bel 0.4.0.beta.2 → 0.4.0.beta.3

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 4c82f900aa4d19f2c484ea7c16fed41b4e4ff30e
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data/lib/bel/resource/namespace_value.rb

@@ -1,4 +1,4 @@
-require_relative '../resource'
+require_relative 'namespaces'
 
 module BEL
   module Resource
@@ -25,20 +25,54 @@ module BEL
                             each.map(&:predicate).uniq
       end
 
-      def equivalents
-        return to_enum(:equivalents) unless block_given?
-				@rdf_repository.
-					query(@eq_query) { |solution|
-						yield NamespaceValue.new(@rdf_repository, solution.object)
-					}
+      def equivalents(target_namespaces = :all)
+        return to_enum(:equivalents, target_namespaces) unless block_given?
+        if target_namespaces == :all
+          @rdf_repository.
+            query(@eq_query) { |solution|
+              yield NamespaceValue.new(@rdf_repository, solution.object)
+            }
+        else
+          target_namespaces = Namespaces.new(@rdf_repository).
+            find([target_namespaces].flatten).to_a
+          target_namespaces.compact!
+          target_namespaces.map! { |ns| ns.uri }
+
+          @rdf_repository.
+            query(@eq_query).map { |solution|
+              NamespaceValue.new(@rdf_repository, solution.object)
+            }.select { |value|
+              scheme_uri = value.inScheme
+              target_namespaces.include?(scheme_uri)
+            }.each { |value|
+              yield value
+            }
+        end
 			end
 
-      def orthologs
-        return to_enum(:orthologs) unless block_given?
-				@rdf_repository.
-					query(@ortho_query) { |solution|
-						yield NamespaceValue.new(@rdf_repository, solution.object)
-					}
+      def orthologs(target_namespaces = :all)
+        return to_enum(:orthologs, target_namespaces) unless block_given?
+        if target_namespaces == :all
+          @rdf_repository.
+            query(@ortho_query) { |solution|
+              yield NamespaceValue.new(@rdf_repository, solution.object)
+            }
+        else
+          target_namespaces = Namespaces.new(@rdf_repository).
+            find([target_namespaces].flatten).to_a
+          target_namespaces.compact!
+          target_namespaces.map! { |ns| ns.uri }
+
+          @rdf_repository.
+            query(@ortho_query).map { |solution|
+              NamespaceValue.new(@rdf_repository, solution.object)
+            }.select { |value|
+              scheme_uri = value.inScheme
+              target_namespaces.include?(scheme_uri)
+            }.each { |value|
+              yield value
+            }
+        end
 			end
 
       def hash

data/lib/bel/resource/namespaces.rb

@@ -1,4 +1,3 @@
-require_relative '../resource'
 require_relative 'namespace'
 
 module BEL

data/lib/bel/version.rb

@@ -1,3 +1,3 @@
 module BEL
-  VERSION = '0.4.0.beta.2'
+  VERSION = '0.4.0.beta.3'
 end

metadata

@@ -1,34 +1,34 @@
 --- !ruby/object:Gem::Specification
 name: bel
 version: !ruby/object:Gem::Version
-  version: 0.4.0.beta.2
+  version: 0.4.0.beta.3
 platform: ruby
 authors:
 - Anthony Bargnesi
 - Natalie Catlett
 - Nick Bargnesi
 - William Hayes
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
 date: 2015-12-02 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
@@ -163,7 +163,7 @@ homepage: https://github.com/OpenBEL/bel.rb
 licenses:
 - Apache-2.0
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options:
 - "--title"
 - BEL Ruby Documentation
@@ -197,10 +197,9 @@ 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: