Class: Tool

Inherits:
Object
  • Object
show all
Defined in:
lib/protk/tool.rb

Direct Known Subclasses

ManageDBTool, SearchTool, SetupTool

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(option_support = {:help=>true}) ⇒ Tool

Creates an empty options object to hold commandline options Also creates an option_parser with default options common to all tools



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# File 'lib/protk/tool.rb', line 52

def initialize(option_support={:help=>true})
  @jobid_prefix = "x"
  @options = OpenStruct.new
  options.library = []
  options.inplace = false
  options.encoding = "utf8"
  options.transfer_type = :auto
  options.verbose = false
  
  @option_parser=OptionParser.new do |opts|
    
    if ( option_support[:prefix_suffix]==true)
    
      @options.output_prefix = ""
      opts.on( '-b', '--output-prefix pref', 'A string to prepend to the name of output files' ) do |prefix|
        @options.output_prefix = prefix
      end

      @options.output_suffix = ""
      opts.on( '-e', '--output-suffix suff', 'A string to append to the name of output files' ) do |suffix|
        @options.output_suffix = suffix
      end
      
    end
    
    if ( option_support[:explicit_output]==true)
      @options.explicit_output = nil
      opts.on( '-o', '--output out', 'An explicitly named output file.' ) do |out|
        @options.explicit_output = out
      end
    end
       
    if ( option_support[:over_write]==true)
          
      @options.over_write=false
      opts.on( '-r', '--replace-output', 'Dont skip analyses for which the output file already exists' ) do  
        @options.over_write = true
      end
      
    end

    if ( option_support[:background]==true)

      @options.background = false
      opts.on( '-z', '--background', 'Run jobs in the background using pbs' ) do  
        @options.background = true
      end
      
    end
    
    if ( option_support[:help]==true)
     
      opts.on( '-h', '--help', 'Display this screen' ) do
        puts opts
        exit
      end
    end
     
  end
  
end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method

#method_missing(meth, *args, &block) ⇒ Object

Provides direct access to options through methods of the same name



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# File 'lib/protk/tool.rb', line 37

def method_missing(meth, *args, &block)
  if ( args.length==0 && block==nil)
    @options.send meth
  else
    super
  end
end

Instance Attribute Details

#option_parser ⇒ Object (readonly)

The option parser used to parse command-line options.



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# File 'lib/protk/tool.rb', line 21

def option_parser
  @option_parser
end

#options ⇒ Object (readonly)

Options set from the command-line



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# File 'lib/protk/tool.rb', line 17

def options
  @options
end

Instance Method Details

#input_base_path(input_file, ext = nil) ⇒ Object

Create a full base path (without extension) representing the input file for this analysis Optionally provide the extension to be removed (if not provided it will be inferred)



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# File 'lib/protk/tool.rb', line 141

def input_base_path(input_file,ext=nil)
  input_path=Pathname.new(input_file)
  throw "Error: Input directory #{input_path.dirname} does not exist" unless input_path.dirname.exist?
  dir=input_path.dirname.realpath.to_s
  if ( ext==nil)
    ext=input_path.extname    
  end
  base_name=input_path.basename.to_s.gsub(/#{ext}$/,"")
  "#{dir}/#{base_name}"
end

#jobid_from_filename(filename) ⇒ Object 



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# File 'lib/protk/tool.rb', line 173

def jobid_from_filename(filename)
  jobid="protk"
  jobnum_match=filename.match(/(.{1,10})\.d/)
  if (jobnum_match!=nil)
    jobid="#{self.jobid_prefix}#{jobnum_match[1]}"
  end
  return jobid
end

#jobid_prefix ⇒ Object

Prefix for background jobs x = X!Tandem, o=OMSSA, p=“Phenyx”, m=“Mascot” Can’t use attr_accessor here because we want this available to subclasses



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# File 'lib/protk/tool.rb', line 27

def jobid_prefix
  @jobid_prefix
end

#jobid_prefix=(p) ⇒ Object 



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

def jobid_prefix=(p)
  @jobid_prefix=p
end

#output_base_path(output_file, ext = nil) ⇒ Object

Create and return a full base path (without extension) representing the output file for this analysis Optionally provide the extension to be removed (if not provided it will be inferred)



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# File 'lib/protk/tool.rb', line 121

def output_base_path(output_file,ext=nil)

  output_path=Pathname.new(output_file)
  throw "Error: Output directory #{output_path.dirname} does not exist" unless output_path.dirname.exist?
  dir=output_path.dirname.realpath.to_s
  basename=output_path.basename.to_s
  if ( ext==nil)
    ext=output_path.extname    
  end
  base_name=basename.gsub(/#{ext}$/,"")

  "#{dir}/#{@options.output_prefix}#{base_name}#{@options.output_suffix}"
end

#run(cmd, genv, job_params = nil, jobscript_path = nil, autodelete = true) ⇒ Object

Run the search tool using the given command string and global environment



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# File 'lib/protk/tool.rb', line 156

def run(cmd,genv,job_params=nil,jobscript_path=nil,autodelete=true)
  if ( @options.background )
    throw "Error: Background option was selected but this host does not support background jobs" unless genv.has_pbs
    # Send this job off to be run in a batch queuer
    
    cmd_runner=CommandRunner.new(genv)
    
 
    
    cmd_runner.run_batch(cmd,job_params,jobscript_path,autodelete)
    
  else 
    cmd_runner=CommandRunner.new(genv)
    cmd_runner.run_local(cmd)
  end
end