restucture

dfci · Oct 1, 2018 · f9f80ae · f9f80ae
1 parent 46ac3b5
commit f9f80ae
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Showing 20 changed files with 23 additions and 20 deletions.
diff --git 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
diff --git a/cbioportal-mysql/mysql-data/.gitignore → mountpoints/cbioportal-mysql-data/.gitignore b/cbioportal-mysql/mysql-data/.gitignore → mountpoints/cbioportal-mysql-data/.gitignore
diff --git a/host/.gitignore → mountpoints/host/.gitignore b/host/.gitignore → mountpoints/host/.gitignore
diff --git a/scripts/generate_self_signed_keys_for_nginx.sh 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 → services/cancerhotspots/Dockerfile b/cancerhotspots/Dockerfile → services/cancerhotspots/Dockerfile
diff --git a/cbioportal-mysql/Dockerfile → services/cbioportal-mysql/Dockerfile b/cbioportal-mysql/Dockerfile → services/cbioportal-mysql/Dockerfile
diff --git a/cbioportal-mysql/custom.cnf → services/cbioportal-mysql/custom.cnf b/cbioportal-mysql/custom.cnf → services/cbioportal-mysql/custom.cnf
diff --git a/cbioportal/Dockerfile → services/cbioportal/Dockerfile b/cbioportal/Dockerfile → services/cbioportal/Dockerfile
diff --git a/cbioportal/context.xml → services/cbioportal/context.xml b/cbioportal/context.xml → services/cbioportal/context.xml
diff --git a/cbioportal/entrypoint.sh → services/cbioportal/entrypoint.sh b/cbioportal/entrypoint.sh → services/cbioportal/entrypoint.sh
diff --git a/cbioportal/resources/portal.properties → ...es/cbioportal/resources/portal.properties b/cbioportal/resources/portal.properties → ...es/cbioportal/resources/portal.properties
diff --git a/genome-nexus-mongodb/Dockerfile → services/genome-nexus-mongodb/Dockerfile b/genome-nexus-mongodb/Dockerfile → services/genome-nexus-mongodb/Dockerfile
diff --git a/genome-nexus/Dockerfile → services/genome-nexus/Dockerfile b/genome-nexus/Dockerfile → services/genome-nexus/Dockerfile
diff --git a/nginx-wrapper/Dockerfile → services/nginx-wrapper/Dockerfile b/nginx-wrapper/Dockerfile → services/nginx-wrapper/Dockerfile
diff --git a/nginx-wrapper/nginx.conf → services/nginx-wrapper/nginx.conf b/nginx-wrapper/nginx.conf → services/nginx-wrapper/nginx.conf
diff --git a/oncokb-mysql/Dockerfile → services/oncokb-mysql/Dockerfile b/oncokb-mysql/Dockerfile → services/oncokb-mysql/Dockerfile
diff --git a/oncokb/Dockerfile → services/oncokb/Dockerfile b/oncokb/Dockerfile → services/oncokb/Dockerfile
diff --git a/session-service-mongodb/Dockerfile → services/session-service-mongodb/Dockerfile b/session-service-mongodb/Dockerfile → services/session-service-mongodb/Dockerfile
diff --git a/session-service/Dockerfile → services/session-service/Dockerfile b/session-service/Dockerfile → services/session-service/Dockerfile