search_biomodel 1.0.0 → 1.0.1

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

@@ -1,589 +0,0 @@
-require 'shellwords'
-require 'optparse'
-
-require 'rake/task_manager'
-require 'rake/win32'
-
-module Rake
-
-  ######################################################################
-  # Rake main application object.  When invoking +rake+ from the
-  # command line, a Rake::Application object is created and run.
-  #
-  class Application
-    include TaskManager
-
-    # The name of the application (typically 'rake')
-    attr_reader :name
-
-    # The original directory where rake was invoked.
-    attr_reader :original_dir
-
-    # Name of the actual rakefile used.
-    attr_reader :rakefile
-
-    # List of the top level task names (task names from the command line).
-    attr_reader :top_level_tasks
-
-    DEFAULT_RAKEFILES = ['rakefile', 'Rakefile', 'rakefile.rb', 'Rakefile.rb'].freeze
-
-    # Initialize a Rake::Application object.
-    def initialize
-      super
-      @name = 'rake'
-      @rakefiles = DEFAULT_RAKEFILES.dup
-      @rakefile = nil
-      @pending_imports = []
-      @imported = []
-      @loaders = {}
-      @default_loader = Rake::DefaultLoader.new
-      @original_dir = Dir.pwd
-      @top_level_tasks = []
-      add_loader('rb', DefaultLoader.new)
-      add_loader('rf', DefaultLoader.new)
-      add_loader('rake', DefaultLoader.new)
-      @tty_output = STDOUT.tty?
-    end
-
-    # Run the Rake application.  The run method performs the following
-    # three steps:
-    #
-    # * Initialize the command line options (+init+).
-    # * Define the tasks (+load_rakefile+).
-    # * Run the top level tasks (+run_tasks+).
-    #
-    # If you wish to build a custom rake command, you should call
-    # +init+ on your application.  Then define any tasks.  Finally,
-    # call +top_level+ to run your top level tasks.
-    def run
-      standard_exception_handling do
-        init
-        load_rakefile
-        top_level
-      end
-    end
-
-    # Initialize the command line parameters and app name.
-    def init(app_name='rake')
-      standard_exception_handling do
-        @name = app_name
-        handle_options
-        collect_tasks
-      end
-    end
-
-    # Find the rakefile and then load it and any pending imports.
-    def load_rakefile
-      standard_exception_handling do
-        raw_load_rakefile
-      end
-    end
-
-    # Run the top level tasks of a Rake application.
-    def top_level
-      standard_exception_handling do
-        if options.show_tasks
-          display_tasks_and_comments
-        elsif options.show_prereqs
-          display_prerequisites
-        else
-          top_level_tasks.each { |task_name| invoke_task(task_name) }
-        end
-      end
-    end
-
-    # Add a loader to handle imported files ending in the extension
-    # +ext+.
-    def add_loader(ext, loader)
-      ext = ".#{ext}" unless ext =~ /^\./
-      @loaders[ext] = loader
-    end
-
-    # Application options from the command line
-    def options
-      @options ||= OpenStruct.new
-    end
-
-    # private ----------------------------------------------------------------
-
-    def invoke_task(task_string)
-      name, args = parse_task_string(task_string)
-      t = self[name]
-      t.invoke(*args)
-    end
-
-    def parse_task_string(string)
-      if string =~ /^([^\[]+)(\[(.*)\])$/
-        name = $1
-        args = $3.split(/\s*,\s*/)
-      else
-        name = string
-        args = []
-      end
-      [name, args]
-    end
-
-    # Provide standard exception handling for the given block.
-    def standard_exception_handling
-      begin
-        yield
-      rescue SystemExit => ex
-        # Exit silently with current status
-        raise
-      rescue OptionParser::InvalidOption => ex
-        $stderr.puts ex.message
-        exit(false)
-      rescue Exception => ex
-        # Exit with error message
-        display_error_message(ex)
-        exit(false)
-      end
-    end
-
-    # Display the error message that caused the exception.
-    def display_error_message(ex)
-      $stderr.puts "#{name} aborted!"
-      $stderr.puts ex.message
-      if options.trace
-        $stderr.puts ex.backtrace.join("\n")
-      else
-        $stderr.puts rakefile_location(ex.backtrace)
-      end
-      $stderr.puts "Tasks: #{ex.chain}" if has_chain?(ex)
-      $stderr.puts "(See full trace by running task with --trace)" unless options.trace
-    end
-
-    # Warn about deprecated usage.
-    #
-    # Example:
-    #    Rake.application.deprecate("import", "Rake.import", caller.first)
-    #
-    def deprecate(old_usage, new_usage, call_site)
-      return if options.ignore_deprecate
-      $stderr.puts "WARNING: '#{old_usage}' is deprecated.  " +
-        "Please use '#{new_usage}' instead.\n" +
-        "    at #{call_site}"
-    end
-
-    # Does the exception have a task invocation chain?
-    def has_chain?(exception)
-      exception.respond_to?(:chain) && exception.chain
-    end
-    private :has_chain?
-
-    # True if one of the files in RAKEFILES is in the current directory.
-    # If a match is found, it is copied into @rakefile.
-    def have_rakefile
-      @rakefiles.each do |fn|
-        if File.exist?(fn)
-          others = Dir.glob(fn, File::FNM_CASEFOLD)
-          return others.size == 1 ? others.first : fn
-        elsif fn == ''
-          return fn
-        end
-      end
-      return nil
-    end
-
-    # True if we are outputting to TTY, false otherwise
-    def tty_output?
-      @tty_output
-    end
-
-    # Override the detected TTY output state (mostly for testing)
-    def tty_output=( tty_output_state )
-      @tty_output = tty_output_state
-    end
-
-    # We will truncate output if we are outputting to a TTY or if we've been
-    # given an explicit column width to honor
-    def truncate_output?
-      tty_output? || ENV['RAKE_COLUMNS']
-    end
-
-    # Display the tasks and comments.
-    def display_tasks_and_comments
-      displayable_tasks = tasks.select { |t|
-        t.comment && t.name =~ options.show_task_pattern
-      }
-      case options.show_tasks
-      when :tasks
-        width = displayable_tasks.collect { |t| t.name_with_args.length }.max || 10
-        max_column = truncate_output? ? terminal_width - name.size - width - 7 : nil
-        displayable_tasks.each do |t|
-          printf "#{name} %-#{width}s  # %s\n",
-            t.name_with_args, max_column ? truncate(t.comment, max_column) : t.comment
-        end
-      when :describe
-        displayable_tasks.each do |t|
-          puts "#{name} #{t.name_with_args}"
-          t.full_comment.split("\n").each do |line|
-            puts "    #{line}"
-          end
-          puts
-        end
-      when :lines
-        displayable_tasks.each do |t|
-          t.locations.each do |loc|
-            printf "#{name} %-30s %s\n",t.name_with_args, loc
-          end
-        end
-      else
-        fail "Unknown show task mode: '#{options.show_tasks}'"
-      end
-    end
-
-    def terminal_width
-      if ENV['RAKE_COLUMNS']
-        result = ENV['RAKE_COLUMNS'].to_i
-      else
-        result = unix? ? dynamic_width : 80
-      end
-      (result < 10) ? 80 : result
-    rescue
-      80
-    end
-
-    # Calculate the dynamic width of the
-    def dynamic_width
-      @dynamic_width ||= (dynamic_width_stty.nonzero? || dynamic_width_tput)
-    end
-
-    def dynamic_width_stty
-      %x{stty size 2>/dev/null}.split[1].to_i
-    end
-
-    def dynamic_width_tput
-      %x{tput cols 2>/dev/null}.to_i
-    end
-
-    def unix?
-      RbConfig::CONFIG['host_os'] =~ /(aix|darwin|linux|(net|free|open)bsd|cygwin|solaris|irix|hpux)/i
-    end
-
-    def windows?
-      Win32.windows?
-    end
-
-    def truncate(string, width)
-      if string.length <= width
-        string
-      else
-        ( string[0, width-3] || "" ) + "..."
-      end
-    end
-
-    # Display the tasks and prerequisites
-    def display_prerequisites
-      tasks.each do |t|
-        puts "#{name} #{t.name}"
-        t.prerequisites.each { |pre| puts "    #{pre}" }
-      end
-    end
-
-    # A list of all the standard options used in rake, suitable for
-    # passing to OptionParser.
-    def standard_rake_options
-      [
-        ['--classic-namespace', '-C', "Put Task and FileTask in the top level namespace",
-          lambda { |value|
-            require 'rake/classic_namespace'
-            options.classic_namespace = true
-          }
-        ],
-        ['--describe', '-D [PATTERN]', "Describe the tasks (matching optional PATTERN), then exit.",
-          lambda { |value|
-            options.show_tasks = :describe
-            options.show_task_pattern = Regexp.new(value || '')
-            TaskManager.record_task_metadata = true
-          }
-        ],
-        ['--dry-run', '-n', "Do a dry run without executing actions.",
-          lambda { |value|
-            Rake.verbose(true)
-            Rake.nowrite(true)
-            options.dryrun = true
-            options.trace = true
-          }
-        ],
-        ['--execute',  '-e CODE', "Execute some Ruby code and exit.",
-          lambda { |value|
-            eval(value)
-            exit
-          }
-        ],
-        ['--execute-print',  '-p CODE', "Execute some Ruby code, print the result, then exit.",
-          lambda { |value|
-            puts eval(value)
-            exit
-          }
-        ],
-        ['--execute-continue',  '-E CODE',
-          "Execute some Ruby code, then continue with normal task processing.",
-          lambda { |value| eval(value) }
-        ],
-        ['--libdir', '-I LIBDIR', "Include LIBDIR in the search path for required modules.",
-          lambda { |value| $:.push(value) }
-        ],
-        ['--no-search', '--nosearch', '-N', "Do not search parent directories for the Rakefile.",
-          lambda { |value| options.nosearch = true }
-        ],
-        ['--prereqs', '-P', "Display the tasks and dependencies, then exit.",
-          lambda { |value| options.show_prereqs = true }
-        ],
-        ['--quiet', '-q', "Do not log messages to standard output.",
-          lambda { |value| Rake.verbose(false) }
-        ],
-        ['--rakefile', '-f [FILE]', "Use FILE as the rakefile.",
-          lambda { |value|
-            value ||= ''
-            @rakefiles.clear
-            @rakefiles << value
-          }
-        ],
-        ['--rakelibdir', '--rakelib', '-R RAKELIBDIR',
-          "Auto-import any .rake files in RAKELIBDIR. (default is 'rakelib')",
-          lambda { |value| options.rakelib = value.split(':') }
-        ],
-        ['--require', '-r MODULE', "Require MODULE before executing rakefile.",
-          lambda { |value|
-            begin
-              require value
-            rescue LoadError => ex
-              begin
-                rake_require value
-              rescue LoadError
-                raise ex
-              end
-            end
-          }
-        ],
-        ['--rules', "Trace the rules resolution.",
-          lambda { |value| options.trace_rules = true }
-        ],
-        ['--silent', '-s', "Like --quiet, but also suppresses the 'in directory' announcement.",
-          lambda { |value|
-            Rake.verbose(false)
-            options.silent = true
-          }
-        ],
-        ['--system',  '-g',
-          "Using system wide (global) rakefiles (usually '~/.rake/*.rake').",
-          lambda { |value| options.load_system = true }
-        ],
-        ['--no-system', '--nosystem', '-G',
-          "Use standard project Rakefile search paths, ignore system wide rakefiles.",
-          lambda { |value| options.ignore_system = true }
-        ],
-        ['--tasks', '-T [PATTERN]', "Display the tasks (matching optional PATTERN) with descriptions, then exit.",
-          lambda { |value|
-            options.show_tasks = :tasks
-            options.show_task_pattern = Regexp.new(value || '')
-            Rake::TaskManager.record_task_metadata = true
-          }
-        ],
-        ['--trace', '-t', "Turn on invoke/execute tracing, enable full backtrace.",
-          lambda { |value|
-            options.trace = true
-            Rake.verbose(true)
-          }
-        ],
-        ['--verbose', '-v', "Log message to standard output.",
-          lambda { |value| Rake.verbose(true) }
-        ],
-        ['--version', '-V', "Display the program version.",
-          lambda { |value|
-            puts "rake, version #{RAKEVERSION}"
-            exit
-          }
-        ],
-        ['--where', '-W [PATTERN]', "Describe the tasks (matching optional PATTERN), then exit.",
-          lambda { |value|
-            options.show_tasks = :lines
-            options.show_task_pattern = Regexp.new(value || '')
-            Rake::TaskManager.record_task_metadata = true
-          }
-        ],
-        ['--no-deprecation-warnings', '-X', "Disable the deprecation warnings.",
-          lambda { |value|
-            options.ignore_deprecate = true
-          }
-        ],
-      ]
-    end
-
-    # Read and handle the command line options.
-    def handle_options
-      options.rakelib = ['rakelib']
-
-      OptionParser.new do |opts|
-        opts.banner = "rake [-f rakefile] {options} targets..."
-        opts.separator ""
-        opts.separator "Options are ..."
-
-        opts.on_tail("-h", "--help", "-H", "Display this help message.") do
-          puts opts
-          exit
-        end
-
-        standard_rake_options.each { |args| opts.on(*args) }
-        opts.environment('RAKEOPT')
-      end.parse!
-
-      # If class namespaces are requested, set the global options
-      # according to the values in the options structure.
-      if options.classic_namespace
-        $show_tasks = options.show_tasks
-        $show_prereqs = options.show_prereqs
-        $trace = options.trace
-        $dryrun = options.dryrun
-        $silent = options.silent
-      end
-    end
-
-    # Similar to the regular Ruby +require+ command, but will check
-    # for *.rake files in addition to *.rb files.
-    def rake_require(file_name, paths=$LOAD_PATH, loaded=$")
-      fn = file_name + ".rake"
-      return false if loaded.include?(fn)
-      paths.each do |path|
-        full_path = File.join(path, fn)
-        if File.exist?(full_path)
-          Rake.load_rakefile(full_path)
-          loaded << fn
-          return true
-        end
-      end
-      fail LoadError, "Can't find #{file_name}"
-    end
-
-    def find_rakefile_location
-      here = Dir.pwd
-      while ! (fn = have_rakefile)
-        Dir.chdir("..")
-        if Dir.pwd == here || options.nosearch
-          return nil
-        end
-        here = Dir.pwd
-      end
-      [fn, here]
-    ensure
-      Dir.chdir(Rake.original_dir)
-    end
-
-    def print_rakefile_directory(location)
-      $stderr.puts "(in #{Dir.pwd})" unless
-        options.silent or original_dir == location
-    end
-
-    def raw_load_rakefile # :nodoc:
-      rakefile, location = find_rakefile_location
-      if (! options.ignore_system) &&
-          (options.load_system || rakefile.nil?) &&
-          system_dir && File.directory?(system_dir)
-        print_rakefile_directory(location)
-        glob("#{system_dir}/*.rake") do |name|
-          add_import name
-        end
-      else
-        fail "No Rakefile found (looking for: #{@rakefiles.join(', ')})" if
-          rakefile.nil?
-        @rakefile = rakefile
-        Dir.chdir(location)
-        print_rakefile_directory(location)
-        $rakefile = @rakefile if options.classic_namespace
-        Rake.load_rakefile(File.expand_path(@rakefile)) if @rakefile && @rakefile != ''
-        options.rakelib.each do |rlib|
-          glob("#{rlib}/*.rake") do |name|
-            add_import name
-          end
-        end
-      end
-      load_imports
-    end
-
-    def glob(path, &block)
-      Dir[path.gsub("\\", '/')].each(&block)
-    end
-    private :glob
-
-    # The directory path containing the system wide rakefiles.
-    def system_dir
-      @system_dir ||=
-        begin
-          if ENV['RAKE_SYSTEM']
-            ENV['RAKE_SYSTEM']
-          else
-            standard_system_dir
-          end
-        end
-    end
-
-    # The standard directory containing system wide rake files.
-    if Win32.windows?
-      def standard_system_dir #:nodoc:
-        Win32.win32_system_dir
-      end
-    else
-      def standard_system_dir #:nodoc:
-        File.join(File.expand_path('~'), '.rake')
-      end
-    end
-    private :standard_system_dir
-
-    # Collect the list of tasks on the command line.  If no tasks are
-    # given, return a list containing only the default task.
-    # Environmental assignments are processed at this time as well.
-    def collect_tasks
-      @top_level_tasks = []
-      ARGV.each do |arg|
-        if arg =~ /^(\w+)=(.*)$/
-          ENV[$1] = $2
-        else
-          @top_level_tasks << arg unless arg =~ /^-/
-        end
-      end
-      @top_level_tasks.push("default") if @top_level_tasks.size == 0
-    end
-
-    # Add a file to the list of files to be imported.
-    def add_import(fn)
-      @pending_imports << fn
-    end
-
-    # Load the pending list of imported files.
-    def load_imports
-      while fn = @pending_imports.shift
-        next if @imported.member?(fn)
-        if fn_task = lookup(fn)
-          fn_task.invoke
-        end
-        ext = File.extname(fn)
-        loader = @loaders[ext] || @default_loader
-        loader.load(fn)
-        @imported << fn
-      end
-    end
-
-    # Warn about deprecated use of top level constant names.
-    def const_warning(const_name)
-      @const_warning ||= false
-      if ! @const_warning
-        $stderr.puts %{WARNING: Deprecated reference to top-level constant '#{const_name}' } +
-          %{found at: #{rakefile_location}} # '
-        $stderr.puts %{    Use --classic-namespace on rake command}
-        $stderr.puts %{    or 'require "rake/classic_namespace"' in Rakefile}
-      end
-      @const_warning = true
-    end
-
-    def rakefile_location backtrace = caller
-      backtrace.map { |t| t[/([^:]+):/,1] }
-
-      re = /^#{@rakefile}$/
-      re = /#{re.source}/i if windows?
-
-      backtrace.find { |str| str =~ re } || ''
-    end
-  end
-end

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

@@ -1,9 +0,0 @@
-# The following classes used to be in the top level namespace.
-# Loading this file enables compatibility with older Rakefile that
-# referenced Task from the top level.
-
-warn "WARNING: Classic namespaces are deprecated and will be removed from future versions of Rake."
-Task = Rake::Task
-FileTask = Rake::FileTask
-FileCreationTask = Rake::FileCreationTask
-RakeApp = Rake::Application

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

@@ -1,31 +0,0 @@
-# The 'rake/clean' file defines two file lists (CLEAN and CLOBBER) and
-# two rake tasks (:clean and :clobber).
-#
-# [:clean] Clean up the project by deleting scratch files and backup
-#          files.  Add files to the CLEAN file list to have the :clean
-#          target handle them.
-#
-# [:clobber] Clobber all generated and non-source files in a project.
-#            The task depends on :clean, so all the clean files will
-#            be deleted as well as files in the CLOBBER file list.
-#            The intent of this task is to return a project to its
-#            pristine, just unpacked state.
-
-require 'rake'
-
-CLEAN = Rake::FileList["**/*~", "**/*.bak", "**/core"]
-CLEAN.clear_exclude.exclude { |fn|
-  fn.pathmap("%f") == 'core' && File.directory?(fn)
-}
-
-desc "Remove any temporary products."
-task :clean do
-  CLEAN.each { |fn| rm_r fn rescue nil }
-end
-
-CLOBBER = Rake::FileList.new
-
-desc "Remove any generated file."
-task :clobber => [:clean] do
-  CLOBBER.each { |fn| rm_r fn rescue nil }
-end

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

@@ -1,25 +0,0 @@
-module Rake
-  # ##########################################################################
-  # Mixin for creating easily cloned objects.
-  #
-  module Cloneable
-    # Clone an object by making a new object and setting all the instance
-    # variables to the same values.
-    def dup
-      sibling = self.class.new
-      instance_variables.each do |ivar|
-        value = self.instance_variable_get(ivar)
-        new_value = value.clone rescue value
-        sibling.instance_variable_set(ivar, new_value)
-      end
-      sibling.taint if tainted?
-      sibling
-    end
-
-    def clone
-      sibling = dup
-      sibling.freeze if frozen?
-      sibling
-    end
-  end
-end

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

@@ -1,21 +0,0 @@
-module Rake
-
-  # Manage several publishers as a single entity.
-  class CompositePublisher
-    def initialize
-      @publishers = []
-    end
-
-    # Add a publisher to the composite.
-    def add(pub)
-      @publishers << pub
-    end
-
-    # Upload all the individual publishers.
-    def upload
-      @publishers.each { |p| p.upload }
-    end
-  end
-
-end
-