RubyGems - search_biomodel - Versions diffs - 1.0.0 → 1.0.1 - Mend

search_biomodel 1.0.0 → 1.0.1

Files changed (1054) hide show

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

@@ -1,113 +0,0 @@
-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 DELETED Viewed

@@ -1,58 +0,0 @@
-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 DELETED Viewed

@@ -1,60 +0,0 @@
-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 DELETED Viewed

@@ -1,480 +0,0 @@
-# -*- 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