Module: GeneValidatorApp

Defined in:
lib/genevalidatorapp/config.rb,
lib/genevalidatorapp.rb,
lib/genevalidatorapp/logger.rb,
lib/genevalidatorapp/routes.rb,
lib/genevalidatorapp/server.rb,
lib/genevalidatorapp/version.rb,
lib/genevalidatorapp/database.rb,
lib/genevalidatorapp/exceptions.rb,
lib/genevalidatorapp/genevalidator.rb

Overview

This file defines all possible exceptions that can be thrown by GeneValidatorApp 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: RunGeneValidator Classes: BIN_DIR_NOT_FOUND, BLAST_DATABASE_ERROR, BLAST_NOT_COMPATIBLE, BLAST_NOT_EXECUTABLE, BLAST_NOT_INSTALLED, CONFIG_FILE_ERROR, Config, DATABASE_DIR_NOT_FOUND, DATABASE_DIR_NOT_SET, Database, ENOENT, EXTENSION_FILE_NOT_FOUND, Logger, MAFFT_NOT_INSTALLED, NO_BLAST_DATABASE_FOUND, NO_PROTEIN_BLAST_DATABASE_FOUND, NUM_THREADS_INCORRECT, Routes, Server

Constant Summary collapse

MINIMUM_BLAST_VERSION =

Use a fixed minimum version of BLAST+

'2.11.0+'.freeze
VERSION = 
'2.1.8'.freeze

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/genevalidatorapp.rb', line 53

def config
  @config
end

.public_dir ⇒ Object (readonly)

Returns the value of attribute public_dir.



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# File 'lib/genevalidatorapp.rb', line 53

def public_dir
  @public_dir
end

.temp_dir ⇒ Object (readonly)

Returns the value of attribute temp_dir.



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# File 'lib/genevalidatorapp.rb', line 53

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/genevalidatorapp.rb', line 90

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

.environment ⇒ Object 



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# File 'lib/genevalidatorapp.rb', line 18

def environment
  ENV['RACK_ENV']
end

.init(config = {}) ⇒ Object

Setting up the environment before running the app…



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# File 'lib/genevalidatorapp.rb', line 39

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

  init_binaries
  init_database

  init_dirs

  load_extension
  check_num_threads
  check_max_characters
  self
end

.logger ⇒ Object 



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

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

.on_start ⇒ Object 



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# File 'lib/genevalidatorapp.rb', line 71

def on_start
  puts '** GeneValidator 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/genevalidatorapp.rb', line 78

def on_stop
  puts
  puts '** Thank you for using GeneValidator :).'
  puts '   Please cite: '
  puts '        Dragan M, Moghul MI, Priyam A, Bustos C, Wurm Y. 2016.'
  puts '        GeneValidator: identify problems with protein-coding gene'
  puts '        predictions. Bioinformatics, doi: 10.1093/bioinformatics/btw015.'
end

.root ⇒ Object 



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# File 'lib/genevalidatorapp.rb', line 26

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

.run ⇒ Object

Starting the app manually



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# File 'lib/genevalidatorapp.rb', line 56

def run
  check_host
  Server.run(self)
rescue Errno::EADDRINUSE
  puts "** Could not bind to port #{config[:port]}."
  puts "   Is GeneValidator already accessible at #{server_url}?"
  puts '   No? Try running GeneValidator on another port, like so:'
  puts
  puts '       genevalidator app -p 4570.'
rescue Errno::EACCES
  puts "** Need root privilege to bind to port #{config[:port]}."
  puts '   It is not advisable to run GeneValidator as root.'
  puts '   Please use Apache/Nginx to bind to a privileged port.'
end

.ssl? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/genevalidatorapp.rb', line 30

def ssl?
  @config[:ssl]
end

.verbose? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/genevalidatorapp.rb', line 22

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