RubyGems - search_biomodel - Versions diffs - 0.1.2 → 1.0.0 - Mend

search_biomodel 0.1.2 → 1.0.0

Files changed (1059) hide show

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

@@ -0,0 +1,113 @@
+require 'erb'
+require 'rack/request'
+require 'rack/utils'
+module Rack
+  # Rack::ShowStatus catches all empty responses the app it wraps and
+  # replaces them with a site explaining the error.
+  #
+  # Additional details can be put into <tt>rack.showstatus.detail</tt>
+  # and will be shown as HTML.  If such details exist, the error page
+  # is always rendered, even if the reply was not empty.
+  class ShowStatus
+    def initialize(app)
+      @app = app
+      @template = ERB.new(TEMPLATE)
+    end
+    def call(env)
+      status, headers, body = @app.call(env)
+      headers = Utils::HeaderHash.new(headers)
+      empty = headers['Content-Length'].to_i <= 0
+      # client or server error, or explicit message
+      if (status.to_i >= 400 && empty) || env["rack.showstatus.detail"]
+        # 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.
+        req = req = Rack::Request.new(env)
+        message = Rack::Utils::HTTP_STATUS_CODES[status.to_i] || status.to_s
+        # 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.
+        detail = detail = env["rack.showstatus.detail"] || message
+        body = @template.result(binding)
+        size = Rack::Utils.bytesize(body)
+        [status, headers.merge("Content-Type" => "text/html", "Content-Length" => size.to_s), [body]]
+      else
+        [status, headers, body]
+      end
+    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" />
+  <title><%=h message %> at <%=h req.script_name + req.path_info %></title>
+  <meta name="robots" content="NONE,NOARCHIVE" />
+  <style type="text/css">
+    html * { padding:0; margin:0; }
+    body * { padding:10px 20px; }
+    body * * { padding:0; }
+    body { font:small sans-serif; background:#eee; }
+    body>div { border-bottom:1px solid #ddd; }
+    h1 { font-weight:normal; margin-bottom:.4em; }
+    h1 span { font-size:60%; color:#666; font-weight:normal; }
+    table { border:none; border-collapse: collapse; width:100%; }
+    td, th { vertical-align:top; padding:2px 3px; }
+    th { width:12em; text-align:right; color:#666; padding-right:.5em; }
+    #info { background:#f6f6f6; }
+    #info ol { margin: 0.5em 4em; }
+    #info ol li { font-family: monospace; }
+    #summary { background: #ffc; }
+    #explanation { background:#eee; border-bottom: 0px none; }
+  </style>
+</head>
+<body>
+  <div id="summary">
+    <h1><%=h message %> <span>(<%= status.to_i %>)</span></h1>
+    <table class="meta">
+      <tr>
+        <th>Request Method:</th>
+        <td><%=h req.request_method %></td>
+      </tr>
+      <tr>
+        <th>Request URL:</th>
+      <td><%=h req.url %></td>
+      </tr>
+    </table>
+  </div>
+  <div id="info">
+    <p><%= detail %></p>
+  </div>
+  <div id="explanation">
+    <p>
+    You're seeing this error because you use <code>Rack::ShowStatus</code>.
+    </p>
+  </div>
+</body>
+</html>
+HTML
+    # :startdoc:
+  end
+end

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

@@ -0,0 +1,58 @@
+module Rack
+  # The Rack::Static middleware intercepts requests for static files
+  # (javascript files, images, stylesheets, etc) based on the url prefixes or
+  # route mappings passed in the options, and serves them using a Rack::File
+  # object. This allows a Rack stack to serve both static and dynamic content.
+  #
+  # Examples:
+  #
+  # Serve all requests beginning with /media from the "media" folder located
+  # in the current directory (ie media/*):
+  #
+  #     use Rack::Static, :urls => ["/media"]
+  #
+  # Serve all requests beginning with /css or /images from the folder "public"
+  # in the current directory (ie public/css/* and public/images/*):
+  #
+  #     use Rack::Static, :urls => ["/css", "/images"], :root => "public"
+  #
+  # Serve all requests to / with "index.html" from the folder "public" in the
+  # current directory (ie public/index.html):
+  #
+  #     use Rack::Static, :urls => {"/" => 'index.html'}, :root => 'public'
+  #
+  # Set a fixed Cache-Control header for all served files:
+  #
+  #     use Rack::Static, :root => 'public', :cache_control => 'public'
+  #
+  class Static
+    def initialize(app, options={})
+      @app = app
+      @urls = options[:urls] || ["/favicon.ico"]
+      root = options[:root] || Dir.pwd
+      cache_control = options[:cache_control]
+      @file_server = Rack::File.new(root, cache_control)
+    end
+    def call(env)
+      path = env["PATH_INFO"]
+      unless @urls.kind_of? Hash
+        can_serve = @urls.any? { |url| path.index(url) == 0 }
+      else
+        can_serve = @urls.key? path
+      end
+      if can_serve
+        env["PATH_INFO"] = @urls[path] if @urls.kind_of? Hash
+        @file_server.call(env)
+      else
+        @app.call(env)
+      end
+    end
+  end
+end

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

@@ -0,0 +1,60 @@
+module Rack
+  # Rack::URLMap takes a hash mapping urls or paths to apps, and
+  # dispatches accordingly.  Support for HTTP/1.1 host names exists if
+  # the URLs start with <tt>http://</tt> or <tt>https://</tt>.
+  #
+  # URLMap modifies the SCRIPT_NAME and PATH_INFO such that the part
+  # relevant for dispatch is in the SCRIPT_NAME, and the rest in the
+  # PATH_INFO.  This should be taken care of when you need to
+  # reconstruct the URL in order to create links.
+  #
+  # URLMap dispatches in such a way that the longest paths are tried
+  # first, since they are most specific.
+  class URLMap
+    NEGATIVE_INFINITY = -1.0 / 0.0
+    def initialize(map = {})
+      remap(map)
+    end
+    def remap(map)
+      longest_path_first = lambda do |(host, location, _, _)|
+        [host ? -host.size : NEGATIVE_INFINITY, -location.size]
+      end
+      @mapping = map.map { |location, app|
+        if location =~ %r{\Ahttps?://(.*?)(/.*)}
+          host, location = $1, $2
+        else
+          host = nil
+        end
+        unless location[0] == ?/
+          raise ArgumentError, "paths need to start with /"
+        end
+        location = location.chomp('/')
+        match = Regexp.new("^#{Regexp.quote(location).gsub('/', '/+')}(.*)", nil, 'n')
+        [host, location, match, app]
+      }.sort_by(&longest_path_first)
+    end
+    def call(env)
+      path = env["PATH_INFO"]
+      script_name = env['SCRIPT_NAME']
+      hHost, sName, sPort = env.values_at('HTTP_HOST','SERVER_NAME','SERVER_PORT')
+      @mapping.each { |host, location, match, app|
+        next unless (hHost == host || sName == host \
+          || (host.nil? && (hHost == sName || hHost == sName+':'+sPort)))
+        next unless path.to_s =~ match && rest = $1
+        next unless rest.empty? || rest[0] == ?/
+        env.merge!('SCRIPT_NAME' => (script_name + location), 'PATH_INFO' => rest)
+        return app.call(env)
+      }
+      [404, {"Content-Type" => "text/plain", "X-Cascade" => "pass"}, ["Not Found: #{path}"]]
+    ensure
+      env.merge! 'PATH_INFO' => path, 'SCRIPT_NAME' => script_name
+    end
+  end
+end

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

@@ -0,0 +1,480 @@
+# -*- encoding: binary -*-
+require 'fileutils'
+require 'set'
+require 'tempfile'
+require 'rack/multipart'
+if RUBY_VERSION[/^\d+\.\d+/] == '1.8'
+  # pull in backports
+  require 'rack/backports/uri/common'
+else
+  require 'uri/common'
+end
+module Rack
+  # Rack::Utils contains a grab-bag of useful methods for writing web
+  # applications adopted from all kinds of Ruby libraries.
+  module Utils
+    # URI escapes a string. (CGI style space to +)
+    def escape(s)
+      URI.encode_www_form_component(s)
+    end
+    module_function :escape
+    # Like URI escaping, but with %20 instead of +. Strictly speaking this is
+    # true URI escaping.
+    def escape_path(s)
+      escape(s).gsub('+', '%20')
+    end
+    module_function :escape_path
+    # Unescapes a URI escaped string.
+    def unescape(s)
+      URI.decode_www_form_component(s)
+    end
+    module_function :unescape
+    DEFAULT_SEP = /[&;] */n
+    # Stolen from Mongrel, with some small modifications:
+    # Parses a query string by breaking it up at the '&'
+    # and ';' characters.  You can also use this to parse
+    # cookies by changing the characters used in the second
+    # parameter (which defaults to '&;').
+    def parse_query(qs, d = nil)
+      params = {}
+      (qs || '').split(d ? /[#{d}] */n : DEFAULT_SEP).each do |p|
+        k, v = p.split('=', 2).map { |x| unescape(x) }
+        if cur = params[k]
+          if cur.class == Array
+            params[k] << v
+          else
+            params[k] = [cur, v]
+          end
+        else
+          params[k] = v
+        end
+      end
+      return params
+    end
+    module_function :parse_query
+    def parse_nested_query(qs, d = nil)
+      params = {}
+      (qs || '').split(d ? /[#{d}] */n : DEFAULT_SEP).each do |p|
+        k, v = p.split('=', 2).map { |s| unescape(s) }
+        normalize_params(params, k, v)
+      end
+      return params
+    end
+    module_function :parse_nested_query
+    def normalize_params(params, name, v = nil)
+      name =~ %r(\A[\[\]]*([^\[\]]+)\]*)
+      k = $1 || ''
+      after = $' || ''
+      return if k.empty?
+      if after == ""
+        params[k] = v
+      elsif after == "[]"
+        params[k] ||= []
+        raise TypeError, "expected Array (got #{params[k].class.name}) for param `#{k}'" unless params[k].is_a?(Array)
+        params[k] << v
+      elsif after =~ %r(^\[\]\[([^\[\]]+)\]$) || after =~ %r(^\[\](.+)$)
+        child_key = $1
+        params[k] ||= []
+        raise TypeError, "expected Array (got #{params[k].class.name}) for param `#{k}'" unless params[k].is_a?(Array)
+        if params[k].last.is_a?(Hash) && !params[k].last.key?(child_key)
+          normalize_params(params[k].last, child_key, v)
+        else
+          params[k] << normalize_params({}, child_key, v)
+        end
+      else
+        params[k] ||= {}
+        raise TypeError, "expected Hash (got #{params[k].class.name}) for param `#{k}'" unless params[k].is_a?(Hash)
+        params[k] = normalize_params(params[k], after, v)
+      end
+      return params
+    end
+    module_function :normalize_params
+    def build_query(params)
+      params.map { |k, v|
+        if v.class == Array
+          build_query(v.map { |x| [k, x] })
+        else
+          "#{escape(k)}=#{escape(v)}"
+        end
+      }.join("&")
+    end
+    module_function :build_query
+    def build_nested_query(value, prefix = nil)
+      case value
+      when Array
+        value.map { |v|
+          build_nested_query(v, "#{prefix}[]")
+        }.join("&")
+      when Hash
+        value.map { |k, v|
+          build_nested_query(v, prefix ? "#{prefix}[#{escape(k)}]" : escape(k))
+        }.join("&")
+      when String
+        raise ArgumentError, "value must be a Hash" if prefix.nil?
+        "#{prefix}=#{escape(value)}"
+      else
+        prefix
+      end
+    end
+    module_function :build_nested_query
+    ESCAPE_HTML = {
+      "&" => "&amp;",
+      "<" => "&lt;",
+      ">" => "&gt;",
+      "'" => "&#x27;",
+      '"' => "&quot;",
+      "/" => "&#x2F;"
+    }
+    ESCAPE_HTML_PATTERN = Regexp.union(*ESCAPE_HTML.keys)
+    # Escape ampersands, brackets and quotes to their HTML/XML entities.
+    def escape_html(string)
+      string.to_s.gsub(ESCAPE_HTML_PATTERN){|c| ESCAPE_HTML[c] }
+    end
+    module_function :escape_html
+    def select_best_encoding(available_encodings, accept_encoding)
+      # http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html
+      expanded_accept_encoding =
+        accept_encoding.map { |m, q|
+          if m == "*"
+            (available_encodings - accept_encoding.map { |m2, _| m2 }).map { |m2| [m2, q] }
+          else
+            [[m, q]]
+          end
+        }.inject([]) { |mem, list|
+          mem + list
+        }
+      encoding_candidates = expanded_accept_encoding.sort_by { |_, q| -q }.map { |m, _| m }
+      unless encoding_candidates.include?("identity")
+        encoding_candidates.push("identity")
+      end
+      expanded_accept_encoding.find_all { |m, q|
+        q == 0.0
+      }.each { |m, _|
+        encoding_candidates.delete(m)
+      }
+      return (encoding_candidates & available_encodings)[0]
+    end
+    module_function :select_best_encoding
+    def set_cookie_header!(header, key, value)
+      case value
+      when Hash
+        domain  = "; domain="  + value[:domain] if value[:domain]
+        path    = "; path="    + value[:path]   if value[:path]
+        # According to RFC 2109, we need dashes here.
+        # N.B.: cgi.rb uses spaces...
+        expires = "; expires=" +
+          rfc2822(value[:expires].clone.gmtime) if value[:expires]
+        secure = "; secure"  if value[:secure]
+        httponly = "; HttpOnly" if value[:httponly]
+        value = value[:value]
+      end
+      value = [value] unless Array === value
+      cookie = escape(key) + "=" +
+        value.map { |v| escape v }.join("&") +
+        "#{domain}#{path}#{expires}#{secure}#{httponly}"
+      case header["Set-Cookie"]
+      when nil, ''
+        header["Set-Cookie"] = cookie
+      when String
+        header["Set-Cookie"] = [header["Set-Cookie"], cookie].join("\n")
+      when Array
+        header["Set-Cookie"] = (header["Set-Cookie"] + [cookie]).join("\n")
+      end
+      nil
+    end
+    module_function :set_cookie_header!
+    def delete_cookie_header!(header, key, value = {})
+      case header["Set-Cookie"]
+      when nil, ''
+        cookies = []
+      when String
+        cookies = header["Set-Cookie"].split("\n")
+      when Array
+        cookies = header["Set-Cookie"]
+      end
+      cookies.reject! { |cookie|
+        if value[:domain]
+          cookie =~ /\A#{escape(key)}=.*domain=#{value[:domain]}/
+        else
+          cookie =~ /\A#{escape(key)}=/
+        end
+      }
+      header["Set-Cookie"] = cookies.join("\n")
+      set_cookie_header!(header, key,
+                 {:value => '', :path => nil, :domain => nil,
+                   :expires => Time.at(0) }.merge(value))
+      nil
+    end
+    module_function :delete_cookie_header!
+    # Return the bytesize of String; uses String#size under Ruby 1.8 and
+    # String#bytesize under 1.9.
+    if ''.respond_to?(:bytesize)
+      def bytesize(string)
+        string.bytesize
+      end
+    else
+      def bytesize(string)
+        string.size
+      end
+    end
+    module_function :bytesize
+    # Modified version of stdlib time.rb Time#rfc2822 to use '%d-%b-%Y' instead
+    # of '% %b %Y'.
+    # It assumes that the time is in GMT to comply to the RFC 2109.
+    #
+    # NOTE: I'm not sure the RFC says it requires GMT, but is ambigous enough
+    # that I'm certain someone implemented only that option.
+    # Do not use %a and %b from Time.strptime, it would use localized names for
+    # weekday and month.
+    #
+    def rfc2822(time)
+      wday = Time::RFC2822_DAY_NAME[time.wday]
+      mon = Time::RFC2822_MONTH_NAME[time.mon - 1]
+      time.strftime("#{wday}, %d-#{mon}-%Y %H:%M:%S GMT")
+    end
+    module_function :rfc2822
+    # Parses the "Range:" header, if present, into an array of Range objects.
+    # Returns nil if the header is missing or syntactically invalid.
+    # Returns an empty array if none of the ranges are satisfiable.
+    def byte_ranges(env, size)
+      # See <http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html#sec14.35>
+      http_range = env['HTTP_RANGE']
+      return nil unless http_range
+      ranges = []
+      http_range.split(/,\s*/).each do |range_spec|
+        matches = range_spec.match(/bytes=(\d*)-(\d*)/)
+        return nil  unless matches
+        r0,r1 = matches[1], matches[2]
+        if r0.empty?
+          return nil  if r1.empty?
+          # suffix-byte-range-spec, represents trailing suffix of file
+          r0 = [size - r1.to_i, 0].max
+          r1 = size - 1
+        else
+          r0 = r0.to_i
+          if r1.empty?
+            r1 = size - 1
+          else
+            r1 = r1.to_i
+            return nil  if r1 < r0  # backwards range is syntactically invalid
+            r1 = size-1  if r1 >= size
+          end
+        end
+        ranges << (r0..r1)  if r0 <= r1
+      end
+      ranges
+    end
+    module_function :byte_ranges
+    # Context allows the use of a compatible middleware at different points
+    # in a request handling stack. A compatible middleware must define
+    # #context which should take the arguments env and app. The first of which
+    # would be the request environment. The second of which would be the rack
+    # application that the request would be forwarded to.
+    class Context
+      attr_reader :for, :app
+      def initialize(app_f, app_r)
+        raise 'running context does not respond to #context' unless app_f.respond_to? :context
+        @for, @app = app_f, app_r
+      end
+      def call(env)
+        @for.context(env, @app)
+      end
+      def recontext(app)
+        self.class.new(@for, app)
+      end
+      def context(env, app=@app)
+        recontext(app).call(env)
+      end
+    end
+    # A case-insensitive Hash that preserves the original case of a
+    # header when set.
+    class HeaderHash < Hash
+      def self.new(hash={})
+        HeaderHash === hash ? hash : super(hash)
+      end
+      def initialize(hash={})
+        super()
+        @names = {}
+        hash.each { |k, v| self[k] = v }
+      end
+      def each
+        super do |k, v|
+          yield(k, v.respond_to?(:to_ary) ? v.to_ary.join("\n") : v)
+        end
+      end
+      def to_hash
+        Hash[*map do |k, v|
+          [k, v.respond_to?(:to_ary) ? v.to_ary.join("\n") : v]
+        end.flatten]
+      end
+      def [](k)
+        super(k) || super(@names[k.downcase])
+      end
+      def []=(k, v)
+        canonical = k.downcase
+        delete k if @names[canonical] && @names[canonical] != k # .delete is expensive, don't invoke it unless necessary
+        @names[k] = @names[canonical] = k
+        super k, v
+      end
+      def delete(k)
+        canonical = k.downcase
+        result = super @names.delete(canonical)
+        @names.delete_if { |name,| name.downcase == canonical }
+        result
+      end
+      def include?(k)
+        @names.include?(k) || @names.include?(k.downcase)
+      end
+      alias_method :has_key?, :include?
+      alias_method :member?, :include?
+      alias_method :key?, :include?
+      def merge!(other)
+        other.each { |k, v| self[k] = v }
+        self
+      end
+      def merge(other)
+        hash = dup
+        hash.merge! other
+      end
+      def replace(other)
+        clear
+        other.each { |k, v| self[k] = v }
+        self
+      end
+    end
+    # Every standard HTTP code mapped to the appropriate message.
+    # Generated with:
+    #   curl -s http://www.iana.org/assignments/http-status-codes | \
+    #     ruby -ane 'm = /^(\d{3}) +(\S[^\[(]+)/.match($_) and
+    #                puts "      #{m[1]}  => \x27#{m[2].strip}x27,"'
+    HTTP_STATUS_CODES = {
+      100  => 'Continue',
+      101  => 'Switching Protocols',
+      102  => 'Processing',
+      200  => 'OK',
+      201  => 'Created',
+      202  => 'Accepted',
+      203  => 'Non-Authoritative Information',
+      204  => 'No Content',
+      205  => 'Reset Content',
+      206  => 'Partial Content',
+      207  => 'Multi-Status',
+      226  => 'IM Used',
+      300  => 'Multiple Choices',
+      301  => 'Moved Permanently',
+      302  => 'Found',
+      303  => 'See Other',
+      304  => 'Not Modified',
+      305  => 'Use Proxy',
+      306  => 'Reserved',
+      307  => 'Temporary Redirect',
+      400  => 'Bad Request',
+      401  => 'Unauthorized',
+      402  => 'Payment Required',
+      403  => 'Forbidden',
+      404  => 'Not Found',
+      405  => 'Method Not Allowed',
+      406  => 'Not Acceptable',
+      407  => 'Proxy Authentication Required',
+      408  => 'Request Timeout',
+      409  => 'Conflict',
+      410  => 'Gone',
+      411  => 'Length Required',
+      412  => 'Precondition Failed',
+      413  => 'Request Entity Too Large',
+      414  => 'Request-URI Too Long',
+      415  => 'Unsupported Media Type',
+      416  => 'Requested Range Not Satisfiable',
+      417  => 'Expectation Failed',
+      422  => 'Unprocessable Entity',
+      423  => 'Locked',
+      424  => 'Failed Dependency',
+      426  => 'Upgrade Required',
+      500  => 'Internal Server Error',
+      501  => 'Not Implemented',
+      502  => 'Bad Gateway',
+      503  => 'Service Unavailable',
+      504  => 'Gateway Timeout',
+      505  => 'HTTP Version Not Supported',
+      506  => 'Variant Also Negotiates',
+      507  => 'Insufficient Storage',
+      510  => 'Not Extended',
+    }
+    # Responses with HTTP status codes that should not have an entity body
+    STATUS_WITH_NO_ENTITY_BODY = Set.new((100..199).to_a << 204 << 304)
+    SYMBOL_TO_STATUS_CODE = Hash[*HTTP_STATUS_CODES.map { |code, message|
+      [message.downcase.gsub(/\s|-/, '_').to_sym, code]
+    }.flatten]
+    def status_code(status)
+      if status.is_a?(Symbol)
+        SYMBOL_TO_STATUS_CODE[status] || 500
+      else
+        status.to_i
+      end
+    end
+    module_function :status_code
+    Multipart = Rack::Multipart
+  end
+end