search_biomodel 0.1.2 → 1.0.0

data/search_biomodel/ruby/1.8/gems/builder-3.0.0/test/test_namecollision.rb

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+#!/usr/bin/env ruby
+
+#--
+# Portions copyright 2004 by Jim Weirich (jim@weirichhouse.org).
+# Portions copyright 2005 by Sam Ruby (rubys@intertwingly.net).
+# All rights reserved.
+
+# Permission is granted for use, copying, modification, distribution,
+# and distribution of modified versions of this work as long as the
+# above copyright notice is included.
+#++
+
+require 'test/unit'
+require 'builder/xchar'
+
+class TestNameCollisions < Test::Unit::TestCase
+  module Collide
+    def xchr
+    end
+  end
+
+  def test_no_collision
+    assert_nothing_raised do
+      Builder.check_for_name_collision(Collide, :not_defined)
+    end
+  end
+
+  def test_collision
+    assert_raise RuntimeError do
+      Builder.check_for_name_collision(Collide, "xchr")
+    end
+  end
+
+  def test_collision_with_symbol
+    assert_raise RuntimeError do
+      Builder.check_for_name_collision(Collide, :xchr)
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/builder-3.0.0/test/test_xchar.rb

@@ -0,0 +1,77 @@
+#!/usr/bin/env ruby
+
+#--
+# Portions copyright 2004 by Jim Weirich (jim@weirichhouse.org).
+# Portions copyright 2005 by Sam Ruby (rubys@intertwingly.net).
+# All rights reserved.
+
+# Permission is granted for use, copying, modification, distribution,
+# and distribution of modified versions of this work as long as the
+# above copyright notice is included.
+#++
+
+#!/usr/bin/env ruby
+
+require 'test/unit'
+require 'builder/xchar'
+
+if String.method_defined?(:encode)
+  class String
+    ENCODING_BINARY = Encoding.find('BINARY')
+
+    # shim method for testing purposes
+    def to_xs(escape=true)
+      raise NameError.new('to_xs') unless caller[0].index(__FILE__)
+
+      result = Builder::XChar.encode(self)
+      if escape
+        result.gsub(/[^\u0000-\u007F]/) {|c| "&##{c.ord};"}
+      else
+        # really only useful for testing purposes
+        result.force_encoding(ENCODING_BINARY)
+      end
+    end
+  end
+end
+
+class TestXmlEscaping < Test::Unit::TestCase
+  REPLACEMENT_CHAR = Builder::XChar::REPLACEMENT_CHAR.to_xs
+
+  def test_ascii
+    assert_equal 'abc', 'abc'.to_xs
+  end
+
+  def test_predefined
+    assert_equal '&amp;', '&'.to_xs              # ampersand
+    assert_equal '&lt;',  '<'.to_xs              # left angle bracket
+    assert_equal '&gt;',  '>'.to_xs              # right angle bracket
+  end
+
+  def test_invalid
+    assert_equal REPLACEMENT_CHAR, "\x00".to_xs               # null
+    assert_equal REPLACEMENT_CHAR, "\x0C".to_xs               # form feed
+    assert_equal REPLACEMENT_CHAR, "\xEF\xBF\xBF".to_xs       # U+FFFF
+  end
+
+  def test_iso_8859_1
+    assert_equal '&#231;', "\xE7".to_xs          # small c cedilla
+    assert_equal '&#169;', "\xA9".to_xs          # copyright symbol
+  end
+
+  def test_win_1252
+    assert_equal '&#8217;', "\x92".to_xs         # smart quote
+    assert_equal '&#8364;', "\x80".to_xs         # euro
+  end
+
+  def test_utf8
+    assert_equal '&#8217;', "\xE2\x80\x99".to_xs # right single quote
+    assert_equal '&#169;',  "\xC2\xA9".to_xs     # copy
+  end
+ 
+  def test_utf8_verbatim
+    assert_equal "\xE2\x80\x99", "\xE2\x80\x99".to_xs(false)  # right single quote
+    assert_equal "\xC2\xA9",  "\xC2\xA9".to_xs(false)         # copy
+    assert_equal "\xC2\xA9&amp;\xC2\xA9",
+      "\xC2\xA9&\xC2\xA9".to_xs(false)                        # copy with ampersand
+  end
+end

data/search_biomodel/ruby/1.8/gems/git-1.2.5/README

@@ -0,0 +1,240 @@
+== Git Library for Ruby
+
+Library for using Git in Ruby. Test.
+
+= Homepage
+
+Git public hosting of the project source code is at:
+
+http://github.com/schacon/ruby-git
+
+= Install
+
+You can install Ruby/Git like this:
+
+$ sudo gem install git
+
+= Major Objects
+
+Git::Base - this is the object returned from a Git.open or Git.clone.  
+Most major actions are called from this object.
+
+Git::Object - this is the base object for your tree, blob and commit objects,
+returned from @git.gtree or @git.object calls.  the Git::AbstractObject will
+have most of the calls in common for all those objects.
+
+Git::Diff - returns from a @git.diff command.  It is an Enumerable that returns
+Git::Diff:DiffFile objects from which you can get per file patches and insertion/deletion
+statistics.  You can also get total statistics from the Git::Diff object directly.
+
+Git::Status - returns from a @git.status command.  It is an Enumerable that returns
+Git:Status::StatusFile objects for each object in git, which includes files in the working
+directory, in the index and in the repository.  Similar to running 'git status' on the command
+line to determine untracked and changed files.
+
+Git::Branches - Enumerable object that holds Git::Branch objects.  You can call .local or .remote
+on it to filter to just your local or remote branches.
+
+Git::Remote - A reference to a remote repository that is tracked by this repository.
+
+Git::Log - An Enumerable object that references all the Git::Object::Commit objects that encompass
+your log query, which can be constructed through methods on the Git::Log object, like:
+
+ @git.log(20).object("some_file").since("2 weeks ago").between('v2.6', 'v2.7').each { |commit| [block] } 
+
+= Examples
+
+Here are a bunch of examples of how to use the Ruby/Git package. 
+
+First you have to remember to require rubygems if it's not.  Then include the 'git' gem.
+
+   require 'rubygems'
+   require 'git'
+
+Here are the operations that need read permission only.
+      
+   g = Git.open (working_dir, :log => Logger.new(STDOUT))
+   
+   g.index
+   g.index.readable?
+   g.index.writable?
+   g.repo
+   g.dir
+   
+   g.log   # returns array of Git::Commit objects
+   g.log.since('2 weeks ago')
+   g.log.between('v2.5', 'v2.6')
+   g.log.each {|l| puts l.sha }
+   g.gblob('v2.5:Makefile').log.since('2 weeks ago')
+   
+   g.object('HEAD^').to_s  # git show / git rev-parse
+   g.object('HEAD^').contents
+   g.object('v2.5:Makefile').size
+   g.object('v2.5:Makefile').sha
+   
+   g.gtree(treeish)
+   g.gblob(treeish)
+   g.gcommit(treeish)
+   
+   
+   commit = g.gcommit('1cc8667014381')
+    commit.gtree
+    commit.parent.sha
+    commit.parents.size
+    commit.author.name
+    commit.author.email
+    commit.author.date.strftime("%m-%d-%y")
+    commit.committer.name
+    commit.date.strftime("%m-%d-%y")
+    commit.message
+   
+  tree = g.gtree("HEAD^{tree}")
+    tree.blobs
+    tree.subtrees
+    tree.children # blobs and subtrees
+   
+   g.revparse('v2.5:Makefile')
+   
+   g.branches # returns Git::Branch objects
+   g.branches.local
+   g.branches.remote
+   g.branches[:master].gcommit
+   g.branches['origin/master'].gcommit
+   
+   g.grep('hello')  # implies HEAD
+   g.blob('v2.5:Makefile').grep('hello')
+   g.tag('v2.5').grep('hello', 'docs/')
+   
+   g.diff(commit1, commit2).size
+   g.diff(commit1, commit2).stats
+   g.gtree('v2.5').diff('v2.6').insertions
+   g.diff('gitsearch1', 'v2.5').path('lib/')
+   g.diff('gitsearch1', @git.gtree('v2.5'))
+   g.diff('gitsearch1', 'v2.5').path('docs/').patch
+   g.gtree('v2.5').diff('v2.6').patch
+   
+   g.gtree('v2.5').diff('v2.6').each do |file_diff|
+     puts file_diff.path
+     puts file_diff.patch
+     puts file_diff.blob(:src).contents
+   end
+   
+   g.config('user.name')  # returns 'Scott Chacon'
+   g.config # returns whole config hash
+   
+   g.tag # returns array of Git::Tag objects
+   
+   
+   
+And here are the operations that will need to write to your git repository.
+   
+   
+   g = Git.init
+     Git.init('project')
+     Git.init('/home/schacon/proj', 
+	 	  { :git_dir => '/opt/git/proj.git', 
+		     :index_file => '/tmp/index'} )
+ 	  
+   g = Git.clone(URI, :name => 'name', :path => '/tmp/checkout')   
+   g.config('user.name', 'Scott Chacon')
+   g.config('user.email', 'email@email.com')      
+   
+   g.add('.')
+   g.add([file1, file2])
+   
+   g.remove('file.txt')
+   g.remove(['file.txt', 'file2.txt'])
+		     
+   g.commit('message')
+   g.commit_all('message')
+   
+   g = Git.clone(repo, 'myrepo')
+   g.chdir do
+    new_file('test-file', 'blahblahblah')
+    g.status.changed.each do |file|
+     puts file.blob(:index).contents
+    end
+   end
+   
+   g.reset # defaults to HEAD
+   g.reset_hard(Git::Commit)
+   
+   g.branch('new_branch') # creates new or fetches existing
+   g.branch('new_branch').checkout
+   g.branch('new_branch').delete
+   g.branch('existing_branch').checkout
+   
+   g.checkout('new_branch')
+   g.checkout(g.branch('new_branch'))
+   
+   g.branch(name).merge(branch2)
+   g.branch(branch2).merge  # merges HEAD with branch2
+   
+   g.branch(name).in_branch(message) { # add files }  # auto-commits
+   g.merge('new_branch')
+   g.merge('origin/remote_branch')
+   g.merge(b.branch('master'))
+   g.merge([branch1, branch2])
+   
+   r = g.add_remote(name, uri)  # Git::Remote
+   r = g.add_remote(name, Git::Base)  # Git::Remote
+   
+   g.remotes  # array of Git::Remotes
+   g.remote(name).fetch
+   g.remote(name).remove
+   g.remote(name).merge
+   g.remote(name).merge(branch)
+   
+   g.fetch
+   g.fetch(g.remotes.first)
+   
+   g.pull
+   g.pull(Git::Repo, Git::Branch) # fetch and a merge
+   
+   g.add_tag('tag_name') # returns Git::Tag
+   
+   g.repack
+
+   g.push
+   g.push(g.remote('name'))
+
+
+Some examples of more low-level index and tree operations
+
+   g.with_temp_index do 
+
+     g.read_tree(tree3) # calls self.index.read_tree
+     g.read_tree(tree1, :prefix => 'hi/')
+
+     c = g.commit_tree('message')
+     # or #
+     t = g.write_tree
+     c = g.commit_tree(t, :message => 'message', :parents => [sha1, sha2])
+
+     g.branch('branch_name').update_ref(c)
+     g.update_ref(branch, c)
+
+     g.with_temp_working do # new blank working directory
+       g.checkout
+       g.checkout(another_index)
+       g.commit # commits to temp_index
+     end    
+   end
+
+   g.set_index('/path/to/index')
+   
+   
+   g.with_index(path) do 
+     # calls set_index, then switches back after
+   end
+   
+   g.with_working(dir) do
+   # calls set_working, then switches back after
+   end
+   
+   g.with_temp_working(dir) do
+     g.checkout_index(:prefix => dir, :path_limiter => path)
+     # do file work
+     g.commit # commits to index
+   end
+   

data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git.rb

@@ -0,0 +1,156 @@
+
+# Add the directory containing this file to the start of the load path if it
+# isn't there already.
+$:.unshift(File.dirname(__FILE__)) unless
+  $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
+
+require 'git/base'
+require 'git/path'
+require 'git/lib'
+
+require 'git/repository'
+require 'git/index'
+require 'git/working_directory'
+
+require 'git/log'
+require 'git/object'
+
+require 'git/branches'
+require 'git/branch'
+require 'git/remote'
+
+require 'git/diff'
+require 'git/status'
+require 'git/author'
+
+require 'git/stashes'
+require 'git/stash'
+
+lib = Git::Lib.new(nil, nil)
+unless lib.meets_required_version?
+  $stderr.puts "[WARNING] The git gem requires git #{lib.required_command_version.join('.')} or later, but only found #{lib.current_command_version.join('.')}. You should probably upgrade."
+end
+
+# Git/Ruby Library
+#
+# This provides bindings for working with git in complex
+# interactions, including branching and merging, object
+# inspection and manipulation, history, patch generation
+# and more.  You should be able to do most fundamental git
+# operations with this library.
+#
+# This module provides the basic functions to open a git 
+# reference to work with. You can open a working directory,
+# open a bare repository, initialize a new repo or clone an
+# existing remote repository.
+#
+# Author::    Scott Chacon (mailto:schacon@gmail.com)
+# License::   MIT License
+module Git
+
+  VERSION = '1.0.4'
+  
+  # open a bare repository
+  #
+  # this takes the path to a bare git repo
+  # it expects not to be able to use a working directory
+  # so you can't checkout stuff, commit things, etc.
+  # but you can do most read operations
+  def self.bare(git_dir, options = {})
+    Base.bare(git_dir, options)
+  end
+    
+  # open an existing git working directory
+  # 
+  # this will most likely be the most common way to create
+  # a git reference, referring to a working directory.
+  # if not provided in the options, the library will assume
+  # your git_dir and index are in the default place (.git/, .git/index)
+  #
+  # options
+  #   :repository => '/path/to/alt_git_dir'
+  #   :index => '/path/to/alt_index_file'
+  def self.open(working_dir, options = {})
+    Base.open(working_dir, options)
+  end
+
+  # initialize a new git repository, defaults to the current working directory
+  #
+  # options
+  #   :repository => '/path/to/alt_git_dir'
+  #   :index => '/path/to/alt_index_file'
+  def self.init(working_dir = '.', options = {})
+    Base.init(working_dir, options)
+  end
+
+  # clones a remote repository
+  #
+  # options
+  #   :bare => true (does a bare clone)
+  #   :repository => '/path/to/alt_git_dir'
+  #   :index => '/path/to/alt_index_file'
+  #
+  # example
+  #  Git.clone('git://repo.or.cz/rubygit.git', 'clone.git', :bare => true)
+  #
+  def self.clone(repository, name, options = {})
+    Base.clone(repository, name, options)
+  end
+  
+  # Export the current HEAD (or a branch, if <tt>options[:branch]</tt>
+  # is specified) into the +name+ directory, then remove all traces of git from the
+  # directory.
+  #
+  # See +clone+ for options.  Does not obey the <tt>:remote</tt> option,
+  # since the .git info will be deleted anyway; always uses the default
+  # remote, 'origin.'
+  def self.export(repository, name, options = {})
+    options.delete(:remote)
+    repo = clone(repository, name, {:depth => 1}.merge(options))
+    repo.checkout("origin/#{options[:branch]}") if options[:branch]
+    Dir.chdir(repo.dir.to_s) { FileUtils.rm_r '.git' }
+  end
+
+  #g.config('user.name', 'Scott Chacon') # sets value
+  #g.config('user.email', 'email@email.com')  # sets value
+  #g.config('user.name')  # returns 'Scott Chacon'
+  #g.config # returns whole config hash
+  def config(name = nil, value = nil)
+    lib = Git::Lib.new
+    if(name && value)
+      # set value
+      lib.config_set(name, value)
+    elsif (name)
+      # return value
+      lib.config_get(name)
+    else
+      # return hash
+      lib.config_list
+    end
+  end
+
+  # Same as g.config, but forces it to be at the global level
+  #
+  #g.config('user.name', 'Scott Chacon') # sets value
+  #g.config('user.email', 'email@email.com')  # sets value
+  #g.config('user.name')  # returns 'Scott Chacon'
+  #g.config # returns whole config hash
+  def self.global_config(name = nil, value = nil)
+    lib = Git::Lib.new(nil, nil)
+    if(name && value)
+      # set value
+      lib.global_config_set(name, value)
+    elsif (name)
+      # return value
+      lib.global_config_get(name)
+    else
+      # return hash
+      lib.global_config_list
+    end
+  end
+
+  def global_config(name = nil, value = nil)
+    self.class.global_config(name, value)
+  end
+    
+end