From f9f80ae406166e70434334ae1ec7fe14aeb0c48b Mon Sep 17 00:00:00 2001 From: Eric Marriott Date: Mon, 1 Oct 2018 10:31:38 -0400 Subject: [PATCH] restucture --- docker-compose.yml | 36 +++++++++---------- generate_self_signed_keys_for_nginx.sh | 2 -- .../cbioportal-mysql-data}/.gitignore | 0 {host => mountpoints/host}/.gitignore | 0 .../generate_self_signed_keys_for_nginx.sh | 5 +++ .../cancerhotspots}/Dockerfile | 0 .../cbioportal-mysql}/Dockerfile | 0 .../cbioportal-mysql}/custom.cnf | 0 .../cbioportal}/Dockerfile | 0 .../cbioportal}/context.xml | 0 .../cbioportal}/entrypoint.sh | 0 .../cbioportal}/resources/portal.properties | 0 .../genome-nexus-mongodb}/Dockerfile | 0 .../genome-nexus}/Dockerfile | 0 .../nginx-wrapper}/Dockerfile | 0 .../nginx-wrapper}/nginx.conf | 0 .../oncokb-mysql}/Dockerfile | 0 {oncokb => services/oncokb}/Dockerfile | 0 .../session-service-mongodb}/Dockerfile | 0 .../session-service}/Dockerfile | 0 20 files changed, 23 insertions(+), 20 deletions(-) delete mode 100755 generate_self_signed_keys_for_nginx.sh rename {cbioportal-mysql/mysql-data => mountpoints/cbioportal-mysql-data}/.gitignore (100%) rename {host => mountpoints/host}/.gitignore (100%) create mode 100755 scripts/generate_self_signed_keys_for_nginx.sh rename {cancerhotspots => services/cancerhotspots}/Dockerfile (100%) rename {cbioportal-mysql => services/cbioportal-mysql}/Dockerfile (100%) rename {cbioportal-mysql => services/cbioportal-mysql}/custom.cnf (100%) rename {cbioportal => services/cbioportal}/Dockerfile (100%) rename {cbioportal => services/cbioportal}/context.xml (100%) rename {cbioportal => services/cbioportal}/entrypoint.sh (100%) rename {cbioportal => services/cbioportal}/resources/portal.properties (100%) rename {genome-nexus-mongodb => services/genome-nexus-mongodb}/Dockerfile (100%) rename {genome-nexus => services/genome-nexus}/Dockerfile (100%) rename {nginx-wrapper => services/nginx-wrapper}/Dockerfile (100%) rename {nginx-wrapper => services/nginx-wrapper}/nginx.conf (100%) rename {oncokb-mysql => services/oncokb-mysql}/Dockerfile (100%) rename {oncokb => services/oncokb}/Dockerfile (100%) rename {session-service-mongodb => services/session-service-mongodb}/Dockerfile (100%) rename {session-service => services/session-service}/Dockerfile (100%) diff --git a/docker-compose.yml b/docker-compose.yml index fbfefdd..a9ab47a 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -3,21 +3,21 @@ services: nginx-wrapper: image: cbioportal-cloud-nginx-wrapper:latest build: - context: ./nginx-wrapper + context: services/nginx-wrapper ports: - "80:80" - "443:443" volumes: - type: bind - source: ./nginx-wrapper/nginx.conf + source: ./services/nginx-wrapper/nginx.conf target: /etc/nginx/conf.d/default.conf read_only: true - type: bind - source: ./nginx-wrapper/cert.crt + source: ./services/nginx-wrapper/cert.crt target: /etc/nginx/cert.crt read_only: true - type: bind - source: ./nginx-wrapper/cert.key + source: ./services/nginx-wrapper/cert.key target: /etc/nginx/cert.key read_only: true depends_on: @@ -29,7 +29,7 @@ services: cbioportal: image: cbioportal-cloud:latest build: - context: ./cbioportal + context: services/cbioportal args: BRANCH: master DB_HOST: cbioportal-mysql @@ -40,11 +40,11 @@ services: restart: always volumes: - type: bind - source: ./host + source: ./mountpoints/host target: /host read_only: false - type: bind - source: ./cbioportal/context.xml + source: ./services/cbioportal/context.xml target: /usr/local/tomcat/cont/context.xml read_only: true depends_on: @@ -63,22 +63,22 @@ services: cbioportal-mysql: image: cbioportal-cloud-cbioportal-mysql:latest build: - context: ./cbioportal-mysql + context: services/cbioportal-mysql environment: MYSQL_ROOT_PASSWORD: *mysql_root_password MYSQL_DATABASE: *mysql_database restart: always volumes: - type: bind - source: ./host + source: ./mountpoints/host target: /host read_only: false - type: bind - source: ./cbioportal-mysql/custom.cnf + source: ./services/cbioportal-mysql/custom.cnf target: /etc/mysql/conf.d/custom.cnf read_only: true - type: bind - source: ./cbioportal-mysql/mysql-data + source: ./mountpoints/cbioportal-mysql-data target: /var/lib/mysql read_only: false networks: @@ -87,7 +87,7 @@ services: oncokb: image: cbioportal-cloud-oncokb:latest build: - context: ./oncokb + context: services/oncokb args: BRANCH: &oncokb_branch v0.3.1 DB_HOST: oncokb-mysql @@ -105,7 +105,7 @@ services: oncokb-mysql: image: cbioportal-cloud-oncokb-mysql:latest build: - context: oncokb-mysql + context: services/oncokb-mysql args: BRANCH: *oncokb_branch environment: @@ -117,7 +117,7 @@ services: genome-nexus: image: cbioportal-cloud-genome-nexus:latest build: - context: ./genome-nexus + context: services/genome-nexus args: BRANCH: master environment: @@ -135,7 +135,7 @@ services: genome-nexus-mongodb: image: cbioportal-cloud-genome-nexus-mongodb:latest build: - context: ./genome-nexus-mongodb + context: services/genome-nexus-mongodb args: BRANCH: v0.4 restart: always @@ -144,7 +144,7 @@ services: session-service: image: cbioportal-cloud-session-service:latest build: - context: ./session-service + context: services/session-service args: BRANCH: master environment: @@ -162,14 +162,14 @@ services: session-service-mongodb: image: cbioportal-cloud-session-service-mongodb:latest build: - context: ./session-service-mongodb + context: services/session-service-mongodb restart: always networks: - cbio-bridge cancerhotspots: image: cbioportal-cloud-cancerhotspots:latest build: - context: ./cancerhotspots + context: services/cancerhotspots args: BRANCH: master restart: always diff --git a/generate_self_signed_keys_for_nginx.sh b/generate_self_signed_keys_for_nginx.sh deleted file mode 100755 index 610c310..0000000 --- a/generate_self_signed_keys_for_nginx.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/usr/bin/env bash -openssl req -x509 -nodes -days 365 -newkey rsa:2048 -keyout ./nginx-wrapper/cert.key -out ./nginx-wrapper/cert.crt diff --git a/cbioportal-mysql/mysql-data/.gitignore b/mountpoints/cbioportal-mysql-data/.gitignore similarity index 100% rename from cbioportal-mysql/mysql-data/.gitignore rename to mountpoints/cbioportal-mysql-data/.gitignore diff --git a/host/.gitignore b/mountpoints/host/.gitignore similarity index 100% rename from host/.gitignore rename to mountpoints/host/.gitignore diff --git a/scripts/generate_self_signed_keys_for_nginx.sh b/scripts/generate_self_signed_keys_for_nginx.sh new file mode 100755 index 0000000..4e26461 --- /dev/null +++ b/scripts/generate_self_signed_keys_for_nginx.sh @@ -0,0 +1,5 @@ +#!/usr/bin/env bash +MAIN_PATH=$(dirname $(dirname $(readlink -f "$0"))) +openssl req -x509 -nodes -days 365 -newkey rsa:2048 \ + -keyout ${MAIN_PATH}/services/nginx-wrapper/cert.key \ + -out ${MAIN_PATH}/services/nginx-wrapper/cert.crt diff --git a/cancerhotspots/Dockerfile b/services/cancerhotspots/Dockerfile similarity index 100% rename from cancerhotspots/Dockerfile rename to services/cancerhotspots/Dockerfile diff --git a/cbioportal-mysql/Dockerfile b/services/cbioportal-mysql/Dockerfile similarity index 100% rename from cbioportal-mysql/Dockerfile rename to services/cbioportal-mysql/Dockerfile diff --git a/cbioportal-mysql/custom.cnf b/services/cbioportal-mysql/custom.cnf similarity index 100% rename from cbioportal-mysql/custom.cnf rename to services/cbioportal-mysql/custom.cnf diff --git a/cbioportal/Dockerfile b/services/cbioportal/Dockerfile similarity index 100% rename from cbioportal/Dockerfile rename to services/cbioportal/Dockerfile diff --git a/cbioportal/context.xml b/services/cbioportal/context.xml similarity index 100% rename from cbioportal/context.xml rename to services/cbioportal/context.xml diff --git a/cbioportal/entrypoint.sh b/services/cbioportal/entrypoint.sh similarity index 100% rename from cbioportal/entrypoint.sh rename to services/cbioportal/entrypoint.sh diff --git a/cbioportal/resources/portal.properties b/services/cbioportal/resources/portal.properties similarity index 100% rename from cbioportal/resources/portal.properties rename to services/cbioportal/resources/portal.properties diff --git a/genome-nexus-mongodb/Dockerfile b/services/genome-nexus-mongodb/Dockerfile similarity index 100% rename from genome-nexus-mongodb/Dockerfile rename to services/genome-nexus-mongodb/Dockerfile diff --git a/genome-nexus/Dockerfile b/services/genome-nexus/Dockerfile similarity index 100% rename from genome-nexus/Dockerfile rename to services/genome-nexus/Dockerfile diff --git a/nginx-wrapper/Dockerfile b/services/nginx-wrapper/Dockerfile similarity index 100% rename from nginx-wrapper/Dockerfile rename to services/nginx-wrapper/Dockerfile diff --git a/nginx-wrapper/nginx.conf b/services/nginx-wrapper/nginx.conf similarity index 100% rename from nginx-wrapper/nginx.conf rename to services/nginx-wrapper/nginx.conf diff --git a/oncokb-mysql/Dockerfile b/services/oncokb-mysql/Dockerfile similarity index 100% rename from oncokb-mysql/Dockerfile rename to services/oncokb-mysql/Dockerfile diff --git a/oncokb/Dockerfile b/services/oncokb/Dockerfile similarity index 100% rename from oncokb/Dockerfile rename to services/oncokb/Dockerfile diff --git a/session-service-mongodb/Dockerfile b/services/session-service-mongodb/Dockerfile similarity index 100% rename from session-service-mongodb/Dockerfile rename to services/session-service-mongodb/Dockerfile diff --git a/session-service/Dockerfile b/services/session-service/Dockerfile similarity index 100% rename from session-service/Dockerfile rename to services/session-service/Dockerfile