diff options
Diffstat (limited to 'example.rb')
-rwxr-xr-x | example.rb | 24 |
1 files changed, 12 insertions, 12 deletions
@@ -3,11 +3,11 @@ require 'lib/test_util.rb' class Example - @@file=File.new("data/hamster_carcinogenicity.yaml","r") + @@file=File.new("data/hamster_carcinogenicity.csv","r") @@file_type="text/x-yaml" @@model=File.join CONFIG[:services]["opentox-model"],"1" #@@feature= URI.encode("http://local-ot/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)") - @@feature= File.join CONFIG[:services]["opentox-dataset"],"1/feature/hamster_carcinogenicity" + @@feature= File.join CONFIG[:services]["opentox-dataset"],"1/feature/Hamster%2520Carcinogenicity" #@@predicted_feature= URI.encode("http://local-ot/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)_lazar_classification") @@alg = File.join CONFIG[:services]["opentox-algorithm"],"lazar" @@alg_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") @@ -58,12 +58,15 @@ class Example #TODO subjectid = nil + Ohm.flush + task = OpenTox::Task.create("prepare examples", "n/a") do |task| @@summary = "" + #delete validations - log "delete validations" - Lib::Validation.auto_migrate! - Lib::Crossvalidation.auto_migrate! + #log "delete validations" + #Lib::Validation.auto_migrate! + #Lib::Crossvalidation.auto_migrate! #ActiveRecord::Base.logger = Logger.new("/dev/null") #ActiveRecord::Migrator.migrate('db/migrate', 0 ) #ActiveRecord::Migrator.migrate('db/migrate', 1 ) @@ -80,10 +83,7 @@ class Example halt 400,"File not found: "+@@file.path.to_s unless File.exist?(@@file.path) #data = File.read(@@file.path) #data_uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:content_type => @@file_type},data).chomp("\n") - data = File.read(@@file.path) - dataset = OpenTox::Dataset.create - dataset.load_yaml(data) - dataset.save + dataset = OpenTox::Dataset.create_from_csv_file(@@file.path,nil) data_uri = dataset.uri log "-> "+data_uri task.progress(20) @@ -92,7 +92,7 @@ class Example #delete_all(CONFIG[:services]["opentox-model"]) OpenTox::RestClientWrapper.delete CONFIG[:services]["opentox-model"] - split_params = Validation::Util.train_test_dataset_split(data_uri, URI.decode(@@feature), 0.9, 1) + split_params = Validation::Util.train_test_dataset_split(data_uri, URI.decode(@@feature), nil, 0.9, 1) v = Validation::Validation.new :training_dataset_uri => split_params[:training_dataset_uri], :validation_type => "test_set_validation", :test_dataset_uri => split_params[:test_dataset_uri], @@ -102,7 +102,7 @@ class Example v.validate_algorithm( @@alg_params, OpenTox::SubTask.new(task, 20, 40) ) log "crossvalidation" - cv = Validation::Crossvalidation.new({ :dataset_uri => data_uri, :algorithm_uri => @@alg, :num_folds => 5, :stratified => false }) + cv = Validation::Crossvalidation.create({ :dataset_uri => data_uri, :algorithm_uri => @@alg, :num_folds => 5, :stratified => false }) cv.perform_cv( URI.decode(@@feature), @@alg_params, OpenTox::SubTask.new(task, 40, 70) ) log "create validation report" @@ -124,7 +124,7 @@ class Example log "done" @@summary end - return_task(task) + task end # performs all curl calls listed in examples after ">>>", next line is added if line ends with "\" |