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require 'test/test_examples_util.rb'
class Class
def humanize
self.to_s.gsub(/.*::/, "").gsub(/([^^A-Z_])([A-Z])/, '\1-\2').gsub(/_/,"-")
end
end
module ValidationExamples
########################################################################################################
class ABSTRACTHamsterSplit < SplitTestValidation
def initialize
@dataset_file = File.new("data/hamster_carcinogenicity.yaml","r")
@prediction_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
end
end
class LazarHamsterSplit < ABSTRACTHamsterSplit
def initialize
@algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
@algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
super
end
end
class MajorityHamsterSplit < ABSTRACTHamsterSplit
def initialize
@algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
super
end
end
########################################################################################################
class ABSTRACTHamsterTrainingTest < TrainingTestValidation
def initialize
@test_target_dataset_file = File.new("data/hamster_carcinogenicity.yaml","r")
@training_dataset_file = File.new("data/hamster_carcinogenicity.train.yaml","r")
@test_dataset_file = File.new("data/hamster_carcinogenicity.test.yaml","r")
@prediction_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
end
end
class MajorityHamsterTrainingTest < ABSTRACTHamsterTrainingTest
def initialize
@algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
super
end
end
class LazarHamsterTrainingTest < ABSTRACTHamsterTrainingTest
def initialize
@algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
@algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
super
end
end
########################################################################################################
class ABSTRACTHamsterCrossvalidation < CrossValidation
def initialize
@dataset_file = File.new("data/hamster_carcinogenicity.yaml","r")
@prediction_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
end
end
class MajorityHamsterCrossvalidation < ABSTRACTHamsterCrossvalidation
def initialize
@algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
super
end
end
class LazarHamsterCrossvalidation < ABSTRACTHamsterCrossvalidation
def initialize
@algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
@algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
super
end
end
########################################################################################################
class ABSTRACT_ISTHamsterCrossvalidationInsilico < CrossValidation
def initialize
@dataset_uri = "http://webservices.in-silico.ch/dataset/108"
@prediction_feature = "http://toxcreate.org/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
end
end
class MajorityISTHamsterCrossvalidation < ABSTRACT_ISTHamsterCrossvalidationInsilico
def initialize
@algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
super
end
end
class LazarISTHamsterCrossvalidation < ABSTRACT_ISTHamsterCrossvalidationInsilico
def initialize
@algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
@algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
super
end
end
class ISTLazarISTHamsterCrossvalidation < ABSTRACT_ISTHamsterCrossvalidationInsilico
def initialize
@algorithm_uri = "http://webservices.in-silico.ch/algorithm/lazar"
@algorithm_params = "feature_generation_uri=http://webservices.in-silico.ch/algorithm/fminer"
super
end
end
########################################################################################################
class LR_AmbitCacoModel < ModelValidation
def initialize
@model_uri = "http://apps.ideaconsult.net:8080/ambit2/model/33"
@test_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/R545"
#@prediction_feature=http://apps.ideaconsult.net:8080/ambit2/feature/22200
end
end
########################################################################################################
class ABSTRACTCacoTrainingTest < TrainingTestValidation
def initialize
@training_dataset_uri = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/R7798"
@test_dataset_uri = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/R8353"
@prediction_feature = "http://ambit.uni-plovdiv.bg:8080/ambit2/feature/255510"
end
end
class LR_AmbitCacoTrainingTest < ABSTRACTCacoTrainingTest
def initialize
@algorithm_uri = "http://ambit.uni-plovdiv.bg:8080/ambit2/algorithm/LR"
super
end
end
class MLR_NTUA_CacoTrainingTest < ABSTRACTCacoTrainingTest
def initialize
@algorithm_uri = "http://opentox.ntua.gr:3003/algorithm/mlr"
super
end
end
class MLR_NTUA2_CacoTrainingTest < ABSTRACTCacoTrainingTest
def initialize
@algorithm_uri = "http://opentox.ntua.gr:3004/algorithm/mlr"
super
end
end
class MajorityCacoTrainingTest < ABSTRACTCacoTrainingTest
def initialize
@algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/regr/algorithm")
super
end
end
########################################################################################################
@@list = {
"1" => [ LazarHamsterSplit, MajorityHamsterSplit ],
"1a" => [ LazarHamsterSplit ],
"1b" => [ MajorityHamsterSplit ],
"2" => [ LazarHamsterTrainingTest, MajorityHamsterTrainingTest ],
"2a" => [ LazarHamsterTrainingTest ],
"2b" => [ MajorityHamsterTrainingTest ],
"3" => [ LazarHamsterCrossvalidation, MajorityHamsterCrossvalidation ],
"3a" => [ LazarHamsterCrossvalidation ],
"3b" => [ MajorityHamsterCrossvalidation ],
"4" => [ MajorityISTHamsterCrossvalidation, LazarISTHamsterCrossvalidation, ISTLazarISTHamsterCrossvalidation ],
"4a" => [ MajorityISTHamsterCrossvalidation ],
"4b" => [ LazarISTHamsterCrossvalidation ],
"4c" => [ ISTLazarISTHamsterCrossvalidation ],
"5a" => [ LR_AmbitCacoModel ],
"6" => [ LR_AmbitCacoTrainingTest, MLR_NTUA_CacoTrainingTest, MLR_NTUA2_CacoTrainingTest, MajorityCacoTrainingTest ],
"6a" => [ LR_AmbitCacoTrainingTest ],
"6b" => [ MLR_NTUA_CacoTrainingTest ],
"6c" => [ MLR_NTUA2_CacoTrainingTest ],
"6d" => [ MajorityCacoTrainingTest ],
}
def self.list
@@list.sort.collect{|k,v| k+":\t"+v.collect{|vv| vv.humanize}.join("\n\t")+"\n"} #.join("\n")
end
def self.select(csv_keys)
res = []
if csv_keys!=nil and csv_keys.size>0
csv_keys.split(",").each do |k|
raise "no key "+k.to_s unless @@list.has_key?(k)
res << @@list[k]
end
end
return res
end
end
#puts ValidationExamples.list
#puts ValidationExamples.select("1,2a").inspect
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