bio 1.0.0 → 1.1.0

data/lib/bio/shell/rails/public/robots.txt

@@ -1 +0,0 @@
-# See http://www.robotstxt.org/wc/norobots.html for documentation on how to use the robots.txt file

data/lib/bio/shell/rails/public/stylesheets/main.css

@@ -1,187 +0,0 @@
-body { background-color: #fff; color: #333; }
-
-body, p, td {
-  font-family: verdana, arial, helvetica, sans-serif;
-  font-size:   13px;
-  line-height: 18px;
-}
-
-pre {
-  background-color: #eee;
-  padding: 10px;
-  font-size: 11px;
-}
-
-a { color: #000; }
-a:visited { color: #666; }
-a:hover { color: #fff; background-color:#000; }
-
-.fieldWithErrors {
-  padding: 2px;
-  background-color: red;
-  display: table;
-}
-
-table {
-     text-align: top;
-     }
-
-#ErrorExplanation {
-  width: 400px;
-  border: 2px solid red;
-  padding: 7px;
-  padding-bottom: 12px;
-  margin-bottom: 20px;
-  background-color: #f0f0f0;
-}
-
-#ErrorExplanation h2 {
-  text-align: left;
-  font-weight: bold;
-  padding: 5px 5px 5px 15px;
-  font-size: 12px;
-  margin: -7px;
-  background-color: #c00;
-  color: #fff;
-}
-
-#ErrorExplanation p {
-  color: #333;
-  margin-bottom: 0;
-  padding: 5px;
-}
-
-#ErrorExplanation ul li {
-  font-size: 12px;
-  list-style: square;
-}
-
-h1{
-    color: #333;
-    padding: 10px;
-    margin: 12px;
-    }
-
-#banner{
-         margin-left: 5em;
-         margin-right: -6px;
-         text-align: center;
-         font-size: 30px;
-         border-top: 1px solid silver;
-         border-bottom: 1px solid silver;
-         padding: 10px 0px 10px 0px;
-         }
-
-tr{
-    vertical-align: top;
-    text-align: left;
-    }
-
-#side img{
-           background-color: black;
-           width:12em;
-           }
-
-#side{
-       position: absolute;
-       margin: -13px;
-       top: 1em;
-       left: 1em;
-       width: 10em;
-       }
-
-#side ul{
-          font-size: 13px;
-          margin: 0em;
-          }
-
-#side h2{
-          font-size: 12px;
-          text-align: center;
-          width: 13em;
-          background-color: black;
-          color: white;
-          }
-#side input{
-             text-align: center;
-             }
-
-#main {
-        margin-left: 10em;
-        padding-top: 4x;
-        padding-left: 2em;
-        background: white;
-        }
-
-.main {
-        margin-left: 10em;
-        padding-top: 4x;
-        padding-left: 2em;
-        background: white;
-        }
-
-#menu {
-        margin-left: 10em;
-        padding-top: 4x;
-        padding-left: 2em;
-        background: white;
-        }
-
-div.uploadStatus {
-  margin: 5px;
-}
-
-div.progressBar {
-  margin: 5px;
-}
-
-div.progressBar div.border {
-  background-color: #fff;
-  border: 1px solid grey;
-  width: 100%;
-}
-
-div.progressBar div.background {
-  background-color: #333;
-  height: 18px;
-  width: 0%;
-}
-
-.tabs {
-        position:relative;
-        height: 20px;
-        margin: 0;
-        padding: 0;
-        background: #aaa repeat-x;
-        overflow:hidden
-        }
-
-.tabs li {
-           display:inline;
-           }
-
-.tabs a:hover, .tabs a.tab-active {
-                                    color:#333;
-                                    background:#fff url("bar_on.gif") repeat-x;
-                                    border-right: 1px solid #fff
-                                    }
-
-
-.tabs a  {
-           height: 27px;
-           font:12px verdana, helvetica, sans-serif;
-           font-weight:bold;
-           position:relative;
-           padding:6px 10px 10px 10px;
-           margin: 0px -4px 0px 0px;
-           color:#333;
-           text-decoration:none;
-           border-left:1px solid #fff;
-           border-right:1px solid #333;
-           }
-.tab-container {
-                 background: #fff;
-                 border:1px solid #555;
-                 }
-.tab-panes {
-             margin: 3px }

data/lib/bio/shell/rails/script/about

@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-require File.dirname(__FILE__) + '/../config/boot'
-require 'commands/about'

data/lib/bio/shell/rails/script/breakpointer

@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-require File.dirname(__FILE__) + '/../config/boot'
-require 'commands/breakpointer'

data/lib/bio/shell/rails/script/console

@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-require File.dirname(__FILE__) + '/../config/boot'
-require 'commands/console'

data/lib/bio/shell/rails/script/destroy

@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-require File.dirname(__FILE__) + '/../config/boot'
-require 'commands/destroy'

data/lib/bio/shell/rails/script/generate

@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-require File.dirname(__FILE__) + '/../config/boot'
-require 'commands/generate'

data/lib/bio/shell/rails/script/performance/benchmarker

@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-require File.dirname(__FILE__) + '/../../config/boot'
-require 'commands/performance/benchmarker'

data/lib/bio/shell/rails/script/performance/profiler

@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-require File.dirname(__FILE__) + '/../../config/boot'
-require 'commands/performance/profiler'

data/lib/bio/shell/rails/script/plugin

@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-require File.dirname(__FILE__) + '/../config/boot'
-require 'commands/plugin'

data/lib/bio/shell/rails/script/process/reaper

@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-require File.dirname(__FILE__) + '/../../config/boot'
-require 'commands/process/reaper'

data/lib/bio/shell/rails/script/process/spawner

@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-require File.dirname(__FILE__) + '/../../config/boot'
-require 'commands/process/spawner'

data/lib/bio/shell/rails/script/process/spinner

@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-require File.dirname(__FILE__) + '/../../config/boot'
-require 'commands/process/spinner'

data/lib/bio/shell/rails/script/runner

@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-require File.dirname(__FILE__) + '/../config/boot'
-require 'commands/runner'

data/lib/bio/shell/rails/script/server

@@ -1,42 +0,0 @@
-#!/usr/bin/env ruby
-#
-# = BioRuby shell on Rails server - GUI for the BioRuby shell
-#
-# Copyright::   Copyright (C) 2006
-#               Nobuya Tanaka <t@chemruby.org>,
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     Ruby's
-#
-# $Id: server,v 1.1 2006/02/27 11:16:23 k Exp $
-#
-
-require 'bio/shell'
-require 'drb/drb'
-
-require './app/models/shell_connection'
-$drb_server = ShellConnection.new
-
-## Access Control List
-#
-# require 'drb/acl'
-#
-# list = %w(deny all
-#           allow 127.0.0.1
-#          )
-# acl = ACL.new(list, ACL::DENY_ALLOW)
-# DRb.install_acl(acl)
-#
-
-STDOUT.sync = true
-
-#uri = "druby://localhost:0"
-uri = 'druby://localhost:81064' # baioroji-
-DRb.start_service(uri, $drb_server)
-puts DRb.uri
-
-puts "starting ..."
-
-require './config/boot'
-require 'commands/server'
-
-puts "exiting ..."

data/lib/bio/shell/rails/test/test_helper.rb

@@ -1,28 +0,0 @@
-ENV["RAILS_ENV"] = "test"
-require File.expand_path(File.dirname(__FILE__) + "/../config/environment")
-require 'test_help'
-
-class Test::Unit::TestCase
-  # Transactional fixtures accelerate your tests by wrapping each test method
-  # in a transaction that's rolled back on completion.  This ensures that the
-  # test database remains unchanged so your fixtures don't have to be reloaded
-  # between every test method.  Fewer database queries means faster tests.
-  #
-  # Read Mike Clark's excellent walkthrough at
-  #   http://clarkware.com/cgi/blosxom/2005/10/24#Rails10FastTesting
-  #
-  # Every Active Record database supports transactions except MyISAM tables
-  # in MySQL.  Turn off transactional fixtures in this case; however, if you
-  # don't care one way or the other, switching from MyISAM to InnoDB tables
-  # is recommended.
-  self.use_transactional_fixtures = true
-
-  # Instantiated fixtures are slow, but give you @david where otherwise you
-  # would need people(:david).  If you don't want to migrate your existing
-  # test cases which use the @david style and don't mind the speed hit (each
-  # instantiated fixtures translates to a database query per test method),
-  # then set this back to true.
-  self.use_instantiated_fixtures  = false
-
-  # Add more helper methods to be used by all tests here...
-end