Class: TAO::RDFizer

Inherits:
Object
  • Object
show all
Defined in:
lib/tao_rdfizer/tao_rdfizer.rb

Instance Method Summary collapse

Constructor Details

#initialize(mode = nil) ⇒ RDFizer

if mode == :spans then produces span descriptions if mode == :annotations then produces annotation descriptions if mode == nil then produces both



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# File 'lib/tao_rdfizer/tao_rdfizer.rb', line 10

def initialize(mode = nil)
	@mode = mode
	template = if !mode.nil? && mode == :spans
		ERB_SPANS_TTL
	else
		ERB_ANNOTATIONS_TTL
	end

	@tao_ttl_erb = ERB.new(template, nil, '-')
	@prefix_ttl_erb = ERB.new(ERB_PREFIXES_TTL, nil, '-')
end

Instance Method Details

#rdfize(annotations_col, with_prefix = true) ⇒ Object 



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# File 'lib/tao_rdfizer/tao_rdfizer.rb', line 22

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 = {}

	anns = annotations_col.first
	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]
		namespaces[prefix_for_this] = project_uri + '/'
	end

	denotations = []
	attributes = []
	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] || []
		_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
			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)
				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
		end

		unless @mode == :annotations
			# collect spans
			_spans = _denotations.map{|d| d[:span]}
			_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 spans
			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][:children] = []
			end

			(0 ... num).each do |i|
				# find the first following span
				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]
					end
					j += 1
				end

				# find adjacent positions
				fp = _spans[i][:end]
				fp += 1 while fp < len && text[fp].match(/\s/)
				next if fp == len

				# index adjacent spans
				while j < num && _spans[j][:begin] == fp
					_spans[i][:followings] << _spans[j]
					j += 1
				end
			end
		end

		denotations += _denotations
		relations += _relations
		spans += _spans unless @mode == :annotations
	end

	ttl  = ''
	ttl += @prefix_ttl_erb.result(binding) if with_prefix
	ttl += @tao_ttl_erb.result(binding)
end