bahuvrihi-ms-data_explorer 0.0.3 → 0.1.0

data/lib/ms/data_explorer/convert/dat_to_ascii.rb

@@ -1,10 +1,11 @@
+require 'tap/tasks/file_task'
 require 'ms/data_explorer'
 
 module Ms
   module DataExplorer
     module Convert
   
-      # :startdoc::manifest converts .dat file to ascii text
+      # :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
@@ -12,15 +13,33 @@ module Ms
       # the same directory as the input file).
       #
       # DatToAscii is based on the getdeascii.pl script.
-      class DatToAscii < Tap::FileTask
+      class DatToAscii < Tap::Tasks::FileTask
         include DataExplorer
       
-        config :output_dir, nil, &c.string_or_nil     # the output dir
-      
+        config :output_dir, nil, &c.string_or_nil     # the output dir
+        
+        def updated_files
+          @updated_files ||= []
+        end
+        
+        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
+        
         def process(*input_files)
-          @updated_files = []
           input_files.collect do |input_file|
-            check_terminate
+            app.check_terminate
             
             output_file = if output_dir
               File.join(output_dir, basename(input_file, ".txt"))
@@ -51,25 +70,13 @@ module Ms
                 # TODO -- add debug logging for this...
               end
 
-              @updated_files << output_file
+              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

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: bahuvrihi-ms-data_explorer
 version: !ruby/object:Gem::Version 
-  version: 0.0.3
+  version: 0.1.0
 platform: ruby
 authors: 
 - Simon Chiang
@@ -9,20 +9,42 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2008-10-27 00:00:00 -07:00
+date: 2009-04-08 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: tap
+  type: :runtime
   version_requirement: 
   version_requirements: !ruby/object:Gem::Requirement 
     requirements: 
-    - - ~>
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.17.0
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: tap-tasks
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.1.0
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: tap-test
+  type: :development
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
       - !ruby/object:Gem::Version 
-        version: "0.11"
+        version: 0.1.0
     version: 
 - !ruby/object:Gem::Dependency 
   name: mspire
+  type: :runtime
   version_requirement: 
   version_requirements: !ruby/object:Gem::Requirement 
     requirements: