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|
class Example
@@file=File.new("data/hamster_carcinogenicity.owl","r")
@@model=File.join @@config[:services]["opentox-model"],"1"
@@feature="http://www.epa.gov/NCCT/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster"
@@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"
@@summary=""
# replaces placeholdes ( in <> brackets ) in EXAMPLE file with uris and ids
def self.transform_example
file = File.new("EXAMPLES", "r")
res = ""
while (line = file.gets)
res += line
end
file.close
sub = { "validation_service" => @@config[:services]["opentox-validation"].chomp("/"),
"validation_id" => "1",
"model_uri" => @@model,
"dataset_uri" => @@data,
"training_dataset_uri" => @@train_data,
"test_dataset_uri" => @@test_data,
"prediction_feature" => @@feature,
"algorithm_uri" => @@alg,
"algorithm_params" => @@alg_params,
"crossvalidation_id" => "1",
"validation_report_id" => "1",
"crossvalidation_report_id" => "1",
}
sub.each do |k,v|
res.gsub!(/<#{k}>/,v)
end
res
end
# creates the resources that are requested by the examples
def self.prepare_example_resources
@@summary = ""
delete_all(@@config[:services]["opentox-dataset"])
log "upload dataset"
data = File.read(@@file.path)
data_uri = OpenTox::RestClientWrapper.post @@config[:services]["opentox-dataset"], data, :content_type => "application/rdf+xml"
log "train-test-validation"
Lib::Validation.auto_migrate!
delete_all(@@config[:services]["opentox-model"])
split_params = Validation::Util.train_test_dataset_split(data_uri, 0.9, 1)
v = Validation::Validation.new :training_dataset_uri => split_params[:training_dataset_uri],
:test_dataset_uri => split_params[:test_dataset_uri],
:prediction_feature => @@feature
v.validate_algorithm( @@alg, @@alg_params)
log "crossvalidation"
Lib::Crossvalidation.auto_migrate!
cv = Validation::Crossvalidation.new({ :dataset_uri => data_uri, :algorithm_uri => @@alg, :num_folds => 5, :stratified => false })
cv.create_cv_datasets( @@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.uri)
log "create crossvalidation report"
rep.delete_all_reports("crossvalidation")
rep.create_report("crossvalidation",cv.uri)
log "done"
@@summary
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")
curl_call = false
curl_calls = []
lines.each do |line|
if line =~ /^\s*>>>\s*.*/
line.gsub!(/^\s*>>>\s*/,"")
if line =~ /.*\s*\\s*$/
curl_call = true
line.gsub!(/\s*\\s*$/," ")
else
curl_call = false
end
curl_calls.push( line )
elsif curl_call
if line =~ /.*\s*\\s*$/
curl_call = true
line.gsub!(/\s*\\s*$/," ")
else
curl_call = false
end
curl_calls[-1] = curl_calls[-1]+line
end
end
@@summary = ""
num = 0
suc = 0
curl_calls.each do |cmd|
num += 1
log "testing: "+cmd
result = ""
IO.popen(cmd.to_s+" 2> /dev/null") do |f|
while line = f.gets
result += line
end
end
result.gsub!(/\n/, " \\n ")
if ($?==0)
log "ok ( " +result.to_s[0,50]+" )"
suc += 1
else
log "failed ( " +result.to_s[0,50]+" )"
end
end
log num.to_s+"/"+num.to_s+" curls succeeded"
@@summary
end
private
# deletes resources listed by service
def self.delete_all(uri_list_service)
uri_list = OpenTox::RestClientWrapper.get(uri_list_service)
uri_list.split("\n").each do |uri|
OpenTox::RestClientWrapper.delete(uri)
end
end
# logs string and and adds to summary
def self.log(log_string)
LOGGER.info log_string
@@summary += log_string+"\n"
end
end
|
