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class Lazar < Model
attr_accessor :dataset, :predictions
def classify(compound_uri)
@dataset = OpenTox::Dataset.new
@predictions = {}
lazar = YAML.load yaml
compound = OpenTox::Compound.new(:uri => compound_uri)
compound_matches = compound.match lazar[:features]
conf = 0.0
neighbors = []
classification = nil
lazar[:fingerprints].each do |uri,matches|
sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(compound_matches,matches,lazar[:p_values])
if sim > 0.3
neighbors << uri
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/neighbors.size
if conf > 0.0
classification = true
elsif conf < 0.0
classification = false
end
compound = @dataset.find_or_create_compound(compound_uri)
feature = @dataset.find_or_create_feature(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[:endpoint] => { :lazar_prediction => {
:classification => classification,
:confidence => conf,
:neighbors => neighbors,
: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
@dataset = OpenTox::Dataset.new
@predictions = {}
c = @dataset.find_or_create_compound(compound_uri)
f = @dataset.find_or_create_feature(lazar[:endpoint])
v = db_activities.join(',')
@dataset.add c,f,v
@predictions[compound_uri] = { lazar[:endpoint] => {:measured_activities => db_activities}}
true
else
false
end
end
end
post '/?' do # create model
#model = Lazar.new(:task_uri => params[:task_uri])
#model.uri = url_for("/#{model.id}", :full)
model = Lazar.new
model.save
model.uri = url_for("/#{model.id}", :full)
# model.uri
#end
#
#put '/:id/?' do # create model from yaml representation
# model = Lazar.first(params[:id])
case request.content_type
when /yaml/
input = request.env["rack.input"].read
model.yaml = input
lazar = OpenTox::Model::Lazar.from_yaml(input)
lazar.uri = model.uri
model.owl = lazar.rdf
model.save
else
halt 400, "MIME type \"#{request.content_type}\" not supported."
end
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) # FEHLER
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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