BioDSL 1.0.0

data/lib/BioDSL/serializer.rb

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+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                #
+#                                                                              #
+# This program is free software; you can redistribute it and/or                #
+# modify it under the terms of the GNU General Public License                  #
+# as published by the Free Software Foundation; either version 2               #
+# of the License, or (at your option) any later version.                       #
+#                                                                              #
+# This program is distributed in the hope that it will be useful,              #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of               #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                #
+# GNU General Public License for more details.                                 #
+#                                                                              #
+# You should have received a copy of the GNU General Public License            #
+# along with this program; if not, write to the Free Software                  #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,    #
+#  USA.                                                                        #
+#                                                                              #
+# http://www.gnu.org/copyleft/gpl.html                                         #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# This software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+# Namespace for BioDSL.
+module BioDSL
+  # Error class for Serializer.
+  SerializerError = Class.new(StandardError)
+
+  # Class for serializing and de-serializing data using Marshal.
+  class Serializer
+    include Enumerable
+
+    # Constructor for serializer.
+    #
+    # @param io    [IO]   IO object.
+    # @param block [Proc] Block context.
+    #
+    # @raise [SerializerError] if no block given.
+    #
+    # @return [Serializer] class instance.
+    def initialize(io, &block)
+      @io = io
+
+      fail SerializerError, 'No block given' unless block
+
+      block.call(self)
+    end
+
+    # Method to write serialized data using Marshal to a given IO.
+    #
+    # @param obj [Object] Object to serialize.
+    #
+    # @example
+    #   File.open("foo.dat", 'wb') do |io|
+    #     BioDSL::Serializer.new(io) do |s|
+    #       s << {"foo": 0}
+    #       s << {"bar": 1}
+    #     end
+    #   end
+    def <<(obj)
+      data = Marshal.dump(obj)
+      @io.write([data.size].pack('N'))
+      @io.write(data)
+    end
+
+    alias_method :writei, :<<
+
+    # Iterator for reading and de-serialized data from a given IO.
+    #
+    # @example
+    #   File.open("foo.dat", 'rb') do |io|
+    #     BioDSL::Serializer.new(io) do |s|
+    #       s.each do |record|
+    #         puts record
+    #       end
+    #     end
+    #   end
+    #
+    # @yield [Object]
+    def each
+      yield next_entry until @io.eof?
+    end
+
+    # Read next entry from serialized stream.
+    #
+    # @return [Object] Deserialized Object.
+    def next_entry
+      size = @io.read(4)
+      fail EOFError unless size
+      data = @io.read(size.unpack('N').first)
+      Marshal.load(data)
+    end
+  end
+end

data/lib/BioDSL/stream.rb

@@ -0,0 +1,113 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                #
+#                                                                              #
+# This program is free software; you can redistribute it and/or                #
+# modify it under the terms of the GNU General Public License                  #
+# as published by the Free Software Foundation; either version 2               #
+# of the License, or (at your option) any later version.                       #
+#                                                                              #
+# This program is distributed in the hope that it will be useful,              #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of               #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                #
+# GNU General Public License for more details.                                 #
+#                                                                              #
+# You should have received a copy of the GNU General Public License            #
+# along with this program; if not, write to the Free Software                  #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,    #
+# USA.                                                                         #
+#                                                                              #
+# http://www.gnu.org/copyleft/gpl.html                                         #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# This software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+# Namespace for BioDSL.
+module BioDSL
+  # Class for Inter Process Communication between forked processes using msgpack
+  # to serialize and deserialize objects.
+  class Stream
+    require 'msgpack'
+
+    include Enumerable
+
+    # Create a pair of connected pipe endpoints. The connection uses msgpack
+    # allowing objects to be written and read.
+    #
+    # Stream.pipe ->  [read_io, write_io]
+    def self.pipe
+      read, write = IO.pipe(Encoding::BINARY)
+
+      [new(read), new(write)]
+    end
+
+    def initialize(io)
+      @io = io
+    end
+
+    def close
+      @io.close
+    end
+
+    def closed?
+      @io.closed?
+    end
+
+    def each
+      yield read until @io.eof?
+    end
+
+    def read
+      size = @io.read(4)
+      fail EOFError unless size
+      size = size.unpack('I').first
+      msg  = @io.read(size)
+      MessagePack.unpack(msg, symbolize_keys: true)
+    end
+
+    def write(obj)
+      msg = MessagePack.pack(obj)
+      @io.write([msg.size].pack('I'))
+      @io.write(msg)
+    end
+
+    alias_method :<<, :write
+  end
+
+  class Channel
+    include Enumerable
+
+    def self.pair
+      queue = Queue.new
+
+      [new(queue), new(queue)]
+    end
+
+    def initialize(queue)
+      @queue = queue
+    end
+
+    def each
+      while (obj = read)
+        yield obj
+      end
+    end
+
+    def read
+      @queue.pop
+    end
+
+    def write(obj)
+      @queue << obj
+    end
+
+    def terminate
+      @queue << nil
+    end
+
+    alias_method :<<, :write
+  end
+end