bio 0.7.1 → 1.0.0

data/lib/bio/shell/plugin/flatfile.rb

@@ -1,29 +1,11 @@
 #
 # = bio/shell/plugin/flatfile.rb - plugin for flatfile database
 #
-# Copyright::	Copyright (C) 2005
-#		Toshiaki Katayama <k@bioruby.org>
-# License::	LGPL
+# Copyright::   Copyright (C) 2005
+#               Toshiaki Katayama <k@bioruby.org>
+# License:      Ruby's
 #
-# $Id: flatfile.rb,v 1.11 2005/11/30 01:57:18 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
-#
-#++
+# $Id: flatfile.rb,v 1.12 2006/02/09 20:48:53 k Exp $
 #
 
 module Bio::Shell
@@ -86,8 +68,8 @@ module Bio::Shell
   end
 
   def flatindex(dbname, *flatfiles)
-    dir = Bio::Shell.create_flat_dir(dbname)
     begin
+      dir = Bio::Shell.create_flat_dir(dbname)
       print "Creating BioFlat index (#{dir}) ... "
       bdb = format = options = nil
       Bio::FlatFileIndex.makeindex(bdb, dir, format, options, *flatfiles)

data/lib/bio/shell/plugin/keggapi.rb

@@ -1,29 +1,11 @@
 #
 # = bio/shell/plugin/keggapi.rb - plugin for KEGG API
 #
-# Copyright::	Copyright (C) 2005
-#		Toshiaki Katayama <k@bioruby.org>
-# License::	LGPL
+# Copyright::   Copyright (C) 2005
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     Ruby's
 #
-# $Id: keggapi.rb,v 1.8 2005/12/18 15:47:33 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
-#
-#++
+# $Id: keggapi.rb,v 1.10 2006/02/09 20:48:53 k Exp $
 #
 
 module Bio::Shell
@@ -40,8 +22,13 @@ module Bio::Shell
 
   private
 
-  def keggapi
-    @keggapi ||= Bio::KEGG::API.new  
+  def keggapi(wsdl = nil)
+    if wsdl
+      @keggapi = Bio::KEGG::API.new(wsdl)
+    else
+      @keggapi ||= Bio::KEGG::API.new
+    end
+    return @keggapi
   end
 
   # DBGET

data/lib/bio/shell/plugin/midi.rb

@@ -1,30 +1,12 @@
 #
 # = bio/shell/plugin/midi.rb - Sequence to MIDI converter
 #
-# Copyright::	Copyright (C) 2003, 2005
-#		Natsuhiro Ichinose <ichinose@genome.ist.i.kyoto-u.ac.jp>,
-#		Toshiaki Katayama <k@bioruby.org>
-# License::	LGPL
+# Copyright::   Copyright (C) 2003, 2005
+#               Natsuhiro Ichinose <ichinose@genome.ist.i.kyoto-u.ac.jp>,
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     Ruby's
 #
-# $Id: midi.rb,v 1.6 2005/11/28 12:06:18 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
-#
-#++
+# $Id: midi.rb,v 1.7 2006/02/09 20:48:53 k Exp $
 #
 
 #--

data/lib/bio/shell/plugin/obda.rb

@@ -1,29 +1,11 @@
 #
 # = bio/shell/plugin/obda.rb - plugin for OBDA
 #
-# Copyright::	Copyright (C) 2005
-#		Toshiaki Katayama <k@bioruby.org>
-# License::	LGPL
+# Copyright::   Copyright (C) 2005
+#               Toshiaki Katayama <k@bioruby.org>
+# License:      Ruby's
 #
-# $Id: obda.rb,v 1.8 2005/11/30 02:01:04 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
-#
-#++
+# $Id: obda.rb,v 1.9 2006/02/09 20:48:53 k Exp $
 #
 
 module Bio::Shell

data/lib/bio/shell/plugin/seq.rb

@@ -1,29 +1,11 @@
 #
 # = bio/shell/plugin/seq.rb - plugin for biological sequence manipulations
 #
-# Copyright::	Copyright (C) 2005
-#		Toshiaki Katayama <k@bioruby.org>
-# License::	LGPL
+# Copyright::   Copyright (C) 2005
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     Ruby's
 #
-# $Id: seq.rb,v 1.16 2005/12/19 01:20:06 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
-#
-#++
+# $Id: seq.rb,v 1.17 2006/02/09 20:48:53 k Exp $
 #
 
 module Bio::Shell
@@ -210,14 +192,14 @@ class String
     while n < self.length
       pos = self[n, size].rindex(separater)
 
-      if self[n, size].length < size	# last line of the folded str
+      if self[n, size].length < size    # last line of the folded str
         pos = nil
       end
 
       if pos
         ary << self[n, pos+separater.length]
         n += pos + separater.length
-      else				# line too long or the last line
+      else                              # line too long or the last line
         ary << self[n, size]
         n += size
       end

data/lib/bio/shell/rails/Rakefile

@@ -0,0 +1,10 @@
+# Add your own tasks in files placed in lib/tasks ending in .rake,
+# for example lib/tasks/switchtower.rake, and they will automatically be available to Rake.
+
+require(File.join(File.dirname(__FILE__), 'config', 'boot'))
+
+require 'rake'
+require 'rake/testtask'
+require 'rake/rdoctask'
+
+require 'tasks/rails'

data/lib/bio/shell/rails/app/controllers/application.rb

@@ -0,0 +1,4 @@
+# Filters added to this controller will be run for all controllers in the application.
+# Likewise, all the methods added will be available for all controllers.
+class ApplicationController < ActionController::Base
+end

data/lib/bio/shell/rails/app/controllers/shell_controller.rb

@@ -0,0 +1,94 @@
+class DocumentRegistry
+
+  @@registry = []
+
+  def self.[](class_name)
+    @@registry.each do |block|
+      url = block.call(class_name)
+      return url if url
+    end
+    ""
+  end
+
+  def self.register &block
+    @@registry.push(block)
+  end
+
+end
+
+DocumentRegistry.register() do |class_name|
+  if m = /Bio::(.+)/.match(class_name)
+    "http://bioruby.org/rdoc/classes/Bio/#{m[1].split('::').join('/')}.html"
+  else
+    false
+  end
+end
+
+DocumentRegistry.register do |class_name|
+  if m = /Chem::(.+)/.match(class_name)
+    "http://chemruby.org/rdoc/classes/Chem/#{m[1].split('::').join('/')}.html"
+  else
+    false
+  end
+end
+
+DocumentRegistry.register do |class_name|
+  "http://www.ruby-doc.org/core/classes/#{class_name.split('::').join('/')}.html"
+end
+
+
+class ShellController < ApplicationController
+
+  layout 'shell'  #, :except => [:rss_feed, :rss_with_content]
+
+  def index
+    setup
+  end
+
+  def show
+    setup
+    @obj = $drb_server[params[:id]]
+    if @obj.nil?
+      @inheritance = "<h1>Unknown local variable! : #{params[:var]}</h1>"
+    else
+      @inheritance = get_inheritance @obj.class
+      if @obj.respond_to?(:to_html)
+        @contents = @obj.to_html
+      else
+        @contents = "Undefined :to_html"
+      end
+    end
+    @title = params[:id]
+  end
+
+=begin
+  def history
+    setup
+    @history = File.read("session/history")
+  end
+=end
+
+  private
+
+  def setup
+    @local_vars = $drb_server.registry
+  end
+  
+  def get_inheritance obj
+    #    mods = obj.included_modules - [PP::ObjectMixin, Bio::Shell, WEBrick]
+    mods = obj.included_modules
+    module_links = mods.collect{|m|
+      " [<a href=#{DocumentRegistry[m.to_s]}>#{m.to_s}</a>] "
+    }.join("|")
+
+    inherit = []
+    loop do
+      inherit.push(" [<a href=#{DocumentRegistry[obj.to_s]}>#{obj.to_s}</a>] ")
+      break if obj == Object
+      obj = obj.superclass
+    end
+    "<table><tr><th>Inheritance</th><td>" +  inherit.join(" &lt; ") + "</td></tr>" +
+      "<tr><th>Mix-in</th><td>" + module_links + "</td</tr></table>"
+  end
+
+end

data/lib/bio/shell/rails/app/helpers/application_helper.rb

@@ -0,0 +1,3 @@
+# Methods added to this helper will be available to all templates in the application.
+module ApplicationHelper
+end

data/lib/bio/shell/rails/app/models/shell_connection.rb

@@ -0,0 +1,30 @@
+# Model object for rails
+class ShellConnection
+
+# include DRb::DRbObservable
+
+  attr_reader :registry
+
+  def puts_remote(str)
+    STDOUT.puts(str)
+  end
+
+  def initialize
+    @connected = false
+    @registry = {}
+  end
+
+  def [] o_id
+    @registry[o_id]
+  end
+
+  def []=(name, obj)
+    @registry[name] = obj
+  end
+
+  def delete(name)
+    @registry.delete(name)
+  end
+
+end
+

data/lib/bio/shell/rails/app/views/layouts/shell.rhtml

@@ -0,0 +1,37 @@
+<html>
+<head>
+  <title>BioRuby shell on Rails</title>
+  <link href="/stylesheets/main.css" media="screen" rel="Stylesheet" type="text/css" />
+</head>
+<body>
+
+<div id="side">
+  <img src="/images/icon.png">
+  <br>
+<!--
+  <h2>Status</h2>
+  <ul><li><%= @connected ? "Not Connected" : "Connected" %></li></ul>
+  <h2>History</h2>
+  <ul>
+    <li>
+      <%= link_to "History", :action => "history" %>
+    </li>
+  </ul>
+-->
+  <h2>Local variables</h2>
+  <ul>
+  <% @local_vars.each do |idx, var| %>
+  <li><%= link_to idx, {:action => "show", :id => idx}%></li>
+  <% end %>
+  </ul>
+
+</div>
+
+<div id="banner">
+  BioRuby shell on Rails
+</div>
+
+<div id="main">
+  <%= @content_for_layout %>
+</div>
+</body>

data/lib/bio/shell/rails/app/views/shell/history.rhtml

@@ -0,0 +1,5 @@
+<!-- this file is temprally not used -- see shell_controller.rb#history -->
+<pre>
+<%= @history %>
+</pre>
+

data/lib/bio/shell/rails/app/views/shell/index.rhtml

@@ -0,0 +1,2 @@
+
+<h2>Connected!</h2>

data/lib/bio/shell/rails/app/views/shell/show.rhtml

@@ -0,0 +1,13 @@
+<%= @inheritance %>
+
+<%= @contents %>
+
+<%= form_tag(:action => "show")%>
+<!--
+<table>
+  <tr><th>Memo</th></tr>
+  <tr><td><input type="submit"></td></tr>
+</table>
+-->
+<%= end_form_tag %>
+

data/lib/bio/shell/rails/config/boot.rb

@@ -0,0 +1,19 @@
+# Don't change this file. Configuration is done in config/environment.rb and config/environments/*.rb
+
+unless defined?(RAILS_ROOT)
+  root_path = File.join(File.dirname(__FILE__), '..')
+  unless RUBY_PLATFORM =~ /mswin32/
+    require 'pathname'
+    root_path = Pathname.new(root_path).cleanpath(true).to_s
+  end
+  RAILS_ROOT = root_path
+end
+
+if File.directory?("#{RAILS_ROOT}/vendor/rails")
+  require "#{RAILS_ROOT}/vendor/rails/railties/lib/initializer"
+else
+  require 'rubygems'
+  require 'initializer'
+end
+
+Rails::Initializer.run(:set_load_path)