bel 0.7.0 → 1.0.0

data/lib/bel/gen.rb

@@ -3,7 +3,7 @@ require          'bel'
 module BEL
 
   # The {Gen} module defines submodules that generate random data that
-  # represent parts of the {::BEL::Model evidence model}.
+  # represent parts of a {::BEL::Nanopub nanopub}.
   module Gen
 
     # Requires +paths+ treated as a soft dependency to bel.rb.
@@ -45,7 +45,7 @@ require_relative 'gen/namespace'
 require_relative 'gen/parameter'
 require_relative 'gen/term'
 require_relative 'gen/statement'
-require_relative 'gen/evidence'
+require_relative 'gen/nanopub'
 require_relative 'gen/sample_resources'
 
 # vim: ts=2 sw=2:

data/lib/bel/gen/annotation.rb

@@ -5,7 +5,7 @@ module BEL
   module Gen
 
     # The {Annotation} module defines methods that generate random annotations
-    # to be used in an evidence's {BEL::Model::ExperimentContext}.
+    # to be used in a nanopub's {BEL::Nanopub::ExperimentContext}.
     module Annotation
 
       # Array of the latest OpenBEL {BEL::Annotation::AnnotationDefinition}.
@@ -23,7 +23,7 @@ module BEL
       end
 
       # Returns a random annotation as a hash of +:name+ and +:value+. These
-      # can be added directly to an evidence's {BEL::Model::ExperimentContext}.
+      # can be added directly to a nanopub's {BEL::Nanopub::ExperimentContext}.
       #
       # @return [Hash] random annotation; hash of +:name+ and +:value+
       def annotation

data/lib/bel/gen/citation.rb

@@ -5,7 +5,7 @@ module BEL
   module Gen
 
     # The {Citation} module defines methods that generate random citation
-    # fields. See {Citation#citation} to generate a {BEL::Model::Citation}.
+    # fields. See {Citation#citation} to generate a {BEL::Nanopub::Citation}.
     module Citation
 
       # Returns a random citation type.
@@ -63,13 +63,13 @@ module BEL
         }
       end
 
-      # Returns a random {BEL::Model::Citation}.
+      # Returns a random {BEL::Nanopub::Citation}.
       #
       # Note: This method has a good chance to return the last generated
-      # {BEL::Model::Citation}. This behavior better models curated BEL
-      # Evidence where many BEL statements have the same citation.
+      # {BEL::Nanopub::Citation}. This behavior better models curated BEL
+      # nanopubs where many BEL statements have the same citation.
       #
-      # @return [BEL::Model::Citation] a random citation
+      # @return [BEL::Nanopub::Citation] a random citation
       def citation
         choice = 
           @citation_hash == nil ?
@@ -92,7 +92,7 @@ module BEL
           }
         end
 
-        ::BEL::Model::Citation.new(@citation_hash)
+        ::BEL::Nanopub::Citation.new(@citation_hash)
       end
     end
   end

data/lib/bel/gen/document_header.rb

@@ -5,7 +5,7 @@ module BEL
   module Gen
 
     # The {DocumentHeader} module defines methods that generate a random
-    # document header for the {BEL::Model::Evidence} metadata.
+    # document header for the {BEL::Nanopub::Nanopub} metadata.
     module DocumentHeader
 
       # Returns a randomly chosen document name.

data/lib/bel/gen/{evidence.rb → nanopub.rb}

@@ -13,11 +13,11 @@ BEL::Gen.soft_require('rantly')
 module BEL
   module Gen
 
-    # The {Evidence} module defines methods that generate random
-    # {BEL::Model::Evidence evidence}.
-    module Evidence
+    # The {Nanopub} module defines methods that generate random
+    # {BEL::Nanopub::Nanopub nanopubs}.
+    module Nanopub
 
-      # Include other generators needed to create {BEL::Model::Evidence}.
+      # Include other generators needed to create {BEL::Nanopub::Nanopub}.
       include BEL::Gen::DocumentHeader
       include BEL::Gen::Annotation
       include BEL::Gen::Citation
@@ -26,21 +26,21 @@ module BEL
       include BEL::Gen::Statement
       include BEL::Gen::Term
 
-      # Returns a random {BEL::Model::Evidence}.
+      # Returns a random {BEL::Nanopub::Nanopub}.
       #
-      # @return [BEL::Model::Evidence] a random evidence
-      def evidence
-        evidence = BEL::Model::Evidence.new
+      # @return [BEL::Nanopub::Nanopub] a random nanopub
+      def nanopub
+        nanopub = BEL::Nanopub::Nanopub.new
 
-        evidence.bel_statement      = bel_statement
-        evidence.citation           = citation
-        evidence.summary_text       = BEL::Model::SummaryText.new(
+        nanopub.bel_statement      = bel_statement
+        nanopub.citation           = citation
+        nanopub.support            = BEL::Nanopub::Support.new(
           Rantly { sized(120) {string(:alpha)} }
         )
-        evidence.experiment_context = BEL::Model::ExperimentContext.new(
+        nanopub.experiment_context = BEL::Nanopub::ExperimentContext.new(
           (1..5).to_a.sample.times.map { annotation }
         )
-        evidence.references         = BEL::Model::References.new({
+        nanopub.references         = BEL::Nanopub::References.new({
           :namespaces  => referenced_namespaces.map { |prefix, ns_def|
             {
               :keyword => prefix,
@@ -55,11 +55,11 @@ module BEL
             }
           }
         })
-        evidence.metadata           = BEL::Model::Metadata.new({
+        nanopub.metadata           = BEL::Nanopub::Metadata.new({
           :document_header => document_header
         })
 
-        evidence
+        nanopub
       end
     end
   end

data/lib/bel/gen/parameter.rb

@@ -6,14 +6,14 @@ module BEL
   module Gen
 
     # The {Parameter} module defines methods that generate random BEL
-    # {BEL::Model::Parameter parameters}.
+    # {BEL::Nanopub::Parameter parameters}.
     module Parameter
       include BEL::Gen::Namespace
 
       # Returns a BEL parameter from a random namespace. The value will be
       # a random string and not necessarily part of the namespace.
       #
-      # @return [BEL::Model::Parameter] a randomly generated parameter with
+      # @return [BEL::Nanopub::Parameter] a randomly generated parameter with
       #         a namespace
       def bel_parameter_with_namespace
         ns    = namespace
@@ -22,7 +22,7 @@ module BEL
             string(/[[:alnum:]]|[[:blank:]]|[[:punct:]]/)
           }
         }
-        BEL::Model::Parameter.new(
+        BEL::Nanopub::Parameter.new(
           ns,
           value,
           :A
@@ -32,7 +32,7 @@ module BEL
       # Returns a BEL parameter without a namespace. The value will be
       # a random string.
       #
-      # @return [BEL::Model::Parameter] a randomly generated parameter
+      # @return [BEL::Nanopub::Parameter] a randomly generated parameter
       #         without a namespace
       def bel_parameter_without_namespace
         value = Rantly.value {
@@ -40,7 +40,7 @@ module BEL
             string(/[[:alnum:]]|[[:blank:]]|[[:punct:]]/)
           }
         }
-        BEL::Model::Parameter.new(
+        BEL::Nanopub::Parameter.new(
           nil,
           value,
           :A
@@ -54,7 +54,7 @@ module BEL
       #
       # @see #bel_parameter_with_namespace
       # @see #bel_parameter_without_namespace
-      # @return [BEL::Model::Parameter] a parameter that may or may not have
+      # @return [BEL::Nanopub::Parameter] a parameter that may or may not have
       #         a namespace
       def bel_parameter
         with_namespace    = bel_parameter_with_namespace

data/lib/bel/gen/sample_resources.rb

@@ -7,7 +7,7 @@ module BEL
     # The {SampleResources} module defines methods that sample data from actual
     # resources.
     #
-    # {BEL::Model::Parameter BEL parameters} are sampled from a
+    # {BEL::Nanopub::Parameter BEL parameters} are sampled from a
     # {BEL::Namespace::NamespaceDefinition}.
     #
     # Annotations are sampled from a {BEL::Annotation::AnnotationDefinition}.
@@ -15,7 +15,7 @@ module BEL
       include BEL::Gen::Annotation
 
       # Returns a sampled annotation as a hash of +:name+ and +:value+. These
-      # can be added directly to an evidence's {BEL::Model::ExperimentContext}.
+      # can be added directly to a nanopubs's {BEL::Nanopub::ExperimentContext}.
       #
       # @return [Hash] sampled annotation; hash of +:name+ and +:value+
       def annotation
@@ -35,13 +35,13 @@ module BEL
 
       # Returns a BEL parameter with a value sampled from a random namespace.
       #
-      # @return [BEL::Model::Parameter] a parameter with value sampled from a
+      # @return [BEL::Nanopub::Parameter] a parameter with value sampled from a
       #         random namespace
       def bel_parameter_with_namespace
         ns    = namespace
         value = ns.values.keys.sample
         enc   = ns.values[value]
-        BEL::Model::Parameter.new(
+        BEL::Nanopub::Parameter.new(
           ns,
           value,
           enc

data/lib/bel/gen/statement.rb

@@ -6,7 +6,7 @@ module BEL
   module Gen
 
     # The {Statement} module defines methods that generate random BEL
-    # {BEL::Model::Statement statements}.
+    # {BEL::Nanopub::Statement statements}.
     module Statement
       include BEL::Gen::Term
 

data/lib/bel/gen/term.rb

@@ -6,7 +6,7 @@ module BEL
   module Gen
 
     # The {Term} module defines methods that generate random BEL
-    # {BEL::Model::Term terms}.
+    # {BEL::Nanopub::Term terms}.
     module Term
       include BEL::Gen::Parameter
 

data/lib/bel/language.rb

@@ -615,26 +615,6 @@ module BEL
       :translatedTo           => :translatedTo,
       :translocates           => :translocates,
     }
-
-    def self.include_bel_dsl
-      RELATIONSHIPS.each do |rel, long_form|
-        BEL::Model::Term.send(:define_method, rel) do |another|
-          s = BEL::Model::Statement.new self
-          s.relationship = long_form
-          s.object = another
-          s
-        end
-      end
-      FUNCTIONS.each do |fx, metadata|
-        func = Function.new(metadata)
-        Language.send(:define_method, fx) do |*args|
-          BEL::Model::Term.new(func, *args)
-        end
-        Language.send(:define_method, metadata[:long_form]) do |*args|
-          BEL::Model::Term.new(func, *args)
-        end
-      end
-    end
   end
 end
 # vim: ts=2 sw=2:

data/lib/bel/namespace.rb

@@ -250,6 +250,10 @@ module BEL
         @values = nil
       end
 
+      def rdf_uri
+        @rdf_uri ||= DEFAULT_URI
+      end
+
       def values
         unless @values
           reload(@url)
@@ -262,16 +266,16 @@ module BEL
         reload(@url) if not @values
         sym = value.to_sym
         encoding = @values[sym] || :''
-        Model::Parameter.new(self, sym, encoding)
+        Nanopub::Parameter.new(self, sym, encoding)
       end
 
       def each &block
         reload(@url) if not @values
         @values.each do |val, enc|
           if block_given?
-            block.call(Model::Parameter.new(self, val, enc))
+            block.call(Nanopub::Parameter.new(self, val, enc))
           else
-            yield Model::Parameter.new(self, val, enc)
+            yield Nanopub::Parameter.new(self, val, enc)
           end
         end
       end

data/lib/bel/nanopub.rb

@@ -0,0 +1,15 @@
+# Expression model (from bel_parser)
+require          'bel_parser/expression/model'
+
+# Nanopub model
+require_relative 'nanopub/nanopub'
+require_relative 'nanopub/citation'
+require_relative 'nanopub/support'
+require_relative 'nanopub/experiment_context'
+require_relative 'nanopub/metadata'
+
+# Nanopub utilities
+require_relative 'nanopub/buffering_nanopub_combiner'
+require_relative 'nanopub/map_references_combiner'
+require_relative 'nanopub/streaming_nanopub_combiner'
+require_relative 'nanopub/util'

data/lib/bel/{evidence_model/buffering_evidence_combiner.rb → nanopub/buffering_nanopub_combiner.rb}

@@ -1,13 +1,13 @@
 require_relative 'hash_map_references'
 
 module BEL
-  module Model
+  module Nanopub
 
-    # EvidenceReferenceCombiner is responsible for disambiguating evidence
+    # NanopubReferenceCombiner is responsible for disambiguating nanopubs
     # with overlapping sets of annotation/namespace references. This can occur
     # when documents use the same keyword to refer to more than one reference.
     #
-    # For example, evidence A may be annotated with:
+    # For example, nanopub A may be annotated with:
     #
     #    {
     #      :keyword => :Species,
@@ -15,7 +15,7 @@ module BEL
     #      :domain  => 'file:///20131211/annotation/species-taxonomy-id.belanno'
     #    }
     #
-    # while evidence B may be annotated with:
+    # while nanopub B may be annotated with:
     #
     #    {
     #      :keyword => :Species,
@@ -28,26 +28,23 @@ module BEL
     #
     # @abstract Subclass and override {#map_namespace_reference} to implement
     # mapping of namespaces.
-    class BufferingEvidenceCombiner
+    class BufferingNanopubCombiner
 
       attr_reader :annotation_references, :namespace_references
 
-      def initialize(evidence_collection)
-        @evidence_collection = evidence_collection
+      def initialize(nanopub_collection)
+        @nanopub_collection = nanopub_collection
       end
 
       def each
         if block_given?
-          evidence_array, map_references =
-            combine_references(@evidence_collection)
+          nanopub_array, map_references =
+            combine_references(@nanopub_collection)
           @annotation_references = map_references.annotation_references
           @namespace_references  = map_references.namespace_references
 
-          evidence_array.each do |evidence|
-            if evidence.bel_statement.is_a?(String)
-              evidence.bel_statement = BEL::Model::Evidence.parse_statement(evidence)
-            end
-            yield rewrite_evidence!(evidence, map_references)
+          nanopub_array.each do |nanopub|
+            yield rewrite_nanopub!(nanopub, map_references)
           end
         else
           to_enum(:each)
@@ -56,33 +53,33 @@ module BEL
 
       protected
 
-      def combine_references(evidence_collection)
+      def combine_references(nanopub_collection)
         annotation_reference_map = {}
         namespace_reference_map  = {}
         annotations = []
         namespaces  = []
-        buffered_evidence = evidence_collection.each.map { |evidence|
+        buffered_nanopub = nanopub_collection.each.map { |nanopub|
           annotations, remap =
-            BEL::Model.union_annotation_references(
+            BEL::Nanopub.union_annotation_references(
               annotations,
-              evidence.references.annotations,
+              nanopub.references.annotations,
               'incr'
             )
           annotation_reference_map.merge!(remap)
 
           namespaces, remap =
-            BEL::Model.union_namespace_references(
+            BEL::Nanopub.union_namespace_references(
               namespaces,
-              evidence.references.namespaces,
+              nanopub.references.namespaces,
               'incr'
             )
           namespace_reference_map.merge!(remap)
 
-          evidence
+          nanopub
         }.to_a
 
         [
-          buffered_evidence,
+          buffered_nanopub,
           HashMapReferences.new(
             annotation_reference_map,
             namespace_reference_map
@@ -90,26 +87,28 @@ module BEL
         ]
       end
 
-      def rewrite_evidence!(evidence, map_references)
+      def rewrite_nanopub!(nanopub, map_references)
         rewrite_experiment_context!(
-          evidence.experiment_context,
-          evidence.references.annotations,
+          nanopub.experiment_context,
+          nanopub.references.annotations,
           map_references
         )
 
         rewrite_statement!(
-          evidence.bel_statement,
-          evidence.references.namespaces,
+          nanopub.bel_statement,
+          nanopub.references.namespaces,
           map_references
         )
 
-        evidence
+        nanopub
       end
 
       def rewrite_statement!(statement, namespace_references, map_references)
+        return if statement.nil?
+
         keyword_to_reference = Hash[
           namespace_references.map { |reference|
-            [reference[:keyword], reference]
+            [reference.keyword, reference]
           }
         ]
 
@@ -121,9 +120,9 @@ module BEL
         obj = statement.object
         if obj
           case obj
-          when ::BEL::Model::Statement
+          when ::BELParser::Expression::Model::Statement
             rewrite_statement!(obj, namespace_references, map_references)
-          when ::BEL::Model::Term
+          when ::BELParser::Expression::Model::Term
             rewrite_term!(obj, keyword_to_reference, map_references)
           end
         end
@@ -134,24 +133,19 @@ module BEL
 
         term.arguments.each do |arg|
           case arg
-          when ::BEL::Model::Parameter
-            if arg.ns
-              prefix =
-                if arg.ns.respond_to?(:prefix)
-                  arg.ns.prefix
-                else
-                  arg.ns[:prefix]
-                end
+          when ::BELParser::Expression::Model::Parameter
+            if arg.namespace
+              prefix        = arg.namespace.keyword
               reference     = keyword_to_reference[prefix.to_sym]
               new_reference = map_references.map_namespace_reference(reference)
               if new_reference
-                arg.ns = BEL::Namespace::NamespaceDefinition.new(
-                  new_reference[:keyword],
-                  new_reference[:uri]
-                )
+                arg.namespace =
+                  BELParser::Expression::Model::Namespace.new(
+                    new_reference[:keyword],
+                    new_reference[:uri])
               end
             end
-          when ::BEL::Model::Term
+          when ::BELParser::Expression::Model::Term
             rewrite_term!(arg, keyword_to_reference, map_references)
           end
         end
@@ -164,7 +158,7 @@ module BEL
       )
         references = Hash[
           annotation_references.map { |reference|
-            [reference[:keyword], reference]
+            [reference.keyword, reference]
           }
         ]
         experiment_context.values.each do |annotation|