bel_parser 1.0.0.alpha.1 → 1.0.0.alpha.2

checksums.yaml

@@ -1,7 +1,7 @@
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-  metadata.gz: fda715b53e000aa7ea548ec0431879d74daac35d
-  data.tar.gz: 303d2234ea34a28ee8b2aba781ff56793930b538
+  metadata.gz: 90ab686251113e217ed255a26b59b00aa9b6a947
+  data.tar.gz: 87f55444534d215b579b4aec8d657cf38479ae1b
 SHA512:
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+  metadata.gz: 959bbb33f76a1888cabec4bc7bef6a00c130a45aeeac7a175e550403e2b14a78c9f75d147208e500a4aa400d5562e08d42a7733a6f53db38b688d0ba0c85a4e4
+  data.tar.gz: 4c43a80f6ad4263753a5e49d76e6bbb57237a32cb61cb6af3dc8349a417ca2d049df3b18af9f1fddfedc3ff89b5e4bc2f7661b39a751aed790eae0dd596ef4b7

data/.gemspec

@@ -11,7 +11,7 @@ Gem::Specification.new do |spec|
                                  'Anthony Bargnesi',
                                  'Nick Bargnesi',
                                ]
-  spec.date                  = %q{2016-04-05}
+  spec.date                  = %q{2016-04-08}
   spec.email                 = %q{abargnesi@selventa.com}
   spec.files                 = [
                                  Dir.glob('lib/**/*.{rb,rl}'),

data/VERSION

@@ -1 +1 @@
-1.0.0.alpha.1
+1.0.0.alpha.2

data/bin/bel2_termcheck

@@ -2,7 +2,7 @@
 $:.unshift(File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
 
 require 'bel_parser'
-require 'bel_parser/language/version2'
+require 'bel_parser/language/version2_0'
 require 'bel_parser/language/semantics/analyzer'
 
 module BELParser
@@ -16,7 +16,7 @@ module BELParser
 
       def each(io)
         if block_given?
-          v2           = BELParser::Language::Version2::Specification.new
+          v2           = BELParser::Language::Version2_0::Specification.new
           filtered_ast = FILTER.each(BELParser::ASTGenerator.new.each(io))
           filtered_ast.each do |results|
             term = results.last.first

data/lib/bel_parser/expression/term_semantics.rb

@@ -1,7 +1,7 @@
 require_relative '../ast_filter'
 require_relative '../ast_generator'
 require_relative '../parsers/expression'
-require_relative '../language/version2'
+require_relative '../language/version2_0'
 require_relative '../language/semantics/analyzer'
 
 module BELParser
@@ -15,7 +15,7 @@ module BELParser
 
       def each(io)
         if block_given?
-          v2           = BELParser::Language::Version2::Specification.new
+          v2           = BELParser::Language::Version2_0::Specification.new
           filtered_ast = FILTER.each(BELParser::ASTGenerator.new.each(io))
           filtered_ast.each do |results|
             term = results.last.first

data/lib/bel_parser/language/expression_validator.rb

@@ -0,0 +1,42 @@
+module BELParser
+  module Language
+    class ExpressionValidator
+      def initialize(spec)
+        @spec = spec
+      end
+
+      def validate(expression_ast)
+        node_errors = check_syntax(expression_ast)
+        if !node_errors.empty?
+          node_errors.each do |node_error|
+            puts "Syntax error (#{node_error.syntax_errors}) with #{node_error.type}."
+          end
+        else
+          check_semantics(expression_ast)
+        end
+      end
+
+      private
+
+      def check_syntax(ast)
+        # Clear syntax checks.
+        ast.traverse.each do |node|
+          node.syntax_errors.clear
+        end
+
+        # Run syntax checks, sets syntax_errors on nodes.
+        @spec.syntax.each do |syntax|
+          syntax.match(ast)
+        end
+
+        ast.traverse.select do |node|
+          !node.syntax_errors.empty?
+        end
+      end
+
+      def check_semantics(ast)
+        BELParser::Language::Semantics.check_term(ast, @spec)
+      end
+    end
+  end
+end

data/lib/bel_parser/language/function.rb

@@ -27,6 +27,14 @@ module BELParser
         raise NotImplementedError, "#{__method__} is not implemented."
       end
 
+      # Indicates whether this function is deprecated. Override in your
+      # function to mark as deprecated.
+      #
+      # @return [Boolean] false
+      def deprecated?
+        false
+      end
+
       def ===(other)
         return false if other.nil?
         short == other || long == other

data/lib/bel_parser/language/relationship.rb

@@ -0,0 +1,57 @@
+module BELParser
+  module Language
+    # Relationship allows you to describe the type of BEL Relationship.
+    #
+    # BEL Relationships represent an interaction between a subject and object
+    # in the BEL expression.
+    module Relationship
+      def short
+        raise NotImplementedError, "#{__method__} is not implemented."
+      end
+
+      def long
+        raise NotImplementedError, "#{__method__} is not implemented."
+      end
+
+      def description
+        raise NotImplementedError, "#{__method__} is not implemented."
+      end
+
+      # Indicates whether this relationship is deprecated. Override in your
+      # relationship to mark as deprecated.
+      #
+      # @return [Boolean] false
+      def deprecated?
+        false
+      end
+
+      def ===(other)
+        return false if other.nil?
+        short == other || long == other
+      end
+
+      def to_sym(form = :short)
+        value = _form_value(form)
+        return nil unless value
+        value.to_s
+      end
+
+      def to_s(form = :short)
+        value = _form_value(form)
+        return nil unless value
+        value.to_s
+      end
+
+      private
+
+      def _form_value(form = :short)
+        case form
+        when :short
+          short
+        when :long
+          long
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/{semantic_ast.rb → semantics/semantic_ast.rb}

@@ -1,5 +1,6 @@
-require_relative 'quoting'
-require_relative '../parsers/ast/node'
+require_relative 'semantic_match'
+require_relative '../quoting'
+require_relative '../../parsers/ast/node'
 
 module BELParser
   module Language
@@ -49,29 +50,6 @@ module BELParser
         match_results.flatten
       end
 
-      # MatchResult holds the results of an input AST to semantic AST match.
-      class MatchResult
-        attr_reader :input_node, :semantic_node
-
-        def initialize(success, input_node, semantic_node)
-          @success       = success
-          @input_node    = input_node
-          @semantic_node = semantic_node
-        end
-
-        def success?
-          @success
-        end
-
-        def failure?
-          !@success
-        end
-
-        def to_s
-          msg
-        end
-      end
-
       # Builder contains methods to build semantic AST nodes.
       # A convenient {Builder.build} method allows you to use these
       # methods within a block scope.
@@ -211,11 +189,11 @@ module BELParser
         end
 
         def success(node)
-          [MatchResult.new(true, node, self)]
+          [SemanticMatch.new(true, node, self)]
         end
 
         def failure(node)
-          [MatchResult.new(false, node, self)]
+          [SemanticMatch.new(false, node, self)]
         end
       end
 

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

@@ -0,0 +1,28 @@
+module BELParser
+  module Language
+    module Semantics
+      # SemanticMatch holds the results of an input AST to semantic AST match.
+      class SemanticMatch
+        attr_reader :input_node, :semantic_node
+
+        def initialize(success, input_node, semantic_node)
+          @success       = success
+          @input_node    = input_node
+          @semantic_node = semantic_node
+        end
+
+        def success?
+          @success
+        end
+
+        def failure?
+          !@success
+        end
+
+        def to_s
+          msg
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/semantics.rb

@@ -0,0 +1,2 @@
+require_relative 'semantics/semantic_ast'
+require_relative 'semantics/analyzer'

data/lib/bel_parser/language/specification.rb

@@ -7,43 +7,67 @@ module BELParser
         @indexed_functions[short_or_long_form]
       end
 
+      def relationship(short_or_long_form)
+        @indexed_relationships[short_or_long_form]
+      end
+
       def return_type(return_type)
         @indexed_return_types[return_type]
       end
 
       def functions(*short_or_long_form)
         if short_or_long_form.empty?
-          @functions
+          @functions.freeze
         else
           @indexed_functions.values_at(*short_or_long_form)
         end
       end
 
+      def relationships(*short_or_long_form)
+        if short_or_long_form.empty?
+          @relationships.freeze
+        else
+          @indexed_relationships.values_at(*short_or_long_form)
+        end
+      end
+
       def return_types(*return_types)
         if return_types.empty?
-          @return_types
+          @return_types.freeze
         else
           @indexed_return_types.values_at(*return_types)
         end
       end
 
-      def index_functions(functions)
+      def syntax
+        @syntax
+      end
+
+      # @param [Array<#long,#short>] language_objects to be indexed by
+      # +long+ and +short+ method return
+      def index_long_short(language_objects)
         Hash[
-          functions.flat_map do |function|
-            [[function.short, function], [function.long, function]]
+          language_objects.flat_map do |obj|
+            [[obj.short, obj], [obj.long, obj]]
           end
         ]
       end
-      protected :index_functions
+      protected :index_long_short
 
-      def index_return_types(return_types)
+      # @param [Array<#to_sym>] language_objects to be indexed by
+      # +to_sym+ method return
+      def index_sym(language_objects)
         Hash[
-          return_types.map do |return_type|
-            [return_type.to_sym, return_type]
+          language_objects.map do |obj|
+            [obj.to_sym, obj]
           end
         ]
       end
-      protected :index_return_types
+      protected :index_sym
+
+      def version
+        @version
+      end
     end
   end
 end

data/lib/bel_parser/language/{version1 → version1_0}/functions/abundance.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version1_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module Functions
         # Abundance: Denotes the abundance of an entity
         class Abundance
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :a
           LONG        = :abundance
-          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::Abundance
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Abundance
           DESCRIPTION = 'Denotes the abundance of an entity'.freeze
 
           def self.short

data/lib/bel_parser/language/{version1 → version1_0}/functions/biological_process.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version1_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module Functions
         # BiologicalProcess: Denotes a process or population of events
         class BiologicalProcess
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :bp
           LONG        = :biologicalProcess
-          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::BiologicalProcess
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::BiologicalProcess
           DESCRIPTION = 'Denotes a process or population of events'.freeze
 
           def self.short

data/lib/bel_parser/language/{version1 → version1_0}/functions/catalytic_activity.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version1_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module Functions
         # CatalyticActivity: Denotes the frequency or abundance of events where a member acts as an enzymatic catalyst of biochecmial reactions
         class CatalyticActivity
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :cat
           LONG        = :catalyticActivity
-          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::CatalyticActivity
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::CatalyticActivity
           DESCRIPTION = 'Denotes the frequency or abundance of events where a member acts as an enzymatic catalyst of biochecmial reactions'.freeze
 
           def self.short
@@ -52,7 +52,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version1::ReturnTypes::ComplexAbundance))))))              
+                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))              
               end
               private_constant :AST
 
@@ -82,7 +82,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version1::ReturnTypes::ProteinAbundance))))))              
+                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))              
               end
               private_constant :AST
 

data/lib/bel_parser/language/{version1 → version1_0}/functions/cell_secretion.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version1_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module Functions
         # CellSecretion: Denotes the frequency or abundance of events in which members of an abundance move from cells to regions outside of the cells
         class CellSecretion
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :sec
           LONG        = :cellSecretion
-          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::Abundance
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Abundance
           DESCRIPTION = 'Denotes the frequency or abundance of events in which members of an abundance move from cells to regions outside of the cells'.freeze
 
           def self.short
@@ -52,7 +52,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version1::ReturnTypes::Abundance))))))              
+                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))              
               end
               private_constant :AST
 

data/lib/bel_parser/language/{version1 → version1_0}/functions/cell_surface_expression.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version1_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module Functions
         # CellSurfaceExpression: Denotes the frequency or abundance of events in which members of an abundance move to the surface of cells
         class CellSurfaceExpression
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :surf
           LONG        = :cellSurfaceExpression
-          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::Abundance
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Abundance
           DESCRIPTION = 'Denotes the frequency or abundance of events in which members of an abundance move to the surface of cells'.freeze
 
           def self.short
@@ -52,7 +52,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version1::ReturnTypes::Abundance))))))              
+                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))              
               end
               private_constant :AST
 

data/lib/bel_parser/language/{version1 → version1_0}/functions/chaperone_activity.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version1_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module Functions
         # ChaperoneActivity: Denotes the frequency or abundance of events in which a member binds to some substrate and acts as a chaperone for the substrate
         class ChaperoneActivity
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :chap
           LONG        = :chaperoneActivity
-          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::ChaperoneActivity
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::ChaperoneActivity
           DESCRIPTION = 'Denotes the frequency or abundance of events in which a member binds to some substrate and acts as a chaperone for the substrate'.freeze
 
           def self.short
@@ -52,7 +52,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version1::ReturnTypes::ComplexAbundance))))))              
+                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))              
               end
               private_constant :AST
 
@@ -82,7 +82,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version1::ReturnTypes::ProteinAbundance))))))              
+                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))              
               end
               private_constant :AST
 

data/lib/bel_parser/language/{version1 → version1_0}/functions/complex_abundance.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version1_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module Functions
         # ComplexAbundance: Denotes the abundance of a molecular complex
         class ComplexAbundance
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :complex
           LONG        = :complexAbundance
-          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::ComplexAbundance
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance
           DESCRIPTION = 'Denotes the abundance of a molecular complex'.freeze
 
           def self.short
@@ -87,7 +87,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version1::ReturnTypes::Abundance))))))              
+                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))              
               end
               private_constant :AST
 

data/lib/bel_parser/language/{version1 → version1_0}/functions/composite_abundance.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version1_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module Functions
         # CompositeAbundance: Denotes the frequency or abundance of events in which members are present
         class CompositeAbundance
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :composite
           LONG        = :compositeAbundance
-          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::Abundance
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Abundance
           DESCRIPTION = 'Denotes the frequency or abundance of events in which members are present'.freeze
 
           def self.short
@@ -52,7 +52,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version1::ReturnTypes::Abundance))))))              
+                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))              
               end
               private_constant :AST
 

data/lib/bel_parser/language/{version1 → version1_0}/functions/degradation.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version1_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module Functions
         # Degradation: Denotes the frequency or abundance of events in which a member is degraded in some way such that it is no longer a member
         class Degradation
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :deg
           LONG        = :degradation
-          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::Abundance
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Abundance
           DESCRIPTION = 'Denotes the frequency or abundance of events in which a member is degraded in some way such that it is no longer a member'.freeze
 
           def self.short
@@ -52,7 +52,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version1::ReturnTypes::Abundance))))))              
+                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))              
               end
               private_constant :AST
 

data/lib/bel_parser/language/{version1 → version1_0}/functions/fusion.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version1_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module Functions
         # Fusion: Specifies the abundance of a protein translated from the fusion of a gene
         class Fusion
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :fus
           LONG        = :fusion
-          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::Fusion
+          RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Fusion
           DESCRIPTION = 'Specifies the abundance of a protein translated from the fusion of a gene'.freeze
 
           def self.short