diff options
| -rw-r--r-- | application.rb | 2 | ||||
| -rw-r--r-- | report/environment.rb | 4 | ||||
| -rw-r--r-- | test/test_examples.rb | 26 | ||||
| -rw-r--r-- | validation/validation_application.rb | 2 | ||||
| -rw-r--r-- | validation/validation_test.rb | 14 |
5 files changed, 35 insertions, 13 deletions
diff --git a/application.rb b/application.rb index 820fc83..7f6cfbd 100644 --- a/application.rb +++ b/application.rb @@ -1,6 +1,6 @@ require 'rubygems' gem 'opentox-ruby-api-wrapper', '= 1.5.7' -[ 'sinatra', 'sinatra/url_for', 'opentox-ruby-api-wrapper', 'logger' ].each do |lib| +[ 'sinatra', 'sinatra/url_for', 'opentox-ruby-api-wrapper' ].each do |lib| require lib end diff --git a/report/environment.rb b/report/environment.rb index 7c9aa8b..714cebe 100644 --- a/report/environment.rb +++ b/report/environment.rb @@ -1,7 +1,7 @@ ['rubygems', 'logger', 'fileutils', 'sinatra', 'sinatra/url_for', 'rest_client', - 'yaml', 'opentox-ruby-api-wrapper', 'fileutils', 'mime/types', 'abbrev', - 'rexml/document', 'active_record', 'ar-extensions', 'ruby-plot'].each do |g| + 'yaml', 'fileutils', 'mime/types', 'abbrev', + 'rexml/document', 'ruby-plot', 'active_record', 'ar-extensions', 'opentox-ruby-api-wrapper' ].each do |g| require g end gem 'ruby-plot', '= 0.0.2' diff --git a/test/test_examples.rb b/test/test_examples.rb index e65e03d..a23ce0f 100644 --- a/test/test_examples.rb +++ b/test/test_examples.rb @@ -133,21 +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") @@ -155,14 +155,30 @@ 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 ######################################################################################################## @@ -244,6 +260,8 @@ module ValidationExamples "7b" => [ MajorityIrisSplit ], "8b" => [ MajorityIrisCrossvalidation ], + + "9a" => [ ISTLazarISTIrisCrossvalidation ], } def self.list diff --git a/validation/validation_application.rb b/validation/validation_application.rb index cadfa43..a10b75a 100644 --- a/validation/validation_application.rb +++ b/validation/validation_application.rb @@ -1,5 +1,5 @@ -[ 'rubygems', 'sinatra', 'sinatra/url_for', 'opentox-ruby-api-wrapper', 'logger', 'active_record', 'ar-extensions' ].each do |lib| +[ 'rubygems', 'sinatra', 'sinatra/url_for', 'active_record', 'ar-extensions', 'opentox-ruby-api-wrapper' ].each do |lib| require lib end diff --git a/validation/validation_test.rb b/validation/validation_test.rb index a6ddb90..3ae1460 100644 --- a/validation/validation_test.rb +++ b/validation/validation_test.rb @@ -1,4 +1,3 @@ -require "logger" require "uri" require "yaml" ENV['RACK_ENV'] = 'test' @@ -7,8 +6,11 @@ require 'test/unit' require 'rack/test' require 'lib/test_util.rb' require 'test/test_examples.rb' + LOGGER = MyLogger.new(STDOUT) LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S " +LOGGER.formatter = Logger::Formatter.new + class ValidationTest < Test::Unit::TestCase include Rack::Test::Methods @@ -17,18 +19,20 @@ class ValidationTest < Test::Unit::TestCase def test_it $test_case = self - - get "/crossvalidation/4/statistics" + #get "/crossvalidation/4/statistics" # post "",:model_uri=>"http://localhost/model/1",:test_dataset_uri=>"http://localhost/dataset/3", # :test_target_dataset_uri=>"http://localhost/dataset/1" #get "/crossvalidation/1",nil,'HTTP_ACCEPT' => "application/rdf+xml" - puts last_response.body + #puts last_response.body # post "/test_validation",:select=>"6d" #,:report=>"yes,please" # puts last_response.body - #run_test("8b") #,"http://localhost/validation/report/validation/36") #, "http://localhost/validation/321") + #run_test("9a") #,"http://localhost/validation/report/validation/36") #, "http://localhost/validation/321") + + run_test("9a","http://localhost/validation/crossvalidation/10") #, "http://localhost/validation/321") + #run_test("8b", "http://localhost/validation/crossvalidation/4") #puts Nightly.build_nightly("1") |