jandot-bio 1.2.1

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb

@@ -0,0 +1,144 @@
+class BiorubyController < ApplicationController
+
+  HIDE_METHODS = Object.methods + [ "singleton_method_added" ]
+
+  HIDE_MODULES = [
+    Base64::Deprecated, Base64, PP::ObjectMixin, Bio::Shell,
+  ]
+  HIDE_MODULES << WEBrick if defined?(WEBrick)
+
+  HIDE_VARIABLES = [
+    "_", "irb", "_erbout",
+  ]
+
+  SECURITY_NOTICE = "For security purposes, this functionality is only available to local requests."
+
+  def index
+    unless local_request?
+      flash[:notice] = SECURITY_NOTICE
+    end
+  end
+
+  def evaluate
+    if local_request?
+      begin
+        @script = params[:script].strip
+
+        # write out to history
+        Bio::Shell.store_history(@script)
+
+        # evaluate ruby script
+        @result = eval(@script, Bio::Shell.cache[:binding])
+
+        # *TODO* need to handle with output of print/puts/p/pp etc. here
+        @output = nil
+      rescue
+        @result = $!
+        @output = nil
+      end
+    else
+      @result = SECURITY_NOTICE
+      @output = nil
+    end
+
+    @number = Bio::Shell.cache[:results].store(@script, @result, @output)
+
+    render :update do |page|
+      render_log(page)
+    end
+  end
+
+  def list_methods
+    number = params[:number].to_i
+
+    script, result, output = Bio::Shell.cache[:results].restore(number)
+    @class = result.class
+    @methods = (result.methods - HIDE_METHODS).sort
+
+    render :update do |page|
+      page.replace_html "methods_#{number}", :partial => "methods"
+      page.visual_effect :toggle_blind, "methods_#{number}", :duration => 0.5
+    end
+  end
+
+  def list_classes
+    number = params[:number].to_i
+
+    script, result, output = Bio::Shell.cache[:results].restore(number)
+    class_name = result.class
+    @class = class_name
+    @classes = []
+    loop do
+      @classes.unshift(class_name)
+      if class_name == Object
+        break
+      else
+        class_name = class_name.superclass
+      end
+    end
+
+    render :update do |page|
+      page.replace_html "classes_#{number}", :partial => "classes"
+      page.visual_effect :toggle_blind, "classes_#{number}", :duration => 0.5
+    end
+  end
+
+  def list_modules
+    number = params[:number].to_i
+
+    script, result, output = Bio::Shell.cache[:results].restore(number)
+    @class = result.class
+    @modules = result.class.included_modules - HIDE_MODULES
+
+    render :update do |page|
+      page.replace_html "modules_#{number}", :partial => "modules"
+      page.visual_effect :toggle_blind, "modules_#{number}", :duration => 0.5
+    end
+  end
+
+  def reload_script
+    number = params[:number].to_i
+
+    script, result, output = Bio::Shell.cache[:results].restore(number)
+
+    render :update do |page|
+      page.replace_html :script, script
+    end
+  end
+
+  def results
+    if Bio::Shell.cache[:results].number > 0
+      limit = params[:limit].to_i
+      max_num = Bio::Shell.cache[:results].number
+      min_num = [ max_num - limit + 1, 1 ].max
+      min_num = 1 if limit == 0
+
+      render :update do |page|
+        # delete all existing results in the current DOM for clean up
+        page.select(".log").each do |element|
+          #page.hide element
+          page.remove element
+        end
+
+        # add selected results to the current DOM
+        min_num.upto(max_num) do |@number|
+          #page.show "log_#{@number}"
+          @script, @result, @output = Bio::Shell.cache[:results].restore(@number)
+          if @script
+            render_log(page)
+          end
+        end
+      end
+    end
+  end
+
+  def commands
+    @bioruby_commands = Bio::Shell.private_instance_methods.sort
+  end
+
+  def history
+    @history = File.readlines(Bio::Shell.history_file)
+  end
+
+end
+

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb

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+module BiorubyHelper
+
+  include Bio::Shell
+
+  def project_workdir
+    if Bio::Shell.cache[:savedir].match(/\.bioruby$/)
+      Bio::Shell.cache[:workdir]
+    else
+      Bio::Shell.cache[:savedir]
+    end
+  end
+
+  def have_results
+    Bio::Shell.cache[:results].number > 0
+  end
+
+  def local_variables
+    eval("local_variables", Bio::Shell.cache[:binding]) -
+      BiorubyController::HIDE_VARIABLES
+  end
+
+  def render_log(page)
+    page.insert_html :top, :logs, :partial => "log"
+    page.replace_html "variables", :partial => "variables"
+    page.hide "methods_#{@number}"
+    page.hide "classes_#{@number}"
+    page.hide "modules_#{@number}"
+  end
+
+  def reference_link(class_or_module)
+    name = class_or_module.to_s
+    case name
+    when /Bio::(.+)/
+      path = $1.split('::').join('/')
+      url = "http://bioruby.org/rdoc/classes/Bio/#{path}.html"
+    when /Chem::(.+)/
+      path = $1.split('::').join('/')
+      url = "http://chemruby.org/rdoc/classes/Chem/#{path}.html"
+    else
+      path = name.split('::').join('/')
+      url = "http://www.ruby-doc.org/core/classes/#{path}.html"
+    end
+    return "<a href='#{url}'>#{name}</a>"
+  end
+
+end
+

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml

@@ -0,0 +1,8 @@
+<div id="command">
+<h2>BioRuby shell commands</h2>
+<ul>
+  <% @bioruby_commands.each do |cmd| %>
+  <li><%= cmd %></li>
+  <% end %>
+</ul>
+</div>

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml

@@ -0,0 +1,10 @@
+<div id="history">
+<h2>Command history</h2>
+<% @history.each do |line| %>
+<%   if line[/^# /] %>
+<div class="histtime"><%= line %></div>
+<%   else %>
+<div class="histline"><%= line %></div>
+<%   end %>
+<% end %>
+</div>

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml

@@ -0,0 +1,26 @@
+<div id="console">
+ <%- if flash[:notice] -%>
+  <div id="notice"><p><%= flash[:notice] %></p></div><br>
+ <%- end -%>
+ <% form_remote_tag(:url => {:action => "evaluate"}, :position => "top",
+      :before => %(Element.show('spinner')),
+      :complete => %(Element.hide('spinner'))) do %>
+  <img id="spinner" src="/images/bioruby/spinner.gif" style="display:none">
+  <b>BioRuby script:</b>
+  <br/>
+  <textarea id="script" name="script" rows=10 cols=80></textarea>
+  <br/>
+  <input type="submit" value="Evaluate">
+  <input type="reset" value="Clear">
+  &nbsp;&nbsp;
+  Show [
+  <%= link_to_remote "All",    :url => {:action => "results", :limit => 0} %> |
+  <%= link_to_remote "Last 5", :url => {:action => "results", :limit => 5} %> |
+  <%= link_to_remote "Previous", :url => {:action => "results", :limit => 1} %>
+  ] or <%= link_to "Hide", :action => "index" %> results<br/>
+ <% end %>
+</div>
+
+<div id="logs">
+</div>
+

data/lib/bio/shell/script.rb

@@ -0,0 +1,25 @@
+#
+# = bio/shell/script.rb - script mode for the BioRuby shell
+#
+# Copyright::   Copyright (C) 2006
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: script.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
+#
+
+module Bio::Shell
+
+  class Script
+
+    def initialize(script)
+      Bio::Shell.cache[:binding] = TOPLEVEL_BINDING
+      Bio::Shell.load_session
+      eval(File.read(script), TOPLEVEL_BINDING)
+      exit
+    end
+
+  end # Script
+
+end
+

data/lib/bio/shell/setup.rb

@@ -0,0 +1,109 @@
+#
+# = bio/shell/setup.rb - setup initial environment for the BioRuby shell
+#
+# Copyright::   Copyright (C) 2006
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: setup.rb,v 1.8 2007/06/28 11:21:40 k Exp $
+#
+
+require 'getoptlong'
+
+class Bio::Shell::Setup
+
+  def initialize
+    check_ruby_version
+
+    # command line options
+    getoptlong
+
+    # setup working directory
+    savedir = setup_savedir
+
+    # load configuration and plugins
+    Bio::Shell.configure(savedir)
+
+    # set default to irb mode
+    Bio::Shell.cache[:mode] = @mode || :irb
+
+    case Bio::Shell.cache[:mode]
+    when :web
+      # setup rails server
+      Bio::Shell::Web.new
+    when :irb
+      # setup irb server
+      Bio::Shell::Irb.new
+    when :script
+      # run bioruby shell script
+      Bio::Shell::Script.new(@script)
+    end
+  end
+
+  def check_ruby_version
+    if RUBY_VERSION < "1.8.2"
+      raise "BioRuby shell runs on Ruby version >= 1.8.2"
+    end
+  end
+
+  # command line argument (working directory or bioruby shell script file)
+  def getoptlong
+    opts = GetoptLong.new
+    opts.set_options(
+      [ '--rails',   '-r',  GetoptLong::NO_ARGUMENT ],
+      [ '--web',     '-w',  GetoptLong::NO_ARGUMENT ],
+      [ '--console', '-c',  GetoptLong::NO_ARGUMENT ],
+      [ '--irb',     '-i',  GetoptLong::NO_ARGUMENT ]
+    )
+    opts.each_option do |opt, arg|
+      case opt
+      when /--rails/, /--web/
+        @mode = :web
+      when /--console/, /--irb/
+        @mode = :irb
+      end
+    end
+  end
+
+  def setup_savedir
+    arg = ARGV.shift
+
+    # Options after the '--' argument are not parsed by GetoptLong and
+    # are passed to irb or rails.  This hack preserve the first option
+    # when working directory of the project is not given.
+    if arg and arg[/^-/]
+      ARGV.unshift arg
+      arg = nil
+    end
+
+    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
+
+end # Setup

data/lib/bio/shell/web.rb

@@ -0,0 +1,102 @@
+#
+# = bio/shell/web.rb - GUI for the BioRuby shell
+#
+# Copyright::   Copyright (C) 2006
+#               Nobuya Tanaka <t@chemruby.org>,
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: web.rb,v 1.5 2007/06/26 08:38:38 k Exp $
+#
+
+
+module Bio::Shell
+
+  class Web
+
+    def initialize
+      Bio::Shell.cache[:binding] = binding
+      Bio::Shell.cache[:results] ||= Results.new
+      install_rails
+      setup_rails
+      start_rails
+    end
+
+    private
+
+    def setup_rails
+      puts
+      puts ">>>"
+      puts ">>>  open http://localhost:3000/bioruby"
+      puts ">>>"
+      puts
+      puts '(You can change the port number by adding "-- -p 4000" option)'
+      puts
+    end
+
+    def install_rails
+      savedir = Bio::Shell.cache[:savedir]
+      path = File.join(savedir, "script", "generate")
+      unless File.exist?(path)
+        puts "Installing Rails application for BioRuby shell ... "
+        system("rails #{savedir}")
+        puts "done"
+      end
+      path = File.join(savedir, "app", "controllers", "bioruby_controller.rb")
+      unless File.exist?(path)
+        basedir = File.dirname(__FILE__)
+        puts "Installing Rails plugin for BioRuby shell ... "
+        FileUtils.cp_r("#{basedir}/rails/.", savedir)
+        Dir.chdir(savedir) do 
+          system("./script/generate bioruby shell")
+        end
+        puts "done"
+      end
+    end
+
+    def start_rails
+      begin
+        Bio::Shell.cache[:rails] = Thread.new do
+          Dir.chdir(Bio::Shell.cache[:savedir]) do
+            require './config/boot'
+            require 'commands/server'
+          end
+        end
+      end
+    end
+
+    class Results
+      attr_accessor :number, :script, :result, :output
+
+      def initialize
+        @number = 0
+        @script = []
+        @result = []
+        @output = []
+      end
+
+      def store(script, result, output)
+        @number += 1
+        @script[@number] = script
+        @result[@number] = result
+        @output[@number] = output
+        return @number
+      end
+
+      def restore(number)
+        return @script[number], @result[number], @output[number]
+      end
+    end
+
+  end
+
+  private
+
+  # *TODO* stop irb and start rails?
+  #def web
+  #end
+
+end
+
+
+