[BioRuby-cvs] bioruby/bin bioruby,1.16,1.17

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/bin
In directory dev.open-bio.org:/tmp/cvs-serv9398/bin

Modified Files:
	bioruby 
Log Message:
* New BioRuby shell with Ruby on Rails generator functionality is integrated.


Index: bioruby
===================================================================
RCS file: /home/repository/bioruby/bioruby/bin/bioruby,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** bioruby	25 Jul 2006 18:16:28 -0000	1.16
--- bioruby	24 Dec 2006 08:32:08 -0000	1.17
***************
*** 15,151 ****
  rescue LoadError
  end
- 
- 
- ### BioRuby shell setup
- 
  require 'bio/shell'
  
  include Bio::Shell
  
! # command line argument (working directory or bioruby shell script file)
! workdir = nil
! script = nil
! if arg = ARGV.shift
!   if File.directory?(arg)
!     # directory or symlink to directory
!     workdir = arg
!     Dir.chdir(workdir)
!   elsif File.exists?(arg)
!     # BioRuby shell script (load script after the previous session is restored)
!     workdir = File.dirname(arg)
!     script = File.basename(arg)
!     Dir.chdir(workdir)
!   else
!     workdir = arg
!     Dir.mkdir(workdir)
!     Dir.chdir(workdir)
!   end
! else
!   unless File.exists?(Bio::Shell.history)
!     message = "Are you sure to start new session in this directory? [y/n] "
!     unless Bio::Shell.ask_yes_or_no(message)
!       exit
!     end
!   end
! end
! 
! # loading configuration and plugins
! Bio::Shell.setup
! 
! 
! ### IRB setup
! 
! require 'irb'
! begin
!   require 'irb/completion'
!   Bio::Shell.cache[:readline] = true
! rescue LoadError
!   Bio::Shell.cache[:readline] = false
! end
! 
! IRB.setup(nil)
! 
! # set application name
! IRB.conf[:AP_NAME] = 'bioruby'
! 
! # change prompt for bioruby
! $_ = Bio::Shell.esc_seq
! IRB.conf[:PROMPT][:BIORUBY_COLOR] = {
!   :PROMPT_I => "bio#{$_[:ruby]}ruby#{$_[:none]}> ",
!   :PROMPT_S => "bio#{$_[:ruby]}ruby#{$_[:none]}%l ",
!   :PROMPT_C => "bio#{$_[:ruby]}ruby#{$_[:none]}+ ",
!   :RETURN   => "  ==> %s\n"
! }
! IRB.conf[:PROMPT][:BIORUBY] = {
!   :PROMPT_I => "bioruby> ",
!   :PROMPT_S => "bioruby%l ",
!   :PROMPT_C => "bioruby+ ",
!   :RETURN   => "  ==> %s\n"
! }
! if Bio::Shell.config[:color]
!   IRB.conf[:PROMPT_MODE] = :BIORUBY_COLOR
! else
!   IRB.conf[:PROMPT_MODE] = :BIORUBY
! end
! IRB.conf[:ECHO] = Bio::Shell.config[:echo] || false
! 
! # irb/input-method.rb >= v1.5 (not in 1.8.2)
! #IRB.conf[:SAVE_HISTORY] = 100000
! 
! # not beautifully works
! #IRB.conf[:AUTO_INDENT] = true
! 
! 
! ### Start IRB
! 
! irb = IRB::Irb.new
! 
! # needed for method completion
! IRB.conf[:MAIN_CONTEXT] = irb.context
  
  # loading workspace and command history
  Bio::Shell.load_session
  
- if script
-   load script
-   exit
- end
- 
- Bio::Shell.create_save_dir
- 
- $history_file = File.open(Bio::Shell.history, "a")
- $history_file.sync = true
- 
- # overwrite gets to store history with time stamp
- io = IRB.conf[:MAIN_CONTEXT].io
- 
- io.class.class_eval do
-   alias_method :irb_original_gets, :gets
- end
- 
- def io.gets
-   line = irb_original_gets
-   $history_file.puts "#{Time.now}\t#{line}" if line
-   line
- end
- 
  # main loop
! Signal.trap("SIGINT") do
!   irb.signal_handle
! end
! 
! catch(:IRB_EXIT) do
!   irb.eval_input
! end
! 
! $history_file.close if $history_file
  
! # shut down the rails server
! if $web_server
!   $web_server.each do |io|
!     io.close
    end
-   $web_access_log.close if $web_access_log
-   $web_error_log.close if $web_error_log
  end
  
--- 15,40 ----
  rescue LoadError
  end
  require 'bio/shell'
  
+ # required to run commands (getseq, ls etc.)
  include Bio::Shell
  
! # setup command line options, working directory, and irb configurations
! Bio::Shell::Setup.new
  
  # loading workspace and command history
  Bio::Shell.load_session
  
  # main loop
! if Bio::Shell.cache[:rails]
!   Bio::Shell.cache[:rails].join
! else
!   Signal.trap("SIGINT") do
!     Bio::Shell.cache[:irb].signal_handle
!   end
  
!   catch(:IRB_EXIT) do
!     Bio::Shell.cache[:irb].eval_input
    end
  end
  
***************
*** 153,160 ****
  Bio::Shell.save_session
  
- if workdir
-   puts "Leaving directory '#{workdir}'."
-   puts "History is saved in '#{workdir}/#{Bio::Shell.history}'."
- end
- 
- 
--- 42,43 ----