bel 0.3.3 → 0.4.0.beta1

data/lib/bel/evidence_model/evidence.rb

@@ -13,7 +13,7 @@ module BEL
       def self.create(hash)
         ev = Evidence.new
         ev.bel_statement      = hash[:bel_statement] || nil
-        ev.citation           = Citation.create(hash[:citation] || {})
+        ev.citation           = Citation.new(hash[:citation] || {})
         ev.summary_text.value = hash[:summary_text] || nil
         ev.experiment_context = ExperimentContext.new(hash[:experiment_context] || [])
         ev.references         = References.new(hash[:references] || {})
@@ -77,7 +77,7 @@ module BEL
             :summary_text       => @summary_text.value,
             :experiment_context => @experiment_context.values,
             :references         => @references.values,
-            :metadata           => @metadata.values
+            :metadata           => @metadata.to_a
           }
         )
         hash

data/lib/bel/evidence_model/experiment_context.rb

@@ -3,6 +3,7 @@ require 'forwardable'
 module BEL
   module Model
     class ExperimentContext
+
       attr_reader :values
 
       extend Forwardable

data/lib/bel/evidence_model/metadata.rb

@@ -9,10 +9,14 @@ module BEL
       extend Forwardable
       include Enumerable
 
-      DOCUMENT_HEADER        = :document_header
+      DOCUMENT_HEADER = :document_header
 
       def initialize(values = {})
-        @values = values
+        if values.is_a? Array
+          @values = Hash[values.map { |item| item.values_at(:name, :value) }]
+        else
+          @values = values
+        end
       end
 
       def document_header
@@ -23,6 +27,15 @@ module BEL
         @values[DOCUMENT_HEADER] = document_header
       end
 
+      def to_a
+        @values.each_pair.map { |key, value|
+          {
+            name:  key,
+            value: value
+          }
+        }
+      end
+
       def_delegators :@values, :[],    :"[]=", :delete_if, :each, :each_pair,
                                :fetch, :keys,  :size,      :sort, :store
     end

data/lib/bel/evidence_model/references.rb

@@ -9,27 +9,27 @@ module BEL
       extend Forwardable
       include Enumerable
 
-      ANNOTATION_DEFINITIONS = :annotation_definitions
-      NAMESPACE_DEFINITIONS  = :namespace_definitions
+      ANNOTATIONS = :annotations
+      NAMESPACES  = :namespaces
 
       def initialize(values = {})
         @values = values
       end
 
-      def annotation_definitions
-        @values[ANNOTATION_DEFINITIONS] ||= {}
+      def annotations
+        @values[ANNOTATIONS] ||= {}
       end
 
-      def annotation_definitions=(annotation_definitions)
-        @values[ANNOTATION_DEFINITIONS] = annotation_definitions
+      def annotations=(annotations)
+        @values[ANNOTATIONS] = annotations
       end
 
-      def namespace_definitions
-        @values[NAMESPACE_DEFINITIONS] ||= {}
+      def namespaces
+        @values[NAMESPACES] ||= {}
       end
 
-      def namespace_definitions=(namespace_definitions)
-        @values[NAMESPACE_DEFINITIONS] = namespace_definitions
+      def namespaces=(namespaces)
+        @values[NAMESPACES] = namespaces
       end
 
       def_delegators :@values, :[],    :"[]=", :delete_if,   :each, :each_pair,

data/lib/bel/json.rb

@@ -0,0 +1,63 @@
+# TODO Document.
+#
+# What does this abstraction provide?
+# Why is it here?
+# 
+module BEL::JSON
+
+  # TODO Document.
+  #
+  # Reads JSON data. Leverages JSON adapters which implement the same signature.
+  def self.read(data, options = {})
+    @adapter ||= self.adapter
+    instance = @adapter.new
+
+    if block_given?
+      instance.read(data, options) { |obj|
+        yield obj
+      }
+    else
+      instance.read(data, options)
+    end
+  end
+
+  # TODO Document.
+  #
+  # Writes JSON data. Leverages JSON adapters which implement the same signature.
+  def self.write(data, output_io, options = {})
+    @adapter ||= self.adapter
+    instance = @adapter.new
+    instance.write(data, output_io, options)
+  end
+
+  # Load the most suitable JSON implementation available within ruby.
+  # The load order attempted is:
+  # - oj              (provides stream parsing utilizing event callbacks)
+  # - multi_json      (simple buffering abstraction over multiple ruby libraries)
+  # - json            (stock ruby implementation)
+  def self.adapter
+    implementations = [
+      'json/adapter/oj',
+      'json/adapter/multi_json',
+      'json/adapter/ruby_json'
+    ]
+
+    load_success = implementations.any? { |impl|
+      begin
+        require_relative impl
+        true
+      rescue LoadError
+        # Could not load +impl_module+; try the next one
+        false
+      end
+    }
+
+    if load_success
+      BEL::JSON::Implementation
+    else
+      mod_s = impl_modules.join(', ')
+      msg   = "Could not load any JSON implementation (tried: #{mod_s})."
+      raise LoadError.new(msg)
+    end
+  end
+end

data/lib/bel/json/adapter/multi_json.rb

@@ -0,0 +1,36 @@
+require 'multi_json'
+
+require_relative '../reader'
+require_relative '../writer'
+
+module BEL::JSON
+
+  class Implementation
+
+    include Reader
+    include Writer
+
+    def read(data, options = {})
+      if block_given?
+        options = { :symbolize_keys => true }.merge!(options)
+        MultiJson.load(data, options).each do |obj|
+          yield obj
+        end
+      else
+        to_enum(:read, data, options)
+      end
+    end
+
+    def write(data, output_io, options = {})
+      json = MultiJson.dump(json_object)
+      if output_io
+        # write json and return IO
+        output_io.write json
+        output_io
+      else
+        # return json string
+        json
+      end
+    end
+  end
+end

data/lib/bel/json/adapter/oj.rb

@@ -0,0 +1,65 @@
+require 'oj'
+
+require_relative '../reader'
+require_relative '../writer'
+
+module BEL::JSON
+
+  class Implementation
+
+    include Reader
+    include Writer
+
+    def read(data, options = {}, &block)
+      if block_given?
+        options = { :symbol_keys => true }.merge!(options)
+        Oj.sc_parse(StreamHandler.new(block), data, options)
+      else
+        to_enum(:read, data, options)
+      end
+    end
+
+    def write(data, output_io, options = {})
+      Oj.to_stream(output_io, data)
+    end
+  end
+
+  class StreamHandler < Oj::ScHandler
+
+    def initialize(callable)
+      @callable = callable
+    end
+
+    def hash_start
+      {}
+    end
+
+    def hash_end
+      @callable.call @hash 
+    end
+
+    def hash_set(hash, key, value)
+      hash[key]  = value
+      @hash = hash
+    end
+
+    def array_start
+      @array = []
+      @array
+    end
+
+    def array_append(array, value)
+      array << value
+      @array = array
+    end
+
+    def array_end()
+      @callable.call @array
+    end
+
+    def error(message, line, column)
+      msg = "Parse error at line #{line}, column #{column}: #{message}"
+      raise Oj::ParseError.new(msg)
+    end
+  end
+end

data/lib/bel/json/adapter/ruby_json.rb

@@ -0,0 +1,28 @@
+require 'json'
+
+require_relative '../reader'
+require_relative '../writer'
+
+module BEL::JSON
+
+  class Implementation
+
+    include Reader
+    include Writer
+
+    def read(data, options = {})
+      if block_given?
+        options = { :symbolize_names => true }.merge!(options)
+        JSON.load(data, nil, options).each do |obj|
+          yield obj
+        end
+      else
+        to_enum(:read, data, options)
+      end
+    end
+
+    def write(data, output_io, options = {})
+      JSON.dump(data, output_io)
+    end
+  end
+end

data/lib/bel/json/reader.rb

@@ -0,0 +1,9 @@
+module BEL::JSON
+
+  module Reader
+
+    def read(input, options = {})
+      raise NotImplementedError.new("#{__method__} is not implemented.")
+    end
+  end
+end

data/lib/bel/json/writer.rb

@@ -0,0 +1,9 @@
+module BEL::JSON
+
+  module Writer
+
+    def write(data, output, options = {})
+      raise NotImplementedError.new("#{__method__} is not implemented.")
+    end
+  end
+end

data/lib/bel/libbel.rb

@@ -12,7 +12,6 @@ module BEL
         defined?(RUBY_ENGINE) && ("rbx" == RUBY_ENGINE)
       end
 
-      # @api_private
       # Determine FFI constant for this ruby engine.
       def find_ffi
         if rubinius?
@@ -26,7 +25,6 @@ module BEL
         end
       end
 
-      # @api_private
       # Extend with the correct ffi implementation.
       def load_ffi
         ffi_module = BEL::LibBEL::find_ffi
@@ -34,7 +32,6 @@ module BEL
         ffi_module
       end
 
-      # @api_private
       # Loads the libbel shared library.
       def load_libBEL
         ffi_module = find_ffi
@@ -123,7 +120,7 @@ module BEL
     attach_function :bel_tokenize_term,       [:string                                      ], :pointer
 
     # parse
-    attach_function :bel_parse_statement,     [:string                                      ], :pointer
+    #attach_function :bel_parse_statement,     [:string                                      ], :pointer
     attach_function :bel_parse_term,          [:string                                      ], :pointer
 
     def self.parse_statement(bel_string)

data/lib/bel/parser.rb

@@ -3,12 +3,12 @@ require_relative 'libbel'
 module BEL
   module Parser
 
-    # Parses BEL expressions to a {BelAst}.
+    # Parses BEL expressions to a {BEL::LibBEL::BelAst}.
     #
     # If +bel_expression+ is +nil+ then +nil+ is returned.
     #
     # @param bel_expression [responds to #to_s] the bel expression to parse
-    # @return [BelAst]
+    # @return [BEL::LibBEL::BelAst]
     def self.parse(bel_expression, options = {})
       if !bel_expression
         return nil

data/lib/bel/rdf_repository.rb

@@ -0,0 +1,18 @@
+module BEL
+  module RdfRepository
+
+    module Plugins; end
+
+    extend LittlePlugger(
+      :path   => 'bel/rdf_repository/plugins',
+      :module => BEL::RdfRepository::Plugins
+    )
+
+    module ClassMethods
+
+      def create_repository(options = {})
+        raise NotImplementedError.new("#{__method__} is not implemented.")
+      end
+    end
+  end
+end

data/lib/bel/rdf_repository/plugins/memory.rb

@@ -0,0 +1,28 @@
+# Load RDF library dependencies
+require 'rdf'
+require 'rdf/mongo'
+require 'addressable/uri'
+require 'uuid'
+
+module BEL::RdfRepository::Plugins
+
+  module Memory
+
+    extend ::BEL::RdfRepository::ClassMethods
+
+    NAME        = 'In-memory RDF Repository'
+    DESCRIPTION = 'An in-memory repository provided by default in RDF.rb.'
+
+    def self.create_repository(options = {})
+      RDF::Repository.new(options)
+    end
+
+    def self.name
+      NAME
+    end
+
+    def self.description
+      DESCRIPTION
+    end
+  end
+end

data/lib/bel/rdf_repository/plugins/mongo.rb

@@ -0,0 +1,28 @@
+# Load RDF library dependencies
+require 'rdf'
+require 'rdf/mongo'
+require 'addressable/uri'
+require 'uuid'
+
+module BEL::RdfRepository::Plugins
+
+  module Mongo
+
+    extend ::BEL::RdfRepository::ClassMethods
+
+    NAME        = 'Mongo RDF Repository'
+    DESCRIPTION = 'A repository of RDF data on MongoDB.'
+
+    def self.create_repository(options = {})
+      RDF::Mongo::Repository.new(options)
+    end
+
+    def self.name
+      NAME
+    end
+
+    def self.description
+      DESCRIPTION
+    end
+  end
+end

data/lib/bel/resource.rb

@@ -0,0 +1,24 @@
+require 'rdf'
+
+module BEL
+  module Resource
+
+    class BELV < RDF::StrictVocabulary('http://www.openbel.org/vocabulary/')
+      term     :AnnotationConcept
+      term     :AnnotationConceptScheme
+      term     :NamespaceConcept
+      term     :NamespaceConceptScheme
+
+      property :prefix
+      property :domain
+      property :species
+      property :inScheme
+      property :orthologousMatch
+    end
+  end
+end
+
+require_relative 'resource/namespaces'
+require_relative 'resource/namespace'
+require_relative 'resource/namespace_value'
+require_relative 'resource/search'