search_biomodel 0.1.2 → 1.0.0

data/search_biomodel/ruby/1.8/gems/rack-1.3.0/lib/rack/auth/abstract/handler.rb

@@ -0,0 +1,37 @@
+module Rack
+  module Auth
+    # Rack::Auth::AbstractHandler implements common authentication functionality.
+    #
+    # +realm+ should be set for all handlers.
+
+    class AbstractHandler
+
+      attr_accessor :realm
+
+      def initialize(app, realm=nil, &authenticator)
+        @app, @realm, @authenticator = app, realm, authenticator
+      end
+
+
+      private
+
+      def unauthorized(www_authenticate = challenge)
+        return [ 401,
+          { 'Content-Type' => 'text/plain',
+            'Content-Length' => '0',
+            'WWW-Authenticate' => www_authenticate.to_s },
+          []
+        ]
+      end
+
+      def bad_request
+        return [ 400,
+          { 'Content-Type' => 'text/plain',
+            'Content-Length' => '0' },
+          []
+        ]
+      end
+
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/rack-1.3.0/lib/rack/auth/abstract/request.rb

@@ -0,0 +1,43 @@
+require 'rack/request'
+
+module Rack
+  module Auth
+    class AbstractRequest
+
+      def initialize(env)
+        @env = env
+      end
+
+      def request
+        @request ||= Request.new(@env)
+      end
+
+      def provided?
+        !authorization_key.nil?
+      end
+
+      def parts
+        @parts ||= @env[authorization_key].split(' ', 2)
+      end
+
+      def scheme
+        @scheme ||= parts.first.downcase.to_sym
+      end
+
+      def params
+        @params ||= parts.last
+      end
+
+
+      private
+
+      AUTHORIZATION_KEYS = ['HTTP_AUTHORIZATION', 'X-HTTP_AUTHORIZATION', 'X_HTTP_AUTHORIZATION']
+
+      def authorization_key
+        @authorization_key ||= AUTHORIZATION_KEYS.detect { |key| @env.has_key?(key) }
+      end
+
+    end
+
+  end
+end

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

@@ -0,0 +1,58 @@
+require 'rack/auth/abstract/handler'
+require 'rack/auth/abstract/request'
+
+module Rack
+  module Auth
+    # Rack::Auth::Basic implements HTTP Basic Authentication, as per RFC 2617.
+    #
+    # Initialize with the Rack application that you want protecting,
+    # and a block that checks if a username and password pair are valid.
+    #
+    # See also: <tt>example/protectedlobster.rb</tt>
+
+    class Basic < AbstractHandler
+
+      def call(env)
+        auth = Basic::Request.new(env)
+
+        return unauthorized unless auth.provided?
+
+        return bad_request unless auth.basic?
+
+        if valid?(auth)
+          env['REMOTE_USER'] = auth.username
+
+          return @app.call(env)
+        end
+
+        unauthorized
+      end
+
+
+      private
+
+      def challenge
+        'Basic realm="%s"' % realm
+      end
+
+      def valid?(auth)
+        @authenticator.call(*auth.credentials)
+      end
+
+      class Request < Auth::AbstractRequest
+        def basic?
+          :basic == scheme
+        end
+
+        def credentials
+          @credentials ||= params.unpack("m*").first.split(/:/, 2)
+        end
+
+        def username
+          credentials.first
+        end
+      end
+
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/rack-1.3.0/lib/rack/auth/digest/md5.rb

@@ -0,0 +1,129 @@
+require 'rack/auth/abstract/handler'
+require 'rack/auth/digest/request'
+require 'rack/auth/digest/params'
+require 'rack/auth/digest/nonce'
+require 'digest/md5'
+
+module Rack
+  module Auth
+    module Digest
+      # Rack::Auth::Digest::MD5 implements the MD5 algorithm version of
+      # HTTP Digest Authentication, as per RFC 2617.
+      #
+      # Initialize with the [Rack] application that you want protecting,
+      # and a block that looks up a plaintext password for a given username.
+      #
+      # +opaque+ needs to be set to a constant base64/hexadecimal string.
+      #
+      class MD5 < AbstractHandler
+
+        attr_accessor :opaque
+
+        attr_writer :passwords_hashed
+
+        def initialize(app, realm=nil, opaque=nil, &authenticator)
+          @passwords_hashed = nil
+          if opaque.nil? and realm.respond_to? :values_at
+            realm, opaque, @passwords_hashed = realm.values_at :realm, :opaque, :passwords_hashed 
+          end
+          super(app, realm, &authenticator)
+          @opaque = opaque
+        end
+
+        def passwords_hashed?
+          !!@passwords_hashed
+        end
+
+        def call(env)
+          auth = Request.new(env)
+
+          unless auth.provided?
+            return unauthorized
+          end
+
+          if !auth.digest? || !auth.correct_uri? || !valid_qop?(auth)
+            return bad_request
+          end
+
+          if valid?(auth)
+            if auth.nonce.stale?
+              return unauthorized(challenge(:stale => true))
+            else
+              env['REMOTE_USER'] = auth.username
+
+              return @app.call(env)
+            end
+          end
+
+          unauthorized
+        end
+
+
+        private
+
+        QOP = 'auth'.freeze
+
+        def params(hash = {})
+          Params.new do |params|
+            params['realm'] = realm
+            params['nonce'] = Nonce.new.to_s
+            params['opaque'] = H(opaque)
+            params['qop'] = QOP
+
+            hash.each { |k, v| params[k] = v }
+          end
+        end
+
+        def challenge(hash = {})
+          "Digest #{params(hash)}"
+        end
+
+        def valid?(auth)
+          valid_opaque?(auth) && valid_nonce?(auth) && valid_digest?(auth)
+        end
+
+        def valid_qop?(auth)
+          QOP == auth.qop
+        end
+
+        def valid_opaque?(auth)
+          H(opaque) == auth.opaque
+        end
+
+        def valid_nonce?(auth)
+          auth.nonce.valid?
+        end
+
+        def valid_digest?(auth)
+          pw = @authenticator.call(auth.username)
+          pw && digest(auth, pw) == auth.response
+        end
+
+        def md5(data)
+          ::Digest::MD5.hexdigest(data)
+        end
+
+        alias :H :md5
+
+        def KD(secret, data)
+          H([secret, data] * ':')
+        end
+
+        def A1(auth, password)
+          [ auth.username, auth.realm, password ] * ':'
+        end
+
+        def A2(auth)
+          [ auth.method, auth.uri ] * ':'
+        end
+
+        def digest(auth, password)
+          password_hash = passwords_hashed? ? password : H(A1(auth, password))
+
+          KD(password_hash, [ auth.nonce, auth.nc, auth.cnonce, QOP, H(A2(auth)) ] * ':')
+        end
+
+      end
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/rack-1.3.0/lib/rack/auth/digest/nonce.rb

@@ -0,0 +1,51 @@
+require 'digest/md5'
+
+module Rack
+  module Auth
+    module Digest
+      # Rack::Auth::Digest::Nonce is the default nonce generator for the
+      # Rack::Auth::Digest::MD5 authentication handler.
+      #
+      # +private_key+ needs to set to a constant string.
+      #
+      # +time_limit+ can be optionally set to an integer (number of seconds),
+      # to limit the validity of the generated nonces.
+
+      class Nonce
+
+        class << self
+          attr_accessor :private_key, :time_limit
+        end
+
+        def self.parse(string)
+          new(*string.unpack("m*").first.split(' ', 2))
+        end
+
+        def initialize(timestamp = Time.now, given_digest = nil)
+          @timestamp, @given_digest = timestamp.to_i, given_digest
+        end
+
+        def to_s
+          [([ @timestamp, digest ] * ' ')].pack("m*").strip
+        end
+
+        def digest
+          ::Digest::MD5.hexdigest([ @timestamp, self.class.private_key ] * ':')
+        end
+
+        def valid?
+          digest == @given_digest
+        end
+
+        def stale?
+          !self.class.time_limit.nil? && (@timestamp - Time.now.to_i) < self.class.time_limit
+        end
+
+        def fresh?
+          !stale?
+        end
+
+      end
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/rack-1.3.0/lib/rack/auth/digest/params.rb

@@ -0,0 +1,53 @@
+module Rack
+  module Auth
+    module Digest
+      class Params < Hash
+
+        def self.parse(str)
+          Params[*split_header_value(str).map do |param|
+            k, v = param.split('=', 2)
+            [k, dequote(v)]
+          end.flatten]
+        end
+
+        def self.dequote(str) # From WEBrick::HTTPUtils
+          ret = (/\A"(.*)"\Z/ =~ str) ? $1 : str.dup
+          ret.gsub!(/\\(.)/, "\\1")
+          ret
+        end
+
+        def self.split_header_value(str)
+          str.scan( /(\w+\=(?:"[^\"]+"|[^,]+))/n ).collect{ |v| v[0] }
+        end
+
+        def initialize
+          super()
+
+          yield self if block_given?
+        end
+
+        def [](k)
+          super k.to_s
+        end
+
+        def []=(k, v)
+          super k.to_s, v.to_s
+        end
+
+        UNQUOTED = ['nc', 'stale']
+
+        def to_s
+          map do |k, v|
+            "#{k}=" + (UNQUOTED.include?(k) ? v.to_s : quote(v))
+          end.join(', ')
+        end
+
+        def quote(str) # From WEBrick::HTTPUtils
+          '"' << str.gsub(/[\\\"]/o, "\\\1") << '"'
+        end
+
+      end
+    end
+  end
+end
+

data/search_biomodel/ruby/1.8/gems/rack-1.3.0/lib/rack/auth/digest/request.rb

@@ -0,0 +1,40 @@
+require 'rack/auth/abstract/request'
+require 'rack/auth/digest/params'
+require 'rack/auth/digest/nonce'
+
+module Rack
+  module Auth
+    module Digest
+      class Request < Auth::AbstractRequest
+
+        def method
+          @env['rack.methodoverride.original_method'] || @env['REQUEST_METHOD']
+        end
+
+        def digest?
+          :digest == scheme
+        end
+
+        def correct_uri?
+          request.fullpath == uri
+        end
+
+        def nonce
+          @nonce ||= Nonce.parse(params['nonce'])
+        end
+
+        def params
+          @params ||= Params.parse(parts.last)
+        end
+
+        def method_missing(sym)
+          if params.has_key? key = sym.to_s
+            return params[key]
+          end
+          super
+        end
+
+      end
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/rack-1.3.0/lib/rack/backports/uri/common.rb

@@ -0,0 +1,64 @@
+# :stopdoc:
+
+# Stolen from ruby core's uri/common.rb, with modifications to support 1.8.x
+#
+# https://github.com/ruby/ruby/blob/trunk/lib/uri/common.rb
+#
+#
+
+module URI
+  TBLENCWWWCOMP_ = {} # :nodoc:
+  TBLDECWWWCOMP_ = {} # :nodoc:
+
+  # Encode given +str+ to URL-encoded form data.
+  #
+  # This method doesn't convert *, -, ., 0-9, A-Z, _, a-z, but does convert SP
+  # (ASCII space) to + and converts others to %XX.
+  #
+  # This is an implementation of
+  # http://www.w3.org/TR/html5/forms.html#url-encoded-form-data
+  #
+  # See URI.decode_www_form_component, URI.encode_www_form
+  def self.encode_www_form_component(str)
+    if TBLENCWWWCOMP_.empty?
+      tbl = {}
+      256.times do |i|
+        tbl[i.chr] = '%%%02X' % i
+      end
+      tbl[' '] = '+'
+      begin
+        TBLENCWWWCOMP_.replace(tbl)
+        TBLENCWWWCOMP_.freeze
+      rescue
+      end
+    end
+    str = str.to_s
+    str.gsub(/[^*\-.0-9A-Z_a-z]/) {|m| TBLENCWWWCOMP_[m]}
+  end
+
+  # Decode given +str+ of URL-encoded form data.
+  #
+  # This decods + to SP.
+  #
+  # See URI.encode_www_form_component, URI.decode_www_form
+  def self.decode_www_form_component(str, enc=nil)
+    if TBLDECWWWCOMP_.empty?
+      tbl = {}
+      256.times do |i|
+        h, l = i>>4, i&15
+        tbl['%%%X%X' % [h, l]] = i.chr
+        tbl['%%%x%X' % [h, l]] = i.chr
+        tbl['%%%X%x' % [h, l]] = i.chr
+        tbl['%%%x%x' % [h, l]] = i.chr
+      end
+      tbl['+'] = ' '
+      begin
+        TBLDECWWWCOMP_.replace(tbl)
+        TBLDECWWWCOMP_.freeze
+      rescue
+      end
+    end
+    raise ArgumentError, "invalid %-encoding (#{str})" unless /\A(?:%[0-9a-fA-F]{2}|[^%]+)*\z/ =~ str
+    str.gsub(/\+|%[0-9a-fA-F]{2}/) {|m| TBLDECWWWCOMP_[m]}
+  end
+end