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require 'lib/test_util.rb'
class Example
@@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%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")
@@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=""
# 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" => "2",
"css_file" => @@css_file,
"prediction_dataset_uri" => @@prediction_data,
#"predicted_feature" => @@predicted_feature,
"qmrf_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
#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!
#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"
raise OpenTox::BadRequestError.new"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")
dataset = OpenTox::Dataset.create_from_csv_file(@@file.path,nil)
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), 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],
:prediction_feature => URI.decode(@@feature),
:algorithm_uri => @@alg
v.validate_algorithm( @@alg_params, OpenTox::SubTask.new(task, 20, 40) )
log "crossvalidation"
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"
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
task
end
# performs all curl calls listed in examples after ">>>", next line is added if line ends with "\"
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 = []
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
Spork.spork(:logger => LOGGER) do
@@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 if result.size<50
end
end
result.chomp!
result.gsub!(/\n/, " \\n ")
if ($?==0)
if result.task_uri?
log "wait for task: "+result
result = Lib::TestUtil.wait_for_task(result)
end
log "ok ( " +result.to_s[0,50]+" )"
suc += 1
else
log "failed ( " +result.to_s[0,50]+" )"
end
end
log suc.to_s+"/"+num.to_s+" curls succeeded"
@@summary
end
"testing in background, check log for results"
end
private
# deletes resources listed by service
def self.delete_all(uri_list_service)
uri_list = OpenTox::RestClientWrapper.get(uri_list_service)
LOGGER.debug "deleting: "+uri_list.inspect
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 "EXAMPLE: "+log_string
@@summary += log_string+"\n"
end
end
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