Class: Ms::DataExplorer::Convert::DatToAscii

Inherits:
Tap::Tasks::FileTask
  • Object
show all
Includes:
Ms::DataExplorer
Defined in:
lib/ms/data_explorer/convert/dat_to_ascii.rb

Overview

:startdoc::task converts .dat file to ascii text

Uses the Applied Biosystems DataExplorer software to extract an ASCII spectrum from a ‘.dat’ file. Each input file should be a dat file; ascii files will be placed in the output directory, with a ‘.txt’ extension (by default the output directory is the same directory as the input file).

DatToAscii is based on the getdeascii.pl script.

Instance Method Summary collapse

Methods included from Ms::DataExplorer

#close_data_explorer, #data_explorer, #data_explorer_version

Instance Method Details

#call(*args) ⇒ Object 



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# File 'lib/ms/data_explorer/convert/dat_to_ascii.rb', line 25

def call(*args)
  @updated_files = []
  
  results = super
  close_data_explorer

  # Ensure de has time to close, then make sure all the output files are dated later than the inputs
  # This rigmarole is necessary because the output file is created while the input file is open in
  # DataExplorer, and apparently DataExplorer doesn't release the file until it completely exits.
  sleep 1 unless @updated_files.empty?
  @updated_files.each {|file| FileUtils.touch(file) }
  @updated_files = nil
  results
end

#process(*input_files) ⇒ Object 



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# File 'lib/ms/data_explorer/convert/dat_to_ascii.rb', line 40

def process(*input_files)
  input_files.collect do |input_file|
    app.check_terminate
    
    output_file = if output_dir
      File.join(output_dir, basename(input_file, ".txt"))
    else
      input_file.chomp(File.extname(input_file)) + ".txt"
    end
  
    if uptodate?(output_file, input_file)
      log_basename(:skip, input_file)
    else
      log_basename :ascii, input_file
      
      prepare output_file

      # This block of code raises an unexpected WIN32OLERuntimeError upon the 'close'
      # operation.  The error may be XP-related or DataExplorer 4.0-related as it is not raised on a 
      # Win2k computer using DataExplorer 4.9.  
      # 
      # I believe that the issue is with XP, however, due to articles I read online 
      # (see http://support.microsoft.com/kb/289737) as well as the fact that if you 
      # enact the open-close routine in irb multiple times, it will only raise the 0x80010105
      # error the first time for any given document.
      begin
        spectrum = data_explorer.documents.open(File.expand_path(input_file))
        spectrum.specview.exportasciispectrum(File.expand_path(output_file))
        spectrum.close
      rescue WIN32OLERuntimeError
        # TODO -- add debug logging for this...
      end

      updated_files << output_file
    end
  
    output_file
  end
end

#updated_files ⇒ Object 



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# File 'lib/ms/data_explorer/convert/dat_to_ascii.rb', line 21

def updated_files
  @updated_files ||= []
end