bio 0.7.0

data/lib/bio/shell.rb

@@ -0,0 +1,51 @@
+#
+# = bio/shell.rb - Loading all BioRuby shell features
+#
+# Copyright::	Copyright (C) 2005
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: shell.rb,v 1.11 2005/12/07 05:12:06 k Exp $
+#
+#--
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library 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
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#++
+#
+
+require 'bio'
+require 'yaml'
+require 'open-uri'
+require 'pp'
+
+module Bio::Shell
+
+  require 'bio/shell/core'
+  require 'bio/shell/session'
+  require 'bio/shell/plugin/entry'
+  require 'bio/shell/plugin/seq'
+  require 'bio/shell/plugin/midi'
+  require 'bio/shell/plugin/codon'
+  require 'bio/shell/plugin/flatfile'
+  require 'bio/shell/plugin/obda'
+  require 'bio/shell/plugin/keggapi'
+
+  extend Ghost
+  extend Private
+
+end
+
+

data/lib/bio/shell/core.rb

@@ -0,0 +1,512 @@
+#
+# = bio/shell/core.rb - internal methods for the BioRuby shell
+#
+# Copyright::	Copyright (C) 2005
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: core.rb,v 1.16 2005/12/07 10:54:23 k Exp $
+#
+#--
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library 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
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#++
+#
+
+module Bio::Shell::Ghost
+
+  CONFIG  = "config"
+  OBJECT  = "object"
+  HISTORY = "history"
+  SCRIPT  = "script.rb"
+  PLUGIN  = "plugin/"
+  BIOFLAT = "bioflat/"
+
+  SITEDIR = "/etc/bioinformatics/bioruby/"
+  USERDIR = "#{ENV['HOME']}/.bioinformatics/bioruby/"
+  SAVEDIR = ".bioruby/"
+
+  MARSHAL = [ Marshal::MAJOR_VERSION, Marshal::MINOR_VERSION ]
+
+  MESSAGE = "...BioRuby in the shell..."
+
+  ESC_SEQ = {
+    :k => "\e[30m",  :black   => "\e[30m",
+    :r => "\e[31m",  :red     => "\e[31m",  :ruby  => "\e[31m",
+    :g => "\e[32m",  :green   => "\e[32m",
+    :y => "\e[33m",  :yellow  => "\e[33m",
+    :b => "\e[34m",  :blue    => "\e[34m",
+    :m => "\e[35m",  :magenta => "\e[35m",
+    :c => "\e[36m",  :cyan    => "\e[36m",
+    :w => "\e[37m",  :white   => "\e[37m",
+    :n => "\e[00m",  :none    => "\e[00m",  :reset => "\e[00m",
+  }
+
+  def esc_seq
+    ESC_SEQ
+  end
+
+  ### save/restore the environment
+
+  def setup
+    @config = {}
+    @cache  = {}
+    check_version
+    check_marshal
+    load_config
+    load_plugin
+  end
+ 
+  # A hash to store persistent configurations
+  attr_accessor :config
+
+  # A hash to store temporal (per session) configurations
+  attr_accessor :cache
+
+  def load
+    load_object
+    load_history
+    opening_splash
+  end
+
+  def save
+    closing_splash
+    save_history
+    save_object
+    save_config
+  end
+
+  #--
+  # *TODO* How to prevent terminal collapse and suppress loading messages?
+  #++
+  def load_thread
+    message = ''
+    begin
+      t1 = Thread.new do
+        require 'stringio'
+        sio = StringIO.new('')
+        begin
+          stdout_save = STDOUT.clone
+          STDOUT.reopen(sio)
+          load_object
+          load_history
+        ensure
+          STDOUT.reopen(stdout_save)
+          stdout_save.close
+          message = sio.read
+          sio.close
+        end
+      end
+      t2 = Thread.new do
+        opening_splash
+      end
+      t1.join
+      t2.join
+    rescue
+    end
+    puts message
+  end
+
+  ### setup
+
+  def check_version
+    if RUBY_VERSION < "1.8.2"
+      raise "BioRuby shell runs on Ruby version >= 1.8.2"
+    end
+  end
+
+  def check_marshal
+    if @config[:marshal] and @config[:marshal] != MARSHAL
+      raise "Marshal version mismatch"
+    end
+  end
+
+  def create_save_dir
+    dir = ask_save_dir
+    create_real_dir(dir)
+    create_real_dir(dir + PLUGIN)
+    create_real_dir(dir + BIOFLAT)
+    return dir
+  end
+
+  # 1. ask to save in SAVEDIR directory in the current directory
+  # 2. otherwise save in USERDIR directory
+  # 3. remember the choice in @cache[:savedir] once per session
+  def ask_save_dir
+    if @cache[:savedir]
+      dir = @cache[:savedir]
+    else
+      dir = SAVEDIR
+      if ! File.directory?(dir)
+        loop do
+          print "Save in \"#{dir}\" directory? [y/n]: "
+          answer = gets
+          if /^\s*[Yy]/.match(answer)
+            break
+          elsif /^\s*[Nn]/.match(answer)
+            dir = USERDIR
+            break
+          end
+        end
+      end
+      @cache[:savedir] = dir
+    end
+    return dir
+  end
+
+  def create_real_dir(dir)
+    unless File.directory?(dir)
+      begin
+        print "Creating directory (#{dir}) ... "
+        Dir.mkdir(dir)
+        puts "done"
+      rescue
+        warn "Error: Failed to create #{dir} : #{$!}"
+      end
+    end
+  end
+
+  ### bioflat
+
+  def create_flat_dir(dbname)
+    if prefix = create_save_dir
+      return prefix + BIOFLAT + dbname.to_s.strip
+    else
+      return nil
+    end
+  end
+
+  def find_flat_dir(dbname)
+    dir = SAVEDIR + BIOFLAT + dbname.to_s.strip
+    dir = USERDIR + BIOFLAT + dbname.to_s.strip unless File.exists?(dir)
+    if File.exists?(dir)
+      return dir
+    else
+      return nil
+    end
+  end
+
+  ### config
+
+  def load_config
+    load_config_file(SITEDIR + CONFIG)
+    load_config_file(USERDIR + CONFIG)
+    load_config_file(SAVEDIR + CONFIG)
+  end
+
+  def load_config_file(file)
+    if File.exists?(file)
+      print "Loading config (#{file}) ... "
+      if hash = YAML.load(File.read(file))
+        @config.update(hash)
+      end
+      puts "done"
+    end
+  end
+
+  def save_config
+    dir = create_save_dir
+    save_config_file(dir + CONFIG)
+  end
+
+  def save_config_file(file)
+    begin
+      print "Saving config (#{file}) ... "
+      File.open(file, "w") do |f|
+        f.puts @config.to_yaml
+      end
+      puts "done"
+    rescue
+      warn "Error: Failed to save (#{file}) : #{$!}"
+    end
+  end
+
+  def config_show
+    @config.each do |k, v|
+      puts "#{k}\t= #{v.inspect}"
+    end
+  end
+
+  def config_echo
+    bind = IRB.conf[:MAIN_CONTEXT].workspace.binding
+    flag = ! @config[:echo]
+    @config[:echo] = IRB.conf[:ECHO] = flag
+    eval("conf.echo = #{flag}", bind)
+    puts "Echo #{flag ? 'on' : 'off'}"
+  end
+
+  def config_color
+    bind = IRB.conf[:MAIN_CONTEXT].workspace.binding
+    flag = ! @config[:color]
+    @config[:color] = flag
+    if flag
+      IRB.conf[:PROMPT_MODE] = :BIORUBY_COLOR
+      eval("conf.prompt_mode = :BIORUBY_COLOR", bind)
+    else
+      IRB.conf[:PROMPT_MODE] = :BIORUBY
+      eval("conf.prompt_mode = :BIORUBY", bind)
+    end
+  end
+
+  def config_pager(cmd = nil)
+    @config[:pager] = cmd
+  end
+
+  def config_message(str = nil)
+    str ||= MESSAGE
+    @config[:message] = str
+  end
+
+  ### plugin
+
+  def load_plugin
+    load_plugin_dir(SITEDIR + PLUGIN)
+    load_plugin_dir(USERDIR + PLUGIN)
+    load_plugin_dir(SAVEDIR + PLUGIN)
+  end
+
+  def load_plugin_dir(dir)
+    if File.directory?(dir)
+      Dir.glob("#{dir}/*.rb").sort.each do |file|
+        print "Loading plugin (#{file}) ... "
+        load file
+        puts "done"
+      end
+    end
+  end
+
+  ### object
+
+  def load_object
+    load_object_file(SITEDIR + OBJECT)
+    load_object_file(USERDIR + OBJECT)
+    load_object_file(SAVEDIR + OBJECT)
+  end
+
+  def load_object_file(file)
+    if File.exists?(file)
+      print "Loading object (#{file}) ... "
+      begin
+        bind = IRB.conf[:MAIN_CONTEXT].workspace.binding
+        hash = Marshal.load(File.read(file))
+        hash.each do |k, v|
+          begin
+            Thread.current[:restore_value] = v
+            eval("#{k} = Thread.current[:restore_value]", bind)
+          rescue
+            puts "Warning: object '#{k}' couldn't be loaded : #{$!}"
+          end
+        end
+      rescue
+        warn "Error: Failed to load (#{file}) : #{$!}"
+      end
+      puts "done"
+    end
+  end
+  
+  def save_object
+    dir = create_save_dir
+    save_object_file(dir + OBJECT)
+  end
+
+  def save_object_file(file)
+    begin
+      print "Saving object (#{file}) ... "
+      File.open(file, "w") do |f|
+        begin
+          bind = IRB.conf[:MAIN_CONTEXT].workspace.binding
+          list = eval("local_variables", bind)
+          list -= ["_"]
+          hash = {}
+          list.each do |elem|
+            value = eval(elem, bind)
+            if value
+              begin
+                Marshal.dump(value)
+                hash[elem] = value
+              rescue
+                # value could not be dumped.
+              end
+            end
+          end
+          Marshal.dump(hash, f)
+          @config[:marshal] = MARSHAL
+        rescue
+          warn "Error: Failed to dump (#{file}) : #{$!}"
+        end
+      end
+      puts "done"
+    rescue
+      warn "Error: Failed to save (#{file}) : #{$!}"
+    end
+  end
+
+  ### history
+
+  def load_history
+    if @cache[:readline]
+      load_history_file(SITEDIR + HISTORY)
+      load_history_file(USERDIR + HISTORY)
+      load_history_file(SAVEDIR + HISTORY)
+    end
+  end
+
+  def load_history_file(file)
+    if File.exists?(file)
+      print "Loading history (#{file}) ... "
+      File.open(file).each do |line|
+        Readline::HISTORY.push line.chomp
+      end
+      puts "done"
+    end
+  end
+  
+  def save_history
+    if @cache[:readline]
+      dir = create_save_dir
+      save_history_file(dir + HISTORY)
+    end
+  end
+
+  def save_history_file(file)
+    begin
+      print "Saving history (#{file}) ... "
+      File.open(file, "w") do |f|
+        f.puts Readline::HISTORY.to_a
+      end
+      puts "done"
+    rescue
+      warn "Error: Failed to save (#{file}) : #{$!}"
+    end
+  end
+
+  ### script
+
+  def script(mode = nil)
+    case mode
+    when :begin, "begin", :start, "start"
+      @cache[:script] = true
+      script_begin
+    when :end, "end", :stop, "stop"
+      @cache[:script] = false
+      script_end
+      save_script
+    else
+      if @cache[:script]
+        @cache[:script] = false
+        script_end
+        save_script
+      else
+        @cache[:script] = true
+        script_begin
+      end
+    end
+  end
+
+  def script_begin
+    puts "-- 8< -- 8< -- 8< --  Script  -- 8< -- 8< -- 8< --"
+    @script_begin = Readline::HISTORY.size
+  end
+
+  def script_end
+    puts "-- >8 -- >8 -- >8 --  Script  -- >8 -- >8 -- >8 --"
+    @script_end = Readline::HISTORY.size - 2
+  end
+
+  def save_script
+    if @script_begin and @script_end and @script_begin <= @script_end
+      dir = create_save_dir
+      save_script_file(dir + SCRIPT)
+    else
+      puts "Error: script range #{@script_begin}..#{@script_end} is invalid"
+    end
+  end
+
+  def save_script_file(file)
+    begin
+      print "Saving script (#{file}) ... "
+        File.open(file, "w") do |f|
+        f.print "#!/usr/bin/env ruby\n\n"
+        f.print "require 'bioruby'\n\n"
+        f.puts Readline::HISTORY.to_a[@script_begin..@script_end]
+        f.print "\n\n"
+      end
+      puts "done"
+    rescue
+      @script_begin = nil
+      warn "Error: Failed to save (#{file}) : #{$!}"
+    end
+  end
+
+  ### splash
+
+  def splash_message
+    @config[:message] ||= MESSAGE
+    @config[:message].to_s.split(//).join(" ")
+  end
+
+  def splash_message_color
+    str = splash_message
+    ruby = ESC_SEQ[:ruby]
+    none = ESC_SEQ[:none]
+    return str.sub(/R u b y/) { "#{ruby}R u b y#{none}" }
+  end
+
+  def splash_message_action
+    s = splash_message
+    l = s.length
+    c = ESC_SEQ
+    x = " "
+    0.step(l,2) do |i|
+      l1 = l-i;  l2 = l1/2;  l4 = l2/2
+      STDERR.print "#{c[:n]}#{s[0,i]}#{x*l1}#{c[:y]}#{s[i,1]}\r"
+      sleep(0.001)
+      STDERR.print "#{c[:n]}#{s[0,i]}#{x*l2}#{c[:g]}#{s[i,1]}#{x*(l1-l2)}\r"
+      sleep(0.002)
+      STDERR.print "#{c[:n]}#{s[0,i]}#{x*l4}#{c[:r]}#{s[i,1]}#{x*(l2-l4)}\r"
+      sleep(0.004)
+      STDERR.print "#{c[:n]}#{s[0,i+1]}#{x*l4}\r"
+      sleep(0.008)
+    end
+  end
+
+  def opening_splash
+    print "\n"
+    if @config[:color]
+      splash_message_action
+    end
+    if @config[:color]
+      print splash_message_color
+    else
+      print splash_message
+    end
+    print "\n\n"
+    print "  Version : BioRuby #{Bio::BIORUBY_VERSION.join(".")}"
+    print " / Ruby #{RUBY_VERSION}\n\n"
+  end
+
+  def closing_splash
+    print "\n\n"
+    if @config[:color]
+      print splash_message_color
+    else
+      print splash_message
+    end
+    print "\n\n"
+  end
+
+end
+