bel 0.1.0

data/lib/bel/namespace.rb

@@ -0,0 +1,106 @@
+# vim: ts=2 sw=2:
+require 'open-uri'
+require_relative './language' 
+
+class String
+  def split_by_last(char=" ")
+    pos = self.rindex(char)
+    pos != nil ? [self[0...pos], self[pos+1..-1]] : [self]
+  end
+end
+
+module BEL
+  module Namespace
+
+    NAMESPACE_HASH = {
+      HGU95AV2:  'http://resource.belframework.org/belframework/1.0/namespace/affy-hg-u95av2.belns',
+      HGU133P2:  'http://resource.belframework.org/belframework/1.0/namespace/affy-hg-u133-plus2.belns',
+      HGU133AB:  'http://resource.belframework.org/belframework/1.0/namespace/affy-hg-u133ab.belns',
+      MGU74ABC:  'http://resource.belframework.org/belframework/1.0/namespace/affy-mg-u74abc.belns',
+      MG430AB:   'http://resource.belframework.org/belframework/1.0/namespace/affy-moe430ab.belns',
+      MG4302:    'http://resource.belframework.org/belframework/1.0/namespace/affy-mouse430-2.belns',
+      MG430A2:   'http://resource.belframework.org/belframework/1.0/namespace/affy-mouse430a-2.belns',
+      RG230AB:   'http://resource.belframework.org/belframework/1.0/namespace/affy-rae230ab-2.belns',
+      RG2302:    'http://resource.belframework.org/belframework/1.0/namespace/affy-rat230-2.belns',
+      CHEBIID:   'http://resource.belframework.org/belframework/1.0/namespace/chebi-ids.belns',
+      CHEBI:     'http://resource.belframework.org/belframework/1.0/namespace/chebi-names.belns',
+      EGID:      'http://resource.belframework.org/belframework/1.0/namespace/entrez-gene-ids-hmr.belns',
+      GOAC:      'http://resource.belframework.org/belframework/1.0/namespace/go-biological-processes-accession-numbers.belns',
+      GO:        'http://resource.belframework.org/belframework/1.0/namespace/go-biological-processes-names.belns',
+      GOCCACC:   'http://resource.belframework.org/belframework/1.0/namespace/go-cellular-component-accession-numbers.belns',
+      GOCCTERM:  'http://resource.belframework.org/belframework/1.0/namespace/go-cellular-component-terms.belns',
+      HGNC:      'http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns',
+      MESHPP:    'http://resource.belframework.org/belframework/1.0/namespace/mesh-biological-processes.belns',
+      MESHCL:    'http://resource.belframework.org/belframework/1.0/namespace/mesh-cellular-locations.belns',
+      MESHD:     'http://resource.belframework.org/belframework/1.0/namespace/mesh-diseases.belns',
+      MGI:       'http://resource.belframework.org/belframework/1.0/namespace/mgi-approved-symbols.belns',
+      RGD:       'http://resource.belframework.org/belframework/1.0/namespace/rgd-approved-symbols.belns',
+      SCHEM:     'http://resource.belframework.org/belframework/1.0/namespace/selventa-legacy-chemical-names.belns',
+      SDIS:      'http://resource.belframework.org/belframework/1.0/namespace/selventa-legacy-diseases.belns',
+      NCH:       'http://resource.belframework.org/belframework/1.0/namespace/selventa-named-human-complexes.belns',
+      PFH:       'http://resource.belframework.org/belframework/1.0/namespace/selventa-named-human-protein-families.belns',
+      NCM:       'http://resource.belframework.org/belframework/1.0/namespace/selventa-named-mouse-complexes.belns',
+      PFM:       'http://resource.belframework.org/belframework/1.0/namespace/selventa-named-mouse-protein-families.belns',
+      NCR:       'http://resource.belframework.org/belframework/1.0/namespace/selventa-named-rat-complexes.belns',
+      PFR:       'http://resource.belframework.org/belframework/1.0/namespace/selventa-named-rat-protein-families.belns',
+      SPAC:      'http://resource.belframework.org/belframework/1.0/namespace/swissprot-accession-numbers.belns',
+      SP:        'http://resource.belframework.org/belframework/1.0/namespace/swissprot-entry-names.belns'
+    }
+
+    class NamespaceDefinition
+      include Enumerable
+
+      attr_reader :url
+      attr_reader :values
+
+      def initialize(prefix, url)
+        @prefix = prefix
+        @url = url
+        @values = nil
+      end
+
+      def [](value)
+        return nil unless value
+
+        reload(@url) if not @values
+        sym = value.to_sym
+        Language::Parameter.new(@prefix, sym,
+                                @values[sym]) if @values.key?(sym)
+      end
+
+      def each &block
+        reload(@url) if not @values
+        ns = @prefix.to_sym
+        @values.each do |val, enc|
+          if block_given?
+            block.call(Language::Parameter.new(ns, val, enc))
+          else
+            yield Language::Parameter.new(ns, val, enc)
+          end
+        end
+      end
+
+      private
+      # the backdoor
+      def reload(url)
+        @values = {}
+        open(url).
+          drop_while { |i| not i.start_with? "[Values]" }.
+          drop(1).
+          each do |s|
+            val_enc = s.strip!.split_by_last('|').map(&:to_sym)
+            @values[val_enc[0]] = val_enc[1]
+          end
+      end
+    end
+
+    # create classes for each standard prefix
+    DEFAULT_NAMESPACES = [
+      NAMESPACE_HASH.collect do |prefix, default_url|
+        ns_definition = NamespaceDefinition.new(prefix, default_url)
+        Namespace.const_set(prefix, ns_definition)
+        ns_definition
+      end
+    ]
+  end
+end

data/lib/bel/script.rb

@@ -0,0 +1,184 @@
+# vim: ts=2 sw=2:
+require_relative 'grammar/lexer.rb'
+require_relative 'grammar/parser.rb'
+
+module BEL
+  module Script
+    DocumentProperty            = Struct.new(:property, :value) 
+    NamespaceDefinition         = Struct.new(:keyword, :url, :default?)   
+    AnnotationListDefinition    = Struct.new(:keyword, :values)
+    AnnotationPatternDefinition = Struct.new(:keyword, :pattern)
+    AnnotationUrlDefinition     = Struct.new(:keyword, :url)
+    SetStatementGroup           = Struct.new(:name)
+    UnsetStatementGroup         = Struct.new(:name)
+    SetAnnotation               = Struct.new(:keyword, :value)
+    ParameterDefinition         = Struct.new(:namespace, :value)
+    TermDefinition              = Struct.new(:function, :arguments)
+    StatementDefinition         = Struct.new(:subject, :rel, :object,
+                                             :comment) do
+      def subject_only?
+        !rel
+      end
+      def simple?
+        object.is_a? TermDefinition
+      end
+      def nested?
+        object.is_a? StatementDefinition
+      end
+    end
+
+    module Parser
+
+      def self.parse(source)
+        return nil if not source
+
+        antlr_parser = BEL::Script::Parser::Parser.new(source)
+        if block_given? then
+          yield from_tree(antlr_parser.document.tree)
+        else
+          from_tree(antlr_parser.document.tree)
+        end
+      end
+
+      def self.parse_record(source)
+        return nil if not source
+
+        BEL::Script::Parser::Parser.new(source)
+        if block_given?
+          source.each_line do |line|
+            antlr_parser = BEL::Script::Parser::Parser.new(line)
+            record_ret = antlr_parser.record
+            if record_ret.tree.length > 0
+              yield from_tree(record_ret.tree)
+            end
+          end
+        else
+          parsed_lines = []
+          source.each_line do |line|
+            line.tr!("\r\n", '')
+            antlr_parser = BEL::Script::Parser::Parser.new(line)
+            record_ret = antlr_parser.record
+            if record_ret.tree.length > 0
+              parsed_lines << from_tree(record_ret.tree)
+            end
+          end
+          return parsed_lines
+        end
+      end
+
+      private
+
+      def self.from_tree(tree)
+        case tree.name
+        when 'DOCDEF'
+          tree.children.map { |x| from_tree(x) }
+        when 'DOCSET_ID'
+          BEL::Script::DocumentProperty.new(
+            tree.children[0].text,
+            tree.children[1].text)
+        when 'DOCSET_QV'
+          value = tree.children[1].text[1...-1]
+          BEL::Script::DocumentProperty.new(
+            tree.children[0].text,
+            value)
+        when 'DOCSET_LIST'
+          values = tree.children[1].text[1...-1].split(' ,')
+          BEL::Script::DocumentProperty.new(
+            tree.children[0].text,
+            values)
+        when 'NSDEF'
+          BEL::Script::NamespaceDefinition.new(
+            tree.children[0].text,
+            tree.children[1].text,
+            false)
+        when 'DFLT_NSDEF'
+          BEL::Script::NamespaceDefinition.new(
+            tree.children[0].text,
+            tree.children[1].text,
+            true)
+        when 'ANNO_DEF_LIST'
+          values = tree.children[1].text[1...-1].split(' ,')
+          BEL::Script::AnnotationListDefinition.new(
+            tree.children[0].text,
+            values)
+        when 'ANNO_DEF_PTRN'
+          BEL::Script::AnnotationListDefinition.new(
+            tree.children[0].text,
+            tree.children[1].text)
+        when 'ANNO_DEF_URL'
+          BEL::Script::AnnotationListDefinition.new(
+            tree.children[0].text,
+            tree.children[1].text)
+        when 'ANNO_SET_ID'
+          BEL::Script::SetAnnotation.new(
+            tree.children[0].text,
+            tree.children[1].text)
+        when 'ANNO_SET_LIST'
+          values = tree.children[1].text[1...-1].split(' ,')
+          BEL::Script::SetAnnotation.new(
+            tree.children[0].text,
+            values)
+        when 'ANNO_SET_QV'
+          BEL::Script::SetAnnotation.new(
+            tree.children[0].text,
+            tree.children[1].text)
+        when 'SG_SET_ID'
+          BEL::Script::SetStatementGroup.new(tree.children[0].text)
+        when 'SG_SET_QV'
+          value = tree.children[0].text[1...-1]
+          BEL::Script::SetStatementGroup.new(value)
+        when 'PARAM_DEF_ID'
+          if tree.children.length == 2
+            BEL::Script::ParameterDefinition.new(
+              tree.children[0].text,
+              tree.children[1].text)
+          else
+            BEL::Script::ParameterDefinition.new(
+              nil,
+              tree.children[0].text)
+          end
+        when 'PARAM_DEF_QV'
+          if tree.children.length == 2
+            value = tree.children[1].text[1...-1]
+            BEL::Script::ParameterDefinition.new(
+              tree.children[0].text,
+              value)
+          else
+            value = tree.children[0].text[1...-1]
+            BEL::Script::ParameterDefinition.new(
+              nil,
+              value)
+          end
+        when 'TERMDEF'
+          func = tree.children[0].text
+          args = tree.children[1..-1].map { |x| from_tree(x) }
+          BEL::Script::TermDefinition.new(func, args)
+        when 'STMTDEF'
+          comment = nil
+          if tree.children[0].text.start_with? '//'
+            comment = tree.children[0].text[2..-1]
+            tree.children.shift
+          end
+
+          if tree.children.length == 1
+            sub = from_tree(tree.children[0])
+            BEL::Script::StatementDefinition.new(sub, nil, nil, comment)
+          else
+            obj = from_tree(tree.children.pop)
+            while tree.children.length > 0
+              rel = tree.children.pop
+              sub = from_tree(tree.children.pop)
+              obj = BEL::Script::StatementDefinition.new(sub, rel, obj)
+            end
+            obj.comment = comment
+            obj
+          end
+        when 'UNSET_SG'
+          BEL::Script::UnsetStatementGroup.new('')
+        else
+          nil
+        end
+      end
+    end
+  end
+end

metadata

@@ -0,0 +1,148 @@
+--- !ruby/object:Gem::Specification
+name: bel
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+  prerelease: 
+platform: ruby
+authors:
+- Anthony Bargnesi
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-07-18 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: antlr3
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.10.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.10.0
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 10.1.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 10.1.0
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.14.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.14.0
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.8.7.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.8.7.0
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 4.0.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 4.0.0
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.3.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.3.0
+description: The BEL gem allows the reading, writing, and processing of BEL (Biological
+  Expression Language) with a natural DSL.
+email: abargnesi@selventa.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- lib/bel.rb
+- lib/bel/grammar/lexer.rb
+- lib/bel/grammar/parser.rb
+- lib/bel/namespace.rb
+- lib/bel/language.rb
+- lib/bel/script.rb
+homepage: https://github.com/OpenBEL/bel.rb
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.25
+signing_key: 
+specification_version: 3
+summary: Process BEL with ruby.
+test_files: []
+has_rdoc: