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module OpenTox
module Model
class Generic
MODEL_ATTRIBS = [:uri, :title, :creator, :date, :format, :predictedVariables, :independentVariables, :dependentVariables, :trainingDataset, :algorithm]
MODEL_ATTRIBS.each{ |a| attr_accessor(a) }
def self.find(uri)
owl = OpenTox::Owl.from_uri(uri, "Model")
return self.new(owl)
end
def self.to_rdf(model)
owl = OpenTox::Owl.create 'Model', model.uri
(MODEL_ATTRIBS - [:uri]).each do |a|
owl.set(a.to_s,model.send(a.to_s))
end
owl.rdf
end
protected
def initialize(owl)
MODEL_ATTRIBS.each do |a|
self.send("#{a.to_s}=".to_sym, owl.get(a.to_s)) unless a==:uri
end
@uri = owl.uri
if ENV['RACK_ENV'] =~ /test|debug/
begin
raise "uri invalid" unless Utils.is_uri?(@uri)
raise "no predicted variables" unless @predictedVariables and @predictedVariables.size>0
rescue => ex
RestClientWrapper.raise_uri_error "invalid model: '"+ex.message+"'\n"+self.to_yaml+"\n",@uri.to_s
end
LOGGER.warn "model has no dependent variable" unless @dependentVariables and @dependentVariables.size>0
LOGGER.warn "model has no algorithm" unless @algorithm and @algorithm.size>0
LOGGER.warn "model has no indenpendent variables" unless @independentVariables
end
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
LOGGER.debug "Build model done: "+uri.to_s
RestClientWrapper.raise_uri_error("Invalid build model result: '"+uri.to_s+"'", algorithm_uri, algorithm_params ) unless Utils.model_uri?(uri)
return PredictionModel.find(uri)
end
def predict_dataset( dataset_uri )
LOGGER.debug "Predict dataset: "+dataset_uri.to_s+" with model "+@uri.to_s
uri = RestClientWrapper.post(@uri, {:accept => "text/uri-list", :dataset_uri=>dataset_uri})
RestClientWrapper.raise_uri_error("Prediciton result no dataset uri: "+uri.to_s, @uri, {:dataset_uri=>dataset_uri} ) unless Utils.dataset_uri?(uri)
uri
end
def classification?
#HACK replace with request to ontology server
if @title =~ /(?i)classification/
return true
elsif @title =~ /(?i)regression/
return false
elsif @uri =~/ntua/ and @title =~ /mlr/
return false
elsif @uri =~/tu-muenchen/ and @title =~ /regression|M5P|GaussP/
return false
elsif @uri =~/ambit2/ and @title =~ /pKa/ || @title =~ /Regression|Caco/
return false
elsif @uri =~/majority/
return (@uri =~ /class/) != nil
else
raise "unknown model, uri:'"+@uri.to_s+"' title:'"+@title.to_s+"'"
end
end
end
class Lazar < Generic
attr_accessor :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
RestClientWrapper.get(@@config[:services]["opentox-model"]).chomp.split("\n")
end
def self.predict(compound_uri,model_uri)
#RestClientWrapper.post(model_uri,{:compound_uri => compound_uri, :accept => 'application/x-yaml'})
`curl -X POST -d 'compound_uri=#{compound_uri}' -H 'Accept:application/x-yaml' #{model_uri}`
end
end
class PropertyLazar < Generic
attr_accessor :feature_dataset_uri, :properties, :features, :activities#, :effects, :p_values
def initialize
@source = "http://github.com/helma/opentox-model"
@algorithm = File.join(@@config[:services]["opentox-algorithm"],"property_lazar")
#@independent_variables = File.join(@@config[:services]["opentox-algorithm"],"fminer#BBRC_representative")
@features = []
#@effects = {}
@activities = {}
#@p_values = {}
@properties = {}
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
RestClientWrapper.get(@@config[:services]["opentox-model"]).chomp.split("\n")
end
def self.predict(compound_uri,model_uri)
#RestClientWrapper.post(model_uri,{:compound_uri => compound_uri, :accept => 'application/x-yaml'})
`curl -X POST -d 'compound_uri=#{compound_uri}' -H 'Accept:application/x-yaml' #{model_uri}`
end
end
end
end
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