bel 0.4.0.beta.7 → 0.4.0.beta.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: d0b4945512529e67124a858ba03f03b18c617ee5
-  data.tar.gz: a57e2e8142d0ed1ef080e4ff206aaf76e69243b4
+  metadata.gz: e22bc8ddb611afaba61076e5e2ac66dc89ff9a59
+  data.tar.gz: 54c075abe536cd62000858f19e88cdaad4b1ab79
 SHA512:
-  metadata.gz: 860f4fa04e20ae6614701eb4714e6cf525781e23cffe1da36307894d62fa26916b5b8d78795b1d90d973c8aa57cd80c792c943d3305e14e9c29b23f8fc2db29c
-  data.tar.gz: 7c68969a47cb4d4a21642c6cc3bfbe825373cf7dab2cf087d410972fb07e5c569a13b88b574e62ffb5d0c921ab6ea2783494bde813cd58c01b04aa4cbaf025d1
+  metadata.gz: e994fee183fbcedbcec2b6728a9095299eb506e3ec0d8e9a2935b589eaff302498c3318fe5ffd25919490b80803db1d5cf4b9ede339099cb6630efc96d2e27ab
+  data.tar.gz: d6573b1c9965ee341f154a03f11c1a50f9392db3d5264c984d6e976435090e6c4f70c8e186e85e46228676791fe46514e6c5610a2e45c22df1b42739f33e02c9

data/lib/bel/completion_rule.rb

@@ -194,9 +194,11 @@ module BEL
               namespace = BEL::Namespace::NAMESPACE_LATEST[prefix_token.value.to_sym]
               if namespace
                 scheme_uri = namespace[1]
-                return search.search_namespace(
-                  URI(scheme_uri),
+                return search.search(
                   "#{active_token.value}*",
+                  :namespace_concept,
+                  URI(scheme_uri),
+                  nil,
                   :start => 0,
                   :size  => 10
                 ).
@@ -207,7 +209,10 @@ module BEL
             end
           else
             return search.search(
-              active_token.value,
+              "#{active_token.value}*",
+              :namespace_concept,
+              nil,
+              nil,
               :start => 0,
               :size  => 10
             ).

data/lib/bel/json/adapter/multi_json.rb

@@ -27,7 +27,7 @@ module BEL::JSON
     end
 
     def write(data, output_io, options = {})
-      json = MultiJson.dump(json_object)
+      json = MultiJson.dump(data)
       if output_io
         # write json and return IO
         output_io.write json

data/lib/bel/rdf_repository/plugins/memory.rb

@@ -1,8 +1,6 @@
 # Load RDF library dependencies
 require 'rdf'
 require 'rdf/mongo'
-require 'addressable/uri'
-require 'uuid'
 
 module BEL::RdfRepository::Plugins
 

data/lib/bel/rdf_repository/plugins/mongo.rb

@@ -1,8 +1,6 @@
 # Load RDF library dependencies
 require 'rdf'
 require 'rdf/mongo'
-require 'addressable/uri'
-require 'uuid'
 
 module BEL::RdfRepository::Plugins
 

data/lib/bel/translator/plugins/rdf/bel_schema.rb

@@ -9,19 +9,20 @@ module BEL::Translator::Plugins
         # uri prefixes
         BELR    = ::RDF::Vocabulary.new('http://www.openbel.org/bel/')
         BELV    = ::RDF::Vocabulary.new('http://www.openbel.org/vocabulary/')
+        BELE    = ::RDF::Vocabulary.new('http://www.openbel.org/evidence/')
         PUBMED  = ::RDF::Vocabulary.new('http://bio2rdf.org/pubmed:')
         RDF     = ::RDF
         RDFS    = ::RDF::RDFS
 
         # annotations
-        Anatomy       = ::RDF::Vocabulary.new('http://www.openbel.org/bel/annotation/anatomy/')
-        Cell          = ::RDF::Vocabulary.new('http://www.openbel.org/bel/annotation/cell/')
-        CellLine      = ::RDF::Vocabulary.new('http://www.openbel.org/bel/annotation/cell-line/')
-        CellStructure = ::RDF::Vocabulary.new('http://www.openbel.org/bel/annotation/cell-structure/')
-        Disease       = ::RDF::Vocabulary.new('http://www.openbel.org/bel/annotation/disease/')
-        MeSHAnatomy   = ::RDF::Vocabulary.new('http://www.openbel.org/bel/annotation/mesh-anatomy/')
-        MeSHDisease   = ::RDF::Vocabulary.new('http://www.openbel.org/bel/annotation/mesh-diseases/')
-        Species       = ::RDF::Vocabulary.new('http://www.openbel.org/bel/annotation/species-taxonomy-id/')
+        Anatomy       = 'http://www.openbel.org/bel/annotation/anatomy/'
+        Cell          = 'http://www.openbel.org/bel/annotation/cell/'
+        CellLine      = 'http://www.openbel.org/bel/annotation/cell-line/'
+        CellStructure = 'http://www.openbel.org/bel/annotation/cell-structure/'
+        Disease       = 'http://www.openbel.org/bel/annotation/disease/'
+        MeSHAnatomy   = 'http://www.openbel.org/bel/annotation/mesh-anatomy/'
+        MeSHDisease   = 'http://www.openbel.org/bel/annotation/mesh-diseases/'
+        Species       = 'http://www.openbel.org/bel/annotation/species-taxonomy-id/'
 
         # maps outer function to bel/vocabulary class
         FUNCTION_TYPE = {

data/lib/bel/translator/plugins/rdf/monkey_patch.rb

@@ -1,3 +1,5 @@
+require_relative 'uuid'
+
 module BEL::Translator::Plugins
 
   module Rdf
@@ -155,8 +157,8 @@ module BEL::Translator::Plugins
         @arguments.find_all{ |x|
           x.is_a? ::BEL::Model::Parameter and x.ns != nil
         }.each do |param|
-          concept_uri = param.ns.to_rdf_vocabulary[param.value.to_s]
-          statements << [uri, BEL::RDF::BELV.hasConcept, BEL::RDF::RDF::URI(Addressable::URI.encode(concept_uri))]
+          concept_uri = param.ns.to_uri + param.value.to_s
+          statements << [uri, BEL::RDF::BELV.hasConcept, BEL::RDF::RDF::URI(URI.encode(concept_uri))]
         end
 
         # BEL::RDF::BELV.hasChild]
@@ -254,10 +256,10 @@ module BEL::Translator::Plugins
         statements << [uri, ::RDF::RDFS.label, to_s.force_encoding('UTF-8')]
 
         # evidence
-        evidence_bnode = BEL::RDF::RDF::Node.uuid
-        statements << [evidence_bnode, BEL::RDF::RDF.type, BEL::RDF::BELV.Evidence]
-        statements << [uri, BEL::RDF::BELV.hasEvidence, evidence_bnode]
-        statements << [evidence_bnode, BEL::RDF::BELV.hasStatement, uri]
+        evidence    = BEL::RDF::BELE[Rdf.generate_uuid]
+        statements << [evidence, BEL::RDF::RDF.type, BEL::RDF::BELV.Evidence]
+        statements << [uri, BEL::RDF::BELV.hasEvidence, evidence]
+        statements << [evidence, BEL::RDF::BELV.hasStatement, uri]
 
         # citation
         citation = @annotations.delete('Citation')
@@ -266,9 +268,9 @@ module BEL::Translator::Plugins
           if citation and value[0] == 'PubMed'
             pid = value[2]
             statements << [
-              evidence_bnode,
+              evidence,
               BEL::RDF::BELV.hasCitation,
-              BEL::RDF::RDF::URI(BEL::RDF::PUBMED[pid])
+              BEL::RDF::PUBMED[pid]
             ]
           end
         end
@@ -277,7 +279,7 @@ module BEL::Translator::Plugins
         evidence_text = @annotations.delete('Evidence')
         if evidence_text
           value = evidence_text.value.gsub('"', '').force_encoding('UTF-8')
-          statements << [evidence_bnode, BEL::RDF::BELV.hasEvidenceText, value]
+          statements << [evidence, BEL::RDF::BELV.hasEvidenceText, value]
         end
 
         # annotations
@@ -287,8 +289,8 @@ module BEL::Translator::Plugins
           if BEL::RDF::const_defined? name
             annotation_scheme = BEL::RDF::const_get name
             [anno.value].flatten.map{|x| x.gsub('"', '')}.each do |val|
-              value_uri = BEL::RDF::RDF::URI(Addressable::URI.encode(annotation_scheme[val.to_s]))
-              statements << [evidence_bnode, BEL::RDF::BELV.hasAnnotation, value_uri]
+              value_uri = BEL::RDF::RDF::URI(URI.encode(annotation_scheme + val.to_s))
+              statements << [evidence, BEL::RDF::BELV.hasAnnotation, value_uri]
             end
           end
         end

data/lib/bel/translator/plugins/rdf/translator.rb

@@ -1,13 +1,6 @@
-# Load RDF library dependencies
-begin
-  require 'rdf'
-  require 'addressable/uri'
-  require 'uuid'
-rescue LoadError => e
-  # Raise LoadError if the requirements were not met.
-  raise
-end
+require 'rdf'
 
+require_relative 'uuid'
 require_relative 'bel_schema'
 require_relative 'monkey_patch'
 require_relative 'reader'
@@ -26,8 +19,8 @@ module BEL::Translator::Plugins
       end
 
       def write(objects, writer = StringIO.new, options = {})
-        format = options[:format] || :ntriples
-        rdf_writer = Writer::RDFYielder.new(writer, format)
+        # format = options[:format] || :ntriples
+        rdf_writer = Writer::RDFYielder.new(writer, :nquads)
 
         objects.each do |evidence|
           rdf_writer << evidence

data/lib/bel/translator/plugins/rdf/uuid.rb

@@ -0,0 +1,21 @@
+module BEL::Translator::Plugins
+
+  module Rdf
+
+    unless self.methods.include?(:generate_uuid)
+
+      # Dynamically defines an efficient UUID method for the current ruby.
+      if RUBY_ENGINE =~ /^jruby/i
+        java_import 'java.util.UUID'
+        define_singleton_method(:generate_uuid) do
+          Java::JavaUtil::UUID.random_uuid.to_s
+        end
+      else
+        require 'uuid'
+        define_singleton_method(:generate_uuid) do
+          UUID.generate
+        end
+      end
+    end
+  end
+end

data/lib/bel/translator/plugins/rdf/writer.rb

@@ -1,3 +1,5 @@
+require_relative 'uuid'
+
 module BEL::Translator::Plugins
 
   module Rdf::Writer
@@ -5,15 +7,18 @@ module BEL::Translator::Plugins
     class RDFYielder
       attr_reader :writer
 
+      Rdf = ::BEL::Translator::Plugins::Rdf
+
       def initialize(io, format)
         rdf_writer = find_writer(format)
         @writer = rdf_writer.new(io, { :stream => true })
       end
 
       def <<(evidence)
+        graph = RDF::URI("http://www.openbel.org/evidence-graphs/#{Rdf.generate_uuid}")
         triples = evidence.bel_statement.to_rdf[1]
         triples.each do |triple|
-          @writer.write_statement(::RDF::Statement(*triple))
+          @writer.write_statement(::RDF::Statement(*triple, :graph_name => graph))
         end
       end
 
@@ -26,18 +31,18 @@ module BEL::Translator::Plugins
       def find_writer(format)
         case format.to_s.to_sym
         when :nquads
-          BEL::RDF::RDF::NQuads::Writer
+          RDF::NQuads::Writer
         when :turtle
           begin
             require 'rdf/turtle'
-            BEL::RDF::RDF::Turtle::Writer
+            RDF::Turtle::Writer
           rescue LoadError
             $stderr.puts """Turtle format not supported.
     Install the 'rdf-turtle' gem."""
             raise
           end
         when :ntriples
-          Rdf::BEL::RDF::RDF::NTriples::Writer
+          RDF::NTriples::Writer
         end
       end
     end

data/lib/bel/translator/plugins/xbel/translator.rb

@@ -14,10 +14,20 @@ module BEL::Translator::Plugins
       end
 
       def write(objects, writer = StringIO.new, options = {})
-        XBELYielder.new(objects).each { |xml_data|
-          writer << xml_data
-          writer.flush
-        }
+        if block_given?
+          XBELYielder.new(objects).each { |xml_data|
+            yield xml_data
+          }
+        else
+          if writer
+            XBELYielder.new(objects).each { |xml_data|
+              writer << xml_data
+              writer.flush
+            }
+          else
+            XBELYielder.new(objects)
+          end
+        end
       end
     end
   end

data/lib/bel/version.rb

@@ -1,3 +1,3 @@
 module BEL
-  VERSION = '0.4.0.beta.7'
+  VERSION = '0.4.0.beta.8'
 end

metadata

@@ -1,34 +1,34 @@
 --- !ruby/object:Gem::Specification
 name: bel
 version: !ruby/object:Gem::Version
-  version: 0.4.0.beta.7
+  version: 0.4.0.beta.8
 platform: ruby
 authors:
 - Anthony Bargnesi
 - Natalie Catlett
 - Nick Bargnesi
 - William Hayes
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2015-12-03 00:00:00.000000000 Z
+date: 2015-12-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: ffi
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.9.8
-  type: :runtime
+  name: ffi
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.9.8
-description: " The BEL gem allows the reading, writing, and processing of BEL (Biological
-  Expression Language) with a natural DSL. "
+description: " The BEL gem allows the reading, writing, and processing of BEL (Biological\
+  \ Expression Language) with a natural DSL. "
 email:
 - abargnesi@selventa.com
 - ncatlett@selventa.com
@@ -152,6 +152,7 @@ files:
 - lib/bel/translator/plugins/rdf/monkey_patch.rb
 - lib/bel/translator/plugins/rdf/reader.rb
 - lib/bel/translator/plugins/rdf/translator.rb
+- lib/bel/translator/plugins/rdf/uuid.rb
 - lib/bel/translator/plugins/rdf/writer.rb
 - lib/bel/translator/plugins/xbel.rb
 - lib/bel/translator/plugins/xbel/evidence_handler.rb
@@ -166,7 +167,7 @@ homepage: https://github.com/OpenBEL/bel.rb
 licenses:
 - Apache-2.0
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options:
 - "--title"
 - BEL Ruby Documentation
@@ -200,10 +201,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: 1.3.1
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.4.5.1
-signing_key: 
+rubyforge_project:
+rubygems_version: 2.4.8
+signing_key:
 specification_version: 4
 summary: Process BEL with ruby.
 test_files: []
-has_rdoc: 
+has_rdoc: