tao_rdfizer 0.9.9 → 0.9.10

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: 0254770e5fbff5ef2071765b19a324af5ad1a3cd
-  data.tar.gz: 639d52929cfe8123766b540cc4f2a92ccf616f36
+SHA256:
+  metadata.gz: 839f30915cc8896477342a8cfdb87d8d4f23d8ffbbc133b9b0b087939050befe
+  data.tar.gz: bfa3efcbae03859f8a778afbf81f37daffec3467b537671cf5282c0905ed1d5f
 SHA512:
-  metadata.gz: c9feeec71d327a4781036d16d5d2773f1fd77678ef23ae2f01b627bdb41f2ab04bf401c57204fdd96c27d237c65c8a9ec9da3060fd2206c4d43d7ca1cad4da50
-  data.tar.gz: 67cd10929f38deb58b0e988547f7bde80fb8dd88e3c771fc034274ef374233bfbe13a5d72c8fd26127a1e8cf5c18c34d158493e11c16d718310b5ca40f37651b
+  metadata.gz: 2a9744b372d7a9774774262a17771c43533b44c3a95ad19cd7e60add25d6135afb3c85ecad8d6933ffdff61b39632be0386ecf9d85340f1f0bea1efc9176e8d5
+  data.tar.gz: 77f1d13bf567b6e5ed28668034da90e0810520358e2aa2d27dc747ce78f090316b1519be8f1b2a30050fce5a20408b46a932887c955979a217304c4a53cd709e

data/lib/tao_rdfizer/tao_rdfizer.rb

@@ -4,11 +4,11 @@ require 'erb'
 module TAO; end unless defined? TAO
 
 class TAO::RDFizer
-  # if mode == :spans then produces span descriptions
-  # if mode == :annotations then produces annotation descriptions
-  # if mode == nil then produces both
-  def initialize(mode = nil)
-  	@mode = mode
+	# if mode == :spans then produces span descriptions
+	# if mode == :annotations then produces annotation descriptions
+	# if mode == nil then produces both
+	def initialize(mode = nil)
+		@mode = mode
 		template = if !mode.nil? && mode == :spans
 			ERB_SPANS_TTL
 		else
@@ -17,7 +17,7 @@ class TAO::RDFizer
 
 		@tao_ttl_erb = ERB.new(template, nil, '-')
 		@prefix_ttl_erb = ERB.new(ERB_PREFIXES_TTL, nil, '-')
-  end
+	end
 
 	def rdfize(annotations_col)
 		# namespaces
@@ -57,19 +57,23 @@ class TAO::RDFizer
 				end
 			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]}"
-				d[:cls_uri] = find_uri(d[:obj], namespaces, prefix_for_this)
-			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
 
-			# 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)
+				end
+			rescue ArgumentError => e
+				raise ArgumentError, "[#{sourcedb}-#{sourceid}] " + e
 			end
 
 			unless @mode == :annotations
@@ -158,6 +162,7 @@ class TAO::RDFizer
 	end
 
 	def find_uri (label, namespaces, prefix_for_this)
+		raise ArgumentError, "A label including a whitespace character found: #{label}." if label.match(/\s/)
 		delimiter_position = label.index(':')
 		if !delimiter_position.nil? && namespaces.keys.include?(label[0...delimiter_position])
 			label
@@ -193,7 +198,7 @@ class TAO::RDFizer
 		<% s[:children].each do |s| -%>
 			tao:contains <%= s[:span_uri] %> ;
 		<% end -%>
-			tao:has_text <%= s[:text].dump %> ;
+			tao:has_text <%= s[:text].inspect %> ;
 			tao:belongs_to <<%= s[:source_uri] %>> ;
 			tao:begins_at <%= s[:begin] %> ;
 			tao:ends_at <%= s[:end] %> .

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: tao_rdfizer
 version: !ruby/object:Gem::Version
-  version: 0.9.9
+  version: 0.9.10
 platform: ruby
 authors:
 - Jin-Dong Kim
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-01-24 00:00:00.000000000 Z
+date: 2019-07-11 00:00:00.000000000 Z
 dependencies: []
 description: It uses TAO (text annotation ontology) for representation of annotations
   to text.
@@ -41,7 +41,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.11
+rubygems_version: 2.7.9
 signing_key: 
 specification_version: 4
 summary: A RDF statement generator for annotations in the PubAnnotation JSON format.