jandot-bio 1.2.1

data/lib/bio/shell.rb

@@ -0,0 +1,44 @@
+#
+# = bio/shell.rb - Loading all BioRuby shell features
+#
+# Copyright::   Copyright (C) 2005, 2006
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: shell.rb,v 1.20 2007/07/09 11:17:09 k Exp $
+#
+
+require 'bio'
+require 'yaml'
+require 'open-uri'
+require 'fileutils'
+require 'pp'
+
+module Bio::Shell
+
+  require 'bio/shell/setup'
+  require 'bio/shell/irb'
+  require 'bio/shell/web'
+  require 'bio/shell/script'
+  require 'bio/shell/core'
+  require 'bio/shell/interface'
+  require 'bio/shell/object'
+  require 'bio/shell/demo'
+  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/das'
+  require 'bio/shell/plugin/keggapi'
+  require 'bio/shell/plugin/soap'
+  require 'bio/shell/plugin/emboss'
+  require 'bio/shell/plugin/blast'
+  require 'bio/shell/plugin/psort'
+
+  extend Ghost
+
+end
+
+

data/lib/bio/shell/core.rb

@@ -0,0 +1,578 @@
+#
+# = bio/shell/core.rb - internal methods for the BioRuby shell
+#
+# Copyright::   Copyright (C) 2005, 2006
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: core.rb,v 1.27 2007/06/28 11:21:40 k Exp $
+#
+
+module Bio::Shell::Core
+
+  SHELLDIR = "shell"
+  DATADIR  = "data"
+  SESSION  = File.join(SHELLDIR, "session")
+  PLUGIN   = File.join(SHELLDIR, "plugin")
+  SCRIPT   = File.join(SHELLDIR, "script.rb")
+  CONFIG   = File.join(SESSION, "config")
+  OBJECT   = File.join(SESSION, "object")
+  HISTORY  = File.join(SESSION, "history")
+  BIOFLAT  = File.join(DATADIR, "bioflat")
+
+  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 colors
+    ESC_SEQ
+  end
+
+  def shell_dir
+    File.join(@cache[:savedir], SHELLDIR)
+  end
+
+  def data_dir
+    File.join(@cache[:savedir], DATADIR)
+  end
+
+  def session_dir
+    File.join(@cache[:savedir], SESSION)
+  end
+
+  def plugin_dir
+    File.join(@cache[:savedir], PLUGIN)
+  end
+
+  def script_file
+    File.join(@cache[:savedir], SCRIPT)
+  end
+
+  def script_dir
+    File.dirname(script_file)
+  end
+
+  def config_file
+    File.join(@cache[:savedir], CONFIG)
+  end
+
+  def object_file
+    File.join(@cache[:savedir], OBJECT)
+  end
+
+  def history_file
+    File.join(@cache[:savedir], HISTORY)
+  end
+
+  def bioflat_dir
+    File.join(@cache[:savedir], BIOFLAT)
+  end
+
+  def ask_yes_or_no(message)
+    loop do
+      STDERR.print "#{message}"
+      answer = gets
+      if answer.nil?
+        # readline support might be broken
+        return false
+      elsif /^\s*[Nn]/.match(answer)
+        return false
+      elsif /^\s*[Yy]/.match(answer)
+        return true
+      else
+        # loop
+      end
+    end
+  end
+
+end
+
+
+module Bio::Shell::Ghost
+
+  include Bio::Shell::Core
+
+  # A hash to store persistent configurations
+  attr_accessor :config
+
+  # A hash to store temporal (per session) configurations
+  attr_accessor :cache
+
+  ### save/restore the environment
+
+  def configure(savedir)
+    @config = {}
+    @cache  = {
+      :savedir => savedir,
+      :workdir => Dir.pwd,
+    }
+    create_save_dir
+    load_config
+    load_plugin
+  end
+ 
+  def load_session
+    load_object
+    unless @cache[:mode] == :script
+      load_history
+      opening_splash
+      open_history
+    end
+  end
+
+  def save_session
+    unless @cache[:mode] == :script
+      closing_splash
+    end
+    if create_save_dir_ask
+      #save_history	# changed to use our own...
+      close_history
+      save_object
+      save_config
+    end
+    #STDERR.puts "Leaving directory '#{@cache[:workdir]}'"
+  end
+
+  ### directories
+
+  def create_save_dir
+    create_real_dir(session_dir)
+    create_real_dir(plugin_dir)
+    create_real_dir(data_dir)
+  end
+
+  def create_save_dir_ask
+    if File.directory?(session_dir)
+      @cache[:save] = true
+    end
+    unless @cache[:save]
+      if ask_yes_or_no("Save session in '#{@cache[:workdir]}' directory? [y/n] ")
+        create_real_dir(session_dir)
+        create_real_dir(plugin_dir)
+        create_real_dir(data_dir)
+        create_real_dir(bioflat_dir)
+        @cache[:save] = true
+      else
+        @cache[:save] = false
+      end
+    end
+    return @cache[:save]
+  end
+
+  def create_real_dir(dir)
+    unless File.directory?(dir)
+      begin
+        STDERR.print "Creating directory (#{dir}) ... "
+        FileUtils.makedirs(dir)
+        STDERR.puts "done"
+      rescue
+        warn "Error: Failed to create directory (#{dir}) : #{$!}"
+      end
+    end
+  end
+
+  ### bioflat
+
+  def create_flat_dir(dbname)
+    dir = File.join(bioflat_dir, dbname.to_s.strip)
+    unless File.directory?(dir)
+      FileUtils.makedirs(dir)
+    end
+    return dir
+  end
+
+  def find_flat_dir(dbname)
+    dir = File.join(bioflat_dir, dbname.to_s.strip)
+    if File.exists?(dir)
+      return dir
+    else
+      return nil
+    end
+  end
+
+  ### config
+
+  def load_config
+    load_config_file(config_file)
+  end
+
+  def load_config_file(file)
+    if File.exists?(file)
+      STDERR.print "Loading config (#{file}) ... "
+      if hash = YAML.load(File.read(file))
+        @config.update(hash)
+      end
+      STDERR.puts "done"
+    end
+  end
+
+  def save_config
+    save_config_file(config_file)
+  end
+
+  def save_config_file(file)
+    begin
+      STDERR.print "Saving config (#{file}) ... "
+      File.open(file, "w") do |f|
+        f.puts @config.to_yaml
+      end
+      STDERR.puts "done"
+    rescue
+      warn "Error: Failed to save (#{file}) : #{$!}"
+    end
+  end
+
+  def config_show
+    @config.each do |k, v|
+      STDERR.puts "#{k}\t= #{v.inspect}"
+    end
+  end
+
+  def config_echo
+    bind = Bio::Shell.cache[:binding]
+    flag = ! @config[:echo]
+    @config[:echo] = IRB.conf[:ECHO] = flag
+    eval("conf.echo = #{flag}", bind)
+    STDERR.puts "Echo #{flag ? 'on' : 'off'}"
+  end
+
+  def config_color
+    bind = Bio::Shell.cache[: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_splash
+    flag = ! @config[:splash]
+    @config[:splash] = flag
+    STDERR.puts "Splash #{flag ? 'on' : 'off'}"
+    opening_splash
+  end
+
+  def config_message(str = nil)
+    str ||= MESSAGE
+    @config[:message] = str
+    opening_splash
+  end
+
+  ### plugin
+
+  def load_plugin
+    load_plugin_dir(plugin_dir)
+  end
+
+  def load_plugin_dir(dir)
+    if File.directory?(dir)
+      Dir.glob("#{dir}/*.rb").sort.each do |file|
+        STDERR.print "Loading plugin (#{file}) ... "
+        load file
+        STDERR.puts "done"
+      end
+    end
+  end
+
+  ### object
+
+  def check_marshal
+    if @config[:marshal] and @config[:marshal] != MARSHAL
+      raise "Marshal version mismatch"
+    end
+  end
+
+  def load_object
+    begin
+      check_marshal
+      load_object_file(object_file)
+    rescue
+      warn "Error: Load aborted : #{$!}"
+    end
+  end
+
+  def load_object_file(file)
+    if File.exists?(file)
+      STDERR.print "Loading object (#{file}) ... "
+      begin
+        bind = Bio::Shell.cache[:binding]
+        hash = Marshal.load(File.read(file))
+        hash.each do |k, v|
+          begin
+            Thread.current[:restore_value] = v
+            eval("#{k} = Thread.current[:restore_value]", bind)
+          rescue
+            STDERR.puts "Warning: object '#{k}' couldn't be loaded : #{$!}"
+          end
+        end
+      rescue
+        warn "Error: Failed to load (#{file}) : #{$!}"
+      end
+      STDERR.puts "done"
+    end
+  end
+
+  def save_object
+    save_object_file(object_file)
+  end
+
+  def save_object_file(file)
+    begin
+      STDERR.print "Saving object (#{file}) ... "
+      File.rename(file, "#{file}.old") if File.exist?(file)
+      File.open(file, "w") do |f|
+        bind = Bio::Shell.cache[:binding]
+        list = eval("local_variables", bind)
+        list -= ["_"]
+        hash = {}
+        list.each do |elem|
+          value = eval(elem, bind)
+          if value
+            begin
+              Marshal.dump(value)
+              hash[elem] = value
+            rescue
+              # value could not be dumped.
+            end
+          end
+        end
+        Marshal.dump(hash, f)
+        @config[:marshal] = MARSHAL
+      end
+      STDERR.puts "done"
+    rescue
+      File.rename("#{file}.old", file) if File.exist?("#{file}.old")
+      warn "Error: Failed to save (#{file}) : #{$!}"
+    end
+  end
+
+  ### history
+
+  def open_history
+    @cache[:histfile] = File.open(history_file, "a")
+    @cache[:histfile].sync = true
+  end
+
+  def store_history(line)
+    Bio::Shell.cache[:histfile].puts "# #{Time.now}"
+    Bio::Shell.cache[:histfile].puts line
+  end
+
+  def close_history
+    if @cache[:histfile]
+      STDERR.print "Saving history (#{history_file}) ... "
+      @cache[:histfile].close
+      STDERR.puts "done"
+    end
+  end
+
+  def load_history
+    if @cache[:readline]
+      load_history_file(history_file)
+    end
+  end
+
+  def load_history_file(file)
+    if File.exists?(file)
+      STDERR.print "Loading history (#{file}) ... "
+      File.open(file).each do |line|
+        unless line[/^# /]
+          Readline::HISTORY.push line.chomp
+        end
+      end
+      STDERR.puts "done"
+    end
+  end
+  
+  # not used (use open_history/close_history instead)
+  def save_history
+    if @cache[:readline]
+      save_history_file(history_file)
+    end
+  end
+
+  def save_history_file(file)
+    begin
+      STDERR.print "Saving history (#{file}) ... "
+      File.open(file, "w") do |f|
+        f.puts Readline::HISTORY.to_a
+      end
+      STDERR.puts "done"
+    rescue
+      warn "Error: Failed to save (#{file}) : #{$!}"
+    end
+  end
+
+  ### script
+
+  def script(mode = nil)
+    case mode
+    when :begin, "begin", :start, "start"
+      @cache[:script] = true
+      script_begin
+    when :end, "end", :stop, "stop"
+      @cache[:script] = false
+      script_end
+      save_script
+    else
+      if @cache[:script]
+        @cache[:script] = false
+        script_end
+        save_script
+      else
+        @cache[:script] = true
+        script_begin
+      end
+    end
+  end
+
+  def script_begin
+    STDERR.puts "-- 8< -- 8< -- 8< --  Script  -- 8< -- 8< -- 8< --"
+    @script_begin = Readline::HISTORY.size
+  end
+
+  def script_end
+    STDERR.puts "-- >8 -- >8 -- >8 --  Script  -- >8 -- >8 -- >8 --"
+    @script_end = Readline::HISTORY.size - 2
+  end
+
+  def save_script
+    if @script_begin and @script_end and @script_begin <= @script_end
+      if File.exists?(script_file)
+        message = "Overwrite script file (#{script_file})? [y/n] "
+      else
+        message = "Save script file (#{script_file})? [y/n] "
+      end
+      if ask_yes_or_no(message)
+        save_script_file(script_file)
+      else
+        STDERR.puts " ... save aborted."
+      end
+    elsif @script_begin and @script_end and @script_begin - @script_end == 1
+      STDERR.puts " ... script aborted."
+    else
+      STDERR.puts "Error: Script range #{@script_begin}..#{@script_end} is invalid"
+    end
+  end
+
+  def save_script_file(file)
+    begin
+      STDERR.print "Saving script (#{file}) ... "
+      File.open(file, "w") do |f|
+        f.puts "#!/usr/bin/env bioruby"
+        f.puts
+        f.puts Readline::HISTORY.to_a[@script_begin..@script_end]
+        f.puts
+      end
+      STDERR.puts "done"
+    rescue
+      @script_begin = nil
+      warn "Error: Failed to save (#{file}) : #{$!}"
+    end
+  end
+
+  ### splash
+
+  def splash_message
+    @config[:message] ||= MESSAGE
+    @config[:message].to_s.split(//).join(" ")
+  end
+
+  def splash_message_color
+    str = splash_message
+    ruby = colors[:ruby]
+    none = colors[:none]
+    return str.sub(/R u b y/) { "#{ruby}R u b y#{none}" }
+  end
+
+  def splash_message_action(message = nil)
+    s = message || splash_message
+    l = s.length
+    x = " "
+    0.step(l,2) do |i|
+      l1 = l-i;  l2 = l1/2;  l4 = l2/2
+      STDERR.print "#{s[0,i]}#{x*l1}#{s[i,1]}\r"
+      sleep(0.001)
+      STDERR.print "#{s[0,i]}#{x*l2}#{s[i,1]}#{x*(l1-l2)}\r"
+      sleep(0.002)
+      STDERR.print "#{s[0,i]}#{x*l4}#{s[i,1]}#{x*(l2-l4)}\r"
+      sleep(0.004)
+      STDERR.print "#{s[0,i+1]}#{x*l4}\r"
+      sleep(0.008)
+    end
+  end
+
+  def splash_message_action_color(message = nil)
+    s = message || splash_message
+    l = s.length
+    c = colors
+    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
+    STDERR.puts
+    if @config[:splash]
+      if @config[:color]
+        splash_message_action_color
+      else
+        splash_message_action
+      end
+    end
+    if @config[:color]
+      STDERR.print splash_message_color
+    else
+      STDERR.print splash_message
+    end
+    STDERR.puts
+    STDERR.puts
+    STDERR.print "  Version : BioRuby #{Bio::BIORUBY_VERSION.join(".")}"
+    STDERR.print " / Ruby #{RUBY_VERSION}"
+    STDERR.puts
+    STDERR.puts
+  end
+
+  def closing_splash
+    STDERR.puts
+    STDERR.puts
+    if @config[:color]
+      STDERR.print splash_message_color
+    else
+      STDERR.print splash_message
+    end
+    STDERR.puts
+    STDERR.puts
+  end
+
+end
+