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module OpenTox
module Model
class Lazar
attr_accessor :dependent_variable, :activity_dataset_uri, :feature_dataset_uri, :effects, :activities, :p_values, :fingerprints, :features
def initialize
@source = "http://github.com/helma/opentox-model"
@algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
#@independent_variables = File.join(@@config[:services]["opentox-algorithm"],"fminer#BBRC_representative")
@features = []
@effects = {}
@activities = {}
@p_values = {}
@fingerprints = {}
end
def save
@features.uniq!
resource = RestClient::Resource.new(@@config[:services]["opentox-model"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
resource.post(self.to_yaml, :content_type => "application/x-yaml").chomp.to_s
end
def self.find_all
RestClient.get(@@config[:services]["opentox-model"]).chomp.split("\n")
end
=begin
include Owl
# Create a new prediction model from a dataset
def initialize
super
self.source = "http://github.com/helma/opentox-model"
self.algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
self.independentVariables = File.join(@@config[:services]["opentox-algorithm"],"fminer#BBRC_representative") # TODO read this from dataset
end
def self.from_yaml(yaml)
yaml = YAML.load yaml
lazar = Lazar.new
lazar.title = "lazar model for #{yaml[:endpoint]}"
lazar.parameters = {
"Dataset URI" => { :scope => "mandatory", :value => "dataset_uri=#{yaml[:activity_dataset]}" },
"Feature URI for dependent variable" => { :scope => "mandatory", :value => "feature_uri=#{yaml[:endpoint]}" },
"Feature generation URI" => { :scope => "mandatory", :value => "feature_generation_uri=#{File.join(@@config[:services]["opentox-algorithm"],"fminer")}"} #TODO write to yaml
}
lazar.algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
lazar.trainingDataset = yaml[:activity_dataset]
lazar.dependentVariables = yaml[:endpoint]
lazar.predictedVariables = yaml[:endpoint] + "_lazar_prediction"
lazar
end
def self.find(uri)
yaml = RestClient.get(uri, :accept => "application/x-yaml")
OpenTox::Model::Lazar.from_yaml(yaml)
end
# Predict a compound
def predict(compound)
# nicht absichern??
resource = RestClient::Resource.new(@uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
resource.post(:compound_uri => compound.uri)
end
def self.base_uri
File.join @@config[:services]["opentox-model"],'lazar'
end
def self.create(data)
resource = RestClient::Resource.new(@@config[:services]["opentox-model"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
resource.post(data, :content_type => "application/x-yaml").chomp.to_s
end
def delete
resource = RestClient::Resource.new(self.uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
resource.delete
#RestClient.delete @uri if @uri
#RestClient.delete model.task_uri if model.task_uri
end
# def self.create(task)
# @uri = RestClient.post(@@config[:services]["opentox-model"], :task_uri => task.uri)
# end
# def yaml=(data)
# RestClient.put(@@uri, data, :content_type => "application/x-yaml").to_s
# end
def endpoint
YAML.load(RestClient.get(uri))[:endpoint]
end
def algorithm=(algorithm)
me = @model.subject(RDF['type'],OT[self.owl_class])
@model.add me, OT['algorithm'], Redland::Uri.new(algorithm) # untyped individual comes from this line, why??
@model.add Redland::Uri.new(algorithm), RDF['type'], OT['Algorithm']
end
def trainingDataset=(trainingDataset)
me = @model.subject(RDF['type'],OT[self.owl_class])
@model.add me, OT['trainingDataset'], Redland::Uri.new(trainingDataset) # untyped individual comes from this line, why??
@model.add Redland::Uri.new(trainingDataset), RDF['type'], OT['Dataset']
end
def dependentVariables=(dependentVariables)
me = @model.subject(RDF['type'],OT[self.owl_class])
@model.add me, OT['dependentVariables'], Redland::Uri.new(dependentVariables) # untyped individual comes from this line, why??
@model.add Redland::Uri.new(dependentVariables), RDF['type'], OT['Feature']
end
def independentVariables=(independentVariables)
me = @model.subject(RDF['type'],OT[self.owl_class])
@model.add me, OT['independentVariables'], Redland::Uri.new(independentVariables) # untyped individual comes from this line, why??
@model.add Redland::Uri.new(independentVariables), RDF['type'], OT['Feature']
end
def predictedVariables=(predictedVariables)
me = @model.subject(RDF['type'],OT[self.owl_class])
@model.add me, OT['predictedVariables'], Redland::Uri.new(predictedVariables) # untyped individual comes from this line, why??
@model.add Redland::Uri.new(predictedVariables), RDF['type'], OT['Feature']
end
=end
end
end
end
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