diff options
Diffstat (limited to 'lib/ontology.rb')
| -rw-r--r-- | lib/ontology.rb | 114 |
1 files changed, 98 insertions, 16 deletions
diff --git a/lib/ontology.rb b/lib/ontology.rb index fa4ea6f..ad7ba7b 100644 --- a/lib/ontology.rb +++ b/lib/ontology.rb @@ -1,11 +1,9 @@ module OpenTox module Ontology module Echa -=begin - require 'sparql/client' - @sparql = SPARQL::Client.new("http://apps.ideaconsult.net:8080/ontology") - def self.qs(classname="Endpoints") - return "PREFIX ot:<http://www.opentox.org/api/1.1#> + + def self.querystring(classname="Endpoints") + return CGI.escape("PREFIX ot:<http://www.opentox.org/api/1.1#> PREFIX ota:<http://www.opentox.org/algorithms.owl#> PREFIX owl:<http://www.w3.org/2002/07/owl#> PREFIX dc:<http://purl.org/dc/elements/1.1/> @@ -17,29 +15,44 @@ module OpenTox where { ?endpoint rdfs:subClassOf otee:#{classname}. ?endpoint dc:title ?title. - }" + }") end - + def self.make_option_list(endpoint="Endpoints", level=1) - out = "" - results = @sparql.query(qs(endpoint)) rescue results = [] + out = "" + results = echa_endpoints(endpoint) rescue results = [] results.each do |result| - endpointname = result.Endpoints.to_s.split('#').last - title = result.bound?(:title) ? result.title : endpointname - out += "<option value='#{title}' id='#{endpointname}' class='level_#{level}'>#{title}</option>\n" + r = result.split(',') + endpointname = r.first.split("#").last + title = r[1..r.size-1] + out += "<option value='#{r.first}' id='#{endpointname}' class='level_#{level}'>#{title}</option>\n" out += make_option_list(endpointname, level + 1) end return out end - - def self.get_endpoint_selectlist(include_blank=true) + + def self.endpoint_option_list(include_blank=true) out = "<select id='endpoint' name='endpoint'>\n" out += "<option value='' id='please_select'>Please select</option>\n" if include_blank out += make_option_list out += "</select>\n" return out end -=end + + # Gets Endpoints of specific level from ontology service + # Top level with endpoint="Endpoints" + # e.G. Ecotoxic effects endpoints with endpoint="EcotoxicEffects" + # if ontology service is not reachable it returns an empty array + # @param [String] endpoint + # @return [Array] of endpoints: e.G. "http://www.opentox.org/echaEndpoints.owl#EcotoxicEffects,Ecotoxic effects" + def self.echa_endpoints(endpoint) + begin + RestClientWrapper.get("#{ONTOLOGY_SERVER}?query=#{querystring(endpoint)}",:accept => "text/csv").collect{|l| l.gsub("\r\n", "") if l.match(/^http/)}.uniq.compact.sort + rescue + LOGGER.warn "OpenTox::Ontology::Echa.echa_endpoints ontology service is not reachable." + [] + end + end def self.endpoints RestClientWrapper.get("http://apps.ideaconsult.net:8080/ambit2/query/ndatasets_endpoint",:accept => "text/csv").collect { |line| line.split(',').first if line.match(/^http/) }.compact @@ -51,5 +64,74 @@ module OpenTox end + #Model Class for OpenTox::Ontology to register/deregister and check models in the ontology service + #@example Register a model URI to the ontology service, check if model URI exists and delete it + # uri = "http://mymodelservice.net/model/1" # model uri will be checked by the ontology service itself + # OpenTox::Ontology::Model.register(uri) + # puts OpenTox::Ontology::Model.exists?(uri) # => should return true + # OpenTox::Ontology::Model.delete(uri) + # puts OpenTox::Ontology::Model.exists?(uri) # => should return false + module Model + + # Register an OpenTox resource into ontology service + # @param [String] uri, URI of recource to register + # @param [String] subjectid + def self.register(uri, subjectid=nil) + begin + RestClientWrapper.post(ONTOLOGY_SERVER, {:uri => uri}, {:subjectid => CGI.escape(subjectid)}) + rescue + LOGGER.warn "OpenTox::Ontology::Model.register ontology service is not reachable. Failed to register URI: #{uri} with subjectid: #{subjectid}" + false + end + end + + # Deregister an OpenTox resource into ontology service + # @param [String] uri, URI of recource to deregister/delete + # @param [String] subjectid + def self.delete(uri, subjectid=nil) + begin + RestClientWrapper.delete("#{ONTOLOGY_SERVER}?uri=#{CGI.escape(uri)}", {:subjectid => CGI.escape(subjectid)}) + rescue + LOGGER.warn "OpenTox::Ontology::Model.exists ontology service is not reachable. Failed to delete URI: #{uri} with subjectid: #{subjectid}" + false + end + end + + # Find an OpenTox resource in the ontology service + # @param [String] uri, URI of recource to find + # @param [String] subjectid + def self.exists?(uri, subjectid=nil) + begin + out = RestClientWrapper.get("#{ONTOLOGY_SERVER}?query=#{querystring(uri)}",:accept => "text/csv").collect{|l| l.gsub("\r\n", "") if l.match(/^http/)}.uniq.compact + return true if out.size > 0 + false + rescue + LOGGER.warn "OpenTox::Ontology::Model.exists ontology service is not reachable. Failed to check for URI: #{uri} with subjectid: #{subjectid}" + false + end + end + + private + # Query string to find a registered model + # @param [String] uri, model URI + def self.querystring(uri) + return CGI.escape("PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> + PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> + PREFIX owl:<http://www.w3.org/2002/07/owl#> + PREFIX dc:<http://purl.org/dc/elements/1.1/> + PREFIX dcterms:<http://purl.org/dc/terms/> + PREFIX ot:<http://www.opentox.org/api/1.1#> + select distinct ?model ?title ?creator ?trainingDataset ?algorithm + where { + ?model rdf:type ot:Model; + OPTIONAL {?model dc:title ?title}. + OPTIONAL {?model dc:creator ?creator}. + OPTIONAL {?model ot:trainingDataset ?trainingDataset}. + OPTIONAL {?model ot:algorithm ?algorithm }. + FILTER (?model = <#{uri}>) + }") + end + end + end -end +end
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