search_biomodel 1.0.0 → 1.0.1

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

@@ -1,468 +0,0 @@
-begin
-  old_verbose = $VERBOSE
-  $VERBOSE = nil
-  require 'session'
-rescue LoadError
-  if File::ALT_SEPARATOR
-    puts "Unable to run functional tests on MS Windows. Skipping."
-  else
-    puts "Unable to run functional tests -- please run \"gem install session\""
-  end
-ensure
-  $VERBOSE = old_verbose
-end
-
-if defined?(Session)
-  if File::ALT_SEPARATOR
-    puts "Unable to run functional tests on MS Windows. Skipping."
-  end
-end
-
-require File.expand_path('../helper', __FILE__)
-require 'fileutils'
-
-# Version 2.1.9 of session has a bug where the @debug instance
-# variable is not initialized, causing warning messages.  This snippet
-# of code fixes that problem.
-module Session
-  class AbstractSession
-    alias old_initialize initialize
-    def initialize(*args)
-      @debug = nil
-      old_initialize(*args)
-    end
-  end
-end if defined? Session
-
-class TestRakeFunctional < Rake::TestCase
-
-  RUBY_COMMAND = 'ruby'
-
-  def setup
-    super
-
-    @rake_path = File.expand_path("bin/rake")
-    lib_path = File.expand_path("lib")
-    @ruby_options = ["-I#{lib_path}", "-I."]
-    @verbose = ! ENV['VERBOSE'].nil?
-
-    if @verbose
-      puts
-      puts
-      puts "--------------------------------------------------------------------"
-      puts name
-      puts "--------------------------------------------------------------------"
-    end
-  end
-
-  def test_rake_default
-    Dir.chdir("test/data/default") do rake end
-    assert_match(/^DEFAULT$/, @out)
-    assert_status
-  end
-
-  def test_rake_error_on_bad_task
-    Dir.chdir("test/data/default") do rake "xyz" end
-    assert_match(/rake aborted/, @err)
-    assert_status(1)
-  end
-
-  def test_env_available_at_top_scope
-    Dir.chdir("test/data/default") do rake "TESTTOPSCOPE=1" end
-    assert_match(/^TOPSCOPE$/, @out)
-    assert_status
-  end
-
-  def test_env_available_at_task_scope
-    Dir.chdir("test/data/default") do rake "TESTTASKSCOPE=1 task_scope" end
-    assert_match(/^TASKSCOPE$/, @out)
-    assert_status
-  end
-
-  def test_multi_desc
-    in_environment(
-      'RAKE_COLUMNS' => "80",
-      "PWD" => "test/data/multidesc"
-      ) do
-      rake "-T"
-    end
-    assert_match %r{^rake a *# A / A2 *$}, @out
-    assert_match %r{^rake b *# B *$}, @out
-    refute_match %r{^rake c}, @out
-    assert_match %r{^rake d *# x{65}\.\.\.$}, @out
-  end
-
-  def test_long_description
-    in_environment("PWD" => "test/data/multidesc") do
-      rake "--describe"
-    end
-    assert_match %r{^rake a\n *A / A2 *$}m, @out
-    assert_match %r{^rake b\n *B *$}m, @out
-    assert_match %r{^rake d\n *x{80}}m, @out
-    refute_match %r{^rake c\n}m, @out
-  end
-
-  def test_proper_namespace_access
-    in_environment("PWD" => "test/data/access") do
-      rake
-    end
-    assert_not_match %r{^BAD:}, @out
-  end
-
-  def test_rbext
-    in_environment("PWD" => "test/data/rbext") do
-      rake "-N"
-    end
-    assert_match %r{^OK$}, @out
-  end
-
-  def test_system
-    in_environment('RAKE_SYSTEM' => 'test/data/sys') do
-      rake '-g', "sys1"
-    end
-    assert_match %r{^SYS1}, @out
-  end
-
-  def test_system_excludes_rakelib_files_too
-    in_environment('RAKE_SYSTEM' => 'test/data/sys') do
-      rake '-g', "sys1", '-T', 'extra'
-    end
-    refute_match %r{extra:extra}, @out
-  end
-
-  def test_by_default_rakelib_files_are_included
-    in_environment('RAKE_SYSTEM' => 'test/data/sys', "PWD" => 'test/data/extra') do
-      rake '-T', 'extra', '--trace'
-    end
-    assert_match %r{extra:extra}, @out
-  end
-
-  def test_implicit_system
-    in_environment('RAKE_SYSTEM' => File.expand_path('test/data/sys'), "PWD" => "/") do
-      rake "sys1", "--trace"
-    end
-    assert_match %r{^SYS1}, @out
-  end
-
-  def test_no_system
-    in_environment('RAKE_SYSTEM' => 'test/data/sys', "PWD" => "test/data/extra") do
-      rake '-G', "sys1"
-    end
-    assert_match %r{^Don't know how to build task}, @err # emacs wart: '
-  end
-
-  def test_nosearch_with_rakefile_uses_local_rakefile
-    in_environment("PWD" => "test/data/default") do
-      rake "--nosearch"
-    end
-    assert_match %r{^DEFAULT}, @out
-  end
-
-  def test_nosearch_without_rakefile_finds_system
-    in_environment(
-      "PWD" => "test/data/nosearch",
-      "RAKE_SYSTEM" => File.expand_path("test/data/sys")
-      ) do
-      rake "--nosearch", "sys1"
-    end
-    assert_match %r{^SYS1}, @out
-  end
-
-  def test_nosearch_without_rakefile_and_no_system_fails
-    in_environment("PWD" => "test/data/nosearch", "RAKE_SYSTEM" => "not_exist") do
-      rake "--nosearch"
-    end
-    assert_match %r{^No Rakefile found}, @err
-  end
-
-  def test_invalid_command_line_options
-    in_environment("PWD" => "test/data/default") do
-      rake "--bad-options"
-    end
-    assert_match %r{invalid +option}i, @err
-  end
-
-  def test_inline_verbose_default_should_show_command
-    in_environment("PWD" => "test/data/verbose") do
-      rake "inline_verbose_default"
-    end
-    assert_match(/ruby -e/, @err)
-  end
-
-  def test_inline_verbose_true_should_show_command
-    in_environment("PWD" => "test/data/verbose") do
-      rake "inline_verbose_true"
-    end
-    assert_match(/ruby -e/, @err)
-  end
-
-  def test_inline_verbose_false_should_not_show_command
-    in_environment("PWD" => "test/data/verbose") do
-      rake "inline_verbose_false"
-    end
-    refute_match(/ruby -e/, @err)
-  end
-
-  def test_block_verbose_false_should_not_show_command
-    in_environment("PWD" => "test/data/verbose") do
-      rake "block_verbose_false"
-    end
-    refute_match(/ruby -e/, @err)
-  end
-
-  def test_block_verbose_true_should_show_command
-    in_environment("PWD" => "test/data/verbose") do
-      rake "block_verbose_true"
-    end
-    assert_match(/ruby -e/, @err)
-  end
-
-  def test_standalone_verbose_true_should_show_command
-    in_environment("PWD" => "test/data/verbose") do
-      rake "standalone_verbose_true"
-    end
-    assert_match(/ruby -e/, @err)
-  end
-
-  def test_standalone_verbose_false_should_not_show_command
-    in_environment("PWD" => "test/data/verbose") do
-      rake "standalone_verbose_false"
-    end
-    refute_match(/ruby -e/, @err)
-  end
-
-  def test_dry_run
-    in_environment("PWD" => "test/data/default") do rake "-n", "other" end
-    assert_match %r{Execute \(dry run\) default}, @err
-    assert_match %r{Execute \(dry run\) other}, @err
-    refute_match %r{DEFAULT}, @out
-    refute_match %r{OTHER}, @out
-  end
-
-  # Test for the trace/dry_run bug found by Brian Chandler
-  def test_dry_run_bug
-    in_environment("PWD" => "test/data/dryrun") do
-      rake
-    end
-    FileUtils.rm_f "test/data/dryrun/temp_one"
-    in_environment("PWD" => "test/data/dryrun") do
-      rake "--dry-run"
-    end
-    refute_match(/No such file/, @out)
-    assert_status
-  end
-
-  # Test for the trace/dry_run bug found by Brian Chandler
-  def test_trace_bug
-    in_environment("PWD" => "test/data/dryrun") do
-      rake
-    end
-    FileUtils.rm_f "test/data/dryrun/temp_one"
-    in_environment("PWD" => "test/data/dryrun") do
-      rake "--trace"
-    end
-    refute_match(/No such file/, @out)
-    assert_status
-  end
-
-  def test_imports
-    open("test/data/imports/static_deps", "w") do |f|
-      f.puts 'puts "STATIC"'
-    end
-    FileUtils.rm_f "test/data/imports/dynamic_deps"
-    in_environment("PWD" => "test/data/imports") do
-      rake
-    end
-    assert File.exist?("test/data/imports/dynamic_deps"),
-      "'dynamic_deps' file should exist"
-    assert_match(/^FIRST$\s+^DYNAMIC$\s+^STATIC$\s+^OTHER$/, @out)
-    assert_status
-    FileUtils.rm_f "test/data/imports/dynamic_deps"
-    FileUtils.rm_f "test/data/imports/static_deps"
-  end
-
-  def test_rules_chaining_to_file_task
-    remove_chaining_files
-    in_environment("PWD" => "test/data/chains") do
-      rake
-    end
-    assert File.exist?("test/data/chains/play.app"),
-      "'play.app' file should exist"
-    assert_status
-    remove_chaining_files
-  end
-
-  def test_file_creation_task
-    in_environment("PWD" => "test/data/file_creation_task") do
-      rake "prep"
-      rake "run"
-      rake "run"
-    end
-    assert(@err !~ /^cp src/, "Should not recopy data")
-  end
-
-  def test_dash_f_with_no_arg_foils_rakefile_lookup
-    rake "-I test/data/rakelib -rtest1 -f"
-    assert_match(/^TEST1$/, @out)
-  end
-
-  def test_dot_rake_files_can_be_loaded_with_dash_r
-    rake "-I test/data/rakelib -rtest2 -f"
-    assert_match(/^TEST2$/, @out)
-  end
-
-  def test_can_invoke_task_in_toplevel_namespace
-    in_environment("PWD" => "test/data/namespace") do
-      rake "copy"
-    end
-    assert_match(/^COPY$/, @out)
-  end
-
-  def test_can_invoke_task_in_nested_namespace
-    in_environment("PWD" => "test/data/namespace") do
-      rake "nest:copy"
-      assert_match(/^NEST COPY$/, @out)
-    end
-  end
-
-  def test_tasks_can_reference_task_in_same_namespace
-    in_environment("PWD" => "test/data/namespace") do
-      rake "nest:xx"
-      assert_match(/^NEST COPY$/m, @out)
-    end
-  end
-
-  def test_tasks_can_reference_task_in_other_namespaces
-    in_environment("PWD" => "test/data/namespace") do
-      rake "b:run"
-      assert_match(/^IN A\nIN B$/m, @out)
-    end
-  end
-
-  def test_anonymous_tasks_can_be_invoked_indirectly
-    in_environment("PWD" => "test/data/namespace") do
-      rake "anon"
-      assert_match(/^ANON COPY$/m, @out)
-    end
-  end
-
-  def test_rake_namespace_refers_to_toplevel
-    in_environment("PWD" => "test/data/namespace") do
-      rake "very:nested:run"
-      assert_match(/^COPY$/m, @out)
-    end
-  end
-
-  def test_file_task_are_not_scoped_by_namespaces
-    in_environment("PWD" => "test/data/namespace") do
-      rake "xyz.rb"
-      assert_match(/^XYZ1\nXYZ2$/m, @out)
-    end
-  end
-
-  def test_file_task_dependencies_scoped_by_namespaces
-    in_environment("PWD" => "test/data/namespace") do
-      rake "scopedep.rb"
-      assert_match(/^PREPARE\nSCOPEDEP$/m, @out)
-    end
-  ensure
-    remove_namespace_files
-  end
-
-  def test_rake_returns_status_error_values
-    in_environment("PWD" => "test/data/statusreturn") do
-      rake "exit5"
-      assert_status(5)
-    end
-  end
-
-  def test_rake_returns_no_status_error_on_normal_exit
-    in_environment("PWD" => "test/data/statusreturn") do
-      rake "normal"
-      assert_status(0)
-    end
-  end
-
-  def test_comment_before_task_acts_like_desc
-    in_environment("PWD" => "test/data/comments") do
-      rake "-T"
-    end
-    refute_match(/comment for t1/, @out)
-  end
-
-  def test_comment_separated_from_task_by_blank_line_is_not_picked_up
-    Dir.chdir("test/data/comments") { rake("-T")}
-    assert_not_match("t2", @out)
-  end
-
-  def test_comment_after_desc_is_ignored
-    Dir.chdir("test/data/comments") { rake("-T")}
-    assert_match("override comment for t3", @out)
-  end
-
-  def test_comment_before_desc_is_ignored
-    Dir.chdir("test/data/comments") { rake("-T")}
-    assert_match("override comment for t4", @out)
-  end
-
-  def test_correct_number_of_tasks_reported
-    Dir.chdir("test/data/comments") { rake("-T")}
-    assert_equal(2, @out.split(/\n/).grep(/t\d/).size)
-  end
-
-  def test_file_list_is_requirable_separately
-    ruby "-rrake/file_list", "-e 'puts Rake::FileList[\"a\"].size'"
-    assert_equal "1\n", @out
-    assert_equal 0, @status
-  end
-
-  private
-
-  def assert_not_match(pattern, string, comment="'#{pattern}' was found (incorrectly) in '#{string}.inspect")
-    assert_nil Regexp.new(pattern).match(string), comment
-  end
-
-  def remove_chaining_files
-    %w(play.scpt play.app base).each do |fn|
-      FileUtils.rm_f File.join("test/data/chains", fn)
-    end
-  end
-
-  def remove_namespace_files
-    %w(scopedep.rb).each do |fn|
-      FileUtils.rm_f File.join("test/data/namespace", fn)
-    end
-  end
-
-  # Run a shell Ruby command with command line options (using the
-  # default test options). Output is captured in @out, @err and
-  # @status.
-  def ruby(*option_list)
-    run_ruby(@ruby_options + option_list)
-  end
-
-  # Run a command line rake with the give rake options.  Default
-  # command line ruby options are included.  Output is captured in
-  # @out, @err and @status.
-  def rake(*rake_options)
-    run_ruby @ruby_options + [@rake_path] + rake_options
-  end
-
-  # Low level ruby command runner ...
-  def run_ruby(option_list)
-    shell = Session::Shell.new
-    command = "#{RUBY_COMMAND} " + option_list.join(' ')
-    puts "COMMAND: [#{command}]" if @verbose
-    @out, @err = shell.execute command
-    @status = shell.exit_status
-    puts "STATUS:  [#{@status}]" if @verbose
-    puts "OUTPUT:  [#{@out}]" if @verbose
-    puts "ERROR:   [#{@err}]" if @verbose
-    puts "PWD:     [#{Dir.pwd}]" if @verbose
-    shell.close
-  end
-
-  def assert_status(expected_status=0)
-    assert_equal expected_status, @status
-  end
-end if defined?(Session)

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

@@ -1,52 +0,0 @@
-require File.expand_path('../helper', __FILE__)
-
-class TestRakeInvocationChain < Rake::TestCase
-
-  def setup
-    super
-
-    @empty = Rake::InvocationChain::EMPTY
-
-    @first_member = "A"
-    @second_member = "B"
-    @one = @empty.append(@first_member)
-    @two = @one.append(@second_member)
-  end
-
-  def test_append
-    chain = @empty.append("A")
-
-    assert_equal 'TOP => A', chain.to_s # HACK
-  end
-
-  def test_append_one_circular
-    ex = assert_raises RuntimeError do
-      @one.append(@first_member)
-    end
-    assert_match(/circular +dependency/i, ex.message)
-    assert_match(/A.*=>.*A/, ex.message)
-  end
-
-  def test_append_two_circular
-    ex = assert_raises RuntimeError do
-      @two.append(@first_member)
-    end
-    assert_match(/A.*=>.*B.*=>.*A/, ex.message)
-  end
-
-  def test_member_eh_one
-    assert @one.member?(@first_member)
-  end
-
-  def test_member_eh_two
-    assert @two.member?(@first_member)
-    assert @two.member?(@second_member)
-  end
-
-  def test_to_s_empty
-    assert_equal "TOP", @empty.to_s
-    assert_equal "TOP => A", @one.to_s
-  end
-
-end
-

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

@@ -1,23 +0,0 @@
-require File.expand_path('../helper', __FILE__)
-require 'rake/loaders/makefile'
-
-class TestRakeMakefileLoader < Rake::TestCase
-  include Rake
-
-  def test_parse
-    Task.clear
-    loader = Rake::MakefileLoader.new
-    loader.load("test/data/sample.mf")
-    %w(a b c d).each do |t|
-      assert Task.task_defined?(t), "#{t} should be a defined task"
-    end
-    assert_equal %w(a1 a2 a3 a4 a5 a6 a7).sort, Task['a'].prerequisites.sort
-    assert_equal %w(b1 b2 b3 b4 b5 b6 b7).sort, Task['b'].prerequisites.sort
-    assert_equal %w(c1).sort, Task['c'].prerequisites.sort
-    assert_equal %w(d1 d2).sort, Task['d'].prerequisites.sort
-    assert_equal %w(e1 f1).sort, Task['e'].prerequisites.sort
-    assert_equal %w(e1 f1).sort, Task['f'].prerequisites.sort
-    assert_equal ["g1", "g 2", "g 3", "g4"].sort, Task['g 0'].prerequisites.sort
-    assert_equal 7, Task.tasks.size
-  end
-end

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

@@ -1,51 +0,0 @@
-require File.expand_path('../helper', __FILE__)
-require 'thread'
-
-class TestRakeMultiTask < Rake::TestCase
-  include Rake
-  include Rake::DSL
-
-  def setup
-    super
-
-    Task.clear
-    @runs = Array.new
-    @mutex = Mutex.new
-  end
-
-  def add_run(obj)
-    @mutex.synchronize do
-      @runs << obj
-    end
-  end
-
-  def test_running_multitasks
-    task :a do 3.times do |i| add_run("A#{i}"); sleep 0.01; end end
-    task :b do 3.times do |i| add_run("B#{i}"); sleep 0.01;  end end
-    multitask :both => [:a, :b]
-    Task[:both].invoke
-    assert_equal 6, @runs.size
-    assert @runs.index("A0") < @runs.index("A1")
-    assert @runs.index("A1") < @runs.index("A2")
-    assert @runs.index("B0") < @runs.index("B1")
-    assert @runs.index("B1") < @runs.index("B2")
-  end
-
-  def test_all_multitasks_wait_on_slow_prerequisites
-    task :slow do 3.times do |i| add_run("S#{i}"); sleep 0.05 end end
-    task :a => [:slow] do 3.times do |i| add_run("A#{i}"); sleep 0.01 end end
-    task :b => [:slow] do 3.times do |i| add_run("B#{i}"); sleep 0.01 end end
-    multitask :both => [:a, :b]
-    Task[:both].invoke
-    assert_equal 9, @runs.size
-    assert @runs.index("S0") < @runs.index("S1")
-    assert @runs.index("S1") < @runs.index("S2")
-    assert @runs.index("S2") < @runs.index("A0")
-    assert @runs.index("S2") < @runs.index("B0")
-    assert @runs.index("A0") < @runs.index("A1")
-    assert @runs.index("A1") < @runs.index("A2")
-    assert @runs.index("B0") < @runs.index("B1")
-    assert @runs.index("B1") < @runs.index("B2")
-  end
-end
-

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

@@ -1,43 +0,0 @@
-require File.expand_path('../helper', __FILE__)
-
-class TestRakeNameSpace < Rake::TestCase
-
-  class TM
-    include Rake::TaskManager
-  end
-
-  def test_namespace_creation
-    mgr = TM.new
-    ns = Rake::NameSpace.new(mgr, [])
-    refute_nil ns
-  end
-
-  def test_namespace_lookup
-    mgr = TM.new
-    ns = mgr.in_namespace("n") do
-      mgr.define_task(Rake::Task, "t")
-    end
-
-    refute_nil ns["t"]
-    assert_equal mgr["n:t"], ns["t"]
-  end
-
-  def test_namespace_reports_tasks_it_owns
-    mgr = TM.new
-    nns = nil
-    ns = mgr.in_namespace("n") do
-      mgr.define_task(Rake::Task, :x)
-      mgr.define_task(Rake::Task, :y)
-      nns = mgr.in_namespace("nn") do
-        mgr.define_task(Rake::Task, :z)
-      end
-    end
-    mgr.in_namespace("m") do
-      mgr.define_task(Rake::Task, :x)
-    end
-
-    assert_equal ["n:nn:z", "n:x", "n:y"],
-      ns.tasks.map { |tsk| tsk.name }
-    assert_equal ["n:nn:z"], nns.tasks.map {|t| t.name}
-  end
-end