bel_parser 1.0.0.alpha.12 → 1.0.0.alpha.13

data/lib/bel_parser/resource/resource_file_reader.rb

@@ -0,0 +1,134 @@
+require 'open-uri'
+require_relative 'reader'
+require_relative 'eager_reader'
+require_relative 'dataset'
+require_relative 'http_cache'
+require_relative 'value'
+
+module BELParser
+  module Resource
+    # ResourceFileReader retrieves {Dataset datasets} and {Value values} from
+    # Annotation (i.e. belanno extension) and Namespace (i.e. belns extension)
+    # files.
+    #
+    # Only supports resource identifiers with an HTTP or HTTPS scheme.
+    class ResourceFileReader
+      include Reader
+      prepend EagerReader
+
+      DEFAULT_RESOURCE_VALUE_DELIMITER = '|'
+      private_constant :DEFAULT_RESOURCE_VALUE_DELIMITER
+
+      def initialize
+        @http_cache = HTTPCache.new
+      end
+
+      def retrieve_resource(resource_identifier)
+        read_resource(resource_identifier)
+      end
+
+      def retrieve_value_from_resource(resource_identifier, value)
+        file_resource = read_resource(resource_identifier)
+
+        io = @http_cache.get(resource_identifier)
+        delimiter = DEFAULT_RESOURCE_VALUE_DELIMITER
+        io.each_line do |line|
+          case line
+          when /^DelimiterString *=(.*)/
+            delimiter = Regexp.last_match[1]
+          when /^#{Regexp.escape('[Values]')}/
+            break
+          end
+        end
+
+        value_match = "#{value}#{delimiter}"
+        value_line  = io.each_line.find do |line|
+          line.start_with?(value_match)
+        end
+        return nil unless value_line
+        value, encoding = value_line.strip.split(delimiter)
+        FileResourceValue.new(file_resource, value, encoding)
+      end
+
+      def retrieve_values_from_resource(resource_identifier)
+        file_resource = read_resource(resource_identifier)
+
+        io = @http_cache.get(resource_identifier)
+        delimiter = DEFAULT_RESOURCE_VALUE_DELIMITER
+        io.each_line do |line|
+          case line
+          when /^DelimiterString *=(.*)/
+            delimiter = Regexp.last_match[1]
+          when /^#{Regexp.escape('[Values]')}/
+            break
+          end
+        end
+
+        io.each_line.map do |line|
+          value, encoding = line.strip.split(delimiter)
+          FileResourceValue.new(file_resource, value, encoding)
+        end
+      end
+
+      private
+
+      def read_resource(url)
+        io = @http_cache.get(url)
+
+        type, name, keyword, domain = nil
+        io.each_line do |line|
+          case line
+          when /^#{Regexp.escape('[AnnotationDefinition]')}/
+            type = Dataset::ANNOTATION
+          when /^#{Regexp.escape('[Namespace]')}/
+            type = Dataset::NAMESPACE
+          when /^NameString *= *(.*)$/
+            name = Regexp.last_match[1]
+          when /^Keyword *= *(.*)$/
+            keyword = Regexp.last_match[1]
+          when /^DomainString *= *(.*)$/
+            domain = Regexp.last_match[1]
+          when /^#{Regexp.escape('[Values]')}/
+            break
+          end
+        end
+        FileResource.new(url, domain, keyword, name, type)
+      end
+
+      # FileResource is a {Dataset} description obtained from a Annotation or
+      # Namespace file.
+      class FileResource
+        include Dataset
+
+        attr_reader :identifier, :domain, :keyword, :name, :types
+
+        def initialize(identifier, domain, keyword, name, type)
+          @identifier = identifier.to_s
+          @domain     = domain.to_s
+          @keyword    = keyword.to_s
+          @name       = name.to_s
+          @types      = [type]
+        end
+      end
+
+      # FileResourceValue is a {Value} obtained from a Annotation or Namespace
+      # file.
+      class FileResourceValue
+        include Value
+
+        attr_reader :dataset, :name, :encodings
+
+        def initialize(dataset, name, encodings)
+          @dataset   = dataset
+          @name      = name
+          @encodings =
+            if dataset.annotation_resource? && !dataset.namespace_resource?
+              nil
+            else
+              encodings.chars.map(&:to_sym)
+            end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/resource/sparql_reader.rb

@@ -0,0 +1,178 @@
+require 'erb'
+require 'net/http'
+require 'sparql/client'
+require 'uri'
+
+require_relative 'reader'
+require_relative 'lru_reader'
+require_relative 'concept'
+require_relative 'concept_scheme'
+
+module BELParser
+  module Resource
+    # SPARQLReader
+    class SPARQLReader
+      include Reader
+      prepend LRUReader
+
+      SCHEMES      = [URI::HTTP, URI::HTTPS].freeze
+      ALLOW_HEADER = 'Allow'.freeze
+
+      def initialize(sparql_endpoint_url, validate_url = true)
+        validate_sparql_endpoint_url(sparql_endpoint_url) if validate_url
+        @sparql_repository = SPARQL::Client.new(sparql_endpoint_url)
+      end
+
+      def retrieve_resource(resource_identifier)
+        uri              = URI(resource_identifier.to_s)
+        template_binding = binding
+        sparql_query     = RESOLVE_CONCEPT_SCHEME.result(template_binding)
+        hash_to_concept_scheme(resource_identifier,
+          execute_select(sparql_query).first)
+      end
+
+      def retrieve_value_from_resource(resource_identifier, value)
+        uri              = URI(resource_identifier.to_s)
+        template_binding = binding
+        sparql_query     = RESOLVE_CONCEPT.result(template_binding)
+        concept_scheme   = retrieve_resource(resource_identifier)
+        to_concept       = method(:hash_to_concept).to_proc.curry[concept_scheme]
+
+        execute_select(sparql_query).map(&to_concept)
+      end
+
+      def retrieve_values_from_resource(resource_identifier)
+        uri              = URI(resource_identifier.to_s)
+        template_binding = binding
+        sparql_query     = RESOLVE_CONCEPTS.result(template_binding)
+        concept_scheme   = retrieve_resource(resource_identifier)
+        to_concept       = method(:hash_to_concept).to_proc.curry[concept_scheme]
+
+        execute_select(sparql_query).map(&to_concept)
+      end
+
+      protected
+
+      def execute_select(sparql_query)
+        @sparql_repository.query(sparql_query).map do |solution|
+          solution.to_hash
+        end
+      end
+
+      def hash_to_concept_scheme(resource_identifier, hash)
+        ConceptScheme.new(resource_identifier, 
+          *hash.values_at(:domain, :prefix, :prefLabel, :types))
+      end
+
+      def hash_to_concept(concept_scheme, hash)
+        Concept.new(concept_scheme, 
+          *hash.values_at(:concept, :prefLabel, :identifier, :title,
+            :altLabels, :types))
+      end
+
+      def validate_sparql_endpoint_url(url)
+        url_s = url.to_s
+        scheme, host, port = URI(url_s).select(:scheme, :host, :port)
+        validate_uri_scheme(scheme, url_s)
+
+        options_request  = Net::HTTP::Options.new(url_s)
+        options_response = Net::HTTP.start(host, port) do |http|
+          http.request(Net::HTTP::Options.new(url_s))
+        end
+        validate_200(options_response, url_s)
+        validate_allowed_methods(options_response, url_s)
+      end
+
+      def validate_uri_scheme(scheme, url_s)
+        unless SCHEMES.include?(URI.scheme_list[scheme.upcase])
+          raise ArgumentError,
+            "expected HTTP or HTTPS scheme for url: #{url_s}"
+        end
+      end
+
+      def validate_200(response, url_s)
+        unless response.code_type == Net::HTTPOK
+          raise ArgumentError,
+            <<-MSG.gsub(/ {14}/, '').delete("\n")
+              expected URL to respond 200 (received #{response.code}) for 
+              OPTIONS request to: #{url_s}"
+            MSG
+        end
+      end
+
+      def validate_allowed_methods(response, url_s)
+        unless response[ALLOW_HEADER].to_s =~ /GET|POST/
+          raise ArgumentError,
+            "expected URL to allow GET or POST: #{url_s}"
+        end
+      end
+
+      RESOLVE_CONCEPT_SCHEME = ERB.new(<<-SPARQL)
+        prefix belv: <http://www.openbel.org/vocabulary/>
+        prefix dct:  <http://purl.org/dc/terms/>
+        prefix rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+        prefix skos: <http://www.w3.org/2004/02/skos/core#>
+        select ?domain ?prefix ?prefLabel (group_concat(?type;separator='|') as ?types)
+        where {
+            <<%= uri %>> rdf:type       skos:ConceptScheme .
+            <<%= uri %>> rdf:type       ?type .
+            <<%= uri %>> belv:domain    ?domain .
+            <<%= uri %>> belv:prefix    ?prefix .
+            <<%= uri %>> skos:prefLabel ?prefLabel .
+        }
+        group by ?domain ?prefix ?prefLabel
+      SPARQL
+
+      RESOLVE_CONCEPT = ERB.new(<<-SPARQL)
+        prefix belv: <http://www.openbel.org/vocabulary/>
+        prefix dct:  <http://purl.org/dc/terms/>
+        prefix rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+        prefix skos: <http://www.w3.org/2004/02/skos/core#>
+        select ?concept ?prefLabel ?identifier ?title
+          (group_concat(distinct(?type);separator='|') as ?types)
+          (group_concat(distinct(?altLabel);separator='|') as ?altLabels)
+        where {
+            {?concept    skos:prefLabel "<%= value %>"}
+              UNION
+            {?concept    dct:identifier "<%= value %>"}
+              UNION
+            {?concept    dct:title      "<%= value %>"}
+              UNION
+            {?concept    skos:altLabel  "<%= value %>"}
+
+            ?concept     skos:inScheme  <<%= uri %>> .
+            ?concept     rdf:type       ?type .
+
+            ?concept     skos:prefLabel ?prefLabel .
+            ?concept     dct:identifier ?identifier .
+            optional {
+              ?concept     dct:title      ?title .
+              ?concept     skos:altLabel  ?altLabel .
+            }
+        }
+        group by ?concept ?prefLabel ?identifier ?title
+      SPARQL
+
+      RESOLVE_CONCEPTS = ERB.new(<<-SPARQL)
+        prefix belv: <http://www.openbel.org/vocabulary/>
+        prefix dct:  <http://purl.org/dc/terms/>
+        prefix rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+        prefix skos: <http://www.w3.org/2004/02/skos/core#>
+        select ?concept ?prefLabel ?identifier ?title
+          (group_concat(distinct(?type);separator='|') as ?types)
+          (group_concat(distinct(?altLabel);separator='|') as ?altLabels)
+        where {
+            ?concept skos:inScheme  <<%= uri %>> .
+            ?concept rdf:type       ?type .
+            ?concept skos:prefLabel ?prefLabel .
+            optional {
+              ?concept dct:identifier ?identifier .
+              ?concept dct:title      ?title .
+              ?concept skos:altLabel  ?altLabel
+            }
+        }
+        group by ?concept ?prefLabel ?identifier ?title
+      SPARQL
+    end
+  end
+end

data/lib/bel_parser/resource/value.rb

@@ -0,0 +1,31 @@
+module BELParser
+  module Resource
+    # Value
+    module Value
+
+      def dataset
+        raise NotImplementedError, "#{__method__} is not implemented."
+      end
+
+      def name
+        raise NotImplementedError, "#{__method__} is not implemented."
+      end
+
+      def identifier
+        nil
+      end
+
+      def title
+        nil
+      end
+
+      def synonyms
+        []
+      end
+
+      def encodings
+        raise NotImplementedError, "#{__method__} is not implemented."
+      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.12
+  version: 1.0.0.alpha.13
 platform: ruby
 authors:
 - Anthony Bargnesi
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-04-15 00:00:00.000000000 Z
+date: 2016-04-27 00:00:00.000000000 Z
 dependencies: []
 description: Implements language versions 1.0 and 2.0.
 email: abargnesi@selventa.com
@@ -31,10 +31,11 @@ files:
 - lib/bel_parser/expression/validator.rb
 - lib/bel_parser/language.rb
 - lib/bel_parser/language/amino_acid.rb
+- lib/bel_parser/language/apply_namespace_encoding.rb
+- lib/bel_parser/language/base_specification.rb
 - lib/bel_parser/language/covalent_protein_modification.rb
 - lib/bel_parser/language/expression_validator.rb
 - lib/bel_parser/language/function.rb
-- lib/bel_parser/language/quoting.rb
 - lib/bel_parser/language/relationship.rb
 - lib/bel_parser/language/semantics.rb
 - lib/bel_parser/language/semantics/deeply_nested_statement.rb
@@ -47,9 +48,11 @@ files:
 - lib/bel_parser/language/semantics/relationship_not_listable.rb
 - lib/bel_parser/language/semantics/signature_mapping.rb
 - lib/bel_parser/language/semantics_ast.rb
+- lib/bel_parser/language/semantics_ast_warnings.rb
 - lib/bel_parser/language/semantics_function.rb
 - lib/bel_parser/language/semantics_match.rb
 - lib/bel_parser/language/semantics_result.rb
+- lib/bel_parser/language/semantics_type_warning.rb
 - lib/bel_parser/language/semantics_warning.rb
 - lib/bel_parser/language/signature.rb
 - lib/bel_parser/language/specification.rb
@@ -57,6 +60,7 @@ files:
 - lib/bel_parser/language/syntax/invalid_function.rb
 - lib/bel_parser/language/syntax/invalid_relationship.rb
 - lib/bel_parser/language/syntax/undefined_namespace.rb
+- lib/bel_parser/language/syntax/undefined_namespace_value.rb
 - lib/bel_parser/language/syntax_error.rb
 - lib/bel_parser/language/syntax_function.rb
 - lib/bel_parser/language/syntax_result.rb
@@ -147,7 +151,15 @@ files:
 - lib/bel_parser/language/version1_0/return_types/transcriptional_activity.rb
 - lib/bel_parser/language/version1_0/return_types/transport_activity.rb
 - lib/bel_parser/language/version1_0/return_types/truncation.rb
-- lib/bel_parser/language/version1_0/syntax/function.rb
+- lib/bel_parser/language/version1_0/value_encodings/abundance.rb
+- lib/bel_parser/language/version1_0/value_encodings/any.rb
+- lib/bel_parser/language/version1_0/value_encodings/biological_process.rb
+- lib/bel_parser/language/version1_0/value_encodings/complex_abundance.rb
+- lib/bel_parser/language/version1_0/value_encodings/gene_abundance.rb
+- lib/bel_parser/language/version1_0/value_encodings/micro_rna_abundance.rb
+- lib/bel_parser/language/version1_0/value_encodings/pathology.rb
+- lib/bel_parser/language/version1_0/value_encodings/protein_abundance.rb
+- lib/bel_parser/language/version1_0/value_encodings/rna_abundance.rb
 - lib/bel_parser/language/version2_0.rb
 - lib/bel_parser/language/version2_0/functions/abundance.rb
 - lib/bel_parser/language/version2_0/functions/activity.rb
@@ -225,6 +237,18 @@ files:
 - lib/bel_parser/language/version2_0/return_types/rna_abundance.rb
 - lib/bel_parser/language/version2_0/return_types/to_location.rb
 - lib/bel_parser/language/version2_0/return_types/variant.rb
+- lib/bel_parser/language/version2_0/value_encodings/abundance.rb
+- lib/bel_parser/language/version2_0/value_encodings/activity.rb
+- lib/bel_parser/language/version2_0/value_encodings/any.rb
+- lib/bel_parser/language/version2_0/value_encodings/biological_process.rb
+- lib/bel_parser/language/version2_0/value_encodings/complex_abundance.rb
+- lib/bel_parser/language/version2_0/value_encodings/gene_abundance.rb
+- lib/bel_parser/language/version2_0/value_encodings/location.rb
+- lib/bel_parser/language/version2_0/value_encodings/micro_rna_abundance.rb
+- lib/bel_parser/language/version2_0/value_encodings/pathology.rb
+- lib/bel_parser/language/version2_0/value_encodings/protein_abundance.rb
+- lib/bel_parser/language/version2_0/value_encodings/protein_modification.rb
+- lib/bel_parser/language/version2_0/value_encodings/rna_abundance.rb
 - lib/bel_parser/mixin/line_continuator.rb
 - lib/bel_parser/mixin/line_mapping.rb
 - lib/bel_parser/parser.rb
@@ -272,6 +296,20 @@ files:
 - lib/bel_parser/parsers/line_parser.rb
 - lib/bel_parser/parsers/mixin/buffer.rb
 - lib/bel_parser/parsers/nonblocking_io_wrapper.rb
+- lib/bel_parser/quoting.rb
+- lib/bel_parser/resource/concept.rb
+- lib/bel_parser/resource/concept_scheme.rb
+- lib/bel_parser/resource/dataset.rb
+- lib/bel_parser/resource/eager_reader.rb
+- lib/bel_parser/resource/eager_sparql_reader.rb
+- lib/bel_parser/resource/http_cache.rb
+- lib/bel_parser/resource/jena_tdb_reader.rb
+- lib/bel_parser/resource/lru_cache.rb
+- lib/bel_parser/resource/lru_reader.rb
+- lib/bel_parser/resource/reader.rb
+- lib/bel_parser/resource/resource_file_reader.rb
+- lib/bel_parser/resource/sparql_reader.rb
+- lib/bel_parser/resource/value.rb
 - lib/bel_parser/script/parser.rb
 - lib/bel_parser/vendor/ast.rb
 - lib/bel_parser/vendor/ast/node.rb

data/lib/bel_parser/language/version1_0/syntax/function.rb

@@ -1,28 +0,0 @@
-require 'bel_parser/parsers/ast/node'
-
-module BELParser
-  module Language
-    module Version1_0
-      module Syntax
-        # Function will add syntax errors to
-        # {BELParser::Parsers::AST::Function} nodes that do not have a valid
-        # BEL 1.0 functon name.
-        class Function
-          private_class_method :new
-
-          V1 = ::BELParser::Language::Version1_0::Specification.new
-
-          def self.match(input_ast)
-            input_ast.traverse do |node|
-              next unless node.is_a?(BELParser::Parsers::AST::Function)
-              function_name = node.identifier.string_literal
-              unless V1.function(function_name.to_sym)
-                node.add_syntax_error(:FunctionV1)
-              end
-            end
-          end
-        end
-      end
-    end
-  end
-end