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module OpenTox
class Owl
attr_reader :uri, :ot_class
def initialize(ot_class,uri)
# read OT Ontology
#@parser.parse_into_model(@model,"http://opentox.org/data/documents/development/RDF%20files/OpenToxOntology/at_download/file")
#@parser.parse_string_into_model(@model,File.read(File.join(File.dirname(__FILE__),"opentox.owl")),'/')
@model = Redland::Model.new Redland::MemoryStore.new
@parser = Redland::Parser.new
@ot_class = ot_class
@uri = Redland::Uri.new(uri.chomp)
@model.add @uri, RDF['type'], OT[@ot_class]
end
def method_missing(name, *args)
methods = ['title', 'source', 'identifier', 'algorithm', 'independentVariables', 'dependentVariable']
if methods.include? name.to_s.sub(/=/,'')
if /=/ =~ name.to_s # setter
name = name.to_s.sub(/=/,'')
begin # delete existing entry
t = @model.object(@uri, DC[name])
@model.delete @uri, DC[name], t
rescue
end
@model.add @uri, DC[name], args.first
else # getter
@model.object(@uri, DC['title']).to_s
end
else
raise "Method '#{name.to_s}' not found."
end
end
def parameters=(params)
params.each do |name, settings|
parameter = @model.create_resource
@model.add parameter, RDF['type'], OT['Parameter']
@model.add parameter, DC['title'], name
@model.add parameter, OT['paramScope'], settings[:scope]
@model.add parameter, OT['paramValue'], settings[:value]
end
end
def add_data_entries(compound_uri,features)
# add compound
compound = @model.subject(DC["identifier"], compound_uri)
if compound.nil?
compound = @model.create_resource(compound_uri)
@model.add compound, RDF['type'], OT["Compound"]
@model.add compound, DC["identifier"], compound_uri
end
features.each do |f|
f.each do |feature_uri,value|
# add feature
feature = find_or_create_feature feature_uri
if value.class.to_s == 'Hash'
# create tuple
tuple = @model.create_resource
@model.add tuple, RDF['type'], OT["Tuple"]
@model.add tuple, OT['feature'], feature
value.each do |uri,v|
f = find_or_create_feature uri
complex_value = @model.create_resource
@model.add tuple, OT['complexValue'], complex_value
@model.add complex_value, RDF['type'], OT["FeatureValue"]
@model.add complex_value, OT['feature'], f
@model.add complex_value, OT['value'], v.to_s
end
# add data entry
data_entry = @model.subject OT['compound'], compound
if data_entry.nil?
data_entry = @model.create_resource
@model.add @uri, OT['dataEntry'], data_entry
@model.add data_entry, RDF['type'], OT["DataEntry"]
@model.add data_entry, OT['compound'], compound
end
@model.add data_entry, OT['values'], tuple
else
data_entry = @model.subject OT['compound'], compound
if data_entry.nil?
data_entry = @model.create_resource
@model.add @uri, OT['dataEntry'], data_entry
@model.add data_entry, RDF['type'], OT["DataEntry"]
@model.add data_entry, OT['compound'], compound
end
values = @model.create_resource
@model.add data_entry, OT['values'], values
@model.add values, RDF['type'], OT['FeatureValue']
@model.add values, OT['feature'], feature
@model.add values, OT['value'], value.to_s
end
end
end
end
def find_or_create_feature(feature_uri)
feature = @model.subject(DC["identifier"], feature_uri)
if feature.nil?
feature = @model.create_resource(feature_uri)
@model.add feature, RDF['type'], OT["Feature"]
@model.add feature, DC["identifier"], feature_uri
@model.add feature, DC["title"], File.basename(feature_uri).split(/#/)[1]
@model.add feature, DC['source'], feature_uri
end
feature
end
def rdf
@model.to_string
end
=begin
def to_ntriples
@serializer.model_to_string(Redland::Uri.new(@uri), @model)
end
def uri=(uri)
@uri = uri.chomp
# rewrite uri
@model.subjects(RDF['type'],OT[@ot_class]).each do |me|
@model.delete(me,RDF['type'],OT[@ot_class])
@model.add(uri,RDF['type'],OT[@ot_class])
id = @model.object(me, DC['identifier'])
@model.delete me, DC['identifier'], id
# find/replace metadata
@model.find(me, nil, nil) do |s,p,o|
@model.delete s,p,o
@model.add uri,p,o
end
@model.add uri, DC['identifier'], @uri
end
end
def read(uri)
@parser.parse_into_model(@model,uri)
@uri = uri
end
def identifier
me = @model.subject(RDF['type'],OT[@ot_class])
@model.object(me, DC['identifier']).to_s unless me.nil?
end
def title=(title)
me = @model.subject(RDF['type'],OT[@ot_class])
begin
t = @model.object(me, DC['title'])
@model.delete me, DC['title'], t
rescue
end
@model.add me, DC['title'], title
end
def source=(source)
me = @model.subject(RDF['type'],OT[@ot_class])
begin
t = @model.object(me, DC['source'])
@model.delete me, DC['source'], t
rescue
end
@model.add me, DC['source'], source
end
def title
# I have no idea, why 2 subjects are returned
# iterating over all subjects leads to memory allocation problems
# SPARQL queries also do not work
#me = @model.subjects(RDF['type'],OT[@ot_class])[1]
me = @model.subject(RDF['type'],OT[@ot_class])
@model.object(me, DC['title']).to_s
end
def source
me = @model.subject(RDF['type'],OT[@ot_class])
@model.object(me, DC['source']).to_s unless me.nil?
end
def create_owl_statement(name,value)
r = @model.create_resource
dc_class = DC[name.gsub(/^[a-z]/) { |a| a.upcase }] # capitalize only the first letter
#puts "DC:" + name.gsub(/^[a-z]/) { |a| a.upcase }
@model.add dc_class, RDF['type'], OWL["Class"]
@model.add r, RDF['type'], dc_class
@model.add r, DC[name], value
end
def method_missing(name, *args)
# create magic setter methods
if /=/ =~ name.to_s
create_owl_statement name.to_s.sub(/=/,''), args.first
else
raise "No method #{name}"
end
end
=end
end
end
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