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-rwxr-xr-x[-rw-r--r--]test/test_examples.rb382
1 files changed, 351 insertions, 31 deletions
diff --git a/test/test_examples.rb b/test/test_examples.rb
index bbe6ddd..3c6f00e 100644..100755
--- a/test/test_examples.rb
+++ b/test/test_examples.rb
@@ -19,15 +19,15 @@ module ValidationExamples
class MajorityIrisCrossvalidation < IrisCrossvalidation
def initialize
- @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/regr/algorithm")
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/regr/algorithm")
super
end
end
class LazarIrisCrossvalidation < IrisCrossvalidation
def initialize
- @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
- @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+ @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer")
super
end
end
@@ -43,15 +43,65 @@ module ValidationExamples
class LazarIrisSplit < IrisSplit
def initialize
- @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
- @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
+ @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 MajorityIrisSplit < IrisSplit
def initialize
- @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/regr/algorithm")
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/regr/algorithm")
+ super
+ end
+ end
+
+ ########################################################################################################
+
+ class EPAFHMSplit < SplitTestValidation
+ def initialize
+ @dataset_file = File.new("data/EPAFHM.csv","r")
+ #@prediction_feature = "http://ot-dev.in-silico.ch/toxcreate/feature#IRIS%20unit%20risk"
+ @split_ratio = 0.95
+ end
+ end
+
+ class LazarEPAFHMSplit < EPAFHMSplit
+ def initialize
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+ @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
+ super
+ end
+ end
+
+ class MajorityEPAFHMSplit < EPAFHMSplit
+ def initialize
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/regr/algorithm")
+ super
+ end
+ end
+
+ ########################################################################################################
+
+ class EPAFHMCrossvalidation < CrossValidation
+ def initialize
+ @dataset_file = File.new("data/EPAFHM.csv","r")
+ #@prediction_feature = "http://ot-dev.in-silico.ch/toxcreate/feature#IRIS%20unit%20risk"
+ @num_folds = 10
+ end
+ end
+
+ class MajorityEPAFHMCrossvalidation < EPAFHMCrossvalidation
+ def initialize
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/regr/algorithm")
+ super
+ end
+ end
+
+ class LazarEPAFHMCrossvalidation < EPAFHMCrossvalidation
+ def initialize
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+ @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
super
end
end
@@ -60,48 +110,85 @@ module ValidationExamples
class HamsterSplit < SplitTestValidation
def initialize
- @dataset_file = File.new("data/hamster_carcinogenicity.yaml","r")
- @prediction_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
+ #@dataset_file = File.new("data/hamster_carcinogenicity.yaml","r")
+ @dataset_file = File.new("data/hamster_carcinogenicity.csv","r")
+
+ #@prediction_feature = "http://local-ot/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
+ #@prediction_feature = "http://local-ot/dataset/1/feature/hamster_carcinogenicity"
end
end
class LazarHamsterSplit < HamsterSplit
def initialize
- @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
- @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+ @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
super
end
end
class MajorityHamsterSplit < HamsterSplit
def initialize
- @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
super
end
end
########################################################################################################
+
+ class HamsterBootstrapping < BootstrappingValidation
+ def initialize
+ #@dataset_file = File.new("data/hamster_carcinogenicity.yaml","r")
+ @dataset_file = File.new("data/hamster_carcinogenicity.csv","r")
+
+ #@prediction_feature = "http://local-ot/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
+ #@prediction_feature = "http://local-ot/dataset/1/feature/hamster_carcinogenicity"
+ end
+ end
+
+ class LazarHamsterBootstrapping < HamsterBootstrapping
+ def initialize
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+ @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
+ super
+ end
+ end
+
+ class MajorityHamsterBootstrapping < HamsterBootstrapping
+ def initialize
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
+ super
+ end
+ end
+
+ ########################################################################################################
class HamsterTrainingTest < 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)"
+# @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")
+
+ @test_target_dataset_file = File.new("data/hamster_carcinogenicity.csv","r")
+ @training_dataset_file = File.new("data/hamster_carcinogenicity.train.csv","r")
+ @test_dataset_file = File.new("data/hamster_carcinogenicity.test.csv","r")
+
+
+ #@prediction_feature = "http://local-ot/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
+ #@prediction_feature = "http://local-ot/dataset/1/feature/hamster_carcinogenicity"
end
end
class MajorityHamsterTrainingTest < HamsterTrainingTest
def initialize
- @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
super
end
end
class LazarHamsterTrainingTest < HamsterTrainingTest
def initialize
- @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
- @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+ @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
super
end
end
@@ -110,23 +197,26 @@ module ValidationExamples
class HamsterCrossvalidation < CrossValidation
def initialize
- @dataset_file = File.new("data/hamster_carcinogenicity.yaml","r")
- @prediction_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
+ #@dataset_file = File.new("data/hamster_carcinogenicity.yaml","r")
+ @dataset_file = File.new("data/hamster_carcinogenicity.csv","r")
+
+ #@prediction_feature = "http://local-ot/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
+ #@prediction_feature = "http://local-ot/dataset/1/feature/hamster_carcinogenicity"
@num_folds = 10
end
end
class MajorityHamsterCrossvalidation < HamsterCrossvalidation
def initialize
- @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
super
end
end
class LazarHamsterCrossvalidation < HamsterCrossvalidation
def initialize
- @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
- @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+ @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
super
end
end
@@ -142,15 +232,15 @@ module ValidationExamples
class MajorityISTHamsterCrossvalidation < ISTHamsterCrossvalidation
def initialize
- @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/class/algorithm")
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
super
end
end
class LazarISTHamsterCrossvalidation < ISTHamsterCrossvalidation
def initialize
- @algorithm_uri = File.join(@@config[:services]["opentox-algorithm"],"lazar")
- @algorithm_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+ @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer")
super
end
end
@@ -182,6 +272,22 @@ module ValidationExamples
########################################################################################################
+ class ISTRatLiverCrossvalidation < CrossValidation
+ def initialize
+ @dataset_uri = "http://webservices.in-silico.ch/dataset/26"
+ @prediction_feature = "http://toxcreate.org/feature#chr_rat_liver_proliferativelesions"
+ end
+ end
+
+ class MajorityISTRatLiverCrossvalidation < ISTRatLiverCrossvalidation
+ def initialize
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
+ super
+ end
+ end
+
+ ########################################################################################################
+
class ISTEpaCrossvalidation < CrossValidation
def initialize
@dataset_uri = "http://ot-dev.in-silico.ch/dataset/69"
@@ -198,12 +304,19 @@ module ValidationExamples
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"
+# @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
+
+ @model_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/model/33"
+ @test_dataset_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R545"
+
end
end
@@ -240,13 +353,183 @@ module ValidationExamples
class MajorityCacoTrainingTest < CacoTrainingTest
def initialize
- @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/regr/algorithm")
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/regr/algorithm")
super
end
end
########################################################################################################
-
+
+ class NtuaModel < ModelValidation
+ def initialize
+ @model_uri = "http://opentox.ntua.gr:4000/model/0d8a9a27-3481-4450-bca1-d420a791de9d"
+ @test_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/54"
+ #@prediction_feature=http://apps.ideaconsult.net:8080/ambit2/feature/22200
+ end
+ end
+
+ ########################################################################################################
+
+ class TumModel < ModelValidation
+ def initialize
+ @model_uri = "http://opentox-dev.informatik.tu-muenchen.de:8080/OpenTox-sec/sec/model/TUMOpenToxModel_M5P_5"
+ @test_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/99488"
+ end
+ end
+
+ ########################################################################################################
+
+ class AmbitModelValidation < ModelValidation
+ def initialize
+ @model_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/model/39319"
+ #@model_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/model/29139"
+ @test_dataset_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R401577?max=3"
+ end
+ end
+
+ class AmbitBursiModelValidation < ModelValidation
+ def initialize
+ @model_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/model/35194"
+ @test_dataset_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R401577"
+ end
+ end
+
+ class AmbitAquaticModelValidation < ModelValidation
+ def initialize
+ @model_uri = "http://apps.ideaconsult.net:8080/ambit2/model/130668"
+ @test_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/186293?feature_uris[]=http://apps.ideaconsult.net:8080/ambit2/feature/430904&feature_uris[]=http://apps.ideaconsult.net:8080/ambit2/feature/430905"
+ @prediction_feature = "http://apps.ideaconsult.net:8080/ambit2/feature/430905"
+ end
+ end
+
+ class AmbitTrainingTest < TrainingTestValidation
+ def initialize
+ @training_dataset_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R401560"
+ #@training_dataset_uri = "http://opentox.informatik.uni-freiburg.de/dataset/317"
+ @test_dataset_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R401560"
+ @prediction_feature = "https://ambit.uni-plovdiv.bg:8443/ambit2/feature/22190"
+ @algorithm_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/algorithm/LR"
+ end
+ end
+
+ class AmbitBursiTrainingTest < TrainingTestValidation
+ def initialize
+ @test_dataset_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R401577"
+ @training_dataset_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R401577"
+ @prediction_feature = "https://ambit.uni-plovdiv.bg:8443/ambit2/feature/26221"
+ @algorithm_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/algorithm/J48"
+ end
+ end
+
+ class AmbitJ48TrainingTest < TrainingTestValidation
+ def initialize
+ @test_dataset_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/39914"
+ @training_dataset_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/39914"
+ @prediction_feature = "https://ambit.uni-plovdiv.bg:8443/ambit2/feature/221726"
+ @algorithm_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/algorithm/J48"
+ end
+ end
+
+ class AmbitTrainingTestSplit < SplitTestValidation
+ def initialize
+ #@model_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/model/29139"
+ @dataset_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R401560"
+ #@test_dataset_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R401560"
+ @prediction_feature = "https://ambit.uni-plovdiv.bg:8443/ambit2/feature/22190"
+ @algorithm_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/algorithm/LR"
+ end
+ end
+
+ class AmbitBursiTrainingTestSplit < SplitTestValidation
+ def initialize
+ @dataset_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R401577"
+ @prediction_feature = "https://ambit.uni-plovdiv.bg:8443/ambit2/feature/26221"
+ @algorithm_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/algorithm/J48"
+ end
+ end
+
+ class AmbitJ48TrainingTestSplit < SplitTestValidation
+ def initialize
+ @dataset_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/39914"
+ @prediction_feature = "https://ambit.uni-plovdiv.bg:8443/ambit2/feature/221726"
+ @algorithm_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/algorithm/J48"
+ end
+ end
+
+
+ ########################################################################################################
+
+ class HamsterTrainingTest < 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")
+
+ @test_target_dataset_file = File.new("data/hamster_carcinogenicity.csv","r")
+ @training_dataset_file = File.new("data/hamster_carcinogenicity.train.csv","r")
+ @test_dataset_file = File.new("data/hamster_carcinogenicity.test.csv","r")
+
+
+ #@prediction_feature = "http://local-ot/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
+ #@prediction_feature = "http://local-ot/dataset/1/feature/hamster_carcinogenicity"
+ end
+ end
+
+ class MajorityHamsterTrainingTest < HamsterTrainingTest
+ def initialize
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
+ super
+ end
+ end
+
+ ########################################################################################################
+
+ class RepdoseSplit < SplitTestValidation
+ def initialize
+ @dataset_file = File.new("data/repdose_classification.csv","r")
+ end
+ end
+
+ class LazarRepdoseSplit < RepdoseSplit
+ def initialize
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+ @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
+ super
+ end
+ end
+
+ class MajorityRepdoseSplit < RepdoseSplit
+ def initialize
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
+ super
+ end
+ end
+
+ ########################################################################################################
+
+ class RepdoseCrossValidation < CrossValidation
+ def initialize
+ @dataset_file = File.new("data/repdose_classification.csv","r")
+ end
+ end
+
+ class LazarRepdoseCrossValidation < RepdoseCrossValidation
+ def initialize
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
+ @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
+ super
+ end
+ end
+
+ class MajorityRepdoseCrossValidation < RepdoseCrossValidation
+ def initialize
+ @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm")
+ super
+ end
+ end
+
+ ########################################################################################################
+
@@list = {
"1" => [ LazarHamsterSplit, MajorityHamsterSplit ],
"1a" => [ LazarHamsterSplit ],
@@ -276,11 +559,48 @@ module ValidationExamples
"7a" => [ LazarIrisSplit ],
"7b" => [ MajorityIrisSplit ],
+ "8a" => [ LazarIrisCrossvalidation ],
"8b" => [ MajorityIrisCrossvalidation ],
"9a" => [ ISTLazarISTIrisCrossvalidation ],
"10a" => [ ISTLazarISTEpaCrossvalidation ],
+
+ "11b" => [ MajorityISTRatLiverCrossvalidation ],
+
+ "12" => [ LazarHamsterBootstrapping, MajorityHamsterBootstrapping ],
+ "12a" => [ LazarHamsterBootstrapping ],
+ "12b" => [ MajorityHamsterBootstrapping ],
+
+ "13a" => [ LazarEPAFHMSplit ],
+ "13b" => [ MajorityEPAFHMSplit ],
+
+ "14a" => [ LazarEPAFHMCrossvalidation ],
+ "14b" => [ MajorityEPAFHMCrossvalidation ],
+
+ "15a" => [ NtuaModel ],
+
+ "16" => [ LazarRepdoseSplit, MajorityRepdoseSplit ],
+ "16a" => [ LazarRepdoseSplit ],
+ "16b" => [ MajorityRepdoseSplit ],
+
+ "17" => [ LazarRepdoseCrossValidation, MajorityRepdoseCrossValidation ],
+ "17a" => [ LazarRepdoseCrossValidation ],
+ "17b" => [ MajorityRepdoseCrossValidation ],
+
+ "18a" => [ TumModel ],
+
+ "19a" => [ AmbitModelValidation ],
+ "19b" => [ AmbitTrainingTest ],
+ "19c" => [ AmbitTrainingTestSplit ],
+ "19d" => [ AmbitBursiTrainingTest ],
+ "19e" => [ AmbitBursiModelValidation ],
+ "19f" => [ AmbitBursiTrainingTestSplit ],
+ "19g" => [ AmbitJ48TrainingTest ],
+ "19h" => [ AmbitJ48TrainingTestSplit ],
+ "19i" => [ AmbitAquaticModelValidation ],
+
+
}
def self.list
@@ -301,4 +621,4 @@ module ValidationExamples
end
#puts ValidationExamples.list
-#puts ValidationExamples.select("1,2a").inspect \ No newline at end of file
+#puts ValidationExamples.select("1,2a").inspect
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-04 14:25:28 +0000