tao_rdfizer 0.9.11 → 0.10.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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data/lib/tao_rdfizer/tao_rdfizer.rb

@@ -19,7 +19,12 @@ class TAO::RDFizer
 		@prefix_ttl_erb = ERB.new(ERB_PREFIXES_TTL, nil, '-')
 	end
 
-	def rdfize(annotations_col)
+	def rdfize(annotations_col, with_prefix = true)
+		# check the format
+		annotations_col.each do |annotations|
+			raise "'target' is missing" unless annotations.has_key? :target
+		end
+
 		# namespaces
 		namespaces = {}
 
@@ -27,6 +32,7 @@ class TAO::RDFizer
 		anns[:namespaces].each {|n| namespaces[n[:prefix]] = n[:uri]} unless anns[:namespaces].nil?
 
 		unless @mode ==:spans
+			raise ArgumentError, "A project name has to be specified." unless anns.has_key?(:project)
 			prefix_for_this = anns[:project].downcase.gsub(/ /, '_')
 			raise ArgumentError, "'#{prefix_for_this}' is a reserved prefix for this project." if namespaces.has_key?(prefix_for_this)
 			project_uri = 'http://pubannotation.org/projects/' + anns[:project]
@@ -34,6 +40,7 @@ class TAO::RDFizer
 		end
 
 		denotations = []
+		attributes = []
 		relations = []
 		spans = []
 
@@ -46,34 +53,57 @@ class TAO::RDFizer
 			end
 
 			# denotations and relations
-			_denotations = annotations[:denotations]
-			_relations = annotations[:relations]
-			_denotations = [] if _denotations.nil?
-			_relations = [] if _relations.nil?
+			_denotations = annotations[:denotations] || []
+			_attributes = annotations[:attributes] || []
+			_relations = annotations[:relations] || []
 			if @mode == :spans && annotations.has_key?(:tracks)
 				annotations[:tracks].each do |track|
 					_denotations += track[:denotations]
+					_attributes += track[:attributes]
 					_relations += track[:relations]
 				end
 			end
 
 			begin
-				# denotations preprocessing
-				_denotations.each do |d|
-					span_uri = "<#{text_uri}/spans/#{d[:span][:begin]}-#{d[:span][:end]}>"
-					d[:span_uri] = span_uri
-					d[:obj_uri] = "#{prefix_for_this}:#{text_id}-#{d[:id]}"
-					d[:cls_uri] = find_uri(d[:obj], namespaces, prefix_for_this)
-				end
+				if @mode == :annotations
+					# index attributes
+					attributesh = _attributes.inject({}) do |h, a|
+						if a[:pred].end_with?('_id')
+							subj = a[:subj]
+							h[subj] = [] unless h.has_key? subj
+							h[subj] << a[:obj]
+						end
+						h
+					end
+
+					# denotations preprocessing
+					_denotations.each do |d|
+						span_uri = "<#{text_uri}/spans/#{d[:span][:begin]}-#{d[:span][:end]}>"
+						d[:span_uri] = span_uri
+						d[:obj_uri] = "#{prefix_for_this}:#{text_id}-#{d[:id]}"
+						class_uris = (attributesh[d[:id]] || []).push(d[:obj])
+						d[:class_uris] = class_uris.map{|uri| find_uri(uri, namespaces, prefix_for_this)}
+					rescue ArgumentError => e
+						raise ArgumentError, "[#{sourcedb}-#{sourceid}-#{d[:id]}] " + e.message
+					end
 
-				# relations preprocessing
-				_relations.each do |r|
-					r[:subj_uri] = "#{prefix_for_this}:#{text_id}-#{r[:subj]}"
-					r[:obj_uri] = "#{prefix_for_this}:#{text_id}-#{r[:obj]}"
-					r[:pred_uri] = find_uri(r[:pred], namespaces, prefix_for_this)
+					# relations preprocessing
+					_relations.each do |r|
+						r[:subj_uri] = "#{prefix_for_this}:#{text_id}-#{r[:subj]}"
+						r[:obj_uri] = "#{prefix_for_this}:#{text_id}-#{r[:obj]}"
+						r[:pred_uri] = find_uri(r[:pred], namespaces, prefix_for_this)
+					rescue ArgumentError => e
+						raise ArgumentError, "[#{sourcedb}-#{sourceid}-#{r[:id]}] " + e.message
+					end
+				else
+					# denotations preprocessing
+					_denotations.each do |d|
+						span_uri = "<#{text_uri}/spans/#{d[:span][:begin]}-#{d[:span][:end]}>"
+						d[:span_uri] = span_uri
+					rescue ArgumentError => e
+						raise ArgumentError, "[#{sourcedb}-#{sourceid}-#{d[:id]}] " + e.message
+					end
 				end
-			rescue ArgumentError => e
-				raise ArgumentError, "[#{sourcedb}-#{sourceid}] " + e
 			end
 
 			unless @mode == :annotations
@@ -88,7 +118,7 @@ class TAO::RDFizer
 					s[:text] = text[s[:begin] ... s[:end]]
 				end
 
-				# index
+				# index spans
 				spanh = _spans.inject({}){|r, s| r[s[:span_uri]] = s; r}
 
 				# add denotation information
@@ -142,7 +172,9 @@ class TAO::RDFizer
 			spans += _spans unless @mode == :annotations
 		end
 
-		ttl = @prefix_ttl_erb.result(binding) + @tao_ttl_erb.result(binding)
+		ttl  = ''
+		ttl += @prefix_ttl_erb.result(binding) if with_prefix
+		ttl += @tao_ttl_erb.result(binding)
 	end
 
 	private
@@ -172,7 +204,7 @@ class TAO::RDFizer
 			clabel = if label.match(/^\W+$/)
 				'SYM'
 			else
-				label.sub(/^\W+/, '').sub(/\W+$/, '').gsub(/ +/, '_')
+				label.sub(/^\W+/, '').sub(/[^a-zA-Z0-9_)]+$/, '').gsub(/ +/, '_')
 			end
 			namespaces.has_key?('_base') ? "<#{clabel}>" : "#{prefix_for_this}:#{clabel.gsub('(', '\(').gsub(')', '\)')}"
 		end
@@ -181,7 +213,7 @@ class TAO::RDFizer
 	ERB_ANNOTATIONS_TTL = <<~HEREDOC
 		<% denotations.each do |d| -%>
 		<%= d[:obj_uri] %> tao:denoted_by <%= d[:span_uri] %> ;
-			rdf:type <%= d[:cls_uri] %> .
+		<%= d[:class_uris].map{|c| "\trdf:type " + c}.join(" ;\n") + " ." %>
 		<% end -%>
 		<%# relations -%>
 		<% relations.each do |r| -%>

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: tao_rdfizer
 version: !ruby/object:Gem::Version
-  version: 0.9.11
+  version: 0.10.2
 platform: ruby
 authors:
 - Jin-Dong Kim
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-07-17 00:00:00.000000000 Z
+date: 2021-05-15 00:00:00.000000000 Z
 dependencies: []
 description: It uses TAO (text annotation ontology) for representation of annotations
   to text.
@@ -40,8 +40,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.9
+rubygems_version: 3.0.9
 signing_key: 
 specification_version: 4
 summary: A RDF statement generator for annotations in the PubAnnotation JSON format.