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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=""
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
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
def self.log(log_string)
LOGGER.debug log_string
@@summary += log_string+"\n"
end
def self.prepare_example_resources
@@summary = ""
delete_all(@@config[:services]["opentox-dataset"])
data = File.read(@@file.path)
data_uri = OpenTox::RestClientWrapper.post @@config[:services]["opentox-dataset"], data, :content_type => "application/rdf+xml"
log "uploaded dataset "+data_uri
raise "failed to prepare demo" unless data_uri==@@data
Lib::Validation.auto_migrate!
delete_all(@@config[:services]["opentox-model"])
vali_uri = OpenTox::RestClientWrapper.post File.join(@@config[:services]["opentox-validation"],'/training_test_split'), { :dataset_uri => data_uri,
:algorithm_uri => @@alg,
:prediction_feature => @@feature,
:algorithm_params => @@alg_params }
log "created validation via training test split "+vali_uri
raise "failed to prepare demo" unless vali_uri==File.join(@@config[:services]["opentox-validation"],'/1')
Lib::Crossvalidation.auto_migrate!
cv_uri = OpenTox::RestClientWrapper.post File.join(@@config[:services]["opentox-validation"],'/crossvalidation'), { :dataset_uri => data_uri,
:algorithm_uri => @@alg,
:prediction_feature => @@feature,
:algorithm_params => @@alg_params,
:num_folds => 5, :stratified => false }
log "created crossvalidation "+cv_uri
raise "failed to prepare demo" unless cv_uri==File.join(@@config[:services]["opentox-validation"],'/crossvalidation/1')
delete_all(File.join(@@config[:services]["opentox-validation"],"/report/validation"))
val_report_uri = OpenTox::RestClientWrapper.post File.join(@@config[:services]["opentox-validation"],'/report/validation'), { :validation_uris => vali_uri }
log "created validation report: "+val_report_uri
raise "failed to prepare demo" unless val_report_uri==File.join(@@config[:services]["opentox-validation"],'/report/validation/1')
delete_all(File.join(@@config[:services]["opentox-validation"],"/report/crossvalidation"))
cv_report_uri = OpenTox::RestClientWrapper.post File.join(@@config[:services]["opentox-validation"],'/report/crossvalidation'), { :validation_uris => cv_uri }
log "created crossvalidation report: "+cv_report_uri
raise "failed to prepare demo" unless cv_report_uri==File.join(@@config[:services]["opentox-validation"],'/report/crossvalidation/1')
log "done"
@@summary
end
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
end
|
