command.rb in bio-1.4.3

- old
+ new

@@ -230,23 +230,41 @@
   # ---
   # *Arguments*:
   # * (required) _cmd_: Array containing String objects
   # * (optional) _options_: Hash
   # *Returns*:: (undefined)
-  def call_command_popen(cmd, options = {})
+  def call_command_popen(cmd, options = {}, &block)
     if RUBY_VERSION >= "1.9.0" then
-      # For Ruby 1.9 or later, using command line array with options.
-      dir = options[:chdir]
-      cmd = safe_command_line_array(cmd)
-      if dir then
-        cmd = cmd + [ { :chdir => dir } ]
+      if RUBY_ENGINE == 'jruby' then
+        _call_command_popen_jruby19(cmd, options, &block)
+      else
+        _call_command_popen_ruby19(cmd, options, &block)
       end
-      r = IO.popen(cmd, "r+") do |io|
-        yield io
-      end
-      return r
+    else
+      _call_command_popen_ruby18(cmd, options, &block)
     end
+  end
+
+  # This method is internally called from the call_command method.
+  # In normal case, use call_command, and do not call this method directly.
+  #
+  # Executes the program via IO.popen.
+  # A block must be given. An IO object is passed to the block.
+  #
+  # See the document of call_command for available options.
+  #
+  # The method is written for Ruby 1.8.
+  #
+  # In Ruby 1.8, although shell unsafe characters are escaped,
+  # if inescapable characters exists, it raises RuntimeError.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _cmd_: Array containing String objects
+  # * (optional) _options_: Hash
+  # *Returns*:: (undefined)
+  def _call_command_popen_ruby18(cmd, options = {})
     # For Ruby 1.8, using command line string.
     str = make_command_line(cmd)
     # processing options
     if dir = options[:chdir] then
       if windows_platform?
@@ -265,14 +283,74 @@
     IO.popen(str, "w+") do |io|
       io.sync = true
       yield io
     end
   end
+  private :_call_command_popen_ruby18
 
   # This method is internally called from the call_command method.
   # In normal case, use call_command, and do not call this method directly.
   #
+  # Executes the program via IO.popen.
+  # A block must be given. An IO object is passed to the block.
+  #
+  # See the document of call_command for available options.
+  #
+  # The method can be run only on Ruby (MRI) 1.9 or later versions.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _cmd_: Array containing String objects
+  # * (optional) _options_: Hash
+  # *Returns*:: (undefined)
+  def _call_command_popen_ruby19(cmd, options = {})
+    # For Ruby 1.9 or later, using command line array with options.
+    dir = options[:chdir]
+    cmd = safe_command_line_array(cmd)
+    if dir then
+      cmd = cmd + [ { :chdir => dir } ]
+    end
+    r = IO.popen(cmd, "r+") do |io|
+      yield io
+    end
+    return r
+  end
+  private :_call_command_popen_ruby19
+
+  # This method is internally called from the call_command method.
+  # In normal case, use call_command, and do not call this method directly.
+  #
+  # Executes the program via IO.popen.
+  # A block must be given. An IO object is passed to the block.
+  #
+  # See the document of call_command for available options.
+  #
+  # The method is written for the workaround of the JRuby bugs:
+  # * {JRUBY-6195}[http://jira.codehaus.org/browse/JRUBY-6195] Process.spawn
+  #   (and related methods) ignore option hash
+  # * {JRUBY-6818}[http://jira.codehaus.org/browse/JRUBY-6818] Kernel.exec,
+  #   Process.spawn (and IO.popen etc.) raise error when program is an array
+  #   containing two strings
+  # This method may be removed after the bugs are resolved.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _cmd_: Array containing String objects
+  # * (optional) _options_: Hash
+  # *Returns*:: (undefined)
+  def _call_command_popen_jruby19(cmd, options = {}, &block)
+    if !options.empty? or cmd.size == 1 then
+      _call_command_popen_ruby18(cmd, options, &block)
+    else
+      _call_command_popen_ruby19(cmd, options, &block)
+    end
+  end
+  private :_call_command_popen_jruby19
+
+  # This method is internally called from the call_command method.
+  # In normal case, use call_command, and do not call this method directly.
+  #
   # Executes the program via fork (by using IO.popen("-")) and exec.
   # A block must be given. An IO object is passed to the block.
   #
   # See the document of call_command for available options.
   #
@@ -545,37 +623,41 @@
   # is destroyed by GC.
   #
   # BioRuby library internal use only.
   class Tmpdir
 
-    # Returns finalizer object for Tmpdir class.
-    # Internal use only. Users should not call this method directly.
-    # 
-    # Acknowledgement: The essense of the code is taken from tempfile.rb
-    # in Ruby 1.8.7.
+    # Internal use only. Users should not use this class directly.
     #
-    # ---
-    # *Arguments*:
-    # * (required) _data_: Array containing internal data
-    # *Returns*:: Proc object
-    def self.callback(data)
-      pid = $$
-      lambda {
-        path, = *data
-        if pid == $$
-          $stderr.print "removing ", path, " ..." if $DEBUG
-          if path and !path.empty? and
-              File.directory?(path) and
-              !File.symlink?(path) then
-            Bio::Command.remove_entry_secure(path)
-            $stderr.print "done\n" if $DEBUG
-          else
-            $stderr.print "skipped\n" if $DEBUG
-          end
+    # Bio::Command::Tmpdir::Remover is a class to remove temporary
+    # directory.
+    #
+    # Acknowledgement: The essense of the code is taken from tempfile.rb
+    # in Ruby trunk (svn 34413) and in Ruby 1.8.7.
+    class Remover
+      # Internal use only. Users should not call this method.
+      def initialize(data)
+        @pid = $$
+        @data = data
+      end
+
+      # Internal use only. Users should not call this method.
+      def call(*args)
+        return if @pid != $$
+
+        path, = *@data
+
+        STDERR.print "removing ", path, "..." if $DEBUG
+        if path and !path.empty? and
+            File.directory?(path) and
+            !File.symlink?(path) then
+          Bio::Command.remove_entry_secure(path)
+          $stderr.print "done\n" if $DEBUG
+        else
+          $stderr.print "skipped\n" if $DEBUG
         end
-      }
-    end
+      end
+    end #class Remover
 
     # Creates a new Tmpdir object.
     # The arguments are the same as Bio::Command.mktmpdir.
     #
     # ---
@@ -583,10 +665,10 @@
     # * (optional) <em>prefix_suffix</em>: String (or Array)
     # * (optional) <em>tmpdir</em>: String: temporary directory's path
     # *Returns*:: Tmpdir object
     def initialize(prefix_suffix = nil, tmpdir = nil)
       @data = []
-      @clean_proc = self.class.callback(@data)
+      @clean_proc = Remover.new(@data)
       ObjectSpace.define_finalizer(self, @clean_proc)
       @data.push(@path = Bio::Command.mktmpdir(prefix_suffix, tmpdir).freeze)
     end
 
     # Path to the temporay directory