diff options
Diffstat (limited to 'example.rb')
| -rwxr-xr-x[-rw-r--r--] | example.rb | 156 |
1 files changed, 96 insertions, 60 deletions
diff --git a/example.rb b/example.rb index ceb1329..07151a8 100644..100755 --- a/example.rb +++ b/example.rb @@ -5,15 +5,16 @@ class Example @@file=File.new("data/hamster_carcinogenicity.yaml","r") @@file_type="text/x-yaml" - @@model=File.join @@config[:services]["opentox-model"],"1" - @@feature= URI.encode("http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)") - @@predicted_feature= URI.encode("http://localhost/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") - @@data=File.join @@config[:services]["opentox-dataset"],"1" - @@train_data=File.join @@config[:services]["opentox-dataset"],"2" - @@test_data=File.join @@config[:services]["opentox-dataset"],"3" - @@prediction_data=File.join @@config[:services]["opentox-dataset"],"5" + @@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" + #@@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") + @@data=File.join CONFIG[:services]["opentox-dataset"],"1" + @@train_data=File.join CONFIG[:services]["opentox-dataset"],"2" + @@test_data=File.join CONFIG[:services]["opentox-dataset"],"3" + @@prediction_data=File.join CONFIG[:services]["opentox-dataset"],"5" @@css_file="http://apps.ideaconsult.net:8080/ToxPredict/style/global.css" @@summary="" @@ -28,7 +29,7 @@ class Example end file.close - sub = { "validation_service" => @@config[:services]["opentox-validation"].chomp("/"), + sub = { "validation_service" => CONFIG[:services]["opentox-validation"].chomp("/"), "validation_id" => "1", "model_uri" => @@model, "dataset_uri" => @@data, @@ -39,10 +40,11 @@ class Example "algorithm_params" => @@alg_params, "crossvalidation_id" => "1", "validation_report_id" => "1", - "crossvalidation_report_id" => "1", + "crossvalidation_report_id" => "2", "css_file" => @@css_file, "prediction_dataset_uri" => @@prediction_data, - "predicted_feature" => @@predicted_feature } + #"predicted_feature" => @@predicted_feature, + "qmrf_id" => "1"} sub.each do |k,v| res.gsub!(/<#{k}>/,v) @@ -53,55 +55,88 @@ class Example # creates the resources that are requested by the examples def self.prepare_example_resources - @@summary = "" - #delete validations - log "delete validations" - ActiveRecord::Base.logger = Logger.new("/dev/null") - ActiveRecord::Migrator.migrate('db/migrate', 0 ) - ActiveRecord::Migrator.migrate('db/migrate', 1 ) - ActiveRecord::Migrator.migrate('db/migrate', 2 ) + #TODO + subjectid = nil - #delete_all(@@config[:services]["opentox-dataset"]) - log OpenTox::RestClientWrapper.delete @@config[:services]["opentox-dataset"] - - log "upload dataset" - 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") - - log "train-test-validation" - #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) - v = Validation::Validation.new :training_dataset_uri => split_params[:training_dataset_uri], - :test_dataset_uri => split_params[:test_dataset_uri], - :test_target_dataset_uri => data_uri, - :prediction_feature => URI.decode(@@feature), - :algorithm_uri => @@alg - v.validate_algorithm( @@alg_params ) - - log "crossvalidation" - cv = Validation::Crossvalidation.new({ :dataset_uri => data_uri, :algorithm_uri => @@alg, :num_folds => 5, :stratified => false }) - cv.create_cv_datasets( URI.decode(@@feature) ) - cv.perform_cv( @@alg_params ) - - log "create validation report" - rep = Reports::ReportService.new(File.join(@@config[:services]["opentox-validation"],"report")) - rep.delete_all_reports("validation") - rep.create_report("validation",v.validation_uri) - - log "create crossvalidation report" - rep.delete_all_reports("crossvalidation") - rep.create_report("crossvalidation",cv.crossvalidation_uri) - - log "done" - @@summary + task = OpenTox::Task.create("prepare examples", "n/a") do |task| + @@summary = "" + #delete validations + 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 ) + #ActiveRecord::Migrator.migrate('db/migrate', 2 ) + + #delete all qmrf reports + ReachReports::QmrfReport.auto_migrate! + + #delete_all(CONFIG[:services]["opentox-dataset"]) + log OpenTox::RestClientWrapper.delete CONFIG[:services]["opentox-dataset"] + task.progress(10) + + log "upload dataset" + 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 + data_uri = dataset.uri + log "-> "+data_uri + task.progress(20) + + log "train-test-validation" + #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) + 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], + :test_target_dataset_uri => data_uri, + :prediction_feature => URI.decode(@@feature), + :algorithm_uri => @@alg + 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.perform_cv( URI.decode(@@feature), @@alg_params, OpenTox::SubTask.new(task, 40, 70) ) + + log "create validation report" + rep = Reports::ReportService.instance(File.join(CONFIG[:services]["opentox-validation"],"report")) + rep.delete_all_reports("validation", subjectid) + rep.create_report("validation",v.validation_uri) + task.progress(80) + + log "create crossvalidation report" + rep.delete_all_reports("crossvalidation", subjectid) + rep.create_report("crossvalidation",cv.crossvalidation_uri) + task.progress(90) + + log "build qmrf" + t = ReachReports.create_report("QMRF",{:model_uri=>@@model}) + Lib::TestUtil.wait_for_task(t) + task.progress(100) + + log "done" + @@summary + end + return_task(task) end # performs all curl calls listed in examples after ">>>", next line is added if line ends with "\" - def self.test_examples - lines = transform_example.split("\n") + def self.test_examples(example_uri=nil) + + if (example_uri) + examples = OpenTox::RestClientWrapper.get(example_uri) + else + examples = transform_example # use local examples + end + + lines = examples.split("\n") curl_call = false curl_calls = [] @@ -136,12 +171,13 @@ class Example result = "" IO.popen(cmd.to_s+" 2> /dev/null") do |f| while line = f.gets - result += line + result += line if result.size<50 end end + result.chomp! result.gsub!(/\n/, " \\n ") if ($?==0) - if OpenTox::Utils.task_uri?(result) + if result.task_uri? log "wait for task: "+result result = Lib::TestUtil.wait_for_task(result) end @@ -151,7 +187,7 @@ class Example log "failed ( " +result.to_s[0,50]+" )" end end - log num.to_s+"/"+num.to_s+" curls succeeded" + log suc.to_s+"/"+num.to_s+" curls succeeded" @@summary end "testing in background, check log for results" |