bel_parser 1.0.8-java → 1.1.1-java

data/lib/bel_parser/language/apply_namespace_encoding.rb

@@ -69,11 +69,11 @@ module BELParser
 
       def on_value(value_node)
         return value_node unless @namespace
+
         value_node.prefix    = @prefix
         value_node.namespace = @namespace
-
-        value_literal        = value_node.children[0].string_literal
-        value                = @namespace[value_literal]
+        string_literal       = value_literal(value_node.children[0])
+        value                = @namespace[string_literal]
 
         if value
           value_node.encoding =
@@ -86,6 +86,17 @@ module BELParser
         end
         value_node
       end
+
+      private
+
+      def value_literal(node)
+        case node.type
+        when :identifier
+          node.string_literal
+        when :string
+          node.string_value
+        end
+      end
     end
   end
 end

data/lib/bel_parser/language/expression_validator.rb

@@ -123,7 +123,7 @@ module BELParser
         end
 
         def semantics_errors_s
-          return nil if @semantics_results.empty?
+          return nil if @semantics_results.nil? || @semantics_results.empty?
 
           report = "Semantic errors\n"
           @semantics_results.each { |res| report += "#{res}\n" }
@@ -406,7 +406,6 @@ module BELParser
         end
 
         def to_s
-          report = @object_result.to_s
           <<-HEADER.gsub(/^ {12}/, '')
             Syntax:    #{valid_syntax?    ? 'Valid' : 'Invalid'}
             Semantics: #{valid_semantics? ? 'Valid' : 'Invalid'}

data/lib/bel_parser/language/function.rb

@@ -60,6 +60,10 @@ module BELParser
         })
       end
 
+      def =~(regexp)
+        short =~ regexp || long =~ regexp
+      end
+
       private
 
       def _form_value(form = :short)

data/lib/bel_parser/language/relationship.rb

@@ -93,6 +93,10 @@ module BELParser
         })
       end
 
+      def =~(regexp)
+        short =~ regexp || long =~ regexp
+      end
+
       private
 
       def _form_value(form = :short)

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

@@ -14,6 +14,7 @@ module BELParser
 
         def self.map(node, spec, _namespaces)
           return nil unless node.is_a?(BELParser::Parsers::AST::Function)
+          return nil unless node.identifier
 
           function_name = node.identifier.string_literal
           func          = spec.function(function_name.to_sym)

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

@@ -19,6 +19,8 @@ module BELParser
           list_func = spec.function(:list)
           return nil unless list_func
 
+          return nil unless node.term.function
+          return nil unless node.term.function.identifier
           func_name = node.term.function.identifier.string_literal
           sub_func  = spec.function(func_name.to_sym)
           ListFunctionSubjectWarning.new(node, spec) if sub_func == list_func

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

@@ -13,6 +13,7 @@ module BELParser
 
         def self.map(stmt_node, spec, _namespaces)
           return nil unless stmt_node.is_a?(BELParser::Parsers::AST::Statement)
+          return nil unless stmt_node.relationship?
           return nil if stmt_node.relationship.string_literal.nil?
           rel = spec.relationship(stmt_node.relationship.string_literal.to_sym)
           return nil unless rel
@@ -20,6 +21,7 @@ module BELParser
 
           list_func = spec.function(:list)
           return nil unless list_func
+          return nil unless stmt_node.object?
           return nil unless stmt_node.object.term?
 
           map_subject_object(stmt_node, rel, spec)
@@ -29,7 +31,8 @@ module BELParser
           sub_term  = stmt_node.subject.term
           list_term = stmt_node.object.child
 
-          if list_term.arguments.any? { |arg| sub_term == arg.child }
+          return nil if list_term.arguments.empty?
+          if list_term.arguments.any? { |arg| arg.child && sub_term == arg.child }
             MultipleSubjectObjectWarning.new(stmt_node, spec, rel)
           end
         end

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

@@ -0,0 +1,43 @@
+require 'bel_parser/parsers/ast/node'
+
+module BELParser
+  module Language
+    module Semantics
+      # NestedStatementWithoutObject implements a {SemanticsFunction} that maps a
+      # nested {BELParser::Parsers::AST::Statement} to {SemanticsWarning} if
+      # the nested statement does not have an object.
+      class NestedStatementWithoutObject
+        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?
+
+          nested = node.object.child
+
+          if nested.object?
+            NestedStatementWithoutObjectWarning.new(node, spec)
+          end
+        end
+      end
+
+      # Represents a {SemanticsWarning} when a nested
+      # {BELParser::Parsers::AST::Statement} does not have an object.
+      class NestedStatementWithoutObjectWarning < SemanticsWarning
+        attr_reader :non_causal_relationship
+
+        def initialize(stmt_node, spec)
+          super(stmt_node, spec)
+        end
+
+        def to_s
+          <<-MSG.gsub(/ {12}/, '')
+            Nested statement does not have an object.
+          MSG
+        end
+      end
+    end
+  end
+end

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

@@ -13,6 +13,8 @@ module BELParser
 
         def self.map(stmt_node, spec, _namespaces)
           return nil unless stmt_node.is_a?(BELParser::Parsers::AST::Statement)
+          return nil unless stmt_node.relationship?
+          return nil unless stmt_node.object?
           return nil if stmt_node.relationship.string_literal.nil?
 
           list_func = spec.function(:list)
@@ -31,6 +33,7 @@ module BELParser
             spec,
             rel) unless obj_node.term?
 
+          return nil unless obj_node.child.function
           obj_func = obj_node.child.function.identifier.string_literal
           NonObjectListWarning.new(
             obj_node,

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

@@ -14,6 +14,7 @@ module BELParser
         def self.map(node, spec, _namespaces)
           return nil unless node.is_a?(BELParser::Parsers::AST::Statement)
           return nil unless node.relationship?
+          return nil unless node.object?
           return nil unless node.object.term?
 
           map_statement(node, spec)
@@ -22,6 +23,7 @@ module BELParser
         def self.map_statement(stmt_node, spec)
           list_func = spec.function(:list)
           return nil unless list_func
+          return nil unless stmt_node.object.child.function
 
           obj_func = stmt_node.object.child.function.identifier.string_literal
           return nil unless spec.function(obj_func.to_sym) == list_func

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

@@ -19,6 +19,8 @@ module BELParser
         # includes both successful and failed signature matches.
         def self.map(term_node, spec, _namespaces)
           return nil unless term_node.is_a?(BELParser::Parsers::AST::Term)
+          return nil unless term_node.function
+          return nil unless term_node.function.identifier
 
           function_name = term_node.function.identifier.string_literal
           function      = spec.function(function_name.to_sym)

data/lib/bel_parser/language/semantics_ast.rb

@@ -69,18 +69,11 @@ module BELParser
 
           builder = _builder_class.new
           builder.instance_eval(&block)
-          builder.result
         end
 
         def self._builder_class
           Class.new do
             include Builder
-
-            attr_reader :result
-
-            def term(function, *arguments, **properties)
-              @result = super
-            end
           end
         end
         private_class_method :_builder_class

data/lib/bel_parser/language/syntax/invalid_function.rb

@@ -13,7 +13,12 @@ module BELParser
         def self.map(func_node, spec, _namespaces)
           return nil unless func_node.is_a?(BELParser::Parsers::AST::Function)
 
-          function_name = func_node.identifier.string_literal
+          function_name =
+            if func_node.identifier
+              func_node.identifier.string_literal
+            else
+              ''
+            end
           unless spec.function(function_name.to_sym)
             InvalidFunctionSyntaxError.new(func_node, spec, function_name)
           end

data/lib/bel_parser/language/syntax/invalid_relationship.rb

@@ -12,6 +12,7 @@ module BELParser
 
         def self.map(stmt_node, spec, _namespaces)
           return nil unless stmt_node.is_a?(BELParser::Parsers::AST::Statement)
+          return nil unless stmt_node.relationship?
 
           rel_name = stmt_node.relationship.string_literal
           return nil if rel_name.nil?

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

@@ -17,15 +17,15 @@ module BELParser
 
           SHORT       = :actsIn
           LONG        = :actsIn
-          DESCRIPTION = ' +A actsIn f(A)+ -  This relationship links an
-          bundance term to the activity term for the same
-          bundance. This relationship is direct because
-          t is a _self_ relationship, the abundance acts
-          n its own activity. For protein abundance p(A)
-          nd its molecular activity kin(p(A), +p(A) actsIn
-          in(p(A))+. This relationship is introduced by the
-          EL Compiler and may not be used by statements in
-          EL documents.'.freeze
+          DESCRIPTION = <<-DOC
+ActsIn:  +A actsIn f(A)+ -  This relationship links
+an abundance term to the activity term for the same
+abundance. This relationship is direct because it is a _self_
+relationship, the abundance acts in its own activity. For
+protein abundance p(A) and its molecular activity kin(p(A),
++p(A) actsIn kin(p(A))+. This relationship is introduced by the
+BEL Compiler and may not be used by statements in BEL documents.
+          DOC
 
           def self.short
             SHORT

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

@@ -14,10 +14,12 @@ module BELParser
 
           SHORT       = :analogous
           LONG        = :analogous
-          DESCRIPTION = ' +A analogous B+ -  For terms A and B, +A
-          nalogousTo B+ indicates that A and B represent
-          bundances or molecular activities in different
-          pecies which function in a similar manner.'.freeze
+          DESCRIPTION = <<-DOC
+Analogous:  +A analogous B+ -  For terms A and B, +A analogousTo
+B+ indicates that A and B represent abundances or molecular
+activities in different species which function in a similar
+manner.
+DOC
 
           def self.short
             SHORT

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

@@ -16,13 +16,14 @@ module BELParser
 
           SHORT       = :'--'
           LONG        = :association
-          DESCRIPTION = ' +A -- B+ -  For terms A and B, +A association B+
-          r +A -- B+ indicates that A and B are associated
-          n an unspecified manner. This relationship
-          s used when not enough information about the
-          ssociation is available to describe it using
-          ore specific relationships, like increases or
-          ositiveCorrelation.'.freeze
+          DESCRIPTION = <<-DOC
+Association:  +A -- B+ -  For terms A and B, +A association
+B+ or +A -- B+ indicates that A and B are associated in an
+unspecified manner. This relationship is used when not enough
+information about the association is available to describe
+it using more specific relationships, like increases or
+positiveCorrelation.
+          DOC
 
           def self.short
             SHORT

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

@@ -14,11 +14,12 @@ module BELParser
 
           SHORT       = :biomarkerFor
           LONG        = :biomarkerFor
-          DESCRIPTION = ' +A biomarkerFor P+ -  For term A and process
-          erm P, +A biomarkerFor P+ indicates that changes
-          n or detection of A is used in some way to be
-           biomarker for pathology or biological process
-          .'.freeze
+          DESCRIPTION = <<-DOC
+BiomarkerFor:  +A biomarkerFor P+ -  For term A and process term
+P, +A biomarkerFor P+ indicates that changes in or detection
+of A is used in some way to be a biomarker for pathology or
+biological process P.
+          DOC
 
           def self.short
             SHORT

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

@@ -16,13 +16,14 @@ module BELParser
 
           SHORT       = :causesNoChange
           LONG        = :causesNoChange
-          DESCRIPTION = ' +A causesNoChange B+ -  For terms A and B, +A
-          ausesNoChange B+ indicates that B was observed not
-          o change in response to changes in A. Statements
-          sing this relationship correspond to cases where
-          xplicit measurement of B demonstrates lack of
-          ignificant change, not for cases where the state
-          f B is unknown.'.freeze
+          DESCRIPTION = <<-DOC
+CausesNoChange:  +A causesNoChange B+ -  For terms A and B,
++A causesNoChange B+ indicates that B was observed not to
+change in response to changes in A. Statements using this
+relationship correspond to cases where explicit measurement
+of B demonstrates lack of significant change, not for cases
+where the state of B is unknown.
+          DOC
 
           def self.short
             SHORT

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

@@ -20,18 +20,19 @@ module BELParser
 
           SHORT       = :'-|'
           LONG        = :decreases
-          DESCRIPTION = ' +A -| B+ -  For terms A and B, +A decreases B
-          r A -| B+ indicates that increases in A have been
-          bserved to cause decreases in B. +A decreases
-          + also represents cases where decreases in A
-          ave been observed to cause increases in B, for
-          xample, in recording the results of gene deletion
-          r other inhibition experiments. A is a BEL Term
-          nd B is either a BEL Term or a BEL Statement. The
-          elationship does not indicate that the changes
-          n A are either necessary for changes in B, nor
-          oes it indicate that changes in A are sufficient
-          o cause changes in B.'.freeze
+
+          DESCRIPTION = <<-DOC
+Decreases:  +A -| B+ -  For terms A and B, +A decreases B or
+A -| B+ indicates that increases in A have been observed to
+cause decreases in B. +A decreases B+ also represents cases
+where decreases in A have been observed to cause increases in B,
+for example, in recording the results of gene deletion or other
+inhibition experiments. A is a BEL Term and B is either a BEL
+Term or a BEL Statement. The relationship does not indicate
+that the changes in A are either necessary for changes in B,
+nor does it indicate that changes in A are sufficient to cause
+changes in B.
+          DOC
 
           def self.short
             SHORT

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

@@ -15,12 +15,14 @@ module BELParser
 
           SHORT       = :'=|'
           LONG        = :directlyDecreases
-          DESCRIPTION = ' +A =| B+ -  For terms A and B,
-          A directlyDecreases B or A =| B+ indicates A
-          ecreases B and that the mechanism of the causal
-          elationship is based on physical interaction
-          f entities related to A and B. This is a direct
-          ersion of the decreases relationship.'.freeze
+
+          DESCRIPTION = <<-DOC
+DirectlyDecreases:  +A =| B+ -  For terms A and B, +A
+directlyDecreases B or A =| B+ indicates A decreases B and that
+the mechanism of the causal relationship is based on physical
+interaction of entities related to A and B. This is a direct
+version of the decreases relationship.
+          DOC
 
           def self.short
             SHORT

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

@@ -15,12 +15,14 @@ module BELParser
 
           SHORT       = :'=>'
           LONG        = :directlyIncreases
-          DESCRIPTION = ' +A => B+ -  For terms A and B,
-          A directlyIncreases B or A => B+ indicate A
-          ncreases B and that the mechanism of the causal
-          elationship is based on physical interaction
-          f entities related to A and B. This is a direct
-          ersion of the increases relationship.'.freeze
+
+          DESCRIPTION = <<-DOC
+DirectlyIncreases:  +A => B+ -  For terms A and B, +A
+directlyIncreases B or A => B+ indicate A increases B and that
+the mechanism of the causal relationship is based on physical
+interaction of entities related to A and B. This is a direct
+version of the increases relationship.
+          DOC
 
           def self.short
             SHORT

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

@@ -21,20 +21,20 @@ module BELParser
 
           SHORT       = :hasComponent
           LONG        = :hasComponent
-          DESCRIPTION = ' +A hasComponent A1+ -  For complexAbundance
-          erm A and abundance term B, +A hasComponent B+
-          esignates B as a component of A, that complexes
-          hat are instances of A have instances of B as
-          ossible components. Note that, the stoichiometry
-          f A is not described, nor is it stated that B
-          s a required component. The use of hasComponent
-          elationships is complementary to the use of
-          unctionally composed complexes and is intended to
-          nable the assignment of components to complexes
-          esignated by names in external vocabularies. The
-          ssignment of components can potentially enable
-          he reconciliation of equivalent complexes at
-          nowledge assembly time.'.freeze
+
+          DESCRIPTION = <<-DOC
+HasComponent:  +A hasComponent A1+ -  For complexAbundance
+term A and abundance term B, +A hasComponent B+ designates
+B as a component of A, that complexes that are instances of
+A have instances of B as possible components. Note that, the
+stoichiometry of A is not described, nor is it stated that B is
+a required component. The use of hasComponent relationships is
+complementary to the use of functionally composed complexes and
+is intended to enable the assignment of components to complexes
+designated by names in external vocabularies. The assignment
+of components can potentially enable the reconciliation of
+equivalent complexes at knowledge assembly time.
+          DOC
 
           def self.short
             SHORT

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

@@ -19,17 +19,18 @@ module BELParser
 
           SHORT       = :hasComponents
           LONG        = :hasComponents
-          DESCRIPTION = ' +A hasComponents (B, C, D)+ -  The hasComponents
-          elationship is a special form which enables
-          he assignment of multiple complex components
-          n a single statement where the object of the
-          tatement is a set of abundance terms. A statement
-          sing hasComponents is exactly equivalent to
-          ultiple hasComponent statements. A term may not
-          ppear in both the subject and object of the same
-          asComponents statement. For the abundance terms A,
-          , C and D, +A hasComponents B, C, D+ indicates
-          hat A has components B, C and D.'.freeze
+
+          DESCRIPTION = <<-DOC
+HasComponents:  +A hasComponents (B, C, D)+ -  The hasComponents
+relationship is a special form which enables the assignment
+of multiple complex components in a single statement where
+the object of the statement is a set of abundance terms. A
+statement using hasComponents is exactly equivalent to multiple
+hasComponent statements. A term may not appear in both the
+subject and object of the same hasComponents statement. For
+the abundance terms A, B, C and D, +A hasComponents B, C, D+
+indicates that A has components B, C and D.
+          DOC
 
           def self.short
             SHORT

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

@@ -17,14 +17,16 @@ module BELParser
 
           SHORT       = :hasMember
           LONG        = :hasMember
-          DESCRIPTION = ' +A hasMember A1+ -  For term abundances A and B,
-          A hasMember B+ designates B as a member class of
-          . A member class is a distinguished sub-class. A is
-          efined as a group by all of the members assigned to
-          t. The member classes may or may not be overlapping
-          nd may or may not entirely cover all instances
-          f A. A term may not appear in both the subject
-          nd object of the same hasMember statement.'.freeze
+
+          DESCRIPTION = <<-DOC
+HasMember:  +A hasMember A1+ -  For term abundances A and B,
++A hasMember B+ designates B as a member class of A. A member
+class is a distinguished sub-class. A is defined as a group
+by all of the members assigned to it. The member classes may
+or may not be overlapping and may or may not entirely cover
+all instances of A. A term may not appear in both the subject
+and object of the same hasMember statement.
+          DOC
 
           def self.short
             SHORT

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

@@ -19,18 +19,19 @@ module BELParser
 
           SHORT       = :hasMembers
           LONG        = :hasMembers
-          DESCRIPTION = ' +A hasMembers (B, C, D)+ -  The hasMembers
-          elationship is a special form which enables the
-          ssignment of multiple member classes in a single
-          tatement where the object of the statement is a set
-          f abundance terms. A statement using hasMembers
-          s exactly equivalent to multiple hasMember
-          tatements. A term may not appear in both the
-          ubject and object of a of the same hasMembers
-          tatement. For the abundance terms A, B, C and D,
-          A hasMembers B, C, D+ indicates that A is defined
-          y its member abundance classes B, C and D.'.freeze
 
+          DESCRIPTION = <<-DOC
+HasMembers:  +A hasMembers (B, C, D)+ -  The hasMembers
+relationship is a special form which enables the assignment of
+multiple member classes in a single statement where the object
+of the statement is a set of abundance terms. A statement
+using hasMembers is exactly equivalent to multiple hasMember
+statements. A term may not appear in both the subject and
+object of a of the same hasMembers statement. For the abundance
+terms A, B, C and D, +A hasMembers B, C, D+ indicates that A
+is defined by its member abundance classes B, C and D.
+          DOC
+          
           def self.short
             SHORT
           end

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

@@ -16,13 +16,15 @@ module BELParser
 
           SHORT       = :hasModification
           LONG        = :hasModification
-          DESCRIPTION = ' +p(A) hasModification p(A, pmod(P, S, 473))+ -
-          his relationship links abundance terms modified by
-          he +pmod()+ function to the unmodified abundance
-          erm. This is a direct relationship because it
-          s a _self_ relationship. This relationship is
-          ntroduced by the BEL Compiler and may not be used
-          y statements in BEL documents.'.freeze
+
+          DESCRIPTION = <<-DOC
+HasModification:  +p(A) hasModification p(A, pmod(P, S, 473))+
+-  This relationship links abundance terms modified by the
++pmod()+ function to the unmodified abundance term. This is a
+direct relationship because it is a _self_ relationship. This
+relationship is introduced by the BEL Compiler and may not be
+used by statements in BEL documents.
+          DOC
 
           def self.short
             SHORT

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

@@ -17,14 +17,16 @@ module BELParser
 
           SHORT       = :hasProduct
           LONG        = :hasProduct
-          DESCRIPTION = ' +reaction(reactants(A), products(B)) hasProduct
-          + -  This relationship links abundance terms
-          rom the +products(<list>)+ in a reaction to the
-          eaction. This is a direct relationship because it
-          s a _self_ relationship. Products are produced
-          irectly by a reaction. This relationship is
-          ntroduced by the BEL Compiler and may not be used
-          y statements in BEL documents.'.freeze
+
+          DESCRIPTION = <<-DOC
+HasProduct:  +reaction(reactants(A), products(B))
+hasProduct B+ -  This relationship links abundance
+terms from the +products(<list>)+ in a reaction to the
+reaction. This is a direct relationship because it is a _self_
+relationship. Products are produced directly by a reaction. This
+relationship is introduced by the BEL Compiler and may not be
+used by statements in BEL documents.
+          DOC
 
           def self.short
             SHORT