[BioRuby-cvs] bioruby/lib/bio/shell core.rb, 1.26, 1.27 setup.rb, 1.7, 1.8

Thu Jun 28 11:21:42 UTC 2007

Update of /home/repository/bioruby/bioruby/lib/bio/shell
In directory dev.open-bio.org:/tmp/cvs-serv2894

Modified Files:
	core.rb setup.rb 
Log Message:
* fixed to accept absolute path in the command line option of the session
  storing directory. e.g. following 2 examples run as expected.

    $ bioruby foo/bar
    $ bioruby /tmp/foo/bar

* Bio::Shell.cache[:savedir] always stores the bioruby shell storing directory,
  Bio::Shell.cache[:workdir] always stores the working directory at start up
  (both are converted to full path allowing user to use Dir.chdir in the 
  shell session).

* if --rails (-r) option is applied, bioruby command will run in the rails mode,
  and rails server will start in the :savedir, otherwise run in the current
  directory in the irb mode.

Note: "session" means shell/session/{config,history,object} files
in the following explanations.

=== IRB mode ===

1. run in the current directory and the session will be saved
   in the ~/.bioruby directory

     $ bioruby

2. run in the current directory and the session will be saved
   in the foo/bar directory

     $ bioruby foo/bar

3. run in the current directory and the session will be saved
   in the /tmp/foo/bar directory

     $ bioruby /tmp/foo/bar

=== Rails mode ===

4. run in the ~/.bioruby directory and the session will be also saved
   in the ~/.bioruby directory

    $ bioruby -r

5. run in the foo/bar directory and the session will be also saved
   in the foo/bar directory

    $ bioruby -r foo/bar

6. run in the /tmp/foo/bar directory and the session will be also saved
   in the /tmp/foo/bar directory

    $ bioruby -r /tmp/foo/bar

=== Script mode ===

7. run in the current directory using the session saved
   in the ~/.bioruby directory.

    $ bioruby ~/.bioruby/shell/script.rb

7'. run in the current directory using the session saved
   in the foo/bar directory.

    $ bioruby foo/bar/shell/script.rb

7''. run in the current directory using the session saved
   in the /tmp/foo/bar directory.

    $ bioruby /tmp/foo/bar/shell/script.rb

Essentially, no difference among these three (7, 7', and 7'') examples.

Index: setup.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/setup.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** setup.rb	26 Jun 2007 08:38:38 -0000	1.7
--- setup.rb	28 Jun 2007 11:21:40 -0000	1.8
***************
*** 20,28 ****

      # setup working directory
!     workdir = setup_workdir

      # load configuration and plugins
!     #Dir.chdir(workdir) if workdir # changed not chdir
!     Bio::Shell.configure(workdir)

      # set default to irb mode
--- 20,27 ----

      # setup working directory
!     savedir = setup_savedir

      # load configuration and plugins
!     Bio::Shell.configure(savedir)

      # set default to irb mode
***************
*** 67,71 ****
    end

!   def setup_workdir
      arg = ARGV.shift

--- 66,70 ----
    end

!   def setup_savedir
      arg = ARGV.shift

***************
*** 80,104 ****
      if arg.nil?
        # run in the current directory
!       workdir = File.join(ENV['HOME'].to_s, ".bioruby")
!       install_workdir(workdir)
!     elsif File.directory?(arg)
!       # run in the existing directory
!       workdir = File.join(Dir.pwd, arg)
      elsif File.file?(arg)
!       # run file as a bioruby shell script (slightly tricky)
!       workdir = File.join(File.dirname(arg), "..")
        @script = arg
        @mode = :script
      else
!       # run in new directory
!       workdir = File.join(Dir.pwd, arg)
!       install_workdir(workdir)
      end

!     return workdir
    end

!   def install_workdir(workdir)
!     FileUtils.mkdir_p(workdir)
    end

--- 79,108 ----
      if arg.nil?
        # run in the current directory
!       if File.exist?(Bio::Shell::Core::HISTORY)
!         savedir = Dir.pwd
!       else
!         savedir = File.join(ENV['HOME'].to_s, ".bioruby")
!         install_savedir(savedir)
!       end
      elsif File.file?(arg)
!       # run file as a bioruby shell script
!       savedir = File.join(File.dirname(arg), "..")
        @script = arg
        @mode = :script
      else
!       # run in new or existing directory
!       if arg[/^#{File::SEPARATOR}/]
!         savedir = arg
!       else
!         savedir = File.join(Dir.pwd, arg)
!       end
!       install_savedir(savedir)
      end

!     return savedir
    end

!   def install_savedir(savedir)
!     FileUtils.makedirs(savedir)
    end

Index: core.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/core.rb,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** core.rb	26 Jun 2007 08:38:38 -0000	1.26
--- core.rb	28 Jun 2007 11:21:40 -0000	1.27
***************
*** 11,19 ****
  module Bio::Shell::Core

-   # TODO:
-   # * load history from current and savedir
-   # * don'nt show history saved when exit 'no save' mode
-   # * replace File to Pathname
-   
    SHELLDIR = "shell"
    DATADIR  = "data"
--- 11,14 ----
***************
*** 118,132 ****
    ### save/restore the environment

!   def configure(workdir)
!     if workdir == File.join(ENV['HOME'].to_s, ".bioruby")
!       savedir = workdir
!       workdir = Dir.pwd
!     else
!       savedir = workdir
!     end
      @config = {}
      @cache  = {
-       :workdir => workdir,
        :savedir => savedir,
      }
      create_save_dir
--- 113,121 ----
    ### save/restore the environment

!   def configure(savedir)
      @config = {}
      @cache  = {
        :savedir => savedir,
+       :workdir => Dir.pwd,
      }
      create_save_dir
***************
*** 146,159 ****
    def save_session
      unless @cache[:mode] == :script
-       close_history
        closing_splash
      end
      if create_save_dir_ask
        #save_history	# changed to use our own...
        save_object
        save_config
      end
      #STDERR.puts "Leaving directory '#{@cache[:workdir]}'"
-     STDERR.puts "History is saved in '#{history_file}'"
    end

--- 135,147 ----
    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

***************
*** 188,192 ****
        begin
          STDERR.print "Creating directory (#{dir}) ... "
!         FileUtils.mkdir_p(dir)
          STDERR.puts "done"
        rescue
--- 176,180 ----
        begin
          STDERR.print "Creating directory (#{dir}) ... "
!         FileUtils.makedirs(dir)
          STDERR.puts "done"
        rescue
***************
*** 201,205 ****
      dir = File.join(bioflat_dir, dbname.to_s.strip)
      unless File.directory?(dir)
!       FileUtils.mkdir_p(dir)
      end
      return dir
--- 189,193 ----
      dir = File.join(bioflat_dir, dbname.to_s.strip)
      unless File.directory?(dir)
!       FileUtils.makedirs(dir)
      end
      return dir
***************
*** 392,396 ****

    def close_history
!     @cache[:histfile].close if @cache[:histfile]
    end

--- 380,388 ----

    def close_history
!     if @cache[:histfile]
!       STDERR.print "Saving history (#{history_file}) ... "
!       @cache[:histfile].close
!       STDERR.puts "done"
!     end
    end

***************
*** 409,414 ****
          end
        end
      end
-     STDERR.puts "done"
    end

--- 401,406 ----
          end
        end
+       STDERR.puts "done"
      end
    end