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module OpenTox
module Model
class Generic
attr_accessor :uri, :title, :source, :identifier, :predicted_variables, :independent_variables, :dependent_variables, :activity_dataset_uri, :feature_dataset_uri, :effects, :activities, :p_values, :fingerprints, :features, :algorithm
def self.find(uri)
owl = OpenTox::Owl.from_uri(uri)
return self.new(owl)
end
protected
def initialize(owl)
@title = owl.title
@source = owl.source
@identifier = owl.identifier.sub(/^\[/,'').sub(/\]$/,'')
@uri = owl.uri.to_s #@identifier
@algorithm = owl.algorithm
@dependent_variables = owl.dependentVariables
@independent_variables = owl.independentVariables
@predicted_variables = owl.predictedVariables
raise "invalid model:\n"+self.to_yaml+"\n" unless Utils.is_uri?(@uri) && @dependent_variables.to_s.size>0 &&
@independent_variables.to_s.size>0 && @predicted_variables.to_s.size>0 if ENV['RACK_ENV'] =~ /test|debug/
end
end
class PredictionModel < Generic
def self.build( algorithm_uri, algorithm_params )
LOGGER.debug "Build model, algorithm_uri:"+algorithm_uri.to_s+", algorithm_parms: "+algorithm_params.inspect.to_s
uri = OpenTox::RestClientWrapper.post(algorithm_uri,algorithm_params).to_s
if uri.to_s =~ /ambit.*task|tu-muenchen.*task/
uri = PredictionModel.redirect_task(uri)
elsif Utils.task_uri?(uri)
uri = OpenTox::Task.find(uri).wait_for_resource.to_s
end
raise "invalid build model result: "+uri.to_s unless uri =~ /model/
return PredictionModel.find(uri)
end
def self.redirect_task( uri )
raise "no redirect task uri: "+uri.to_s unless uri.to_s =~ /ambit.*task|tu-muenchen.*task/
while (uri.to_s =~ /ambit.*task|tu-muenchen.*task/)
#HACK handle redirect
LOGGER.debug "REDIRECT TASK: "+uri.to_s
redirect = ""
while (redirect.size == 0)
IO.popen("bin/redirect.sh "+uri.to_s) do |f|
while line = f.gets
redirect += line.chomp
end
end
sleep 0.3
end
uri = redirect
LOGGER.debug "REDIRECT TO: "+uri.to_s
end
return uri
end
def predict_dataset( dataset_uri )
LOGGER.debug "Predict dataset: "+dataset_uri.to_s+" with model "+@uri.to_s
#HACK using curl
uri = ""
IO.popen("curl -X POST -d dataset_uri='"+dataset_uri+"' "+@uri.to_s+" 2> /dev/null") do |f|
while line = f.gets
uri += line
end
end
if uri.to_s =~ /ambit.*task|tu-muenchen.*task/
uri = PredictionModel.redirect_task(uri)
raise "invalid redirect result: " unless uri =~ /ambit.*dataset/
return uri
else
uri = OpenTox::Task.find(uri).wait_for_resource.to_s if Utils.task_uri?(uri)
return uri if Utils.dataset_uri?(uri)
raise "not sure about prediction result: "+uri.to_s
end
end
def classification?
#HACK replace with request to ontology server
if @title =~ /lazar classification/
return true
elsif @uri =~/ntua/ and @title =~ /mlr/
return false
elsif @uri =~/tu-muenchen/ and @title =~ /regression/
return false
else
raise "unknown model, uri:'"+@uri.to_s+"' title:'"+@title.to_s+"'"
end
end
end
class Lazar < Generic
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
# 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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