ngoto-bio 1.2.9.9001

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

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+/* body */
+
+body {
+	margin: 0;
+	color: #555555;
+	background: url("/images/bioruby/bg.gif") repeat-y center;
+	font-family: "trebuchet ms", verdana, arial, helvetica, sans-serif;
+	font-size: 12px;
+}
+
+div#content {
+	width: 750px;
+	height: auto;
+	margin: 0 auto 0 auto;
+	text-align: left;
+}
+
+/* title */
+
+div#title {
+	width: 550px;
+	padding-right: 200px;
+	margin-bottom: 20px;
+	text-align: left;
+	background: url("/images/bioruby/gem.png") no-repeat left bottom;
+}
+
+div#title .titletop {
+	color: #736451;
+	font-size: 30px;
+	font-weight: normal;
+	text-align: left;
+	text-indent: 70px;
+	margin: 0;
+	padding: 0;
+	padding-top: 20px;
+	margin-bottom: 10px;
+}
+
+div#title .titlesub {
+	color: #000000;
+	font-size: 15px;
+	font-weight: normal;
+	text-align: left;
+	text-indent: 70px;
+	margin: 0;
+	padding: 0;
+	border-bottom: 1px solid #eeeeee;
+}
+
+/* main */
+
+div#main {
+	width: 550px;
+	background-color: #ffffff;
+	padding-top: 0px;
+	padding-left: 10px;
+}
+
+div#notice {
+	background-color: #fcc;
+	border: 1px solid #f00;
+}
+
+div#notice p {
+	margin: 0;
+	padding: 10px;
+}
+
+pre {
+	color: #6e8377;
+	background-color: #eaedeb;
+	border-color: #6e8377;
+	border-style: dashed;
+	border-width: 1px;
+	padding: 5px;
+	width: 500px;
+	overflow: auto;
+}
+
+div.log {
+	width: 500px;
+	margin-top: 15px;
+	padding-top: 5px;
+	border-top: 1px dotted #333333;
+}
+
+div.log div.input pre.script {
+	background-color: #ffffeb;
+	border-style: solid;
+}
+
+div.log div.output div.methods {
+	padding: 5px;
+	background-color: #ffffdd;
+	border: 1px solid #ffcc00;
+}
+
+div.log div.output div.classes {
+	padding: 5px;
+	background-color: #ccffcc;
+	border: 1px solid #00ff00;
+}
+
+div.log div.output div.modules {
+	padding: 5px;
+	background-color: #ffcccc;
+	border: 1px solid #ff0000;
+}
+
+div.log div.output pre.result {
+	border-style: dashed;
+}
+
+div.log div.output pre.output {
+	border-style: dashed;
+}
+
+div.log hr.log {
+	border-style: dotted none none none;
+	border-top-width: 1px;
+	border-color: #6e8377;
+	width: 200px;
+	height: 1px;
+}
+
+/* side */
+
+div#side {
+	width: 150px;
+	float: right;
+	margin-top: 20px;
+	text-align: left;
+	font-size: 12px;
+	color: #e44268;
+}
+
+div#side div.title {
+	font-weight: normal;
+	color: #e44268;
+	text-align: left;
+	border-width: 0px 0px 1px 0px;
+	border-bottom: 1px solid #e44268;
+}
+
+div#side a:link {
+	color: #ffffff;
+	text-decoration: none;
+}
+
+div#side a:visited {
+	color: #ffffff;
+	text-decoration: none;
+}
+
+div#side a:hover {
+	color: #cccccc;
+	text-decoration: underline;
+}
+
+div#side ol,ul {
+	margin: 10px;
+	padding-left: 10px;
+}
+
+div#side li {
+	color: #e44268;
+}
+
+div#side img {
+	padding: 5px;
+	/* centering */
+	display: block;
+	margin-left: auto;
+	margin-right: auto;
+	border: 0px;
+}
+
+/* history */
+
+div#history {
+	width: 500px;
+}
+
+div#history div.histtime {
+	background-color: #eaedeb;
+	padding: 5px;
+}
+
+div#history div.histline {
+	background-color: #ffffeb;
+	padding: 5px;
+	font-family: monospace;
+	white-space: pre;
+}
+
+/* command */
+
+div#command {
+	width: 500px;
+}
+
+/* image */
+
+img {
+}
+
+/* em */
+
+em {
+	color: #6e8377;
+	font-style: normal;
+}
+
+/* link */
+
+a {
+	text-decoration: none;
+}
+
+a:link {
+	color: #669933;
+}
+
+a:visited {
+	color: #669933;
+}
+
+a:hover {
+	text-decoration: underline;
+}
+
+/* header */
+
+h1 {
+	font-size: 180%;
+	color: #ffffff;
+	background-color: #6e8377;
+	line-height: 64px;
+	text-align: left;
+	padding-left: 20px;
+}
+
+h2 {
+	font-size: 160%;
+	color: #6e8377;
+	border-color: #b9c3be;
+	border-style: dashed;
+	border-width: 0px 0px 1px 0px;
+}
+
+h3 {
+	font-size: 140%;
+	color: #6e8377;
+	border-color: #b9c3be;
+	border-style: dotted;
+	border-width: 0px 0px 1px 0px;
+}
+
+h4 {
+	font-size: 130%;
+	color: #6e8377;
+	border-color: #b9c3be;
+	border-style: solid;
+	border-width: 0px 0px 1px 0px;
+}
+
+h5 {
+	font-size: 120%;
+	color: #6e8377;
+}
+
+h6 {
+	font-size: 110%;
+	color: #6e8377;
+}
+
+/* list */
+
+dt {
+	color: #6e8377;
+	border-color: #b9c3be;
+	border-style: dashed;
+	border-width: 1px;
+	padding: 5px;
+}
+
+ul {
+	color: #6e8377;
+}
+
+/* table */
+
+table {
+	border: 1px solid #cccccc;
+	border-collapse: collapse;
+}
+
+th {
+	vertical-align: top;
+	padding: 5px;
+}
+
+td {
+	vertical-align: top;
+	padding: 5px;
+}
+
+div#method_list table {
+	border: none;
+}
+
+
+/* form */
+
+input {
+	background-color: #FFFFFF;
+	padding: 2px;
+	font-size: 10px;
+	color: #666666;
+	border: 1px solid #611022;
+	margin-bottom: 2px;
+}
+
+input[type=submit] {
+	background-color: #FFFFFF;
+	padding: 2px;
+	font-size: 10px;
+	color: #ffffff;
+	border: 1px solid #611022;
+	background-color: #E44268;
+	margin-bottom: 2px;
+}
+
+/* textarea */
+
+textarea {
+	background-color: #eaedeb;
+	font-family: monospace;
+	font-size: 12px;
+	overflow: auto;
+	width: 500px;
+	padding: 5px;
+}
+
+
+/* blockquote */
+
+blockquote {
+	color: #6e8377;
+	background-color: #eaedeb;
+	border-color: #6e8377;
+	border-style: dashed;
+	border-width: 1px;
+}
+
+/* media */
+
+@media print {
+	div#main	{ margin-left: 0px; }
+	div#side	{ display: none; }
+}
+
+@media screen {
+	div#main	{ margin-left: 0px; }
+	div#side	{ display: block; }
+}
+

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

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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />	
+<title>BioRuby shell on Rails</title>
+<%= stylesheet_link_tag "bioruby.css" %>
+<%= javascript_include_tag :defaults %>
+</head>
+
+<body>
+
+<div id="content">
+
+ <div id="side">
+  <div class="title">Project</div>
+  <ul>
+   <li><%= link_to "#{File.basename(project_workdir)}", "file://#{project_workdir}" %>
+  </ul>
+
+  <div class="title">Functions</div>
+  <ul>
+    <li><%= link_to "Console", :action => "index" %></li>
+    <li><%= link_to "History", :action => "history" %></li>
+    <li><%= link_to "Commands", :action => "commands" %></li>
+  </ul>
+
+  <div class="title">Local variables</div>
+  <%= render :partial => "variables" %>
+
+  <br>
+  <a href="http://bioruby.org/"><img src="/images/bioruby/link.gif" border=0></a>
+ </div><!-- side -->
+
+ <div id="title">
+  <p class="titletop">BioRuby shell on Rails</p>
+  <p class="titlesub">Web interface for the BioRuby library</p>
+ </div><!-- title -->
+
+ <div id="main">
+<%= yield %>
+ </div><!-- main -->
+
+</div><!-- content -->
+
+</body>
+
+</html>

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

@@ -0,0 +1,47 @@
+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
+