bahuvrihi-ms-data_explorer 0.0.2 → 0.0.3

data/MIT-LICENSE

@@ -0,0 +1,21 @@
+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/ms/data_explorer/convert/dat_to_ascii.rb

@@ -0,0 +1,76 @@
+require 'ms/data_explorer'
+
+module Ms
+  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 (by default the output directory is
+      # the same directory as the input file).
+      #
+      # DatToAscii is based on the getdeascii.pl script.
+      class DatToAscii < Tap::FileTask
+        include DataExplorer
+      
+        config :output_dir, nil, &c.string_or_nil     # the output dir
+      
+        def process(*input_files)
+          @updated_files = []
+          input_files.collect do |input_file|
+            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
+
+        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
+end

data/lib/ms/data_explorer/format/ascii.rb

@@ -0,0 +1,34 @@
+require 'ms/data'
+require 'ms/spectrum'
+
+module Ms
+  module DataExplorer
+  
+    # ::format (.dat)
+    # 
+    module Format
+      class Ascii < Spectrum
+        class << self
+          def parse(str)
+            headers = {}
+            data = []
+            
+            str.split(/\r?\n/).each do |line|
+              line = line.strip
+              next if line.empty?
+              
+              key, value = line.split(/\s+/, 2)
+              if key =~ /^\d/
+                data << [key.to_f, value.to_f]
+              else
+                headers[key] = value
+              end
+            end
+            
+            new(Data.new(data, :transposed), headers)
+          end
+        end
+      end
+    end
+  end
+end

data/lib/ms/data_explorer.rb

@@ -0,0 +1,54 @@
+require 'win32ole'
+require 'Win32API'
+
+module Ms
+  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
+end

data/test/tap_test_suite.rb

@@ -0,0 +1,5 @@
+$:.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

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: bahuvrihi-ms-data_explorer
 version: !ruby/object:Gem::Version 
-  version: 0.0.2
+  version: 0.0.3
 platform: ruby
 authors: 
 - Simon Chiang
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2008-08-13 00:00:00 -07:00
+date: 2008-10-27 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -19,7 +19,16 @@ dependencies:
     requirements: 
     - - ~>
       - !ruby/object:Gem::Version 
-        version: 0.10.0
+        version: "0.11"
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: mspire
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: "0.5"
     version: 
 description: 
 email: simon.a.chiang@gmail.com
@@ -32,6 +41,7 @@ extra_rdoc_files:
 files: 
 - lib/ms/data_explorer.rb
 - lib/ms/data_explorer/convert/dat_to_ascii.rb
+- lib/ms/data_explorer/format/ascii.rb
 - tap.yml
 - MIT-LICENSE
 has_rdoc: true