diff options
Diffstat (limited to 'test')
-rw-r--r-- | test/test_examples.rb | 97 | ||||
-rw-r--r-- | test/test_examples_util.rb | 8 |
2 files changed, 99 insertions, 6 deletions
diff --git a/test/test_examples.rb b/test/test_examples.rb index ae4f617..34a9f67 100644 --- a/test/test_examples.rb +++ b/test/test_examples.rb @@ -9,6 +9,53 @@ end module ValidationExamples + class IrisCrossvalidation < CrossValidation + def initialize + @dataset_file = File.new("data/IRIS_unitrisk.yaml","r") + @prediction_feature = "http://ot-dev.in-silico.ch/toxcreate/feature#IRIS%20unit%20risk" + @num_folds = 10 + end + end + + class MajorityIrisCrossvalidation < IrisCrossvalidation + def initialize + @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") + super + end + end + + ######################################################################################################## + + class IrisSplit < SplitTestValidation + def initialize + @dataset_file = File.new("data/IRIS_unitrisk.yaml","r") + @prediction_feature = "http://ot-dev.in-silico.ch/toxcreate/feature#IRIS%20unit%20risk" + end + end + + 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") + super + end + end + + class MajorityIrisSplit < IrisSplit + def initialize + @algorithm_uri = File.join(@@config[:services]["opentox-majority"],"/regr/algorithm") + super + end + end + ######################################################################################################## class HamsterSplit < SplitTestValidation @@ -86,21 +133,21 @@ module ValidationExamples ######################################################################################################## - class ISTHamsterCrossvalidationInsilico < CrossValidation + class ISTHamsterCrossvalidation < 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 < ISTHamsterCrossvalidationInsilico + class MajorityISTHamsterCrossvalidation < ISTHamsterCrossvalidation def initialize @algorithm_uri = File.join(CONFIG[:services]["opentox-majority"],"/class/algorithm") super end end - class LazarISTHamsterCrossvalidation < ISTHamsterCrossvalidationInsilico + 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") @@ -108,14 +155,47 @@ module ValidationExamples end end - class ISTLazarISTHamsterCrossvalidation < ISTHamsterCrossvalidationInsilico + class ISTLazarISTHamsterCrossvalidation < ISTHamsterCrossvalidation 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 ISTIrisCrossvalidation < CrossValidation + def initialize + @dataset_uri = "http://ot-dev.in-silico.ch/dataset/39" + @prediction_feature = "http://ot-dev.in-silico.ch/toxcreate/feature#IRIS%20unit%20risk" + end + end + + class ISTLazarISTIrisCrossvalidation < ISTIrisCrossvalidation + def initialize + @algorithm_uri = "http://ot-dev.in-silico.ch/algorithm/lazar" + @algorithm_params = "feature_generation_uri=http://ot-dev.in-silico.ch/algorithm/fminer" + super + end + end + + ######################################################################################################## + + class ISTEpaCrossvalidation < CrossValidation + def initialize + @dataset_uri = "http://ot-dev.in-silico.ch/dataset/69" + @prediction_feature = "http://ot-dev.in-silico.ch/toxcreate/feature#EPA%20FHM" + end + end + + class ISTLazarISTEpaCrossvalidation < ISTEpaCrossvalidation + def initialize + @algorithm_uri = "http://ot-dev.in-silico.ch/algorithm/lazar" + @algorithm_params = "feature_generation_uri=http://ot-dev.in-silico.ch/algorithm/fminer" + super + end + end ######################################################################################################## @@ -192,6 +272,15 @@ module ValidationExamples "6b" => [ MLR_NTUA_CacoTrainingTest ], "6c" => [ MLR_NTUA2_CacoTrainingTest ], "6d" => [ MajorityCacoTrainingTest ], + + "7a" => [ LazarIrisSplit ], + "7b" => [ MajorityIrisSplit ], + + "8b" => [ MajorityIrisCrossvalidation ], + + "9a" => [ ISTLazarISTIrisCrossvalidation ], + + "10a" => [ ISTLazarISTEpaCrossvalidation ], } def self.list diff --git a/test/test_examples_util.rb b/test/test_examples_util.rb index 3d4d605..7eb69ff 100644 --- a/test/test_examples_util.rb +++ b/test/test_examples_util.rb @@ -114,11 +114,15 @@ module ValidationExamples assert_int_equal(predictions, num_instances-num_unpredicted) else regr_stats = val["regression_statistics".to_sym] - assert regr_stats!=nil + assert_not_nil regr_stats end end - private + private + def self.assert_not_nil(val,msg_suffix=nil) + raise msg_suffix.to_s+" is nil" if val==nil + end + def self.assert_int_equal(val1,val2,msg_suffix=nil) raise msg_suffix.to_s+" not equal: "+val1.to_s+" != "+val2.to_s unless val1==val2 end |