bahuvrihi-biomass-data_explorer 0.0.2

data/MIT-LICENSE

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+Copyright (c) 2006-2008, Regents of the University of Colorado.
+Developer:: Simon Chiang, Biomolecular Structure Program, Hansen Lab
+Support:: CU Denver School of Medicine Deans Academic Enrichment Fund
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this
+software and associated documentation files (the "Software"), to deal in the Software
+without restriction, including without limitation the rights to use, copy, modify, merge,
+publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons
+to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or
+substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.

data/lib/data_explorer.rb

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+require 'win32ole'
+require 'Win32API'
+
+module DataExplorer 
+  @@data_explorer_instance = nil
+  
+  def data_explorer
+    @@data_explorer_instance = WIN32OLE.new('DataExplorer.Application') unless @@data_explorer_instance
+    @@data_explorer_instance
+  end
+
+  def close_data_explorer
+    if @@data_explorer_instance
+      data_explorer.quit
+      data_explorer.ole_free
+      @@data_explorer_instance = nil
+    end
+  end
+
+  def data_explorer_version
+    # Gets the version information for a windows executable
+    # trivially modified from: http://blade.nagaokaut.ac.jp/cgi-bin/scat.rb/ruby/ruby-talk/161140
+    #fname = 'D:\ruby\bin\ruby.exe'  
+    fname = data_explorer.fullname
+    get_file_version_info_size = Win32API.new('Version', 'GetFileVersionInfoSize', 'PP', 'L')
+    get_file_version_info     = Win32API.new('Version', 'GetFileVersionInfo', 'PLLP', 'L')
+    ver_query_value          = Win32API.new('Version', 'VerQueryValue', 'PPPP', 'I')
+    memcpy = Win32API.new('msvcrt', 'memcpy', 'PLL', 'L')
+
+    addr = "\0"*4
+
+    v_info_sz = get_file_version_info_size.call(fname, addr)
+
+    raise 'GFVIS failed' if v_info_sz == 0
+    v_info = "\0"*v_info_sz
+    get_file_version_info.call(fname, 0, v_info_sz, v_info)
+
+    v_val_sz = "\0"*4
+    ver_query_value.call(v_info, '\\', addr, v_val_sz)
+    v_bufsz = v_val_sz.unpack('L')[0]
+    v_buf = "\0" * v_bufsz
+    v_src = addr.unpack('L')[0]
+    ret = memcpy.call(v_buf, v_src, v_bufsz)
+    raise 'memcpy failed' if ret == 0
+
+    raise 'Oops' unless v_buf[0, 4].unpack('L')[0] == 0xFEEF04BD
+    #p v_buf[0x08, 8].unpack('S*').values_at(1,0,3,2)  #-> [1, 8, 2, 0]
+    #p v_buf[0x10, 8].unpack('S*').values_at(1,0,3,2)  #-> [1, 8, 2, 0]
+    v_buf[0x08, 8].unpack('S*').values_at(1,0,3,2).join('.')
+  end
+
+end

data/lib/data_explorer/convert/dat_to_ascii.rb

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+require 'data_explorer'
+
+module DataExplorer
+  module Convert
+  
+    # :startdoc::manifest 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.
+    #
+    # DatToAscii is based on the getdeascii.pl script.
+    class DatToAscii < Tap::FileTask
+      include DataExplorer
+      
+      config :output_dir, nil, &c.string_or_nil
+      
+      def process(*input_files)
+        @updated_files = []
+        input_files.collect do |input_file|
+          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
+            end
+
+            @updated_files << output_file
+          end
+          
+          output_file
+        end
+      end
+
+      protected
+
+      def after_execute
+        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
+      end
+    end
+  end
+end

data/test/tap_test_suite.rb

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+$:.unshift File.join(File.dirname(__FILE__), '../lib')
+
+# runs all subsets (see Tap::Test::SubsetMethods)
+ENV["ALL"] = "true"
+Dir.glob("./**/*_test.rb").each {|test| require test}

metadata

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+--- !ruby/object:Gem::Specification 
+name: bahuvrihi-biomass-data_explorer
+version: !ruby/object:Gem::Version 
+  version: 0.0.2
+platform: ruby
+authors: 
+- Simon Chiang
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2008-07-08 00:00:00 -07:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: tap
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 0.10.0
+    version: 
+description: 
+email: simon.a.chiang@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- MIT-LICENSE
+files: 
+- lib/data_explorer.rb
+- lib/data_explorer/convert/dat_to_ascii.rb
+- tap.yml
+- MIT-LICENSE
+has_rdoc: true
+homepage: http://github.com/bahuvrihi/biomass-data_explorer/wikis
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: bioactive
+rubygems_version: 1.2.0
+signing_key: 
+specification_version: 2
+summary: data_explorer task library
+test_files: 
+- test/tap_test_suite.rb