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class Lazar < Model
attr_accessor :dataset, :predictions
def classify(compound_uri)
#unless @dataset
#@dataset = OpenTox::Dataset.new
@predictions = {}
#end
lazar = YAML.load self.yaml
compound = OpenTox::Compound.new(:uri => compound_uri)
compound_matches = compound.match lazar.features
conf = 0.0
similarities = {}
classification = nil
lazar.fingerprints.each do |uri,matches|
sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(compound_matches,matches,lazar.p_values)
LOGGER.debug sim
if sim > 0#.3
similarities[uri] = sim
lazar.activities[uri].each do |act|
case act.to_s
when 'true'
conf += OpenTox::Utils.gauss(sim)
when 'false'
conf -= OpenTox::Utils.gauss(sim)
end
end
end
end
conf = conf/similarities.size
if conf > 0.0
classification = true
elsif conf < 0.0
classification = false
end
LOGGER.debug conf
#compound = @dataset.compounds[compound_uri]
#feature = @dataset.features[lazar.endpoint]
if (classification != nil)
#tuple = @dataset.create_tuple(feature,{ 'lazar#classification' => classification, 'lazar#confidence' => conf})
#@dataset.add_tuple compound,tuple
@predictions[compound_uri] = { lazar.dependent_variable => { :lazar_prediction => {
:classification => classification,
:confidence => conf,
:similarities => similarities,
:features => compound_matches
} } }
end
end
def database_activity?(compound_uri)
# find database activities
lazar = YAML.load self.yaml
db_activities = lazar.activities[compound_uri]
if db_activities
@predictions = {:compound_uri => { lazar.dependent_variable => {:measured_activities => db_activities}}}
true
else
false
end
end
end
post '/?' do # create model
halt 400, "MIME type \"#{request.content_type}\" not supported." unless request.content_type.match(/yaml/)
model = Lazar.new
model.save
model.uri = url_for("/#{model.id}", :full)
model.yaml = request.env["rack.input"].read
model.save
model.uri
end
post '/:id/?' do # create prediction
lazar = Lazar.get(params[:id])
halt 404, "Model #{params[:id]} does not exist." unless lazar
halt 404, "No compound_uri or dataset_uri parameter." unless compound_uri = params[:compound_uri] or dataset_uri = params[:dataset_uri]
if compound_uri
lazar.classify(compound_uri) unless lazar.database_activity?(compound_uri)
elsif dataset_uri
input_dataset = OpenTox::Dataset.find(dataset_uri)
input_dataset.compounds.each do |compound_uri|
lazar.classify(compound_uri) unless lazar.database_activity?(compound_uri)
end
end
case request.env['HTTP_ACCEPT']
when /yaml/
lazar.predictions.to_yaml
else
if params[:compound_uri]
lazar.dataset.rdf
elsif params[:dataset_uri]
lazar.dataset.save
end
end
end
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