search_biomodel 0.1.2 → 1.0.0

data/search_biomodel/ruby/1.8/gems/rack-1.3.0/lib/rack/session/memcache.rb

@@ -0,0 +1,93 @@
+# AUTHOR: blink <blinketje@gmail.com>; blink#ruby-lang@irc.freenode.net
+
+require 'rack/session/abstract/id'
+require 'memcache'
+
+module Rack
+  module Session
+    # Rack::Session::Memcache provides simple cookie based session management.
+    # Session data is stored in memcached. The corresponding session key is
+    # maintained in the cookie.
+    # You may treat Session::Memcache as you would Session::Pool with the
+    # following caveats.
+    #
+    # * Setting :expire_after to 0 would note to the Memcache server to hang
+    #   onto the session data until it would drop it according to it's own
+    #   specifications. However, the cookie sent to the client would expire
+    #   immediately.
+    #
+    # Note that memcache does drop data before it may be listed to expire. For
+    # a full description of behaviour, please see memcache's documentation.
+
+    class Memcache < Abstract::ID
+      attr_reader :mutex, :pool
+
+      DEFAULT_OPTIONS = Abstract::ID::DEFAULT_OPTIONS.merge \
+        :namespace => 'rack:session',
+        :memcache_server => 'localhost:11211'
+
+      def initialize(app, options={})
+        super
+
+        @mutex = Mutex.new
+        mserv = @default_options[:memcache_server]
+        mopts = @default_options.reject{|k,v| !MemCache::DEFAULT_OPTIONS.include? k }
+
+        @pool = options[:cache] || MemCache.new(mserv, mopts)
+        unless @pool.active? and @pool.servers.any?{|c| c.alive? }
+          raise 'No memcache servers'
+        end
+      end
+
+      def generate_sid
+        loop do
+          sid = super
+          break sid unless @pool.get(sid, true)
+        end
+      end
+
+      def get_session(env, sid)
+        with_lock(env, [nil, {}]) do
+          unless sid and session = @pool.get(sid)
+            sid, session = generate_sid, {}
+            unless /^STORED/ =~ @pool.add(sid, session)
+              raise "Session collision on '#{sid.inspect}'"
+            end
+          end
+          [sid, session]
+        end
+      end
+
+      def set_session(env, session_id, new_session, options)
+        expiry = options[:expire_after]
+        expiry = expiry.nil? ? 0 : expiry + 1
+
+        with_lock(env, false) do
+          @pool.set session_id, new_session, expiry
+          session_id
+        end
+      end
+
+      def destroy_session(env, session_id, options)
+        with_lock(env) do
+          @pool.delete(session_id)
+          generate_sid unless options[:drop]
+        end
+      end
+
+      def with_lock(env, default=nil)
+        @mutex.lock if env['rack.multithread']
+        yield
+      rescue MemCache::MemCacheError, Errno::ECONNREFUSED
+        if $VERBOSE
+          warn "#{self} is unable to find memcached server."
+          warn $!.inspect
+        end
+        default
+      ensure
+        @mutex.unlock if @mutex.locked?
+      end
+
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/rack-1.3.0/lib/rack/session/pool.rb

@@ -0,0 +1,79 @@
+# AUTHOR: blink <blinketje@gmail.com>; blink#ruby-lang@irc.freenode.net
+# THANKS:
+#   apeiros, for session id generation, expiry setup, and threadiness
+#   sergio, threadiness and bugreps
+
+require 'rack/session/abstract/id'
+require 'thread'
+
+module Rack
+  module Session
+    # Rack::Session::Pool provides simple cookie based session management.
+    # Session data is stored in a hash held by @pool.
+    # In the context of a multithreaded environment, sessions being
+    # committed to the pool is done in a merging manner.
+    #
+    # The :drop option is available in rack.session.options if you wish to
+    # explicitly remove the session from the session cache.
+    #
+    # Example:
+    #   myapp = MyRackApp.new
+    #   sessioned = Rack::Session::Pool.new(myapp,
+    #     :domain => 'foo.com',
+    #     :expire_after => 2592000
+    #   )
+    #   Rack::Handler::WEBrick.run sessioned
+
+    class Pool < Abstract::ID
+      attr_reader :mutex, :pool
+      DEFAULT_OPTIONS = Abstract::ID::DEFAULT_OPTIONS.merge :drop => false
+
+      def initialize(app, options={})
+        super
+        @pool = Hash.new
+        @mutex = Mutex.new
+      end
+
+      def generate_sid
+        loop do
+          sid = super
+          break sid unless @pool.key? sid
+        end
+      end
+
+      def get_session(env, sid)
+        with_lock(env, [nil, {}]) do
+          unless sid and session = @pool[sid]
+            sid, session = generate_sid, {}
+            @pool.store sid, session
+          end
+          [sid, session]
+        end
+      end
+
+      def set_session(env, session_id, new_session, options)
+        with_lock(env, false) do
+          @pool.store session_id, new_session
+          session_id
+        end
+      end
+
+      def destroy_session(env, session_id, options)
+        with_lock(env) do
+          @pool.delete(session_id)
+          generate_sid unless options[:drop]
+        end
+      end
+
+      def with_lock(env, default=nil)
+        @mutex.lock if env['rack.multithread']
+        yield
+      rescue
+        default
+      ensure
+        @mutex.unlock if @mutex.locked?
+      end
+
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/rack-1.3.0/lib/rack/showexceptions.rb

@@ -0,0 +1,378 @@
+require 'ostruct'
+require 'erb'
+require 'rack/request'
+require 'rack/utils'
+
+module Rack
+  # Rack::ShowExceptions catches all exceptions raised from the app it
+  # wraps.  It shows a useful backtrace with the sourcefile and
+  # clickable context, the whole Rack environment and the request
+  # data.
+  #
+  # Be careful when you use this on public-facing sites as it could
+  # reveal information helpful to attackers.
+
+  class ShowExceptions
+    CONTEXT = 7
+
+    def initialize(app)
+      @app = app
+      @template = ERB.new(TEMPLATE)
+    end
+
+    def call(env)
+      @app.call(env)
+    rescue StandardError, LoadError, SyntaxError => e
+      exception_string = dump_exception(e)
+
+      env["rack.errors"].puts(exception_string)
+      env["rack.errors"].flush
+
+      if prefers_plain_text?(env)
+        content_type = "text/plain"
+        body = [exception_string]
+      else
+        content_type = "text/html"
+        body = pretty(env, e)
+      end
+
+      [500,
+       {"Content-Type" => content_type,
+        "Content-Length" => Rack::Utils.bytesize(body.join).to_s},
+       body]
+    end
+
+    def prefers_plain_text?(env)
+      env["HTTP_X_REQUESTED_WITH"] == "XMLHttpRequest" && (!env["HTTP_ACCEPT"] || !env["HTTP_ACCEPT"].include?("text/html"))
+    end
+
+    def dump_exception(exception)
+      string = "#{exception.class}: #{exception.message}\n"
+      string << exception.backtrace.map { |l| "\t#{l}" }.join("\n")
+      string
+    end
+
+    def pretty(env, exception)
+      req = Rack::Request.new(env)
+
+      # This double assignment is to prevent an "unused variable" warning on
+      # Ruby 1.9.3.  Yes, it is dumb, but I don't like Ruby yelling at me.
+      path = path = (req.script_name + req.path_info).squeeze("/")
+
+      # This double assignment is to prevent an "unused variable" warning on
+      # Ruby 1.9.3.  Yes, it is dumb, but I don't like Ruby yelling at me.
+      frames = frames = exception.backtrace.map { |line|
+        frame = OpenStruct.new
+        if line =~ /(.*?):(\d+)(:in `(.*)')?/
+          frame.filename = $1
+          frame.lineno = $2.to_i
+          frame.function = $4
+
+          begin
+            lineno = frame.lineno-1
+            lines = ::File.readlines(frame.filename)
+            frame.pre_context_lineno = [lineno-CONTEXT, 0].max
+            frame.pre_context = lines[frame.pre_context_lineno...lineno]
+            frame.context_line = lines[lineno].chomp
+            frame.post_context_lineno = [lineno+CONTEXT, lines.size].min
+            frame.post_context = lines[lineno+1..frame.post_context_lineno]
+          rescue
+          end
+
+          frame
+        else
+          nil
+        end
+      }.compact
+
+      [@template.result(binding)]
+    end
+
+    def h(obj)                  # :nodoc:
+      case obj
+      when String
+        Utils.escape_html(obj)
+      else
+        Utils.escape_html(obj.inspect)
+      end
+    end
+
+    # :stopdoc:
+
+# adapted from Django <djangoproject.com>
+# Copyright (c) 2005, the Lawrence Journal-World
+# Used under the modified BSD license:
+# http://www.xfree86.org/3.3.6/COPYRIGHT2.html#5
+TEMPLATE = <<'HTML'
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html lang="en">
+<head>
+  <meta http-equiv="content-type" content="text/html; charset=utf-8" />
+  <meta name="robots" content="NONE,NOARCHIVE" />
+  <title><%=h exception.class %> at <%=h path %></title>
+  <style type="text/css">
+    html * { padding:0; margin:0; }
+    body * { padding:10px 20px; }
+    body * * { padding:0; }
+    body { font:small sans-serif; }
+    body>div { border-bottom:1px solid #ddd; }
+    h1 { font-weight:normal; }
+    h2 { margin-bottom:.8em; }
+    h2 span { font-size:80%; color:#666; font-weight:normal; }
+    h3 { margin:1em 0 .5em 0; }
+    h4 { margin:0 0 .5em 0; font-weight: normal; }
+    table {
+        border:1px solid #ccc; border-collapse: collapse; background:white; }
+    tbody td, tbody th { vertical-align:top; padding:2px 3px; }
+    thead th {
+        padding:1px 6px 1px 3px; background:#fefefe; text-align:left;
+        font-weight:normal; font-size:11px; border:1px solid #ddd; }
+    tbody th { text-align:right; color:#666; padding-right:.5em; }
+    table.vars { margin:5px 0 2px 40px; }
+    table.vars td, table.req td { font-family:monospace; }
+    table td.code { width:100%;}
+    table td.code div { overflow:hidden; }
+    table.source th { color:#666; }
+    table.source td {
+        font-family:monospace; white-space:pre; border-bottom:1px solid #eee; }
+    ul.traceback { list-style-type:none; }
+    ul.traceback li.frame { margin-bottom:1em; }
+    div.context { margin: 10px 0; }
+    div.context ol {
+        padding-left:30px; margin:0 10px; list-style-position: inside; }
+    div.context ol li {
+        font-family:monospace; white-space:pre; color:#666; cursor:pointer; }
+    div.context ol.context-line li { color:black; background-color:#ccc; }
+    div.context ol.context-line li span { float: right; }
+    div.commands { margin-left: 40px; }
+    div.commands a { color:black; text-decoration:none; }
+    #summary { background: #ffc; }
+    #summary h2 { font-weight: normal; color: #666; }
+    #summary ul#quicklinks { list-style-type: none; margin-bottom: 2em; }
+    #summary ul#quicklinks li { float: left; padding: 0 1em; }
+    #summary ul#quicklinks>li+li { border-left: 1px #666 solid; }
+    #explanation { background:#eee; }
+    #template, #template-not-exist { background:#f6f6f6; }
+    #template-not-exist ul { margin: 0 0 0 20px; }
+    #traceback { background:#eee; }
+    #requestinfo { background:#f6f6f6; padding-left:120px; }
+    #summary table { border:none; background:transparent; }
+    #requestinfo h2, #requestinfo h3 { position:relative; margin-left:-100px; }
+    #requestinfo h3 { margin-bottom:-1em; }
+    .error { background: #ffc; }
+    .specific { color:#cc3300; font-weight:bold; }
+  </style>
+  <script type="text/javascript">
+  //<!--
+    function getElementsByClassName(oElm, strTagName, strClassName){
+        // Written by Jonathan Snook, http://www.snook.ca/jon;
+        // Add-ons by Robert Nyman, http://www.robertnyman.com
+        var arrElements = (strTagName == "*" && document.all)? document.all :
+        oElm.getElementsByTagName(strTagName);
+        var arrReturnElements = new Array();
+        strClassName = strClassName.replace(/\-/g, "\\-");
+        var oRegExp = new RegExp("(^|\\s)" + strClassName + "(\\s|$$)");
+        var oElement;
+        for(var i=0; i<arrElements.length; i++){
+            oElement = arrElements[i];
+            if(oRegExp.test(oElement.className)){
+                arrReturnElements.push(oElement);
+            }
+        }
+        return (arrReturnElements)
+    }
+    function hideAll(elems) {
+      for (var e = 0; e < elems.length; e++) {
+        elems[e].style.display = 'none';
+      }
+    }
+    window.onload = function() {
+      hideAll(getElementsByClassName(document, 'table', 'vars'));
+      hideAll(getElementsByClassName(document, 'ol', 'pre-context'));
+      hideAll(getElementsByClassName(document, 'ol', 'post-context'));
+    }
+    function toggle() {
+      for (var i = 0; i < arguments.length; i++) {
+        var e = document.getElementById(arguments[i]);
+        if (e) {
+          e.style.display = e.style.display == 'none' ? 'block' : 'none';
+        }
+      }
+      return false;
+    }
+    function varToggle(link, id) {
+      toggle('v' + id);
+      var s = link.getElementsByTagName('span')[0];
+      var uarr = String.fromCharCode(0x25b6);
+      var darr = String.fromCharCode(0x25bc);
+      s.innerHTML = s.innerHTML == uarr ? darr : uarr;
+      return false;
+    }
+    //-->
+  </script>
+</head>
+<body>
+
+<div id="summary">
+  <h1><%=h exception.class %> at <%=h path %></h1>
+  <h2><%=h exception.message %></h2>
+  <table><tr>
+    <th>Ruby</th>
+    <td>
+<% if first = frames.first %>
+      <code><%=h first.filename %></code>: in <code><%=h first.function %></code>, line <%=h frames.first.lineno %>
+<% else %>
+      unknown location
+<% end %>
+    </td>
+  </tr><tr>
+    <th>Web</th>
+    <td><code><%=h req.request_method %> <%=h(req.host + path)%></code></td>
+  </tr></table>
+
+  <h3>Jump to:</h3>
+  <ul id="quicklinks">
+    <li><a href="#get-info">GET</a></li>
+    <li><a href="#post-info">POST</a></li>
+    <li><a href="#cookie-info">Cookies</a></li>
+    <li><a href="#env-info">ENV</a></li>
+  </ul>
+</div>
+
+<div id="traceback">
+  <h2>Traceback <span>(innermost first)</span></h2>
+  <ul class="traceback">
+<% frames.each { |frame| %>
+      <li class="frame">
+        <code><%=h frame.filename %></code>: in <code><%=h frame.function %></code>
+
+          <% if frame.context_line %>
+          <div class="context" id="c<%=h frame.object_id %>">
+              <% if frame.pre_context %>
+              <ol start="<%=h frame.pre_context_lineno+1 %>" class="pre-context" id="pre<%=h frame.object_id %>">
+                <% frame.pre_context.each { |line| %>
+                <li onclick="toggle('pre<%=h frame.object_id %>', 'post<%=h frame.object_id %>')"><%=h line %></li>
+                <% } %>
+              </ol>
+              <% end %>
+
+            <ol start="<%=h frame.lineno %>" class="context-line">
+              <li onclick="toggle('pre<%=h frame.object_id %>', 'post<%=h frame.object_id %>')"><%=h frame.context_line %><span>...</span></li></ol>
+
+              <% if frame.post_context %>
+              <ol start='<%=h frame.lineno+1 %>' class="post-context" id="post<%=h frame.object_id %>">
+                <% frame.post_context.each { |line| %>
+                <li onclick="toggle('pre<%=h frame.object_id %>', 'post<%=h frame.object_id %>')"><%=h line %></li>
+                <% } %>
+              </ol>
+              <% end %>
+          </div>
+          <% end %>
+      </li>
+<% } %>
+  </ul>
+</div>
+
+<div id="requestinfo">
+  <h2>Request information</h2>
+
+  <h3 id="get-info">GET</h3>
+  <% unless req.GET.empty? %>
+    <table class="req">
+      <thead>
+        <tr>
+          <th>Variable</th>
+          <th>Value</th>
+        </tr>
+      </thead>
+      <tbody>
+          <% req.GET.sort_by { |k, v| k.to_s }.each { |key, val| %>
+          <tr>
+            <td><%=h key %></td>
+            <td class="code"><div><%=h val.inspect %></div></td>
+          </tr>
+          <% } %>
+      </tbody>
+    </table>
+  <% else %>
+    <p>No GET data.</p>
+  <% end %>
+
+  <h3 id="post-info">POST</h3>
+  <% unless req.POST.empty? %>
+    <table class="req">
+      <thead>
+        <tr>
+          <th>Variable</th>
+          <th>Value</th>
+        </tr>
+      </thead>
+      <tbody>
+          <% req.POST.sort_by { |k, v| k.to_s }.each { |key, val| %>
+          <tr>
+            <td><%=h key %></td>
+            <td class="code"><div><%=h val.inspect %></div></td>
+          </tr>
+          <% } %>
+      </tbody>
+    </table>
+  <% else %>
+    <p>No POST data.</p>
+  <% end %>
+
+
+  <h3 id="cookie-info">COOKIES</h3>
+  <% unless req.cookies.empty? %>
+    <table class="req">
+      <thead>
+        <tr>
+          <th>Variable</th>
+          <th>Value</th>
+        </tr>
+      </thead>
+      <tbody>
+        <% req.cookies.each { |key, val| %>
+          <tr>
+            <td><%=h key %></td>
+            <td class="code"><div><%=h val.inspect %></div></td>
+          </tr>
+        <% } %>
+      </tbody>
+    </table>
+  <% else %>
+    <p>No cookie data.</p>
+  <% end %>
+
+  <h3 id="env-info">Rack ENV</h3>
+    <table class="req">
+      <thead>
+        <tr>
+          <th>Variable</th>
+          <th>Value</th>
+        </tr>
+      </thead>
+      <tbody>
+          <% env.sort_by { |k, v| k.to_s }.each { |key, val| %>
+          <tr>
+            <td><%=h key %></td>
+            <td class="code"><div><%=h val %></div></td>
+          </tr>
+          <% } %>
+      </tbody>
+    </table>
+
+</div>
+
+<div id="explanation">
+  <p>
+    You're seeing this error because you use <code>Rack::ShowExceptions</code>.
+  </p>
+</div>
+
+</body>
+</html>
+HTML
+
+    # :startdoc:
+  end
+end