bel 0.3.1-x86-mingw32 → 0.3.2-x86-mingw32

checksums.yaml

@@ -1,15 +1,7 @@
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data/README.md

@@ -3,6 +3,14 @@ bel ruby
 
 [![Gem Version](https://badge.fury.io/rb/bel.svg)](http://badge.fury.io/rb/bel)
 
+[![Changelog](https://img.shields.io/badge/bel.rb-changelog-brightgreen.svg)](https://github.com/OpenBEL/bel.rb/blob/master/CHANGELOG.md)
+
+[![Issues](https://img.shields.io/github/issues/OpenBEL/bel.rb.svg)](https://github.com/OpenBEL/bel.rb/issues)
+
+[![Dependencies](https://img.shields.io/gemnasium/OpenBEL/bel.rb.svg)]()
+
+[![Join the chat at https://gitter.im/OpenBEL/bel.rb](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/OpenBEL/bel.rb?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+
 The bel ruby gem allows the reading, writing, and processing of BEL (Biological Expression Language) with a natural DSL.
 
 Learn more on [BEL](http://www.openbel.org/content/bel-lang-language).
@@ -22,6 +30,8 @@ Dependencies
 
 Install / Build: See [INSTALL](INSTALL.md).
 
+A changelog is maintained at [CHANGELOG][CHANGELOG].
+
 branches
 --------
 
@@ -53,7 +63,7 @@ executable commands
       upgrade
 
 
-    bel 0.3.1
+    bel 0.3.2
     Copyright (C) 2015 OpenBEL
     Apache License, Version 2.0, January 2004
     http://www.apache.org/licenses/
@@ -355,3 +365,5 @@ api examples
       end  
     end
 ```
+
+[CHANGELOG]: https://github.com/OpenBEL/bel.rb/blob/master/CHANGELOG.md

data/bel.gemspec

@@ -57,12 +57,15 @@ Gem::Specification.new do |spec|
   spec.add_dependency             'ffi',           '1.9.8'
 
   # test rdf functionality
-  spec.add_development_dependency 'uuid',          '~> 2.3'
   spec.add_development_dependency 'addressable',   '~> 2.3'
   spec.add_development_dependency 'rdf',           '~> 1.1'
   spec.add_development_dependency 'rdf-turtle',    '~> 1.1'
+  spec.add_development_dependency 'uuid',          '~> 2.3'
 
   # development gems
+  spec.add_development_dependency 'byebug',        '~> 5.0'
+  spec.add_development_dependency 'minitest',      '~> 5.7'
+  spec.add_development_dependency 'pry-byebug',    '~> 3.2'
   spec.add_development_dependency 'rake',          '~> 10.4'
   spec.add_development_dependency 'rake-compiler', '~> 0.9'
   spec.add_development_dependency 'rdoc',          '~> 4.2'

data/bin/bel

@@ -1,4 +1,5 @@
 #!/usr/bin/env ruby
+$: << File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib')
 require 'erb'
 require 'bel'
 require 'bel/vendor/trollop'

data/bin/bel2rdf.rb

@@ -128,9 +128,9 @@ end
 # read bel content
 content =
   if options[:bel]
-    File.open(options[:bel]).read
+    File.open(options[:bel], :external_encoding => 'UTF-8')
   else
-    $stdin.read
+    $stdin
   end
 
 # parse and write rdf

data/bin/bel_compare.rb

@@ -46,11 +46,11 @@ threads = []
 first_groups = {}
 second_groups = {}
 threads << Thread.new {
-  first_groups.update(fetch_groups(File.read(ARGV[0])))
+  first_groups.update(fetch_groups(File.open(ARGV[0], :external_encoding => 'UTF-8')))
 }
 
 threads << Thread.new {
-  second_groups.update(fetch_groups(File.read(ARGV[1])))
+  second_groups.update(fetch_groups(File.open(ARGV[1], :external_encoding => 'UTF-8')))
 }
 
 threads.each { |t| t.join }

data/bin/bel_parse.rb

@@ -35,7 +35,7 @@ end
 # read bel content
 content =
 if options[:bel]
-  File.open(options[:bel])
+  File.open(options[:bel], :external_encoding => 'UTF-8')
 else
   $stdin
 end

data/bin/bel_summarize.rb

@@ -21,7 +21,7 @@ end.parse!
 # read bel content
 content =
   if options[:bel]
-    File.open(options[:bel])
+    File.open(options[:bel], :external_encoding => 'UTF-8')
   else
     $stdin
   end

data/bin/bel_upgrade.rb

@@ -52,7 +52,7 @@ end
 # read bel content
 content =
 if options[:bel]
-  File.open(options[:bel])
+  File.open(options[:bel], :external_encoding => 'UTF-8')
 else
   $stdin
 end
@@ -60,7 +60,7 @@ end
 # read change log
 changelog = nil
 if File.exists? options[:change_log]
-  File.open(options[:change_log]) do |f|
+  File.open(options[:change_log], :external_encoding => 'UTF-8') do |f|
     changelog = JSON.parse(f.read)
   end
 else

data/lib/bel/evidence_model/bel_parameter.rb

@@ -6,7 +6,7 @@ module BEL
       def valid?
         return false unless value
         return true unless @ns
-        @ns.respond_to?(:values) && ns.values.include?(value)
+        @ns.respond_to?(:values) && ns.values.include?(value.to_sym)
       end
     end
 

data/lib/bel/evidence_model/bel_term.rb

@@ -9,10 +9,56 @@ module BEL
         @arguments = (arguments ||= []).flatten
       end
 
+      def initialize(fx, *arguments)
+        @fx = case fx
+        when String
+          BEL::Language::Function.new(FUNCTIONS[fx.to_sym])
+        when Symbol
+          BEL::Language::Function.new(FUNCTIONS[fx.to_sym])
+        when BEL::Language::Function
+          fx
+        when nil
+          raise ArgumentError, 'fx must not be nil'
+        end
+        @arguments = (arguments ||= []).flatten
+        @signature = Signature.new(
+          @fx[:short_form],
+          *@arguments.map { |arg|
+            case arg
+            when Term
+              F.new(arg.fx.return_type)
+            when Parameter
+              E.new(arg.enc)
+            when nil
+              NullE.new
+            end
+          })
+      end
+
       def <<(item)
         @arguments << item
       end
 
+      def valid?
+        invalid_signatures = @arguments.find_all { |arg|
+          arg.is_a? Term
+        }.find_all { |term|
+          not term.valid?
+        }
+        return false if not invalid_signatures.empty?
+
+        sigs = @fx.signatures
+        sigs.any? do |sig| (@signature <=> sig) >= 0 end
+      end
+
+      def valid_signatures
+        @fx.signatures.find_all { |sig| (@signature <=> sig) >= 0 }
+      end
+
+      def invalid_signatures
+        @fx.signatures.find_all { |sig| (@signature <=> sig) < 0 }
+      end
+
       def hash
         [@fx, @arguments].hash
       end
@@ -25,9 +71,10 @@ module BEL
 
       def to_bel
         arguments = [@arguments].flatten.map(&:to_bel).join(',') 
-        "#@fx(#{arguments})"
+        "#{@fx.short_form}(#{arguments})"
       end
       alias_method :to_s, :to_bel
     end
   end
 end
+

data/lib/bel/extensions/jgf.rb

@@ -129,6 +129,7 @@ module BEL::Extension::Format
       bel_statements.map { |bel_statement|
         graph_name = graph[:label] || graph[:id] || 'BEL Graph'
         metadata   = ::BEL::Model::Metadata.new
+        references = ::BEL::Model::References.new
 
         # establish document header
         metadata.document_header[:Name]        = graph_name
@@ -153,7 +154,7 @@ module BEL::Extension::Format
             }
           ]
         end
-        metadata.annotation_definitions = annotations if annotations
+        references.annotation_definitions = annotations if annotations
 
         # establish namespace definitions
         namespaces = graph.fetch(:metadata, {}).
@@ -170,11 +171,12 @@ module BEL::Extension::Format
             }
           ]
         end
-        metadata.namespace_definitions = namespaces if namespaces
+        references.namespace_definitions = namespaces if namespaces
 
         ::BEL::Model::Evidence.create(
           :bel_statement => bel_statement,
-          :metadata      => metadata
+          :metadata      => metadata,
+          :references    => references
         )
       }
     end

data/lib/bel/extensions/rdf/bel_rdf.rb

@@ -27,147 +27,163 @@ module BEL
     # maps outer function to bel/vocabulary class
     FUNCTION_TYPE = {
       a:                       BELV.Abundance,
-      abundance:               BELV.Abundance,
-      g:                       BELV.GeneAbundance,
-      geneAbundance:           BELV.GeneAbundance,
-      p:                       BELV.ProteinAbundance,
-      proteinAbundance:        BELV.ProteinAbundance,
-      r:                       BELV.RNAAbundance,
-      rnaAbundance:            BELV.RNAAbundance,
-      m:                       BELV.microRNAAbundance,
-      microRNAAbundance:       BELV.microRNAAbundance,
+      act:                     BELV.AbundanceActivity,
+      bp:                      BELV.BiologicalProcess,
+      cat:                     BELV.AbundanceActivity,
+      chap:                    BELV.AbundanceActivity,
       complex:                 BELV.ComplexAbundance,
-      complexAbundance:        BELV.ComplexAbundance,
       composite:               BELV.CompositeAbundance,
-      compositeAbundance:      BELV.CompositeAbundance,
-      bp:                      BELV.BiologicalProcess,
-      biologicalProcess:       BELV.BiologicalProcess,
+      deg:                     BELV.Degradation,
+      fus:                     BELV.Fusion,
+      g:                       BELV.GeneAbundance,
+      gtp:                     BELV.AbundanceActivity,
+      kin:                     BELV.AbundanceActivity,
+      m:                       BELV.microRNAAbundance,
+      p:                       BELV.ProteinAbundance,
       path:                    BELV.Pathology,
-      pathology:               BELV.Pathology,
+      pep:                     BELV.AbundanceActivity,
+      phos:                    BELV.AbundanceActivity,
+      pmod:                    BELV.ProteinModification,
+      r:                       BELV.RNAAbundance,
+      ribo:                    BELV.AbundanceActivity,
       rxn:                     BELV.Reaction,
-      reaction:                BELV.Reaction,
-      tloc:                    BELV.Translocation,
-      translocation:           BELV.Translocation,
       sec:                     BELV.CellSecretion,
-      cellSecretion:           BELV.CellSecretion,
-      deg:                     BELV.Degradation,
-      degradation:             BELV.Degradation,
-      cat:                     BELV.AbundanceActivity,
+      sub:                     BELV.Substitution,
+      surf:                    BELV.CellSurfaceExpression,
+      tloc:                    BELV.Translocation,
+      tport:                   BELV.AbundanceActivity,
+      tscript:                 BELV.AbundanceActivity,
+      abundance:               BELV.Abundance,
+      biologicalProcess:       BELV.BiologicalProcess,
       catalyticActivity:       BELV.AbundanceActivity,
-      chap:                    BELV.AbundanceActivity,
+      cellSecretion:           BELV.CellSecretion,
+      cellSurfaceExpression:   BELV.CellSurfaceExpression,
       chaperoneActivity:       BELV.AbundanceActivity,
-      gtp:                     BELV.AbundanceActivity,
+      complexAbundance:        BELV.ComplexAbundance,
+      compositeAbundance:      BELV.CompositeAbundance,
+      degradation:             BELV.Degradation,
+      fusion:                  BELV.Fusion,
+      geneAbundance:           BELV.GeneAbundance,
       gtpBoundActivity:        BELV.AbundanceActivity,
-      kin:                     BELV.AbundanceActivity,
       kinaseActivity:          BELV.AbundanceActivity,
-      act:                     BELV.AbundanceActivity,
+      list:                    BELV.List,
+      microRNAAbundance:       BELV.microRNAAbundance,
       molecularActivity:       BELV.AbundanceActivity,
-      pep:                     BELV.AbundanceActivity,
+      pathology:               BELV.Pathology,
       peptidaseActivity:       BELV.AbundanceActivity,
-      phos:                    BELV.AbundanceActivity,
       phosphataseActivity:     BELV.AbundanceActivity,
-      ribo:                    BELV.AbundanceActivity,
+      products:                BELV.Products,
+      proteinAbundance:        BELV.ProteinAbundance,
+      proteinModification:     BELV.ProteinModification,
+      reactants:               BELV.Reactants,
+      reaction:                BELV.Reaction,
       ribosylationActivity:    BELV.AbundanceActivity,
-      tscript:                 BELV.AbundanceActivity,
+      rnaAbundance:            BELV.RNAAbundance,
+      substitution:            BELV.Substitution,
       transcriptionalActivity: BELV.AbundanceActivity,
-      tport:                   BELV.AbundanceActivity,
-      transportActivity:       BELV.AbundanceActivity
+      translocation:           BELV.Translocation,
+      transportActivity:       BELV.AbundanceActivity,
+      truncation:              BELV.Truncation,
     }
 
     RELATIONSHIP_TYPE = {
-        'association'            => BELV.Association,
         '--'                     => BELV.Association,
+        '-|'                     => BELV.Decreases,
+        '=|'                     => BELV.DirectlyDecreases,
+        '=>'                     => BELV.DirectlyIncreases,
+        '->'                     => BELV.Increases,
+        ':>'                     => BELV.TranscribedTo,
+        '>>'                     => BELV.TranslatedTo,
+        'actsIn'                 => BELV.ActsIn,
+        'analogous'              => BELV.Analogous,
+        'association'            => BELV.Association,
         'biomarkerFor'           => BELV.BiomarkerFor,
         'causesNoChange'         => BELV.CausesNoChange,
         'decreases'              => BELV.Decreases,
-        '-|'                     => BELV.Decreases,
         'directlyDecreases'      => BELV.DirectlyDecreases,
-        '=|'                     => BELV.DirectlyDecreases,
         'directlyIncreases'      => BELV.DirectlyIncreases,
-        '=>'                     => BELV.DirectlyIncreases,
         'hasComponent'           => BELV.HasComponent,
+        'hasComponents'          => BELV.HasComponents,
         'hasMember'              => BELV.HasMember,
+        'hasMembers'             => BELV.HasMembers,
+        'hasModification'        => BELV.HasModification,
+        'hasProduct'             => BELV.HasProduct,
+        'hasVariant'             => BELV.HasVariant,
+        'includes'               => BELV.Includes,
         'increases'              => BELV.Increases,
-        '->'                     => BELV.Increases,
         'isA'                    => BELV.IsA,
         'negativeCorrelation'    => BELV.NegativeCorrelation,
+        'orthologous'            => BELV.Orthologous,
         'positiveCorrelation'    => BELV.PositiveCorrelation,
         'prognosticBiomarkerFor' => BELV.PrognosticBiomarkerFor,
         'rateLimitingStepOf'     => BELV.RateLimitingStepOf,
+        'reactantIn'             => BELV.ReactantIn,
         'subProcessOf'           => BELV.SubProcessOf,
-        ':>'                     => BELV.TranscribedTo,
-        '>>'                     => BELV.TranslatedTo,
-
-        # Supported by schema
-        # 'actsIn'               => BELV.ActsIn, # (BELV.hasChild)
-
-        # Unsupported in schema
-        #'analogous'              => BELV.Analogous,
-        #'hasModification'        => BELV.HasModification,
-        #'hasProduct'             => BELV.HasProduct,
-        #'hasVariant'             => BELV.HasVariant,
-        #'includes'               => BELV.Includes,
-        #'orthologous'            => BELV.Orthologous,
-        #'reactantIn'             => BELV.ReactantIn,
-        #'transcribedTo'          => BELV.TranscribedTo,
-        #'translatedTo'           => BELV.TranslatedTo,
-        #'translocates'           => BELV.Translocates,
-
-        # Macro statements - TODO needs parser AST translation
-        #'hasComponents'          => BELV.HasComponents,
-        #'hasMembers'             => BELV.HasMembers,
+        'transcribedTo'          => BELV.TranscribedTo,
+        'translatedTo'           => BELV.TranslatedTo,
+        'translocates'           => BELV.Translocates,
     }
 
     RELATIONSHIP_CLASSIFICATION = {
-        :'association'            => BELV.CorrelativeRelationship,
         :'--'                     => BELV.CorrelativeRelationship,
+        :'-|'                     => BELV.Decreases,
+        :'=|'                     => BELV.DirectlyDecreases,
+        :'=>'                     => BELV.DirectlyIncreases,
+        :'->'                     => BELV.Increases,
+        :'association'            => BELV.CorrelativeRelationship,
         :'biomarkerFor'           => BELV.BiomarkerFor,
         :'causesNoChange'         => BELV.CausesNoChange,
         :'decreases'              => BELV.Decreases,
-        :'-|'                     => BELV.Decreases,
         :'directlyDecreases'      => BELV.DirectlyDecreases,
-        :'=|'                     => BELV.DirectlyDecreases,
         :'directlyIncreases'      => BELV.DirectlyIncreases,
-        :'=>'                     => BELV.DirectlyIncreases,
         :'hasComponent'           => BELV.HasComponent,
         :'hasMember'              => BELV.HasMember,
         :'increases'              => BELV.Increases,
-        :'->'                     => BELV.Increases,
         :'isA'                    => BELV.IsA,
         :'negativeCorrelation'    => BELV.NegativeCorrelation,
         :'positiveCorrelation'    => BELV.PositiveCorrelation,
         :'prognosticBiomarkerFor' => BELV.PrognosticBiomarkerFor,
         :'rateLimitingStepOf'     => BELV.RateLimitingStepOf,
-        :'subProcessOf'           => BELV.SubProcessOf
+        :'subProcessOf'           => BELV.SubProcessOf,
     }
 
     ACTIVITY_TYPE = {
-      cat: BELV.Catalytic,
-      chap: BELV.Chaperone,
-      gtp: BELV.GtpBound,
-      kin: BELV.Kinase,
-      act: BELV.Activity,
-      pep: BELV.Peptidase,
-      phos: BELV.Phosphatase,
-      ribo: BELV.Ribosylase,
-      tscript: BELV.Transcription,
-      tport: BELV.Transport
+      act:                     BELV.Activity,
+      cat:                     BELV.Catalytic,
+      chap:                    BELV.Chaperone,
+      gtp:                     BELV.GtpBound,
+      kin:                     BELV.Kinase,
+      pep:                     BELV.Peptidase,
+      phos:                    BELV.Phosphatase,
+      ribo:                    BELV.Ribosylase,
+      tport:                   BELV.Transport,
+      tscript:                 BELV.Transcription,
+      catalyticActivity:       BELV.Catalytic,
+      chaperoneActivity:       BELV.Chaperone,
+      gtpBoundActivity:        BELV.GtpBound,
+      kinaseActivity:          BELV.Kinase,
+      molecularActivity:       BELV.Activity,
+      peptidaseActivity:       BELV.Peptidase,
+      phosphataseActivity:     BELV.Phosphatase,
+      ribosylationActivity:    BELV.Ribosylase,
+      transcriptionalActivity: BELV.Transcription,
+      transportActivity:       BELV.Transport,
     }
 
     # maps modification types to bel/vocabulary class
     MODIFICATION_TYPE = {
-      'P,S' => BELV.PhosphorylationSerine,
-      'P,T' => BELV.PhosphorylationThreonine,
-      'P,Y' => BELV.PhosphorylationTyrosine,
       'A'   => BELV.Acetylation,
       'F'   => BELV.Farnesylation,
       'G'   => BELV.Glycosylation,
       'H'   => BELV.Hydroxylation,
       'M'   => BELV.Methylation,
       'P'   => BELV.Phosphorylation,
+      'P,S' => BELV.PhosphorylationSerine,
+      'P,T' => BELV.PhosphorylationThreonine,
+      'P,Y' => BELV.PhosphorylationTyrosine,
       'R'   => BELV.Ribosylation,
       'S'   => BELV.Sumoylation,
-      'U'   => BELV.Ubiquitination
+      'U'   => BELV.Ubiquitination,
     }
 
     # protein variant