - bwhc_data:/bwhc-backend/data/ diff --git a/ccp/modules/dnpm-setup.sh b/ccp/modules/dnpm-setup.sh index ce39731..c6c2b29 100644 --- a/ccp/modules/dnpm-setup.sh +++ b/ccp/modules/dnpm-setup.sh @@ -12,5 +12,15 @@ if [ -n "${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 diff --git a/dnpm/dnpm-compose-beamconnect.yml b/dnpm/dnpm-compose-beamconnect.yml deleted file mode 100644 index 57c46eb..0000000 --- a/dnpm/dnpm-compose-beamconnect.yml +++ /dev/null @@ -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 diff --git a/dnpm/dnpm-compose-bwhc.yml b/dnpm/dnpm-compose-bwhc.yml deleted file mode 100644 index 60fe3f0..0000000 --- a/dnpm/dnpm-compose-bwhc.yml +++ /dev/null @@ -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: ${ZPM_SITE} - noproxy: dnpm-frontend,connect - # PLAY_HTTP_PORT: 9000 - # PLAY_HTTP_ADDRESS: 0.0.0.0 - volumes: - - ../dnpm/origin/logback.xml:/bwhc-backend/logback.xml:ro - - /etc/bridgehead/dnpm/bwhcConnectorConfig.xml:/bwhc-backend/bwhcConnectorConfig.xml:ro - - /etc/bridgehead/dnpm/production.conf:/bwhc-backend/production.conf:ro - - bwhc_data:/bwhc-backend/data/ - - bwhc_hgnc_data:/bwhc-backend/hgnc_data/ - -volumes: - bwhc_data: - bwhc_hgnc_data: diff --git a/dnpm/dnpm-setup.sh b/dnpm/dnpm-setup.sh deleted file mode 100644 index ff32c68..0000000 --- a/dnpm/dnpm-setup.sh +++ /dev/null @@ -1,16 +0,0 @@ -#!/bin/bash - -function dnpmSetup() { - if [ -e /etc/bridgehead/dnpm/local_targets.json ]; then - log INFO "DNPM setup detected (Beam.Connect) -- will start Beam.Connect for DNPM." - OVERRIDE+=" -f ./dnpm/dnpm-compose-beamconnect.yml" - DNPM_APPLICATION_SECRET="$(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 -} diff --git a/dnpm/origin/logback.xml b/dnpm/origin/logback.xml deleted file mode 100644 index c25cda6..0000000 --- a/dnpm/origin/logback.xml +++ /dev/null @@ -1,37 +0,0 @@ - - - - - - - - - - %d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n - - - - - - - - - - diff --git a/dnpm/vars b/dnpm/vars deleted file mode 100644 index 69c2220..0000000 --- a/dnpm/vars +++ /dev/null @@ -1 +0,0 @@ -DNPM_DISCOVERY_URL=https://dnpm.medizin.uni-tuebingen.de/sites diff --git a/dnpm/origin/Backend.Dockerfile b/minimal/modules/dnpm-backend.Dockerfile similarity index 100% rename from dnpm/origin/Backend.Dockerfile rename to minimal/modules/dnpm-backend.Dockerfile diff --git a/minimal/modules/dnpm-compose-bwhc.yml b/minimal/modules/dnpm-compose-bwhc.yml index 9ba1357..a264728 100644 --- a/minimal/modules/dnpm-compose-bwhc.yml +++ b/minimal/modules/dnpm-compose-bwhc.yml @@ -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: ${ZPM_SITE} @@ -43,7 +40,6 @@ services: # PLAY_HTTP_PORT: 9000 # PLAY_HTTP_ADDRESS: 0.0.0.0 volumes: - - ../dnpm/origin/logback.xml:/bwhc-backend/logback.xml:ro - /etc/bridgehead/dnpm/bwhcConnectorConfig.xml:/bwhc-backend/bwhcConnectorConfig.xml:ro - /etc/bridgehead/dnpm/production.conf:/bwhc-backend/production.conf:ro - bwhc_data:/bwhc-backend/data/ diff --git a/dnpm/origin/Frontend.Dockerfile b/minimal/modules/dnpm-frontend.Dockerfile similarity index 100% rename from dnpm/origin/Frontend.Dockerfile rename to minimal/modules/dnpm-frontend.Dockerfile diff --git a/minimal/modules/dnpm-setup.sh b/minimal/modules/dnpm-setup.sh index db1969a..ca98542 100644 --- a/minimal/modules/dnpm-setup.sh +++ b/minimal/modules/dnpm-setup.sh @@ -15,5 +15,15 @@ if [ -n "${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