biosample2ttl.rb v0.2

biosample2ttl.rb

#!/usr/bin/env ruby

require 'nokogiri'
require 'erb'
#require 'uri'
#require 'pp'

class BioSampleSet

	include Enumerable

	def initialize(xml)
		@xml =xml
	end

	def each
		@doc = []
		IO.foreach(@xml) do |line|
			next if line =~/\<\?xml|BioSampleSet/
			@doc.push('<?xml version="1.0" encoding="UTF-8"?>') if line =~/^\s*<BioSample/
			@doc.push(line.chomp)
			if line =~/\<\/BioSample\>/
				docs = @doc.join("\n").to_s
				yield BioSample.new(docs)
				@doc = []
			end
		end
	end

	def to_ttl
		self.each_with_index do |biosample,i|
			if i == 0
				puts biosample.to_ttl_prefix
			end
			puts biosample.to_ttl
		end
	end
end

class BioSample
	def initialize(xml)
		@biosample = Nokogiri::XML(xml).css("BioSample")
		raise NameError, "biosample element not found" unless @biosample

		doc = Nokogiri::XML(xml)
		biosample = doc.xpath("/BioSample")

		if @biosample.attribute("id").nil?
			@ddbj = true
		else
			@ddbj = false
		end
	end

	def id
		if @ddbj
			nil
		else
			@biosample.attribute("id").value
		end
		# @biosample.attribute("id").nil? ?
		#         '' : @biosample.attribute("id").value
	end

	def accession
		if @ddbj
			@biosample.at_css('Ids > Id[namespace="BioSample"]').inner_text
		else
			#@biosample.attribute("accession").value
			if @biosample.at_css('Ids > Id[db="BioSample"]').nil?
				nil
			else
				@biosample.at_css('Ids > Id[db="BioSample"]').inner_text
			end
		end
	end

	def access
		@biosample.attribute("access").value
	end

	def publication_date
		if  @biosample.attribute("publication_date").nil?
			''
		else
			@biosample.attribute("publication_date").value
		end
	end

	def last_update
		@biosample.attribute("last_update").value
	end

	def title
		if @ddbj 
			@biosample.css('Description > SampleName' ).inner_text
		else
			@biosample.css('Description > Title' ).inner_text
		end
	end

	def comment
		if @ddbj
			@biosample.css('Description > Title' ).inner_text
		else
                        #exception: SAMN00000186
                        if @biosample.at_css('Description > Comment > Paragraph' ).nil?
				''
			else
				@biosample.at_css('Description > Comment > Paragraph' ).inner_text
			end
		end
	end 

	def organism
		if @ddbj 
			@biosample.css('Organism > OrganismName').inner_text
		else
			@biosample.css('Description > Organism').attribute('taxonomy_name').value
		end
	end

	def taxid
		@biosample.css('Description > Organism').attribute('taxonomy_id').value
	end

	def model
		@biosample.css('Models > Model').inner_text
	end

	def owner
		@biosample.css('Owner > Name').inner_text
	end

	def to_ttl
		erb = accession ? self.template : self.template_blank
		puts erb.result(binding)
	end

	def template
		tpl = <<EOF
<http://identifiers.org/biosample/<%= self.accession %>>
	rdf:type insdc:BioSample ;
	rdfs:label "<%= self.title %>" ;
	rdfs:comment "<%= self.comment -%>" ;
	insdc:organism "<%= self.organism -%>" ;
	obo:RO_0002162 <http:identifiers.org/taxonomy/<%= self.taxid -%>> ; #RO:in taxon
	owl:sameAs <http://trace.ddbj.nig.ac.jp/BSSearch/biosample?acc=<%= self.accession %>> ;
	owl:sameAs <http://www.ebi.ac.uk/ena/data/view/<%= self.accession %>> ;
	owl:sameAs <http://www.ncbi.nlm.nih.gov/biosample?term=<%= self.accession %>> ;
	biosample:model "<%= self.model %>" ;
	biosample:owner "<%= self.owner %>" ;
<% self.sample_attributes.each do |attribute| -%>
	biosample:<%= attribute[:name] %> "<%= attribute[:value] %>" ;
<% end -%>
<% self.sample_ids.each do |id| -%>
	biosample:dblink "<%= id[:name] %>:<%= id[:value] %>" ;
<% end -%>
<% self.sample_links.each do |link| -%>
	biosample:db_xref "<%= link[:name] %>:<%= link[:value] %>" ;
<% end -%>
	biosample:access "<%= self.access %>" ;
	biosample:publication_date "<%= self.publication_date %>" ;
	biosample:last_update "<%= self.last_update %>" .
EOF
  ERB.new(tpl, nil, '-')
	end

	def template_blank
                tpl = <<EOF
[
	rdf:type insdc:BioSample ;
	rdfs:label "<%= self.title %>" ;
	rdfs:comment "<%= self.comment -%>" ;
	insdc:organism "<%= self.organism -%>" ;
	obo:RO_0002162 <http:identifiers.org/taxonomy/<%= self.taxid -%>> ; #RO:in taxon
	biosample:access "<%= self.access %>" ;
	biosample:publication_date "<%= self.publication_date %>" ;
	biosample:last_update "<%= self.last_update %>" ;
	biosample:model "<%= self.model %>" ;
	biosample:owner "<%= self.owner %>" ;
<% self.sample_attributes.each do |attribute| -%>
	biosample:<%= attribute[:name] %> "<%= attribute[:value] %>" ;
<% end -%>
<% self.sample_ids.each do |id| -%>
	biosample:dblink "<%= id[:name] %>:<%= id[:value] %>" ;
<% end -%>
<% self.sample_links.each do |link| -%>
	biosample:db_xref "<%= link[:name] %>:<%= link[:value] %>" ;
<% end -%>
	biosample:access "<%= self.access %>" ;
	biosample:publication_date "<%= self.publication_date %>" ;
	biosample:last_update "<%= self.last_update %>" ;
]
.
EOF
  ERB.new(tpl, nil, '-')
        end



	def sample_attributes
		#      doc.xpath("/BioSample/Attributes/Attribute").each do |element|
		#         children = element.children.to_s
		#         attribute_name = element.attribute("attribute_name").value
		#         harmonized_name = element.attribute("harmonized_name").nil? ?
		#              '' : element.attribute("harmonized_name").value
		#         display_name = element.attribute('display_name').nil? ?
		#              '' : element.attribute("display_name").value
		#         #puts [accession,id,attribute_name,harmonized_name,display_name,children].join("\t")
		#         puts "biosample:attributes##{URI.escape(attribute_name)}>\t\"#{children.gsub('"','\\"')}\" ;"
		#      end
		@biosample.css('Attributes > Attribute').map do |node|
                        {
			name: self.uri_escaped(node.attribute('attribute_name').value),
			value:  self.ttl_escaped(node.inner_text.to_s)
			}
		end
	end

	def sample_ids
		ids = @biosample.css('Ids > Id').map do |node|
			children = node.inner_text.to_s
			if @ddbj
                                {
				name: self.uri_escaped(node.attribute("namespace").value),
				value: self.ttl_escaped(node.inner_text.to_s)
				}
			else
				db = node.attribute("db").nil? ? node.attribute("db_label").value : node.attribute("db").value 
				{
				name: self.uri_escaped(db),
				value: self.ttl_escaped(node.inner_text.to_s)
				}
			end
		end
		#      doc.xpath("/BioSample/Ids/Id").each do |element|
		#         children = element.children.to_s
		#         #attribute_name = element.attribute("namespace").value #DDBJ
		#         attribute_name = element.attribute("namespace") ? attribute_name = element.attribute("namespace").value : attribute_name = element.attribute("db").value
		#         puts "\tdcterms:identifier\t\"#{URI.escape(attribute_name)}:#{children}\" ;"
		#      end
	end

	def sample_links
		#      #doc.xpath('/BioSample/Links/Link').each do |element| # DDBJ
		#      doc.xpath('/BioSample/Links/Link[@type="url"]').each do |element| #NCBI
		#         children = element.children.to_s
		#         attribute_name = element.attribute("label").value #DDBJ
		#         #puts "\t<http://ddbj.nig.ac.jp/ontologies/biosample/link##{URI.escape(attribute_name)}>\t\"#{children}\" ;"
		#         puts "\tdcterms:identifier\t\"#{URI.escape(attribute_name)}:#{children}\" ;"
		#      end
		if @ddbj
			@biosample.css('Links > Link').map do |node|
				{
				name: self.uri_escaped(node.attribute("label").value),
				value: self.ttl_escaped(node.inner_text.to_s)
				}
			end
		else
			@biosample.css('Links > Link[type="url"]').map do |node|
				label = node.attribute("label").nil? ? node.attribute("target").value : node.attribute("label").value
				{
				name: self.uri_escaped(label),
				value: self.ttl_escaped(node.inner_text.to_s)
				}
			end
		end
	end 

        def uri_escaped(string)
            require 'uri'
            URI.escape(string)
        end
        # seeAlso: http://rdf.greggkellogg.net/yard/RDF/Writer.html#escaped-instance_method
	def ttl_escaped(string)
		string.gsub('\\', '\\\\\\\\').
		gsub("\b", '\\b').
		gsub("\f", '\\f').
		gsub("\t", '\\t').
		gsub("\n", '\\n').
		gsub("\r", '\\r').
		gsub('"', '\\"')
	end

	# TODO
	def related_link
		@study.css("RELATED_LINK").map do |node|
			{ db: node.css("DB").inner_text,
				id: node.css("ID").inner_text,
			label: node.css("LABEL").inner_text }
		end
	end
		def to_ttl_prefix
		<<HEADER
@prefix : <http://identifiers.org/dataset/> .
@prefix owl:  <http://www.w3.org/2002/07/owl#>.
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix void: <http://rdfs.org/ns/void#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix obo:  <http://purl.obolibrary.org/obo/> .
@prefix insdc: <http://ddbj.nig.ac.jp/ontologies/nucleotide/> . 
@prefix biosample: <http://ddbj.nig.ac.jp/biosample/> . 
@prefix dcterms: <http://purl.org/dc/terms/>.

HEADER
    end
end

xml =  ARGV[0] || 'biosample_ddbj.xml'
bss = BioSampleSet.new(xml)
bss.to_ttl