bel 0.3.3 → 0.4.0.beta1

data/lib/bel/vendor/little-plugger.rb

@@ -0,0 +1,323 @@
+
+# == Synopsis
+# LittlePlugger is a module that provides Gem based plugin management.
+# By extending your own class or module with LittlePlugger you can easily
+# manage the loading and initializing of plugins provided by other gems.
+#
+# == Details
+# Plugins are great! They allow other developers to add functionality to
+# an application but relieve the application developer of the responsibility
+# for mainting some other developer's plugin code. LittlePlugger aims to
+# make it dead simple to manage external plugins as gems.
+#
+# === Naming
+# Every plugin managed by LittlePlugger will have a name represented as a
+# Symbol. This name is used to register the plugin, load the plugin file,
+# and manage the plugin class/module. Here are the three rules for plugin
+# names:
+#
+# 1) all lowercase with underscores
+# 2) maps to a file of the same name with an '.rb' extension
+# 3) converting the name to camel case yields the plugin class / module
+#
+# These rules are essentially the standard ruby practice of naming files
+# after the class / module the file defines.
+#
+# === Finding & Loading
+# Plugins are found by searching through the lib folders of all installed
+# gems; these gems are not necessarily loaded - just searched. If the lib
+# folder has a subdirectory that matches the +plugin_path+, then all ruby
+# files in the gem's +plugin_path+ are noted for later loading.
+#
+# A file is only loaded if the basename of the file matches one of the
+# registered plugin names. If no plugins are registered, then every file in
+# the +plugin_path+ is loaded.
+#
+# The plugin classes / modules are all expected to live in the same
+# namespace for a particular application. For example, all plugins for the
+# "Foo" application should reside in a "Foo::Plugins" namespace. This allows
+# the plugins to be automatically initialized by LittlePlugger.
+#
+# === Initializing
+# Optionally, plugins can provide an initialization method for running any
+# setup code needed by the plugin. This initialize method should be named as
+# follows: "initializer_#{plugin_name}" where the name of the plugin is
+# appended to the end of the initializer method name.
+#
+# If this method exists, it will be called automatically when plugins are
+# loaded. The order of loading of initialization is not strictly defined, so
+# do not rely on another plugin being initialized for your own plugin
+# successfully initialize.
+#
+# == Usage
+# LittlePlugger is used by extending your own class or module with the
+# LittlePlugger module.
+#
+#    module Logging
+#      extend LittlePlugger
+#    end
+#
+# This defines a +plugin_path+ and a +plugin_module+ for our Logging module.
+# The +plugin_path+ is set to "logging/plugins", and therefore, the
+# +plugin_modlue+ is defined as Logging::Plugins. All plugins for the
+# Logging module should be found underneath this plugin module.
+#
+# The plugins for the Logging module are loaded and initialized by calling
+# the +initialize_plugins+ method.
+#
+#    Logging.initialize_plugins
+#
+# If you only want to load the plugin files but not initialize the plugin
+# classes / modules then you can call the +load_plugins+ method.
+#
+#    Logging.load_plugins
+#
+# Finally, you can get a hash of all the loaded plugins.
+#
+#    Logging.plugins
+#
+# This returns a hash keyed by the plugin names with the plugin class /
+# module as the value.
+#
+# If you only want a certain set of plugins to be loaded, then pass the
+# names to the +plugin+ method.
+#
+#    Logging.plugin :foo, :bar, :baz
+#
+# Now only three plugins for the Logging module will be loaded.
+#
+# === Customizing
+# LittlePlugger allows the use of a custom plugin path and module. These are
+# specified when extending with LilttlePlugger by passing the specific path
+# and module to LittlePlugger.
+#
+#    class Hoe
+#      extend LittlePlugger( :path => 'hoe', :module => Hoe )
+#
+#      plugin(
+#          :clean, :debug, :deps, :flay, :flog, :package,
+#          :publish, :rcov, :signing, :test
+#      )
+#    end
+#
+# All ruby files found under the "hoe" directory will be treated as
+# plugins, and the plugin classes / modules should reside directly under the
+# Hoe namespace.
+#
+# We also specify a list of plugins to be loaded. Only these plugins will be
+# loaded and initialized by the LittlePlugger module. The +plugin+ method
+# can be called multiple times to add more plugins.
+#
+module LittlePlugger
+
+  VERSION = '1.1.4'  # :nodoc:
+
+  # Returns the version string for the library.
+  #
+  def self.version
+    VERSION
+  end
+
+  module ClassMethods
+
+    # Add the _names_ to the list of plugins that will be loaded.
+    #
+    def plugin( *names )
+      plugin_names.concat(names.map! {|n| n.to_sym})
+    end
+
+    # Add the _names_ to the list of plugins that will *not* be loaded. This
+    # list prevents the plugin system from loading unwanted or unneeded
+    # plugins.
+    #
+    # If a plugin name appears in both the 'disregard_plugin' list and the
+    # 'plugin' list, the disregard list takes precedence; that is, the plugin
+    # will not be loaded.
+    #
+    def disregard_plugin( *names )
+      @disregard_plugin ||= []
+      @disregard_plugin.concat(names.map! {|n| n.to_sym})
+      @disregard_plugin
+    end
+    alias :disregard_plugins :disregard_plugin
+
+    # Returns the array of plugin names that will be loaded. If the array is
+    # empty, then any plugin found in the +plugin_path+ will be loaded.
+    #
+    def plugin_names
+      @plugin_names ||= []
+    end
+
+    # Loads the desired plugins and returns a hash. The hash contains all
+    # the plugin classes and modules keyed by the plugin name.
+    #
+    def plugins
+      load_plugins
+      pm = plugin_module
+      names = pm.constants.map { |s| s.to_s }
+      names.reject! { |n| n =~ %r/^[A-Z_]+$/ }
+
+      h = {}
+      names.each do |name|
+        sym = ::LittlePlugger.underscore(name).to_sym
+        next unless plugin_names.empty? or plugin_names.include? sym
+        next if disregard_plugins.include? sym
+        h[sym] = pm.const_get name
+      end
+      h
+    end
+
+    # Iterate over the loaded plugin classes and modules and call the
+    # initialize method for each plugin. The plugin's initialize method is
+    # defeind as +initialize_plugin_name+, where the plugin name is unique
+    # to each plugin.
+    #
+    def initialize_plugins
+      plugins.each do |name, klass|
+        msg = "initialize_#{name}"
+        klass.send msg if klass.respond_to? msg
+      end
+    end
+
+    # Iterate through all installed gems looking for those that have the
+    # +plugin_path+ in their "lib" folder, and load all .rb files found in
+    # the gem's plugin path. Each .rb file should define one class or module
+    # that will be used as a plugin.
+    #
+    def load_plugins
+      @loaded ||= {}
+      found = {}
+
+      Gem.find_files(File.join(plugin_path, '*.rb')).sort!.reverse_each do |path|
+        name = File.basename(path, '.rb').to_sym
+        found[name] = path unless found.key? name
+      end
+
+      :keep_on_truckin while found.map { |name, path|
+        next unless plugin_names.empty? or plugin_names.include? name
+        next if disregard_plugins.include? name
+        next if @loaded[name]
+        begin
+          @loaded[name] = load path
+        rescue ScriptError, StandardError => err
+          warn "Error loading #{path.inspect}: #{err.message}. skipping..."
+        end
+      }.any?
+    end
+
+    # The path to search in a gem's 'lib' folder for plugins.
+    #
+    def plugin_path
+      ::LittlePlugger.default_plugin_path(self)
+    end
+
+    # This module or class where plugins are located.
+    #
+    def plugin_module
+      ::LittlePlugger.default_plugin_module(plugin_path)
+    end
+
+  end  # module ClassMethods
+
+  # :stopdoc:
+
+  # Called when another object extends itself with LittlePlugger.
+  #
+  def self.extended( other )
+    other.extend ClassMethods
+  end
+
+  # Convert the given string from camel case to snake case. Method liberally
+  # stolen from ActiveSupport.
+  #
+  #    underscore( "FooBar" )    #=> "foo_bar"
+  #
+  def self.underscore( string )
+    string.to_s.
+        gsub(%r/::/, '/').
+        gsub(%r/([A-Z]+)([A-Z][a-z])/,'\1_\2').
+        gsub(%r/([a-z\d])([A-Z])/,'\1_\2').
+        tr('-', '_').
+        downcase
+  end
+
+  # For a given object returns a default plugin path. The path is
+  # created by splitting the object's class name on the namespace separator
+  # "::" and converting each part of the namespace into an underscored
+  # string (see the +underscore+ method). The strings are then joined using
+  # the File#join method to give a filesystem path. Appended to this path is
+  # the 'plugins' directory.
+  #
+  #    default_plugin_path( FooBar::Baz )    #=> "foo_bar/baz/plugins"
+  #
+  def self.default_plugin_path( obj )
+    obj = obj.class unless obj.is_a? Module
+    File.join(underscore(obj.name), 'plugins')
+  end
+
+  # For a given path returns the class or module corresponding to the
+  # path. This method assumes a correspondence between directory names and
+  # Ruby namespaces.
+  #
+  #    default_plugin_module( "foo_bar/baz/plugins" )  #=> FooBar::Baz::Plugins
+  #
+  # This method will fail if any of the namespaces have not yet been
+  # defined.
+  #
+  def self.default_plugin_module( path )
+    path.split(File::SEPARATOR).inject(Object) do |mod, const|
+      const = const.split('_').map { |s| s.capitalize }.join
+      mod.const_get const
+    end
+  end
+  # :startdoc:
+
+end  # module LittlePlugger
+
+
+module Kernel
+
+  # call-seq:
+  #    LittlePlugger( opts = {} )
+  #
+  # This method allows the user to override some of LittlePlugger's default
+  # settings when mixed into a module or class.
+  #
+  # See the "Customizing" section of the LittlePlugger documentation for an
+  # example of how this method is used.
+  #
+  # ==== Options
+  #
+  # * :path <String>
+  #    The default plugin path. Defaults to "module_name/plugins".
+  #
+  # * :module <Module>
+  #    The module where plugins will be loaded. Defaults to
+  #    ModuleName::Plugins.
+  #
+  # * :plugins <Array>
+  #    The array of default plugins to load. Only the plugins listed in this
+  #    array will be loaded by LittlePlugger.
+  # 
+  def LittlePlugger( opts = {} )
+    return ::LittlePlugger::ClassMethods if opts.empty?
+    Module.new {
+      include ::LittlePlugger::ClassMethods
+
+      if opts.key?(:path)
+        eval %Q{def plugin_path() #{opts[:path].to_s.inspect} end}
+      end
+
+      if opts.key?(:module)
+        eval %Q{def plugin_module() #{opts[:module].name} end}
+      end
+
+      if opts.key?(:plugins)
+        plugins = Array(opts[:plugins]).map {|val| val.to_sym.inspect}.join(',')
+        eval %Q{def plugin_names() @plugin_names ||= [#{plugins}] end}
+      end
+    }
+  end
+end  # module Kernel
+
+# EOF

data/lib/bel/version.rb

@@ -1,3 +1,3 @@
 module BEL
-  VERSION = '0.3.3'
+  VERSION = '0.4.0.beta1'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel
 version: !ruby/object:Gem::Version
-  version: 0.3.3
+  version: 0.4.0.beta1
 platform: ruby
 authors:
 - Anthony Bargnesi
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-08-07 00:00:00.000000000 Z
+date: 2015-12-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -27,146 +27,6 @@ dependencies:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.9.8
-- !ruby/object:Gem::Dependency
-  name: addressable
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '2.3'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '2.3'
-- !ruby/object:Gem::Dependency
-  name: rdf
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.1'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.1'
-- !ruby/object:Gem::Dependency
-  name: rdf-turtle
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.1'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.1'
-- !ruby/object:Gem::Dependency
-  name: uuid
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '2.3'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '2.3'
-- !ruby/object:Gem::Dependency
-  name: minitest
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '5.7'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '5.7'
-- !ruby/object:Gem::Dependency
-  name: rake
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '10.4'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '10.4'
-- !ruby/object:Gem::Dependency
-  name: rake-compiler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '0.9'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '0.9'
-- !ruby/object:Gem::Dependency
-  name: rdoc
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '4.2'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '4.2'
-- !ruby/object:Gem::Dependency
-  name: rspec
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.2'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.2'
-- !ruby/object:Gem::Dependency
-  name: yard
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '0.8'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '0.8'
 description: " The BEL gem allows the reading, writing, and processing of BEL (Biological
   Expression Language) with a natural DSL. "
 email:
@@ -215,6 +75,7 @@ files:
 - ext/mri/libbel.def
 - lib/bel.rb
 - lib/bel/completion.rb
+- lib/bel/completion/value_match_rule.rb
 - lib/bel/completion_rule.rb
 - lib/bel/evidence_model.rb
 - lib/bel/evidence_model/bel_parameter.rb
@@ -226,19 +87,12 @@ files:
 - lib/bel/evidence_model/metadata.rb
 - lib/bel/evidence_model/references.rb
 - lib/bel/evidence_model/summary_text.rb
-- lib/bel/extension.rb
-- lib/bel/extension_format.rb
-- lib/bel/extensions/bel.rb
-- lib/bel/extensions/jgf.rb
-- lib/bel/extensions/json/jrjackson.rb
-- lib/bel/extensions/json/json.rb
-- lib/bel/extensions/json/multi_json.rb
-- lib/bel/extensions/json/oj.rb
-- lib/bel/extensions/json/ruby_json.rb
-- lib/bel/extensions/rdf/bel_rdf.rb
-- lib/bel/extensions/rdf/rdf.rb
-- lib/bel/extensions/xbel.rb
-- lib/bel/format.rb
+- lib/bel/json.rb
+- lib/bel/json/adapter/multi_json.rb
+- lib/bel/json/adapter/oj.rb
+- lib/bel/json/adapter/ruby_json.rb
+- lib/bel/json/reader.rb
+- lib/bel/json/writer.rb
 - lib/bel/language.rb
 - lib/bel/libbel.rb
 - lib/bel/libbel/bel_ast_structs.rb
@@ -269,8 +123,40 @@ files:
 - lib/bel/nonblocking_io_wrapper.rb
 - lib/bel/parser.rb
 - lib/bel/quoting.rb
+- lib/bel/rdf_repository.rb
+- lib/bel/rdf_repository/plugins/memory.rb
+- lib/bel/rdf_repository/plugins/mongo.rb
+- lib/bel/resource.rb
+- lib/bel/resource/namespace.rb
+- lib/bel/resource/namespace_value.rb
+- lib/bel/resource/namespaces.rb
+- lib/bel/resource/search.rb
+- lib/bel/resource/search/api.rb
+- lib/bel/resource/search/search_result.rb
 - lib/bel/script.rb
+- lib/bel/translate.rb
+- lib/bel/translator.rb
+- lib/bel/translator/plugins/bel_script.rb
+- lib/bel/translator/plugins/bel_script/bel_yielder.rb
+- lib/bel/translator/plugins/bel_script/evidence_yielder.rb
+- lib/bel/translator/plugins/bel_script/translator.rb
+- lib/bel/translator/plugins/jgf.rb
+- lib/bel/translator/plugins/jgf/translator.rb
+- lib/bel/translator/plugins/json_evidence.rb
+- lib/bel/translator/plugins/json_evidence/translator.rb
+- lib/bel/translator/plugins/rdf.rb
+- lib/bel/translator/plugins/rdf/bel_schema.rb
+- lib/bel/translator/plugins/rdf/monkey_patch.rb
+- lib/bel/translator/plugins/rdf/reader.rb
+- lib/bel/translator/plugins/rdf/translator.rb
+- lib/bel/translator/plugins/rdf/writer.rb
+- lib/bel/translator/plugins/xbel.rb
+- lib/bel/translator/plugins/xbel/evidence_handler.rb
+- lib/bel/translator/plugins/xbel/evidence_yielder.rb
+- lib/bel/translator/plugins/xbel/translator.rb
+- lib/bel/translator/plugins/xbel/xbel_yielder.rb
 - lib/bel/util.rb
+- lib/bel/vendor/little-plugger.rb
 - lib/bel/vendor/trollop.rb
 - lib/bel/version.rb
 homepage: https://github.com/OpenBEL/bel.rb
@@ -307,12 +193,12 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: 2.0.0
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - ">"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.5
+rubygems_version: 2.4.5.1
 signing_key: 
 specification_version: 4
 summary: Process BEL with ruby.