tao_rdfizer 0.9.1

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 5e3d5c4f2fea0db166fcd917ed89667233b10cd3
+  data.tar.gz: 0216a19ec23514d036319e1f9125694d50dfb0e9
+SHA512:
+  metadata.gz: 028c6d291dfd986350c641f5265b014231876fa12d7b828df2b468a8fd1b995798ab2fedc2a493482c27aea420293bd8a8c47aa0521cdbd871f539d0483341a0
+  data.tar.gz: 3bd1f003d591cb8c849db4751ac168176020b395bdd3e4a3712faf83e204020ab1762e74391bfa1c9f0ed2ae6b590a202284ee972d47c52bf133a7a9ff645b0a

data/bin/tao_rdfizer

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+#!/usr/bin/env ruby
+require 'tao_rdfizer'
+require 'json'
+
+begin
+	annotations = JSON.parse File.read(ARGV[0]), :symbolize_names => true
+	annotations = [annotations] unless annotations.class == Array
+	# mode = :annotations
+	mode = :spans
+	rdfizer = TAO::RDFizer.new(mode)
+	puts rdfizer.rdfize(annotations)
+rescue ArgumentError, IOError => e
+	puts e.message
+end

data/lib/tao_rdfizer.rb

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+require 'tao_rdfizer/tao_rdfizer'

data/lib/tao_rdfizer/tao_rdfizer.rb

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+#!/usr/bin/env ruby
+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
+		template_filename = unless mode.nil?
+			if mode == :annotations
+				'view/tao_annotations_ttl.erb'
+			elsif mode == :spans
+				'view/tao_spans_ttl.erb'
+			else
+				'view/tao_ttl.erb'
+			end
+		else
+			'view/tao_ttl.erb'
+		end
+		@tao_ttl_erb = ERB.new(File.read(template_filename), nil, '-')
+		@prefix_ttl_erb = ERB.new(File.read("view/prefixes_ttl.erb"), nil, '-')
+  end
+
+	def rdfize(annotations_col)
+		# namespaces
+		namespaces = {}
+		anns = annotations_col.first
+		anns[:namespaces].each {|n| namespaces[n[:prefix]] = n[:uri]} unless anns[:namespaces].nil?
+		raise ArgumentError, "'prj' is a reserved prefix." if namespaces.has_key?('prj')
+
+		unless @mode ==:spans
+			project_uri = 'http://pubannotation.org/projects/' + anns[:project] unless @mode ==:spans
+			namespaces['prj'] = project_uri + '/' 
+		end
+
+		denotations = []
+		relations = []
+		spans = []
+
+		annotations_col.each do |annotations|
+			text = annotations[:text]
+			text_uri = annotations[:target]
+			text_id = begin
+				sourcedb, sourceid, divid = get_target_info(text_uri)
+				divid.nil? ? "#{sourcedb}-#{sourceid}" : "#{sourcedb}-#{sourceid}-#{divid}"
+			end
+
+			# denotations and relations
+			_denotations = annotations[:denotations]
+			_relations = annotations[:relations]
+			_denotations = [] if _denotations.nil?
+			_relations = [] if _relations.nil?
+			if @mode == :spans && annotations.has_key?(:tracks)
+				annotations[:tracks].each do |track|
+					_denotations += track[:denotations]
+					_relations += track[:relations]
+				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] = "prj:#{text_id}-#{d[:id]}"
+				d[:cls_uri] = find_uri(d[:obj], namespaces)
+			end
+
+			# relations preprocessing
+			_relations.each do |r|
+				r[:subj_uri] = "prj:#{text_id}-#{r[:subj]}"
+				r[:obj_uri] = "prj:#{text_id}-#{r[:obj]}"
+				r[:pred_uri] = find_uri(r[:pred], namespaces)
+			end
+
+			unless @mode == :annotations
+				# collect spans
+				_spans = _denotations.map{|d| d[:span]}
+				position = 0
+				annotations[:text].scan(/[^\W]*\W/).each do |tok|
+					_spans << {:begin => position, :end => position + tok.index(/\W/)}
+					position += tok.length
+				end
+				_spans.uniq!
+
+				# add_infomation
+				_spans.each do |s|
+					s[:span_uri] = "<#{text_uri}/spans/#{s[:begin]}-#{s[:end]}>"
+					s[:source_uri] = text_uri
+					s[:text] = text[s[:begin] ... s[:end]]
+				end
+
+				# index
+				spanh = _spans.inject({}){|r, s| r[s[:span_uri]] = s; r}
+
+				# add denotation information
+				_denotations.each do |d|
+					span_uri = d[:span_uri]
+					if spanh[span_uri][:denotations].nil?
+						spanh[span_uri][:denotations] = [d]
+					else
+						spanh[span_uri][:denotations] << d
+					end
+				end
+
+				_spans.sort!{|a, b| (a[:begin] <=> b[:begin]).nonzero? || b[:end] <=> a[:end]}
+
+				## begin indexing
+				len = text.length
+				num = _spans.length
+
+				# initilaize the index
+				(0 ... num).each do |i|
+					_spans[i][:followings] = []
+					_spans[i][:precedings] = []
+					_spans[i][:children] = []
+				end
+
+				(0 ... num).each do |i|
+					# index the embedded spans
+					j = i + 1
+					while j < num && _spans[j][:begin] < _spans[i][:end]
+						unless include_parent?(_spans[i][:children], _spans[j])
+							_spans[i][:children] << _spans[j]
+							_spans[j][:parent] = _spans[i]
+						end
+						j += 1
+					end
+
+					# find the following position
+					fp = _spans[i][:end]
+					fp += 1 while fp < len && text[fp].match(/\s/)
+					next if fp == len
+
+					# index the following spans
+					while j < num && _spans[j][:begin] == fp
+						_spans[i][:followings] << _spans[j]
+						_spans[j][:precedings] << _spans[i]
+						j += 1
+					end 
+				end
+			end
+
+			denotations += _denotations
+			relations += _relations
+			spans += _spans unless @mode == :annotations
+		end
+
+		ttl = @prefix_ttl_erb.result(binding) + @tao_ttl_erb.result(binding)
+	end
+
+	def include_parent?(spans, span)
+		# spans.each{|s| return true if (s[:begin] <= span[:begin] && s[:end] > span[:end]) || (s[:begin] < span[:begin] && s[:end] >= span[:end])}
+		spans.each{|s| return true if s[:begin] <= span[:begin] && s[:end] >= span[:end]}
+		return false
+	end
+
+	def get_target_info (text_uri)
+		sourcedb = (text_uri =~ %r|/sourcedb/([^/]+)|)? $1 : nil
+		sourceid = (text_uri =~ %r|/sourceid/([^/]+)|)? $1 : nil
+		divid    = (text_uri =~ %r|/divs/([^/]+)|)? $1 : nil
+
+		return sourcedb, sourceid, divid
+	end
+
+	def find_uri (label, namespaces)
+		delimiter_position = label.index(':')
+		if !delimiter_position.nil? && namespaces.keys.include?(label[0...delimiter_position])
+			label
+		elsif label =~ %r[^https?://]
+			"<#{label}>"
+		else
+			clabel = if label.match(/^\W+$/)
+				'SYM'
+			else
+				label.sub(/^\W+/, '').sub(/\W+$/, '')
+			end
+			namespaces.has_key?('_base') ? "<#{clabel}>" : "prj:#{clabel}"
+		end
+	end
+end

data/view/prefixes_ttl.erb

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+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix tao: <http://pubannotation.org/ontology/tao.owl#> .
+<%# namespaces -%>
+<% namespaces.each_key do |p| -%>
+<% if p == '_base' -%>
+@base <%= "<#{namespaces[p]}>" %> .
+<% else -%>
+@prefix <%= p %>: <%= "<#{namespaces[p]}>" %> .
+<% end -%>
+<% end -%>

data/view/tao_annotations_ttl.erb

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+<%# denotations -%>
+<% denotations.each do |d| -%>
+<%= d[:obj_uri] %> tao:denoted_by <%= d[:span_uri] %> ;
+	rdf:type <%= d[:cls_uri] %> .
+<% end -%>
+<%# relations -%>
+<% relations.each do |r| -%>
+<%= r[:subj_uri] %> <%= r[:pred_uri] %> <%= r[:obj_uri] %> .
+<% end -%>

data/view/tao_spans_ttl.erb

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+<%# spans -%>
+<% spans.each do |s| -%>
+<%= s[:span_uri] %> rdf:type tao:Text_span ;
+	tao:belongs_to <%= "<#{s[:source_uri]}>" %> ;
+	tao:begins_at <%= s[:begin] %> ;
+	tao:ends_at <%= s[:end] %> ;
+<% s[:precedings].each do |s| -%>
+	tao:follows <%= s[:span_uri] %> ;
+<% end -%>
+<% s[:children].each do |s| -%>
+	tao:contains <%= s[:span_uri] %> ;
+<% end -%>
+	tao:has_text "<%= s[:text] %>" .
+<% end -%>

metadata

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+--- !ruby/object:Gem::Specification
+name: tao_rdfizer
+version: !ruby/object:Gem::Version
+  version: 0.9.1
+platform: ruby
+authors:
+- Jin-Dong Kim
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2017-09-26 00:00:00.000000000 Z
+dependencies: []
+description: It uses TAO (text annotation ontology) for representation of annotations
+  to text.
+email: jindong.kim@gmail.com
+executables:
+- tao_rdfizer
+extensions: []
+extra_rdoc_files: []
+files:
+- bin/tao_rdfizer
+- lib/tao_rdfizer.rb
+- lib/tao_rdfizer/tao_rdfizer.rb
+- view/prefixes_ttl.erb
+- view/tao_annotations_ttl.erb
+- view/tao_spans_ttl.erb
+homepage: https://github.com/pubannotation/tao_rdfizer
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.8
+signing_key: 
+specification_version: 4
+summary: A RDF statement generator for annotations in the PubAnnotation JSON format.
+test_files: []