bel 0.7.0 → 1.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 7af3edc1edfb6d481168297a4799af8c7c9e0128
+  metadata.gz: ee6f5ca76360462e55335f9e1c46479ce56798da
+  data.tar.gz: b0f1a01dddc5d8cccf586b08c957cf153d6d8cfd
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+  data.tar.gz: def4cf7f97273305d73d706b7362f14facdfbf9620a82c1b98731dc064e633fd31bf787ae3b225a71d582cf337173f753a5451576a3dc66d691fbf788f69b0cb

data/{bel.gemspec → .gemspec}

@@ -1,8 +1,8 @@
-require './lib/bel/version'
-
 Gem::Specification.new do |spec|
   spec.name                     = 'bel'
-  spec.version                  = BEL::VERSION
+  spec.version                  = File.read(File.join(
+                                    File.expand_path(File.dirname(__FILE__)),
+                                    'VERSION'))
   spec.summary                  = '''
                                     Process BEL with ruby.
                                   '''.gsub(%r{^\s+}, ' ').gsub(%r{\n}, '')
@@ -36,6 +36,7 @@ Gem::Specification.new do |spec|
                                     'INSTALL_RUBY.md',
                                     'LICENSE',
                                     'README.md',
+                                    'VERSION',
                                   ].flatten!
   spec.executables              = Dir.glob('bin/*').map(&File.method(:basename))
   spec.homepage                 = 'https://github.com/OpenBEL/bel.rb'
@@ -59,7 +60,10 @@ Gem::Specification.new do |spec|
   spec.extensions              << 'ext/mri/extconf.rb'
   spec.required_ruby_version    = '>= 2.0.0'
 
-  spec.add_runtime_dependency 'ffi', '1.9.8'
+  spec.add_runtime_dependency 'bel_parser', '~> 1.0.0'
+  spec.add_runtime_dependency 'rdf',        '~> 2.0.0'
+  spec.add_runtime_dependency 'rdf-vocab',  '~> 2.0.0'
+  spec.add_runtime_dependency 'ffi',        '1.9.8'
 
   # Example post-install message.
   #

data/README.md

@@ -211,7 +211,7 @@ the root of the bel.rb tree:
   
     # reference namespace value using standard prefixes (HGNC, MGI, RGD, etc.)
     HGNC['AKT1']
-    => #<BEL::Model::Parameter:0x00000004df5bc0
+    => #<BEL::Nanopub::Parameter:0x00000004df5bc0
       @enc=:GRP,
       @ns_def="BEL::Namespace::HGNC",
       @value=:AKT1>
@@ -405,14 +405,14 @@ the root of the bel.rb tree:
 
     # parse term
     parser.parse('p(HGNC:AKT1)') do |obj|
-      if obj.is_a? BEL::Model::Term  
+      if obj.is_a? BEL::Nanopub::Term  
         rdf_statements += obj.to_rdf
       end  
     end
 
     # parse statement
     parser.parse("p(HGNC:AKT1) => tscript(g(HGNC:TNF))\n") do |obj|
-      if obj.is_a? BEL::Model::Statement
+      if obj.is_a? BEL::Nanopub::Statement
         rdf_statements += obj.to_rdf
       end  
     end

data/VERSION

@@ -0,0 +1 @@
+1.0.0

data/bin/bel

@@ -6,7 +6,7 @@ require 'bel/util'
 require 'bel/vendor/trollop'
 
 VERSION_BANNER = <<-VERSION
-bel #{BEL::VERSION}
+bel #{BEL::Version}
 Copyright (C) #{Time.now.year} OpenBEL
 Apache License, Version 2.0, January 2004
 http://www.apache.org/licenses/
@@ -247,7 +247,7 @@ Subcommands:
       def run
         parsed_options =
           Trollop::options do
-            synopsis "Translates BEL evidence between formats using translator plugins."
+            synopsis "Translates BEL nanopubs between formats using translator plugins."
             usage    <<-DOC.gsub(/^ {14}/, '')
               [OPTIONS]... translate [OPTIONS] FROM_TRANSLATOR TO_TRANSLATOR
 
@@ -275,7 +275,7 @@ Subcommands:
                   Run "bel remapfile" to get an example of the YAML format.
             DOC
 
-            opt      :'input-file', 'The file containing evidence data to translate. If not specified the default is to read from STDIN.',
+            opt      :'input-file', 'The file containing nanopubs to translate. If not specified the default is to read from STDIN.',
                      :type    => String,
                      :long    => :'input-file',
                      :short   => :i,
@@ -506,21 +506,21 @@ Subcommands:
 
         # require BEL generator and include in GenerateCommand
         require 'bel/gen'
-        self.class.include(BEL::Gen::Evidence)
+        self.class.include(BEL::Gen::Nanopub)
         self.class.include(BEL::Gen::SampleResources) if options[:sample]
 
-        # create enumerator of random evidence
+        # create enumerator of random nanopubs
         limit       = options[:limit].to_i
         random_data = Enumerator.new do |yielder|
           count = 0
           while count != limit do
-            yielder << evidence
+            yielder << nanopub
             count += 1
-            $stderr.puts "#{count} evidence generated..." if count % 500 == 0
+            $stderr.puts "#{count} nanopubs generated..." if count % 500 == 0
           end
         end
 
-        # write random evidence to STDOUT through a translator
+        # write random nanopubs to STDOUT through a translator
         translator_id = options[:translator] || :bel
         translator    = BEL.translator(options[:translator] || :bel)
         unless translator

data/bin/bel2rdf.rb

@@ -28,7 +28,7 @@ options = {
 }
 OptionParser.new do |opts|
   opts.banner = <<-USAGE
-    Converts BEL evidence to RDF...
+    Converts BEL nanopubs to RDF...
 
     From a BEL file.
     Usage: bel2rdf --bel [FILE]

data/bin/bel_summarize.rb

@@ -31,7 +31,7 @@ CSV do |csv_out|
     statement_group_count: 0,
     empty_statement_groups: 0,
     statement_count: 0,
-    evidence_count: 0
+    support_count: 0
   }
 
   FUNCTIONS.each do |k, v|
@@ -53,7 +53,7 @@ CSV do |csv_out|
         report[:empty_statement_groups] += 1
       end
     end
-    if obj.is_a? BEL::Model::Term
+    if obj.is_a? BEL::Nanopub::Term
       fx = obj.fx
       fx = fx.respond_to?(:long_form) ?
              fx.long_form.to_s :
@@ -61,7 +61,7 @@ CSV do |csv_out|
       fx = FUNCTIONS[fx.to_sym][:long_form]
       report["fx_#{fx}"] += 1
     end
-    if obj.is_a? BEL::Model::Statement
+    if obj.is_a? BEL::Nanopub::Statement
       report[:statement_count] += 1
       obj.relationship = case obj.relationship
       when :"->"
@@ -83,7 +83,7 @@ CSV do |csv_out|
       end
     end
     if obj.is_a? BEL::Language::Annotation
-      report[:evidence_count] += 1 if obj.name == 'Evidence'
+      report[:support_count] += 1 if obj.name == 'Support'
     end
   end
 

data/bin/bel_upgrade.rb

@@ -75,7 +75,7 @@ end
 
 class Main
 
-  EvidenceMatcher = Regexp.compile(/SET Evidence = ([0-9a-zA-Z]+)/)
+  SupportMatcher = Regexp.compile(/SET Support = ([0-9a-zA-Z]+)/)
   LostReplaceValues = ['unresolved', 'withdrawn']
   attr_reader :ttl
 
@@ -141,11 +141,11 @@ class Main
         end
       end
 
-      # evidence always needs quoting; backwards-compatibility
+      # support always needs quoting; backwards-compatibility
       if obj.is_a? BEL::Language::Annotation
-        if obj.name == 'Evidence'
+        if obj.name == 'Support'
           ev = obj.to_s
-          ev.gsub!(EvidenceMatcher, 'SET Evidence = "\1"')
+          ev.gsub!(SupportMatcher, 'SET Support = "\1"')
           puts ev.to_s
           next
         # look for replacement values for annotations  
@@ -185,7 +185,7 @@ class Main
         end
       end
 
-      if obj.is_a? BEL::Model::Parameter and obj.ns
+      if obj.is_a? BEL::Nanopub::Parameter and obj.ns
         # first try replacing by existing namespace prefix...
         prefix = obj.ns.prefix.to_s
         replacements = @change_log[prefix]
@@ -225,7 +225,7 @@ class Main
         end
       end
       # do not print Parameter and Term; they are included in Statement
-      if not obj.is_a? BEL::Model::Parameter and not obj.is_a? BEL::Model::Term
+      if not obj.is_a? BEL::Nanopub::Parameter and not obj.is_a? BEL::Nanopub::Term
         puts obj.to_bel
       end
     end

data/lib/bel.rb

@@ -5,7 +5,7 @@ require_relative 'bel/annotation'
 require_relative 'bel/namespace'
 require_relative 'bel/util'
 
-require_relative 'bel/evidence_model'
+require_relative 'bel/nanopub'
 require_relative 'bel/translator'
 require_relative 'bel/translate'
 
@@ -15,9 +15,10 @@ require_relative 'bel/resource'
 require_relative 'bel/script'
 
 require_relative 'bel/libbel.rb'
-require_relative 'bel/parser'
 require_relative 'bel/completion'
 
+require_relative 'bel/dsl'
+
 module BEL
   extend  BEL::Translate::ClassMethods
 end

data/lib/bel/completion.rb

@@ -1,11 +1,12 @@
+require          'bel_parser/language'
 require_relative 'libbel'
 require_relative 'completion_rule'
 require_relative 'language'
 require_relative 'namespace'
 
 module BEL
+  # Completion defines an API for completing BEL Expressions.
   module Completion
-
     # Provides completions on BEL expressions.
     #
     # If +bel_expression+ is +nil+ then its assumed to be the empty string
@@ -26,17 +27,18 @@ module BEL
     #
     # @param bel_expression   [responds to #to_s] the bel expression to
     # complete on
+    # @param specification    [BELParser::Language::Specification] language specification
     # @param search           [#search_namespace, #search] the search object used to
     # provide namespace value completions
     # @param position         [responds to #to_i] the position to complete from
     # @return [Array<Completion>]
-    def self.complete(bel_expression, search, namespaces, position = nil)
-      raise ArgumentError.new(
-        "search should be a BEL::Resource::Search plugin implementation"
-      ) unless search
-      raise ArgumentError.new(
-        "namespaces should be a BEL::Resource::Namespaces object"
-      ) unless namespaces
+    def self.complete(bel_expression, specification, search, namespaces, position = nil)
+      #raise ArgumentError.new(
+      #  "search should be a BEL::Resource::Search plugin implementation"
+      #) unless search
+      #raise ArgumentError.new(
+      #  "namespaces should be a BEL::Resource::Namespaces object"
+      #) unless namespaces
 
       bel_expression = (bel_expression || '').to_s
       position = (position || bel_expression.length).to_i
@@ -58,8 +60,9 @@ module BEL
       }
       BEL::Completion::run_rules(
         tokens, active_index, active_token,
-        :search     => search,
-        :namespaces => namespaces
+        :specification => specification,
+        :search        => search,
+        :namespaces    => namespaces
       )
     end
   end

data/lib/bel/completion_rule.rb

@@ -1,30 +1,31 @@
-require_relative 'language'
 require_relative 'namespace'
 require_relative 'quoting'
 
 module BEL
   module Completion
-
-    SORTED_FUNCTIONS  = BEL::Language::FUNCTIONS.keys.sort.map(&:to_s)
     SORTED_NAMESPACES = BEL::Namespace::NAMESPACE_LATEST.keys.sort.map(&:to_s)
     EMPTY_MATCH       = []
 
+    # Run all defined {Rule rules}.
     def self.run_rules(tokens, active_index, active_token, options = {})
       self.rules.reduce([]) { |completion_results, rule|
         completion_results.concat(
           rule.apply(tokens, active_token, active_index, options)
         )
+        completion_results
       }
     end
 
+    # Retrieve all completion {Rule rules}.
     def self.rules
-      [
-        MatchFunctionRule.new,
-        MatchNamespacePrefixRule.new,
-        MatchNamespaceValueRule.new
-      ]
+      constants.map do |const|
+        obj = const_get(const)
+        obj.new if obj.include?(Rule)
+      end.compact
     end
 
+    # Rule defines the {#apply} API contract and additional helpers to convey
+    # completion actions.
     module Rule
 
       def apply(token_list, active_token, active_token_index, options = {})
@@ -100,21 +101,22 @@ module BEL
       end
     end
 
+    # MatchFunctionRule defines a function completion rule. This rule relies on
+    # a {BELParser::Language::Specification} for the available functions.
     class MatchFunctionRule
       include Rule
 
       def _apply(token_list, active_token, active_token_index, options = {})
         if token_list.empty? or active_token.type == :O_PAREN
-          return SORTED_FUNCTIONS.map { |fx| map_function(fx) }.uniq.sort_by { |fx|
-            fx[:label]
-          }
+          return spec_functions(options[:specification]).map(&method(:map_function))
         end
 
         if active_token.type == :IDENT
-          value = active_token.value.downcase
-          return SORTED_FUNCTIONS.find_all { |x|
-            x.downcase.include? value
-          }.map { |fx| map_function(fx) }.uniq.sort_by { |fx| fx[:label] }
+          value   = active_token.value.downcase
+          matches = spec_functions(options[:specification]).select do |func|
+            func.short.to_s.include?(value) || func.long.to_s.include?(value)
+          end
+          return matches.map(&method(:map_function))
         end
 
         return EMPTY_MATCH
@@ -122,14 +124,17 @@ module BEL
 
       protected
 
-      def map_function(fx_name)
-        fx = BEL::Language::Function.new(BEL::Language::FUNCTIONS[fx_name.to_sym])
-        if fx
+      def spec_functions(spec)
+        spec.functions.sort_by(&:long)
+      end
+
+      def map_function(function)
+        if function
           {
-            :id     => fx.short_form,
+            :id     => function.short,
             :type   => :function,
-            :label  => fx.long_form,
-            :value  => "#{fx.short_form}()",
+            :label  => function.long,
+            :value  => "#{function.short}()",
             :offset => -1
           }
         else
@@ -138,6 +143,8 @@ module BEL
       end
     end
 
+    # MatchNamespacePrefixRule defines a namespace completion rule.
+    # TODO Namespces should be passed as state, not hardcoded.
     class MatchNamespacePrefixRule
       include Rule
 
@@ -176,6 +183,7 @@ module BEL
       end
     end
 
+    # MatchNamespaceValueRule defines a namespace value completion rule.
     class MatchNamespaceValueRule
       include Rule
       include BEL::Quoting

data/lib/bel/dsl.rb

@@ -0,0 +1,75 @@
+require 'bel_parser/expression/model'
+require 'bel_parser/resources'
+
+module BEL
+  # DSL adds BEL functions and relationships as Ruby methods that allows
+  # creation of {BELParser::Expression::Model::Term} and
+  # {BELParser::Expression::Model::Statement} objects.
+  #
+  # DSL is an acronym for "Domain-specific language".
+  #
+  # @see https://en.wikipedia.org/wiki/Domain-specific_language
+  module DSL
+    # Defines ruby methods for BEL functions and relationships on
+    # +another_module+. The functions and relationships from the
+    # {BELParser::Language.default_specification default specification}
+    # are included.
+    #
+    # This method is called when {BEL::DSL} is included, as in:
+    #
+    #    # calls this method
+    #    include BEL::DSL
+    #
+    #    # Can access namespace constants.
+    #    HGNC
+    #
+    #    # Create new terms.
+    #    p(HGNC['AKT1'])
+    #
+    #    # Create new statements.
+    #    p(HGNC['AKT1']).increases bp(GOBP['apoptotic process'])
+    #
+    # @param [Module] another_module the module receiving DSL functionality
+    def self.included(another_module)
+      self.include_in(
+        another_module,
+        BELParser::Language.default_specification)
+    end
+
+    # Defines ruby methods for BEL functions and relationships on _object_. The
+    # functions and relationships from the provided _specification_ are used.
+    #
+    # @param [Object] object the object to include the DSL methods in
+    # @param [BELParser::Language::Specification] spec the BEL specification
+    def self.include_in(object, spec)
+      if [Class, Module].none? { |type| object.is_a?(type) }
+        raise(ArgumentError, "object: expected Class or Module, actual #{object}")
+      end
+
+      BELParser::Resources.included(object)
+      spec.functions.each do |function|
+        self.send(:_define_term_method, object, function.short, function, spec)
+        self.send(:_define_term_method, object, function.long,  function, spec)
+      end
+      nil
+    end
+
+    # @api private
+    def self._define_term_method(object, name, function, spec)
+      object.send(:define_method, name) do |*args|
+        object       = BELParser::Expression::Model::Term.new(function, *args)
+        object_class = object.singleton_class
+        spec.relationships.each do |relationship|
+          object_class.send(:define_method, relationship.long) do |another|
+            s              = BELParser::Expression::Model::Statement.new self
+            s.relationship = relationship
+            s.object       = another
+            s
+          end
+        end
+        object
+      end
+    end
+    private_class_method :_define_term_method
+  end
+end