bel_parser 1.0.0.alpha.8 → 1.0.0.alpha.9

checksums.yaml

@@ -1,7 +1,7 @@
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data/VERSION

@@ -1 +1 @@
-1.0.0.alpha.8
+1.0.0.alpha.9

data/lib/bel_parser/language/relationship.rb

@@ -25,7 +25,52 @@ module BELParser
         false
       end
 
-      def ===(other)
+      def causal?
+        false
+      end
+
+      def correlative?
+        false
+      end
+
+      def decreasing?
+        false
+      end
+
+      def direct?
+        false
+      end
+
+      def directed?
+        false
+      end
+
+      def genomic?
+        false
+      end
+
+      def increasing?
+        false
+      end
+
+      def indirect?
+        false
+      end
+
+      def injected?
+        false
+      end
+
+      def listable?
+        false
+      end
+
+      def self?
+        false
+      end
+
+      def ==(other)
+        return true if self.equal?(other)
         return false if other.nil?
         short == other || long == other
       end

data/lib/bel_parser/language/semantics/non_causal_nested_statement.rb

@@ -0,0 +1,55 @@
+require 'bel_parser/parsers/ast/node'
+
+module BELParser
+  module Language
+    module Semantics
+      # NonCausalNestedStatement implements a {SemanticsFunction} that maps a
+      # nested {BELParser::Parsers::AST::Statement} to {SemanticsWarning} if
+      # the relationship is non-causal.
+      class NonCausalNestedStatement
+        include SemanticsFunction
+
+        private_class_method :new
+
+        def self.map(node, spec, _namespaces)
+          return nil unless node.is_a?(BELParser::Parsers::AST::Statement)
+          return nil unless node.object? && node.object.statement?
+
+          rel = node.relationship.string_literal.to_sym
+          unless spec.causal_relationships.include?(rel)
+            NonCausalNestedStatementWarning.new(node, spec, rel)
+          end
+        end
+      end
+
+      # Represents a {SemanticsWarning} when a nested
+      # {BELParser::Parsers::AST::Statement} has a non-causal relationship.
+      class NonCausalNestedStatementWarning < SemanticsWarning
+        attr_reader :non_causal_relationship
+
+        def initialize(stmt_node, spec, rel)
+          super(stmt_node, spec)
+          @non_causal_relationship = spec.relationship(rel)
+        end
+
+        def to_s
+          causal_relationships =
+            @specification
+            .causal_relationships
+            .map(&:long)
+            .join(', ')
+          <<-MSG.gsub(/ {12}/, '')
+            Nested statement is not a causal relationship.
+             The "#{non_causal_relationship.long}" relationship is not causal.
+             Causal Relationships: #{causal_relationships}
+          MSG
+        end
+
+        private
+
+        def causal_relationships
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/specification.rb

@@ -3,6 +3,8 @@ module BELParser
     # Specification defines the common behavior of any language specification.
     # It includes the syntactic and semantic rules of the language.
     module Specification
+      EMPTY_ARRAY = [].freeze
+
       def function(short_or_long_form)
         @indexed_functions[short_or_long_form]
       end
@@ -43,6 +45,50 @@ module BELParser
         @syntax
       end
 
+      def causal_relationships
+        @causal_relationships || EMPTY_ARRAY
+      end
+
+      def correlative_relationships
+        @correlative_relationships || EMPTY_ARRAY
+      end
+
+      def decreasing_relationships
+        @decreasing_relationships || EMPTY_ARRAY
+      end
+
+      def deprecated_relationships
+        @deprecated_relationships || EMPTY_ARRAY
+      end
+
+      def direct_relationships
+        @direct_relationships || EMPTY_ARRAY
+      end
+
+      def directed_relationships
+        @directed_relationships || EMPTY_ARRAY
+      end
+
+      def genomic_relationships
+        @genomic_relationships || EMPTY_ARRAY
+      end
+
+      def increasing_relationships
+        @increasing_relationships || EMPTY_ARRAY
+      end
+
+      def indirect_relationships
+        @indirect_relationships || EMPTY_ARRAY
+      end
+
+      def listable_relationships
+        @listable_relationships || EMPTY_ARRAY
+      end
+
+      def self_relationships
+        @self_relationships || EMPTY_ARRAY
+      end
+
       # @param [Array<#long,#short>] language_objects to be indexed by
       # +long+ and +short+ method return
       def index_long_short(language_objects)
@@ -65,6 +111,22 @@ module BELParser
       end
       protected :index_sym
 
+      def assign_relationship_categories(relationships)
+        relationships.each do |rel|
+          rel.methods(false).grep(/(.*?)\?/) do |method_name|
+            if rel.method(method_name).call
+              category = method_name.to_s.delete('?')
+              category_ivar = "@#{category}_relationships".to_sym
+              unless instance_variable_defined? category_ivar
+                instance_variable_set(category_ivar, [])
+              end
+              instance_variable_get(category_ivar) << rel
+            end
+          end
+        end
+      end
+      protected :assign_relationship_categories
+
       def version
         @version
       end

data/lib/bel_parser/language/version1_0/relationships/acts_in.rb

@@ -38,6 +38,22 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.injected?
+            true
+          end
+
+          def self.self?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/analogous.rb

@@ -30,6 +30,10 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.genomic?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/biomarker_for.rb

@@ -31,6 +31,10 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/causes_no_change.rb

@@ -35,6 +35,14 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.causal?
+            true
+          end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/decreases.rb

@@ -44,6 +44,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.causal?
+            true
+          end
+
+          def self.decreasing?
+            true
+          end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/directly_decreases.rb

@@ -33,6 +33,22 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.causal?
+            true
+          end
+
+          def self.decreasing?
+            true
+          end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/directly_increases.rb

@@ -33,6 +33,22 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.causal?
+            true
+          end
+
+          def self.increasing?
+            true
+          end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/has_component.rb

@@ -47,6 +47,14 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/has_components.rb

@@ -42,6 +42,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.listable?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/has_member.rb

@@ -37,6 +37,10 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/has_members.rb

@@ -42,6 +42,14 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.directed?
+            true
+          end
+
+          def self.listable?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/has_modification.rb

@@ -35,6 +35,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.injected?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/has_product.rb

@@ -37,6 +37,22 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.injected?
+            true
+          end
+
+          def self.self?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/has_variant.rb

@@ -35,6 +35,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.injected?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/includes.rb

@@ -40,6 +40,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.directed?
+            true
+          end
+
+          def self.injected?
+            true
+          end
+
+          def self.self?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/increases.rb

@@ -44,6 +44,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.causal?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.increasing?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/is_a.rb

@@ -37,6 +37,10 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/negative_correlation.rb

@@ -35,6 +35,14 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.correlative?
+            true
+          end
+
+          def self.decreasing?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/orthologous.rb

@@ -37,6 +37,10 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.genomic?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/positive_correlation.rb

@@ -31,6 +31,14 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.increasing?
+            true
+          end
+
+          def self.correlative?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/prognostic_biomarker_for.rb

@@ -33,6 +33,10 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/rate_limiting_step_of.rb

@@ -38,6 +38,14 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.directed?
+            true
+          end
+
+          def self.increasing?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/reactant_in.rb

@@ -37,6 +37,22 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.injected?
+            true
+          end
+
+          def self.self?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/sub_process_of.rb

@@ -44,6 +44,10 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/transcribed_to.rb

@@ -34,6 +34,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.genomic?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/translated_to.rb

@@ -35,6 +35,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.genomic?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0/relationships/translocates.rb

@@ -38,6 +38,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.directed?
+            true
+          end
+
+          def self.injected?
+            true
+          end
+
+          def self.self?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version1_0.rb

@@ -48,6 +48,7 @@ module BELParser
           end
           @relationships         = rel_classes.compact
           @indexed_relationships = index_long_short(@relationships)
+          assign_relationship_categories(@relationships)
         end
 
         def load_syntax

data/lib/bel_parser/language/version2_0/relationships/acts_in.rb

@@ -38,6 +38,22 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.injected?
+            true
+          end
+
+          def self.self?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/analogous.rb

@@ -34,6 +34,10 @@ module BELParser
           def self.deprecated?
             true
           end
+
+          def self.genomic?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/biomarker_for.rb

@@ -35,6 +35,10 @@ module BELParser
           def self.deprecated?
             true
           end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/causes_no_change.rb

@@ -35,6 +35,14 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.causal?
+            true
+          end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/decreases.rb

@@ -44,6 +44,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.causal?
+            true
+          end
+
+          def self.decreasing?
+            true
+          end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/directly_decreases.rb

@@ -33,6 +33,22 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.causal?
+            true
+          end
+
+          def self.decreasing?
+            true
+          end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/directly_increases.rb

@@ -33,6 +33,22 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.causal?
+            true
+          end
+
+          def self.increasing?
+            true
+          end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/has_component.rb

@@ -47,6 +47,14 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/has_components.rb

@@ -42,6 +42,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.listable?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/has_member.rb

@@ -37,6 +37,10 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/has_members.rb

@@ -42,6 +42,14 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.directed?
+            true
+          end
+
+          def self.listable?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/has_modification.rb

@@ -35,6 +35,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.injected?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/has_product.rb

@@ -37,6 +37,22 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.injected?
+            true
+          end
+
+          def self.self?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/has_variant.rb

@@ -35,6 +35,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.injected?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/includes.rb

@@ -40,6 +40,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.directed?
+            true
+          end
+
+          def self.injected?
+            true
+          end
+
+          def self.self?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/increases.rb

@@ -44,6 +44,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.causal?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.increasing?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/is_a.rb

@@ -37,6 +37,10 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/negative_correlation.rb

@@ -35,6 +35,14 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.correlative?
+            true
+          end
+
+          def self.decreasing?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/orthologous.rb

@@ -37,6 +37,10 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.genomic?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/positive_correlation.rb

@@ -31,6 +31,14 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.increasing?
+            true
+          end
+
+          def self.correlative?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/prognostic_biomarker_for.rb

@@ -37,6 +37,10 @@ module BELParser
           def self.deprecated?
             true
           end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/rate_limiting_step_of.rb

@@ -38,6 +38,14 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.directed?
+            true
+          end
+
+          def self.increasing?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/reactant_in.rb

@@ -37,6 +37,22 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.injected?
+            true
+          end
+
+          def self.self?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/regulates.rb

@@ -36,6 +36,14 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.causal?
+            true
+          end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/sub_process_of.rb

@@ -44,6 +44,10 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.directed?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/transcribed_to.rb

@@ -34,6 +34,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.genomic?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/translated_to.rb

@@ -35,6 +35,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.genomic?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0/relationships/translocates.rb

@@ -38,6 +38,18 @@ module BELParser
           def self.description
             DESCRIPTION
           end
+
+          def self.directed?
+            true
+          end
+
+          def self.injected?
+            true
+          end
+
+          def self.self?
+            true
+          end
         end
       end
     end

data/lib/bel_parser/language/version2_0.rb

@@ -29,6 +29,7 @@ module BELParser
           end
           @relationships         = rel_classes.compact
           @indexed_relationships = index_long_short(@relationships)
+          assign_relationship_categories(@relationships)
 
           # Establish return types
           ret_classes = Version2_0::ReturnTypes.constants.collect do |symbol|

data/lib/bel_parser/parsers/ast/node.rb

@@ -19,7 +19,8 @@ module BELParser
       # _ast_type_. This is equivalent to its _type_ instance variable
       # but the former is not used by the AST library itself.
       #
-      # @see Node.ast_type @see Node.initialize
+      # @see Node.ast_type
+      # @see Node.initialize
       #
       class Node < ::AST::Node
         # AST node type
@@ -62,6 +63,9 @@ module BELParser
         # AST node.
         attr_reader :character_range
 
+        # Get/Set the complete property.
+        attr_accessor :complete
+
         # Get the syntax errors for this AST node.
         def syntax_errors
           (@syntax_errors ||= [])
@@ -120,7 +124,9 @@ module BELParser
 
           if @children == new_children && properties.nil?
             self
-          else
+          elsif instance_of? Node
+            original_dup.send :initialize, @type, new_children, new_properties
+          else # self.is_a? Node
             original_dup.send :initialize, new_children, new_properties
           end
         end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel_parser
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.8
+  version: 1.0.0.alpha.9
 platform: ruby
 authors:
 - Anthony Bargnesi
@@ -38,6 +38,7 @@ files:
 - lib/bel_parser/language/semantics/deeply_nested_statement.rb
 - lib/bel_parser/language/semantics/function_deprecation.rb
 - lib/bel_parser/language/semantics/list_function_subject.rb
+- lib/bel_parser/language/semantics/non_causal_nested_statement.rb
 - lib/bel_parser/language/semantics/relationship_deprecation.rb
 - lib/bel_parser/language/semantics/signature_mapping.rb
 - lib/bel_parser/language/semantics_ast.rb