RubyGems - bel_parser - Versions diffs - 1.0.0.alpha.1 → 1.0.0.alpha.2 - Mend

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

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (184) hide show

data/lib/bel_parser/language/version1_0.rb ADDED Viewed

@@ -0,0 +1,89 @@
+require_relative 'function'
+require_relative 'specification'
+module BELParser
+  module Language
+    module Version1_0
+      # Specification defines the BEL, version 1.0 specification.
+      class Specification
+        include BELParser::Language::Specification
+        def initialize
+          @version = '1.0'.freeze
+          # Collect return types
+          ret_classes = Version1_0::ReturnTypes.constants.collect do |symbol|
+            const = Version1_0::ReturnTypes.const_get(symbol)
+            const if const.respond_to?(:subtypes)
+          end
+          @return_types         = ret_classes.compact
+          @indexed_return_types = index_sym(@return_types)
+          # Collect functions
+          function_classes = Version1_0::Functions.constants.collect do |symbol|
+            const = Version1_0::Functions.const_get(symbol)
+            const if
+              const.respond_to?(:short) &&
+              const.respond_to?(:long)
+          end
+          @functions         = function_classes.compact
+          @indexed_functions = index_long_short(@functions)
+          # Collect relationships
+          rel_classes = Version1_0::Relationships.constants.collect do |symbol|
+            const = Version1_0::Relationships.const_get(symbol)
+            const if
+              const.respond_to?(:short) &&
+              const.respond_to?(:long)
+          end
+          @relationships         = rel_classes.compact
+          @indexed_relationships = index_long_short(@relationships)
+          # Collect syntax checkers.
+          syntax_classes = Version1_0::Syntax.constants.collect do |symbol|
+            const = Version1_0::Syntax.const_get(symbol)
+            const if const.respond_to?(:match)
+          end
+          @syntax = syntax_classes.compact
+          freeze
+        end
+      end
+    end
+  end
+end
+# Require all version 1.0 return types
+Dir[
+  File.join(
+    File.dirname(File.expand_path(__FILE__)),
+    'version1_0', 'return_types', '*.rb')
+].each do |path|
+  require_relative "version1_0/return_types/#{File.basename(path)}"
+end
+# Require all version 1.0 functions.
+Dir[
+  File.join(
+    File.dirname(File.expand_path(__FILE__)),
+    'version1_0', 'functions', '*.rb')
+].each do |path|
+  require_relative "version1_0/functions/#{File.basename(path)}"
+end
+# Require all version 1.0 relationships.
+Dir[
+  File.join(
+    File.dirname(File.expand_path(__FILE__)),
+    'version1_0', 'relationships', '*.rb')
+].each do |path|
+  require_relative "version1_0/relationships/#{File.basename(path)}"
+end
+# Require all version 1.0 syntax checkers.
+Dir[
+  File.join(
+    File.dirname(File.expand_path(__FILE__)),
+    'version1_0', 'syntax', '*.rb')
+].each do |path|
+  require_relative "version1_0/syntax/#{File.basename(path)}"
+end

data/lib/bel_parser/language/{version2 → version2_0}/functions/abundance.rb RENAMED Viewed

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 module BELParser
   module Language
-    module Version2
+    module Version2_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::Version2::ReturnTypes::Abundance
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
           DESCRIPTION = 'Denotes the abundance of an entity.'.freeze
           def self.short
@@ -97,7 +97,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Location))))))
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
               end
               private_constant :AST
@@ -137,7 +137,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::MolecularActivity))))))
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::MolecularActivity))))))
               end
               private_constant :AST

data/lib/bel_parser/language/{version2 → version2_0}/functions/activity.rb RENAMED Viewed

@@ -1,11 +1,11 @@
-require_relative '../../version2'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module Functions
         # Activity: Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale.
         class Activity
@@ -13,7 +13,7 @@ module BELParser
           SHORT       = :act
           LONG        = :activity
-          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Activity
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Activity
           DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale.'.freeze
           def self.short
@@ -52,7 +52,7 @@ module BELParser
                     term(
                       function(
                         identifier(
-                          return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))))
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST
@@ -82,12 +82,12 @@ module BELParser
                     term(
                       function(
                         identifier(
-                          return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))),
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))),
                   argument(
                     term(
                       function(
                         identifier(
-                          return_type_of(BELParser::Language::Version2::ReturnTypes::MolecularActivity))))))
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::MolecularActivity))))))
               end
               private_constant :AST

data/lib/bel_parser/language/{version2 → version2_0}/functions/biological_process.rb RENAMED Viewed

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 module BELParser
   module Language
-    module Version2
+    module Version2_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::Version2::ReturnTypes::BiologicalProcess
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::BiologicalProcess
           DESCRIPTION = 'Denotes a process or population of events.'.freeze
           def self.short

data/lib/bel_parser/language/{version2 → version2_0}/functions/cell_secretion.rb RENAMED Viewed

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 module BELParser
   module Language
-    module Version2
+    module Version2_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::Version2::ReturnTypes::Abundance
+          RETURN_TYPE = BELParser::Language::Version2_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::Version2::ReturnTypes::Abundance))))))
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST

data/lib/bel_parser/language/{version2 → version2_0}/functions/cell_surface_expression.rb RENAMED Viewed

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 module BELParser
   module Language
-    module Version2
+    module Version2_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::Version2::ReturnTypes::Abundance
+          RETURN_TYPE = BELParser::Language::Version2_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::Version2::ReturnTypes::Abundance))))))
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST

data/lib/bel_parser/language/{version2 → version2_0}/functions/complex_abundance.rb RENAMED Viewed

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 module BELParser
   module Language
-    module Version2
+    module Version2_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::Version2::ReturnTypes::ComplexAbundance
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ComplexAbundance
           DESCRIPTION = 'Denotes the abundance of a molecular complex.'.freeze
           def self.short
@@ -97,7 +97,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Location))))))
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
               end
               private_constant :AST
@@ -127,7 +127,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))))
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST
@@ -157,12 +157,12 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))),
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))),
                 argument(
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Location))))))
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
               end
               private_constant :AST

data/lib/bel_parser/language/{version2 → version2_0}/functions/composite_abundance.rb RENAMED Viewed

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 module BELParser
   module Language
-    module Version2
+    module Version2_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::Version2::ReturnTypes::Abundance
+          RETURN_TYPE = BELParser::Language::Version2_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::Version2::ReturnTypes::Abundance))))))
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST

data/lib/bel_parser/language/{version2 → version2_0}/functions/degradation.rb RENAMED Viewed

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 module BELParser
   module Language
-    module Version2
+    module Version2_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::Version2::ReturnTypes::Abundance
+          RETURN_TYPE = BELParser::Language::Version2_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::Version2::ReturnTypes::Abundance))))))
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST

data/lib/bel_parser/language/{version2 → version2_0}/functions/fragment.rb RENAMED Viewed

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module Functions
         # Fragment: Denotes a protein fragment, e.g., a product of proteolytic cleavage.
         class Fragment
@@ -13,7 +13,7 @@ module BELParser
           SHORT       = :frag
           LONG        = :fragment
-          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Fragment
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Fragment
           DESCRIPTION = 'Denotes a protein fragment, e.g., a product of proteolytic cleavage.'.freeze
           def self.short

data/lib/bel_parser/language/{version2 → version2_0}/functions/from_location.rb RENAMED Viewed

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module Functions
         # FromLocation: Denotes the from cellular location of the abundance.
         class FromLocation
@@ -13,7 +13,7 @@ module BELParser
           SHORT       = :fromLoc
           LONG        = :fromLocation
-          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::FromLocation
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::FromLocation
           DESCRIPTION = 'Denotes the from cellular location of the abundance.'.freeze
           def self.short

data/lib/bel_parser/language/{version2 → version2_0}/functions/fusion.rb RENAMED Viewed

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 module BELParser
   module Language
-    module Version2
+    module Version2_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::Version2::ReturnTypes::Fusion
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Fusion
           DESCRIPTION = 'Specifies the abundance of a protein translated from the fusion of a gene.'.freeze
           def self.short

data/lib/bel_parser/language/{version2 → version2_0}/functions/gene_abundance.rb RENAMED Viewed

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module Functions
         # GeneAbundance: Denotes the abundance of a gene.
         class GeneAbundance
@@ -13,7 +13,7 @@ module BELParser
           SHORT       = :g
           LONG        = :geneAbundance
-          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::GeneAbundance
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::GeneAbundance
           DESCRIPTION = 'Denotes the abundance of a gene.'.freeze
           def self.short
@@ -87,7 +87,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Fusion))))))
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Fusion))))))
               end
               private_constant :AST
@@ -127,7 +127,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Location))))))
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
               end
               private_constant :AST
@@ -167,7 +167,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Variant))))))
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))
               end
               private_constant :AST

data/lib/bel_parser/language/{version2 → version2_0}/functions/list.rb RENAMED Viewed

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module Functions
         # List: Groups a list of terms together.
         class List
@@ -13,7 +13,7 @@ module BELParser
           SHORT       = :list
           LONG        = :list
-          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::List
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::List
           DESCRIPTION = 'Groups a list of terms together.'.freeze
           def self.short
@@ -87,7 +87,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))))
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST

data/lib/bel_parser/language/{version2 → version2_0}/functions/location.rb RENAMED Viewed

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module Functions
         # Location: Denotes the cellular location of the abundance.
         class Location
@@ -13,7 +13,7 @@ module BELParser
           SHORT       = :loc
           LONG        = :location
-          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Location
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Location
           DESCRIPTION = 'Denotes the cellular location of the abundance.'.freeze
           def self.short

data/lib/bel_parser/language/{version2 → version2_0}/functions/micro_rna_abundance.rb RENAMED Viewed

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module Functions
         # MicroRNAAbundance: Denotes the abundance of a processed, functional microRNA
         class MicroRNAAbundance
@@ -13,7 +13,7 @@ module BELParser
           SHORT       = :m
           LONG        = :microRNAAbundance
-          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::MicroRNAAbundance
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::MicroRNAAbundance
           DESCRIPTION = 'Denotes the abundance of a processed, functional microRNA'.freeze
           def self.short
@@ -97,7 +97,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Location))))))
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
               end
               private_constant :AST
@@ -137,7 +137,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Variant))))))
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))
               end
               private_constant :AST

data/lib/bel_parser/language/{version2 → version2_0}/functions/molecular_activity.rb RENAMED Viewed

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module Functions
         # MolecularActivity: Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale
         class MolecularActivity
@@ -13,7 +13,7 @@ module BELParser
           SHORT       = :ma
           LONG        = :molecularActivity
-          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::MolecularActivity
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::MolecularActivity
           DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale'.freeze
           def self.short

data/lib/bel_parser/language/{version1 → version2_0}/functions/pathology.rb RENAMED Viewed

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 module BELParser
   module Language
-    module Version1
+    module Version2_0
       module Functions
         # Pathology: Denotes a disease or pathology process
         class Pathology
@@ -13,7 +13,7 @@ module BELParser
           SHORT       = :path
           LONG        = :pathology
-          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::Pathology
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Pathology
           DESCRIPTION = 'Denotes a disease or pathology process'.freeze
           def self.short