search_biomodel 0.1.2 → 1.0.0

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

@@ -0,0 +1,7 @@
+module Rake
+
+  # Error indicating an ill-formed task declaration.
+  class TaskArgumentError < ArgumentError
+  end
+
+end

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

@@ -0,0 +1,74 @@
+module Rake
+
+  ####################################################################
+  # TaskArguments manage the arguments passed to a task.
+  #
+  class TaskArguments
+    include Enumerable
+
+    attr_reader :names
+
+    # Create a TaskArgument object with a list of named arguments
+    # (given by :names) and a set of associated values (given by
+    # :values).  :parent is the parent argument object.
+    def initialize(names, values, parent=nil)
+      @names = names
+      @parent = parent
+      @hash = {}
+      names.each_with_index { |name, i|
+        @hash[name.to_sym] = values[i] unless values[i].nil?
+      }
+    end
+
+    # Create a new argument scope using the prerequisite argument
+    # names.
+    def new_scope(names)
+      values = names.collect { |n| self[n] }
+      self.class.new(names, values, self)
+    end
+
+    # Find an argument value by name or index.
+    def [](index)
+      lookup(index.to_sym)
+    end
+
+    # Specify a hash of default values for task arguments. Use the
+    # defaults only if there is no specific value for the given
+    # argument.
+    def with_defaults(defaults)
+      @hash = defaults.merge(@hash)
+    end
+
+    def each(&block)
+      @hash.each(&block)
+    end
+
+    def method_missing(sym, *args, &block)
+      lookup(sym.to_sym)
+    end
+
+    def to_hash
+      @hash
+    end
+
+    def to_s
+      @hash.inspect
+    end
+
+    def inspect
+      to_s
+    end
+
+    protected
+
+    def lookup(name)
+      if @hash.has_key?(name)
+        @hash[name]
+      elsif @parent
+        @parent.lookup(name)
+      end
+    end
+  end
+
+  EMPTY_TASK_ARGS = TaskArguments.new([], [])
+end

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

@@ -0,0 +1,307 @@
+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

@@ -0,0 +1,22 @@
+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

@@ -0,0 +1,191 @@
+# 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