bel_parser 1.0.0.alpha.47-java → 1.0.0.alpha.48-java

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

@@ -17,7 +17,7 @@ module BELParser
           return nil if prefix_identifier.nil?
 
           prefix = prefix_identifier.string_literal
-          unless namespaces[prefix.downcase]
+          unless namespaces[prefix]
             UndefinedNamespaceError.new(prefix_node, spec, prefix, namespaces)
           end
         end

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

@@ -14,7 +14,8 @@ module BELParser
           return nil unless value_node.is_a?(BELParser::Parsers::AST::Value)
           return nil unless value_node.namespace
 
-          unless value_node.namespace_value
+          nsv = value_node.namespace_value
+          if nsv.nil? || nsv.encoding.nil?
             value = value_node.children[0].string_literal
             UndefinedNamespaceValueWarning.new(value_node, spec, value)
           end

data/lib/bel_parser/language/version2_0/functions/activity.rb

@@ -16,8 +16,8 @@ module BELParser
           LONG        = :activity
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Activity
           DESCRIPTION = 'Denotes the frequency or abundance of events
-          n which a member acts as a causal agent at the
-          olecular scale.'.freeze
+          in which a member acts as a causal agent at the
+          molecular scale.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/biological_process.rb

@@ -15,8 +15,7 @@ module BELParser
           LONG        = :biologicalProcess
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::BiologicalProcess
           B_ENC       = Version2_0::ValueEncodings::BiologicalProcess
-          DESCRIPTION = 'Denotes a process or population of
-          vents.'.freeze
+          DESCRIPTION = 'Denotes a process or population of events.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/cell_secretion.rb

@@ -17,8 +17,8 @@ module BELParser
           LONG        = :cellSecretion
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
           DESCRIPTION = 'Denotes the frequency or abundance of events
-          n which members of an abundance move from cells
-          o regions outside of the cells.'.freeze
+          in which members of an abundance move from cells
+          to regions outside of the cells.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/cell_surface_expression.rb

@@ -17,8 +17,8 @@ module BELParser
           LONG        = :cellSurfaceExpression
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
           DESCRIPTION = 'Denotes the frequency or abundance of events in
-          hich members of an abundance move to the surface
-          f cells.'.freeze
+          which members of an abundance move to the surface
+          of cells.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/complex_abundance.rb

@@ -16,7 +16,7 @@ module BELParser
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ComplexAbundance
           C_ENC       = Version2_0::ValueEncodings::ComplexAbundance
           DESCRIPTION = 'Denotes the abundance of a molecular
-          omplex.'.freeze
+          complex.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/composite_abundance.rb

@@ -16,7 +16,7 @@ module BELParser
           LONG        = :compositeAbundance
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
           DESCRIPTION = 'Denotes the frequency or abundance of events
-          n which members are present.'.freeze
+          in which members are present.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/degradation.rb

@@ -17,8 +17,8 @@ module BELParser
           LONG        = :degradation
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
           DESCRIPTION = 'Denotes the frequency or abundance of events
-          n which a member is degraded in some way such
-          hat it is no longer a member.'.freeze
+          in which a member is degraded in some way such
+          that it is no longer a member.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/fragment.rb

@@ -16,7 +16,7 @@ module BELParser
           LONG        = :fragment
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Fragment
           DESCRIPTION = 'Denotes a protein fragment, e.g., a product of
-          roteolytic cleavage.'.freeze
+          proteolytic cleavage.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/from_location.rb

@@ -17,7 +17,7 @@ module BELParser
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::FromLocation
           L_ENC       = Version2_0::ValueEncodings::Location
           DESCRIPTION = 'Denotes the from cellular location of the
-          bundance.'.freeze
+          abundance.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/fusion.rb

@@ -19,7 +19,7 @@ module BELParser
           P_ENC       = Version2_0::ValueEncodings::ProteinAbundance
           R_ENC       = Version2_0::ValueEncodings::RNAAbundance
           DESCRIPTION = 'Specifies the abundance of a protein translated
-          rom the fusion of a gene.'.freeze
+          from the fusion of a gene.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/micro_rna_abundance.rb

@@ -17,7 +17,7 @@ module BELParser
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::MicroRNAAbundance
           M_ENC       = Version2_0::ValueEncodings::MicroRNAAbundance
           DESCRIPTION = 'Denotes the abundance of a processed, functional
-          icroRNA'.freeze
+          microRNA'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/molecular_activity.rb

@@ -18,7 +18,7 @@ module BELParser
           T_ENC       = Version2_0::ValueEncodings::Activity
           DESCRIPTION = 'Denotes the frequency or abundance of events
           n which a member acts as a causal agent at the
-          olecular scale'.freeze
+          molecular scale'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/protein_modification.rb

@@ -18,7 +18,7 @@ module BELParser
           RETURN_TYPE = Version2_0::ReturnTypes::ProteinModification
           E_ENC       = Version2_0::ValueEncodings::ProteinModification
           DESCRIPTION = 'Denotes a covalently modified protein
-          bundance'.freeze
+          abundance'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/reaction.rb

@@ -16,7 +16,7 @@ module BELParser
           LONG        = :reaction
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
           DESCRIPTION = 'Denotes the frequency or abundance of events
-          n a reaction'.freeze
+          in a reaction'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/to_location.rb

@@ -16,7 +16,7 @@ module BELParser
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ToLocation
           L_ENC       = Version2_0::ValueEncodings::Location
           DESCRIPTION = 'Denotes the to cellular location of the
-          bundance.'.freeze
+          abundance.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/translocation.rb

@@ -16,7 +16,7 @@ module BELParser
           LONG        = :translocation
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
           DESCRIPTION = 'Denotes the frequency or abundance of events
-          n which members move between locations'.freeze
+          in which members move between locations'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/variant.rb

@@ -15,7 +15,7 @@ module BELParser
           LONG        = :variant
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Variant
           DESCRIPTION = 'Denotes a sequence variant of the specified
-          bundance.'.freeze
+          abundance.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/resource.rb

@@ -5,8 +5,7 @@ require_relative 'resource/resource_url_reader'
 module BELParser
   module Resource
 
-    DEFAULT_SPARQL_ENDPOINT = 'http://build.openbel.org/sparql'
-    #DEFAULT_SPARQL_ENDPOINT = 'http://localhost:3030/identifiers/sparql'
+    DEFAULT_SPARQL_ENDPOINT = 'http://resources.openbel.org/sparql'
 
     READER_LOCK       = Mutex.new
     private_constant :READER_LOCK
@@ -15,27 +14,30 @@ module BELParser
     URISTRING_PATTERN = /^URIString *= *(.*)$/
     private_constant :URISTRING_PATTERN
 
+    @default_uri_reader = SPARQLReader.new(DEFAULT_SPARQL_ENDPOINT, false)
+    @default_url_reader = ResourceURLReader.new
+
     def self.default_uri_reader
       READER_LOCK.synchronize do
-        @default_uri_reader ||= SPARQLReader.new(DEFAULT_SPARQL_ENDPOINT)
+        @default_uri_reader
       end
     end
 
     def self.default_uri_reader=(uri_reader)
       READER_LOCK.synchronize do
-        @default_uri_reader ||= uri_reader
+        @default_uri_reader = uri_reader
       end
     end
 
     def self.default_url_reader
       READER_LOCK.synchronize do
-        @default_url_reader ||= ResourceURLReader.new
+        @default_url_reader
       end
     end
 
     def self.default_url_reader=(url_reader)
       READER_LOCK.synchronize do
-        @default_url_reader ||= url_reader
+        @default_url_reader = url_reader
       end
     end
 

data/lib/bel_parser/resource/concept_scheme.rb

@@ -16,6 +16,14 @@ module BELParser
         @types      = convert_types(types.to_s)
       end
 
+      def uri?
+        true
+      end
+
+      def url?
+        false
+      end
+
       private
 
       def convert_types(types)

data/lib/bel_parser/resource/dataset.rb

@@ -29,6 +29,30 @@ module BELParser
       def types
         raise NotImplementedError, "#{__method__} is not implemented."
       end
+
+      def uri?
+        raise NotImplementedError, "#{__method__} is not implemented."
+      end
+
+      def url?
+        raise NotImplementedError, "#{__method__} is not implemented."
+      end
+
+      def <=>(another_dataset)
+        keyword <=> another_dataset.keyword
+      end
+
+      def hash
+        [types, identifier, keyword].hash
+      end
+
+      def ==(another_dataset)
+        return false if another_dataset == nil
+        types      == another_dataset.types &&
+        identifier == another_dataset.identifier &&
+        keyword    == another_dataset.keyword
+      end
+      alias :eql? :'=='
     end
   end
 end

data/lib/bel_parser/resource/file_resource.rb

@@ -16,6 +16,14 @@ module BELParser
         @name       = name.to_s
         @types      = [type]
       end
+
+      def uri?
+        false
+      end
+
+      def url?
+        true
+      end
     end
   end
 end

data/lib/bel_parser/resource/file_resource_value.rb

@@ -19,6 +19,7 @@ module BELParser
             encodings.chars.map(&:to_sym)
           end
       end
+
     end
   end
 end

data/lib/bel_parser/resource/sparql_reader.rb

@@ -122,9 +122,11 @@ module BELParser
         where {
             <<%= uri %>> rdf:type       skos:ConceptScheme .
             <<%= uri %>> rdf:type       ?type .
-            <<%= uri %>> belv:domain    ?domain .
             <<%= uri %>> belv:prefix    ?prefix .
             <<%= uri %>> skos:prefLabel ?prefLabel .
+            optional {
+              <<%= uri %>> belv:domain    ?domain .
+            }
         }
         group by ?domain ?prefix ?prefLabel
       SPARQL

data/lib/bel_parser/resource/value.rb

@@ -26,6 +26,26 @@ module BELParser
       def encodings
         raise NotImplementedError, "#{__method__} is not implemented."
       end
+
+      def <=>(another_value)
+        name <=> another_value.name
+      end
+
+      def hash
+        [dataset, name, encodings].hash
+      end
+
+      def ==(another_value)
+        return false if another_value == nil
+        dataset   == another_value.dataset &&
+        name      == another_value.name &&
+        encodings == another_value.encodings
+      end
+      alias :eql? :'=='
+
+      def to_s
+        name
+      end
     end
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel_parser
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.47
+  version: 1.0.0.alpha.48
 platform: java
 authors:
 - Anthony Bargnesi