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LOGGER.progname = File.expand_path(__FILE__)
module OpenTox
module Algorithm
class Fminer
include Owl
def initialize
super
self.uri = File.join(@@config[:services]["opentox-algorithm"],'fminer')
self.title = "fminer"
self.source = "http://github.com/amaunz/libfminer"
self.parameters = {
"Dataset URI" => { :scope => "mandatory", :value => "dataset_uri" },
"Feature URI for dependent variable" => { :scope => "mandatory", :value => "feature_uri" }
}
end
def self.create_feature_dataset(params)
LOGGER.debug File.basename(__FILE__) + ": creating feature dataset"
resource = RestClient::Resource.new(params[:feature_generation_uri], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
resource.post :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri]
end
def self.uri
File.join(@@config[:services]["opentox-algorithm"], "fminer")
end
end
class Lazar
include Owl
def initialize
super
self.uri = File.join(@@config[:services]["opentox-algorithm"],'lazar')
self.title = "lazar"
self.source = "http://github.com/helma/opentox-algorithm"
self.parameters = {
"Dataset URI" =>
{ :scope => "mandatory", :value => "dataset_uri" },
"Feature URI for dependent variable" =>
{ :scope => "mandatory", :value => "feature_uri" },
"Feature generation URI" =>
{ :scope => "mandatory", :value => "feature_generation_uri" }
}
end
def self.create_model(params)
LOGGER.debug params
LOGGER.debug File.basename(__FILE__) + ": creating model"
#@uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "lazar"), :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")
resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "lazar"), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
@uri = resource.post :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer").chomp
end
def self.uri
File.join(@@config[:services]["opentox-algorithm"], "lazar")
end
end
class Similarity
def self.weighted_tanimoto(fp_a,fp_b,p)
common_features = fp_a & fp_b
all_features = fp_a + fp_b
common_p_sum = 0.0
if common_features.size > 0
common_features.each{|f| common_p_sum += p[f]}
all_p_sum = 0.0
all_features.each{|f| all_p_sum += p[f]}
common_p_sum/all_p_sum
else
0.0
end
end
end
end
end
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