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LOGGER.progname = File.expand_path(__FILE__)
module OpenTox
class Dataset
attr_accessor :uri, :title, :source, :identifier, :data, :features, :compounds
def initialize
@data = {}
@features = []
@compounds = []
end
def self.find(uri)
if uri.match(/webservices.in-silico.ch|localhost/) # try to get YAML first
YAML.load RestClient.get(uri, :accept => 'application/x-yaml').to_s
else # get default rdf+xml
owl = OpenTox::Owl.from_uri(uri)
@title = owl.title
@source = owl.source
@identifier = owl.identifier.sub(/^\[/,'').sub(/\]$/,'')
@uri = @identifier
@data = owl.data
halt 404, "Dataset #{uri} empty!" if @data.empty?
@data.each do |compound,features|
@compounds << compound
features.each do |f,v|
@features << f
end
end
@compounds.uniq!
@features.uniq!
end
end
def save
@features.uniq!
@compounds.uniq!
RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0]).post(self.to_yaml, :content_type => "application/x-yaml").chomp.to_s
end
=begin
# create/add to entry from uris or Redland::Resources
def add(compound,feature,value)
compound = self.find_or_create_compound compound unless compound.class == Redland::Resource
feature = self.find_or_create_feature feature unless feature.class == Redland::Resource
data_entry = @model.subject OT['compound'], compound
if data_entry.nil?
data_entry = @model.create_resource
dataset = @model.subject(RDF['type'],OT[self.owl_class])
@model.add dataset, 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
def add_tuple(compound,tuple)
compound = self.find_or_create_compound compound unless compound.class == Redland::Resource
data_entry = @model.subject OT['compound'], compound
if data_entry.nil?
data_entry = @model.create_resource
dataset = @model.subject(RDF['type'],OT[self.owl_class])
@model.add dataset, 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
end
def create_tuple(feature,t)
feature = self.find_or_create_feature feature unless feature.class == Redland::Resource
tuple = @model.create_resource
@model.add tuple, RDF['type'], OT["Tuple"]
@model.add tuple, OT['feature'], feature
t.each do |name,value|
f = self.find_or_create_feature name unless name.class == Redland::Resource
complex_value = @model.create_resource
feature = self.find_or_create_feature(name)
@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'], value.to_s
end
tuple
end
# find or create a new compound and return the resource
def find_or_create_compound(uri)
compound = @model.subject(DC["identifier"], uri)
if compound.nil?
compound = @model.create_resource(uri)
@model.add compound, RDF['type'], OT["Compound"]
@model.add compound, DC["identifier"], uri
end
compound
end
# find or create a new feature and return the resource
def find_or_create_feature(uri)
feature = @model.subject(DC["identifier"], uri)
if feature.nil?
feature = @model.create_resource(uri)
@model.add feature, RDF['type'], OT["Feature"]
@model.add feature, DC["identifier"], uri
@model.add feature, DC["title"], File.basename(uri).split(/#/)[1]
@model.add feature, DC['source'], uri
end
feature
end
def self.create(data, content_type = 'application/rdf+xml')
resource = RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
uri = resource.post data, :content_type => content_type
dataset = Dataset.new
dataset.read uri.chomp.to_s
dataset
end
def features
features = []
@model.subjects(RDF['type'], OT["Feature"]).each do |feature_node|
features << @model.object(feature_node, DC["identifier"])#
end
features
end
def compounds
compounds = []
@model.subjects(RDF['type'], OT["Compound"]).each do |compound_node|
compounds << @model.object(compound_node, DC["identifier"]).to_s
end
compounds
end
# Delete a dataset
def delete
resource = RestClient::Resource.new(@uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
resource.delete
end
def to_owl
end
def from_owl
end
=end
end
end
|
