Module: NeuroHmmerApp

Defined in:
lib/neurohmmerapp/config.rb,
lib/neurohmmerapp.rb,
lib/neurohmmerapp/logger.rb,
lib/neurohmmerapp/routes.rb,
lib/neurohmmerapp/server.rb,
lib/neurohmmerapp/version.rb,
lib/neurohmmerapp/exceptions.rb,
lib/neurohmmerapp/neurohmmer.rb

Overview

This file defines all possible exceptions that can be thrown by NeuroHmmerApp on startup.

Exceptions only ever inform another entity (downstream code or users) of an issue. Exceptions may or may not be recoverable.

Error classes should be seen as: the error code (class name), human readable message (to_s method), and necessary attributes to act on the error.

We define as many error classes as needed to be precise about the issue, thus making it easy for downstream code (bin/genevalidatorapp or config.ru) to act on them.

Defined Under Namespace

Modules: RunNeuroHmmer Classes: BIN_DIR_NOT_FOUND, CONFIG_FILE_ERROR, Config, ENOENT, Logger, NUM_THREADS_INCORRECT, Routes, Server

Constant Summary collapse

MINIMUM_HMMER_VERSION =

Use a fixed minimum version of BLAST+

'3.0.0'
VERSION = 
'0.0.7'

Class Attribute Summary collapse

Class Method Summary collapse

Class Attribute Details

.config ⇒ Object (readonly)

Returns the value of attribute config.



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# File 'lib/neurohmmerapp.rb', line 44

def config
  @config
end

.public_dir ⇒ Object (readonly)

Returns the value of attribute public_dir.



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# File 'lib/neurohmmerapp.rb', line 44

def public_dir
  @public_dir
end

.temp_dir ⇒ Object (readonly)

Returns the value of attribute temp_dir.



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# File 'lib/neurohmmerapp.rb', line 44

def temp_dir
  @temp_dir
end

Class Method Details

.call(env) ⇒ Object

Rack-interface.

Inject our logger in the env and dispatch request to our controller.



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# File 'lib/neurohmmerapp.rb', line 80

def call(env)
  env['rack.logger'] = logger
  Routes.call(env)
end

.environment ⇒ Object 



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# File 'lib/neurohmmerapp.rb', line 17

def environment
  ENV['RACK_ENV']
end

.init(config = {}) ⇒ Object

Setting up the environment before running the app…



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# File 'lib/neurohmmerapp.rb', line 34

def init(config = {})
  @config = Config.new(config)

  init_binaries
  init_dirs
  check_num_threads
  check_max_characters
  self
end

.logger ⇒ Object 



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# File 'lib/neurohmmerapp.rb', line 29

def logger
  @logger ||= Logger.new(STDERR, verbose?)
end

.on_start ⇒ Object 



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# File 'lib/neurohmmerapp.rb', line 62

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

.on_stop ⇒ Object 



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# File 'lib/neurohmmerapp.rb', line 69

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

.root ⇒ Object 



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# File 'lib/neurohmmerapp.rb', line 25

def root
  File.dirname(File.dirname(__FILE__))
end

.run ⇒ Object

Starting the app manually



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# File 'lib/neurohmmerapp.rb', line 47

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

.verbose? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/neurohmmerapp.rb', line 21

def verbose?
  @verbose ||= (environment == 'development')
end