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module OpenTox
module Ontology
module Echa
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/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
PREFIX toxcast:<http://www.opentox.org/toxcast.owl#>
select *
where {
?endpoint rdfs:subClassOf otee:#{classname}.
?endpoint dc:title ?title.
}")
end
def self.make_option_list(endpoint="Endpoints", level=1)
out = ""
results = echa_endpoints(endpoint) rescue results = []
results.each do |result|
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.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
# 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
end
def self.datasets(endpoint)
RestClientWrapper.get("http://apps.ideaconsult.net:8080/ambit2/dataset?feature_sameas=#{URI.encode endpoint}", :accept => "text/uri-list").split("\n")
end
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
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