bio 1.0.0 → 1.1.0

data/lib/bio/shell.rb

@@ -3,22 +3,26 @@
 #
 # Copyright::   Copyright (C) 2005, 2006
 #               Toshiaki Katayama <k@bioruby.org>
-# License:      Ruby's
+# License::     The Ruby License
 #
-# $Id: shell.rb,v 1.15 2006/02/27 09:34:23 k Exp $
+# $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/web'
   require 'bio/shell/demo'
   require 'bio/shell/plugin/entry'
   require 'bio/shell/plugin/seq'
@@ -26,11 +30,14 @@ module Bio::Shell
   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
-  extend Private
 
 end
 

data/lib/bio/shell/core.rb

@@ -3,22 +3,22 @@
 #
 # Copyright::   Copyright (C) 2005, 2006
 #               Toshiaki Katayama <k@bioruby.org>
-# License::     Ruby's
+# License::     The Ruby License
 #
-# $Id: core.rb,v 1.21 2006/02/27 09:09:57 k Exp $
+# $Id: core.rb,v 1.27 2007/06/28 11:21:40 k Exp $
 #
 
+module Bio::Shell::Core
 
-module Bio::Shell::Ghost
-
-  SAVEDIR = "session/"
-  CONFIG  = "config"
-  OBJECT  = "object"
-  HISTORY = "history"
-  SCRIPT  = "script.rb"
-  PLUGIN  = "plugin/"
-  DATADIR = "data/"
-  BIOFLAT = "bioflat/"
+  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 ]
 
@@ -36,80 +36,133 @@ module Bio::Shell::Ghost
     :n => "\e[00m",  :none    => "\e[00m",  :reset => "\e[00m",
   }
 
-  def history
-    SAVEDIR + HISTORY
+  def colors
+    ESC_SEQ
   end
 
-  def datadir
-    DATADIR
+  def shell_dir
+    File.join(@cache[:savedir], SHELLDIR)
   end
 
-  def esc_seq
-    ESC_SEQ
+  def data_dir
+    File.join(@cache[:savedir], DATADIR)
   end
 
-  ### save/restore the environment
+  def session_dir
+    File.join(@cache[:savedir], SESSION)
+  end
 
-  def setup
-    @config = {}
-    @cache  = {}
-    check_version
-    check_marshal
-    load_config
-    load_plugin
+  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
-    load_history
-    opening_splash
+    unless @cache[:mode] == :script
+      load_history
+      opening_splash
+      open_history
+    end
   end
 
   def save_session
-    closing_splash
+    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
 
-  ### 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
+  ### directories
 
   def create_save_dir
-    create_real_dir(SAVEDIR)
-    create_real_dir(DATADIR)
-    create_real_dir(PLUGIN)
+    create_real_dir(session_dir)
+    create_real_dir(plugin_dir)
+    create_real_dir(data_dir)
   end
 
   def create_save_dir_ask
-    if File.directory?(SAVEDIR)
+    if File.directory?(session_dir)
       @cache[:save] = true
     end
-    if @cache[:save].nil?
-      if ask_yes_or_no("Save session in '#{SAVEDIR}' directory? [y/n] ")
-        create_real_dir(SAVEDIR)
-        create_real_dir(DATADIR)
-        create_real_dir(PLUGIN)
-#       create_real_dir(BIOFLAT)
+    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
@@ -118,29 +171,12 @@ module Bio::Shell::Ghost
     return @cache[:save]
   end
 
-  def ask_yes_or_no(message)
-    loop do
-      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
-
   def create_real_dir(dir)
     unless File.directory?(dir)
       begin
-        print "Creating directory (#{dir}) ... "
-        Dir.mkdir(dir)
-        puts "done"
+        STDERR.print "Creating directory (#{dir}) ... "
+        FileUtils.makedirs(dir)
+        STDERR.puts "done"
       rescue
         warn "Error: Failed to create directory (#{dir}) : #{$!}"
       end
@@ -150,18 +186,15 @@ module Bio::Shell::Ghost
   ### bioflat
 
   def create_flat_dir(dbname)
-    dir = BIOFLAT + dbname.to_s.strip
-    unless File.directory?(BIOFLAT)
-      Dir.mkdir(BIOFLAT)
-    end
+    dir = File.join(bioflat_dir, dbname.to_s.strip)
     unless File.directory?(dir)
-      Dir.mkdir(dir)
+      FileUtils.makedirs(dir)
     end
     return dir
   end
 
   def find_flat_dir(dbname)
-    dir = BIOFLAT + dbname.to_s.strip
+    dir = File.join(bioflat_dir, dbname.to_s.strip)
     if File.exists?(dir)
       return dir
     else
@@ -172,30 +205,30 @@ module Bio::Shell::Ghost
   ### config
 
   def load_config
-    load_config_file(SAVEDIR + CONFIG)
+    load_config_file(config_file)
   end
 
   def load_config_file(file)
     if File.exists?(file)
-      print "Loading config (#{file}) ... "
+      STDERR.print "Loading config (#{file}) ... "
       if hash = YAML.load(File.read(file))
         @config.update(hash)
       end
-      puts "done"
+      STDERR.puts "done"
     end
   end
 
   def save_config
-    save_config_file(SAVEDIR + CONFIG)
+    save_config_file(config_file)
   end
 
   def save_config_file(file)
     begin
-      print "Saving config (#{file}) ... "
+      STDERR.print "Saving config (#{file}) ... "
       File.open(file, "w") do |f|
         f.puts @config.to_yaml
       end
-      puts "done"
+      STDERR.puts "done"
     rescue
       warn "Error: Failed to save (#{file}) : #{$!}"
     end
@@ -203,20 +236,20 @@ module Bio::Shell::Ghost
 
   def config_show
     @config.each do |k, v|
-      puts "#{k}\t= #{v.inspect}"
+      STDERR.puts "#{k}\t= #{v.inspect}"
     end
   end
 
   def config_echo
-    bind = IRB.conf[:MAIN_CONTEXT].workspace.binding
+    bind = Bio::Shell.cache[:binding]
     flag = ! @config[:echo]
     @config[:echo] = IRB.conf[:ECHO] = flag
     eval("conf.echo = #{flag}", bind)
-    puts "Echo #{flag ? 'on' : 'off'}"
+    STDERR.puts "Echo #{flag ? 'on' : 'off'}"
   end
 
   def config_color
-    bind = IRB.conf[:MAIN_CONTEXT].workspace.binding
+    bind = Bio::Shell.cache[:binding]
     flag = ! @config[:color]
     @config[:color] = flag
     if flag
@@ -235,7 +268,7 @@ module Bio::Shell::Ghost
   def config_splash
     flag = ! @config[:splash]
     @config[:splash] = flag
-    puts "Splash #{flag ? 'on' : 'off'}"
+    STDERR.puts "Splash #{flag ? 'on' : 'off'}"
     opening_splash
   end
 
@@ -248,115 +281,143 @@ module Bio::Shell::Ghost
   ### plugin
 
   def load_plugin
-    load_plugin_dir(PLUGIN)
+    load_plugin_dir(plugin_dir)
   end
 
   def load_plugin_dir(dir)
     if File.directory?(dir)
       Dir.glob("#{dir}/*.rb").sort.each do |file|
-        print "Loading plugin (#{file}) ... "
+        STDERR.print "Loading plugin (#{file}) ... "
         load file
-        puts "done"
+        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
-    load_object_file(SAVEDIR + 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)
-      print "Loading object (#{file}) ... "
+      STDERR.print "Loading object (#{file}) ... "
       begin
-        bind = IRB.conf[:MAIN_CONTEXT].workspace.binding
+        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
-            puts "Warning: object '#{k}' couldn't be loaded : #{$!}"
+            STDERR.puts "Warning: object '#{k}' couldn't be loaded : #{$!}"
           end
         end
       rescue
         warn "Error: Failed to load (#{file}) : #{$!}"
       end
-      puts "done"
+      STDERR.puts "done"
     end
   end
-  
+
   def save_object
-    save_object_file(SAVEDIR + OBJECT)
+    save_object_file(object_file)
   end
 
   def save_object_file(file)
     begin
-      print "Saving object (#{file}) ... "
+      STDERR.print "Saving object (#{file}) ... "
+      File.rename(file, "#{file}.old") if File.exist?(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
+        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
-          Marshal.dump(hash, f)
-          @config[:marshal] = MARSHAL
-        rescue
-          warn "Error: Failed to dump (#{file}) : #{$!}"
         end
+        Marshal.dump(hash, f)
+        @config[:marshal] = MARSHAL
       end
-      puts "done"
+      STDERR.puts "done"
     rescue
+      File.rename("#{file}.old", file) if File.exist?("#{file}.old")
       warn "Error: Failed to save (#{file}) : #{$!}"
     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(SAVEDIR + HISTORY)
+      load_history_file(history_file)
     end
   end
 
   def load_history_file(file)
     if File.exists?(file)
-      print "Loading history (#{file}) ... "
+      STDERR.print "Loading history (#{file}) ... "
       File.open(file).each do |line|
-        #Readline::HISTORY.push line.chomp
-	date, hist = line.chomp.split("\t")
-        Readline::HISTORY.push hist if hist
+        unless line[/^# /]
+          Readline::HISTORY.push line.chomp
+        end
       end
-      puts "done"
+      STDERR.puts "done"
     end
   end
   
+  # not used (use open_history/close_history instead)
   def save_history
     if @cache[:readline]
-      save_history_file(SAVEDIR + HISTORY)
+      save_history_file(history_file)
     end
   end
 
   def save_history_file(file)
     begin
-      print "Saving history (#{file}) ... "
+      STDERR.print "Saving history (#{file}) ... "
       File.open(file, "w") do |f|
         f.puts Readline::HISTORY.to_a
       end
-      puts "done"
+      STDERR.puts "done"
     rescue
       warn "Error: Failed to save (#{file}) : #{$!}"
     end
@@ -386,44 +447,44 @@ module Bio::Shell::Ghost
   end
 
   def script_begin
-    puts "-- 8< -- 8< -- 8< --  Script  -- 8< -- 8< -- 8< --"
+    STDERR.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 --"
+    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)
-        message = "Overwrite script file (#{SCRIPT})? [y/n] "
+      if File.exists?(script_file)
+        message = "Overwrite script file (#{script_file})? [y/n] "
       else
-        message = "Save script file (#{SCRIPT})? [y/n] "
+        message = "Save script file (#{script_file})? [y/n] "
       end
       if ask_yes_or_no(message)
-        save_script_file(SCRIPT)
+        save_script_file(script_file)
       else
-        puts " ... save aborted."
-      end 
+        STDERR.puts " ... save aborted."
+      end
     elsif @script_begin and @script_end and @script_begin - @script_end == 1
-      puts " ... script aborted."
+      STDERR.puts " ... script aborted."
     else
-      puts "Error: Script range #{@script_begin}..#{@script_end} is invalid"
+      STDERR.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|
+      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
-      puts "done"
+      STDERR.puts "done"
     rescue
       @script_begin = nil
       warn "Error: Failed to save (#{file}) : #{$!}"
@@ -439,8 +500,8 @@ module Bio::Shell::Ghost
 
   def splash_message_color
     str = splash_message
-    ruby = ESC_SEQ[:ruby]
-    none = ESC_SEQ[:none]
+    ruby = colors[:ruby]
+    none = colors[:none]
     return str.sub(/R u b y/) { "#{ruby}R u b y#{none}" }
   end
 
@@ -464,7 +525,7 @@ module Bio::Shell::Ghost
   def splash_message_action_color(message = nil)
     s = message || splash_message
     l = s.length
-    c = ESC_SEQ
+    c = colors
     x = " "
     0.step(l,2) do |i|
       l1 = l-i;  l2 = l1/2;  l4 = l2/2
@@ -480,7 +541,7 @@ module Bio::Shell::Ghost
   end
 
   def opening_splash
-    puts
+    STDERR.puts
     if @config[:splash]
       if @config[:color]
         splash_message_action_color
@@ -489,28 +550,28 @@ module Bio::Shell::Ghost
       end
     end
     if @config[:color]
-      print splash_message_color
+      STDERR.print splash_message_color
     else
-      print splash_message
+      STDERR.print splash_message
     end
-    puts
-    puts
-    print "  Version : BioRuby #{Bio::BIORUBY_VERSION.join(".")}"
-    print " / Ruby #{RUBY_VERSION}"
-    puts
-    puts
+    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
-    puts
-    puts
+    STDERR.puts
+    STDERR.puts
     if @config[:color]
-      print splash_message_color
+      STDERR.print splash_message_color
     else
-      print splash_message
+      STDERR.print splash_message
     end
-    puts
-    puts
+    STDERR.puts
+    STDERR.puts
   end
 
 end