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class Lazar < Model
attr_accessor :prediction_dataset
def classify(compound_uri,prediction)
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)
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
if (classification != nil)
feature_uri = lazar.dependentVariables
prediction.compounds << compound_uri
prediction.features << feature_uri
prediction.data[compound_uri] = [] unless prediction.data[compound_uri]
tuple = {
:classification => classification,
:confidence => conf,
:similarities => similarities,
:features => compound_matches
# uncomment to enable owl-dl serialisation of predictions
# url_for("/lazar#classification") => classification,
# url_for("/lazar#confidence") => conf,
# url_for("/lazar#similarities") => similarities,
# url_for("/lazar#features") => compound_matches
}
prediction.data[compound_uri] << {feature_uri => tuple}
end
end
def database_activity?(compound_uri,prediction)
# find database activities
lazar = YAML.load self.yaml
db_activities = lazar.activities[compound_uri]
if db_activities
prediction.creator = lazar.trainingDataset
feature_uri = lazar.dependentVariables
prediction.compounds << compound_uri
prediction.features << feature_uri
prediction.data[compound_uri] = [] unless prediction.data[compound_uri]
db_activities.each do |act|
prediction.data[compound_uri] << {feature_uri => act}
#tuple = {
# :classification => act}
#:confidence => "experimental"}
#prediction.data[compound_uri] << {feature_uri => tuple}
end
true
else
false
end
end
def to_owl
data = YAML.load(yaml)
activity_dataset = YAML.load(RestClient.get(data.trainingDataset, :accept => 'application/x-yaml').to_s)
feature_dataset = YAML.load(RestClient.get(data.feature_dataset_uri, :accept => 'application/x-yaml').to_s)
owl = OpenTox::Owl.create 'Model', uri
owl.set("creator","http://github.com/helma/opentox-model")
owl.set("title","#{URI.decode(activity_dataset.title)} lazar classification")
owl.set("date",created_at.to_s)
owl.set("algorithm",data.algorithm)
owl.set("dependentVariables",activity_dataset.features.join(', '))
owl.set("independentVariables",feature_dataset.features.join(', '))
owl.set("predictedVariables",activity_dataset.features.join(', ') + "_lazar_classification")
owl.set("trainingDataset",data.trainingDataset)
owl.parameters = {
"Dataset URI" =>
{ :scope => "mandatory", :value => data.trainingDataset },
"Feature URI for dependent variable" =>
{ :scope => "mandatory", :value => activity_dataset.features.join(', ')},
"Feature generation URI" =>
{ :scope => "mandatory", :value => feature_dataset.creator }
}
owl.rdf
end
end
get '/:id/?' do
accept = request.env['HTTP_ACCEPT']
accept = "application/rdf+xml" if accept == '*/*' or accept == '' or accept.nil?
# workaround for browser links
case params[:id]
when /.yaml$/
params[:id].sub!(/.yaml$/,'')
accept = 'application/x-yaml'
when /.rdf$/
params[:id].sub!(/.rdf$/,'')
accept = 'application/rdf+xml'
end
model = Lazar.get(params[:id])
halt 404, "Model #{params[:id]} not found." unless model
case accept
when "application/rdf+xml"
response['Content-Type'] = 'application/rdf+xml'
unless model.owl # lazy owl creation
model.owl = model.to_owl
model.save
end
model.owl
when /yaml/
response['Content-Type'] = 'application/x-yaml'
model.yaml
else
halt 400, "Unsupported MIME type '#{accept}'"
end
end
get '/:id/algorithm/?' do
response['Content-Type'] = 'text/plain'
YAML.load(Lazar.get(params[:id]).yaml).algorithm
end
get '/:id/trainingDataset/?' do
response['Content-Type'] = 'text/plain'
YAML.load(Lazar.get(params[:id]).yaml).trainingDataset
end
get '/:id/feature_dataset/?' do
response['Content-Type'] = 'text/plain'
YAML.load(Lazar.get(params[:id]).yaml).feature_dataset_uri
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]
prediction = OpenTox::Dataset.new
prediction.creator = lazar.uri
prediction.title = URI.decode YAML.load(lazar.yaml).dependentVariables.split(/#/).last
prediction.title += " lazar classification"
if compound_uri
lazar.classify(compound_uri,prediction) unless lazar.database_activity?(compound_uri,prediction)
LOGGER.debug prediction.to_yaml
case request.env['HTTP_ACCEPT']
when /yaml/
prediction.to_yaml
when 'application/rdf+xml'
prediction.to_owl
else
halt 404, "Content type #{request.env['HTTP_ACCEPT']} not available."
end
elsif dataset_uri
response['Content-Type'] = 'text/uri-list'
task_uri = OpenTox::Task.as_task do
input_dataset = OpenTox::Dataset.find(dataset_uri)
input_dataset.compounds.each do |compound_uri|
lazar.classify(compound_uri,prediction) unless lazar.database_activity?(compound_uri,prediction)
end
begin
uri = prediction.save.chomp
rescue
halt 500, "Could not save prediction dataset"
end
end
halt 202,task_uri
end
end
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