bel_parser 1.0.0.alpha.27-java → 1.0.0.alpha.28-java

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 1e921d76566be607de95fcb0cc81def38fb66fbc
-  data.tar.gz: 07403998d6fdaeca6d9a3380a3fc55480470d7f1
+  metadata.gz: 13215ac795faa5077028725921572827bb24953b
+  data.tar.gz: 94c3c72300afd58322ff396a0ddcb30a8d71109f
 SHA512:
-  metadata.gz: 437d7fd653d991fe0e7f3db14e42f210b61744e25f6395b7a673bba701ad43dc5ae920254683916347867402d4c04b3232f518f709ad867cdc3aee0b471338c6
-  data.tar.gz: 61f465297d02cf000a853f1b1048acd359529b3bdef234aa10f9494c58c51e5b042eab8b0f99a0868bdbb387108fda6b1679cf3edfc972db7539c3ba98cff6a3
+  metadata.gz: 68c9dba99dad0c8a19c00dfe78b99d8c882a54c55754f87b421e2353495f42e591e167c0473570ec6df12e76c034f7498c4d4216693e560b9442d1abe61b204d
+  data.tar.gz: c490a891dd8cc5bfc2c2abee8d16d49807d19abebb9695ab486059fff6c5b4bd4022c2c489ce0759a1d3c1deb86c10bafa26b14380729dc06527a52ff44ff77d

data/.gemspec-java

@@ -27,6 +27,7 @@ Gem::Specification.new do |spec|
   spec.required_ruby_version = '>= 2.0.0'
 
   spec.platform              = 'java'
-  spec.add_runtime_dependency  'dbm-mapdb3', '~> 0.6.0.beta'
+  spec.add_runtime_dependency  'sparql-client', '~> 2.0.0'
+  spec.add_runtime_dependency  'dbm-mapdb3',    '~> 0.6.0.beta'
 end
 # vim: ft=ruby

data/VERSION

@@ -1 +1 @@
-1.0.0.alpha.27
+1.0.0.alpha.28

data/lib/bel_parser/expression/model/annotation.rb

@@ -0,0 +1,87 @@
+module BELParser
+  module Expression
+    module Model
+      # Annotation represents a catalog of biological annotation values.
+      class Annotation
+        include Enumerable
+
+        attr_reader :keyword
+        attr_reader :uri
+        attr_reader :url
+
+        def initialize(keyword, uri = nil, url = nil, options = {})
+          raise(ArgumentError, 'keyword is nil') unless keyword
+          @keyword = keyword
+          @uri     = uri
+          @url     = url
+
+          # configure reader for URIs (RDF).
+          @uri_reader =
+            options.fetch(:uri_reader) {
+              BELParser::Resource.default_uri_reader
+            }
+          BELParser::Resource::Reader.assert_reader(@uri_reader, 'uri_reader')
+
+          # configure reader for URLs (Resource files).
+          @url_reader =
+            options.fetch(:url_reader) {
+              BELParser::Resource.default_url_reader
+            }
+          BELParser::Resource::Reader.assert_reader(@url_reader, 'url_reader')
+        end
+
+        def uri?
+          !@uri.nil?
+        end
+
+        def url?
+          !@url.nil?
+        end
+
+        def [](value)
+          if uri?
+            @uri_reader.retrieve_value_from_resource(@uri, value)
+          elsif url?
+            @url_reader.retrieve_value_from_resource(@url, value)
+          else
+            nil
+          end
+        end
+
+        def each
+          if block_given?
+            values =
+              if uri?
+                @uri_reader.retrieve_values_from_resource(@uri)
+              elsif url?
+                @url_reader.retrieve_values_from_resource(@url)
+              else
+                []
+              end
+            values.each do |value|
+              yield value
+            end
+          else
+            to_enum(:each)
+          end
+        end
+
+        def hash
+          [@keyword, @uri, @url].hash
+        end
+
+        def ==(other)
+          return false if other.nil?
+          @keyword == other.keyword && @uri == other.uri && @url == other.url
+        end
+        alias :eql? :'=='
+
+        def to_s
+          @keyword.to_s
+        end
+      end
+    end
+  end
+end
+# vim: ts=2 sw=2:
+# encoding: utf-8

data/lib/bel_parser/expression/model/namespace.rb

@@ -0,0 +1,91 @@
+require 'bel_parser/resource'
+
+module BELParser
+  module Expression
+    module Model
+      # Namespace represents a catalog of biological identifiers that are to
+      # identify parameter values like genes (e.g. _AKT1_),
+      # diseases (e.g. _hypertropia_), and processes (e.g. _anaphase_).
+      class Namespace
+        include Enumerable
+
+        attr_accessor :keyword
+        attr_accessor :uri
+        attr_accessor :url
+
+        def initialize(keyword, uri = nil, url = nil, options = {})
+          raise(ArgumentError, 'keyword is nil') unless keyword
+          @keyword = keyword
+          @uri     = uri
+          @url     = url
+
+          # configure reader for URIs (RDF).
+          @uri_reader =
+            options.fetch(:uri_reader) {
+              BELParser::Resource.default_uri_reader
+            }
+          BELParser::Resource::Reader.assert_reader(@uri_reader, 'uri_reader')
+
+          # configure reader for URLs (Resource files).
+          @url_reader =
+            options.fetch(:url_reader) {
+              BELParser::Resource.default_url_reader
+            }
+          BELParser::Resource::Reader.assert_reader(@url_reader, 'url_reader')
+        end
+
+        def uri?
+          !@uri.nil?
+        end
+
+        def url?
+          !@url.nil?
+        end
+
+        def [](value)
+          if uri?
+            @uri_reader.retrieve_value_from_resource(@uri, value)
+          elsif url?
+            @url_reader.retrieve_value_from_resource(@url, value)
+          else
+            nil
+          end
+        end
+
+        def each
+          if block_given?
+            values =
+              if uri?
+                @uri_reader.retrieve_values_from_resource(@uri)
+              elsif url?
+                @url_reader.retrieve_values_from_resource(@url)
+              else
+                []
+              end
+            values.each do |value|
+              yield value
+            end
+          else
+            to_enum(:each)
+          end
+        end
+
+        def hash
+          [@keyword, @uri, @url].hash
+        end
+
+        def ==(other)
+          return false if other.nil?
+          @keyword == other.keyword && @uri == other.uri && @url == other.url
+        end
+        alias :eql? :'=='
+
+        def to_s
+          @keyword.to_s
+        end
+      end
+    end
+  end
+end
+# vim: ts=2 sw=2:
+# encoding: utf-8

data/lib/bel_parser/expression/model/parameter.rb

@@ -0,0 +1,60 @@
+require 'bel_parser/quoting'
+
+module BELParser
+  module Expression
+    module Model
+
+      class Parameter
+        include BELParser::Quoting
+        include Comparable
+
+        attr_accessor :namespace, :value
+
+        def initialize(namespace, value)
+          raise(ArgumentError, 'value is nil') unless value
+          unless namespace.nil? || namespace.is_a?(Namespace)
+            raise(
+              ArgumentError,
+              "namespace: expected nil or Namespace, actual #{namespace.class}")
+          end
+          @namespace = namespace
+          @value     = value
+        end
+
+        def valid?
+          return false unless @value
+          return true unless @namespace
+          !@namespace[@value].nil?
+        end
+
+        def <=>(other)
+          namespace_compare = @namespace <=> other.namespace
+          if namespace_compare == 0
+            @value <=> other.value
+          else
+            namespace_compare
+          end
+        end
+
+        def hash
+          [@namespace, @value].hash
+        end
+
+        def ==(other)
+          return false if other == nil
+          @namespace == other.namespace && @value == other.value
+        end
+        alias_method :eql?, :'=='
+
+        def to_s(_)
+          if @namespace
+            prefix = "#{@namespace.keyword}:"
+          else
+            prefix = ''
+          end
+          %Q{#{prefix}#{quote_if_needed(@value)}}
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/expression/model/statement.rb

@@ -0,0 +1,114 @@
+module BELParser
+  module Expression
+    module Model
+
+      # A {Statement} captures a BEL statement composed of a subject {Term},
+      # +relationship+, and object {Term}. A {Statement} may be one of the
+      # following common forms:
+      #
+      # - SUBJECT
+      #   - +complex(p(HGNC:F3),p(HGNC:F7))+
+      # - SUBJECT RELATIONSHIP OBJECT(Term)
+      #   - +pep(complex(p(HGNC:F3),p(HGNC:F7))) => pep(p(HGNC:F9))+
+      # - SUBJECT RELATIONSHIP OBJECT(Statement)
+      #   - +p(HGNC:VHL) -> (p(HGNC:TNF) -> bp(GOBP:"cell death"))+
+      class Statement
+        attr_accessor :subject, :relationship, :object, :comment
+
+        # Creates a {Statement} with +subject+, +relationship+, +object+, and
+        # +comment+.
+        #
+        # @param [Term] subject
+        # @param [BELParser::Language::Relationship] relationship
+        # @param [Term, Statement] object
+        # @param [String] comment
+        def initialize(subject, relationship = nil, object = nil, comment = nil)
+          raise(ArgumentError, 'subject is nil') unless subject
+          @subject      = subject
+
+          unless relationship.nil? || relationship.is_a?(BELParser::Language::Relationship)
+            raise(
+              ArgumentError,
+              "relationship: expected nil or Relationship, actual #{@relationship.class}")
+          end
+          @relationship = relationship
+
+          unless object.nil? || [Term, Statement].any?(&object.method(:is_a?))
+            raise(
+              ArgumentError,
+              "object: expected nil, Term, or Statement, actual #{@object.class}")
+          end
+          @object       = object
+          @comment      = comment
+
+          if @relationship && !@object
+            raise(
+              ArgumentError,
+              "object must be set when specifying a relationship")
+          end
+
+          if @object && !@relationship
+            raise(
+              ArgumentError,
+              "relationsihp must be set when specifying an object")
+          end
+        end
+
+        def subject_only?
+          !@relationship
+        end
+
+        def simple?
+          @object && @object.is_a?(Term)
+        end
+
+        def nested?
+          @object && @object.is_a?(Statement)
+        end
+
+        def valid?
+          # TODO Use expression validator.
+        end
+
+        def hash
+          [@subject, @relationship, @object, @comment].hash
+        end
+
+        def ==(other)
+          return false if other == nil
+          @subject      == other.subject &&
+          @relationship == other.relationship &&
+          @object       == other.object &&
+          @comment      == other.comment
+        end
+        alias :eql? :'=='
+
+        def to_s(form = :short)
+          rel =
+            case form
+            when :short
+              @relationship && @relationship.short
+            when :long
+              @relationship && @relationship.long
+            else
+              nil
+            end
+
+          lbl =
+            case
+            when subject_only?
+              @subject.to_s(form)
+            when simple?
+              "#{@subject.to_s(form)} #{rel} #{@object.to_s(form)}"
+            when nested?
+              "#{@subject.to_s(form)} #{rel} (#{@object.to_s(form)})"
+            else
+              ''
+            end
+
+          comment ? lbl + ' //' + comment : lbl
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/expression/model/term.rb

@@ -0,0 +1,52 @@
+module BELParser
+  module Expression
+    module Model
+      class Term
+        include Comparable
+
+        attr_accessor :function, :arguments
+
+        def initialize(function, *arguments)
+          unless function && function.is_a?(BELParser::Language::Function)
+            raise(
+              ArgumentError,
+              %(function: expected Function, actual #{function.class}))
+          end
+          @function  = function
+          @arguments = (arguments ||= []).flatten
+        end
+
+        def <<(item)
+          @arguments << item
+        end
+
+        def valid?
+          # TODO Use expression validator.
+        end
+
+        def hash
+          [@function, @arguments].hash
+        end
+
+        def ==(other)
+          return false if other == nil
+          @function == other.function && @arguments == other.arguments
+        end
+        alias :eql? :'=='
+
+        def to_s(form = :short)
+          args = [@arguments].flatten.map { |arg| arg.to_s(form) }.join(',')
+          case form
+          when :short
+            "#{@function.short}(#{args})"
+          when :long
+            "#{@function.long}(#{args})"
+          else
+            nil
+          end
+        end
+      end
+    end
+  end
+end
+

data/lib/bel_parser/expression/model.rb

@@ -0,0 +1,5 @@
+require_relative 'model/annotation'
+require_relative 'model/namespace'
+require_relative 'model/parameter'
+require_relative 'model/term'
+require_relative 'model/statement'

data/lib/bel_parser/expression.rb

@@ -1,3 +1,4 @@
 require_relative 'expression/filter'
+require_relative 'expression/model'
 require_relative 'expression/parser'
 require_relative 'expression/validator'

data/lib/bel_parser/resource/reader.rb

@@ -2,6 +2,19 @@ module BELParser
   module Resource
     # Reader represents the API for a reader of resource data.
     module Reader
+      def self.assert_reader(reader, var_name)
+        raise ArgumentError, "#{var_name} is nil" unless reader
+        not_impl_methods =
+          Reader.instance_methods.reject do |method|
+            reader.respond_to?(method)
+          end
+        unless not_impl_methods.empty?
+          raise(
+            ArgumentError,
+            "#{var_name} does not respond to #{not_impl_methods.join(', ')}.")
+        end
+      end
+
       def retrieve_resource(resource_identifier)
         raise NotImplementedError, "#{__method__} is not implemented."
       end

data/lib/bel_parser/resource/sparql_reader.rb

@@ -60,12 +60,13 @@ module BELParser
       end
 
       def hash_to_concept_scheme(resource_identifier, hash)
-        return nil if hash[:types].value.empty?
+        return nil if hash.empty? or hash[:types].value.empty?
         ConceptScheme.new(resource_identifier, 
           *hash.values_at(:domain, :prefix, :prefLabel, :types))
       end
 
       def hash_to_concept(concept_scheme, hash)
+        return nil if hash.empty?
         Concept.new(concept_scheme, 
           *hash.values_at(:concept, :prefLabel, :identifier, :title,
             :altLabels, :types))

data/lib/bel_parser/resource.rb

@@ -0,0 +1,37 @@
+require_relative 'resource/sparql_reader'
+require_relative 'resource/resource_url_reader'
+
+module BELParser
+  module Resource
+
+    # DEFAULT_SPARQL_ENDPOINT = 'http://sparql.openbel.org/identifiers/sparql'
+    DEFAULT_SPARQL_ENDPOINT = 'http://localhost:3030/identifiers/sparql'
+
+    READER_LOCK = Mutex.new
+    private_constant :READER_LOCK
+
+    def self.default_uri_reader
+      READER_LOCK.synchronize do
+        @default_uri_reader ||= SPARQLReader.new(DEFAULT_SPARQL_ENDPOINT)
+      end
+    end
+
+    def self.default_uri_reader=(uri_reader)
+      READER_LOCK.synchronize do
+        @default_uri_reader ||= uri_reader
+      end
+    end
+
+    def self.default_url_reader
+      READER_LOCK.synchronize do
+        @default_url_reader ||= ResourceURLReader.new
+      end
+    end
+
+    def self.default_url_reader=(url_reader)
+      READER_LOCK.synchronize do
+        @default_url_reader ||= url_reader
+      end
+    end
+  end
+end

data/lib/bel_parser.rb

@@ -16,7 +16,7 @@ require 'bel_parser/ast_filter'
 # Language; version-independent classes
 require 'bel_parser/language'
 
-# BEL expression support
+# BEL Expression support
 require 'bel_parser/expression'
 
 # BEL Script support

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel_parser
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.27
+  version: 1.0.0.alpha.28
 platform: java
 authors:
 - Anthony Bargnesi
@@ -11,6 +11,20 @@ bindir: bin
 cert_chain: []
 date: 2016-05-09 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.0
+  name: sparql-client
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.0
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
@@ -53,6 +67,12 @@ files:
 - lib/bel_parser/ast_generator.rb
 - lib/bel_parser/expression.rb
 - lib/bel_parser/expression/filter.rb
+- lib/bel_parser/expression/model.rb
+- lib/bel_parser/expression/model/annotation.rb
+- lib/bel_parser/expression/model/namespace.rb
+- lib/bel_parser/expression/model/parameter.rb
+- lib/bel_parser/expression/model/statement.rb
+- lib/bel_parser/expression/model/term.rb
 - lib/bel_parser/expression/parser.rb
 - lib/bel_parser/expression/validator.rb
 - lib/bel_parser/language.rb
@@ -323,6 +343,7 @@ files:
 - lib/bel_parser/parsers/nonblocking_io_wrapper.rb
 - lib/bel_parser/parsers/serializer.rb
 - lib/bel_parser/quoting.rb
+- lib/bel_parser/resource.rb
 - lib/bel_parser/resource/concept.rb
 - lib/bel_parser/resource/concept_scheme.rb
 - lib/bel_parser/resource/dataset.rb