Merge db347d4 into 6963ce0

.travis.yml

@@ -9,11 +9,6 @@ cache:
 addons:
   chrome: stable
 
-node_js:
-  - "6"
-  - "7"
-  - "8"
-
 matrix:
   fast_finish: true
 
@@ -25,6 +20,27 @@ before_install:
 
 install:
   - npm install
+  - sudo apt-get install -y build-essential libssl-dev python-pip python2.7-dev
+  - sudo pip install -U setuptools wheel docker-cloud synapseclient[pandas,pysftp]
+  - docker login --username="$DOCKER_USER" --password="$DOCKER_PASSWORD"
+
+stages:
+  - name: deploy-containers
+  - name: test
 
-script:
-  - npm run ci:travis
+jobs:
+  include:
+    - stage: deploy-containers
+      script:
+        - ./get-data-aws.sh || travis_terminate 1
+        - ./container-build.sh || travis_terminate 1
+        - ./container-deploy.sh || travis_terminate 1
+    - stage: test
+      script: npm run ci:travis
+      node_js: 6
+    - stage: test
+      script: npm run ci:travis
+      node_js: 7
+    - stage: test
+      script: npm run ci:travis
+      node_js: 8

.vscode/launch.json

@@ -5,7 +5,7 @@
             "name": "Launch Chrome against localhost, with sourcemaps",
             "type": "chrome",
             "request": "launch",
-            "url": "http://localhost:3000/*",
+            "url": "http://localhost:8080/*",
             "runtimeArgs": [
               "--disable-web-security",
               "--user-data-dir",
@@ -18,7 +18,7 @@
             "name": "Attach to Chrome, with sourcemaps",
             "type": "chrome",
             "request": "attach",
-            "url": "http://localhost:3000/*",
+            "url": "http://localhost:8080/*",
             "port": 9222,
             "sourceMaps": true,
             "webRoot": "${workspaceRoot}"

Dockerfile

@@ -1,4 +1,4 @@
-FROM node:latest
+FROM node:8.11.4
 
 # See https://crbug.com/795759
 RUN apt-get update && apt-get install -yq libgconf-2-4
@@ -29,8 +29,8 @@ COPY . .
 
 RUN npm run webdriver:update
 
-## The ci:travis script already runs the AoT build, so these two lines build the client and server
-RUN npm run ci:travis
+## These two lines build the client and server
+RUN npm run build:aot
 RUN npm run build:server:docker
 
 COPY ./start-server.sh /ng-app/start-server.sh

README.md

@@ -1,5 +1,5 @@
 [![Coverage Status](https://coveralls.io/repos/github/Sage-Bionetworks/Agora/badge.svg?branch=master)](https://coveralls.io/github/Sage-Bionetworks/Agora?branch=master)
-[![Build Status](https://travis-ci.com/Sage-Bionetworks/Agora.svg?branch=master)](https://travis-ci.com/Sage-Bionetworks/Agora)
+[![Build Status](https://travis-ci.org/Sage-Bionetworks/Agora.svg?branch=master)](https://travis-ci.org/Sage-Bionetworks/Agora)
 [![GitHub version](https://badge.fury.io/gh/Sage-Bionetworks%2FAgora.svg)](https://badge.fury.io/gh/Sage-Bionetworks%2FAgora)
 
 # Agora BETA
@@ -126,7 +126,7 @@ There are two ways to use this application in a remote production environment. O
 
 If you are copying the dist folder, install Node in the remote machine. Then, install MongoDB and populate the needed collections (follow the steps described above). Start the application by running `node` against the `server.js` file.
 
-If you are copying the entire project, install Node and any needed global dependencies in the remote machine. Then, run `npm install` to get all local dependencies installed and just follow the same steps for the local development (see below). You'll need to expose port `3000` so anyone can access the application.
+If you are copying the entire project, install Node and any needed global dependencies in the remote machine. Then, run `npm install` to get all local dependencies installed and just follow the same steps for the local development (see below). You'll need to expose port `8080` so anyone can access the application.
 
 In both cases the final URL will be the remote machine public ip.
 
@@ -170,7 +170,7 @@ npm start
 npm run start:prod
 ```
 
-go to [http://0.0.0.0:3000](http://0.0.0.0:3000) or [http://localhost:3000](http://localhost:3000) in your browser. If you are running in production mode change from `3000` to `8080`.
+go to [http://0.0.0.0:8080](http://0.0.0.0:8080) in your browser.
 
 ## Other commands
 
@@ -302,7 +302,7 @@ We have good experience using these editors:
 ### Visual Studio Code + Debugger for Chrome
 > Install [Debugger for Chrome](https://marketplace.visualstudio.com/items?itemName=msjsdiag.debugger-for-chrome) and see docs for instructions to launch Chrome
 
-The included `.vscode` automatically connects to the webpack development server on port `3000`.
+The included `.vscode` automatically connects to the webpack development server on port `8080`.
 
 # Types
 > When you include a module that doesn't include Type Definitions inside of the module you can include external Type Definitions with @types

config/nginx.conf

@@ -4,6 +4,9 @@
 # the number of hard disk drives that store data, and load pattern. When one is in doubt,
 # setting it to the number of available CPU cores would be a good start (the value “auto” will try to autodetect it).
 worker_processes auto;
+# maximum number of open files (RLIMIT_NOFILE) for worker processes. default is 1024
+# set to (worker_connections * worker_processes).
+worker_rlimit_nofile 65535;
 
 # Keep logs of events http://nginx.org/en/docs/ngx_core_module.html#error_log
 error_log /var/log/nginx-error.log info;
@@ -13,7 +16,7 @@ events {
     # To check your server's limits limits, run these 2 commands ["ulimit -Hn", "ulimit -Sn"]
     # Max # of clients = worker_connections * worker_processes
     # Total # of users you can serve per second = worker_processes * worker_connections / (keepalive_timeout * 2)
-    worker_connections      20000;
+    worker_connections      8096;
 
     # Use epoll, an I/O processing method that can enhance performance an is commonly used within Linux
     # http://nginx.org/en/docs/events.html
@@ -33,7 +36,7 @@ http {
         ip_hash;
 
         # Our 4 replicated servers
-        server agora:5000 max_fails=2 fail_timeout=3s;
+        server agora:8080 max_fails=2 fail_timeout=3s;
     }
 
     # The processing rate of requests coming from a single IP address
@@ -149,4 +152,4 @@ http {
             proxy_read_timeout 600;
         }
     }
-}
+}

config/protractor.conf.js

@@ -6,7 +6,7 @@ require('ts-node/register');
 var helpers = require('./helpers');
 
 exports.config = {
-  baseUrl: 'http://localhost:3000/',
+  baseUrl: 'http://localhost:8080/',
 
   /**
    * Use `npm run e2e`

config/webpack.common.js

@@ -9,6 +9,7 @@ const helpers = require('./helpers');
  *
  * problem with copy-webpack-plugin
  */
+const webpack = require('webpack');
 const DefinePlugin = require('webpack/lib/DefinePlugin');
 const CopyWebpackPlugin = require('copy-webpack-plugin');
 const HtmlElementsPlugin = require('./html-elements-plugin');
@@ -19,6 +20,7 @@ const AngularCompilerPlugin = require('@ngtools/webpack').AngularCompilerPlugin;
 const ProvidePlugin = require('webpack/lib/ProvidePlugin');
 const BundleAnalyzerPlugin = require('webpack-bundle-analyzer').BundleAnalyzerPlugin;
 const StyleLintPlugin = require('stylelint-webpack-plugin');
+const rxPaths = require('rxjs/_esm2015/path-mapping');
 
 const buildUtils = require('./build-utils');
 
@@ -54,10 +56,14 @@ module.exports = function (options) {
      *
      * https://github.com/webpack-contrib/webpack-bundle-analyzer
      */
-    const baPlugin = (METADATA.Analyzer === true) ? [new BundleAnalyzerPlugin({
+    const baPlugin = (METADATA.Analyzer === 'true') ? [new BundleAnalyzerPlugin({
       openAnalyzer: false
     })] : [];
 
+    /*const baPlugin = [new BundleAnalyzerPlugin({
+      openAnalyzer: false
+    })];*/
+
   return {
     /**
      * The entry point for the bundle
@@ -106,7 +112,7 @@ module.exports = function (options) {
        *
        * BE AWARE that not using lettable operators will probably result in significant payload added to your bundle.
        */
-      alias: buildUtils.rxjsAlias(supportES2015)
+      alias: rxPaths()
     },
 
     /**
@@ -201,6 +207,8 @@ module.exports = function (options) {
         'process.env.Docker': JSON.stringify(METADATA.Docker)
       }),
 
+      new webpack.optimize.ModuleConcatenationPlugin(),
+
       /**
        * Plugin: CopyWebpackPlugin
        * Description: Copy files and directories in webpack.

config/webpack.dev.js

@@ -20,7 +20,7 @@ const LoaderOptionsPlugin = require('webpack/lib/LoaderOptionsPlugin');
 module.exports = function (options) {
   const ENV = (process.env.mode = process.env.ENV = process.env.NODE_ENV = 'development');
   const HOST = process.env.HOST || 'localhost';
-  const PORT = process.env.PORT || 3000;
+  const PORT = process.env.PORT || 8080;
   const Docker = process.env.Docker || false;
   const Analyzer = process.env.Analyzer || false;
 

config/webpack.server.js

@@ -16,11 +16,18 @@ const NodemonPlugin = require( 'nodemon-webpack-plugin' );
 
 const ENV = (process.env.mode || process.env.NODE_ENV || process.env.ENV || 'development');
 const Docker = process.env.Docker || false;
+const HOST = process.env.HOST || 'localhost';
+
+const MONGODB_HOST = process.env.MONGODB_HOST || null;
+const MONGODB_PORT = process.env.MONGODB_PORT || null;
+
 const METADATA = Object.assign({}, buildUtils.DEFAULT_METADATA, {
     host: process.env.HOST || 'localhost',
-    port: process.env.PORT || 3000,
+    port: process.env.PORT || 8080,
     ENV: ENV,
-    Docker: Docker
+    Docker: Docker,
+    MONGODB_HOST: MONGODB_HOST,
+    MONGODB_PORT: MONGODB_PORT
 });
 
 module.exports = {
@@ -70,7 +77,9 @@ module.exports = {
         'process.env.NODE_ENV': JSON.stringify(METADATA.ENV),
         'process.env.HOST': JSON.stringify(METADATA.host),
         'process.env.PORT': JSON.stringify(METADATA.port),
-        'process.env.Docker': JSON.stringify(METADATA.Docker)
+        'process.env.Docker': JSON.stringify(METADATA.Docker),
+        'process.env.MONGODB_HOST': JSON.stringify(METADATA.MONGODB_HOST),
+        'process.env.MONGODB_PORT': JSON.stringify(METADATA.MONGODB_PORT)
       })
     ],
     target: 'node',

container-build.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+set -ex
+
+CURRENT_DIR=$(pwd)
+PARENT_DIR=$(dirname "$CURRENT_DIR")
+DATA_DIR=$PARENT_DIR/data
+
+# build docker images
+docker build -t sagebionetworks/agora-app:latest -f ./Dockerfile $CURRENT_DIR
+docker build -t sagebionetworks/agora-nginx:latest -f ./nginx.Dockerfile $CURRENT_DIR
+
+# move docker files to DATA_DIR, otherwise docker builds will fail on travis
+cp -rp $CURRENT_DIR/mongo-seed $DATA_DIR/.
+
+pushd $DATA_DIR
+docker build -t sagebionetworks/agora-mongo_data:latest -f ./mongo-seed/rnaseq_differential_expression.Dockerfile $DATA_DIR
+docker build -t sagebionetworks/agora-mongo_seed_links:latest -f ./mongo-seed/network.Dockerfile $DATA_DIR
+docker build -t sagebionetworks/agora-mongo_seed_info:latest -f ./mongo-seed/gene_info.Dockerfile $DATA_DIR
+docker build -t sagebionetworks/agora-mongo_seed_team:latest -f ./mongo-seed/team_info.Dockerfile $DATA_DIR
+docker build -t sagebionetworks/agora-mongo_seed_team_images:latest -f ./mongo-seed/team_images.Dockerfile $DATA_DIR
+popd
+

container-deploy.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+set -ex
+
+# push images to dockerhub
+docker push sagebionetworks/agora-app:latest
+docker push sagebionetworks/agora-nginx:latest
+docker push sagebionetworks/agora-mongo_data:latest
+docker push sagebionetworks/agora-mongo_seed_links:latest
+docker push sagebionetworks/agora-mongo_seed_info:latest
+docker push sagebionetworks/agora-mongo_seed_team:latest
+docker push sagebionetworks/agora-mongo_seed_team_images:latest
+

docker-compose-app.yml

@@ -1,22 +1,17 @@
 version: '2'
 services:
   agora:
-    build:
-      context: .
-      dockerfile: Dockerfile
+    image: 'sagebionetworks/agora-app'
     environment:
       - MONGO_URI=mongodb://mongodb/agora
     restart: always
     expose:
-      - '5000'
+      - '8080'
     networks:
       - front-tier
   # NGINX will reverse proxy the express application
   nginx:
-    build:
-      # Look for the Dockerfile inside the "nginx" folder
-      context: .
-      dockerfile: nginx.Dockerfile
+    image: 'sagebionetworks/agora-nginx'
     restart: always
     ports:
       - '80:80'
@@ -29,4 +24,4 @@ services:
 networks:
   front-tier:
     external:
-      name: agora_network
+      name: agora_network

docker-compose.yml

@@ -3,35 +3,25 @@ services:
   mongodb:
     container_name: mongodb
     image: 'amd64/mongo'
+    entrypoint:
+        - mongod
+        - --bind_ip_all
     ports:
       - 27017:27017
     networks:
       - front_agora
-  mongod:
-    container_name: mongod
-    build:
-      context: ./mongo-seed
-      dockerfile: ./mongod.Dockerfile
-    links:
-      - mongodb
-    networks:
-      - front_agora
   mongo_data:
     container_name: mongo_data
-    build:
-      context: ../data
-      dockerfile: ../Agora/mongo-seed/rnaseq_differential_expression.Dockerfile
+    image: 'sagebionetworks/agora-mongo_data'
     links:
       - mongodb
     depends_on:
-      - mongod
+      - mongodb
     networks:
       - front_agora
   mongo_seed_links:
     container_name: mongo_seed_links
-    build:
-      context: ../data
-      dockerfile: ../Agora/mongo-seed/network.Dockerfile
+    image: 'sagebionetworks/agora-mongo_seed_links'
     links:
       - mongodb
     depends_on:
@@ -40,9 +30,7 @@ services:
       - front_agora
   mongo_seed_info:
     container_name: mongo_seed_info
-    build:
-      context: ../data
-      dockerfile: ../Agora/mongo-seed/gene_info.Dockerfile
+    image: 'sagebionetworks/agora-mongo_seed_info'
     links:
       - mongodb
     depends_on:
@@ -51,9 +39,7 @@ services:
       - front_agora
   mongo_seed_team:
     container_name: mongo_seed_team
-    build:
-      context: ../data
-      dockerfile: ../Agora/mongo-seed/team_info.Dockerfile
+    image: 'sagebionetworks/agora-mongo_seed_team'
     links:
       - mongodb
     depends_on:
@@ -62,9 +48,7 @@ services:
       - front_agora
   mongo_seed_team_images:
     container_name: mongo_seed_team_images
-    build:
-      context: ../data
-      dockerfile: ../Agora/mongo-seed/team_images.Dockerfile
+    image: 'sagebionetworks/agora-mongo_seed_team_images'
     links:
       - mongodb
     depends_on: