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|
module ValidationExamples
class Util
@@dataset_uris = {}
def self.upload_dataset(file, dataset_service=@@config[:services]["opentox-dataset"], file_type="text/x-yaml")
raise "File not found: "+file.path.to_s unless File.exist?(file.path)
if @@dataset_uris[file.path.to_s]==nil
data = File.read(file.path)
data_uri = OpenTox::RestClientWrapper.post(dataset_service,{:content_type => file_type},data).to_s.chomp
@@dataset_uris[file.path.to_s] = data_uri
LOGGER.debug "uploaded dataset: "+data_uri
else
LOGGER.debug "file already uploaded: "+@@dataset_uris[file.path.to_s]
end
return @@dataset_uris[file.path.to_s]
end
def self.build_compare_report(validation_examples)
@comp = validation_examples[0].algorithm_uri==nil ? :model_uri : :algorithm_uri
return nil if @comp == :model_uri
to_compare = []
validation_examples.each do |v|
to_compare << v.validation_uri if v.validation_uri and v.validation_error==nil
end
return nil if to_compare.size < 2
begin
return validation_post "report/algorithm_comparison",{ :validation_uris => to_compare.join("\n") }
rescue => ex
return "error creating comparison report "+ex.message
end
end
def self.validation_post(uri, params)
if $test_case
#puts "posting: "+uri+","+params.inspect
$test_case.post uri,params
return wait($test_case.last_response.body)
else
return OpenTox::RestClientWrapper.post(File.join(@@config[:services]["opentox-validation"],uri),params)
end
end
def self.wait(uri)
if OpenTox::Utils.task_uri?(uri)
task = OpenTox::Task.find(uri)
task.wait_for_completion
raise "task failed: "+uri.to_s+", error is:\n"+task.description if task.error?
uri = task.resultURI
end
uri
end
end
class ValidationExample
#params
attr_accessor :name,
:prediction_feature,
:algorithm_uri,
:model_uri,
:test_dataset_uri,
:test_dataset_file,
:test_target_dataset_uri,
:test_target_dataset_file,
:training_dataset_uri,
:training_dataset_file,
:dataset_uri,
:dataset_file,
:algorithm_params,
:split_ratio,
:random_seed,
:num_folds,
:stratified
#results
attr_accessor :validation_uri,
:report_uri,
:validation_error,
:report_error
def upload_files
[[:test_dataset_uri, :test_dataset_file],
[:test_target_dataset_uri, :test_target_dataset_file],
[:training_dataset_uri, :training_dataset_file],
[:dataset_uri, :dataset_file]].each do |a|
uri = a[0]
file = a[1]
if send(uri)==nil and send(file)!=nil
send("#{uri.to_s}=".to_sym, Util.upload_dataset(send(file)))
end
end
end
def check_requirements
params.each do |r|
raise "values not set: "+r.to_s if send(r)==nil
end
end
def report
begin
@report_uri = Util.validation_post '/report/'+report_type,{:validation_uris => @validation_uri}
rescue => ex
@report_error = ex.message
end
end
def validate
begin
@validation_uri = Util.validation_post '/'+validation_type, get_params
rescue => ex
@validation_error = ex.message
LOGGER.error ex.message
end
end
def title
self.class.humanize
end
protected
def report_type
"validation"
end
def validation_type
""
end
def get_params
p = {}
( params + opt_params ).each do |pp|
p[pp] = send(pp) if send(pp)!=nil
end
return p
end
end
class ModelValidation < ValidationExample
def params
[:model_uri, :test_dataset_uri]
end
def opt_params
[ :prediction_feature, :test_target_dataset_uri ]
end
end
class TrainingTestValidation < ValidationExample
def params
[:algorithm_uri, :training_dataset_uri, :test_dataset_uri, :prediction_feature]
end
def opt_params
[ :algorithm_params, :test_target_dataset_uri ]
end
end
class SplitTestValidation < ValidationExample
def params
[:algorithm_uri, :dataset_uri, :prediction_feature]
end
def opt_params
[ :algorithm_params, :split_ratio, :random_seed ]
end
def validation_type
"training_test_split"
end
end
class CrossValidation < ValidationExample
def params
[:algorithm_uri, :dataset_uri, :prediction_feature]
end
def opt_params
[ :algorithm_params, :num_folds, :stratified, :random_seed ]
end
def report_type
"crossvalidation"
end
def validation_type
"crossvalidation"
end
end
end
|
