search_biomodel 1.0.0 → 1.0.1

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/lib/rake/task_manager.rb

@@ -1,307 +0,0 @@
-module Rake
-
-  # The TaskManager module is a mixin for managing tasks.
-  module TaskManager
-    # Track the last comment made in the Rakefile.
-    attr_accessor :last_description
-    alias :last_comment :last_description    # Backwards compatibility
-
-    def initialize
-      super
-      @tasks = Hash.new
-      @rules = Array.new
-      @scope = Array.new
-      @last_description = nil
-    end
-
-    def create_rule(*args, &block)
-      pattern, _, deps = resolve_args(args)
-      pattern = Regexp.new(Regexp.quote(pattern) + '$') if String === pattern
-      @rules << [pattern, deps, block]
-    end
-
-    def define_task(task_class, *args, &block)
-      task_name, arg_names, deps = resolve_args(args)
-      task_name = task_class.scope_name(@scope, task_name)
-      deps = [deps] unless deps.respond_to?(:to_ary)
-      deps = deps.collect {|d| d.to_s }
-      task = intern(task_class, task_name)
-      task.set_arg_names(arg_names) unless arg_names.empty?
-      if Rake::TaskManager.record_task_metadata
-        add_location(task)
-        task.add_description(get_description(task))
-      end
-      task.enhance(deps, &block)
-    end
-
-    # Lookup a task.  Return an existing task if found, otherwise
-    # create a task of the current type.
-    def intern(task_class, task_name)
-      @tasks[task_name.to_s] ||= task_class.new(task_name, self)
-    end
-
-    # Find a matching task for +task_name+.
-    def [](task_name, scopes=nil)
-      task_name = task_name.to_s
-      self.lookup(task_name, scopes) or
-        enhance_with_matching_rule(task_name) or
-        synthesize_file_task(task_name) or
-        fail "Don't know how to build task '#{task_name}'"
-    end
-
-    def synthesize_file_task(task_name)
-      return nil unless File.exist?(task_name)
-      define_task(Rake::FileTask, task_name)
-    end
-
-    # Resolve the arguments for a task/rule.  Returns a triplet of
-    # [task_name, arg_name_list, prerequisites].
-    def resolve_args(args)
-      if args.last.is_a?(Hash)
-        deps = args.pop
-        resolve_args_with_dependencies(args, deps)
-      else
-        resolve_args_without_dependencies(args)
-      end
-    end
-
-    # Resolve task arguments for a task or rule when there are no
-    # dependencies declared.
-    #
-    # The patterns recognized by this argument resolving function are:
-    #
-    #   task :t
-    #   task :t, [:a]
-    #   task :t, :a                 (deprecated)
-    #
-    def resolve_args_without_dependencies(args)
-      task_name = args.shift
-      if args.size == 1 && args.first.respond_to?(:to_ary)
-        arg_names = args.first.to_ary
-      else
-        arg_names = args
-      end
-      [task_name, arg_names, []]
-    end
-    private :resolve_args_without_dependencies
-
-    # Resolve task arguments for a task or rule when there are
-    # dependencies declared.
-    #
-    # The patterns recognized by this argument resolving function are:
-    #
-    #   task :t => [:d]
-    #   task :t, [a] => [:d]
-    #   task :t, :needs => [:d]                 (deprecated)
-    #   task :t, :a, :needs => [:d]             (deprecated)
-    #
-    def resolve_args_with_dependencies(args, hash) # :nodoc:
-      fail "Task Argument Error" if hash.size != 1
-      key, value = hash.map { |k, v| [k,v] }.first
-      if args.empty?
-        task_name = key
-        arg_names = []
-        deps = value
-      elsif key == :needs
-        Rake.application.deprecate(
-          "task :t, arg, :needs => [deps]",
-          "task :t, [args] => [deps]",
-          caller.detect { |c| c !~ /\blib\/rake\b/ })
-        task_name = args.shift
-        arg_names = args
-        deps = value
-      else
-        task_name = args.shift
-        arg_names = key
-        deps = value
-      end
-      deps = [deps] unless deps.respond_to?(:to_ary)
-      [task_name, arg_names, deps]
-    end
-    private :resolve_args_with_dependencies
-
-    # If a rule can be found that matches the task name, enhance the
-    # task with the prerequisites and actions from the rule.  Set the
-    # source attribute of the task appropriately for the rule.  Return
-    # the enhanced task or nil of no rule was found.
-    def enhance_with_matching_rule(task_name, level=0)
-      fail Rake::RuleRecursionOverflowError,
-        "Rule Recursion Too Deep" if level >= 16
-      @rules.each do |pattern, extensions, block|
-        if pattern.match(task_name)
-          task = attempt_rule(task_name, extensions, block, level)
-          return task if task
-        end
-      end
-      nil
-    rescue Rake::RuleRecursionOverflowError => ex
-      ex.add_target(task_name)
-      fail ex
-    end
-
-    # List of all defined tasks in this application.
-    def tasks
-      @tasks.values.sort_by { |t| t.name }
-    end
-
-    # List of all the tasks defined in the given scope (and its
-    # sub-scopes).
-    def tasks_in_scope(scope)
-      prefix = scope.join(":")
-      tasks.select { |t|
-        /^#{prefix}:/ =~ t.name
-      }
-    end
-
-    # Clear all tasks in this application.
-    def clear
-      @tasks.clear
-      @rules.clear
-    end
-
-    # Lookup a task, using scope and the scope hints in the task name.
-    # This method performs straight lookups without trying to
-    # synthesize file tasks or rules.  Special scope names (e.g. '^')
-    # are recognized.  If no scope argument is supplied, use the
-    # current scope.  Return nil if the task cannot be found.
-    def lookup(task_name, initial_scope=nil)
-      initial_scope ||= @scope
-      task_name = task_name.to_s
-      if task_name =~ /^rake:/
-        scopes = []
-        task_name = task_name.sub(/^rake:/, '')
-      elsif task_name =~ /^(\^+)/
-        scopes = initial_scope[0, initial_scope.size - $1.size]
-        task_name = task_name.sub(/^(\^+)/, '')
-      else
-        scopes = initial_scope
-      end
-      lookup_in_scope(task_name, scopes)
-    end
-
-    # Lookup the task name
-    def lookup_in_scope(name, scope)
-      n = scope.size
-      while n >= 0
-        tn = (scope[0,n] + [name]).join(':')
-        task = @tasks[tn]
-        return task if task
-        n -= 1
-      end
-      nil
-    end
-    private :lookup_in_scope
-
-    # Return the list of scope names currently active in the task
-    # manager.
-    def current_scope
-      @scope.dup
-    end
-
-    # Evaluate the block in a nested namespace named +name+.  Create
-    # an anonymous namespace if +name+ is nil.
-    def in_namespace(name)
-      name ||= generate_name
-      @scope.push(name)
-      ns = NameSpace.new(self, @scope)
-      yield(ns)
-      ns
-    ensure
-      @scope.pop
-    end
-
-    private
-
-    # Add a location to the locations field of the given task.
-    def add_location(task)
-      loc = find_location
-      task.locations << loc if loc
-      task
-    end
-
-    # Find the location that called into the dsl layer.
-    def find_location
-      locations = caller
-      i = 0
-      while locations[i]
-        return locations[i+1] if locations[i] =~ /rake\/dsl_definition.rb/
-        i += 1
-      end
-      nil
-    end
-
-    # Generate an anonymous namespace name.
-    def generate_name
-      @seed ||= 0
-      @seed += 1
-      "_anon_#{@seed}"
-    end
-
-    def trace_rule(level, message)
-      $stderr.puts "#{"    "*level}#{message}" if Rake.application.options.trace_rules
-    end
-
-    # Attempt to create a rule given the list of prerequisites.
-    def attempt_rule(task_name, extensions, block, level)
-      sources = make_sources(task_name, extensions)
-      prereqs = sources.collect { |source|
-        trace_rule level, "Attempting Rule #{task_name} => #{source}"
-        if File.exist?(source) || Rake::Task.task_defined?(source)
-          trace_rule level, "(#{task_name} => #{source} ... EXIST)"
-          source
-        elsif parent = enhance_with_matching_rule(source, level+1)
-          trace_rule level, "(#{task_name} => #{source} ... ENHANCE)"
-          parent.name
-        else
-          trace_rule level, "(#{task_name} => #{source} ... FAIL)"
-          return nil
-        end
-      }
-      task = FileTask.define_task({task_name => prereqs}, &block)
-      task.sources = prereqs
-      task
-    end
-
-    # Make a list of sources from the list of file name extensions /
-    # translation procs.
-    def make_sources(task_name, extensions)
-      result = extensions.collect { |ext|
-        case ext
-        when /%/
-          task_name.pathmap(ext)
-        when %r{/}
-          ext
-        when /^\./
-          task_name.ext(ext)
-        when String
-          ext
-        when Proc
-          if ext.arity == 1
-            ext.call(task_name)
-          else
-            ext.call
-          end
-        else
-          fail "Don't know how to handle rule dependent: #{ext.inspect}"
-        end
-      }
-      result.flatten
-    end
-
-
-    private
-
-    # Return the current description, clearing it in the process.
-    def get_description(task)
-      desc = @last_description
-      @last_description = nil
-      desc
-    end
-
-    class << self
-      attr_accessor :record_task_metadata
-      TaskManager.record_task_metadata = false
-    end
-  end
-
-end

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/lib/rake/tasklib.rb

@@ -1,22 +0,0 @@
-require 'rake'
-
-module Rake
-
-  # Base class for Task Libraries.
-  class TaskLib
-    include Cloneable
-    include Rake::DSL
-
-    # Make a symbol by pasting two strings together.
-    #
-    # NOTE: DEPRECATED! This method is kinda stupid. I don't know why
-    # I didn't just use string interpolation. But now other task
-    # libraries depend on this so I can't remove it without breaking
-    # other people's code. So for now it stays for backwards
-    # compatibility. BUT DON'T USE IT.
-    def paste(a,b)              # :nodoc:
-      (a.to_s + b.to_s).intern
-    end
-  end
-
-end

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/lib/rake/testtask.rb

@@ -1,191 +0,0 @@
-# Define a task library for running unit tests.
-
-require 'rake'
-require 'rake/tasklib'
-
-module Rake
-
-  # Create a task that runs a set of tests.
-  #
-  # Example:
-  #
-  #   Rake::TestTask.new do |t|
-  #     t.libs << "test"
-  #     t.test_files = FileList['test/test*.rb']
-  #     t.verbose = true
-  #   end
-  #
-  # If rake is invoked with a "TEST=filename" command line option,
-  # then the list of test files will be overridden to include only the
-  # filename specified on the command line.  This provides an easy way
-  # to run just one test.
-  #
-  # If rake is invoked with a "TESTOPTS=options" command line option,
-  # then the given options are passed to the test process after a
-  # '--'.  This allows Test::Unit options to be passed to the test
-  # suite.
-  #
-  # Examples:
-  #
-  #   rake test                           # run tests normally
-  #   rake test TEST=just_one_file.rb     # run just one test file.
-  #   rake test TESTOPTS="-v"             # run in verbose mode
-  #   rake test TESTOPTS="--runner=fox"   # use the fox test runner
-  #
-  class TestTask < TaskLib
-
-    # Name of test task. (default is :test)
-    attr_accessor :name
-
-    # List of directories to added to $LOAD_PATH before running the
-    # tests. (default is 'lib')
-    attr_accessor :libs
-
-    # True if verbose test output desired. (default is false)
-    attr_accessor :verbose
-
-    # Test options passed to the test suite.  An explicit
-    # TESTOPTS=opts on the command line will override this. (default
-    # is NONE)
-    attr_accessor :options
-
-    # Request that the tests be run with the warning flag set.
-    # E.g. warning=true implies "ruby -w" used to run the tests.
-    attr_accessor :warning
-
-    # Glob pattern to match test files. (default is 'test/test*.rb')
-    attr_accessor :pattern
-
-    # Style of test loader to use.  Options are:
-    #
-    # * :rake -- Rake provided test loading script (default).
-    # * :testrb -- Ruby provided test loading script.
-    # * :direct -- Load tests using command line loader.
-    #
-    attr_accessor :loader
-
-    # Array of commandline options to pass to ruby when running test loader.
-    attr_accessor :ruby_opts
-
-    # Explicitly define the list of test files to be included in a
-    # test.  +list+ is expected to be an array of file names (a
-    # FileList is acceptable).  If both +pattern+ and +test_files+ are
-    # used, then the list of test files is the union of the two.
-    def test_files=(list)
-      @test_files = list
-    end
-
-    # Create a testing task.
-    def initialize(name=:test)
-      @name = name
-      @libs = ["lib"]
-      @pattern = nil
-      @options = nil
-      @test_files = nil
-      @verbose = false
-      @warning = false
-      @loader = :rake
-      @ruby_opts = []
-      yield self if block_given?
-      @pattern = 'test/test*.rb' if @pattern.nil? && @test_files.nil?
-      define
-    end
-
-    # Create the tasks defined by this task lib.
-    def define
-      desc "Run tests" + (@name==:test ? "" : " for #{@name}")
-      task @name do
-        FileUtilsExt.verbose(@verbose) do
-          ruby "#{ruby_opts_string} #{run_code} #{file_list_string} #{option_list}"
-        end
-      end
-      self
-    end
-
-    def option_list # :nodoc:
-      (ENV['TESTOPTS'] ||
-        ENV['TESTOPT'] ||
-        ENV['TEST_OPTS'] ||
-        ENV['TEST_OPT'] ||
-        @options ||
-        "")
-    end
-
-    def ruby_opts_string
-      opts = @ruby_opts.dup
-      opts.unshift( "-I\"#{lib_path}\"" ) unless @libs.empty?
-      opts.unshift( "-w" ) if @warning
-      opts.join(" ")
-    end
-
-    def lib_path
-      @libs.join(File::PATH_SEPARATOR)
-    end
-
-    def file_list_string
-      file_list.collect { |fn| "\"#{fn}\"" }.join(' ')
-    end
-
-    def file_list # :nodoc:
-      if ENV['TEST']
-        FileList[ ENV['TEST'] ]
-      else
-        result = []
-        result += @test_files.to_a if @test_files
-        result << @pattern if @pattern
-        result
-      end
-    end
-
-    def fix # :nodoc:
-      case ruby_version
-      when '1.8.2'
-        "\"#{find_file 'rake/ruby182_test_unit_fix'}\""
-      else
-        nil
-      end || ''
-    end
-
-    def ruby_version
-      RUBY_VERSION
-    end
-
-    def run_code
-      case @loader
-      when :direct
-        "-e \"ARGV.each{|f| require f}\""
-      when :testrb
-        "-S testrb #{fix}"
-      when :rake
-        "-I\"#{rake_lib_dir}\" \"#{rake_loader}\""
-      end
-    end
-
-    def rake_loader # :nodoc:
-      find_file('rake/rake_test_loader') or
-        fail "unable to find rake test loader"
-    end
-
-    def find_file(fn) # :nodoc:
-      $LOAD_PATH.each do |path|
-        file_path = File.join(path, "#{fn}.rb")
-        return file_path if File.exist? file_path
-      end
-      nil
-    end
-
-    def rake_lib_dir # :nodoc:
-      find_dir('rake') or
-        fail "unable to find rake lib"
-    end
-
-    def find_dir(fn) # :nodoc:
-      $LOAD_PATH.each do |path|
-        file_path = File.join(path, "#{fn}.rb")
-        return path if File.exist? file_path
-      end
-      nil
-    end
-
-  end
-end

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/lib/rake/version.rb

@@ -1,10 +0,0 @@
-module Rake
-  module Version
-    NUMBERS = [
-      MAJOR = 0,
-      MINOR = 9,
-      BUILD = 2,
-    ]
-  end
-  VERSION = Version::NUMBERS.join('.')
-end

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/lib/rake/win32.rb

@@ -1,55 +0,0 @@
-
-module Rake
-  require 'rake/alt_system'
-
-  # Win 32 interface methods for Rake. Windows specific functionality
-  # will be placed here to collect that knowledge in one spot.
-  module Win32
-
-    # Error indicating a problem in locating the home directory on a
-    # Win32 system.
-    class Win32HomeError < RuntimeError
-    end
-
-    class << self
-      # True if running on a windows system.
-      def windows?
-        AltSystem::WINDOWS
-      end
-
-      # Run a command line on windows.
-      def rake_system(*cmd)
-        AltSystem.system(*cmd)
-      end
-
-      # The standard directory containing system wide rake files on
-      # Win 32 systems. Try the following environment variables (in
-      # order):
-      #
-      # * HOME
-      # * HOMEDRIVE + HOMEPATH
-      # * APPDATA
-      # * USERPROFILE
-      #
-      # If the above are not defined, the return nil.
-      def win32_system_dir #:nodoc:
-        win32_shared_path = ENV['HOME']
-        if win32_shared_path.nil? && ENV['HOMEDRIVE'] && ENV['HOMEPATH']
-          win32_shared_path = ENV['HOMEDRIVE'] + ENV['HOMEPATH']
-        end
-
-        win32_shared_path ||= ENV['APPDATA']
-        win32_shared_path ||= ENV['USERPROFILE']
-        raise Win32HomeError, "Unable to determine home path environment variable." if
-          win32_shared_path.nil? or win32_shared_path.empty?
-        normalize(File.join(win32_shared_path, 'Rake'))
-      end
-
-      # Normalize a win32 path so that the slashes are all forward slashes.
-      def normalize(path)
-        path.gsub(/\\/, '/')
-      end
-
-    end
-  end
-end

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/lib/rake.rb

@@ -1,65 +0,0 @@
-#--
-
-# Copyright 2003-2010 by Jim Weirich (jim.weirich@gmail.com)
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to
-# deal in the Software without restriction, including without limitation the
-# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
-# sell copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
-# IN THE SOFTWARE.
-#++
-
-require 'rake/version'
-
-RAKEVERSION = Rake::VERSION
-
-require 'rbconfig'
-require 'fileutils'
-require 'singleton'
-require 'monitor'
-require 'optparse'
-require 'ostruct'
-
-require 'rake/ext/module'
-require 'rake/ext/string'
-require 'rake/ext/time'
-
-require 'rake/win32'
-
-require 'rake/task_argument_error'
-require 'rake/rule_recursion_overflow_error'
-require 'rake/rake_module'
-require 'rake/pseudo_status'
-require 'rake/task_arguments'
-require 'rake/invocation_chain'
-require 'rake/task'
-require 'rake/file_task'
-require 'rake/file_creation_task'
-require 'rake/multi_task'
-require 'rake/dsl_definition'
-require 'rake/file_utils_ext'
-require 'rake/file_list'
-require 'rake/default_loader'
-require 'rake/early_time'
-require 'rake/name_space'
-require 'rake/task_manager'
-require 'rake/application'
-
-$trace = false
-
-# Some top level Constants.
-
-FileList = Rake::FileList
-RakeFileUtils = Rake::FileUtilsExt

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/test/check_expansion.rb

@@ -1,5 +0,0 @@
-if ARGV[0] != ARGV[1]
-  exit 1
-else
-  exit 0
-end

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/test/check_no_expansion.rb

@@ -1,5 +0,0 @@
-if ARGV[0] != ARGV[1]
-  exit 0
-else
-  exit 1
-end

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/test/data/access/Rakefile

@@ -1,35 +0,0 @@
-TOP_LEVEL_CONSTANT = 0
-
-def a_top_level_function
-end
-
-task :default => [:work, :obj, :const]
-
-task :work do
-  begin
-    a_top_level_function
-    puts "GOOD:M Top level methods can be called in tasks"
-  rescue NameError => ex
-    puts "BAD:M  Top level methods can not be called in tasks"
-  end
-end
-
-# TODO: remove `disabled_' when DeprecatedObjectDSL removed
-task :obj
-task :disabled_obj do
-  begin
-    Object.new.instance_eval { task :xyzzy }
-    puts "BAD:D  Rake DSL are polluting objects"
-  rescue StandardError => ex
-    puts "GOOD:D Rake DSL are not polluting objects"
-  end
-end
-
-task :const do
-  begin
-    TOP_LEVEL_CONSTANT
-    puts "GOOD:C Top level constants are available in tasks"
-  rescue StandardError => ex
-    puts "BAD:C  Top level constants are NOT available in tasks"
-  end
-end