Class: Constants

Inherits:
Object
  • Object
show all
Includes:
Singleton
Defined in:
lib/protk/constants.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initializeConstants

Read the global constants file and initialize our class @env variable Initialize loggers


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# File 'lib/protk/constants.rb', line 128

def initialize() 

  @data_lib_dir="#{File.dirname(__FILE__)}/data"
  @protk_dir="#{Dir.home}/.protk"

  if ( ENV['PROTK_INSTALL_DIR']!=nil )
    p "Using protk install dir from shell"
    @protk_dir=ENV['PROTK_INSTALL_DIR']
  end

  # Load Protk Defaults
  #
  default_config_yml = YAML.load_file "#{File.dirname(__FILE__)}/data/default_config.yml"
  throw "Unable to read the config file at #{File.dirname(__FILE__)}/data/default_config.yml" unless default_config_yml!=nil

  # User-defined defaults override protk defaults
  #
  user_config_yml = nil
  user_config_yml = YAML.load_file "#{@protk_dir}/config.yml" if File.exist? "#{@protk_dir}/config.yml"
  if ( user_config_yml !=nil )
    @env = default_config_yml.merge user_config_yml
  else
    @env=default_config_yml
  end

  protk_tool_dirs=["tpp/bin","omssa","openms/bin","msgfplus","blast/bin","pwiz","tandem/bin"]

  # Construct the PATH variable by prepending our preferred paths
  #
  protk_paths=[]

  # Add PATHs if PROTK_XXX_ROOT is defined
  #
  protk_tool_dirs.each do |tooldir|  
    env_value = ENV["PROTK_#{tooldir.upcase}_ROOT"]
    if ( env_value!=nil)
      protk_paths<<env_value
    end
    protk_paths<<"#{@protk_dir}/tools/#{tooldir}"
  end

  original_path=ENV['PATH']
  protk_paths<<original_path


  ENV['PATH']=protk_paths.join(":")

  # puts "Path #{ENV['PATH']}"
  throw "No data found in config file" unless @env!=nil

  @info_level="fatal"
  @info_level=default_config_yml['message_level'] unless default_config_yml['message_level'].nil?

end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method

#method_missing(method) ⇒ Object

Provides direct access to constants through methods of the same name This will be used for all constants other than paths


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# File 'lib/protk/constants.rb', line 38

def method_missing(method)

  from_env = @env[method.to_s]
  throw "#{method} is undefined" unless from_env!=nil
  from_env
end

Instance Attribute Details

#data_lib_dirObject (readonly)

Returns the value of attribute data_lib_dir


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# File 'lib/protk/constants.rb', line 32

def data_lib_dir
  @data_lib_dir
end

#info_levelObject

Returns the value of attribute info_level


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# File 'lib/protk/constants.rb', line 30

def info_level
  @info_level
end

#protk_dirObject (readonly)

Returns the value of attribute protk_dir


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# File 'lib/protk/constants.rb', line 31

def protk_dir
  @protk_dir
end

Instance Method Details

#binObject

Some constants are paths. They need to be translated into real paths before being returned


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# File 'lib/protk/constants.rb', line 49

def bin
  return "#{@protk_dir}/bin"
end

#blast_rootObject


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# File 'lib/protk/constants.rb', line 111

def blast_root
    "#{@protk_dir}/tools/blast"   
end

#blastdbcmdObject


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# File 'lib/protk/constants.rb', line 88

def blastdbcmd
  path=%x[which blastdbcmd]
  path.chomp
end

#current_database_for_name(dbname) ⇒ Object

Based on the database shortname and global database path, find the most current version of the required database If dbname corresponds to a folder in the dbroot this function returns the path of the database with an extension appropriate to the database type

If dbname is a full path to a file this tool will first import the file as a temporary database and will then return its full path


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# File 'lib/protk/constants.rb', line 247

def current_database_for_name(dbname)
  dbroot=self.protein_database_root
  
  throw "Protein database directory not specified" unless dbroot!=nil
  throw "Protein database directory #{dbroot} does not exist" unless Pathname(dbroot).exist?
  
  # Remove any trailing slashes or spaces from the end of dbroot if present
  #
  dbroot.sub!(/(\/*\s*)$/,"")
  
  return path_for_builtin_database(dbname)

end

#database_downloadsObject


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# File 'lib/protk/constants.rb', line 107

def database_downloads
  return "#{self.protein_database_root}/downloads"
end

#dbexist?(dbname) ⇒ Boolean

Returns:

  • (Boolean)

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# File 'lib/protk/constants.rb', line 236

def dbexist?(dbname)
  Pathname.new("#{self.protein_database_root}/#{dbname}").exist?
end

#import_fasta_database(dbroot, path_to_fasta_file) ⇒ Object


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# File 'lib/protk/constants.rb', line 283

def import_fasta_database(dbroot,path_to_fasta_file)
  
  tmp_dbroot=Pathname.new("#{dbroot}/tmp/")

  dest_fasta_file_name=Pathname.new(path_to_fasta_file).basename
  dest_fasta_file_path=Pathname.new("#{tmp_dbroot}#{dest_fasta_file_name}")

  if ( !dest_fasta_file_path.exist? )

    Dir.mkdir(tmp_dbroot) unless tmp_dbroot.exist? && tmp_dbroot.directory?

    throw "Unable to make temporary database directory #{tmp_dbroot}" unless tmp_dbroot.exist?
    
    link_cmd = "ln -s #{path_to_fasta_file} #{dest_fasta_file_path}"
    
    result= %x[#{link_cmd}]
    p result
  end

  check_cmd="#{self.ncbi_tools_bin}/blastdbcmd -info -db #{dest_fasta_file_path}"
  result = %x[#{check_cmd}]

  if ( result=="")
    
    throw "Unable to create temporary database #{dest_fasta_file_path}" unless dest_fasta_file_path.exist?
    cmd="#{self.makeblastdb} -in #{dest_fasta_file_path} -parse_seqids"
    p cmd
    self.run_local(cmd)
    
  end

  return dest_fasta_file_path.to_s
  
end

#initialize_loggersObject


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# File 'lib/protk/constants.rb', line 195

def initialize_loggers
  log_dir = Pathname.new(self.log_file).dirname
  log_dir.mkpath unless log_dir.exist?

  @stdout_logger=Logger.new(STDOUT)
  @file_logger=Logger.new(self.log_file)

  throw "Unable to create file logger at path #{self.log_file}" unless @file_logger!=nil
  throw "Unable to create stdout logger " unless @stdout_logger!=nil

  case @info_level
  when /info/i
    @stdout_logger.level=Logger::INFO
  when /debug/i    
    @stdout_logger.level=Logger::DEBUG
  when /warn/i
    @stdout_logger.level=Logger::WARN
  when /fatal/i
    @stdout_logger.level=Logger::FATAL
  else
    throw "Unknown log level #{@info_level}"
  end

end

#log(message, level) ⇒ Object

Write a message to all logger objects


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# File 'lib/protk/constants.rb', line 222

def log(message,level)
  if ( @stdout_logger == nil || @file_logger == nil)
    initialize_loggers
  end

 @stdout_logger.send(level,message)
 @file_logger.send(level,message)        
end

#log_fileObject


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# File 'lib/protk/constants.rb', line 115

def log_file
  path=@env['log_file']
  if ( path =~ /^\// )
    return path
  else
    return "#{@protk_dir}/#{@env['log_file']}"
  end
end

#makeblastdbObject


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# File 'lib/protk/constants.rb', line 83

def makeblastdb
  makeblastdbpath=%x[which makeblastdb]
  makeblastdbpath.chomp
end

#mascot2xmlObject


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# File 'lib/protk/constants.rb', line 93

def mascot2xml
  path=%x[which Mascot2XML]
  path.chomp
end

#msgfplus_rootObject


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# File 'lib/protk/constants.rb', line 62

def msgfplus_root
  "#{@protk_dir}/tools/msgfplus"
end

#msgfplusjarObject


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# File 'lib/protk/constants.rb', line 66

def msgfplusjar
  msgfplus_path=%x[which MSGFPlus.jar]
  msgfplus_path.chomp
end

#omssa_rootObject


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# File 'lib/protk/constants.rb', line 58

def omssa_root
    "#{@protk_dir}/tools/omssa"
end

#openms_rootObject


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# File 'lib/protk/constants.rb', line 75

def openms_root
    "#{@protk_dir}/tools/openms"
end

#path_for_builtin_database(dbname) ⇒ Object


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# File 'lib/protk/constants.rb', line 231

def path_for_builtin_database(dbname)
  "#{self.protein_database_root}/#{dbname}/current.fasta"
end

#protein_database_rootObject


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# File 'lib/protk/constants.rb', line 98

def protein_database_root
  path=@env['protein_database_root']
  if ( path =~ /^\// )
    return path
  else
    return "#{@protk_dir}/#{@env['protein_database_root']}"
  end
end

#pwiz_rootObject


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# File 'lib/protk/constants.rb', line 71

def pwiz_root
    return "#{@protk_dir}/tools/pwiz"
end

#run_local(command_string) ⇒ Object

Runs the given command in a local shell


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# File 'lib/protk/constants.rb', line 264

def run_local(command_string)
  self.log("Command: #{command_string} started",:info)
  status = Open4::popen4("#{command_string} ") do |pid, stdin, stdout, stderr|
    puts "PID #{pid}" 

    stdout.each { |line| self.log(line.chomp,:info) }

    stderr.each { |line| self.log(line.chomp,:warn) }

  end
  if ( status!=0 )
    # We terminated with some error code so log as an error
    self.log( "Command: #{command_string} exited with status #{status.to_s}",:error)
  else
    self.log( "Command: #{command_string} exited with status #{status.to_s}",:info)      
  end
  status     
end

#tandem_rootObject


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# File 'lib/protk/constants.rb', line 79

def tandem_root
    "#{@protk_dir}/tools/tandem"
end

#tpp_rootObject


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# File 'lib/protk/constants.rb', line 53

def tpp_root
    "#{@protk_dir}/tools/tpp"
end

#update_user_config(dict) ⇒ Object


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# File 'lib/protk/constants.rb', line 184

def update_user_config(dict)
  user_config_yml = YAML.load_file "#{self.protk_dir}/config.yml" if File.exist? "#{self.protk_dir}/config.yml"

  if ( user_config_yml !=nil )
    dict = user_config_yml.merge dict 
  end

  File.open("#{self.protk_dir}/config.yml", "w") {|file| file.puts(dict.to_yaml) }

end