search_biomodel 1.0.0 → 1.0.1

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

@@ -1,156 +0,0 @@
-
-# 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

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/.gitignore

@@ -1,9 +0,0 @@
-.DS_Store
-.yardoc
-doc
-coverage
-tmp
-*~
-*.gem
-.bundle
-Gemfile.lock

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/.rspec

@@ -1 +0,0 @@
---color

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/.travis.yml

@@ -1,7 +0,0 @@
-script: "rake"
-rvm:
-  - 1.8.7
-  - 1.9.2
-  - ree
-  - rbx
-  - jruby

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/CHANGELOG.md

@@ -1,55 +0,0 @@
-## 0.4.4
-
-* Fix: [issue 6](https://github.com/rubiii/gyoku/issues/6) -
-  `Gyoku.xml` does not modify the original Hash.
-
-## 0.4.3
-
-* Fix: Make sure `require "date"` when necessary.
-
-## 0.4.2
-
-* Fix: `Array.to_xml` so that the given :namespace is applied to every element
-  in an Array.
-
-## 0.4.1
-
-* Fix: Alternative formulas and namespaces.
-
-## 0.4.0
-
-* Feature: Added alternative Symbol conversion formulas. You can choose between
-  :lower_camelcase (the default), :camelcase and :none.
-
-      Gyoku.convert_symbols_to :camelcase
-
-  You can even define your own formula:
-
-      Gyoku.convert_symbols_to { |key| key.upcase }
-
-## 0.3.1
-
-* Feature: Gyoku now calls Proc objects and converts their return value.
-
-## 0.3.0
-
-* Feature: Now when all Hash keys need to be namespaced (like with
-  elementFormDefault), you can use options to to trigger this behavior.
-
-      Gyoku.xml hash,
-        :element_form_default => :qualified,
-        :namespace => :v2
-
-## 0.2.0
-
-* Feature: Added support for self-closing tags. Hash keys ending with a forward
-  slash (regardless of their value) are now converted to self-closing tags.
-
-## 0.1.1
-
-* Fix: Allow people to use new versions of builder.
-
-## 0.1.0
-
-* Initial version. Gyoku was born as a core extension inside the
-  [Savon](http://rubygems.org/gems/savon) library.

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/Gemfile

@@ -1,2 +0,0 @@
-source :rubygems
-gemspec

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/LICENSE

@@ -1,20 +0,0 @@
-Copyright (c) 2010 Daniel Harrington
-
-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.

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/README.md

@@ -1,81 +0,0 @@
-Gyoku ![http://travis-ci.org/rubiii/gyoku](http://travis-ci.org/rubiii/gyoku.png)
-=====
-
-Gyoku translates Ruby Hashes to XML.
-
-[Bugs](http://github.com/rubiii/gyoku/issues) | [Docs](http://rubydoc.info/gems/gyoku/frames)
-
-Installation
-------------
-
-The gem is available through [Rubygems](http://rubygems.org/gems/gyoku) and can be installed via:
-
-    $ gem install gyoku
-
-An example
-----------
-
-    Gyoku.xml :find_user => { :id => 123, "wsdl:Key" => "api" }
-    # => "<findUser><id>123</id><wsdl:Key>api</wsdl:Key></findUser>"
-
-As you might notice, Gyoku follows a couple of conventions for translating Hashes into XML.
-
-Conventions
------------
-
-### Hash keys
-
-* Symbols are converted to lowerCamelCase Strings
-* Strings are not converted and may contain namespaces
-
-### Hash values
-
-* DateTime objects are converted to xs:dateTime Strings
-* Objects responding to :to_datetime (except Strings) are converted to xs:dateTime Strings
-* TrueClass and FalseClass objects are converted to "true" and "false" Strings
-* NilClass objects are converted to xsi:nil tags
-* These conventions are also applied to the return value of objects responding to :call
-* All other objects are converted to Strings using :to_s
-
-Symbols are converted to lowerCamelCase?
-----------------------------------------
-
-That's the default. But you can use one of the other conversion formulas:
-
-    Gyoku.convert_symbols_to :camelcase  # or one of [:none, :lower_camelcase]
-
-or even define you own one:
-
-    Gyoku.convert_symbols_to { |key| key.upcase }
-
-Special characters
-------------------
-
-Gyoku escapes special characters unless the Hash key ends with an exclamation mark:
-
-    Gyoku.xml :escaped => "<tag />", :not_escaped! => "<tag />"
-    # => "<escaped>&lt;tag /&gt;</escaped><notEscaped><tag /></notEscaped>"
-
-Self-closing tags
------------------
-
-Hash Keys ending with a forward slash create self-closing tags:
-
-    Gyoku.xml :"self_closing/" => "", "selfClosing/" => nil
-    # => "<selfClosing/><selfClosing/>"
-
-Sort XML tags
--------------
-
-In case you need the XML tags to be in a specific order, you can specify the order through an additional Array stored under an :order! key:
-
-    Gyoku.xml :name => "Eve", :id => 1, :order! => [:id, :name]
-    # => "<id>1</id><name>Eve</name>"
-
-XML attributes
---------------
-
-Adding XML attributes is rather ugly, but it can be done by specifying an additional Hash stored under an :attributes! key:
-
-    Gyoku.xml :person => "Eve", :attributes! => { :person => { :id => 1 } }
-    # => "<person id=\"1\">Eve</person>"

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/Rakefile

@@ -1,11 +0,0 @@
-require "bundler"
-Bundler::GemHelper.install_tasks
-
-require "rspec/core/rake_task"
-
-RSpec::Core::RakeTask.new do |t|
-  t.rspec_opts = %w(-c)
-end
-
-task :default => :spec
-task :test => :spec

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/gyoku.gemspec

@@ -1,26 +0,0 @@
-$:.push File.expand_path("../lib", __FILE__)
-require "gyoku/version"
-
-Gem::Specification.new do |s|
-  s.name        = "gyoku"
-  s.version     = Gyoku::VERSION
-  s.platform    = Gem::Platform::RUBY
-  s.authors     = "Daniel Harrington"
-  s.email       = "me@rubiii.com"
-  s.homepage    = "http://github.com/rubiii/#{s.name}"
-  s.summary     = %q{Converts Ruby Hashes to XML}
-  s.description = %q{Gyoku converts Ruby Hashes to XML}
-
-  s.rubyforge_project = "gyoku"
-
-  s.add_dependency "builder", ">= 2.1.2"
-
-  s.add_development_dependency "rspec", "~> 2.4.0"
-  s.add_development_dependency "autotest"
-  s.add_development_dependency "mocha", "~> 0.9.9"
-
-  s.files         = `git ls-files`.split("\n")
-  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
-  s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
-  s.require_paths = ["lib"]
-end

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/lib/gyoku/array.rb

@@ -1,45 +0,0 @@
-require "builder"
-
-require "gyoku/hash"
-require "gyoku/xml_value"
-
-module Gyoku
-  class Array
-
-    # Translates a given +array+ to XML. Accepts the XML +key+ to add the elements to,
-    # whether to +escape_xml+ and an optional Hash of +attributes+.
-    def self.to_xml(array, key, escape_xml = true, attributes = {}, options = {})
-      iterate_with_xml array, attributes do |xml, item, attrs, index|
-        case item
-          when ::Hash   then xml.tag!(key, attrs) { xml << Hash.to_xml(item, options) }
-          when NilClass then xml.tag!(key, "xsi:nil" => "true")
-          else               xml.tag!(key, attrs) { xml << XMLValue.create(item, escape_xml) }
-        end
-      end
-    end
-
-  private
-
-    # Iterates over a given +array+ with a Hash of +attributes+ and yields a builder +xml+
-    # instance, the current +item+, any XML +attributes+ and the current +index+.
-    def self.iterate_with_xml(array, attributes)
-      xml = Builder::XmlMarkup.new
-      array.each_with_index do |item, index|
-        yield xml, item, tag_attributes(attributes, index), index
-      end
-      xml.target!
-    end
-
-    # Takes a Hash of +attributes+ and the +index+ for which to return attributes
-    # for duplicate tags.
-    def self.tag_attributes(attributes, index)
-      return {} if attributes.empty?
-
-      attributes.inject({}) do |hash, (key, value)|
-        value = value[index] if value.kind_of? ::Array
-        hash.merge key => value
-      end
-    end
-
-  end
-end

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/lib/gyoku/core_ext/string.rb

@@ -1,19 +0,0 @@
-module Gyoku
-  module CoreExt
-    module String
-
-      # Returns the String in lowerCamelCase.
-      def lower_camelcase
-        self[0].chr.downcase + self.camelcase[1..-1]
-      end
-
-      # Returns the String in CamelCase.
-      def camelcase
-        self.gsub(/\/(.?)/) { "::#{$1.upcase}" }.gsub(/(?:^|_)(.)/) { $1.upcase }
-      end
-
-    end
-  end
-end
-
-String.send :include, Gyoku::CoreExt::String

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/lib/gyoku/hash.rb

@@ -1,55 +0,0 @@
-require "builder"
-
-require "gyoku/array"
-require "gyoku/xml_key"
-require "gyoku/xml_value"
-
-module Gyoku
-  class Hash
-
-    # Translates a given +hash+ with +options+ to XML.
-    def self.to_xml(hash, options = {})
-      iterate_with_xml hash do |xml, key, value, attributes|
-        self_closing = key.to_s[-1, 1] == "/"
-        escape_xml = key.to_s[-1, 1] != "!"
-        xml_key = XMLKey.create key, options
-
-        case
-          when ::Array === value  then xml << Array.to_xml(value, xml_key, escape_xml, attributes, options)
-          when ::Hash === value   then xml.tag!(xml_key, attributes) { xml << Hash.to_xml(value, options) }
-          when self_closing       then xml.tag!(xml_key, attributes)
-          when NilClass === value then xml.tag!(xml_key, "xsi:nil" => "true")
-          else                         xml.tag!(xml_key, attributes) { xml << XMLValue.create(value, escape_xml) }
-        end
-      end
-    end
-
-  private
-
-    # Iterates over a given +hash+ and yields a builder +xml+ instance, the current
-    # Hash +key+ and any XML +attributes+.
-    def self.iterate_with_xml(hash)
-      xml = Builder::XmlMarkup.new
-      attributes = hash.delete(:attributes!) || {}
-
-      order(hash).each { |key| yield xml, key, hash[key], (attributes[key] || {}) }
-
-      xml.target!
-    end
-
-    # Deletes and returns an Array of keys stored under the :order! key of a given +hash+.
-    # Defaults to return the actual keys of the Hash if no :order! key could be found.
-    # Raises an ArgumentError in case the :order! Array does not match the Hash keys.
-    def self.order(hash)
-      order = hash.delete :order!
-      order = hash.keys unless order.kind_of? ::Array
-
-      missing, spurious = hash.keys - order, order - hash.keys
-      raise ArgumentError, "Missing elements in :order! #{missing.inspect}" unless missing.empty?
-      raise ArgumentError, "Spurious elements in :order! #{spurious.inspect}" unless spurious.empty?
-
-      order
-    end
-
-  end
-end

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/lib/gyoku/version.rb

@@ -1,5 +0,0 @@
-module Gyoku
-
-  VERSION = "0.4.4"
-
-end

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/lib/gyoku/xml_key.rb

@@ -1,63 +0,0 @@
-require "gyoku/core_ext/string"
-
-module Gyoku
-  module XMLKey
-    class << self
-
-      FORMULAS = {
-        :lower_camelcase => lambda { |key| key.lower_camelcase },
-        :camelcase       => lambda { |key| key.camelcase },
-        :none            => lambda { |key| key }
-      }
-
-      # Converts a given +object+ with +options+ to an XML key.
-      def create(key, options = {})
-        xml_key = chop_special_characters key.to_s
-
-        if unqualified = unqualify?(xml_key)
-          xml_key = xml_key.split(":").last
-        end
-
-        xml_key = symbol_converter.call(xml_key) if Symbol === key
-
-        if !unqualified && qualify?(options) && !xml_key.include?(":")
-          xml_key = "#{options[:namespace]}:#{xml_key}"
-        end
-
-        xml_key
-      end
-
-      # Returns the formula for converting Symbol keys.
-      def symbol_converter
-        @symbol_converter ||= FORMULAS[:lower_camelcase]
-      end
-
-      # Sets the +formula+ for converting Symbol keys.
-      # Accepts one of +FORMULAS+ of an object responding to <tt>:call</tt>.
-      def symbol_converter=(formula)
-        formula = FORMULAS[formula] unless formula.respond_to? :call
-        raise ArgumentError, "Invalid symbol_converter formula" unless formula
-
-        @symbol_converter = formula
-      end
-
-    private
-
-      # Chops special characters from the end of a given +string+.
-      def chop_special_characters(string)
-        ["!", "/"].include?(string[-1, 1]) ? string.chop : string
-      end
-
-      # Returns whether to remove the namespace from a given +key+.
-      def unqualify?(key)
-        key[0, 1] == ":"
-      end
-
-      # Returns whether to namespace all keys (elementFormDefault).
-      def qualify?(options)
-        options[:element_form_default] == :qualified && options[:namespace]
-      end
-
-    end
-  end
-end

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/lib/gyoku/xml_value.rb

@@ -1,28 +0,0 @@
-require "cgi"
-require "date"
-
-module Gyoku
-  module XMLValue
-    class << self
-
-      # xs:dateTime format.
-      XS_DATETIME_FORMAT = "%Y-%m-%dT%H:%M:%S%Z"
-
-      # Converts a given +object+ to an XML value.
-      def create(object, escape_xml = true)
-        if DateTime === object
-          object.strftime XS_DATETIME_FORMAT
-        elsif String === object
-          escape_xml ? CGI.escapeHTML(object) : object
-        elsif object.respond_to?(:to_datetime)
-          create object.to_datetime
-        elsif object.respond_to?(:call)
-          create object.call
-        else
-          object.to_s
-        end
-      end
-
-    end
-  end
-end

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/lib/gyoku.rb

@@ -1,23 +0,0 @@
-require "gyoku/version"
-require "gyoku/hash"
-
-module Gyoku
-  class << self
-
-    # Translates a given +hash+ with +options+ to XML.
-    def xml(hash, options = {})
-      Hash.to_xml hash.dup, options
-    end
-
-    # Yields this object for configuration.
-    def configure
-      yield self
-    end
-
-    # Sets the formula for converting Symbol keys.
-    def convert_symbols_to(formula = nil, &block)
-      XMLKey.symbol_converter = formula ? formula : block
-    end
-
-  end
-end

data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/spec/gyoku/array_spec.rb

@@ -1,53 +0,0 @@
-require "spec_helper"
-
-describe Gyoku::Array do
-
-  describe ".to_xml" do
-    it "returns the XML for an Array of Hashes" do
-      array = [{ :name => "adam" }, { :name => "eve" }]
-      result = "<user><name>adam</name></user><user><name>eve</name></user>"
-
-      to_xml(array, "user").should == result
-    end
-
-    it "returns the XML for an Array of different Objects" do
-      array = [:symbol, "string", 123]
-      result = "<value>symbol</value><value>string</value><value>123</value>"
-
-      to_xml(array, "value").should == result
-    end
-
-    it "defaults to escape special characters" do
-      array = ["<tag />", "adam & eve"]
-      result = "<value>&lt;tag /&gt;</value><value>adam &amp; eve</value>"
-
-      to_xml(array, "value").should == result
-    end
-
-    it "does not escape special characters when told to" do
-      array = ["<tag />", "adam & eve"]
-      result = "<value><tag /></value><value>adam & eve</value>"
-
-      to_xml(array, "value", false).should == result
-    end
-
-    it "adds attributes to a given tag" do
-      array = ["adam", "eve"]
-      result = '<value active="true">adam</value><value active="true">eve</value>'
-
-      to_xml(array, "value", :escape_xml, :active => true).should == result
-    end
-
-    it "adds attributes to duplicate tags" do
-      array = ["adam", "eve"]
-      result = '<value id="1">adam</value><value id="2">eve</value>'
-
-      to_xml(array, "value", :escape_xml, :id => [1, 2]).should == result
-    end
-  end
-
-  def to_xml(*args)
-    Gyoku::Array.to_xml *args
-  end
-
-end