Merge pull request #583 from PecanProject/rails5-unicorn

Rails5 unicorn

Author: gsrohde

Dockerfile

@@ -1,12 +1,14 @@
-FROM ruby:2.1
+FROM ruby:2.3
 MAINTAINER Max Burnette <[email protected]>
 
 # Install dependencies
 RUN apt-get update \
     && apt-get install --no-install-recommends -y \
         curl \
         git \
+        libgeos-dev \
         netcat \
+        nodejs \
         postgresql-client \
     && rm -rf /var/lib/apt/lists/*
 
@@ -15,15 +17,17 @@ WORKDIR /home/bety
 
 # install gems (allowing for caching)
 COPY /Gemfile* /home/bety/
-RUN gem install bundler && \
-    bundle install --without javascript_testing --path vendor/bundle
+RUN gem install bundler \
+    && bundle install --with docker --without "test development production debug javascript_testing"
+
 
 # port that is exposed (standard ruby port)
-EXPOSE 3000
+EXPOSE 8000
 
 # copy rest of the files
 COPY / /home/bety
 COPY /docker/database.yml /home/bety/config/database.yml
+COPY /docker/config.ru /home/bety/config.ru
 
 # download dump.bety and load.bety scripts and configure app
 RUN curl -LOs https://raw.githubusercontent.com/PecanProject/pecan/master/scripts/load.bety.sh \
@@ -41,11 +45,18 @@ ARG BETY_GIT_DATE="unknown"
 ENV LOCAL_SERVER=99 \
     REMOTE_SERVERS="0 1 2 5" \
     RAILS_ENV="production" \
+    RAILS_RELATIVE_URL_ROOT="" \
+    SECRET_KEY_BASE="ThisIsNotReallySuchAGreatSecret" \
+    UNICORN_WORKER_PROCESSES="3" \
+    UNICORN_PORT="8000" \
     BETY_GIT_TAGS=${BETY_GIT_TAGS} \
     BETY_GIT_BRANCH=${BETY_GIT_BRANCH} \
     BETY_GIT_CHECKSUM=${BETY_GIT_CHECKSUM} \
     BETY_GIT_DATE=${BETY_GIT_DATE}
 
+# expose public files
+VOLUME ["/home/bety/public"]
+
 # default command to run bety web-app
 ENTRYPOINT ["/home/bety/docker/entrypoint.sh"]
-CMD ["server"]
+CMD ["unicorn"]

Gemfile

@@ -91,6 +91,10 @@ group :production do
   gem "passenger", "5.1.12"
 end
 
+group :docker do
+  gem 'unicorn'
+end
+
 # API-related Gems:
 
 gem "rspec_api_documentation"

Gemfile.lock

@@ -99,6 +99,7 @@ GEM
     json (2.1.0)
     json-schema (2.8.0)
       addressable (>= 2.4)
+    kgio (2.11.2)
     loofah (2.2.2)
       crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
@@ -164,6 +165,7 @@ GEM
       method_source
       rake (>= 0.8.7)
       thor (>= 0.18.1, < 2.0)
+    raindrops (0.19.0)
     rake (12.3.1)
     rb-fsevent (0.10.3)
     rb-inotify (0.9.10)
@@ -232,6 +234,9 @@ GEM
       thread_safe (~> 0.1)
     uglifier (4.1.9)
       execjs (>= 0.3.0, < 3)
+    unicorn (5.4.0)
+      kgio (~> 2.6)
+      raindrops (~> 0.7)
     websocket-driver (0.6.5)
       websocket-extensions (>= 0.1.0)
     websocket-extensions (0.1.3)
@@ -288,6 +293,10 @@ DEPENDENCIES
   trollop
   tzinfo
   uglifier
+  unicorn
   will_paginate
   yajl-ruby (~> 1.3.1)
   yard
+
+BUNDLED WITH
+   1.16.1

README.md

@@ -9,6 +9,27 @@ This is the source code for the [Biofuel Ecophysiological Traits and Yields data
 The website is primarily written in Ruby-on-Rails, and has a PostgreSQL backend.
 BETYdb provides an interface for contributing and accessing data, and is the informatics backend for the [Predictive Ecosystem Analyzer (PEcAn)](http://www.pecanproject.org).
 
+## Running BETY using Docker
+
+To get started with BETY you can use the docker-compose.yml file included. This will start the database (postgresql with postgis version 9.5) as well as the BETY container. If this is the first time you start it you will need to initialize the database, this can be done using the following commands:
+
+```
+docker-compose -p bety up -d postgres
+docker run --rm --network bety_bety pecan/bety initialize
+```
+
+Once bety finishes inializing the database, or to restart BETY, you can bring up the all the containers using:
+
+```
+docker-compose -p bety up -d
+```
+
+To change the path BETY runs under you can change the path using the environment variable RAILS_RELATIVE_URL_ROOT, for example to just run bety you can use the following command. This will precompile any of the static assets and run BETY.
+
+```
+docker run -e RAILS_RELATIVE_URL_ROOT="/bety" pecan/bety
+```
+
 ## Documentation.
 
 * Technical Documentation: https://pecan.gitbooks.io/betydb-documentation/content/

app/models/experiment.rb

@@ -1,4 +1,5 @@
 class Experiment < ActiveRecord::Base
+  attr_protected []
 
   extend SimpleSearch
 

app/views/layouts/application.html.erb

@@ -178,6 +178,7 @@
                 <li><%= link_to "Citations", citations_path %></li>
                 <li><%= link_to "Covariates", covariates_path %></li>
                 <li><%= link_to "Cultivars", cultivars_path %></li>
+                <li><%= link_to "Experiments", experiments_path %></li>
                 <li><%= link_to "Managements", managements_path %></li>
                 <% if current_user.page_access_level <= 2 %>
                   <li><%= link_to "Methods", methods_path %></li>

config/unicorn.rb

@@ -0,0 +1,97 @@
+# Sample verbose configuration file for Unicorn (not Rack)
+#
+# This configuration file documents many features of Unicorn
+# that may not be needed for some applications. See
+# http://unicorn.bogomips.org/examples/unicorn.conf.minimal.rb
+# for a much simpler configuration file.
+#
+# See http://unicorn.bogomips.org/Unicorn/Configurator.html for complete
+# documentation.
+
+# Go with at least 1 per CPU core, a higher amount will usually help for fast
+# responses such as reading from a cache.
+worker_processes ENV['UNICORN_WORKER_PROCESSES'].to_i
+
+# Help ensure your application will always spawn in the symlinked
+# "current" directory that Capistrano sets up.
+#working_directory "/home/bety" # available in 0.94.0+
+
+# feel free to point this anywhere accessible on the filesystem
+#pid "/home/bety/tmp/pids/unicorn.pid"
+
+# Listen on both a Unix domain socket and a TCP port.
+# If you are load-balancing multiple Unicorn masters, lower the backlog
+# setting to e.g. 64 for faster failover.
+#listen "/home/git/gitlab/tmp/sockets/gitlab.socket", :backlog => 1024
+#listen "127.0.0.1:8080", :tcp_nopush => true
+listen "0.0.0.0:" + ENV['UNICORN_PORT']
+
+# nuke workers after 30 seconds instead of 60 seconds (the default)
+timeout 30
+
+# By default, the Unicorn logger will write to stderr.
+# Additionally, some applications/frameworks log to stderr or stdout,
+# so prevent them from going to /dev/null when daemonized here:
+#stderr_path "/home/bety/log/unicorn.stderr.log"
+#stdout_path "/home/bety/log/unicorn.stdout.log"
+
+# combine Ruby 2.0.0dev or REE with "preload_app true" for memory savings
+# http://rubyenterpriseedition.com/faq.html#adapt_apps_for_cow
+preload_app true
+GC.respond_to?(:copy_on_write_friendly=) and
+  GC.copy_on_write_friendly = true
+
+# Enable this flag to have unicorn test client connections by writing the
+# beginning of the HTTP headers before calling the application.  This
+# prevents calling the application for connections that have disconnected
+# while queued.  This is only guaranteed to detect clients on the same
+# host unicorn runs on, and unlikely to detect disconnects even on a
+# fast LAN.
+check_client_connection false
+
+before_fork do |server, worker|
+  # the following is highly recommended for Rails + "preload_app true"
+  # as there's no need for the master process to hold a connection
+  defined?(ActiveRecord::Base) and
+    ActiveRecord::Base.connection.disconnect!
+
+  # The following is only recommended for memory/DB-constrained
+  # installations.  It is not needed if your system can house
+  # twice as many worker_processes as you have configured.
+  #
+  # This allows a new master process to incrementally
+  # phase out the old master process with SIGTTOU to avoid a
+  # thundering herd (especially in the "preload_app false" case)
+  # when doing a transparent upgrade.  The last worker spawned
+  # will then kill off the old master process with a SIGQUIT.
+  old_pid = "#{server.config[:pid]}.oldbin"
+  if old_pid != server.pid
+    begin
+      sig = (worker.nr + 1) >= server.worker_processes ? :QUIT : :TTOU
+      Process.kill(sig, File.read(old_pid).to_i)
+    rescue Errno::ENOENT, Errno::ESRCH
+    end
+  end
+  #
+  # Throttle the master from forking too quickly by sleeping.  Due
+  # to the implementation of standard Unix signal handlers, this
+  # helps (but does not completely) prevent identical, repeated signals
+  # from being lost when the receiving process is busy.
+  # sleep 1
+end
+
+after_fork do |server, worker|
+  # per-process listener ports for debugging/admin/migrations
+  # addr = "127.0.0.1:#{9293 + worker.nr}"
+  # server.listen(addr, :tries => -1, :delay => 5, :tcp_nopush => true)
+
+  # the following is *required* for Rails + "preload_app true",
+  defined?(ActiveRecord::Base) and
+    ActiveRecord::Base.establish_connection
+
+  # if preload_app is true, then you may also want to check and
+  # restart any other shared sockets/descriptors such as Memcached,
+  # and Redis.  TokyoCabinet file handles are safe to reuse
+  # between any number of forked children (assuming your kernel
+  # correctly implements pread()/pwrite() system calls)
+end

docker-compose.yml

@@ -0,0 +1,46 @@
+version: "3"
+
+services:
+  # BETY rails frontend to the database
+  bety:
+    image: pecan/bety:unicorn
+    networks:
+      - bety
+    ports:
+      - 8000
+    environment:
+      - UNICORN_WORKER_PROCESSES=1
+      - SECRET_KEY_BASE=thisissomereallllllylongsecretkeyandshouldbelongerthanthis
+    depends_on:
+      - postgres
+    restart: unless-stopped
+    deploy:
+      mode: replicated
+      restart_policy:
+        condition: any
+      placement:
+        constraints: [node.role == manager]
+
+  # postgresql + postgis to hold all the data
+  postgres:
+    image: mdillon/postgis:9.5
+    networks:
+      - bety
+    #ports:
+    #  - 5432
+    volumes:
+      - postgres:/var/lib/postgresql/data
+    restart: unless-stopped
+    deploy:
+      mode: replicated
+      restart_policy:
+        condition: any
+      placement:
+        constraints: [node.role == worker]
+
+networks:
+  bety:
+
+volumes:
+  postgres:
+

docker/config.ru

@@ -0,0 +1,7 @@
+# This file is used by Rack-based servers to start the application.
+
+require ::File.expand_path('../config/environment',  __FILE__)
+
+map (ENV['RAILS_RELATIVE_URL_ROOT'] || "") + "/" do
+    run BetyRails3::Application
+end