Merge branch 'next'; Fixes #90 and #91

OpenBEL · Dec 21, 2015 · 9d9448f · 9d9448f
2 parents 3f77265 + 208d7f0
commit 9d9448f
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Showing 6 changed files with 38 additions and 30 deletions.
diff --git a/bin/bel_upgrade.rb b/bin/bel_upgrade.rb
@@ -106,7 +106,7 @@ def initialize(content, change_log)
     BEL::Script.parse(content) do |obj|
       # redefine namespace based on change log's `redefine` blocik
       # use 'namespaces' block, if available
-      if obj.is_a? NamespaceDefinition
+      if obj.is_a? BEL::Namespace::NamespaceDefinition
         if @change_log.has_key? 'redefine'
           redefine = @change_log['redefine']['namespaces']
           if not redefine
@@ -116,7 +116,7 @@ def initialize(content, change_log)
             entry = redefine[obj.prefix.to_s]
             new_keyword = entry['new_keyword'].to_sym
             new_url = entry['new_url']
-            obj = NamespaceDefinition.new(new_keyword, new_url)
+            obj = BEL::Namespace::NamespaceDefinition.new(new_keyword, new_url)
           end
         end
 
@@ -128,21 +128,21 @@ def initialize(content, change_log)
       end
 
       # update annotation definitions
-      if obj.is_a? AnnotationDefinition and obj.type.eql? :url
+      if obj.is_a? BEL::Language::AnnotationDefinition and obj.type.eql? :url
         if @redefine_annotations
           old_url = obj.value
           if @annotation_url_map.has_key? old_url.to_s
             kw = obj.prefix
             new_url = @annotation_url_map[old_url]['new_url']
             prefix = @annotation_url_map[old_url]['prefix']
-            obj = AnnotationDefinition.new(:url, kw, new_url)
+            obj = BEL::Language::AnnotationDefinition.new(:url, kw, new_url)
             @annotation_keyword_map[kw] = prefix # map bel doc annotation kw to set of changelog prefixes
           end
         end
       end
 
       # evidence always needs quoting; backwards-compatibility
-      if obj.is_a? Annotation
+      if obj.is_a? BEL::Language::Annotation
         if obj.name == 'Evidence'
           ev = obj.to_s
           ev.gsub!(EvidenceMatcher, 'SET Evidence = "\1"')
@@ -207,7 +207,7 @@ def initialize(content, change_log)
           if redefinition
             new_prefix = redefinition['new_keyword']
             new_url = redefinition['new_url']
-            obj.ns = NamespaceDefinition.new(new_prefix, new_url)
+            obj.ns = BEL::Namespace::NamespaceDefinition.new(new_prefix, new_url)
 
             # ...and replace value using new namespace prefix
             replacements = @change_log[new_prefix]

diff --git a/gem.deps.rb b/gem.deps.rb
@@ -25,6 +25,7 @@
 gem 'rdf',           '~> 1.1'
 gem 'rdf-turtle',    '~> 1.1'
 gem 'uuid',          '~> 2.3'
+gem 'rdf-mongo',     '1.99.0'
 
 # Platform-specific example.
 # platform(:jruby) {

diff --git a/lib/bel/namespace.rb b/lib/bel/namespace.rb
@@ -42,11 +42,11 @@ module Namespace
       ],
       GOBP: [
         LATEST_PREFIX + 'namespace/go-biological-process.belns',
-        'http://www.openbel.org/bel/namespace/go-biological-processes'
+        'http://www.openbel.org/bel/namespace/go-biological-process'
       ],
       GOBPID: [
         LATEST_PREFIX + 'namespace/go-biological-process-ids.belns',
-        'http://www.openbel.org/bel/namespace/go'
+        'http://www.openbel.org/bel/namespace/go-biological-process'
       ],
       GOCC: [
         LATEST_PREFIX + 'namespace/go-cellular-component.belns',
@@ -68,6 +68,14 @@ module Namespace
         LATEST_PREFIX + 'namespace/mesh-cellular-structures-ids.belns',
         'http://www.openbel.org/bel/namespace/mesh-cellular-structures'
       ],
+      MECHC: [
+        LATEST_PREFIX + 'namespace/mesh-chemicals.belns',
+        'http://www.openbel.org/bel/namespace/mesh-chemicals'
+      ],
+      MECHCID: [
+        LATEST_PREFIX + 'namespace/mesh-chemicals-ids.belns',
+        'http://www.openbel.org/bel/namespace/mesh-chemicals'
+      ],
       MESHD: [
         LATEST_PREFIX + 'namespace/mesh-diseases.belns',
         'http://www.openbel.org/bel/namespace/mesh-diseases',
@@ -114,7 +122,7 @@ module Namespace
       ],
       SPID: [
         LATEST_PREFIX + 'namespace/swissprot-ids.belns',
-        'http://www.openbel.org/bel/namespace/swissprot-ids'
+        'http://www.openbel.org/bel/namespace/swissprot'
       ]
     }
 

diff --git a/lib/bel/translator/plugins/rdf/monkey_patch.rb b/lib/bel/translator/plugins/rdf/monkey_patch.rb
@@ -154,7 +154,7 @@ def to_rdf(graph_name = nil)
         @arguments.find_all{ |x|
           x.is_a? ::BEL::Model::Parameter and x.ns != nil
         }.each do |param|
-          concept_uri = param.ns.to_uri + param.value.to_s
+          concept_uri = "#{param.ns.to_uri}/#{param.value}"
           statements << ::RDF::Statement.new(uri, BEL::RDF::BELV.hasConcept, BEL::RDF::RDF::URI(URI.encode(concept_uri)), :graph_name => graph_name)
         end
 

diff --git a/spec/integration/belrdf_spec.rb b/spec/integration/belrdf_spec.rb
@@ -13,7 +13,7 @@
     BEL.translate(bel_file, :bel, :rdf, writer)
 
     rdf_triples = writer.string
-    expect(rdf_triples.each_line.count).to eql(301)
+    expect(rdf_triples.each_line.count).to eql(372)
   end
 end
 

diff --git a/spec/unit/rdf_spec.rb b/spec/unit/rdf_spec.rb
@@ -11,6 +11,8 @@
 include BEL::Model
 include BEL::Namespace
 
+BELV = ::BEL::Translator::Plugins::Rdf::BEL::RDF::BELV
+
 describe 'RDF functionality of BEL language objects' do
 
   before(:all) do
@@ -45,19 +47,19 @@
       expect(triples.size).to eq(4)
       expect(
         triples.count { |x|
-          x.object.uri? and x.object.value == ::BEL::Translator::Plugins::Rdf::BEL::RDF::BELV.AbundanceConcept
+          x.object.uri? and x.object.value == BELV.AbundanceConcept
         }).to eq(1)
       expect(
         triples.count { |x|
-          x.object.uri? and x.object.value == ::BEL::Translator::Plugins::Rdf::BEL::RDF::BELV.GeneConcept
+          x.object.uri? and x.object.value == BELV.GeneConcept
         }).to eq(1)
       expect(
         triples.count { |x|
-          x.object.uri? and x.object.value == ::BEL::Translator::Plugins::Rdf::BEL::RDF::BELV.RNAConcept
+          x.object.uri? and x.object.value == BELV.RNAConcept
         }).to eq(1)
       expect(
         triples.count { |x|
-          x.object.uri? and x.object.value == ::BEL::Translator::Plugins::Rdf::BEL::RDF::BELV.ProteinConcept
+          x.object.uri? and x.object.value == BELV.ProteinConcept
         }).to eq(1)
     end
 
@@ -76,27 +78,27 @@
       expect(term_uri).to eq(term.to_uri)
       expect(rdf_statements.size).to eq(4)
       expect(
-        rdf_statements.include? [term.to_uri, ::BEL::Translator::Plugins::Rdf::BEL::RDF::RDF.type, ::BEL::Translator::Plugins::Rdf::BEL::RDF::BELV.Term]
+        rdf_statements.include? [term.to_uri, RDF.type, BELV.Term]
       ).to be(true)
       expect(
-        rdf_statements.include? [term.to_uri, ::BEL::Translator::Plugins::Rdf::BEL::RDF::RDF.type, term.rdf_type]
+        rdf_statements.include? [term.to_uri, RDF.type, term.rdf_type]
       ).to be(true)
       expect(
-        rdf_statements.include? [term.to_uri, ::BEL::Translator::Plugins::Rdf::BEL::RDF::RDFS.label, term.to_s]
+        rdf_statements.include? [term.to_uri, RDF::RDFS.label, term.to_s]
       ).to be(true)
       expect(
-        rdf_statements.include? [term.to_uri, ::BEL::Translator::Plugins::Rdf::BEL::RDF::BELV.hasConcept, term.arguments[0].to_uri]
+        rdf_statements.include? [term.to_uri, BELV.hasConcept, term.arguments[0].to_uri]
       ).to be(true)
     end
 
     it "forces term labels as UTF-8" do
       (_, rdf_statements) = a(Parameter.new(CHEBI, '5α-androst-16-en-3-one')).to_rdf
       _, _, label_literal = rdf_statements.find { |stmt|
-        stmt[1] == ::BEL::Translator::Plugins::Rdf::BEL::RDF::RDFS.label
+        stmt[1] == RDF::RDFS.label
       }
 
-      expect(label_literal.encoding).to eql(Encoding::UTF_8)
-      expect(label_literal).to          eql(%Q{a(CHEBI:"5α-androst-16-en-3-one")})
+      expect(label_literal.value.encoding).to eql(Encoding::UTF_8)
+      expect(label_literal).to                eql(RDF::Literal.new(%Q{a(CHEBI:"5α-androst-16-en-3-one")}))
     end
   end
 
@@ -115,26 +117,23 @@
       (_, rdf_statements) = statement.to_rdf
 
       type_evidence_statements = rdf_statements.find_all { |stmt|
-        stmt[1] == ::BEL::Translator::Plugins::Rdf::BEL::RDF::RDF.type and stmt[2] == ::BEL::Translator::Plugins::Rdf::BEL::RDF::BELV.Evidence
+        stmt[1] == RDF.type and stmt[2] == BELV.Evidence
       }
       expect(type_evidence_statements.size).to eq(1)
 
       evidence_resource = type_evidence_statements.first[0]
-      expect(evidence_resource).to be_a(::BEL::Translator::Plugins::Rdf::BEL::RDF::RDF::Node)
-
-      evidence_resource_identifier = evidence_resource.to_s.gsub(/^_:/, '')
-      expect(UUID.validate(evidence_resource_identifier)).to be(true)
+      expect(evidence_resource).to be_a(RDF::URI)
     end
 
     it "forces statement labels as UTF-8" do
       (_, rdf_statements) =
         (a(Parameter.new(CHEBI, '5α-androst-16-en-3-one')).association a(Parameter.new(CHEBI, 'luteolin 7-O-β-D-glucosiduronate'))).to_rdf
       _, _, label_literal = rdf_statements.select { |stmt|
-        stmt[1] == ::BEL::Translator::Plugins::Rdf::BEL::RDF::RDFS.label
+        stmt[1] == RDF::RDFS.label
       }.last
 
-      expect(label_literal.encoding).to eql(Encoding::UTF_8)
-      expect(label_literal).to          eql(%Q{a(CHEBI:"5α-androst-16-en-3-one") association a(CHEBI:"luteolin 7-O-β-D-glucosiduronate")})
+      expect(label_literal.value.encoding).to eql(Encoding::UTF_8)
+      expect(label_literal).to                eql(RDF::Literal.new(%Q{a(CHEBI:"5α-androst-16-en-3-one") association a(CHEBI:"luteolin 7-O-β-D-glucosiduronate")}))
     end
 
     it "forces evidence text as UTF-8" do