BioDSL 1.0.0

data/lib/BioDSL/fork.rb

@@ -0,0 +1,145 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# 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).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+# BioDSL namespace.
+module BioDSL
+  # Error class for all Fork errors.
+  ForkError = Class.new(StandardError)
+
+  # Class containing methods to fork in an objective oriented manner.
+  class Fork
+    attr_reader :input, :output
+
+    # Class method to execute a block in a seperate process.
+    #
+    # @param block [Proc] Block to execute.
+    #
+    # @return [Fork] Instance of Fork.
+    def self.execute(&block)
+      parent = new(&block)
+      parent.execute
+    end
+
+    # Constructor for Fork.
+    #
+    # @param block [Proc] Block to execute.
+    #
+    # @raise [ArgumentError] If no block given.
+    #
+    # @return [Fork] Instance of Fork.
+    def initialize(&block)
+      fail ArgumentError, 'No block given' unless block
+
+      @parent = true
+      @alive  = false
+      @pid    = nil
+      @input  = nil
+      @output = nil
+      @block  = block
+    end
+
+    # Execute the block in a separate process.
+    def execute
+      @alive = true
+
+      child_read, parent_write = BioDSL::Stream.pipe
+      parent_read, child_write = BioDSL::Stream.pipe
+
+      pid = fork_process(child_read, child_write, parent_read, parent_write)
+
+      child_write.close
+      child_read.close
+
+      @pid    = pid
+      @input  = parent_read
+      @output = parent_write
+
+      self
+    end
+
+    # Determines if process is running.
+    #
+    # @return [Bool] True if running else nil.
+    def running?
+      @pid
+    end
+
+    # Read object from forked process.
+    #
+    # @raise [ForkError] unless process is running.
+    def read
+      fail BioDSL::ForkError, 'Not running' unless running?
+
+      @input.read
+    end
+
+    # Write object to forked process.
+    #
+    # @raise [ForkError] unless process is running.
+    def write(obj)
+      fail BioDSL::ForkError, 'Not running' unless running?
+
+      @output.write(obj)
+    end
+
+    # Wait for forked process.
+    #
+    # @raise [ForkError] unless process is running.
+    def wait
+      fail BioDSL::ForkError, 'Not running' unless running?
+
+      @input.close  unless @input.closed?
+      @output.close unless @output.closed?
+
+      Process.wait(@pid)
+    end
+
+    private
+
+    # Fork process with IPC.
+    #
+    # @param child_read   [BioDSL::Stream] Child read IO.
+    # @param child_write  [BioDSL::Stream] Child write IO.
+    # @param parent_read  [BioDSL::Stream] Parent read IO.
+    # @param parent_write [BioDSL::Stream] Parent write IO.
+    #
+    # @return [FixNum] Process ID.
+    def fork_process(child_read, child_write, parent_read, parent_write)
+      Process.fork do
+        parent_write.close
+        parent_read.close
+
+        @parent = false
+        @pid    = Process.pid
+        @input  = child_read
+        @output = child_write
+
+        @block.call(self)
+      end
+    end
+  end
+end

data/lib/BioDSL/hamming.rb

@@ -0,0 +1,128 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# 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 all exceptions to do with Hamming.
+  HammingError = Class.new(StandardError)
+
+  # Class for calculating Hamming distance.
+  class Hamming
+    extend Ambiguity
+
+    # Class method for calculating the Hamming distance between
+    # two given strings optionally allowing for IUPAC ambiguity codes.
+    #
+    # @param str1     [String]  String 1.
+    # @param str2     [String]  String 2.
+    # @param options  [Hash]    Options hash.
+    # @option options [Boolean] :ambiguity
+    def self.distance(str1, str2, options = {})
+      check_strings(str1, str2)
+
+      hd = new
+
+      if options[:ambiguity]
+        hd.hamming_distance_ambiguity_C(str1, str2, str1.length)
+      else
+        hd.hamming_distance_C(str1, str2, str1.length)
+      end
+    end
+
+    # Check that string lengths are equal.
+    #
+    # @param str1 [String] String 1.
+    # @param str2 [String] String 2.
+    #
+    # @raise [HammingError] if string lengths mismatch.
+    def self.check_strings(str1, str2)
+      return if str1.length == str2.length
+
+      fail HammingError, "bad string lengths: #{str1.length} != #{str2.length}"
+    end
+
+    # >>>>>>>>>>>>>>> RubyInline C code <<<<<<<<<<<<<<<
+
+    inline do |builder|
+      add_ambiguity_macro(builder)
+
+      # C method for calculating Hamming Distance.
+      builder.c %{
+        VALUE hamming_distance_C(
+          VALUE _str1,   // String 1
+          VALUE _str2,   // String 2
+          VALUE _len     // String length
+        )
+        {
+          char         *str1 = StringValuePtr(_str1);
+          char         *str2 = StringValuePtr(_str2);
+          unsigned int  len  = FIX2UINT(_len);
+
+          unsigned int hamming_dist = 0;
+          unsigned int i            = 0;
+
+          for (i = 0; i < len; i++)
+          {
+            if (str1[i] != str2[i])
+            {
+              hamming_dist++;
+            }
+          }
+
+          return UINT2NUM(hamming_dist);
+        }
+      }
+
+      # C method for calculating Hamming Distance.
+      builder.c %{
+        VALUE hamming_distance_ambiguity_C(
+          VALUE _str1,   // String 1
+          VALUE _str2,   // String 2
+          VALUE _len     // String length
+        )
+        {
+          char         *str1 = StringValuePtr(_str1);
+          char         *str2 = StringValuePtr(_str2);
+          unsigned int  len  = FIX2UINT(_len);
+
+          unsigned int hamming_dist = 0;
+          unsigned int i            = 0;
+
+          for (i = 0; i < len; i++)
+          {
+            if (! MATCH(str1[i], str2[i]))
+            {
+              hamming_dist++;
+            }
+          }
+
+          return UINT2NUM(hamming_dist);
+        }
+      }
+    end
+  end
+end

data/lib/BioDSL/helpers/aux_helper.rb

@@ -0,0 +1,44 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# 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
+  # Namespace for AuxHelper.
+  module AuxHelper
+    BioDSL::AuxiliaryError = Class.new(StandardError)
+
+    # Method that raises if the given command is not found on the system.
+    #
+    # @param command [String] Command that must exist.
+    #
+    # @raise [AuxiliaryError] if command is not found.
+    def aux_exist(command)
+      return if BioDSL::Filesys.which(command)
+      fail AuxiliaryError, "command: #{command} not found"
+    end
+  end
+end

data/lib/BioDSL/helpers/email_helper.rb

@@ -0,0 +1,66 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# 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).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+module BioDSL
+  # Namespace for EmailHelper.
+  module EmailHelper
+    # Send email notification to email address specfied in @options[:email],
+    # including a optional subject specified in @options[:subject], that will
+    # otherwise default to self.to_s. The body of the email will be an HTML
+    # report.
+    #
+    # @param pipeline [BioDSL::Pipeline] Pipeline object
+    def send_email(pipeline)
+      return unless @options[:email]
+
+      html_part = Mail::Part.new do
+        content_type 'text/html; charset=UTF-8'
+        body BioDSL::HtmlReport.new(pipeline).to_html
+      end
+
+      compose_mail(html_part).deliver!
+    end
+
+    # Compose an email.
+    #
+    # @param html_part [Mail::Part] The email body.
+    #
+    # @return [Mail] Mail to be sent.
+    def compose_mail(html_part)
+      mail = Mail.new
+      mail[:from]    = "do-not-reply@#{`hostname -f`.strip}"
+      mail[:to]      = @options[:email]
+      mail[:subject] = @options[:subject] || to_s.first(30)
+      mail.html_part = html_part
+      mail.delivery_method :smtp,
+                           address: 'localhost',
+                           port: 25,
+                           enable_starttls_auto: false
+      mail
+    end
+  end
+end

data/lib/BioDSL/helpers/history_helper.rb

@@ -0,0 +1,40 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# 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).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+module BioDSL
+  # Namespace for HistoryHelper.
+  module HistoryHelper
+    # Save pipeline to history file unless test is set.
+    def save_history
+      return if BioDSL.test
+
+      File.open(BioDSL::Config::HISTORY_FILE, 'a') do |ios|
+        ios.puts to_s
+      end
+    end
+  end
+end

data/lib/BioDSL/helpers/log_helper.rb

@@ -0,0 +1,55 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# 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).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+module BioDSL
+  # Namespace for LogHelper.
+  module LogHelper
+    require 'yaml'
+
+    # Log an OK messge to the log file.
+    def log_ok
+      return if BioDSL.test
+
+      File.open(BioDSL::Config::LOG_FILE, 'a') do |ios|
+        ios.puts to_s
+        ios.puts status.to_yaml
+        ios.puts 'OK'
+      end
+    end
+
+    # Log an ERROR messge to the log file.
+    def log_error(exception)
+      File.open(BioDSL::Config::LOG_FILE, 'a') do |ios|
+        ios.puts to_s
+        ios.puts status.to_yaml if self.respond_to? :status
+        ios.puts 'ERROR'
+        ios.puts exception.message
+        ios.puts exception.backtrace
+      end
+    end
+  end
+end