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|
#TEST_USER = "mgtest"
#TEST_PW = "mgpasswd"
#ENV['RACK_ENV'] = 'test'
require "rubygems"
require "sinatra"
require "uri"
require "yaml"
require 'application.rb'
require 'test/unit'
require 'rack/test'
require 'lib/test_util.rb'
require 'test/test_examples.rb'
TEST_USER = "guest"
TEST_PW = "guest"
#LOGGER = OTLogger.new(STDOUT)
#LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S "
#LOGGER.formatter = Logger::Formatter.new
module Sinatra
set :raise_errors, false
set :show_exceptions, false
end
class Exception
def message
errorCause ? errorCause.to_yaml : to_s
end
end
class ValidationTest < Test::Unit::TestCase
include Rack::Test::Methods
include Lib::TestUtil
def global_setup
puts "login and upload datasets"
if AA_SERVER
@@subjectid = OpenTox::Authorization.authenticate(TEST_USER,TEST_PW)
raise "could not log in" unless @@subjectid
puts "logged in: "+@@subjectid.to_s
else
puts "AA disabled"
@@subjectid = nil
end
f = File.new("data/hamster_carcinogenicity.mini.csv")
@@data_class_mini = ValidationExamples::Util.upload_dataset(f, @@subjectid)
@@feat_class_mini = ValidationExamples::Util.prediction_feature_for_file(f)
end
def global_teardown
puts "delete and logout"
OpenTox::Dataset.find(@@data_class_mini,@@subjectid).delete(@@subjectid) if defined?@@data_class_mini
@@cv.delete(@@subjectid) if defined?@@cv
@@report.delete(@@subjectid) if defined?@@report
@@qmrfReport.delete(@@subjectid) if defined?@@qmrfReport
OpenTox::Authorization.logout(@@subjectid) if AA_SERVER
end
def test_crossvalidation
puts "test_crossvalidation"
#assert_rest_call_error OpenTox::NotFoundError do
# OpenTox::Crossvalidation.find(File.join(CONFIG[:services]["opentox-validation"],"crossvalidation/noexistingid"))
#end
p = {
:dataset_uri => @@data_class_mini,
:algorithm_uri => File.join(CONFIG[:services]["opentox-algorithm"],"lazar"),
:algorithm_params => "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc"),
:prediction_feature => @@feat_class_mini,
:num_folds => 2 }
t = OpenTox::SubTask.new(nil,0,1)
def t.progress(pct)
if !defined?@last_msg or @last_msg+3<Time.new
puts "waiting for crossvalidation: "+pct.to_s
@last_msg=Time.new
end
end
def t.waiting_for(task_uri); end
cv = OpenTox::Crossvalidation.create(p, @@subjectid, t)
assert cv.uri.uri?
if @@subjectid
assert_rest_call_error OpenTox::NotAuthorizedError do
OpenTox::Crossvalidation.find(cv.uri)
end
end
cv = OpenTox::Crossvalidation.find(cv.uri, @@subjectid)
assert cv.uri.uri?
if @@subjectid
assert_rest_call_error OpenTox::NotAuthorizedError do
cv.summary(cv)
end
end
summary = cv.summary(@@subjectid)
assert_kind_of Hash,summary
@@cv = cv
end
def test_crossvalidation_report
#@@cv = OpenTox::Crossvalidation.find("http://local-ot/validation/crossvalidation/48", @@subjectid)
puts "test_crossvalidation_report"
assert defined?@@cv,"no crossvalidation defined"
assert_kind_of OpenTox::Crossvalidation,@@cv
#assert_rest_call_error OpenTox::NotFoundError do
# OpenTox::CrossvalidationReport.find_for_crossvalidation(@@cv.uri)
#end
if @@subjectid
assert_rest_call_error OpenTox::NotAuthorizedError do
OpenTox::CrossvalidationReport.create(@@cv.uri)
end
end
report = OpenTox::CrossvalidationReport.create(@@cv.uri,@@subjectid)
assert report.uri.uri?
if @@subjectid
assert_rest_call_error OpenTox::NotAuthorizedError do
OpenTox::CrossvalidationReport.find(report.uri)
end
end
report = OpenTox::CrossvalidationReport.find(report.uri,@@subjectid)
assert report.uri.uri?
report2 = OpenTox::CrossvalidationReport.find_for_crossvalidation(@@cv.uri,@@subjectid)
assert_equal report.uri,report2.uri
report3_uri = @@cv.find_or_create_report(@@subjectid)
assert_equal report.uri,report3_uri
@report = report2
end
def test_qmrf_report
#@@cv = OpenTox::Crossvalidation.find("http://local-ot/validation/crossvalidation/47", @@subjectid)
puts "test_qmrf_report"
assert defined?@@cv,"no crossvalidation defined"
validations = @@cv.metadata[OT.validation]
assert_kind_of Array,validations
assert validations.size==@@cv.metadata[OT.numFolds]
val = OpenTox::Validation.find(validations[0], @@subjectid)
model_uri = val.metadata[OT.model]
model = OpenTox::Model::Generic.find(model_uri, @@subjectid)
assert model!=nil
#assert_rest_call_error OpenTox::NotFoundError do
# OpenTox::QMRFReport.find_for_model(model_uri, @@subjectid)
#end
@@qmrfReport = OpenTox::QMRFReport.create(model_uri, @@subjectid)
end
################### utils and overrides ##########################
def app
Sinatra::Application
end
# checks RestCallError type
def assert_rest_call_error( ex )
if ex==OpenTox::NotAuthorizedError and @@subjectid==nil
puts "AA disabled: skipping test for not authorized"
return
end
begin
yield
rescue OpenTox::RestCallError => e
report = e.errorCause
while report.errorCause
report = report.errorCause
end
assert_equal report.errorType,ex.to_s
end
end
# hack to have a global_setup and global_teardown
def teardown
if((@@expected_test_count-=1) == 0)
global_teardown
end
end
def setup
unless defined?@@expected_test_count
@@expected_test_count = (self.class.instance_methods.reject{|method| method[0..3] != 'test'}).length
global_setup
end
end
end
|
