neurohmmerapp 0.0.1

data/lib/neurohmmerapp/routes.rb

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+require 'sinatra/base'
+require 'sinatra/cross_origin'
+require 'neurohmmer/version'
+require 'neurohmmerapp/version'
+require 'slim'
+
+module NeuroHmmerApp
+  # The Sinatra Routes
+  class Routes < Sinatra::Base
+    register Sinatra::CrossOrigin
+
+    configure do
+      # We don't need Rack::MethodOverride. Let's avoid the overhead.
+      disable :method_override
+
+      # Ensure exceptions never leak out of the app. Exceptions raised within
+      # the app must be handled by the app. We do this by attaching error
+      # blocks to exceptions we know how to handle and attaching to Exception
+      # as fallback.
+      disable :show_exceptions, :raise_errors
+
+      # Make it a policy to dump to 'rack.errors' any exception raised by the
+      # app so that error handlers don't have to do it themselves. But for it
+      # to always work, Exceptions defined by us should not respond to `code`
+      # or http_status` methods. Error blocks errors must explicitly set http
+      # status, if needed, by calling `status` method.
+      enable :dump_errors
+
+      # We don't want Sinatra do setup any loggers for us. We will use our own.
+      set :logging, nil
+
+      # This is the app root...
+      set :root,          lambda { NeuroHmmerApp.root }
+
+      # This is the full path to the public folder...
+      set :public_folder, lambda { NeuroHmmerApp.public_dir }
+    end
+
+    # Set up global variables for the templates...
+    before '/' do
+      @max_characters             = NeuroHmmerApp.config[:max_characters]
+      @current_neurohmmer_version = '0.1'
+    end
+
+    get '/' do
+      slim :index
+    end
+
+    post '/' do
+      cross_origin # Required for the API to work...
+      RunNeuroHmmer.init(request.url, params)
+      @neurohmmer_results = RunNeuroHmmer.run
+      slim :results, layout: false
+    end
+
+    # This error block will only ever be hit if the user gives us a funny
+    # sequence or incorrect advanced parameter. Well, we could hit this block
+    # if someone is playing around with our HTTP API too.
+    error RunNeuroHmmer::ArgumentError do
+      status 400
+      slim :"500", layout: false
+    end
+
+    # This will catch any unhandled error and some very special errors. Ideally
+    # we will never hit this block. If we do, there's a bug in NeuroHmmerApp
+    # or something really weird going on.
+    # TODO: If we hit this error block we show the stacktrace to the user
+    # requesting them to post the same to our Google Group.
+    error Exception, RunNeuroHmmer::RuntimeError do
+      status 500
+      slim :"500", layout: false
+    end
+
+    not_found do
+      status 404
+      slim :"500" # TODO: Create another Template
+    end
+  end
+end

data/lib/neurohmmerapp/server.rb

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+require 'rack/handler/webrick'
+
+module NeuroHmmerApp
+  # Simple wrapper around WEBrick and Rack::Handler::WEBrick to host
+  # NeuroHmmerApp standalone.
+  class Server
+    class << self
+      def run(*args)
+        new(*args).start
+      end
+    end
+
+    def initialize(app)
+      @app = app
+    end
+
+    attr_reader :app
+
+    # Start server. Raises Errno::EADDRINUSE if port is in use by another
+    # process. Raises Errno::EACCES if binding to the port requires root
+    # privilege.
+    def start
+      setup_signal_handlers
+      @server = WEBrick::HTTPServer.new(options)
+      @server.mount '/', Rack::Handler::WEBrick, app
+      @server.start
+    end
+
+    # Stop server.
+    def stop
+      @server.shutdown
+    end
+
+    # Options Hash passed to WEBrick::HTTPServer.
+    # rubocop:disable Metrics/AbcSize
+    def options
+      @options ||= {
+        :BindAddress      => app.config[:host],
+        :Port             => app.config[:port],
+        :StartCallback    => proc { app.on_start },
+        :StopCallback     => proc { app.on_stop  },
+        :OutputBufferSize => 5,
+        :AccessLog        => [[logdev, WEBrick::AccessLog::COMMON_LOG_FORMAT]],
+        :Logger           => WEBrick::Log.new(logdev)
+      }
+    end
+    # rubocop:enable Metrics/AbcSize
+
+    private
+
+    def setup_signal_handlers
+      [:INT, :TERM].each do |sig|
+        trap sig do
+          stop
+        end
+      end
+    end
+
+    def logdev
+      @logdev ||= app.verbose? ? STDERR : '/dev/null'
+    end
+  end
+end

data/lib/neurohmmerapp/version.rb

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+module NeuroHmmerApp
+  VERSION = '0.0.1'
+end

data/lib/neurohmmerapp.rb

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+require 'yaml'
+require 'fileutils'
+
+require 'neurohmmerapp/config'
+require 'neurohmmerapp/exceptions'
+require 'neurohmmerapp/neurohmmer'
+require 'neurohmmerapp/logger'
+require 'neurohmmerapp/routes'
+require 'neurohmmerapp/server'
+require 'neurohmmerapp/version'
+
+module NeuroHmmerApp
+  # Use a fixed minimum version of BLAST+
+  MINIMUM_HMMER_VERSION = '3.0.0'
+
+  class << self
+    def environment
+      ENV['RACK_ENV']
+    end
+
+    def verbose?
+      @verbose ||= (environment == 'development')
+    end
+
+    def root
+      File.dirname(File.dirname(__FILE__))
+    end
+
+    def logger
+      @logger ||= Logger.new(STDERR, verbose?)
+    end
+
+    # Setting up the environment before running the app...
+    def init(config = {})
+      @config = Config.new(config)
+
+      init_binaries
+      init_dirs
+
+      load_extension
+      check_num_threads
+      check_max_characters
+      self
+    end
+
+    attr_reader :config, :temp_dir, :public_dir
+
+    # Starting the app manually
+    def run
+      check_host
+      Server.run(self)
+    rescue Errno::EADDRINUSE
+      puts "** Could not bind to port #{config[:port]}."
+      puts "   Is NeuroHmmer already accessible at #{server_url}?"
+      puts '   No? Try running NeuroHmmer on another port, like so:'
+      puts
+      puts '       neurohmmerapp -p 4570.'
+    rescue Errno::EACCES
+      puts "** Need root privilege to bind to port #{config[:port]}."
+      puts '   It is not advisable to run NeuroHmmer as root.'
+      puts '   Please use Apache/Nginx to bind to a privileged port.'
+    end
+
+    def on_start
+      puts '** NeuroHmmer is ready.'
+      puts "   Go to #{server_url} in your browser and start analysing genes!"
+      puts '   Press CTRL+C to quit.'
+      open_in_browser(server_url)
+    end
+
+    def on_stop
+      puts
+      puts '** Thank you for using NeuroHmmerApp :).'
+      puts '   Please cite: '
+      puts '        Moghul M.I., Elphick M & Wurm Y (in prep).'
+      puts '        NeuroHmmer: identify Neuropeptide Precursors.'
+    end
+
+    # Rack-interface.
+    #
+    # Inject our logger in the env and dispatch request to our controller.
+    def call(env)
+      env['rack.logger'] = logger
+      Routes.call(env)
+    end
+
+    private
+
+    def init_dirs
+      config[:public_dir] = File.expand_path(config[:public_dir])
+      unique_start_id     = 'NH_' + "#{Time.now.strftime('%Y%m%d-%H-%M-%S')}"
+      @public_dir         = File.join(config[:public_dir], unique_start_id)
+      init_public_dir
+    end
+
+    # Create the Public Dir and copy files from gem root - this public dir
+    #   is served by the app is accessible at URL/...
+    def init_public_dir
+      FileUtils.mkdir_p(File.join(@public_dir, 'NeuroHmmer'))
+      root_web_files = File.join(NeuroHmmerApp.root, 'public/web_files')
+      root_gv        = File.join(NeuroHmmerApp.root, 'public/NeuroHmmer')
+      FileUtils.cp_r(root_web_files, @public_dir)
+      FileUtils.cp_r(root_gv, @public_dir)
+    end
+
+    def init_binaries
+      config[:bin] = init_bins if config[:bin]
+      assert_blast_installed_and_compatible
+      assert_mafft_installed
+    end
+
+    def load_extension
+      return unless config[:require]
+      config[:require] = File.expand_path config[:require]
+      unless File.exist?(config[:require]) && File.file?(config[:require])
+        fail EXTENSION_FILE_NOT_FOUND, config[:require]
+      end
+
+      logger.debug("Loading extension: #{config[:require]}")
+      require config[:require]
+    end
+
+    def check_num_threads
+      num_threads = Integer(config[:num_threads])
+      fail NUM_THREADS_INCORRECT unless num_threads > 0
+
+      logger.debug "Will use #{num_threads} threads to run BLAST."
+      if num_threads > 256
+        logger.warn "Number of threads set at #{num_threads} is unusually high."
+      end
+    rescue
+      raise NUM_THREADS_INCORRECT
+    end
+
+    def check_max_characters
+      if config[:max_characters] != 'undefined'
+        config[:max_characters] = Integer(config[:max_characters])
+      end
+    rescue
+      raise MAX_CHARACTERS_INCORRECT
+    end
+
+    def init_bins
+      bins = []
+      config[:bin].each do |bin|
+        bins << File.expand_path(bin)
+        unless File.exist?(bin) && File.directory?(bin)
+          fail BIN_DIR_NOT_FOUND, config[:bin]
+        end
+        export_bin_dir(bin)
+      end
+      bins
+    end
+
+    ## Checks if dir is in $PATH and if not, it adds the dir to the $PATH.
+    def export_bin_dir(bin_dir)
+      return unless bin_dir
+      return if ENV['PATH'].split(':').include?(bin_dir)
+      ENV['PATH'] = "#{bin_dir}:#{ENV['PATH']}"
+    end
+
+    def assert_blast_installed_and_compatible
+      fail HMMER_NOT_INSTALLED unless command? 'hmmscan'
+      # version = `hmmscan -version`.split[1]
+      # fail HMMER_NOT_COMPATIBLE, version unless version >= MINIMUM_HMMER_VERSION
+    end
+
+    def assert_mafft_installed
+      fail MAFFT_NOT_INSTALLED unless command? 'mafft'
+    end
+
+    # Check and warn user if host is 0.0.0.0 (default).
+    def check_host
+      return unless config[:host] == '0.0.0.0'
+      logger.warn 'Will listen on all interfaces (0.0.0.0).' \
+                  ' Consider using 127.0.0.1 (--host option).'
+    end
+
+    def server_url
+      host = config[:host]
+      host = 'localhost' if host == '127.0.0.1' || host == '0.0.0.0'
+      "http://#{host}:#{config[:port]}"
+    end
+
+    def open_in_browser(server_url)
+      return if using_ssh? || verbose?
+      if RUBY_PLATFORM =~ /linux/ && xdg?
+        system "xdg-open #{server_url}system"
+      elsif RUBY_PLATFORM =~ /darwin/
+        system "open #{server_url}system"
+      end
+    end
+
+    def using_ssh?
+      true if ENV['SSH_CLIENT'] || ENV['SSH_TTY'] || ENV['SSH_CONNECTION']
+    end
+
+    def xdg?
+      true if ENV['DISPLAY'] && command?('xdg-open')
+    end
+
+    # Return `true` if the given command exists and is executable.
+    def command?(command)
+      system("which #{command} > /dev/null 2>&1")
+    end
+  end
+end

data/neurohmmerapp.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'neurohmmerapp/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = 'neurohmmerapp'
+  spec.version       = NeuroHmmerApp::VERSION
+  spec.authors       = ['Ismail Moghul', 'Yannick Wurm']
+  spec.email         = 'y.wurm@qmul.ac.uk'
+  spec.summary       = 'A Web App wrapper for NeuroHmmer.'
+  spec.description   = 'A Web App wrapper for NeuroHmmer, a program for' \
+                       ' validating gene predictions.'
+  spec.homepage      = 'https://github.com/wurmlab/neurohmmerapp'
+  spec.license       = 'AGPL'
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ['lib']
+
+  spec.required_ruby_version = '>= 2.0.0'
+
+  spec.add_development_dependency 'bundler', '~> 1.6'
+  spec.add_development_dependency 'rake', '~>10.3'
+  spec.add_development_dependency('rspec', '~> 2.8', '>= 2.8.0')
+  spec.add_development_dependency 'rack-test', '~> 0.6'
+  spec.add_development_dependency('capybara', '~> 2.4', '>= 2.4.4')
+  spec.add_development_dependency 'w3c_validators', '~>1.1'
+
+  spec.add_dependency 'neurohmmer', '~>0.1'
+  spec.add_dependency 'bio', '~>1.4'
+  spec.add_dependency 'sinatra', '~>1.4'
+  spec.add_dependency 'sinatra-cross_origin', '~> 0.3'
+  spec.add_dependency 'slim', '~>3.0'
+  spec.add_dependency 'slop', '~>3.6'
+  spec.post_install_message = <<INFO
+
+------------------------------------------------------------------------
+  Thank you for Installing the NeuroHmmer App!
+
+  To launch NeuroHmmerApp execute 'neurohmmerapp' from command line.
+
+    $ neurohmmerapp [options]
+
+  Visit https://github.com/wurmlab/neurohmmerapp for more information.
+------------------------------------------------------------------------
+
+INFO
+end

data/public/NeuroHmmer/loading.html

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+<!DOCTYPE html><html><head><title>NeuroHmmer: Identify Neuropeptide Precursors</title><meta content="text/html; charset=utf-8" http-equiv="Content-Type"><link rel="stylesheet" type="text/css" href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.5/flatly/bootstrap.min.css"><link rel="stylesheet" type="text/css" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/css/font-awesome.min.css">
+<style type="text/css">html{position:relative;min-height:100%;}body{margin:0 0 100px;background-color:#F5F5F5}footer{bottom:0;width:100%;margin:0 auto;position:absolute;height:100px;overflow:hidden;border-top:2px solid #DBDBDB;padding-top:10px;color:#b4bcc2}
+</style></head>
+<body>
+<div class="container text-center">
+  <h1 style="font-size: 78px">NeuroHmmer</h1>
+  <h4 style="margin-bottom:3em">Identify Neuropeptide Precursors</h4>
+  <i class="fa fa-spinner fa-spin" style="font-size: 10em"></i>
+  <h2> Calculating...</h2>
+  <p class="results_link"> This may take some time. Please leave this page open.</p>
+</div>
+<footer><div class="container center-block"><p class="text-muted text-center">Please cite: "Moghul MI, Elphick M &amp; Wurm Y <em>(in prep)</em> NeuroHmmer: Identify Neuropeptide Precursors"<br/>  Developed at <a href="https://wurmlab.github.io" target="_blank">Wurm Lab</a>, <a href="http://www.sbcs.qmul.ac.uk" target="_blank">QMUL</a> with funding by <a href="http://www.bbsrc.ac.uk/home/home.aspx" target="_blank">BBSRC</a><br/>This page was created by <a href="https://github.com/wurmlab/neurohmmer" target="_blank" >NeuroHmmer</a> v0.01</p></div></footer></body></html>